Дисертації з теми "Environmental genomic"
Щоб переглянути інші типи публікацій з цієї теми, перейдіть за посиланням: Environmental genomic.
Оформте джерело за APA, MLA, Chicago, Harvard та іншими стилями
Ознайомтеся з топ-50 дисертацій для дослідження на тему "Environmental genomic".
Біля кожної праці в переліку літератури доступна кнопка «Додати до бібліографії». Скористайтеся нею – і ми автоматично оформимо бібліографічне посилання на обрану працю в потрібному вам стилі цитування: APA, MLA, «Гарвард», «Чикаго», «Ванкувер» тощо.
Також ви можете завантажити повний текст наукової публікації у форматі «.pdf» та прочитати онлайн анотацію до роботи, якщо відповідні параметри наявні в метаданих.
Переглядайте дисертації для різних дисциплін та оформлюйте правильно вашу бібліографію.
1
Yang, Bin, and 杨彬. "A novel framework for binning environmental genomic fragments." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2010. http://hub.hku.hk/bib/B45789344.
2
Jackson, Colin John. "The typing and environmental detection of Campylobacter jejuni." Thesis, Manchester Metropolitan University, 1995. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.262007.
3
Herzog, Rebecca [Verfasser]. "Global change genomics - comparative genomic analyses on environmental associated speciation and adaptation processes in Odonata / Rebecca Herzog." Hannover : Gottfried Wilhelm Leibniz Universität, 2021. http://d-nb.info/1238221785/34.
4
Finke, Jan Felix. "Environmental and genomic insights into marine virus populations and communities." Thesis, University of British Columbia, 2017. http://hdl.handle.net/2429/61997.
Анотація:
The full abstract for this thesis is available in the body of the thesis, and will be available when the embargo expires.Science, Faculty of
Earth, Ocean and Atmospheric Sciences, Department of
Graduate
5
Chan, Yu-ki, and 陳裕琪. "Environmental genomic analysis of refuge habitats in hyper-arid deserts." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2011. http://hub.hku.hk/bib/B46917366.
6
Skutas, Jorie L. "Microbial and Genomic Analysis of Environmental Samples in Search of Pathogenic Salmonella." NSUWorks, 2017. http://nsuworks.nova.edu/occ_stuetd/461.
Анотація:
Salmonellosis or “food poisoning” is a foodborne infection brought on by the pathogen Salmonella from the ingestion of the bacterium on contaminated foods such as vegetables. Infection from Salmonella leads to the highest incidence of hospitalizations and deaths each year, compared to any other bacterial foodborne illness. South Florida is the second largest agricultural winter vegetable producer in the United States, and contamination of vegetables is often observed in preharvest practices. A hardy bacterium, Salmonella, has been shown to live up to 6 weeks in soil and water up to 42°C without a host.
The Florida Everglades is a tropical wetland that plays a large role in South Florida’s watershed. It can be divided into agricultural, conservation, and urban areas that connect Lake Okeechobee to Florida Bay by canals, swamps, and rivers. Inland canals tightly regulate water levels in South Florida as a means of flood control for residential and agricultural land. With the influences of anthropomorphic run off from agricultural and urban use, we hypothesized that microbial communities would significantly differ between three select sites in western (Collier county) versus three sites in more urban eastern Florida (Broward county): natural standing water, manmade drainage canal in agricultural areas, and manmade drainage canals in urban areas. We also hypothesized that pathogenic like Salmonella would be present in these habitats. Deep sequencing and ecological genetics analyses of the 16s rRNA V4 region yielded a total of 163,320 unique bacterial OTUs from a total of 139 samples collected monthly for one year in 2015 and part of 2016. Salmonella is not considered an abundant taxon within the microbial population.
With the knowledge that Salmonella resides within the microbial population isolates were cultured from soil and water samples that were taken monthly from each site using a modified version of the Food and Drug Administration Bacterial Analytical Methods manual (FDA-BAM). The culturing resulted in 234 isolates obtained and 31 different serovars of Salmonella. Culturing showed that Salmonella favored months with high standing water and high-water temperatures that would lead to the ideal environment for survival. The most commonly occurring isolates within the sample set are those associated with agricultural animals. Though Salmonella may be a rare taxon within the microbial population given the correct environmental conditions such as warm temperatures it is possible to observe Salmonella year round within the South Florida environment.
7
Gray, Miranda M. "Genomic differentiation of big bluestem (Andropogon gerardii) along the Great Plains’ environmental gradient." Thesis, Kansas State University, 2012. http://hdl.handle.net/2097/14626.
Анотація:
Master of ScienceDepartment of Plant Pathology
Eduard D. Akhunov
Loretta C. Johnson
Big bluestem (Andropogon gerardii Vitman) is an ecologically dominant grass of the North American grasslands with precipitation-dependent productivity. However, climatic predictions for big bluestem’s dominant range in the Great Plains include increased periods of drought. The main objectives of this research were to determine the extent of neutral and non-neutral genetic differentiation and diversity among putative big bluestem ecotypes using amplified fragment length polymorphism (AFLP) markers. This is the first study of both neutral and non-neutral genetic diversity of big bluestem which also includes source populations of well-described ecotypes studied in reciprocal common gardens. A total of 378 plants were genotyped from 11 source prairies, originating from one of three ecoregions (Central Kansas, Eastern Kansas, and Illinois). Using two AFLP primer sets, 387 polymorphic markers (error rate 9.18%) were found. Un-rooted neighbor joining tree and principle-component analyses showed continuous genetic differentiation between Kansas and Illinois putative ecotypes, with genetic overlap occurring between Kansas ecotypes. Analysis of molecular variance showed high diversity within-prairie sites (80%) relative to across-prairies (11%), and across- ecoregions (9%) (p<0.001). Within-prairie genetic diversity levels were similar among ecoregions (84-92%), with the highest genetic variation maintained in Illinois prairies (92%). Population structure analyses supported K=6 genetic clusters across the environmental gradient, with Kansas prairies belonging to three main genetic groups, and Illinois prairies having largely divergent allele frequencies from Kansas prairies. Interestingly, BAYESCAN analysis of the three putative ecotypes identified eight F[subscript]ST-outlier AFLP loci under potential diversifying selection. Frequency patterns of loci under diversifying selection were further linked to geo-environmental descriptors including precipitation, temperature severity, diurnal temperature variation, prairie location, and elevation. The observed allele frequency divergence between Kansas and Illinois ecotypes suggests tallgrass restorations should consider possible maladaptation of non-local ecotypes and genetic swamping. However, high within-prairie genetic variation may help individual big bluestem populations withstand climatic variability.
