Dissertations / Theses: 'Adaptation, biological'

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Herndon, Nic. "Domain adaptation algorithms for biological sequence classification." Diss., Kansas State University, 2016. http://hdl.handle.net/2097/35242.

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Doctor of Philosophy
Department of Computing and Information Sciences
Doina Caragea
The large volume of data generated in the recent years has created opportunities for discoveries in various fields. In biology, next generation sequencing technologies determine faster and cheaper the exact order of nucleotides present within a DNA or RNA fragment. This large volume of data requires the use of automated tools to extract information and generate knowledge. Machine learning classification algorithms provide an automated means to annotate data but require some of these data to be manually labeled by human experts, a process that is costly and time consuming. An alternative to labeling data is to use existing labeled data from a related domain, the source domain, if any such data is available, to train a classifier for the domain of interest, the target domain. However, the classification accuracy usually decreases for the domain of interest as the distance between the source and target domains increases. Another alternative is to label some data and complement it with abundant unlabeled data from the same domain, and train a semi-supervised classifier, although the unlabeled data can mislead such classifier. In this work another alternative is considered, domain adaptation, in which the goal is to train an accurate classifier for a domain with limited labeled data and abundant unlabeled data, the target domain, by leveraging labeled data from a related domain, the source domain. Several domain adaptation classifiers are proposed, derived from a supervised discriminative classifier (logistic regression) or a supervised generative classifier (naïve Bayes), and some of the factors that influence their accuracy are studied: features, data used from the source domain, how to incorporate the unlabeled data, and how to combine all available data. The proposed approaches were evaluated on two biological problems -- protein localization and ab initio splice site prediction. The former is motivated by the fact that predicting where a protein is localized provides an indication for its function, whereas the latter is an essential step in gene prediction.

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Srinivasan, Karunya. "Human adaptation of avian influenza viruses." Thesis, Massachusetts Institute of Technology, 2012. http://hdl.handle.net/1721.1/78139.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2012.
Cataloged from PDF version of thesis.
Includes bibliographical references.
Human adaptation of avian influenza viruses pose an enormous public health challenge as the human population is predominantly naive to avian influenza antigens. As such, constant surveillance is needed to monitor the circulating avian strains. Of particular importance are strains belonging to H5N1, H7N7, H7N2 and H9N2 subtypes that continue to circulate in birds worldwide and have on occasions caused infections in humans. A key step in influenza human adaptation is the accumulation of substitutions/mutations in the viral coat glycoprotein, hemagglutinin (HA), that changes HA's binding specificity and affinity towards glycan receptors in the upper respiratory epithelia (referred to as human receptors). Unlike for the H1, H2, H3 and more recently H5 HA a correlation between the quantitative binding of HA to human receptors and respiratory droplet transmissibility has not been established for H9 and H7 subtypes. This thesis is a systematic investigation of determinants that mediate changes in HA-glycan receptor binding specificity, with focus on the molecular environments within and surrounding the glycan receptor binding site (RBS) of avian HAs, particularly the H9 and H7 subtypes. The glycan receptor binding properties of HA were studied using a combination of biochemical and molecular biology approaches including dose dependent glycan binding, human tissue staining and structural modeling. Using these complementary analyses, it is shown that molecular interactions between amino acids in and proximal to the RBS, including interactions between the RBS and the glycan receptor converge to provide high affinity binding of avian HA to human receptors. For the H9 HA [alpha]2-->6 glycan receptor-binding affinity of a mutant carrying Thr-189-->Ala amino acid change correlated with the respiratory droplet transmission in ferrets conferred by this change. Further, it was demonstrated for the first time that two specific mutations; Gln226-->Leu and Gly228-->Ser in glycan receptor-binding site of H7 HA substantially increase its binding affinity to human receptors. These approaches and findings contribute to a framework for monitoring the evolution of HA and the development of general rules that govern human adaption applicable to strains beyond ones currently under study.
by Karunya Srinivasan.
Ph.D.

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Snipes, Chelsie, and Richard T. Carter. "Sound transmission by the hyoid apparatus during echolocation in bats." Digital Commons @ East Tennessee State University, 2021. https://dc.etsu.edu/asrf/2021/presentations/6.

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Sound transmission by the hyoid apparatus during echolocation in bats Chelsie C.G. Snipes1 and Richard T. Carter1 1 East Tennessee State University, Johnson City TN, USA The morphology of the stylohyal-tympanic bone articulation found in laryngeally echolocating bats is highly indicative of a function associated with signal production. One untested hypothesis is that this morphology allows the transfer of a sound signal from the larynx to the tympanic bones (auditory bulla) via the hyoid apparatus during signal production by the larynx. To test this hypothesis, we used µCT data, CAD editing software, and finite element analysis (FEA) to model the propagation of sound through the hyoid chain into the tympanic bones. This involved making digital segmentations from the µCT data of the tympanic bones and cartilaginous segments and converting it into a digital mesh body. Since the cartilaginous segments are not visible in CTs, we segmented the air in each gap and subsequently used a Boolean function in CAD software to fit each bony end into their respective cartilaginous segment. Further post-processing of the model included a reduction in the number of facets bodies and smoothing surfaces which allowed us to convert it into a solid body model. The solid body geometry was then uploaded into FEA software and assigned material properties for cortical bone, cartilage, and bulla. Additional biomechanical data, including Young’s Modulus, Poisson’s ratio, and speed of sound through each material were defined in previous literature. We ran two FEA analysis with our model: the first was an acoustic analysis that modelled sound propagation through our material (bone and cartilage), and the second was a coupled modal and structural analysis that modelled resonant behavior and sound pressure wave propagation from the hyoid body to the tympanic bones. Our models support the hypothesis that bats use this physical connection between the larynx and auditory bulla to transfer sound (mechanical excitation). Our models show both pressure waves and vibration due to resonance could be used to transfer this signal and this resonance behavior can be modulated by restraining the hyoid apparatus, perhaps through muscle contraction. We propose that by modulating the resonant behavior of the hyoid apparatus, bats can selectively filter which frequencies of sound are transferred from the larynx to the auditory bulla during echolocation signal production.

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Clarke, Sean Aidan. "Hypermutation and adaptation of experimentally evolved marine Vibrio bacteria." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81665.

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Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013.
Cataloged from PDF version of thesis.
Includes bibliographical references (p. 73-83).
Environmental bacteria display tremendous genetic diversity, but we are still learning how this diversity arises and relates to their wide range of habitats. Investigating how bacteria adapt helps us understand their contributions to environmental processes and informs forward engineering of bacteria for industrial applications. Experimental evolution is a powerful approach, with microbes especially, but it has mostly been applied to model organisms and metabolic functions. In the work here, we investigated the possibility, degree, and variability of adaptation of an environmental Vibrio strain by applying a little-used selection method appropriate to a relevant condition, salinity. We successfully isolated mutants with higher salt tolerance by selecting on salt gradient plates. Resequencing the genomes of the evolved strains revealed unprecedented hypermutation in three of nine parallel lineages. These mutator lines arose independently, and each of them accumulated more than 1500 single-base mutations. By comparison, there are only 302 single-base differences between the ancestor strain and another strain isolated in the wild. Hypermutation was associated with a deletion resulting from improper prophage excision. Members of this family of prophages are found in other proteobacteria, including well-studied human pathogens, from very different environments. Mutators are known to arise spontaneously in wild and clinical bacteria, but the extent of their adaptive contribution is unknown. We have preliminary evidence that this mechanism of evolution could be relevant in the environment, where horizontal gene transfer and mobile elements play known, significant roles in bacterial evolution.
by Sean Aidan Clarke.
Ph.D.

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Poole, L. F. "Psychological and biological determinants of emotional adaptation and recovery after cardiac surgery." Thesis, University College London (University of London), 2013. http://discovery.ucl.ac.uk/1384788/.

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How and why depression confers greater risk of impaired adaptation following coronary artery bypass graft (CABG) surgery is not well understood. This PhD aimed to address these issues by: developing and piloting a longitudinal study (the ARCS study) in order to track the recovery of patients undergoing CABG surgery; and conducting an extended version of the ARCS study on which to test the association between pre-operative depression and post-operative recovery and the underlying social-behavioural, cognitive and biological pathways. Outcomes were studied in the early and short term, namely three to five days (216 participants) and two months (154 participants) following surgery. The results indicated that greater pre-operative depression symptoms were predictive of poorer recovery, including longer in-hospital stays, greater emotional distress, physical symptoms and pain in the early term, and greater emotional distress, physical symptoms and pain and impaired health status in the short term, independent of demographic and disease severity factors (all p <0.05). Some associations were limited to subtypes of depression symptoms. Specifically, somatic/affective, but not total or cognitive/affective, depression symptoms were predictive of short-term outcomes. Mediators of the depression-recovery relationship were tested. Social support and behavioural factors were not shown to be mediators, but instead physical activity, body mass index and smoking status all had independent effects on recovery. Cognitive mediation was shown, with greater pre-operative negative illness perceptions mediating the relationship between pre-operative depression symptoms and post-operative anxiety and physical symptoms in the early term, and affective pain and physical symptoms in the short term. Biological mediation was not shown: although depression symptoms were related to neuroendocrine and inflammatory patterns suggestive of poorer physical functioning, these patterns did not consistently relate to recovery. Further work is needed to translate these findings into new ways to approach the measurement, diagnosis and treatment of depressed cardiac surgery patients.

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Welsh, David T. "The role of compatible solutes in the adaptation and survival of Escherichia coli." Thesis, University of Dundee, 1992. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.339281.

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COPPOLECCHIA, DAMIANO. "MICROBIAL INDICATORS OF ADAPTATION IN A ZINC CONTAMINATED SOIL." Doctoral thesis, Università Cattolica del Sacro Cuore, 2011. http://hdl.handle.net/10280/975.

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Scopo di questa tesi è stato di valutare se le attività biologiche possono essere utilizzate come indicatori di adattamento microbico. Le prove condotte sinora in letteratura si sono concentrate unicamente sull’attività di nitrificazione. Pertanto si è voluto valutare se altre attività biologiche possono essere utilizzate come indicatori d’adattamento. Allo scopo si è prima valutata la sensibilità di alcune importanti proprietà biologiche del suolo (nitrification, fluorescein diacetate (FDA)) e attività enzimatiche (urease, nitrate reductase, phosphatase, arylsulfatase, β-galactosidase, phenol-oxidase and dehydrogenase) allo Zn mediante l’impiego di test ecotossicologici Per le attività più sensibili sono state condotte delle prove di adattamento secondo il protocollo di Rusk. Questo esclude le interferenze dovuto all’ aging. Questo protocollo è basato sul reinoculo di un suolo sterile (contaminato con concentrazioni crescenti di Zn) con sottocampioni di suolo che sono stati precedentemente incubati per un periodo di 4 mesi con e senza Zn Il confronto tra i valori di EC50 delle attività biologiche dei suoli reinoculati ci ha permesso di dimostrare un significativo recupero della β-galactosidase, mentre per il nitrate reductase e la nitrificazione potenziale è stato trovato un chiaro e significativo shift delle curve di dose e risposta, anche se con parziale sovrapposizione del range dell’EC50 stimato.
The purpose of this thesis was to assess whether the biological activities can be used as indicators of the microbial adaptation. The tests conducted so far in the literature have focused only nitrification activity. Therefore we wanted to assess whether other biological activities can be used as indicators of adaptation. To do this you first evaluated the sensitivity of some important biological properties of the soil (nitrification, fluorescein diacetate (FDA)) and enzymatic activities (urease, nitrate reductase, phosphatase, arylsulfatase, β-galactosidase, phenol-oxidase and dehydrogenase) Zn through the use of toxicological test. Then the activities most sensitive were tests to evaluate to adapt according to the protocol by Rusk This method to exclude interferences to two chemical aging in soil, This protocol is based on the reinoculation of sterilized soil (contaminated with increasing Zn concentrations) with sub-samples of soil which have been incubated for 4 months with or without Zn. The comparison between the EC50 of the biological properties of reinoculated soils allow us to demonstrate a significant restoration was found for β-galactosidase, while for nitrate reductase and potential nitrification there was a clear and significant shift of dose response curves but with partial overlap of the EC50 ranges estimation.

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8

COPPOLECCHIA, DAMIANO. "MICROBIAL INDICATORS OF ADAPTATION IN A ZINC CONTAMINATED SOIL." Doctoral thesis, Università Cattolica del Sacro Cuore, 2011. http://hdl.handle.net/10280/975.

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Scopo di questa tesi è stato di valutare se le attività biologiche possono essere utilizzate come indicatori di adattamento microbico. Le prove condotte sinora in letteratura si sono concentrate unicamente sull’attività di nitrificazione. Pertanto si è voluto valutare se altre attività biologiche possono essere utilizzate come indicatori d’adattamento. Allo scopo si è prima valutata la sensibilità di alcune importanti proprietà biologiche del suolo (nitrification, fluorescein diacetate (FDA)) e attività enzimatiche (urease, nitrate reductase, phosphatase, arylsulfatase, β-galactosidase, phenol-oxidase and dehydrogenase) allo Zn mediante l’impiego di test ecotossicologici Per le attività più sensibili sono state condotte delle prove di adattamento secondo il protocollo di Rusk. Questo esclude le interferenze dovuto all’ aging. Questo protocollo è basato sul reinoculo di un suolo sterile (contaminato con concentrazioni crescenti di Zn) con sottocampioni di suolo che sono stati precedentemente incubati per un periodo di 4 mesi con e senza Zn Il confronto tra i valori di EC50 delle attività biologiche dei suoli reinoculati ci ha permesso di dimostrare un significativo recupero della β-galactosidase, mentre per il nitrate reductase e la nitrificazione potenziale è stato trovato un chiaro e significativo shift delle curve di dose e risposta, anche se con parziale sovrapposizione del range dell’EC50 stimato.
The purpose of this thesis was to assess whether the biological activities can be used as indicators of the microbial adaptation. The tests conducted so far in the literature have focused only nitrification activity. Therefore we wanted to assess whether other biological activities can be used as indicators of adaptation. To do this you first evaluated the sensitivity of some important biological properties of the soil (nitrification, fluorescein diacetate (FDA)) and enzymatic activities (urease, nitrate reductase, phosphatase, arylsulfatase, β-galactosidase, phenol-oxidase and dehydrogenase) Zn through the use of toxicological test. Then the activities most sensitive were tests to evaluate to adapt according to the protocol by Rusk This method to exclude interferences to two chemical aging in soil, This protocol is based on the reinoculation of sterilized soil (contaminated with increasing Zn concentrations) with sub-samples of soil which have been incubated for 4 months with or without Zn. The comparison between the EC50 of the biological properties of reinoculated soils allow us to demonstrate a significant restoration was found for β-galactosidase, while for nitrate reductase and potential nitrification there was a clear and significant shift of dose response curves but with partial overlap of the EC50 ranges estimation.

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9

Fletcher, David. "Biological invasion risk assessment, considering adaptation at multiple scales : the case of topmouth gudgeon Pseudorasbora parva." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTG029/document.

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Afin de quantifier les risques d’invasion chez le goujon Asiatique Pseudorasbora parva, un petit cyprinidae d’eau douce, j’ai tout d’abord testé une approche corrélative de modélisation de la niche climatique dans laquelle j’ai intégré un proxy relatif à la probabilité d’introduction. Cette approche s’appuie sur des assomptions relatives à l’adaptation des organismes aux conditions environnementales locales ou régionales. J’ai ensuite comparé la niche climatique mesurée de deux lignées génétiques majeures à la fois dans les aires natives et envahies. Puis dans un second temps, par une approche expérimentale j’ai comparé la réponse aux variations de température, des traits d’histoire de vie de populations vivant dans des zones climatiques contrastées. Finalement, je me suis intéressé à la dispersion des goujons Asiatiques afin de mieux comprendre si les populations situées sur les fronts d’invasions avaient des capacités de colonisation plus importante. J’ai donc quantifié et comparé le long d’un gradient d’invasion, le potentiel de dispersion des individus ainsi que des traits pouvant y être liés (activité et morphologie). L’étude des risques d’invasions a montré que de nombreuses zones – au delà des zones déjà envahies - étaient climatiquement favorables au goujon Asiatique. C’était le cas en particulier pour certaines zones comme l’Australie, l’Amérique du Sud et du Nord, indiquant que l’invasion de cette espèce pourrait encore s’étendre. Après avoir pris en compte les probabilités d’introduction, cette étude a montré que l’Amérique du Nord était la zone la plus à risques. Par contre, la niche climatique entre les différentes lignées dans les zones géographiques envahies est très similaire, ce qui laisse à penser qu’il n’y a pas de patrons d’adaptation locale chez cette espèce. Pour autant, la niche climatique observée dans la zone envahie est très différente de celle observée dans la zone native, ce qui suggère un shift climatique important au cours de l’invasion. Les réponses thermiques des traits d’histoire de vie du goujon Asiatique testés expérimentalement n’ont pas varié significativement entre les populations originaires de conditions climatiques continentales et maritime-tempérées. Par exemple, l’effort reproductif global des femelles n’a pas varié entre les températures testées (15-25°C) mais la stratégie temporelle de reproduction a beaucoup varié. L’effort reproductif était plus cours et plus intense à forte température, alors qu’il était plus étalé et avec des pics reproductifs moins forts à faible température. Pour ailleurs, il semble qu’il existe un gradient morphologique fort entre les populations situées à différentes distances du front d’invasion ce qui suggère une forte plasticité morphologique mais qui ne serait pas liée à la capacité de dispersion de ces populations. En effet, cette dernière ne variant pas significativement le long du gradient d’invasion. La capacité de dispersion serait principalement liée à la taille du corps de goujon Asiatique, les individus les plus grands ayant une probabilité plus élevée de disperser.Bien que les prédictions générales du modèle de niche puissent être affectées par de potentielles adaptations à l’échelle de la population ou de la lignée évolutive, les résultats suggèrent qu’une certaine incertitude liée à ces prédictions persiste puisque la distribution native ne prédisait que très mal la distribution actuelle dans les zones envahies. Par ailleurs, mes travaux expérimentaux à plus fine échelle suggèrent que cette espèce est extrêmement adaptable et tolère une large gamme environnementale, ce qui pourrait expliquer son caractère invasif. Les connaissances produites au cours de cette thèse constituent donc des ressources extrêmement pertinentes pour développer des stratégies de gestion visant à contrôler les invasions futures du goujon Asiatique
In this thesis I set out to quantify the risk of invasion from the invasive freshwater fish, Pseudorasbora parva, at a global extent, using traditional correlative ecological niche modelling approaches with the integration of surrogate data representing introduction likelihood (Chapter I). These correlative approaches rely upon key assumptions relating to the presence or absence of local or regional adaptations, and so I subsequently tested for evidence of such adaptations in genetic lineages and in individual populations. This was achieved through analyzing climatic niche differentiation of key genetic lineages in the native and invasive ranges (Chapter II) and by conducting lab experiments comparing thermal responses of important life history traits in populations from contrasting climates (Chapter III). The initial risk assessment did not account for a key factor in invasions; namely, natural dispersal. Natural dispersal has been observed to be subject to selection in vanguard populations of invasive species, and adaptation of dispersal traits can infer additional invasive vigor, allowing the species to spread across the landscape quicker. For this reason, I quantified dispersal, activity and morphological differences, often associated with differential dispersal ability, in populations along a distance-gradient from an invasion front, in order to identify if P. parva is capable of such adaptations.The initial risk mapping study showed that large areas, beyond the current distribution of the species, are climatically suitable. These areas are mainly in North and South America, Australia and New Zealand, and constitute significant scope for spread and impact of this species. When introduction likelihood was included, N. America appears most at risk. I found no evidence to suggest that native genetic lineages represented local adaptations to their respective native climates - there was little or no differentiation of the lineages’ climatic niches in the invasive range. It was also apparent, from the niche comparisons, that the climatic niche in the invaded range constituted a significant shift, compared to the native range. The thermal responses of P. parva life history traits did not differ significantly between populations from a strongly seasonal continental climate and a mild temperate maritime climate. The overall reproductive output of females did not vary according to breeding season temperature, however, temporal reproductive strategy showed a strong response, with lower temperatures inducing a protracted breeding season and higher temperatures inducing rapid and intense reproductive output. The dispersal and morphology-related study identified a strong gradient of morphological change, corresponding with distance from invasion front. This demonstrates a high degree of plasticity in P. parva’s morphology in an invasion context, however this was not linked to either dispersal or activity levels, neither of which was significantly linked to distance from invasion front. Dispersal was best explained by body size, with larger fish more likely to disperse further.Whilst I found no evidence to suggest that the model predictions (Chapter I) were hampered by differentiation at either lineage or population levels, the findings of Chapter II do highlight the uncertainties surrounding the degree of conservatism in such predictions, mainly owing to the fact that past, native, distribution did not accurately predict the current invaded distribution. The results of Chapters II-IV show broad tolerances and great plasticity in P. parva, which likely underpin this species success as a pan-continental invader. The knowledge produced in this thesis provides a useful new resource for the development of management strategies for P. parva and could be usefully enhanced by the additional of analogous studies on native populations, which could help elucidate the source of the observed plasticity

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Clarke, Gregory Stephen. "The Evolution of Competitive Ability Across a Biological Invasion: A Study of Cane Toads in Tropical Australia." Thesis, The University of Sydney, 2019. http://hdl.handle.net/2123/21083.

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Invasive species must adapt to a suite of novel selective pressures as they colonise new territory. For example, theory predicts that selective forces at an invasion front will favour traits that enhance rates of dispersal and population growth, whereas selective forces in the range-core will favour traits that enhance competitive ability. To explore this idea, I conducted competition trials on three life stages of the invasive cane toad (Rhinella marina) from invasion-front and range-core populations in tropical Australia. For larval and early terrestrial-stage animals, I conducted experiments whereby the offspring of invasion-front and range-core adults were placed into mesocosms to compete for limited resources. To enable such experiments, I developed a simple method to mark each cohort of tadpoles, with minimal observed effects on growth or survival. Range-core larvae proved to be better competitors than invasion-front larvae, as predicted by evolutionary theory. Contrary to expectations, invasion-front metamorphs outcompeted range-core metamorphs, growing larger and winning more food. For adults, I focused on the trade-off between rapid dispersal versus success in male-male rivalry. Longer arms reduced the force required to displace an amplecting male from a female. When competing for a female, males with longer arms had lower likelihoods of retaining amplexus. I also explored how visual and acoustic cues influence the behaviour of sexually active males. Male toads used the presence of a chorus to increase their activity levels and as a cue to initiate amplexus. Males also used movement to identify potential mates, with increased rates of amplexus when a target was moving. My thesis presents empirical evidence that the evolutionary forces unleashed by a biological invasion can modify traits important in intraspecific competition at each life stage. My results are relevant to evolutionary theory and are directly translatable into proposed management strategies.

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Perunov, Nikolay. "Statistical physics of biological self-organization : case studies in protein folding and adaptation to time-varying fields." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/103232.

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Thesis: Ph. D., Massachusetts Institute of Technology, Department of Physics, 2016.
Cataloged from PDF version of thesis.
Includes bibliographical references (pages 119-128).
In this thesis, we use the methods of statistical physics to provide quantitative insights into the behavior of biological systems. In the first half of the thesis, we use equilibrium statistical physics to develop a phenomenological model of how the hydrophobic effect impacts the structure of proteins, and in the second half, we study the phenomenon of adaptation and Darwinian selection from the standpoint of nonequilibrium statistical physics. It has been known for a long time that the hydrophobic effect plays a major role in driving protein folding. However, it has been challenging to translate this understanding into a predictive, quantitative theory of how the full pattern of sequence hydrophobicity in a protein helps to determine its structure. Here, we develop and apply a phenomenological theory of the sequence-structure relationship in globular protein domains. In an effort to optimize parameters for the model, we first analyze the patterns of backbone burial found in single-domain crystal structures and discover that classic hydrophobicity scales derived from bulk physicochemical properties of amino acids are already nearly optimal for prediction of burial using the model. Subsequently, we apply the model to studying structural fluctuations in proteins and establish a means of identifying ligand-binding and protein-protein interaction sites using this approach. In the second half of the thesis, we undertake to address the question of adaptation from the standpoint of physics. Building on past fundamental results in nonequilibrium statistical mechanics, we demonstrate a generalization of the Helmholtz free energy for the finite-time stochastic evolution of driven Newtonian matter. By analyzing this expression, we show a general tendency in a broad class of driven many-particle systems toward self-organization into states formed through reliable absorption and dissipation of work energy from the surrounding environment. We demonstrate how this tendency plays out in the familiar example of Darwinian competition between two exponentially growing self-replicators. Subsequently, we illustrate the more general mechanism by which extra dissipation drives adaptation by analyzing the process of random hopping in driven energy landscapes.
by Nikolay Perunov.
Ph. D.

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Coi, Anna Lisa. "A genome based approach to characterize genes involved in yeast adaptation to Sherry-like wines’ biological ageing." Thesis, Montpellier, SupAgro, 2014. http://www.theses.fr/2014NSAM0005/document.

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La fermentation œnologique et le vieillissement oxydatif des vins sous voile représentent des modes de vie très contrastés qui sont effectués par deux lignées différentes de souches de levures de l'espèce Saccharomyces cerevisiae. Dans cette thèse, nous avons comparé le génome de souches de levures de voile à celui de levures de vin afin de détecter leurs spécificités. Nous tout d'abord sélectionné 16 souches (8 levures de vin et 8 levures de voile) isolées en France, Hongrie, Italie et Espagne, pour séquencer leur génome sur une plateforme Illumina (HiSeq2000). Nous avons également développé un ensemble de souches de vin et de voile haploïdes pour l'évaluation moléculaire de différentes cibles. Nous avons également mis au point un milieu synthétique mimant le vin à cette fin. A partir de la comparaison des séquences du génome nous avons établi une phylogénie qui montre que les levures de voile représentent un groupe spécifique de levure, différentes des levures de vin, puis à partir de différentes méthodes (analyse en composantes principale, diversité nucléotidique et D de Tajima) nous avons identifié des régions divergentes. Ces régions variantes comprennent des gènes remplissant plusieurs fonctions clé associées à la croissance en voile. En particulier, des variations alléliques ont été rencontrées chez les levures de voile pour plusieurs gènes impliqués dans la régulation de l'expression de FLO11 tels que les voies MAP kinase, ou des voies Ras/cAMP/PKA, ainsi que pour plusieurs gènes impliqués dans l'homéostasie des cations divalents de métaux de transition tels que le zinc, le cuivre ou le fer. La comparaison des transcriptomes d'une levure de voile et d'une levure de vin sur notre milieu synthétique a révélé des différences d'expression pour les floculines (FLO1, 5, 8, 11) ainsi que pour le transport des hexoses, mais a également suggéré que la levure de voile P3-D5 était en situation de carence en zinc et en inositol par rapport à la levure de vin, tandis que la levure de vin K1 exprimait certains gènes suggérant des défauts mitochondriaux. L'impact de la variation allélique de plusieurs gènes a été évalué dans le phénotype de voile: le transporteur de zinc à haute affinité Zrt1 ainsi que la pyruvate décarboxylase majeure Pdc1
Wine fermentation and flor ageing are performed by two groups of the yeast Saccharomyces cerevisiae, with very different lifestyles. In this thesis we have studied the genome of flor yeast in comparison to wine yeast in order to unravel their specificities. We have first selected 16 strains (8 wine and 8 flor) from France, Hungary, Italy and Spain in order to sequence their genome sequence on an Illumina HiSeq2000 platform. Three flor strains and two wine strains were haploidized in order to obtain a set of haploid flor strains for the molecular evaluation of different targets. We developed as well a synthetic media mimicking wine for that purpose. From the genome sequence we have drawn a phylogeny that showed that flor yeasts represent a specific lineage of yeast, different from the wine strains lineage, and identified divergent regions. These regions contain genes involved in key functions and several associated with velum growth. Remarkably, many genes involved in FLO11 regulation such as MAP kinase, or Ras/PKA pathways were mutated among flor strains and many variations were encountered in genes involved in metal homeostasis such as zinc and divalent metal transporters. A transcriptome analysis comparing one flor and one wine yeast on our wine synthetic media revealed expression differences associated to floculins and hexose transport, but also suggested that flor yeast P3-D5 face a zinc and inositol deficiency, whereas wine yeast K1 presented mitochondrial defects. The impact of allelic variation of several genes coding for the high affinity zinc transporter (ZRT1), and the major pyruvate decarboxylase (PDC1) has been evaluated in order to assess their role in the flor phenotype

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Garmany, Mattea A., Darrell Moore, and Thomas C. Jones. "Effects of Non-photic Zeitgebers on the Circadian Clock in the Common House Spider, Parasteatoda tepidariorum." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/asrf/2019/schedule/149.

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Most eukaryotic organisms have an internal circadian clock which allows them to maintain their physiological and behavioral cycles in phase with the 24-hour day. The ability to synchronize with (entrain to) the 24-hour day prevents mismatch between the internal circadian clock and the daily cycle which could lead to serious health risks. Some spider species, including Parasteatoda tepidariorum, appear to be exempt from the negative consequences of being out of phase with the 24-hour day. Parasteatoda tepidariorum, the common house spider, is a nocturnal species that consistently demonstrates a short-period circadian clock averaging 21.6 hours when left in constant darkness, yet they are able to entrain to the 24-hour light cycle. Here we test if these spiders are able to use cues (Zeitgebers) other than light to entrain to the 24-hour day. These non-photic Zeitgebers included food, disturbance, and temperature changes. The spiders were assigned into groups which received the given external cues at 24-hour intervals for 7 days followed by 7 days without any external cues. Food, disturbance, and temperature were not found to be effective Zeitgebers for the spiders’ entrainment. There were significant results between random feedings with consistent scheduled feedings which suggests that these spiders were able to manipulate the duration of activity based on the consistency and regularity of a food source. Adjusting the span of activity based on availability of food sources would be advantageous for spiders considering that prey availability in natural environments may not be rhythmic. Given that these spiders tend to build webs in dark secluded spaces, it would be a particular advantage for them to be able to use an environmental cue in addition to light to entrain their internal clocks. However, our data to date suggest otherwise.

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Chang, Joshua TsuKang. "Flipping Biological Switches: Solving for Optimal Control: A Dissertation." eScholarship@UMMS, 2015. https://escholarship.umassmed.edu/gsbs_diss/763.

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Switches play an important regulatory role at all levels of biology, from molecular switches triggering signaling cascades to cellular switches regulating cell maturation and apoptosis. Medical therapies are often designed to toggle a system from one state to another, achieving a specified health outcome. For instance, small doses of subpathologic viruses activate the immune system’s production of antibodies. Electrical stimulation revert cardiac arrhythmias back to normal sinus rhythm. In all of these examples, a major challenge is finding the optimal stimulus waveform necessary to cause the switch to flip. This thesis develops, validates, and applies a novel model-independent stochastic algorithm, the Extrema Distortion Algorithm (EDA), towards finding the optimal stimulus. We validate the EDA’s performance for the Hodgkin-Huxley model (an empirically validated ionic model of neuronal excitability), the FitzHugh-Nagumo model (an abstract model applied to a wide range of biological systems that that exhibit an oscillatory state and a quiescent state), and the genetic toggle switch (a model of bistable gene expression). We show that the EDA is able to not only find the optimal solution, but also in some cases excel beyond the traditional analytic approaches. Finally, we have computed novel optimal stimulus waveforms for aborting epileptic seizures using the EDA in cellular and network models of epilepsy. This work represents a first step in developing a new class of adaptive algorithms and devices that flip biological switches, revealing basic mechanistic insights and therapeutic applications for a broad range of disorders.

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Gunnin, R. Davis, Blaine W. Schubert, Joshua X. Samuels, and Keila E. Bredehoeft. "A new genus of desmognathan salamander (Plethodontidae) from the early Pliocene Gray Fossil Site of Northeast Tennessee." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/asrf/2019/schedule/65.

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Many organisms are known to reach high levels of endemism and biodiversity in the temperate forests of Southern Appalachia, especially in the dense forests and rugged terrain of the Blue Ridge physiographic province. Many plants and fungi reach their highest levels of biodiversity in these mountains, as does one group of vertebrates: the lungless salamanders, Plethodontidae. This family of salamanders hosts the most species of any other group of salamanders on earth and has adapted to a wide range of habitats. Only two of the approximately twenty-seven known genera are not found in North or South America, and while we know much about the modern-day biology of this family, few fossils older than ~15,000 years have been recovered, complicating our understanding of the historical distribution of this group and the timing of key evolutionary events within the family. Recently discovered salamander fossils from the Gray Fossil Site provide the foundation of this project. We describe these exceptionally large plethodontid remains to a new genus that belongs to the group containing dusky salamanders, or desmognathans. The morphology of the fossil material resembles Phaeognathus hubrichti, an extant burrowing species from southern Alabama with a suite of primitive characteristics. Comparison of the fossil material to modern desmognathans using geometric statistical methods has revealed that the extinct form was likely similar in lifestyle to P. hubrichti, but considerably larger. It was unparalleled in the southern Appalachians in terms of size and ecology, and reveals a more complex evolutionary history for desmognathan salamanders.