8
Curreem, Oi-ting Shirly. "The study of environmental adaptability of laribacter hongkongensis by genomic and proteomic approach." Click to view the E-thesis via HKUTO, 2009. http://sunzi.lib.hku.hk/hkuto/record/B43931686.
9
Braff, Jennifer C. "Construction and phenotypic screening of mid-size insert marine microbial environmental genomic libraries." Thesis, Massachusetts Institute of Technology, 2008. http://hdl.handle.net/1721.1/43722.
Анотація:
Thesis (S.M.)--Joint Program in Oceanography/Applied Ocean Science and Engineering (Massachusetts Institute of Technology, Dept. of Civil and Environmental Engineering; and the Woods Hole Oceanographic Institution), 2008.Includes bibliographical references (leaves 52-56).
Functional screening of environmental genomic libraries permits the identification of clones expressing activities of interest without requiring prior knowledge of the genes responsible. In this study, protocols were optimized for the construction of mid-size DNA insert, inducible expression environmental genomic plasmid libraries for this purpose. A library with a mean insert size of 5.2 kilobases was constructed with environmental DNA isolated from surface ocean water collected at Hawaii Ocean Time-series station ALOHA in plasmid cloning vector pMCL200 under the inducible control of the PLAC promoter. To begin to evaluate the utility of such libraries for gene expression-based screens, this library was screened phenotypically for clones expressing genes that confer fluorescence or distinctive coloration on colonies of host Escherichia coli cells, and results were compared to those for a fosmid library constructed from the same marine microbial DNA sample. Ecologically relevant sequences were identified in both libraries, and each was observed to offer both advantages and disadvantages. Results of this study suggest that mid-size insert plasmid libraries under the control of inducible promoters can provide a useful and complementary approach for both functional screening and shotgun sequencing of environmental genomic libraries.
by Jennifer C. Braff.
S.M.
10
Tsai, Yeng-Chieh. "The application of two-dimensional genomic DNA nylon matrix for environmental samples analysis." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 67 p, 2009. http://proquest.umi.com/pqdweb?did=1654501591&sid=1&Fmt=2&clientId=8331&RQT=309&VName=PQD.
11
Holden, Lindsay Adrian. "Investigating the Role of Genomic Variation in Susceptibility to Environmental Chemicals across Populations." PDXScholar, 2018. https://pdxscholar.library.pdx.edu/open_access_etds/4371.
Анотація:
No two individuals are identical. This is true at the genetic level and at the phenotypic level. One of the traits that varies between populations is toxicant susceptibility: some individuals are sensitive to the effects of environmental chemical exposure, and others are resistant. This body of work aims to address the impact of genomic copy number variants (CNV)--large (>1 Kb) duplications or deletions across the genome--on the toxicant-susceptibility phenotype.
Herein copy number variants were characterized across three commonly used laboratory strains of zebrafish (Danio rerio) and mRNA expression phenotypes were identified in the same strains. It was found that males and females have only a 14% overlap in differentially expressed mRNA transcripts across three common laboratory strains, congruent with the growing body of work identifying sex- and strain-specific phenotypes in zebrafish. Furthermore, identified were two strain-specific response quantitative trait loci (QTL) that explain about a third of the variation in susceptibility to PCB and tested the response QTL using targeted CRISPR-Cas9 editing of the CNV involved. Overall, this body of work defines CNV and mRNA expression variation across zebrafish strains, identifies CNV causal in the PCB-susceptibility phenotype, and confirms the PCB-susceptibility QTL using targeted genomic editing.
12
Li-Sucholeiki, Xiaocheng 1968. "A technology for detecting unselected mutational spectra in human genomic DNA." Thesis, Massachusetts Institute of Technology, 1999. http://hdl.handle.net/1721.1/84743.
Анотація:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Division of Bioengineering and Environmental Health, 1999.Includes bibliographical references (leaves 186-205).
by Xiaocheng Li-Suckoleiki.
Ph.D.
13
Yang, Qiu. "Multifaceted aspects of MCR-mediated colistin resistance : fitness, virulence, environmental reservoirs and genomic insights." Thesis, Cardiff University, 2018. http://orca.cf.ac.uk/115924/.
Анотація:
To date, eight different mcr-variants have been identified encoding phosphoethanolamine transferases contributing to phosphoethanolamine addition to lipid A and thereby conferring colistin resistance. This novel mechanism of plasmid-mediated colistin resistance provides an efficient way in distributing colistin resistance. This thesis aims to further our understanding of the multifaceted aspects of mcr-like genes using detailed molecular analysis including whole-genome sequencing (WGS) for 17 mcr-positive Klebsiella pneumoniae (MCRPKP) and 219 mcr-positive Escherichia coli (MCRPEC) from Thailand and Vietnam. Fitness is an important factor to predict the spread and development of antibiotic resistance. In chapter 3, the data show that over-producing MCR-1 in E. coli imposes a great fitness loss, observed by slow growth rates, impaired membrane integrity and decreased competitiveness. The fitness burden conferred by mcr-3 seems to be more moderate and mcr-3-positive plasmids are more stable and competitive, than that of mcr-1-carrying plasmids. In addition, I provided evidence that blowflies serve as reservoirs of mcr-genes and 48 mcr-1-positive strains recovered from blowflies have been characterized. In particular, the clonal relationship among 17 MCRPKP strains obtained from blowflies was observed by indistinguishable PFGE patterns and an identical phylogenetic tree. The virulence potential of this MCRPKP clone was measured in the Galleria mellonella model. Furthermore, 219 MCRPEC isolates were characterized using WGS and bioinformatics analysis. WGS analysis shows that MCRPEC isolates are highly diverse, with distinct phylogenetic groups and various accessory genes including heavy-metal/antibiotic resistance determinants, virulence factors and toxin-antitoxin systems. The genetic context analysis on the origin and spread of gene mcr-1 and mcr-3, provides important knowledge of understanding on the movement and dissemination of mcr-like genes bacterial population.
14
BASTAKI, NASMAH K. "Novel Genomic Remodeling Events In Response to Environmental Stress:Clues from Transgenic Arabidopsis and Flax." Case Western Reserve University School of Graduate Studies / OhioLINK, 2015. http://rave.ohiolink.edu/etdc/view?acc_num=case1425659664.