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Musker, Seth. "Dispersal, gene flow, niche divergence and local adaptation in the hyper-diverse ruschioid Aizoaceae: testing alternative modes of speciation in the Knersvlakte quartz field flora of the Succulent Karoo, South Africa." Master's thesis, University of Cape Town, 2017. http://hdl.handle.net/11427/27384.

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What are the roles of alternative modes of speciation in the generation of biological diversity? This question is fundamental to the debate surrounding the origins of extraordinarily diverse regions and clades. Diversification in the Cape flora of South Africa has been intensively studied owing to its remarkable diversity, for which significant roles for both ecological and non-ecological speciation have been invoked as drivers. However, much of this research has focused on the mesic fynbos vegetation, with far less attention paid to its neighboring biodiversity hotspot, the arid Succulent Karoo (SK), which has hosted the spectacular radiation of the ecologically dominant ruschioid Aizoaceae, a succulent group which exhibits extreme morphological diversity and convergence. This thesis focused on ruschioid Aizoaceae in the Knersvlakte, a small region of the SK which holds a diverse and endemic-rich flora specially adapted to the ecologically unusual quartz fields - whose patchy distribution in the landscape suggests that diversification may have been facilitated by divergence of populations isolated on these 'environmental islands' in a similar fashion to serpentine systems such as those in California - and continues from previous work on the Knersvlakte-endemic ruschioid genus Argyroderma which supported an adaptive radiation in allopatry hypothesis. A population genomic approach was used to investigate the scale of seed dispersal (which is thought to be very limited due to the group's highly specialized ballistic dispersal mechanism) as well as correlates of population divergence in two ruschioid quartz-field specialists with very different growth forms (the shrubby Ruschia burtoniae versus the dwarf Conophytum calculus) and which co-occurred at four sites distributed throughout the Knersvlakte. This, in combination with ecological and experimental transplant data to test the adaptive underpinning of edaphically-driven community structure, ecological isolation and niche divergence in these and other quartz field species, made it possible to tease apart the roles of local adaptation and limited dispersal in driving gene flow and speciation in the system. Quartz fields were found to be a highly insular habitat with strong internal edaphic community structure, suggesting that they represent an environmental island system. In addition, intrinsic dispersal ability was very poor in the specialist shrub, which showed complete genetic isolation between the four populations separated by just 17-42 km. This species showed strong local adaptation between the populations as well as some evidence that this inhibited gene flow, though it is more likely that dispersal limitation allowed for fundamental niche divergence. In contrast, the dwarf showed surprisingly good dispersal ability and consequent weak genetic structure, which accounted for the lack of edaphic local adaptation between the populations. The study showed that, contrary to expectation, not all ruschioid Aizoaceae are poor dispersers, and also suggested that the likelihood of ecological speciation in response to edaphic heterogeneity is contingent on dispersal ability. Strongly limited dispersal may thus have contributed to the group's diversification either through non-adaptive radiation or edaphically driven adaptive radiation, but other factors are more likely to have driven diversification in sections of ruschioid Aizoaceae that possess mechanisms of long-distance dispersal. Future work might focus on inferring the scale of dispersal (e.g. based on morphological traits) and whether it predicts diversification rates. Finally, the lack of morphological variation in R. burtoniae belies its strong ecological and genetic divergence; in light of this, systematists are encouraged to investigate cryptic speciation in the group.

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Säfström, Daniel. "Sensorimotor transformations during grasping movements /." Umeå : Department of Integrative Medical Biology, 2006. http://urn.kb.se/resolve?urn=urn:nbn:se:umu:diva-781.

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Steele, Rebecca, Clinton Elmore, Rebecca Wilson, Darrell James Moore, Blaine W. Schubert, and Thomas Charles Jones. "Chronoecology of the Cave Dwelling Orb-Weaver Spider, Meta ovalis (Araneae: Tetragnathidae)." Digital Commons @ East Tennessee State University, 2019. https://dc.etsu.edu/asrf/2019/schedule/198.

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Circadian clocks are endogenous time keeping mechanisms that are ubiquitous among animals. They enable coordination of many essential biological and metabolic processes in relation to the 24 hour light cycle on earth. However, there are many habitats on earth that are not subject to this light cycle. This study aims to look at the potential genetic drift of the circadian rhythm of a subterranean spider, Meta ovalis, as well as gathering general natural history information on this under-studied spider. This study will fill general gaps in knowledge of this spider and its habitat, highlight the importance of studying organisms within a subterranean environment, and place importance on cave conservation and acquiring knowledge of these specialized, and sensitive species. This study integrates circadian and foraging theory to evaluate species as circadian specialists and generalists based on how narrowly or widely their activity is spread over the 24 h cycle. We suggest that M. ovalis benefits from a generalist strategy, showing small bursts of focused activity widely dispersed across the 24 h cycle, allowing it to capture prey opportunistically whenever it is available. Live spiders were collected from area caves, monitored in an environment controlled for light and temperature, and returned to their cave of origin. The activity of each spider was analyzed for differences in circadian activity among and between populations to determine if there is a significant drift of the circadian strategy between isolated populations of Meta ovalis. We expect to see a different circadian strategy implemented between populations due to drift from the spiders being isolated from other populations.

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Waffenschmidt, Tobias [Verfasser], Andreas [Akademischer Betreuer] Menzel, and Ellen [Gutachter] Kuhl. "Modelling and simulation of adaptation and degradation in anisotropic biological tissues / Tobias Waffenschmidt. Betreuer: Andreas Menzel. Gutachter: Ellen Kuhl." Dortmund : Universitätsbibliothek Dortmund, 2013. http://d-nb.info/1108288634/34.

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Ermold, Friederike. "Climate change time machine : Adaptation to 30 years of warming in the Baltic Sea." Doctoral thesis, Uppsala universitet, Zooekologi, 2016. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-271575.

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Earth mean surface temperature has increased by 1 °C since the industrial revolution, and this has already had considerable effects on animal and plant species. Ecological responses to the warming climate – often facilitated via phenotypic plasticity – are ubiquitous. However, even though evolution can occur rapidly there are only few examples of genetic adaptation to climate change. In my thesis, I used a near-natural system to study if and how organisms have adapted to 30 years of warming, and how this has affected competitive species interactions. I investigated Baltic Sea populations of the aquatic snails Galba truncatula and Theodoxus fluviatilis, which had been subjected to cooling water discharge from power plants, resulting in water temperatures 4 to 10 °C higher than in the surrounding sea. G. truncatula had high upper thermal limits and large acclimation potential. This plasticity may have helped the species to survive under the new conditions, allowing evolution through natural selection to take place. I found that the populations of the two thermal origins had diverged in SNP markers associated with warmer temperature, whereas divergence in selectively neutral markers was mainly related to geographical distance. Adaptation occurred from standing genetic variation, emphasizing the importance of genetic diversity and population size in enabling the persistence of populations. Changes in thermal sensitivity of growth and survival were subtle yet significant, and complied with theoretical models of thermal adaptation in ectotherms. At the community level, pre-adaptation to warmer conditions aided the native T. fluviatilis when competing with the alien Potamopyrgus antipodarum. However, interspecific competition limited the snails most in those traits favored under warming, highlighting the challenge of adapting to different selecting forces during global change. The persistence of species and populations under climate change depends on several factors - plasticity allowing for initial survival, evolvability in allowing the genetic changes, and species interactions affecting the new ecological niches. The results of my thesis indicate that persistence under climate change is possible when these factors align, but the relative roles of ecology and plasticity may explain why there are so few observed instances of evolution in response to climate change.

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Alder, Matthew N. "The adaptive immune system of sea lamprey." Thesis, Birmingham, Ala. : University of Alabama at Birmingham, 2008. https://www.mhsl.uab.edu/dt/2009r/alder.pdf.

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Gallien, Laure. "Comprendre et prédire l'expansion géographique des espèces végétales invasives dans les Alpes." Thesis, Grenoble, 2013. http://www.theses.fr/2013GRENV062/document.

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Les invasions biologiques, deuxième menace majeure de la biodiversité, pose d'important défis pour la conservation de la biodiversité, et la recherche en éco-évolution. Les espèces invasives ont en effet été étudiées depuis plus de 150 ans, mais nos capacités à prédire leurs présences aujourd'hui et dans le futur reste rudimentaire. Ce problème est principalement dû à la difficulté d'estimer à la fois les composantes biotiques et abiotiques de la niche des espèces invasives, ainsi que leur évolution dans le temps et l'espace. L'objectif de ma thèse a été de travailler sur ces défis en améliorant les méthodes d'estimation de niche, en enrichissant notre compréhension du rôle des interactions biotiques dans le processus d'invasion, et en étudiant en détail comment les processus évolutifs peuvent affecter la dynamique spatio-temporelle des niches. Plus précisément, (1) à l'aide d'une revue de la littérature, j'ai commencé par décrire les limites des différentes approches de modélisation utilisées pour prédire la distribution des espèces invasives. (2) Ensuite, j'ai proposé un cadre de modélisation permettant d'améliorer l'estimation des niches abiotiques régionales. (3) Puis, je me suis intéressée à la caractérisation des interactions biotiques, et aux méthodes communément utilisées pour identifier les patrons de compétition symétrique en écologie des communautés. J'ai également implémenté un modèle de simulation d'assemblage de communautés pour tester la performance de ces méthodes. (4) Ces premières études m'ont permis d'étudier à la fois les composantes biotiques et abiotiques des communautés de plantes envahies dans les Alpes. (5) Finalement, j'ai étudié l'évolution de la niche environnementale chez une espèce invasive des Alpes françaises Ambrosia artemisiifolia L, à travers une approche reliant niche-trait-génétique. Dans l'ensemble, les résultats de ces études montrent à quel point les différentes facettes de l'écologie et l'évolution en invasion sont fortement intriquées. De plus, ils soulignent la nécessité d'une modélisation intégrant les processus écologiques et évolutifs pour pouvoir comprendre la dynamique des invasions et proposer des outils de protection de la biodiversité efficaces
Biological invasions, the second major threat to biodiversity, pose significant challenges to conservation management and eco-evolutionary research. Even though invasion processes have been studied for more than 150 years, our capacity to predict their presence today and in the future is still rudimentary. This deficiency stems mainly from the difficulty involved in reliably assessing the ecological niche of an invader, i.e. those environmental and biotic conditions that allow the species to maintain viable populations. In particular, disentangling the abiotic and biotic components of the ecological niche and accounting for their changing over space and time due to evolutionary dynamics is difficult, albeit crucial for the quality of predictions. The main objective of my PhD has been to address these challenges by improving methodological approaches of niche estimation, advancing our understanding of the role of biotic interactions for invasion processes and studying in greater detail how evolution may affect spatio-temporal niche dynamics. More precisely, (1) with a comprehensive literature review, I started by describing the limits of the different modelling approaches usually applied to predict invasive species distributions. (2) Then, I provided a modelling framework for improving regional environmental niche estimations. (3) Thirdly, I focused on the identification of biotic interactions, and the methods commonly used to identify patterns of symmetric competition in ecological communities. I also implemented a simulation model of community assembly to test the efficiency of these methods. (4) In a fourth part, I studied invaded alpine plant communities and showed that characteristics of the biotic environment in these communities (e.g. symmetric vs. asymmetric competition) were good predictors of invaders' presence. (5) Finally, I provided a first example of a genetic-based, climatic niche expansion of the invasive weed Ambrosia artemisiifolia L. in the French Alps by combining information on its environmental niche, genetic structure and functional traits. Taken together, the results of these studies highlight how tightly the different facets of invasion ecology and evolution are interrelated and open the way to an integrated modelling approach that would advance both eco-evolutionary research on invasion dynamics and applied tools for biodiversity protection

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Genitoni, Julien. "Acclimatation de l’espèce aquatique invasive, Ludwigia grandiflora, au milieu terrestre : Approches physiologique et épigénétique." Thesis, Rennes, Agrocampus Ouest, 2019. http://www.theses.fr/2019NSARA085.

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Dans un contexte d’expansion des espèces invasives, leur survie et succès sont conditionnés par leur capacité à s’adapter. En France, Ludwigia grandiflora (jussie) a envahi bon nombre de biotopes aquatiques et son déploiement récent dans les prairies humides a conduit à l’apparition de deux morphotypes, l’un aquatique et l’autre dit « terrestre ». L’objectif de cette thèse visait à mieux comprendre les capacités d’acclimatation de la jussie au milieu terrestre en explorant les sources de flexibilité que sont les mécanismes génétiques et épigénétiques. Les réponses des morphotypes aquatique et terrestre à différentes contraintes hydriques ont été évaluées via l’observation des traits morphologiques et développementaux, des dosages de métabolites et de phytohormones. La piste épigénétique a été abordée par l’utilisation d’une drogue hypométhylante, la zébularine. Ces travaux ont montré que L. grandiflora adapte son développement et son métabolisme avec des valeurs de biomasses élevées etLe morphotype terrestre présente des valeurs de traits plus importants que ceux du morphotype aquatique, quelle que soit la condition. Cependant, la plasticité phénotypique est plus importante chez le morphotype aquatique. Enfin, l’épigénétique via la méthylation de l’ADN semble impliquée dans la transition du morphotype aquatique vers le milieu terrestre. Nos résultats suggèrent une implication de la méthylation de l’ADN et de la plasticité phénotypique dans la réponse de la jussie au changement de milieu. Le morphotype terrestre ayant des capacités supérieures au morphotype aquatique, sa
Abstract: In the context of the expansion of invasive species, their survival is conditioned by their ability to adapt. In France, Ludwigia grandiflora has invaded aquatic biotopes and its recent deployment in wet meadows has led to the emergence of two morphotypes, one aquatic and the other called “terrestrial”. The aim of this thesis was to get a better understanding of water primrose acclimation capacities to terrestrial environment through exploring genetic and epigenetic sources of flexibility. The responses of two morphotypes to different water stresses were evaluated by observing physiological traits. The epigenetic pathway was addressed by the use of a hypomethylant drug. This work showed that L. grandiflora adapts its development and metabolism according to environmental conditions.The terrestrial morphotype shows higher trait values than those of the aquatic morphotype, regardless of the condition. However, phenotypic plasticity is higher in the aquatic morphotype. Finally, our results suggest the involvement of DNA methylation and phenotypic plasticity in the response of water primrose to environmental change. Since the terrestrial morphotype has higher capacities than the aquatic morphotype, its management must become a priority. The acquisition of genomic resources in L. grandiflora will make it possible to search for genetic and epigenetic markers of acclimation to the terrestrial environment

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Parrett, Jonathan Michael. "The role of sexual selection in adaptation to novel environments and the effects of environmental change on sexual selection." Thesis, Queen Mary, University of London, 2018. http://qmro.qmul.ac.uk/xmlui/handle/123456789/39761.

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Sexual selection is ubiquitous in all sexually reproducing species and a powerful evolutionary force. The effect of sexual selection on population fitness has caused wide debate and has been proposed to both enhance adaptation rates, but also possibly increase extinction risk. Using experimental evolution, the strength of sexual selection was altered by biasing adult sex ratios in replicated populations of the Indian meal moth, Plodia interpunctella. Under increasing temperatures strong sexual selection and polyandry was associated with increased population fitness. Suggesting sexual selection could provide a buffer against climate change by increasing adaptation rates. However, no effect on male mating success was observed. In contrast, under stable temperatures male mating success was increased by strong sexual selection, however, this did not translate to increased population fitness. These results indicate that female choice is a potentially strong selective pressure in P. interpunctella. Moreover, under stabilising and directional selection the costs and benefits of sexual selection change. In a field study, dung beetle species richness and abundance were compared across a gradient of habitat disturbance, ranging from old-growth rainforest to oil palm plantation. Species persistence within altered habitats was positively associated with expressing horns and relative horn lengths, suggesting male-male competition increases a species ability to persist within modified landscapes. There was not a strong effect of relative testes mass or sexual size dimorphism on the abundance of species. Additionally, by examining the expression of sexually selected traits within species, horn length and testes mass appear to be condition dependent, but only the expression of horns was effected by habitat change. Overall, from both laboratory and field studies it was found that sexual selection can increase adaptation rates and the persistence of species within altered and changing environments. Moreover, both sets of studies suggest pre-copulatory sexual selection to be an important aspect of sexual selection in driving this adaptation.

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Saers, Jacobus Petrus Paulus. "Ontogeny and functional adaptation of trabecular bone in the human foot." Thesis, University of Cambridge, 2017. https://www.repository.cam.ac.uk/handle/1810/270298.