15
Freedman, Adam Joshua Ehrich. "Surveying and harnessing the genetic, (meta)genomic, and metabolic potential of the deep carbonated biosphere." Thesis, Massachusetts Institute of Technology, 2016. http://hdl.handle.net/1721.1/104482.
Анотація:
Thesis: Ph. D. in Environmental Engineering, Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2016.Cataloged from PDF version of thesis.
Includes bibliographical references (pages 165-190).
The interaction between microbes and supercritical (sc) carbon dioxide represents an increasingly compelling area of research due to use of scCO₂ in geologic carbon sequestration (GCS) and as a sustainable chemical solvent. To investigate the long-term effects of GCS on the in situ deep subsurface biosphere, I conducted a taxonomic, geochemical and metagenomic survey of the McElmo Dome sCCO₂ reservoir, which serves as a natural analog for GCS environments. Through 16S rRNA amplicon and metagenome sequencing, I identified Sulfurospirillum, Rhizobium, Desulfovibrio and members of the Clostridiales family associated with reservoir fluids. Annotations of complete genomes extracted from metagenomes predict diverse mechanisms for growth and nutrient cycling in deep subsurface sCCO₂ microbial ecosystems at McElmo Dome. Supercritical CO₂ is frequently used as a solvent for compound extraction and in vitro biocatalysis. However, due to its lethal effects, scCO₂ has previously been considered inaccessible for in vivo microbial bioproduct stripping. Utilizing a bioprospecting approach, I isolated strain Bacillus megaterium SR7 through enrichment culture and serial passaging of McElmo Dome scCO₂ reservoir fluids. I then initiated process improvements including media and culturing optimization under 1 atm CO₂ that increased SR7 growth frequency under scCO₂ . After developing a genetic system enabling inducible heterologous enzyme expression, scCO₂ incubations of SR7 transformed with a two-gene isobutanol biosynthesis pathway generated up to 93.5 mg/1 isobutanol. 5.2% of the total isobutanol was directly extracted by the scCO₂ headspace. This finding demonstrates for the first time the feasibility of active bioproduct synthesis and extraction in a single scCO₂-exposed bioreactor.
by Adam Joshua Ehrich Freedman.
Ph. D. in Environmental Engineering
16
Kunkle, Brian W. "The Potential Role of Environmental Exposures and Genomic Signaling in Development of Central Nervous System Tumors." FIU Digital Commons, 2011. http://digitalcommons.fiu.edu/etd/524.
Анотація:
The etiology of central nervous system tumors (CNSTs) is mainly unknown. Aside from extremely rare genetic conditions, such as neurofibromatosis and tuberous sclerosis, the only unequivocally identified risk factor is exposure to ionizing radiation, and this explains only a very small fraction of cases. Using meta-analysis, gene networking and bioinformatics methods, this dissertation explored the hypothesis that environmental exposures produce genetic and epigenetic alterations that may be involved in the etiology of CNSTs.
A meta-analysis of epidemiological studies of pesticides and pediatric brain tumors revealed a significantly increased risk of brain tumors among children whose mothers had farm-related exposures during pregnancy. A dose response was recognized when this risk estimate was compared to those for risk of brain tumors from maternal exposure to non-agricultural pesticides during pregnancy, and risk of brain tumors among children exposed to agricultural activities. Through meta-analysis of several microarray studies which compared normal tissue to astrocytomas, we were able to identify a list of 554 genes which were differentially expressed in the majority of astrocytomas. Many of these genes have in fact been implicated in development of astrocytoma, including EGFR, HIF-1α, c-Myc, WNT5A, and IDH3A. Reverse engineering of these 554 genes using Bayesian network analysis produced a gene network for each grade of astrocytoma (Grade I-IV), and ‘key genes’ within each grade were identified. Genes found to be most influential to development of the highest grade of astrocytoma, Glioblastoma multiforme (GBM) were: COL4A1, EGFR, BTF3, MPP2, RAB31, CDK4, CD99, ANXA2, TOP2A, and SERBP1. Lastly, bioinformatics analysis of environmental databases and curated published results on GBM was able to identify numerous potential pathways and gene-environment interactions that may play key roles in astrocytoma development.
Findings from this research have strong potential to advance our understanding of the etiology and susceptibility to CNSTs. Validation of our 'key genes' and pathways could potentially lead to useful tools for early detection and novel therapeutic options for these tumors.
17
Greated, Alicia. "The IncP-9 plasmid group : characterisation of genomic sequences and development of tools for environmental monitoring." Thesis, University of Birmingham, 2000. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.366379.
18
Sukup, Jackson Michelle R. "Fluorescent detection of homologous recombination reveals the impact of genetic, physiological, and environmental factors on genomic stability." Thesis, Massachusetts Institute of Technology, 2013. http://hdl.handle.net/1721.1/81671.
Анотація:
Thesis (Ph. D.)--Massachusetts Institute of Technology, Dept. of Biological Engineering, 2013.Page 200 blank. Cataloged from PDF version of thesis.
Includes bibliographical references.
Unless repaired correctly, DNA double strand breaks (DSBs) can cause the loss of millions of base pairs of information and can induce cellular toxicity. DSBs are repaired via mitotic homologous recombination (HR), non-homologous end-joining (NHEJ) or microhomology-mediated end-joining (MMEJ). Here we use the Fluorescent Yellow Direct Repeat (FYDR) mouse to examine these pathways. Specifically, we crossed FYDR mice with mice lacking an essential NHEJ protein. Consistent with in vitro studies, we observed an increase in HR in the NHEJ deficient mice, indicating a shift from one pathway to another. Additionally, FYDR mice deficient in ERCC1, a protein involved in several pathways including nucleotide excision repair and MMEJ, showed an increase in HR. We describe a possible model for this observation. HR is presumed to be largely limited to replicating cells; however, little is known about differences in HR rates between tissues. Thus, we engineered the Rosa26 Direct Repeat-GFP (raDR-GFP) mouse that enables study of HR in many tissues in response to endogenous and exogenous factors. The raDR-GFP mouse harbors two truncated EGFP genes integrated at the ROSA26 locus. HR at the locus yields a full-length EGFP gene and a fluorescent cell. In adult raDR-GFP mice, differences in frequency of recombinant cells among tissues of challenged and unchallenged mice demonstrate the utility of raDR-GFP mice in measuring exposure-induced HR and the importance of multi-tissue studies. We also observed the progressive accumulation of recombinant cells in the pancreas, liver, and colon with age. These data are consistent with the finding that cancer is an age-related disease requiring time to accumulate tumorigenic mutations. To test the hypothesis that chronic inflammation promotes the induction of DSBs, we bred raDR-GFP mice deficient in an anti-inflammatory cytokine. These mice showed an increase in spontaneous HR in the pancreas. Interestingly, 10 week-infection of RAG2-/- raDR-GFP mice with H. hepaticus, and longer-term 20-week infection with H. trogontum did not have the same effect on HR in the pancreas, liver, or colon. Further studies of large-scale sequence rearrangements, point mutations, and small deletions in multiple tissues in response to environmentally-induced inflammation are planned.
by Michelle R. Sukup Jackson.
Ph.D.
19
Villagrasa, Ramírez Eduard. "Heavy metal uptake in the environmental isolated bacterium Ochrobactrum anthropi DE2010: Morphological responses, genomic insights and cellular strategies." Doctoral thesis, Universitat Autònoma de Barcelona, 2021. http://hdl.handle.net/10803/672494.
Анотація:
La contaminació ambiental és una de les condicions extremes que pot alterar els ecosistemes naturals i afectar tots els organismes vius. Entre els contaminants ambientals, els metalls tenen un paper rellevant degut a la seva elevada toxicitat. De fet, es pot considerar que els microorganismes que habiten zones contaminades per metalls formen freqüentment consorcis, la qual cosa els permet desenvolupar estratègies cel·lulars per sobreviure en presència de metalls evitant així els seus efectes nocius.
En els darrers anys, el nostre grup de recerca ha aïllat diferents consorcis de microorganismes dels tapets microbians del delta de l’Ebre (Tarragona). Aquests consorcis estan formats per un únic microorganisme fotòtrof i diferents heteròtrofs. En la present tesi doctoral, a partir del consorci on domina la microalga Scenedesmus sp. DE2009, s’ha aïllat, caracteritzat i identificat un bacteri heteròtrof com a Ochrobactrum anthropi DE2010. En estudis preliminars, aquest bacteri ha mostrat la capacitat per fixar nitrogen atmosfèric, presentar pleomorfisme cel·lular i resistir a antibiòtics del grups dels betalactàmics. Encara que prèviament s’ha investigat l’efecte de diversos metalls pesants en el consorci Scenedesmus sp. DE2009, no se sap res sobre l’efecte d’aquests en la viabilitat cel·lular d’O. antropi DE2010 i el seu paper en la captació de metalls pesants.
Els objectius de la present tesi s’han desenvolupat tenint en compte que O. anthropi DE2010 creix de manera fàcil i ràpida tant en medi líquid com sòlid, esdevenint un model adequat per a la investigació front a toxicitat per metalls pesants. A més a més, s’ha analitzat l’efecte citotòxic i la capacitat de resposta de O. anthropi DE2010 per superar l’estrès front a l’exposició a Cd, Pb(II), Cu(II), Cr(III) i Zn així com els patrons de localització cel·lular d’aquests metalls i les estratègies emprades per aquest bacteri per immobilitzar-los. Aquesta tesi s’ha organitzat en diferents capítols. Concretament, el capítol 2 correspon als articles publicats on els resultats obtinguts de la investigació realitzada es troben a les seccions de la 2.1 a la 2.4 i es discuteixen globalment en el capítol 3.
Els resultats obtinguts en aquest estudi indiquen que O. anthropi DE2010 mostra una elevada resistència als cinc metalls assajats tolerant concentracions de fins a 20 mM de Zn i de 10 mM per a Cd, Pb(II), Cu(II) i Cr(III). A més, aquest bacteri té una gran capacitat per eliminar metalls del medi, captant fins a un 90% de Pb (II) i un 40% de Cr (III), ambdós a 10 mM. Analitzant la seqüencia del genoma d’O. anthropi DE2010 s’ha observat que presenta sis gens relacionats amb el metabolisme del polifosfat, i que l’anàlisi del contingut cel·lular de polyP indica que aquest bacteri el sintetitza i l’acumula de manera directament proporcional a la concentració de metall. D’altra banda, les cèl·lules d’O. anthropi DE2010 immobilitzen metalls pesants en grànuls i/o inclusions de polyP mitjançant tres patrons específics de localització subcel·lular: extracel·lularment en grànuls de polifosfat (Cu (II)); a l’espai periplasmàtic formant cristalls amb el fòsfor (Pb (II)), i intracel·lularment en inclusions de polifosfat (Pb (II), Cr (III) i Zn). Per tant, O. anthropi DE2010 genera respostes cel·lulars (estratègies de supervivència) específiques per a cada metall, com ara bioacumulació en el cas de Pb (II), Cu (II), Cr (III) i Zn, biosorció per al Cr (III) i Cd i biomineralització per al Pb (II). L’elevada resistència i la capacitat de segrestar metalls d’O. anthropi DE2010 posen de manifest el seu gran potencial com a possible agent bioremediador, especialment en zones contaminades per Pb i Cr.La contaminación ambiental es una de las condiciones extremas que puede alterar los ecosistemas naturales y afectar a todos los organismos vivos. Entre los contaminantes ambientales, los metales tienen un papel relevante debido a su elevada toxicidad. De hecho, se puede considerar que los microorganismos que habitan zonas contaminadas por metales forman frecuentemente consorcios, lo que les permite desarrollar estrategias celulares para sobrevivir en presencia de metales evitando así sus efectos nocivos. En los últimos años, nuestro grupo de investigación ha aislado diferentes consorcios de microorganismos de los tapetes microbianos del delta del Ebro (Tarragona). Estos consorcios están formados por un único microorganismo fotótrofo y varios heterótrofos. En la presente tesis doctoral, a partir del consorcio donde domina la microalga Scenedesmus sp. DE2009, se ha aislado, caracterizado e identificado una bacteria heterótrofa como Ochrobactrum anthropi DE2010. En estudios preliminares, esta bacteria ha mostrado la capacidad para fijar nitrógeno atmosférico, presentar pleomorfismo celular y resistir a antibióticos del grupo de los betalactámicos. Aunque previamente se ha investigado el efecto de varios metales pesados en el consorcio Scenedesmus sp. DE2009, poco se conoce del efecto de estos en la viabilidad celular de O. antropi DE2010 y su papel en la captación de metales pesados. Los objetivos de la presente tesis se han desarrollado teniendo en cuenta que O. anthropi DE2010 crece de manera fácil y rápida tanto en medio líquido como sólido, lo que permite considerarlo como modelo para la investigación frente a la toxicidad por metales pesados. Además, se ha analizado el efecto citotóxico y la capacidad de respuesta de O. anthropi DE2010 para superar el estrés frente a la exposición a Cd, Pb(II), Cu(II), Cr(III) y Zn así como los patrones de localización celular de estos metales y las estrategias empleadas por esta bacteria para inmovilizarlos. Esta tesis se ha organizado en diferentes