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Trabecular bone forms the internal scaffolding of most bones, and consists of a microscopic lattice-like structure of interconnected bony struts. Experimental work has demonstrated that trabecular bone adapts its structural rigidity and orientation in response to the strains placed upon the skeleton during life, a concept popularly known as “Wolff’s Law” or “bone functional adaptation”. Anthropological work has focused on correlating variation in primate trabecular bone to locomotor and masticatory function, to provide a context for the interpretation of fossil morphology. However, intraspecies variation and its underlying mechanisms are still poorly understood. In this thesis, variation in trabecular bone structure is examined in the human foot in four archaeological populations. The aim is to tease apart the factors underlying variation in human trabecular microstructure to determine whether it may be a suitable proxy for inferring terrestrial mobility in past populations. μCT scanning is used to image the three-dimensional trabecular structure of the talus, calcaneus, and first metatarsal in samples from four archaeological populations. Trabecular structure is quantified in seventeen volumes of interest placed throughout the foot. Trabecular bone is influenced by a variety of factors including body mass, age, diet, temperature, genetics, sex, and mechanical loading. Before trabecular structure can be used to infer habitual behaviour, the effects of these factors need to be understood and ideally statistically accounted for. Therefore, the effects of variation in bone size and shape, body mass, age, and sex on human trabecular structure are examined in four populations. Significant effects of body mass and age are reported, but little sexual dimorphism was found within populations. Taking these results into account, variation in trabecular structure is compared between archaeological populations that were divided into high and low mobility categories. Results demonstrate that the four populations show similar patterns of trabecular variation throughout the foot, with a signal of terrestrial mobility level superimposed upon it. Terrestrial mobility is associated with greater bone volume fraction and thicker, more widely spaced, and less interconnected trabeculae. Ontogeny of trabecular bone in the human calcaneus is investigated in two archaeological populations in the final chapter of the thesis. Results indicate that calcaneal trabecular bone adapts predictably to changes in loading associated with phases of gait maturation and increases in body mass. This opens the possibility of using trabecular structure to serve as a proxy of neuromuscular development in juvenile hominins. This work demonstrates that trabecular bone may serve as a useful proxy of habitual behaviour in hominin fossils and past populations when all contributing factors are carefully considered and ideally statistically controlled for.

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King, Judy A. "Adaptation of Striped Bass to Sea Water Following Direct Transfer from Freshwater: Morphological, Biochemical, and Physiological Parameters." Digital Commons @ East Tennessee State University, 1987. https://dc.etsu.edu/etd/2932.

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There has been heightened interest in the biology of striped bass (Morone saxatilis) because of increased pollution in their native spawning grounds and because of their extensive use in landlocked sport fisheries. Their euryhalinity makes them an excellent species for osmoregulation studies. The objective of this research was to study the rate of adaptation of striped bass gills to sea water (3% salt) after direct transfer from freshwater using biochemical (ion transport enzyme levels), physiological (chloride efflux), and ultrastructural methods. Striped bass have specialized osmoregulatory cells located on the interlamellar and afferent surfaces of their gill filaments as shown by light microscopy (LM), transmission electron microscopy (TEM), and scanning electron microscopy (SEM). SEM studies show that apical pit (opening of one or more chloride cells) morphology changes during sea water adaptation, and the number of apical pits increases by 32.5% after two weeks in sea water. Chloride cell size and number, extent of basolateral tubular system, and number of mitochondria per chloride cell appear to increase upon adaptation to sea water. Sodium-potassium adenosine triphosphatase (Na,K-ATPase) activity is maximal on day 3 after transfer to sea water. Studies suggest that cortisol may act as a hormonal mediator for long term adaptation to sea water. The general morphology of both freshwater and sea water adapted fish gills were studied. Preliminary studies indicate that the osmium-dimethylsulfoxide-osmium method can be used to investigate intracellular structural changes in striped bass gills. Since the chloride cells are associated with the afferent surface of the filament, the blood supply to that area is also of great interest in osmoregulation studies. Studies of the gill vasculature using corrosion casting (i.e. filling blood vessels with plastic resins) and SEM indicate that the blood vessel distribution in the striped bass gill is similar to that of other euryhaline species with arterio-arterial, arterio-venous, and nutritive pathways. Blood flow may be controlled at a variety of places by sphincters, shunts and cellular contraction. Correlation of these biochemical, physiological and anatomical measurements will aid in the understanding of the process of adaptation to sea water. (Abstract shortened with permission of author.)

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Mougou, Amira. "Interaction Chêne-oïdium : caractérisation moléculaire et adaptation locale du parasite, résistance génétique de l’hôte." Thesis, Bordeaux 1, 2009. http://www.theses.fr/2009BOR13820/document.

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L’oïdium est une des maladies les plus communes sur chêne en Europe. Cette maladie a été signalée à partir du début du 20ème siècle. Toutefois, peu de données sont disponibles sur l’identité de l’agent causal et de son interaction avec l’hôte. L’objectif de cette étude est d’améliorer les connaissances sur ce pathosystème : (1) caractériser son agent causal avec un marqueur moléculaire (ADN ribosomal) et étudier la distribution spatiale des différentes lignées ; (2) étudier l’adaptation locale du parasite à son hôte ; (3) explorer le déterminisme génétique de la résistance de l’hôte. L’étude de l’ADN ribosomal (ITS=Internal transcribed region et IGS= Intergenic spacer) a mis en évidence l’existence de quatre haplotypes, dont trois seulement avaient été associés à des agents d’oïdium sur chêne en Europe. Erysiphe alphitoïdes, classiquement considéré comme responsable de l’épidémie du XXème siècle est bien l’espèce prépondérante (environ 80% des détections), E. hypophylla et Phyllactinia sp étant détectés à fréquence beaucoup plus faible. Un résultat inattendu est la détection d’une quatrième séquence, présentant 100% d’homologie avec celle de plusieurs agents d’oïdium d’arbres tropicaux et avec Erysiphe quercicola, très récemment décrit sur chêne en Asie et Australie mais jusqu’alors inconnu en Europe. L’ITS de E. quercicola est détecté dans toutes les régions de France, à une fréquence non négligeable (de l’ordre de 15% en moyenne). On le trouve dans les mêmes parcelles et parfois sur les mêmes arbres, voire dans les mêmes lésions que E. alphitoides. La mise au point d’une méthode d’inoculation artificielle a permis d’étudier de façon quantitative l’interaction chêne-oïdium. Une expérimentation d’inoculations réciproques montre que les souches d’oïdium sont plus performantes sur les descendants des arbres dont elles ont été isolées que sur ceux d’autres arbres, suggèrant une adaptation trans- générationnelle. Des inoculations artificielles, complétées par des observations en conditions naturelles, ont également permis de démontrer un déterminisme génétique de la résistance des chênes, avec l’identification de plusieurs QTL. Certains de ces QTL co-localisent avec des QTL de phénologie, en accord avec l’importance de la résistance ontogénique des chênes à l’oïdium. L’ensemble de l’étude amène à reconsidérer l’oïdium du chêne comme un probable complexe d’espèces cryptiques, dont l’histoire de l’invasion et la co-existence en Europe restent à préciser. Les résultats acquis sur l’héritabilité de la résistance et l’adaptation locale du parasite constituent une première étape dans la compréhension des interactions démo-génétiques entre hôte et parasite dans ce pathosystème
Powdery mildew is the most common disease on oaks in Europe where it was first recorded at the beginning of the 20th century. Yet, little is known about the identity of the causal agent and his interaction with its host. The objective of this study was: (1) to characterize the species responsible of oak powdery mildew with a molecular marker (ribosomal DNA); to study the spatial distribution of these different lineages and (2) to study local adaptation of the parasite to its host (3) to explore the genetic determinism of host resistance. The study of the ITS (internal transcribed region) and IGS (intergenic spacer) diversity revealed the existence of four haplotypes, only three had been already associated with oak powdery mildew in Europe. Erysiphe alphitoïdes, for a long time considered as sole responsible for the epidemic of the XXth century, was the predominant species (~ 80% of detections), E. hypophylla and Phyllactinia sp. were detected at lower frequencies. An unexpected result is the detection of a fourth sequence which show 100% homology with ITS sequences of several powdery mildew agents of tropical trees and Erysiphe quercicola, recently described on oak in Asia and Australia but previously unknown in Europe. E. quercicola ITS was detected in all French regions, at a significant frequency (~ 15%). The study showed that E. alphitoides was often found in association with different ITS types in the same region, the same tree, and even in the same lesion. The development of an artificial inoculation method allowed the quantitative evaluation of the oak-powdery mildew interaction. A reciprocal inoculation experiment showed that powdery mildew strains were more efficient on their mother tress and their descendants than on the other trees, suggesting a trans-generational adaptation. Artificial inoculations, supplemented by observations in natural conditions, have also demonstrated a genetic determination of resistance of oak trees, with the identification of several QTL. Some of these QTL co-localize with QTL controlling phenology, in agreement with the importance of oaks ontogenic resistance to powdery mildew. The entire study leads to reconsider oak powdery mildew as a probable complex of cryptic species; the invasion history and the co-existence in Europe are still to be determined. The results achieved on the heritability of resistance and localization of the parasite are a first step in understanding the demo-genetic interactions between host and parasite in this pathosystem

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Olazcuaga, Laure. "Réponses adaptatives chez Drosophila suzukii, une espèce généraliste envahissante." Electronic Thesis or Diss., Montpellier, SupAgro, 2019. http://www.theses.fr/2019NSAM0045.

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Comprendre comment évolue l’adéquation entre le phénotype des organismes et leur environnement est un enjeu majeur de la biologie évolutive, notamment dans le contexte des changements globaux. Dans le cadre de cette thèse, j’ai étudié les réponses adaptatives aux pressions environnementales, à différentes échelles géographiques et temporelles de Drosophila suzukii, une espèce généraliste envahissante ravageuse des cultures fruitières. J’ai utilisé des méthodes de génétique évolutive combinant génomique des populations et approches expérimentales centrées sur l’étude des traits d’histoire de vie. A partir d’une analyse d’association entre la différenciation génétique et le statut natif ou invasif de 22 populations échantillonnées à travers le monde, j’ai identifié des gènes candidats présentant des variations alléliques fortement associées à l’invasion de D. suzukii. A une échelle temporelle et géographique plus fine (i.e., au sein d’une région de l’aire envahie), je me suis intéressée à la réponse adaptative de cette espèce à une disponibilité des plantes hôtes hétérogène dans l’espace et dans le temps. En utilisant des approches d’évolution expérimentale, j’ai montré que des patrons d’adaptation locale aux fruits hôtes émergent en moins de 30 générations en laboratoire. De manière surprenante, j’ai détecté un patron semblable d’adaptation locale aux fruits hôtes dans des populations naturelles ayant passé moins de quatre générations sur un même fruit. La rapidité des réponses adaptatives observées in natura soulève de nombreuses questions sur la dynamique des processus influençant l’évolution de l’adaptation locale dans un environnement hétérogène dans l’espace et dans le temps à une échelle géographique fine. Les travaux de cette thèse ont permis d’apporter un ensemble d’éléments conceptuels et méthodologiques novateurs pour améliorer notre compréhension de la dynamique de l’adaptation des insectes phytophages à leurs plantes hôtes et des changements évolutifs ayant lieu au cours d’une invasion
The evolution of the match between the phenotype of organisms and their environment is a major issue in evolutionary biology, especially in a context of global change. During my PhD, I investigated the adaptive response to spatio-temporal environmental heterogeneity at different geographic and temporal scales of the spotted wing drosophila Drosophila suzukii, an invasive generalist pest of fruit crops. I used ecological genetic approaches, that combine populations genomics and experimental approaches focusing on lifehistory trait analyses. Based on an association study between genome-wide allelic variations and the invasive or native status of 22 populations sampled worldwide, I identified candidate genes whose allelic variation was strongly associated with the invasion status of D. suzukii. On a finer time and geographic scale (i.e., within a region of the invaded area), I studied the adaptive response of this species to spatiotemporal heterogeneity in host fruit availability. Using experimental evolution in the lab, I found that local adaptation patterns to host fruits emergence within less than 30 generations. Surprisingly, I detected a similar pattern in natural populations that evolved for less than four generations on the same fruit in the field. The speed of adaptive responses observed in natura raises important questions regarding the nature and the dynamics of processes influencing the evolution of fine geographic scale local adaptation in spatiotemporally heterogeneous environments. This PhD work provides new conceptual and methodological elements that improve our understanding of the dynamics of the adaptation of phytophagous insects to their host plant and of the evolutionary changes occurring during the invasion process

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Erdal, Ufuk Goksin. "The Effects of Temperatures on System Performance and Bacterial Community Structure in a Biological Phosphorus Removal System." Diss., Virginia Tech, 2002. http://hdl.handle.net/10919/26384.

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It is generally accepted that a decrease in temperature causes the rates of chemical and biochemical reactions to slow down, usually resulting in poorer performance of biological wastewater treatment systems. Despite this, early researchers repeatedly showed that excess biological phosphorus removal (EBPR) was more efficient at colder temperatures. Recent studies, however, have demonstrated that the reaction rates of EBPR processes decrease with temperature in accordance with Arrheniusâ Law, resulting in an apparent contradiction in the literature. The objective of this study was to investigate the EBPR temperature controversy. The experimental systems used were two, lab-scale UCT configuration plants fed with acetate as the sole volatile fatty acid (VFA) source. The results showed that EBPR systems do perform more efficiently at colder temperatures, i.e., at 5oC compared to 20oC. The reason for better system performance was determined to be related to reduced competition for substrate in the non-oxic zones that results in an increased population of phosphate accumulating organisms (PAOs) relative to non-PAOs and, therefore, greater EBPR efficiency even though the reaction rates are slower. The proliferation of PAOs relative to non-PAOs at cold temperature indicates that some of the PAOs are psychrophilic, i.e., they have alternate biochemical pathways that give them a competitive advantage over bacteria dependent upon glycogen metabolism. The activated sludge acclimated to 20oC had relatively high polyhydroxyvalerate (PHV) and glycogen contents relative to sludge acclimated to 5oC. It was initially hypothized that there is a significant competition between PAO and glycogen accumulating organisms (GAOs) at 20oC and cold temperature (5oC) nearly eliminates this competition in favor of the PAOs. A series of batch test experiments revealed that despite similar acetate utilization by the sludges grown at the two temperatures nearly 30% less PHA was produced by the sludge taken from the 20oC reactor, indicating that GAOs were a small fraction of the population at 20oC. Transmission electron microscopy pictures showed that the biomass acclimated to 20oC had a much more diverse bacterial population than the biomass acclimated to 5oC. However, no GAO population was detected in electron microscopy samples under any temperature conditions. The decreased P removal efficiency at 20oC was then attributed to the presence of fermentative or other non poly-P bacteria that are capable of utilizing substrate under anaerobic conditions. PHA production greatly increased at 5oC, whereas glycogen metabolism substantially reduced. Even though glycogen is an essential requirement for EBPR mechanism, the EBPR microorganisms have the ability to adapt their metabolic pathways to environmental conditions and greatly reduce their need for glycogen. It is apperant that cold temperature inhibits some of the key enzymes in glycogen metabolism resulting in lower glycogen accumulation that in turn increases the EBPR performance. Therefore temperature not only exerts selective pressure on the dominant population but also alters the metabolic pathways of the EBPR process. Increased glycogen accumulation, as observed in this study at 20oC, may not be related to GAO proliferation as suggested by Filipe et al. (2001) instead it may be related to EBPR bacteria to efficiently use glycogen metabolism. Current models (Brdjanovic et al. 1997; Filipe et al. 2002) consider that GAO metabolism is an integral part of EBPR metabolism and the performance of EBPR processes depends on PAO/GAO fraction in the EBPR system. No GAO proliferation was observed even the A/O process was operated without P addition for more than 3 weeks at 10oC. Therefore such important concept should be further investigated before it is included in EBPR models. EBPR stoichiometry was presumed to be insensitive to temperatures (Brdjanovic et al. 1997). However, observed stoichiometric values of PHA storage per unit glycogen utilization and PHA utilization per unit glycogen rephlenishment were quite different at different temperatures. Temperature, therefore, not only affects the kinetics of EBPR systems but also affects the EBPR stoichiometry. Most prokaryotic cells have the ability to alter their cellular membrane fatty acid composition as temperature decreases to counteract the adverse effects of temperature on membrane fluidity (Becker et al., 1996). This unique ability is known as â homeoviscous adaptationâ . In this study, homeoviscous adaptation by EBPR activated sludge was investigated for a series of temperatures ranging from 20oC to 5oC using one of the lab scale EBPR systems. The fatty acid analysis results showed that the unsaturated to saturated fatty acid ratio increased from 1.40 to 3.61 as temperature dropped from 20 to 5oC. The increased cis-9-hexadecanoic acid (C16:1) at 5oC strongly indicated the presence of homeoviscous adaptation in the EBPR bacterial community. Thus the cell membranes of the EBPR community were still in a fluid state, and solute transport and proton motive force mechanisms were operable even at 5oC. It was concluded that loss of EBPR performance at low temperatures, as reported by McClintock et al. (1992) was not related to the physical state of the cellular membranes, but was probably caused by unsuitable operational conditions. Even though the transport of volatile fatty acids (e.g. acetate) is an integral part of EBPR biochemistry and stoichiometry, this important concept has been ignored. Fleet (1997) concluded that acetate entry into bacterial cells in EBPR sludge was simple passive diffusion based upon the results of a single study (Baronofsky et al. 1984). However, this study showed that neither acetate nor propionate can cross the cell membrane via simple passive diffusion. The existence of apparent saturation curves when the substrate uptake rates (acetate and propionate) were plotted against the substrate concentrations suggested that transport of volatile fatty acids obey facilitated or active transport. Following from the above results, an investigation of the impacts of operational conditions such as low solids retention time (SRT), presence of electron acceptors in the non-oxic zones, low anaerobic detention time, and lack of acclimation was performed. The results showed that the â critical, i.e., wash-outâ SRT increased as temperature decreased, but if the biomass was permitted to acclimate to the lower temperature, a major population shift would occur which would increase the capacity of the system for phosphorus (P) removal. When the 5 oC sludge was allowed to acclimate at a relatively high SRT (18 d), the systemâ s P-removal capacity greatly surpassed that of the 20 oC system. The decrease in EBPR performance because of the presence of nitrates in the non-oxic zones was determined to be greater than what would be predicted based on accepted stoichiometry.
Ph. D.