capítulos. Concretamente, el capítulo 2 corresponde a los artículos publicados donde los resultados obtenidos se encuentran en las secciones de la 2.1 a la 2.4 y se discuten globalmente en el capítulo 3. Los resultados obtenidos en este estudio indican que O. anthropi DE2010 muestra una elevada resistencia a los cinco metales ensayados tolerando concentraciones de hasta 20 mM de Zn y de 10 mM para Cd, Pb(II), Cu(II) y Cr(III). Además, esta bacteria tiene una gran capacidad para eliminar metales del medio, captando hasta un 90% de Pb (II) y un 40% de Cr (III), ambos a 10 mM. Analizando la secuencia del genoma de O. anthropi DE2010 se ha observado que presenta seis genes del metabolismo del polifosfato, y que el análisis del contenido celular de polyP indica que esta bacteria lo sintetiza y acumula de manera directamente proporcional a la concentración de metal. Por otro lado, las células de O. anthropi DE2010 inmovilizan metales pesados en gránulos y/o inclusiones de polyP mediante tres patrones específicos de localización subcelular: extracelularmente en gránulos de polifosfato (Cu (II)); en el espacio periplasmático formando cristales con el fósforo (Pb (II)), e intracelularmente en inclusiones de polyP (Pb (II), Cr (III) y Zn). Por lo tanto, O. anthropi DE2010 genera respuestas celulares (estrategias de supervivencia) específicas para cada metal, como bioacumulación en el caso de Pb (II), Cu (II), Cr (III) y Zn, biosorción para el Cr (III) y Cd y biomineralitzación para el Pb (II). La elevada resistencia y la capacidad de secuestrar metales de O. anthropi DE2010 ponen de manifiesto su gran potencial como posible agente bioremediador, especialmente en zonas contaminadas por Pb y Cr.
Environmental pollution remains as one of the extreme conditions that can disrupt the existing natural ecosystems and affect all the living organisms. Among the environmental stressors, metals play a significant role as potential toxicants. Consequently, it can be considered that the microorganisms inhabiting metal polluted areas frequently form consortia and they can develop cellular strategies to survive in the presence of heavy metals for avoid their negative effects. In the last years, our research group has isolated different consortia of microorganisms from Ebro Delta microbial mats (Tarragona). These consortia are formed by a single type of phototrophic microorganism and different heterotrophic bacteria. In the present doctoral thesis, an heterotrophic bacteria from the consortium dominated by the microalga Scenedesmus sp. DE2009, have been isolated, characterized and identified as Ochrobactrum anthropi DE2010. In preliminary studies, this bacterium showed the ability to fix atmospheric nitrogen, present cellular pleomorphism and beta-lactam antibiotic resistance. Despite the effect of some heavy metals in the microalgae consortium had previously been investigated, nothing is known about the effect of them on the cell viability of O. anthropi DE2010 and the role of this bacterium in heavy metal sequestration. The goals of this thesis have been developed taking into account the fact that O. anthropi DE2010 grows easily and fast in both liquid and solid media culture, which it becomes a suitable model for heavy metal experimental research. Thus, cytotoxic effects of heavy metals and cellular responses on O. anthropi DE2010 cultures exposed to increasing concentrations of Cd, Pb(II), Cu(II), Cr(III), and Zn, and the cellular metal localization patterns and the strategies and pathways used by this bacterium to immobilize them have extensively been analyzed. This thesis has been organized in different Chapters. Specifically, the Chapter 2 correspond to the published articles; thus, the obtained results from the research carried out are therefore in sections from 2.1 to 2.4 and are discussed globally in Chapter 3. The results of this study indicate that O. anthropi DE2010 shows high resistance to the five tested metals, supporting concentrations up to 20 mM of Zn and up to 10 mM for Cd, Pb(II), Cu(II) and Cr(III). Moreover, this bacterium has a high ability to remove metals from the environment, highlighting up to 90% for Pb(II) and 40% for Cr(III) both at 10 mM. Analyzing the sequenced genome of O. anthropi DE2010 it has been observed that it presents six genes linked to the metabolism of the polyphosphate and that the analysis of polyP content indicates that this bacterium synthesizes and accumulates it in a metal concentration-dependent manner. O. anthropi DE2010 cells immobilized heavy metals in polyP granules and/or inclusions in three metal-specific patterns for subcellular localization: extracellular in polyphosphate granules (Cu(II)); in the periplasmic space forming crystals with phosphorus (Pb(II)), and intracellular in polyphosphate inclusions (Pb(II), Cr(III) and Zn). Therefore, O. anthropi DE2010 generates specific cellular responses for each heavy metal as survival strategies, such as bioaccumulation for Pb(II), Cu(II), Cr(III) and Zn, biosorption for Cr(III) and Cd and biomineralization for Pb(II). The high resistance and the capacity to uptake metals evidenced by O. anthropi DE2010 prove its great potential as a possible candidate to bioremediate, especially Pb and Cr polluted areas.
Universitat Autònoma de Barcelona. Programa de Doctorat en Microbiologia
20
Dale, Ryan K. "Temperature and the biological response a multivariate statistical analysis of the variation in genomic organization, oligopeptide frequencies, and environmental temperature /." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 235 p, 2009. http://proquest.umi.com/pqdweb?did=1654488371&sid=7&Fmt=2&clientId=8331&RQT=309&VName=PQD.
21
Lopez, Carlos Julian De Luna. "The relationship between developmental stability, genomic diversity and environmental stress in two Cetacean species : the harbour porpoise (Phocoenaphocoena) and the bottlenose dolphin (Tursiops truncatusl)." Thesis, Durham University, 2005. http://etheses.dur.ac.uk/3010/.
Анотація:
The relationship between developmental stability, genomic diversity and environmental stress in three eastern North Atlantic populations of the harbour porpoise {Phocoena phocoena), and in two populations of the western North Atlantic and one from the Gulf of California of the bottlenose dolphin {Tursiops truncatus) was investigated. In addition, the population structure for the two species from the study areas mentioned was also assessed. Population structure was determined using discriminant function analysis for morphological characters and a Bayesian analysis for microsatellite loci. Consistency of the results was assessed with pairwise comparisons between populations using two indices of population differentiation (F(_st) and Rho(_st)). For the harbour porpoises classification was made into three putative populations: Norwegian, British and Danish. For the bottlenose dolphin significant differentiation was found for the three populations studied. Population differentiation between the two western North Atlantic parapatric populations was the highest among the pairwise comparisons. This result highlights the importance of resource specialisation of bottlenose dolphins in causing population structure for parapatric populations. Developmental stability was assessed by fluctuating asymmetry (FA) measured on morphological traits. Genomic diversity was determined by five indices (mean cf, scaled mean cF, multilocus individual heterozygosity, standardised heterozygosity and internal relatedness). Environmental stress was assessed by the concentration of chemical pollutants in tissues, and from the literature published for chemical pollutants, by-catch rate, parasite load and mean surface ocean temperature. Significant relationships between FA and the indices of genomic diversity were found. The Norwegian population of harbour porpoises and the coastal population of the western North Atlantic of bottlenose dolphin showed the highest level of FA. Both populations also showed the least genetically diverse animals. However, no clarity was obtained in respect of the relationship between FA and environmental stress. British and Norwegian harbour porpoises did not show significant correlations between the concentration of several chemical pollutants in tissues and FA. In addition, the Norwegian population of harbour porpoise inhabits the least impacted areas in respect to the concentration of chemical pollutants in tissues, parasite load and by-catch rates. Environmental stress was difficult to assess on the bottlenose dolphins populations due to the scarcity of data. These results show the influence of genetic diversity on the disruption of developmental stability and they also show the importance of conservation practices in maintaining genetic diversity as an important factor for the subsistence of natural populations.
22
Rain, Franco Angel. "Consequences of environmental disturbances on community structure and functioning of aquatic prokaryotes." Electronic Thesis or Diss., Sorbonne université, 2021. https://theses.hal.science/tel-03730170.
Анотація:
Les microbes sont affectés par les perturbations environnementales qui affectent la stabilité fonctionnelle des communautés microbiennes. Cependant, leurs réponses sont complexes, difficiles à élucider et les mécanismes de la stabilité fonctionnelle sont encore mal compris. Dans cette thèse, j'ai étudié les réponses microbiennes aux perturbations environnementales, des populations uniques aux communautés complexes. Dans le cas d'une population unique, nous avons étudié la réponse transcriptionnelle de populations bactériennes uniques dont la niche varie le long d'un gradient environnemental. Pour aborder les conséquences des perturbations au niveau de la communauté, nous avons établi et testé un protocole de cryoconservation de communautés microbiennes complexes afin d'améliorer la reproductibilité des études expérimentales avec des assemblages de communautés microbiennes aquatiques naturelles comme sources d'inoculum. En outre, nous avons exposé expérimentalement des communautés microbiennes aquatiques complexes à des perturbations pulsées afin d'étudier les conséquences de ces perturbations sur les changements structurels de la communauté et les paramètres fonctionnels généraux, tels que l'efficacité de la croissance bactérienne. Enfin, nous avons inspecté plus en détail les conséquences des perturbations pulsées sur les processus impliqués dans le cycle de l'azote. Au cours de cette thèse, je me suis particulièrement intéressé aux isolats et aux communautés provenant d'habitats aquatiques côtiers qui fournissent d'importants services écosystémiquesMicrobes are impacted by environmental disturbances affecting the functional stability of microbial communities. However, their responses are complex, difficult to elucidate and the mechanics of functional stability are still poorly understood. In this thesis, I investigated microbial responses to environmental disturbances from single populations to complex communities. For the single population approach, we addressed the transcriptional response of single bacterial populations with varying niche breadths along an environmental gradient. To address the consequences of disturbances at the community level, we have established and tested a protocol for cryopreserving complex microbial communities to improve the replicability of experimental studies with natural microbial aquatic community assemblies as inoculum sources. Furthermore, we have experimentally exposed complex aquatic microbial communities to pulsed disturbances to study the consequences of such disturbances on community structural changes and broad functional parameters, such as bacterial growth efficiency. Finally, we have inspected in more detail the consequences of pulsed disturbances on processes involved in nitrogen cycling. During this thesis, I particularly focused on isolates and communities that originated from coastal aquatic habitats that provide important ecosystem services
23
Wagner, Darlene Darlington. "Comparative genomics reveal ecophysiological adaptations of organohalide-respiring bacteria." Diss., Georgia Institute of Technology, 2012. http://hdl.handle.net/1853/45916.
Анотація:
Organohalide-respiring Bacteria (OHRB) play key roles in the reductive
dehalogenation of natural organohalides and anthropogenic chlorinated contaminants. Reductive dehalogenases (RDases) catalyze the cleavage of
carbon-halogen bonds, enabling respiratory energy conservation and growth. Large numbers of RDase genes, a majority lacking experimental characterization
of function, are found on the genomes of OHRB. In silico genomics tools were employed to identify shared sequence features among RDase genes and proteins,
predict RDase functionality, and elucidate RDase evolutionary history. These analyses showed that the RDase superfamily could be divided into proteins
exported to the membrane and cytoplasmic proteins, indicating that not all RDases function in respiration. Further, Hidden Markov models (HMMs) and
multiple sequence alignments (MSAs) based upon biochemically characterized RDases identified previously uncharacterized members of an RDase superfamily,
delineated protein domains and amino acid motifs serving to distinguish RDases from unrelated iron-sulfur proteins. Such conserved and discriminatory features among RDases may facilitate monitoring of organohalide-degrading microbial
communities or improve accuracy of genome annotation. Phylogenetic analyses of RDase superfamily sequences provided evidence of convergent evolution and horizontal gene transfer (HGT) across distinct OHRB
genera. Yet, the low frequency of RDase transfer outside the genus level and the absence of RDase transfer between phyla indicate that RDases evolve primarily
by vertical evolution or HGT is restricted among related OHRB strains. Polyphyletic evolutionary lineages within the RDase superfamily comprise
distantly-related RDases, some exhibiting activities towards the same substrates, suggesting a longstanding history of OHRB adaptation to natural organohalides. Similar functional and phylogenetic analyses provided evidence that nitrous oxide (N₂O, a potent greenhouse gas) reductase (nosZ) genes from versatile OHRB members of the Anaeromyxobacter and Desulfomonile genera comprised a nosZ sub-family evolutionarily distinct from nosZ found in non-OHRB denitrifiers. Hence, elucidation of RDase and NosZ sequence diversity may enhance the mitigation of anthropogenic organohalides and greenhouse gases (i.e., N₂O), respectively. The tetrachloroethene-respiring bacterium Geobacter lovleyi strain SZ exhibited genomic features distinguishing it from non-organohalide-respiring
members of the Geobacter genus, including a conjugative pilus transfer gene cluster, a chromosomal genomic island harboring two RDase genes, and a
diminished set of c-type cytochrome genes. The G. lovleyi strain SZ genome also harbored a 77 kbp plasmid carrying 15 out of the 24 genes involved in biosynthesis of corrinoid, likely related to this strains ability to degrade PCE to cis-DCE in the absence of supplied corrinoid (i.e., vitamin B₁₂). Although corrinoids are essential cofactors to RDases, the strictly organohalide-respiring
Dehalococcoides mccartyi strains are corrinoid auxotrophs and depend upon uptake of extracellular corrinoids via Archaeal and Bacterial salvage pathways. A
key corrinoid salvage gene in D. mccartyi, cbiZ, occurs at duplicated loci adjacent
to RDase genes and appears to have been horizontally-acquired from Archaea. These comparative genome analyses highlight RDase dependencies upon
corrinoids and also suggest mobile genomic elements (e.g., plasmids) are associated with organohalide respiration and corrinoid acquisition among OHRB. In summary, analyses of OHRB genomes promise to enable more complete
modeling of metabolic and evolutionary processes associated with the turnover of organohalides in anoxic environments. These efforts also expand knowledge of
biomarkers for monitoring OHRB activity in anoxic environments, and will improve our understanding of the fate of chlorinated contaminants.