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Leslie, Kevin A. "Evaluation and Adaptation of Live-Cell Interferometry for Applications in Basic, Translational, and Clinical Research." VCU Scholars Compass, 2018. https://scholarscompass.vcu.edu/etd/5562.

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Cell mass is an important indicator of cell health and status. A diverse set of techniques have been developed to precisely measure the masses of single cells, with varying degrees of technical complexity and throughput. Here, the development of a non-invasive, label-free optical technique, termed Live-Cell Interferometry (LCI), is described. Several applications are presented, including an evaluation of LCI’s utility for assessing drug response heterogeneity in patient-derived melanoma lines and the measurement of CD3+ T cell kinetics during hematopoietic stem cell transplantation. The characterization of mast cells during degranulation, the measurement of viral reactivation kinetics in Kaposi’s Sarcoma, and drug response studies in patient-derived xenograft models of triple-negative breast cancer are also discussed. Taken together, data from these studies highlight LCI’s versatility as a tool for clinical, translational, and basic research applications.

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Cogo, Karina 1980. "Avaliação in vitro dos efeitos da nicotina e cotinina sobre a expressão de proteinas e capacidade de adesão e invasão de Porphyromonas gingivalis." [s.n.], 2009. http://repositorio.unicamp.br/jspui/handle/REPOSIP/288971.

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Orientadores: Francisco Carlos Groppo, Reginaldo Bruno Gonçalves
Tese (doutorado) - Universidade Estadual de Campinas, Faculdade de Odontologia de Piracicaba
Made available in DSpace on 2018-08-12T19:00:41Z (GMT). No. of bitstreams: 1 Cogo_Karina_D.pdf: 3355648 bytes, checksum: d8afd799c6d162cda6cbb9bad9d225a5 (MD5) Previous issue date: 2009
Resumo: O uso do cigarro tem sido associado com a progressão da periodontite bem como com a redução da resposta à terapia aplicada a essa doença. Porphyromonas gingivalis é um importante colonizador do biofilme subgengival além de ser um dos principais patógenos envolvidos no estabelecimento e progressão da doença periodontal. No entanto, os possíveis efeitos dos principais derivados do cigarro sobre P. gingivalis ainda não foram totalmente investigados. Dessa forma, os objetivos deste estudo foram avaliar os efeitos da nicotina e cotinina sobre a expressão de proteínas e sobre a capacidade de adesão e invasão celular de P. gingivalis. A fim de avaliar a expressão de proteínas, culturas de P. gingivalis W83 foram expostas à nicotina e cotinina nas concentrações de 6 e 600µg/mL, as proteínas foram extraídas, separadas por eletroforese bidimensional em gel de poliacrilamida (12.5% SDS-PAGE) e identificadas por LC-MS/MS. Os géis e suas corridas eletroforéticas foram feitas em triplicatas e a detecção de proteínas nos mesmos foi feita através de coloração com corante Coomassie. Proteínas diferentemente expressas foram digeridas com tripsina e as amostras de peptídeos sequenciadas utilizando um sistema Q-TOF API LC-MS/MS. A busca MS/MS foi realizada utilizando os bancos de dados MSDB e NCBI através do programa Mascot. Para examinar a capacidade de adesão e invasão de P. gingivalis, monocamadas de células KB e culturas de P. gingivalis ATCC 33277 foram expostas às concentrações de 0.1, 10 e 100 µg/mL de nicotina e cotinina. As células epiteliais foram incubadas por 24 h enquanto P. gingivalis foi exposta a essas substâncias até atingir a fase logarítmica. Após o período de incubação, P. gingivalis foi submetida aos ensaios de adesão e invasão às células KB. O número de bactérias associadas às células foi obtido através de contagem de unidades formadoras de colônia. Os resultados obtidos da análise expressão de proteínas mostraram que a adição de nicotina e cotinina promoveram alterações no proteoma de P. gingivalis. Entre os ± 430 spots de proteínas reproduzíveis detectados em cada gel, 20 proteínas foram menos expressas e 42 foram mais expressas em pelo menos um dos tratamentos (p<0.05; ANOVA - Tukey). Entre as proteínas identificadas, muitas estavam envolvidas em processos como produção de energia celular, síntese de proteínas, estresse oxidativo, virulência, transporte, etc. Em relação aos resultados obtidos nos ensaios de adesão e invasão, foi evidenciado que, quando as células epiteliais foram inoculadas com nicotina e cotinina, nenhuma diferença significativa na colonização de P. gingivalis foi encontrada. Quando P. gingivalis foi exposta à maior concentração de cotinina, sua capacidade de adesão e invasão às células epiteliais aumentou de forma expressiva (p<0.05; ANOVA - Tukey). No entanto, a nicotina e as outras concentrações de cotinina testadas não alteraram a capacidade de colonização. Esses achados indicam que a nicotina e a cotinina podem afetar a expressão de proteínas de P. gingivalis. Ainda, a cotinina pode alterar positivamente a eficiência de adesão e invasão de P. gingivalis.
Abstract: Cigarette smoking is associated with the development of periodontitis and the decreased response to periodontal therapy. P. gingivalis is an important colonizer of the subgingival biofilm and is one of the major pathogens involved in the initiation and progression of periodontal disease. However, the possible effects of major cigarette's derivatives on P. gingivalis were not fully investigated. Thus, the purpose of the present study was to evaluate the effects of nicotine and cotinine on the protein expression and cellular adhesion and invasion abilities of P. gingivalis. To evaluate protein expression, P. gingivalis W83 cultures were exposed to nicotine and cotinine 6 and 600µg/mL concentrations, the proteins were extracted, separated by two-dimensional polyacrylamide gel electrophoresis (12.5% PAGE) and identified with LC-MS/MS. The gels were run in triplicates and detection of proteins was obtained by staining the gels with Coomassie blue. Proteins differentially expressed were digested with trypsin, and the peptide samples sequenced using a Q-TOF API LC-MS/MS system. The MS/MS was searched against the MSDB and NCBI databank using Mascot program. In order to assess P. gingivalis adhesion and invasion abilities, KB cells monolayers and P. gingivalis ATCC 33277 cultures were exposed to 0.1, 10 and 100 µg/mL nicotine and cotinine concentrations. The epithelial cells were incubated for 24 h while P. gingivalis was exposed to these substances until early logarithmic phase. After incubation period, P. gingivalis were submitted to assays to evaluate adhesion to and invasion of KB cells. The number of bacteria associated with these cells was assessed by counting the colony-forming unities. The results from protein expression analyses showed that addition of nicotine and cotinine promoted alterations in proteome profile of P. gingivalis. Among ± 430 protein spots reproducibly detected on each gel, 20 protein spots were downregulated, and 42 were upregulated at least in one treatment (p<0.05; ANOVA - Tukey test). The identified proteins are involved in several processes, i.e. energy production, protein synthesis, oxidative stress, virulence, transport and binding activities. Data obtained from adhesion and invasion assays evidenced that epithelial cells inoculated with nicotine and cotinine did not show any significant differences in P. gingivalis colonization. When P. gingivalis was exposed to the higher concentration of cotinine, adherence and invasion of this bacterium to the epithelial cells markedly increased (p<0.05; ANOVA - Tukey test). However, nicotine and the other concentrations of cotinine did not alter the colonization ability. These findings indicate that nicotine and cotinine may affect P. gingivalis protein expression. In addition, cotinine may alter positively P. gingivalis adhesion and invasion efficiencies.
Doutorado
Farmacologia, Anestesiologia e Terapeutica
Doutor em Odontologia

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Bouteiller, Xavier. "Une histoire écologique et évolutive du robinier faux-acacia (Robinia pseudoacacia L.) depuis son introduction en Europe." Thesis, Bordeaux, 2018. http://www.theses.fr/2018BORD0162/document.

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Robinia pseudoacacia L. est un arbre nordaméricain qui est largement répandu à travers l’Europe. Afin d’évaluer les mécanismes évolutifs pouvant expliquer son potentiel invasif, il est indispensable d’identifier les populations sources de l’introduction et de comprendre quels traits ont contribué à son succès dans l’aire européenne Une étude de génétique des populations a été réalisée, un large échantillonnage a été conduit au sein des deux aires et 818 individus provenant de 63 populations ont été génotypés grâce à 113 marqueurs SNPS. En premier lieu, nous avons démontré que le robinier européen provenait d’un nombre restreint de populations situées au nord du plateau des Appalaches, ce qui est en accord avec les données historiques. Au sein des ÉtatsUnis la structure reflète des processus évolutifs au long cours tandis qu’en Europe, la structure est plus ténue et pourrait être due à l’activité humaine, notamment aux programmes de sélection entrepris en Europe centrale depuis le 18ème siècle. En deuxième lieu, un goulot d’étranglement génétique associé à une perte de diversité a été mis en évidence dans l’aire d’introduction. Enfin un plus fort taux de clonalité a été observé au sein des populations d’Europe Conjointement à cette étude de génétique des populations. Une expérimentation de génétique quantitative a été réalisée afin d’évaluer la différenciation de traits juvéniles entre populations des deux aires (3000 individus de 20 populations) cultivées dans 3 conditions de température différentes (18°C ; 22°C et 31°C). Les résultats ont révélé une augmentation du taux de germination parmi les populations européennes par rapport aux américaines (88% vs 60%) quelles que soient les conditions environnementales. Un scénario possible est que l’Homme aurait sélectionné et propagé les meilleures graines en Europe favorisant alors l’évolution du taux de germination. De plus, les traits phénotypiques juvéniles sont extrêmement plastiques à la température avec une tendance générale à l’augmentation de la valeur du trait avec la température. Cela suggère qu’un réchauffement climatique favoriserait le développement de l’espèce, au moins en conditions d’alimentation en eau non limitante. Cependant, seules les populations américaines montrent un signal une adaptation locale à la température d’origine Dans tous les cas, ils semblent que l’action de l’Homme sur le potentiel reproductif, sexué ou asexué, a probablement influencé le potentiel invasif du robinier en Europe
Robinia pseudoacacia L. is a North American tree which has now broadly spread in Europe. In order to evaluate the evolutionary mechanisms behind its invasiveness, it is crucial to identify the population sources of the introduction and to understand which traits contributed to its success in the European range. To undertake a population genetics study, we performed a large sampling both in the invasive and native ranges; 818 individuals from 63 populations were genotyped using 113 SNPs. First, we demonstrated that European black locust was introduced from only a limited number of populations located in the Northern plateau of the Appalachians Mountains; this is in agreement with historical records. Within America, population structure reflected long time evolutionary processes whereas in Europe, it was largely impacted by human activities. In the European range, the genetic clustering may be a signal of evolution caused by artificial selection due to human oriented mass selection or tree breeding initiated in Central Europe since the 18th century. Second, we evidenced a genetic bottleneck among ranges with a decrease in allelic richness and in the total number of alleles in Europe. Lastly, we found more clonality within the European populations. Conjointly to the population genetic analysis, we conducted a quantitative genetics experiment to evaluate juvenile traits of both native and invasive black locust populations (3000 individuals from 20 populations) grown under 3 different temperature conditions. Results revealed an enhanced germination rate among European populations compared to that of the native American populations whatever the environmental condition (88% vs 60%). Thus a possible scenario may be that Man would have selected and propagated the best seeds in the new range that would have favored an evolution of germination rate through European populations. Phenotypic traits of juvenile development are extremely plastic in response to temperature (18/22/31°C), with a general tendency to increasing trait values with increasing temperature. This suggests that global warming would favor the development of the species, at least under nonlimiting water supply conditions. However, only American populations demonstrated a signal of local adaptation to the temperature at the sampling location. In any case, the human role on the reproductive potential, both sexual and asexual, within the introduced rangewould likely be a key process in the success of black locust dynamics in Europe

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Leblanc, Sylvie. "Réalisation d'électrodes sélectives au NA**(+) et K**(+) en vue d'une adaptation sur des appareils de biologie clinique." Nancy 1, 1986. http://www.theses.fr/1986NAN10355.

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34

McGaughran, Angela. "Polar eveolution: molecular genetic and physiological parameters of Antarctic arthropod populations : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Molecular Biosciences at the Allan Wilson Centre of Molecular Ecology and Evolution, Institute of Molecular Biosciences, Massey University, Palmerston North, New Zealand." Massey University, 2009. http://hdl.handle.net/10179/1163.

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This thesis is presented as a collection of research papers synthesising knowledge gained during the period of candidacy. Its underlying focus is the examination of evolution from a variety of perspectives for terrestrial arthropods (springtails) in an Antarctic setting. These perspectives include investigation of the ways in which springtail populations respond both physiologically and genetically to environmental variability over historical and contemporary time-scales. While the physiological and genetic may seem two worlds apart, this thesis recognises that, in reality the two are inextricably linked. Thus, when genetic differentiation between populations of the same species can be demonstrated, physiological differentiation of these populations may also be predicted (and vice versa). Therefore, across several locations and springtail species, physiological and genetic parameters of individuals and populations are examined both separately and, where possible, in concert. The physiological aspect of this thesis focuses on the springtail Gomphiocephalus hodgsoni from continental Antarctica. In addition to providing the first metabolic rate data for a continental Antarctic springtail, seasonal variation in metabolic rates is examined across multiple temporal and spatial scales to evaluate the ways in which individuals and populations respond to environmental variability. Metabolic activity in this species is intricately linked to a variety of factors, both intrinsic and extrinsic. These include biological function, temperature profiles in the local microclimate, and body mass and genetic differences among populations. In the genetically-focused aspect of this thesis, population genetic patterns of G. hodgsoni from several continental locations and Cryptopygus antarcticus antarcticus from locations across the Antarctica Peninsula are compared. Here, the importance of differing evolutionary histories in influencing patterns of contemporary genetic population structure is highlighted. While both species have been similarly affected genetically by Pleistocene (2 Ma – present) glacial cycling, it is clear that differences in timing of colonisation events and subsequent population expansions have left distinct genetic signatures in each species. In a separate molecular study, phylogenetic analyses are employed to study members of the circum-Antarctic springtail family Isotomidae. Thesis Abstract The genetic ancestry among these closely related species is shown to reflect a diverse evolutionary origin in the Miocene (23 – 5 Ma), subsequent to which both vicariant and dispersal processes have been important. Phylogenetic re-constructions tease out the relationships among sister species, and the identification of several genetically distant lineages suggests that a revision of current species designations is required. Finally, two studies that integrate the physiological and molecular genetic are presented. First, metabolic rate variation across several locations on sub-Antarctic Marion Island in the springtail Cryptopygus antarcticus travei is examined. This variation is related to the genetic structure of populations to show that historical and contemporary environmental characteristics have left their trace in the expression of both genetic and physiological variability of these populations. Second, the perceived association between metabolic rate and genetic (mutation) rate is investigated more closely - a sophisticated Bayesian correlation analysis detects that there is an indirect relationship between metabolic rate and underlying species phylogeny in C. a. travei. Thus, the physiological and molecular genetic elements of this thesis test or advance important hypotheses within their own fields, and the integrated approach applied is a new step in interpreting evidence of physiological adaptation in Antarctic species. In its multi-faceted approach to evolutionary studies, this thesis enhances understanding of the current picture of springtail evolution in polar environments.

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SCHEIN-FATTON, ELISABETH. "L'adaptation des pectinidae a l'ocean profond : des faunes actuelles a l'interpretation des annales paleontologiques." Paris 6, 1987. http://www.theses.fr/1987PA066818.