24
Adhikari, Bishwo. "Genomic Analysis of Nematode-Environment Interaction." BYU ScholarsArchive, 2010. https://scholarsarchive.byu.edu/etd/2578.
Анотація:
The natural environments of organisms present a multitude of biotic and abiotic challenges that require both short-term ecological and long-term evolutionary responses. Though most environmental response studies have focused on effects at the ecosystem, community and organismal levels, the ultimate controls of these responses are located in the genome of the organism. Soil nematodes are highly responsive to, and display a wide variety of responses to changing environmental conditions, making them ideal models for the study of organismal interactions with their environment. In an attempt to examine responses to environmental stress (desiccation and freezing), genomic level analyses of gene expression during anhydrobiosis of the Antarctic nematode Plectus murrayi was undertaken. An EST library representative of the desiccation induced transcripts was established and the transcripts differentially expressed during desiccation stress were identified. The expressed genome of P. murrayi showed that desiccation survival in nematodes involves differential expression of a suite of genes from diverse functional areas, and constitutive expression of a number of stress related genes. My study also revealed that exposure to slow desiccation and freezing plays an important role in the transcription of stress related genes, improves desiccation and freezing survival of nematodes. Deterioration of traits essential for biological control has been recognized in diverse biological control agents including insect pathogenic nematodes. I studied the genetic mechanisms behind such deterioration using expression profiling. My results showed that trait deterioration of insect pathogenic nematode induces substantial overall changes in the nematode transcriptome and exhibits a general pattern of metabolic shift causing massive changes in metabolic and other processes. Finally, through field observations and molecular laboratory experiments the validity of the growth rate hypothesis in natural populations of Antarctic nematodes was tested. My results indicated that elemental stoichiometry influences evolutionary adaptations in gene expression and genome evolution. My study, in addition to providing immediate insight into the mechanisms by which multicellular animals respond to their environment, is transformative in its potential to inform other fundamental ecological and evolutionary questions, such as the evolution of life-history patterns and the relationship between community structure and ecological function in ecosystems.
25
Thiroux, Sarah. "Etudes des interactions entre virus et hôtes archéens hydrothermaux hyperthermophiles Two viruses, MCV1 and MCV2, which infect Marinitoga bacteria isolated from deep‐sea hydrothermal vents: functional and genomic analysis, in Environmental microbiology 20(2), 2018." Thesis, Brest, 2019. http://theses-scd.univ-brest.fr/2019/These-2019-SML-Microbiologie-THIROUX_Sarah.pdf.
Анотація:
Malgré l’importance des virus dans la diversité, l’adaptation et l’évolution des communautés microbiennes, la virosphère des sources hydrothermales océaniques, reste peu caractérisée.Seulement 10 virus, dont 8 bacteriovirus et 2 virus d’archées, ont été décrits à ce jour. C’est dans ce contexte que ce travail de thèse s’inscrit avec pour objectif de caractériser des archaeovirus isolés de la composante microbienne abyssale. Les études ont porté sur des virus de méthanogènes, des producteurs primaires abondants dans ces environnements hydrothermaux. MFV1, premier virus tête-queue hyperthermophile décrit, a été isolé de Methanocaldococcus fervens une méthanogènehyperthermophile issue de sédiments marins profonds. Une caractérisation fonctionnelle et génomique de ce nouveau siphovirus a été conduite.Le caractère infectieux des virions a été démontré sur des Methanocaldococcus. Le plasmide pMEFER01, porté par M. fervens, peut également être empaqueté dans les capsides virales. L’étude d’autres virus de méthanogènes hyperthermophiles hydrothermales a été amorcée. M. vulcanius produit des virions tête-queue tandis que ceux isolés de M.jannaschii ont une morphologie particulière (tigeboucles).En parallèle, l’étude d’un virus en forme de citron, infectant Thermococcus thioreducens, a permis de s’intéresser à un autre ordre archéen, bien représenté au sein des systèmes hydrothermaux marins. De façon surprenante, ce virus semble capable d’infecter des méthanogènes. La mise en évidence de nouveaux systèmes hôtes-virus mais également d’interactions avec différents éléments génétiques mobiles (plasmides, vésicules) a permis d’élargir les connaissances sur le mobilome abyssalDespite the importance of viruses in the diversity, adaptation, and evolution of microbial communities, the virosphere of deep-sea hydrothermal vents remains poorly characterized. To date, only 10 viruses isolated from deep sea hydrothermal vents, including 8 bacterial viruses and 2 archaeal viruses, have been described. In this context, this thesis work focused on gaining insights into the viral interactions with deep-sea autotrophic archaeal component. We aimed to characterize viruses of methanogens, which are abundant primary producers in these hydrothermal environments. MFV1, the first hyperthermophilic head-tail virus described, was isolated from Methanocaldococcus fervens, a hyperthermophilic methanogen from hydrothermal sediments. A functional and genomic characterization of this new siphovirus was conducted.The infectivity of MFV1 was demonstrated on Methanocaldococcus species. The plasmid pMEFER01, carried by M. fervens, can also be packaged in viral capsids. The study of other viruses of hyperthermophilic and hydrothermal methanogens was initiated. M. vulcanius produced head-tailed virions whereas those isolated from M. jannaschii had a particular morphology (stem-loops). In parallel, the study of a lemon-shaped virus, infecting Thermococcus thioreducens, permits to take an interest on another archaeal order, which is wellrepresented in marine hydrothermal systems.Surprisingly, this virus seemed capable of infecting hyperthermophilic methanogens. The characterization of new host-virus systems but also of interactions with different mobile genetic elements (plasmids, vesicles) expanding knowledge about the abyssal mobilome
26
Diemer, Geoffrey Scott. "The Boiling Springs Lake Metavirome: Charting the Viral Sequence-Space of an Extreme Environment Microbial Ecosystem." PDXScholar, 2014. https://pdxscholar.library.pdx.edu/open_access_etds/1640.