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Auteur d'une etude de la systematique des pectinidae vivant actuellement en milieu profond, ce travail developpe differents aspects de leur biogeographie et de leur evolution au sein des pectinacea depuis le paleozoique. On montre l'importance de l'etude de la microstructure du test, de celle des premiers stades ontogeniques et de la comparaison entre formes fossiles et actuelles. On aborde les problemes lies a la systematique et a l'evolution des formes profondes a partir d'un cas extreme d'une espece consideree comme fossile vivant. On propose une systematique qu'on applique aux formes bathyales et abyssales du golfe de gascogne. On recherche dans les annales paleontologiques des formes comparables a celles du milieu profond actuel

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Sherpa, Stéphanie. "Histoire de la colonisation et déterminants du succès invasif des populations du moustique tigre Aedes albopictus en Europe." Electronic Thesis or Diss., Université Grenoble Alpes (ComUE), 2019. http://www.theses.fr/2019GREAV049.

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Le moustique tigre, Aedes albopictus, originaire d’Asie du Sud-Est, a colonisé l’ensemble des continents excepté l’Antarctique depuis les dernières décennies. En revanche, les raisons du succès invasif des populations à l’échelle mondiale sont encore peu connues. Nous nous sommes concentrés sur l’invasion de l’Europe, et avons combiné différentes méthodes d’analyse et des données multi-sources afin de distinguer le rôle des processus historiques et contemporains, neutres et adaptatifs, dans la structuration de la variabilité génétique des populations invasives. L’analyse de la variabilité génétique de 1000 individus appartenant à 150 populations invasives et natives a révélé trois introductions indépendantes en Europe (en Albanie, au Nord de l’Italie, et au Centre de l’Italie), à partir des Etats-Unis (aire envahie) et de la Chine (aire native). Les populations initialement introduites ont constitué des centres de dispersion en Europe et les voies de migration corrèlent avec la géographie des transports humains. Différents évènements d’admixture au moment de l’introduction ou durant l’expansion subséquente, ainsi qu’une forte connectivité des populations, ont favorisé le maintien d’une forte diversité génétique. Des adaptations au froid préexistantes dans l’aire native de l’espèce et un fort conservatisme de niche entre les populations introduites et leurs sources suggèrent que les populations introduites étaient déjà pré-adaptées pour coloniser les environnements tempérés de l’Europe. Néanmoins, des changements de fréquences alléliques le long des gradients environnementaux en Europe suggèrent également une réponse adaptative après l’introduction. Le potentiel adaptatif des populations, ainsi que la dispersion longue distance assistée par l’homme, ont favorisé l’expansion rapide en Europe. Bien que souvent négligée dans le contexte des invasions biologiques, la dispersion naturelle semble également jouer un rôle dans l’expansion des populations à l’échelle du paysage. L’étude des caractéristiques démo-génétiques des populations invasives et des caractéristiques environnementales de l’aire envahie en Europe a permis d’identifier les processus favorisant deux étapes clés du processus d’invasion: l’établissement et l’expansion
The Asian tiger mosquito, Aedes albopictus, is native to Southeast Asia and has colonized all continents but Antarctica in the last decades. However, the factors determining the invasive success of populations at the global scale remain to be elucidated. Focusing on the European invasion, we used a comprehensive framework and multi-source data for distinguishing the role of historical and contemporary processes, both neutral and adaptive, in structuring the genetic variability of invasive populations. Examining the genetic variability of 1,000 individuals from 150 invasive and native populations revealed three independent introduction events in Europe (in Albania, North Italy, and Central Italy), from the United States (previously invaded area) and from China (native range). Primary introduced populations constituted dispersal centers for the colonization of Europe, and migration routes correlate with the geography of human transportation networks. Several admixture events either during introduction or subsequent expansion, as well as high connectivity between invasive populations, promoted the maintenance of high levels of genetic diversity. Pre-existing cold adaptation within the native range of the species and niche conservatism between introduced populations and their sources suggest that these populations were already prepared for establishing under temperate European climate. Nonetheless, shifts in allele frequencies along environmental gradients within Europe suggest post-introduction adaptive changes. The adaptive potential of populations and long-distance human-aided dispersal facilitated the rapid expansion of populations. Although often neglected in the context of biological invasions, natural dispersal at the landscape scale further contributed to range filling in range edge populations. The study of the demo-genetic and environmental characteristics of the European invasion allows a better understanding of processes at play during two key stages of the invasion process: establishment and expansion

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Julou, Thomas. "Evolution, compétition et coopération dans les populations bactériennes." Phd thesis, Ecole Normale Supérieure de Paris - ENS Paris, 2011. http://tel.archives-ouvertes.fr/tel-00600569.

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Les différents facteurs que sont l'environnement, l'héritabilité et la stochasticité contribuent au développement d'individus différents à partir d'une information génétique donnée. Cette variabilité phénotypique modifie l'action de la sélection naturelle sur la variabilité génétique. Un fil conducteur de ce travail est l'étude de l'impact de la variabilité phénotypique sur les dynamiques d'adaptation. Le premier chapitre expose la conception d'une expérience d'évolution de Escherichia coli dans un environnement structuré. Le trait sélectionné est la resistance aux hautes températures. En particulier, nous étudions les effets de la température sur le chimiotactisme ainsi que l'impact de l'acclimatation sur la croissance et la survie à haute température. Le deuxième chapitre porte sur la réalisation d'un dispositif de mesure de population microbienne à basse concentration. Cette mesure est continue et non invasive et sa limite de détection varie selon l'espèce. Pour l'espèce modèle Escherichia ecoli, la limite est environ 5000/mL soit une amélioration d'un facteur 100 par rapport à la photométrie classique. Dans le troisième chapitre, nous étudions la distribution de la pyoverdine entre les individus d'une population clonale de Pseudomonas aeruginosa. La variabilité de la concentration de ce sidérophore considéré comme un "bien commun'' est beaucoup plus grande que celle attendue et ne peut être expliquée en terme de répartition spatiale ou d'héritabilité. Après avoir caractérisé des fluctuations rapides de la concentration en pyoverdine, nous proposons un modèle de switch phénotypique dans le métabolisme de la pyoverdine qui est en très bonne adéquation avec les observations.

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Ségurel, Laure. "Mode de vie et diversité génétique dans les populations humaines d'Asie Centrale." Phd thesis, Université Pierre et Marie Curie - Paris VI, 2010. http://tel.archives-ouvertes.fr/tel-00547600.

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Cette thèse a pour objectif de s'interroger sur l'influence du mode de vie sur la diversité génétique humaine. Nous avons pour cela étudié plusieurs ethnies d'Asie Centrale qui diffèrent de par leur organisation sociale et leur mode de subsistance. Nous avons d'abord comparé la diversité génétique a priori neutre de populations patrilinéaires et cognatiques (populations se définissant par leur ascendance paternelle ou indifféremment par les deux sexes, respectivement). Cette étude, basée sur les autosomes et le chromosome X, nous a permis de montrer que les hommes ont un effectif efficace et un taux de migration réduits par rapport aux femmes chez les patrilinéaires, mais non chez les cognatiques. Ensuite, nous avons testé si les éleveurs et les agriculteurs ont subi différentes pressions de sélection liées à l'alimentation. Pour le gène de la lactase (digestion du lactose) et de l'AGXT (facilitant la digestion de la viande), nous n'avons pas trouvé de différence de diversité génétique entre populations. Cependant, nous avons montré que les éleveurs (représentés par les Kirghiz) présentent près de deux fois plus de résistance à l'insuline, phénotype proposé comme une adaptation aux faibles quantités de glucides dans l'alimentation, que les agriculteurs (représentés par les Tadjiks). Nous avons également mis en évidence des signatures d'adaptation locale entre éleveurs et agriculteurs sur certains gènes associés à la résistance à l'insuline. Ainsi, ces populations semblent s'être adaptées à des régimes alimentaires différents. Cette thèse conforte donc l'hypothèse d'une influence des facteurs culturels sur l'évolution de la diversité génétique des populations humaines.

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Asse, Daphné. "Comprendre et prédire la réponse des écosystèmes forestiers d'altitude aux changements climatiques : apports d'un programme de sciences participatives." Thesis, Montpellier, 2018. http://www.theses.fr/2018MONTG058/document.

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Les régions alpines sont particulièrement sensibles aux changements climatiques en cours. Ainsi, l’ouest des Alpes s’est réchauffé deux fois plus vite que l’hémisphère Nord au cours du XXème siècle. Les rythmes saisonniers des arbres, comme beaucoup d’autres organismes, sont fortement modifiés par le réchauffement climatique. La phénologie et les variations temporelles fines du climat apparaissent comme des composantes incontournables à prendre en compte pour prédire la répartition des espèces. L’objectif principal de ce travail de thèse a été de comprendre la réponse de la phénologie des espèces arborées au réchauffement climatique dans les Alpes et de développer des outils pour évaluer cette réponse dans le futur. Pour atteindre cet objectif nous avons utilisé des données phénologiques (débourrement, floraison, senescence foliaire,) pour le noisetier, le frêne, le bouleau, le mélèze et l’épicéa, issues du programme de sciences participatives Phénoclim.Nos résultats montrent que le réchauffement de l’hiver retarde la levée de la dormance des bourgeons et par conséquent les dates de débourrement et de floraison le long du gradient d’altitude. Cet effet est plus important à basse altitude. La robustesse des projections des modèles de répartition basés sur les processus dépend fortement de la robustesse des modèles phénologiques qu’ils utilisent. En comparant des modèles phénologiques présentant différents niveaux de complexité nous avons montré que les modèles basés sur les processus étaient les plus robustes particulièrement lorsque l’estimation de leurs paramètres reposait sur une estimation directe à l'aide de mesures expérimentales. Les modèles prévoient une réduction des écarts entre les dates de débourrement le long du gradient d'altitude pour toutes les espèces d'ici la fin du 21e siècle. Ceci est dû d’une part à un avancement des dates de débourrement à haute altitude et d’autre part à un retard des dates de débourrement à basse altitude. Nous avons également testé de nouvelles hypothèses sur le déterminisme environnemental de la croissance cellulaire dans les bourgeons, mais aucune des hypothèses testées n’a significativement amélioré les performances des modèles. Nous avons ensuite intégré les modèles phénologiques les plus performants que nous ayons obtenus au modèle d’aire de répartition basé sur les processus PHENOFIT. Nous avons réalisé pour la première fois avec ce modèle des simulations à haute résolution spatiale. Les projections du modèle montrent que les espèces arborées devraient se déplacer vers le haut du gradient d’altitude. Cependant, des phénomènes d’extinction locale pourraient avoir lieu dans les fonds des vallées liés à des dates de floraison trop tardives qui diminuerait le succès reproducteur des individus. Selon les espèces, la limite altitudinale supérieure serait contrôlée par le risque d'exposition au gel tardif des fleurs ou par la longueur de la saison de croissance qui détermine le temps disponible pour la maturation des fruits.L’ensemble de ces résultats nous a permis d’apporter des éléments de réponse sur la dynamique future des écosystèmes forestiers altitudes face au réchauffement climatique. Ils nous ont également permis de montrer que les données du programme Phénoclim étaient de qualité suffisante pour être utilisées dans des travaux de recherche scientifique
Mountainous regions are particularly exposed to the ongoing climate change. Indeed, in the Western Alps the temperature increased twice faster than in the northern hemisphere during the 20th century. Trees’ annual cycle, as in many other organisms, is largely affected by climate change. Phenology and the fine temporal variations of climate appear key to predict species distribution. The main objective of this PhD thesis work was to understand the response of tree phenology to climate change in the Alps and to develop tools to evaluate this response in future conditions. It has been carried out using the phenological observations (budburst, flowering, leaf senescence) of five tree species (hazel, ash, birch, larch and spruce) of the citizen science program Phenoclim.Our results show that warmer winters slow down bud dormancy break, and consequently the budburst and flowering dates along the elevation gradient. This effect is stronger at low elevation. The robustness of process-based species distribution models depends strongly on the robustness of their process-based phenology sub-model. By comparing different phenology models differing in their level of complexity and we showed that process-based models were the most robust especially when their parameter estimates relied on forward estimation using experimental data. Models project a reduction in the phenological cline along the elevation gradient by the end of the 21th century. This is due, on one hand, to an advancement of the budburst dates at high elevation and on the other hand, to a delay of the budburst dates at low elevation. We also tested several hypotheses on the environmental determinism of bud cell growth. However, none of the hypotheses improved significantly the models’ performance. We then implemented the best phenology models we obtained in the process-based species distribution model PHENOFIT. We carried out for the first time simulations at high spatial resolution. Projections showed that species are expected to move up along the elevation gradient in response to climate change. However, local extinction events may occur in the bottom of the valleys due to late flowering dates that would decrease the reproductive success. Depending on the species, the upper altitudinal limit would be controlled by the risk of flowers’ exposure to late spring frost or to the length of growing season, which determine fruit maturation success.All of these results, allowed us to provide some answers on the future dynamics of high altitude ecosystems in the face of global climate change. They also allowed us to show that the Phenoclim data were of sufficient quality to be used to address important scientific questions

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Scarborough, Matthew Edward. "Insular adaptations in the appendicular skeleton of Sicilian and Maltese dwarf elephants." Doctoral thesis, Faculty of Science, 2020. http://hdl.handle.net/11427/32747.

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This thesis investigates the evolution of Pleistocene insular proboscideans from the centralwestern Mediterranean (Palaeoloxodon species from Sicily, Malta, Favignana) and a mammoth (Mammuthus lamarmorai) from Sardinia, with a particular emphasis on the anatomy of the limbs. Differences in the morphology of the limbs are examined across a tenfold reduction in mass (from 3,5m-tall P. antiquus from Germany to 1,2 m-tall P. ex gr. P. falconeri from Spinagallo Cave, Sicily), revealing insights into significant morphological changes in the long and foot-bones, particularly appendicular changes evident in SiculoMaltese P. ex gr. P. falconeri. Notable morphological differences between P. antiquus and its insular descendent P. ex gr. P. falconeri include the functional morphology of the ankle-joint (especially the calcaneus' articular facet for the tibia). Furthermore, morphological similarities found between the femur of young continental elephants (P. antiquus and L. africana) and adult insular dwarfs (P. ex gr. P. falconeri and its probable ancestor Palaeoloxodon sp. from Lparello Fissure, Sicily) suggest evidence of paedomorphism in the limbs. Similarly, comparisons of the ontogenetic allometry of the tibia in L. africana and P. ex gr. P. falconceri include changes which are also consistent with paedomorphism, although other factors could not be ruled out. In the humerus large differences are evident in the morphology of the deltoid tubercule between co-generic insular Palaeoloxodon species, suggesting interspecific differences in the musculo-skeletal system. Furthermore, on the basis of dimensions, morphology and stratigraphy, the large Palaeoloxodon sp. remains from Luparello Fissure, north-western Sicily are suggested to belong to the ancestral chronospecies of P. ex gr. P. falconeri from Sicily, which may have subsequently colonized Malta during the reduced sea-levels of a Middle Pleistocene glacial lowstand (following a corridor with reduced distances between the two islands). Additionally, morphological differences in the calcanei of elephants from Luparello Fissure, Sicily, and Benghisa Gap, Malta may be the result of allopatric speciation between similar-sized elephants during the Middle Pleistocene, or alternatively relate to ecomorphology. These findings suggest that the morphology of the calcaneus may be more informative than hitherto recognised for resolving systematics and taxonomy among the Elephantini. Furthermore, although the absolute chronology of SiculoMaltese elephants remains poorly constrained, preliminary U-Th dating at Alcamo Quarry, western Sicily suggests a tentative early Middle Pleistocene age for Palaeoloxodon sp.

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Ion, Scotta Michela. "Distributions des espèces du genre Trichogramma le long d’un gradient altitudinal et adaptations locales aux basses températures chez l’espèce Trichogramma cacoeciae." Electronic Thesis or Diss., Université Côte d'Azur (ComUE), 2019. http://www.theses.fr/2019AZUR4035.

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Toutes les espèces sont confrontées à une hétérogénéité environnementale dans le temps et/ou dans l’espace et donc à des variations de la qualité de leur environnement local. Selon leurs biologies (capacité de dispersion, plasticité phénotypique, variabilité génétique locale, etc), les espèces répondent différemment mais cette hétérogénéité génère ou maintient in fine des variations inter- ou intra- spécifiques des traits d'histoire de vie. Dans ce contexte, ma thèse s’intéresse à (i) la distribution géographique et écologique des espèces du genre Trichogramma le long d’un gradient altitudinal dans une aire restreinte des Alpes Maritimes ; (ii) la mise en évidence chez l’une des espèces, d’éventuelles adaptations locales en relation avec les basses températures. Concernant ce deuxième volet, trois types d’expériences ont été menées à partir d’un ensemble de souches provenant des deux étages du gradient altitudinal (Méso- et Supra- méditerranéens) ainsi que des souches provenant d’une aire géographique plus septentrionale : (i) comparaison en laboratoire d’indices de tolérance thermique : Ctmin, Chill coma et Recover Activity ; (ii) étude des modalités d’overwintering sur le terrain ; (iii) étude des capacités de diapause. Mes résultats ont tout d’abord mis en évidence que, à l’échelle du transect altitudinal étudié et avec notre protocole d’échantillonnage, T. cacoeciae est l’espèce la plus largement distribuée et la plus abondante. De plus, les souches Supra - méditerranéennes semblent présenter par rapport aux souches Méso - méditerranéennes des différences génétiques, notamment dans leur propension à diapauser et dans leur vitesse de développement à basses températures. Cette différentiation génétique est encore plus marquée dans les souches plus septentrionales notamment pour leurs valeurs de Chill coma qui sont en moyenne plus basses. D’une façon générale, cette étude conclut sans ambiguïté à l’existence d’une variabilité intra-spécifique chez T. cacoeciae pour des traits liés à l’adaptation aux basses températures. Ces résultats, obtenus pour une seule espèce et à une échelle géographique restreinte, ouvrent donc la voie vers une étude plus systématique de ces traits et à la prise en compte/exploitation de leurs variabilités inter- et intra- spécifiques dans l’évaluation des trichogrammes comme auxiliaires de lutte biologique
All species are facing some environmental heterogeneity in time and / or space and thus with variations in the quality of their local environment. According to their biology (dispersal ability, phenotypic plasticity, local genetic variability, etc.), species respond differently but this heterogeneity usually generates or maintains inter-or intra-specific variations in life history traits. In this context, my thesis focuses on (i) the understanding of the geographical and ecological distributions of Trichogramma species along an altitudinal gradient in a narrow area of the department “Alpes-Maritimes”; (ii) –possible local adaptations to low temperatures in one of the encountered species. For this second part, three types of experiments were conducted from a set of strains from the two contrasted areas along the altitudinal gradient (Meso - and Supra - mediterranean) as well as strains from a more northern geographical area: (i) laboratory comparison of thermal tolerance indices: Ctmin, Chill coma and Recover Activity; (ii) study of diapause capabilities; (iii) study of overwintering modalities in the field. My results first showed that, at the scale of the altitudinal transect studied and with our sampling protocol, T. cacoeciae is the most widely distributed and abundant species. In addition, the Supra - mediterranean strains seem to have genetic differences with regard to the Meso - Mediterranean ones, particularly in their rate of development at low temperatures as well as their propensity to diapause. This genetic differentiation is even more marked in the more northern strains especially for their Chill coma values which are on average lower. Taken as a whole, this study unambiguously concludes that there is intra-specific variability in T. cacoeciae for traits related to adaptation to low temperatures. These results, obtained for a single species and on a small geographical scale, thus open the way towards a more systematic study of these traits and the taking into account/exploitation of their inter and intra-specific variabilities in the evaluation of trichograms as auxiliaries for biological control

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Agra, Ana Raquel Santos. "Adaptation of Cladocerans in metal-polluted heterogeneous environments." Doctoral thesis, Universidade de Aveiro, 2010. http://hdl.handle.net/10773/3877.

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Doutoramento em Biologia
No presente trabalho o cladócero Daphnia longispina foi utilizado como organismo modelo para a avaliação dos efeitos ecológicos da adaptação a ambientes contaminados por metais. Foram amostradas populações naturais de D. longispina num local sujeito à contaminação por metais e num local próximo, de referência, ambos localizados no sistema aquático na área envolvente à mina abandonada de São Domingos. Várias linhagens clonais de ambas as populações foram mantidas em laboratório, sob condições controladas, para a execução dos testes. Um dos testes realizados permitiu estudar e quantificar as diferenças na tolerância letal entre as linhagens clonadas de ambas as populações e também avaliar os custos associados. Utilizando vinte linhagens clonais de D. longispina das duas populações verificou-se que apenas clones sensíveis ao cobre estavam presentes na população de referência e clones resistentes ao cobre estavam presentes na população do local contaminado. Os custos associados à tolerância foram ilustrados pela determinação de taxas alimentares mais baixas para a população tolerante quando comparadas com as da população de referência. Outro dos testes realizados permitiu comparar as respostas de clones de populações de ambos os locais – contaminado e referência – à exposição a concentrações sub-letais do metal cobre. A tolerância evidenciada anteriormente ao nível letal foi confirmada ao nível sub-letal, com o clone proveniente da população do local contaminado evidenciando uma maior tolerância ao cobre quando comparado com os restantes clones, para todos os parâmetros analisados (taxas alimentares, consumo de oxigénio, crescimento e reprodução). Os efeitos da aclimatação ao cobre ao longo de várias gerações foram também avaliados num clone de D. longispina. Os resultados evidenciaram a existência de uma adaptação fisiológica ao cobre ao longo das várias gerações que, no entanto, apenas aumentou marginalmente a tolerância a níveis de cobre letais. Para além disso, observou-se também uma grande variação nas respostas do clone de D. longispina estudado, não só entre concentrações de cobre mas também entre gerações. Os resultados obtidos nos vários estudos realizados com linhagens clonais de ambas as populações de D. longispina reforçam a importância de integrar a temática do desenvolvimento de tolerância à poluição aquando da avaliação dos riscos ambientais e ecológicos de compostos químicos, como os metais, no meio ambiente.
In the present study the cladoceran Daphnia longispina was used as a model organism to test the ecological side effects of adaptation to metal contaminated environments. D. longispina natural populations were sampled from a metal contaminated reservoir and from a nearby clean water reservoir, both belonging to the aquatic system surrounding the abandoned São Domingos cupric mine. Clonal lineages were established and maintained in the laboratory by means of asexual reproduction and were used for tests. The comparison of broad sense heritabilities and genetic correlations using up to twenty distinct clonal D. longispina lineages randomly obtained from the metal contaminated reservoir and the reference reservoir showed that only sensitive and resistant lineages to Cu were present in the reference and contaminated site, respectively. For Zn, however, both populations had a similar distribution pattern of sensitivities. Fitness costs of tolerance were illustrated by lower feeding rates of the tolerant population compared to the reference one. Another study assessing life-history responses to sublethal copper contamination in four D. longispina clones, two from a reference site and the other two from a historically copper-exposed site showed that tolerance manifested by D. longispina clones at lethal copper levels was also evident at sublethal concentrations, with the tolerant clone from impacted population showing higher tolerance to copper for all the parameters (feeding, oxygen consumption, growth and reproduction) compared to the rest of clones. The multigenerational effects of acclimation to copper were also evaluated by exposing a single clone of D. longispina originated from the reference population to copper over three consecutive generations. Results from the evaluation of its life-history performance illustrate that physiological adaptation to copper across several generations only increased marginally acute tolerance to copper. Besides that, a high variation in life-history traits was observed not only between copper treatments, but also among generations. For instance, generation had a significantly influence on the observed pattern of age at first reproduction and interact with copper in the observed variation of time and clutch size at first reproduction. Overall, the importance of studying long-term adaptation to metals in natural populations is highlighted in this study as the acquisition of genetically inherited tolerance could have associated ecological costs. The obtained results reinforce the need to integrate these issues when assessing risks posed by chemicals to the environment.
FCT/FSE - SFRH/BD/12324/2003

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Luisi, Pierre 1985. "Positive selection in humans : from singles to interaction maps." Doctoral thesis, Universitat Pompeu Fabra, 2014. http://hdl.handle.net/10803/286921.

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From Darwin’s Origin of the Species to the recent wealth in genomic data, many biologists have focused their research on understanding how natural selection has shaped the variability among and within species. Although theoretical and empirical advances have been remarkable, most biological mechanisms underlying the molecular basis of human adaptation remain to be elucidated. The selectionist view of adaptation accounted for the bias towards independent gene evolution. Most published studies aiming at detecting positive selection using either polymorphism or divergence data have been performed using a gene-candidate or a genome-wide scan approach, as described in the two first articles presented here. However, gene evolution is largely influenced by the biological context in which the encoded protein performs its intrinsic function(s). The phenotype, not the genotype, is at the interface with natural selection. Thus, in order to understand gene evolution, and particularly when considering adaptive selection, it is crucial to reduce the gap between genotype and phenotype. Genes and proteins do not act in isolation, but rather interact one with others in order to perform a given biological function. Therefore, when studying natural selection at molecular level one promising framework is to consider gene networks, as described in the two last articles of the present thesis. Analyses of gene networks describing the Insulin/TOR transduction signalling cascade and the whole protein-protein physical interaction map hold very striking results. Namely, genes acting at the core of both networks, thus having either more effect on a given phenotype or more pleiotropic effects within the organism, are more likely to be targeted by recent positive selection, as inferred using polymorphism data.
Desde el “Origen de las Especies” de Darwin a la reciente revoluci´on gen´omica, muchos bi´ologos han centrado su investigaci´on en la comprensi ´on de c´omo la selecci´on natural ha dado forma a la variabilidad entre y dentro de las especies. Aunque, los avances te´oricos y emp´ıricos han sido notables, la mayor´ıa de los mecanismos biol´ogicos que subyacen a las bases moleculares de la adaptaci´on biol´ogica a´un no est´an suficientemente esclarecidos. La visi´on seleccionista de adaptaci´on marc´o el sesgo de los estudios evolutivos hacia el an´alisis de genes individuales. La mayor´ıa de estudios publicados destinados a la detecci´on de la selecci´on positiva utilizando datos de polimorfismo o de divergencia se han realizado utilizando un gen candidato o un enfoque de exploraci´on gen´omica, como se describe en los dos primeros art´ıculos presentados en la presente tesis. Sin embargo, la evoluci´on de genes est´a muy condicionada por el contexto biol´ogico en el que cada gen realiza su funci´on intr´ınseca, siendo el fenotipo, y no el genotipo, su materia primaria. Por lo tanto, a fin de comprender la evoluci´on de genes, y en particular cuando se considera la evoluci´on adaptativa, es crucial reducir la brecha entre el genotipo y el fenotipo. Los genes y las prote´ınas no act´uan de manera aislada, sino que interact´uan entre s´ı con el fin de realizar una funci´on biol´ogica determinada. Por lo tanto, un marco prometedor al estudiar la selecci´on natural a nivel molecular seria considerar las redes de genes, como se describe en los dos ´ultimos art´ıculos de la presente tesis. Los an´alisis de los datos de polimorfismo gen´etico, tanto de los genes que componen la v´ıa de la insulina, c´omo de los todos los genes descritos en los mapas f´ısicos de interacci´on prote´ına-prote´ına tienen resultados muy sorprendentes: los genes que act´uan en el n´ucleo de ambas redes, teniendo as´ı m´as efecto sobre un determinado fenotipo o m´as efectos ple´otropicos dentro del organismo, tienen m´as probabilidades de ser el blanco de la selecci´on positiva reciente.

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44

Nomura, Erico. "Valor adaptativo do parasitóide Apanteles galleriae (Hymenoptera: Braconidae) de população natural e da população mantida em laboratório /." Rio Claro : [s.n.], 2009. http://hdl.handle.net/11449/106555.

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Resumo: Lagartas das traças-da-cera Galleria mellonella e Achroia grisella foram oferecidas a fêmeas do endoparasitóide solitário Apanteles galleriae de uma população mantida em condições de laboratório (população de laboratório), e a fêmeas de uma população selvagem, formada a partir de casulos coletados em apiários de Rio Claro e Araras, SP, Brasil (população de campo). Os parasitóides de cada população foram criados por 4 gerações consecutivas. Dois parasitóides machos e uma fêmea, emergidos no mesmo dia e da mesma espécie de hospedeiro foram transferidos para frascos de 30 mL, para propiciar o acasalamento. A cada fêmea fecundada de A. galleriae foram oferecidas 5, 10, 15 ou 20 lagartas de Galleria mellonella ou Achroia grisella de 5º e 6º instar, respectivamente, por uma hora. Após este período, a fêmea foi devolvida ao frasco de origem e as lagartas receberam dieta "ad libidum". Tal procedimento foi realizado a cada 2 dias, desde o 3º dia de vida da fêmea, até a sua morte. O objetivo da pesquisa foi comparar as proles obtidas de ambas as populações, em relação ao número de descendentes e à razão sexual, bem como avaliar a capacidade de parasitismo do parasitóide, em função da idade da fêmea e da densidade de hospedeiros submetidos ao parasitismo. Utilizou-se um teste de proporções para comparar as freqüências de lagartas de G. mellonella e A. grisella parasitadas por fêmeas de A. galleriae de cada população (F4 ou Lab) e uma análise de variâncias para testar o efeito da idade das fêmeas das duas populações sobre o número de descendentes emergidos, para as quatro densidades de hospedeiros. Uma análise de correlação de Pearson foi usada para avaliar o efeito da idade materna sobre a razão sexual registrada para os parasitóides obtidos em cada grupo experimental. As maiores eficiências de parasitismo registradas foram 42,59% para... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: Caterpillars of Galleria mellonella and Achroia grisella were offered to females of the solitary endoparasitoid Apanteles galleriae from a population maintained under laboratory conditions (laboratory population), and females from a wild population, formed from cocoons collected in apiaries of Rio Claro and Araras, SP, Brazil (field population). The parasitoids of each population were reared by four consecutive generations. Two males and a female, emerged on the same day and reared in the same host species, were transferred to a 30 mL vial in order to allow mating. Caterpillars of A. grisella (sixth instar) or G. mellonella (fifth instar) were offered for sixty minutes to each mated and expert female, with 2 to 5 days of age, in one of the four host densities used in this research (5, 10, 15 and 20 hosts/female). After this period, the female was given back to the original vial, and the caterpillars received diet "ad libidum". Such procedure was accomplished every 2 days, since the 3rd day of the female life until her death. The objective of this research was to compare the offsprings from both populations, in relation to the number of descendants and sex ratio, and also the capacity of parasitism of A. galleriae in relation to the age of the female and the density of hosts submitted to the parasitism. A test for difference of proportions was applied to compare the frequencies of caterpillars of G. mellonella and A. grisella parasitized by A. galleriae females of each population (F4 or Lab), and an analysis of variances was used to evaluate the effect of the age of females from both populations on the number of descendants emerged, as a function of the host densities. A Pearson's correlation analysis was utilized to test the effect of maternal age on sexual proportion recorded for parasitoids of each experimental group. The highest efficiencies of parasitism recorded were 42.59% to ... (Complete abstract click electronic access below)
Orientador: José Chaud Netto
Coorientador: Nivar Gobbi
Banca: Ana Eugenia de Carvalho Campos Farinha
Banca: Julio Marcos Melges Walder
Banca: Sonia Silveira Ruiz
Banca: Giuliano Grici Zacarin
Doutor

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45

Guthrie, Ruth J. "Patterns of invertebrate distribution and abundance on Cordyline australis in human-modified landscapes." Diss., Lincoln University, 2008. http://hdl.handle.net/10182/1235.

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Fragmentation of forest habitat by urban and rural development has had profound effects on the distribution and abundance of many native species; however, little is known about the ecological processes driving patterns in community structure (species richness and composition) of host-specialised herbivores in modified habitats. I examined patterns in community structure of 9 specialist and 19 generalist invertebrate herbivores of cabbage trees (Cordyline australis Laxmanniaceae) across a highly-modified landscape. I found that, although species richness of specialists was highest in forest sites, the majority of host-specialised species were not restricted to forest habitats and were as widespread as many generalists. In terms of site occupancy, only two specialist and four generalist species were rare. I show that patterns of species occupancy and abundance reflect differing susceptibility to habitat modification, with landscape-level variation an important predictor of abundance for nearly all species. When species occurrences and life history traits were considered I did not find strong evidence for the importance of dispersal ability, which suggests that habitat variability had a stronger organising effect on the community. In a replicated common garden experiment, I found distinct regional patterns in the community structure of the specialist invertebrates occurring on different phylogenetic groups of C. australis. In contrast, community structure of generalist herbivores did not differ significantly among host genotypes. I speculate these patterns are due to historical changes in the distribution of cabbage trees in the Southern phylogenetic region that caused specialised herbivores to become locally adapted on populations of low genetic diversity following expansion after the last glacial maximum. However, this consistent selection pressure did not occur in the Northern region where C. australis habitat has been more consistently available over the past tens of thousands of years, reflected in higher host genetic diversity. This study has advanced our understanding of the patterns in community structure of an indigenous, host-specialised fauna in a highly modified and fragmented urban and rural landscapes.

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46

Nomura, Erico [UNESP]. "Valor adaptativo do parasitóide Apanteles galleriae (Hymenoptera: Braconidae) de população natural e da população mantida em laboratório." Universidade Estadual Paulista (UNESP), 2009. http://hdl.handle.net/11449/106555.

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Lagartas das traças-da-cera Galleria mellonella e Achroia grisella foram oferecidas a fêmeas do endoparasitóide solitário Apanteles galleriae de uma população mantida em condições de laboratório (população de laboratório), e a fêmeas de uma população selvagem, formada a partir de casulos coletados em apiários de Rio Claro e Araras, SP, Brasil (população de campo). Os parasitóides de cada população foram criados por 4 gerações consecutivas. Dois parasitóides machos e uma fêmea, emergidos no mesmo dia e da mesma espécie de hospedeiro foram transferidos para frascos de 30 mL, para propiciar o acasalamento. A cada fêmea fecundada de A. galleriae foram oferecidas 5, 10, 15 ou 20 lagartas de Galleria mellonella ou Achroia grisella de 5º e 6º instar, respectivamente, por uma hora. Após este período, a fêmea foi devolvida ao frasco de origem e as lagartas receberam dieta “ad libidum”. Tal procedimento foi realizado a cada 2 dias, desde o 3º dia de vida da fêmea, até a sua morte. O objetivo da pesquisa foi comparar as proles obtidas de ambas as populações, em relação ao número de descendentes e à razão sexual, bem como avaliar a capacidade de parasitismo do parasitóide, em função da idade da fêmea e da densidade de hospedeiros submetidos ao parasitismo. Utilizou-se um teste de proporções para comparar as freqüências de lagartas de G. mellonella e A. grisella parasitadas por fêmeas de A. galleriae de cada população (F4 ou Lab) e uma análise de variâncias para testar o efeito da idade das fêmeas das duas populações sobre o número de descendentes emergidos, para as quatro densidades de hospedeiros. Uma análise de correlação de Pearson foi usada para avaliar o efeito da idade materna sobre a razão sexual registrada para os parasitóides obtidos em cada grupo experimental. As maiores eficiências de parasitismo registradas foram 42,59% para...
Caterpillars of Galleria mellonella and Achroia grisella were offered to females of the solitary endoparasitoid Apanteles galleriae from a population maintained under laboratory conditions (laboratory population), and females from a wild population, formed from cocoons collected in apiaries of Rio Claro and Araras, SP, Brazil (field population). The parasitoids of each population were reared by four consecutive generations. Two males and a female, emerged on the same day and reared in the same host species, were transferred to a 30 mL vial in order to allow mating. Caterpillars of A. grisella (sixth instar) or G. mellonella (fifth instar) were offered for sixty minutes to each mated and expert female, with 2 to 5 days of age, in one of the four host densities used in this research (5, 10, 15 and 20 hosts/female). After this period, the female was given back to the original vial, and the caterpillars received diet ad libidum. Such procedure was accomplished every 2 days, since the 3rd day of the female life until her death. The objective of this research was to compare the offsprings from both populations, in relation to the number of descendants and sex ratio, and also the capacity of parasitism of A. galleriae in relation to the age of the female and the density of hosts submitted to the parasitism. A test for difference of proportions was applied to compare the frequencies of caterpillars of G. mellonella and A. grisella parasitized by A. galleriae females of each population (F4 or Lab), and an analysis of variances was used to evaluate the effect of the age of females from both populations on the number of descendants emerged, as a function of the host densities. A Pearson’s correlation analysis was utilized to test the effect of maternal age on sexual proportion recorded for parasitoids of each experimental group. The highest efficiencies of parasitism recorded were 42.59% to ... (Complete abstract click electronic access below)

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47

McMillen, David. "Effects of spike-frequency adaptation on neural models, with applications to biologically inspired robotics." Thesis, National Library of Canada = Bibliothèque nationale du Canada, 2000. http://www.collectionscanada.ca/obj/s4/f2/dsk1/tape2/PQDD_0020/NQ53651.pdf.

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48

D'Arcangelo, Silvia. "Persistence and Adaptation of Pseudomonas Aeruginosa in cystic Fibrosis Airway." Doctoral thesis, Università degli studi di Trento, 2017. https://hdl.handle.net/11572/368506.

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Background. Infections caused by Pseudomonas aeruginosa are the main cause of morbidity and mortality in Cystic Fibrosis (CF) patients and occur via primary colonisation of the airway followed by the accumulation of pathoadaptive mutations in the bacterial genome which increase fitness in the lung environment and result in chronicization. A better understanding of i) the evolutionary dynamics occurring during chronic airway infections in CF patients and ii) the genetic adaptation of strains to the CF lung environment, might give further clues for preventive measures or novel therapies to control CF infections in the future. In this work, we obtained genomic sequences of 40 P. aeruginosa isolates from a single CF patient collected over an eight-year period (2007-2014) and analysed the population in terms of clonality of the isolates, phylogenetic relationships, and presence of polymorphisms and variants between the strains. Population structure and microevolution. In silico Multilocus Sequence Typing (MLST) analysis revealed a characteristic single clonal population dominated by a previously characterized sequence type (ST390) and a small number of new, closely related ST variants (ST1863, ST1864, ST1923). EBURST analysis of the sequence types revealed that all members of this population belong to the same clonal lineage and likely evolved from a single ancestral colonizing strain. Furthermore, the phylogenetic analysis based on SNPs also divided the population into two subpopulations derived from the evolution of the first infecting strain. The annotation of SNPs allowed us to identify mutations with moderate or high impact. Genes with high impact variants encoded respiratory nitrate reductase subunit gamma nail, polyprotein signal peptidase lspA, the ABC transporter-binding protein aaltP, the copper resistance protein A precursor pcoAin, and four hypothetical proteins. The evolution of strains in the CF airway is characterized by the loss of many virulence traits, including motility and protease secretion, along with the acquisition of multidrug resistance. Functional phenotypic assays of the collection, including motility and secretion of proteases, showed a decrease over time in the persistent isolates. We also determined the antibiotic susceptibility profile of the collection; while early isolates were found to be susceptible to almost all these antibiotics, resistant phenotypes dramatically increased over time in the population. Functional studies on specific strains. To identify additional functional variations related to pathoadaptive mutations occurring in the course of chronic infection in CF, we then selected three isolates for further characterization: one early CF isolate (TNCF_23 isolated in 2007); one clonal late CF isolate (TNCF_175 isolated in 2014); one clinical isolate (VrPa97) from a non-CF patient belonging to the same sequence type (ST390) as the former isolates. With this approach, we aimed to identify additional phenotypic and functional variations between isolates with a very homogeneous genomic background, in an attempt to find out new pathoadaptive mutations occurring in the course of chronic infection in CF. Specifically, the following traits were investigated: killing of C. elegans and G. mellonella (in vivo virulence); immunomodulatory properties (IL-8 ELISA assay); competitive growth in Artificial Sputum Medium (ASM); functionality of Type Six Secretion System (T6SS). Despite their close genetic relatedness, considerable variations were observed between the three isolates, among which the late isolate TNCF_175 showed several alterations 7 putatively resulting from the adaptation process to the CF lung. TNCF_175 presented a mutation in tssK3, part of H3-T6SS; this mutation (C958T) was therefore introduced in the reference strains PAO1 and PA14, and mutated strains were subsequently complemented; killing rate on C. elegans and growth rate in ASM in mutant and complemented strains were evaluated. Conclusions. A rare feature of this strain collection is the consistent number of clonal isolates obtained from a single patient over a rather long period of 8 eight years, thus providing a model to look at microevolutionary trends within a highly homogenous bacterial population, and avoiding potential biases due to the host genetic background and clinical history. In spite of the close genomic relatedness of all isolates, a surprisingly high diversity was observed for the majority of tested phenotypes. Investigating the competitive ability of early versus late strains we propose a role for T6SS in the adaptation process to the CF lung environment. Our data suggest that once persistence has been established, a strain no longer requires its T6SS, allowing loss of function mutations to occur. Conversely, acute and early CF strains still carry a number of virulence factors, including T6SS that potentially provide an advantage in outcompeting other microorganisms in the initial stage of CF infection.

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49

D'Arcangelo, Silvia. "Persistence and Adaptation of Pseudomonas Aeruginosa in cystic Fibrosis Airway." Doctoral thesis, University of Trento, 2017. http://eprints-phd.biblio.unitn.it/2719/1/Thesis_SDA_FINAL.pdf.

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Abstract:

Background. Infections caused by Pseudomonas aeruginosa are the main cause of morbidity and mortality in Cystic Fibrosis (CF) patients and occur via primary colonisation of the airway followed by the accumulation of pathoadaptive mutations in the bacterial genome which increase fitness in the lung environment and result in chronicization. A better understanding of i) the evolutionary dynamics occurring during chronic airway infections in CF patients and ii) the genetic adaptation of strains to the CF lung environment, might give further clues for preventive measures or novel therapies to control CF infections in the future. In this work, we obtained genomic sequences of 40 P. aeruginosa isolates from a single CF patient collected over an eight-year period (2007-2014) and analysed the population in terms of clonality of the isolates, phylogenetic relationships, and presence of polymorphisms and variants between the strains. Population structure and microevolution. In silico Multilocus Sequence Typing (MLST) analysis revealed a characteristic single clonal population dominated by a previously characterized sequence type (ST390) and a small number of new, closely related ST variants (ST1863, ST1864, ST1923). EBURST analysis of the sequence types revealed that all members of this population belong to the same clonal lineage and likely evolved from a single ancestral colonizing strain. Furthermore, the phylogenetic analysis based on SNPs also divided the population into two subpopulations derived from the evolution of the first infecting strain. The annotation of SNPs allowed us to identify mutations with moderate or high impact. Genes with high impact variants encoded respiratory nitrate reductase subunit gamma nail, polyprotein signal peptidase lspA, the ABC transporter-binding protein aaltP, the copper resistance protein A precursor pcoAin, and four hypothetical proteins. The evolution of strains in the CF airway is characterized by the loss of many virulence traits, including motility and protease secretion, along with the acquisition of multidrug resistance. Functional phenotypic assays of the collection, including motility and secretion of proteases, showed a decrease over time in the persistent isolates. We also determined the antibiotic susceptibility profile of the collection; while early isolates were found to be susceptible to almost all these antibiotics, resistant phenotypes dramatically increased over time in the population. Functional studies on specific strains. To identify additional functional variations related to pathoadaptive mutations occurring in the course of chronic infection in CF, we then selected three isolates for further characterization: one early CF isolate (TNCF_23 isolated in 2007); one clonal late CF isolate (TNCF_175 isolated in 2014); one clinical isolate (VrPa97) from a non-CF patient belonging to the same sequence type (ST390) as the former isolates. With this approach, we aimed to identify additional phenotypic and functional variations between isolates with a very homogeneous genomic background, in an attempt to find out new pathoadaptive mutations occurring in the course of chronic infection in CF. Specifically, the following traits were investigated: killing of C. elegans and G. mellonella (in vivo virulence); immunomodulatory properties (IL-8 ELISA assay); competitive growth in Artificial Sputum Medium (ASM); functionality of Type Six Secretion System (T6SS). Despite their close genetic relatedness, considerable variations were observed between the three isolates, among which the late isolate TNCF_175 showed several alterations 7 putatively resulting from the adaptation process to the CF lung. TNCF_175 presented a mutation in tssK3, part of H3-T6SS; this mutation (C958T) was therefore introduced in the reference strains PAO1 and PA14, and mutated strains were subsequently complemented; killing rate on C. elegans and growth rate in ASM in mutant and complemented strains were evaluated. Conclusions. A rare feature of this strain collection is the consistent number of clonal isolates obtained from a single patient over a rather long period of 8 eight years, thus providing a model to look at microevolutionary trends within a highly homogenous bacterial population, and avoiding potential biases due to the host genetic background and clinical history. In spite of the close genomic relatedness of all isolates, a surprisingly high diversity was observed for the majority of tested phenotypes. Investigating the competitive ability of early versus late strains we propose a role for T6SS in the adaptation process to the CF lung environment. Our data suggest that once persistence has been established, a strain no longer requires its T6SS, allowing loss of function mutations to occur. Conversely, acute and early CF strains still carry a number of virulence factors, including T6SS that potentially provide an advantage in outcompeting other microorganisms in the initial stage of CF infection.

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50

Kremer, Débora. "O GÊNERO TILLANDSIA L. (BROMELIACEAE-TILLANDSIOIDEAE) NO ESTADO DO PARANÁ, BRASIL." UNIVERSIDADE ESTADUAL DE PONTA GROSSA, 2011. http://tede2.uepg.br/jspui/handle/prefix/952.

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Tillandsia L. is the largest genus of the subfamily Tillandsioideae (Bromeliaceae) with ca. 557 species. It is distributed from the southern U. S. A to central Argentina and Chile. Traditionally the genus has been divided into seven subgenera: Tillandsia subg. Allardtia (A. Dietrich) Baker, Tillandsia subg. Anoplophytum (Beer) Baker, Tillandsia subg. Phytarrhiza (Vis.) Baker, Tillandsia subg. Diaphoranthema (Beer) Baker, Tillandsia subg. Tillandsia L., Tillandsia subg. Pseudalcantarea Mez and Tillandsia subg. Pseudo-Catopsis Baker. The taxonomic study of the species Tillandsia in the Paraná state was presented. Were found 17 species in 4 subgenera:Tillandsia subg. Diaphoranthema -Tillandsia loliacea Mart. ex Schult. & Schult.f., Tillandsia recurvata (L.) L, Tillandsia tricholepis Baker and Tillandsia usneoides (L.) L.; Tillandsia subg. Anoplophytum -Tillandsia didisticha (E. Morren) Baker, Tillandsia gardneri Lindley, Tillandsia geminiflora Brong., Tillandsia lineares Vell., Tillandsia lorentziana Griseb.; Tillandsia pohliana Mez, Tillandsia recurvifolia Hooker, Tillandsia stricta Solander, Tillandsia tenuifolia L.; Tillandsia subg. Phytarrhiza - Tillandsia crocata (E. Morren) Baker, Tillandsia streptocarpa Baker; Tillandsia mallemontii Glazou ex Mez e Tillandsia subg. Tillandsia -Tillandsia polystachia (L.) L.. Identification Keys, as well as descriptions, illustrations, comments and distribuition patterns are presented. The results show that the Paraná has a high species richness when compared to neighboring states. Besides the taxonomic study, there were some evolutionary adaptations of species, fitting them in ecophysiological types proposed in the literature. Only T. polystachia presents wide rosette forming tank. The remaining species are characterized by the absence of the tank, the presence or absence of non-root in adulthood and four species were found to be minimized.
Tillandsia L. é o maior gênero da subfamília Tillandsioideae (Bromeliaceae) com 557 espécies, distribuídas desde o sul dos Estados Unidos até a Argentina e o Chile. Tradicionalmente, está dividido em sete subgêneros: Tillandsia subg. Allardtia (A. Dietrich) Baker, Tillandsia subg. Anoplophytum (Beer) Baker, Tillandsia subg. Phytarrhiza (Vis.) Baker, Tillandsia subg. Diaphoranthema (Beer) Baker, Tillandsia subg. Tillandsia L., Tillandsia subg. Pseudalcantarea Mez e Tillandsia subg. Pseudo- Catopsis Baker. Um estudo taxonômico de Tillandsia no Estado do Paraná foi realizado e foram encontrados 17 táxons, distribuídos em 4 subgêneros: Tillandsia subg. Diaphoranthema -Tillandsia loliacea Mart. ex Schult. & Schult.f., Tillandsia recurvata (L.) L, Tillandsia tricholepis Baker e Tillandsia usneoides (L.) L.; Tillandsia subg. Anoplophytum - Tillandsia didisticha (E. Morren) Baker, Tillandsia gardneri Lindley, Tillandsia geminiflora Brong., Tillandsia lineares Vell., Tillandsia lorentziana Griseb.; Tillandsia pohliana Mez, Tillandsia recurvifolia Hooker, Tillandsia stricta Solander, Tillandsia tenuifolia L.; Tillandsia subg. Phytarrhiza - Tillandsia crocata (E. Morren) Baker, Tillandsia streptocarpa Baker; Tillandsia mallemontii Glazou ex Mez e Tillandsia subg. Tillandsia – com apenas uma espécie Tillandsia polystachia (L.) L.. São apresentadas chaves de identificação, descrições, comentários,ilustrações e distribuição geográfica de cada táxon. Os resultados revelaram que a riqueza de espécies de Tillandsia no Paraná é maior quando comparada aos Estados vizinhos. Além do estudo taxonômico, foram observadas algumas adaptações evolutivas das espécies, enquadrando-as nos tipos ecofisiológicos propostos em literatura. Apenas T. polystachia apresenta roseta ampla formando tanque. As demais espécies são caracterizadas pela ausência de tanque, a presença ou não de raiz na fase adulta e quatro delas, foram consideradas espécies minimizadas.

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Dissertations / Theses on the topic 'Adaptation, biological'

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