Анотація:
Viruses are the most abundant organisms on Earth, yet their collective evolutionary history, biodiversity and functional capacity is not well understood. Viral metagenomics offers a potential means of establishing a more comprehensive view of virus diversity and evolution, as vast amounts of new sequence data becomes available for comparative analysis.Metagenomic DNA from virus-sized particles (smaller than 0.2 microns in diameter) was isolated from approximately 20 liters of sediment obtained from Boiling Springs Lake (BSL) and sequenced. BSL is a large, acidic hot-spring (with a pH of 2.2, and temperatures ranging from 50°C to 96°C) located in Lassen Volcanic National Park, USA. BSL supports a purely microbial ecosystem comprised largely of Archaea and Bacteria, however, the lower temperature regions permit the growth of acid- and thermo-tolerant Eukarya. This distinctive feature of the BSL microbial ecosystem ensures that virus types infecting all domains of life will be present. The metagenomic sequence data was used to characterize the types of viruses present within the microbial ecosystem, to ascertain the extent of genetic diversity and novelty comprising the BSL virus assemblage, and to explore the genomic and structural modalities of virus evolution.Metagenomic surveys of natural virus assemblages, including the survey of BSL, have revealed that the diversity within the virosphere far exceeds what has currently been determined through the detailed study of viruses that are relevant to human health and agriculture. The number of as-yet-uncharacterized virus protein families present in the BSL assemblage was estimated by clustering analysis. Genomic context analysis of the predicted viral protein sequences in the BSL dataset indicates that most of the putative uncharacterized proteins are endemic or unique to BSL, and are largely harbored by known virus types. A comparative metagenomic analysis approach identified a set of conserved, yet uncharacterized BSL protein sequences that are commonly found in other similar and dissimilar environments.New sequence data from metagenomic surveys of natural virus assemblages was also used to better characterize and define known virus protein families, as some of the viruses found in the BSL environment represent distant relatives of well-characterized isolates. By comparing viral genes and protein sequences from these highly divergent species, it is possible to better understand the dynamics of adaptation and evolution in the virosphere. Additionally, as structures of virus proteins continue to be experimentally determined by X-ray crystallography and cryo-electron microscopy, a merger of structural and metagenomic sequence data allows the opportunity to observe the structural dynamics underlying virus protein evolution.Capsid (structural) proteins from two distinct Microviridae strains; a globally ubiquitous and highly sequence-diverse virus family, were identified in, and isolated from the BSL metagenomic DNA sample. These BSL capsid protein sequences, along with several other homologous sequences derived from metagenomic surveys and laboratory isolates, were mapped to the solved structure of a closely related capsid protein from the Spiroplasma phage-4 microvirus. Patterns of amino acid sequence conservation, unveiled by structure-based homology modeling analysis, revealed that the protein sequences within this family exhibit a remarkable level of plasticity, while remaining structurally and functionally congruent.Lateral gene transfer is thought to have had a significant impact on the genomic evolution and adaptation of virus families. Genomic context analysis was also utilized to identify interviral gene transfer within the BSL virus assemblage. An ostensibly rare interviral gene transfer event, having transpired between single-stranded RNA and DNA virus types, was detected in the BSL metagenome. Similar genomes were subsequently detected in other ecosystems around the globe. The discovery of this new virus genome dramatically underscores the scope and importance of genetic mobility and genomic mosaicism as major forces driving the evolution of viruses.The analyses conducted herein demonstrate the many ways in which viral metagenomic sequence data may be utilized to not only evaluate the composition of a natural virus assemblage, but to discover new viral genes, and to better understand the dynamics of both genomic and structural evolution within the virosphere.
27
Monjot, Arthur. "Les eucaryotes unicellulaires dans les écosystèmes lacustres : de la diversité fonctionnelle aux interactions hôte-parasites." Electronic Thesis or Diss., Université Clermont Auvergne (2021-...), 2023. http://www.theses.fr/2023UCFA0109.
Анотація:
Au cours des dernières décennies, notre compréhension de la diversité microbienne dans l'environnement a beaucoup progressé notamment avec l'avènement des méthodes de séquençage de nouvelle génération et les approches « -omics ». Leur application a notamment permis de s'affranchir des approches de mise en culture ne contribuant qu'à une évaluation partielle et orientée de la diversité microbienne. Le métabarcoding, basé sur l'étude d'un marqueur unique et ubiquiste, est la méthode la plus utilisée pour l'analyse de la diversité car elle permet une évaluation assez exhaustive des espèces présentes dans un écosystème. En milieu aquatique, elle a en effet permis la mise en évidence d'une diversité considérable et insoupçonnée d'eucaryotes unicellulaires. Toutefois cette approche, essentiellement descriptive, ne permet pas de déterminer la physiologie ni de comprendre le rôle de ces microorganismes dans les écosystèmes. D'autres méthodes, telles que la métatranscriptomique, offrent la possibilité d'étudier leur potentiel métabolique et d'en évaluer les variations en fonction de paramètres environnementaux. Néanmoins, ces approches de séquençage haut débit conduisent à la production d'une quantité colossale de séquences environnementales dont la majeure partie reste inconnue. Afin d'étudier le lien diversité-fonction au sein des eucaryotes unicellulaires et ainsi mieux comprendre leur rôle dans les réseaux trophiques lacustres, largement sous-étudiés en comparaison aux écosystèmes marins, plusieurs approches ont été utilisées.Du métabarcoding couplé à une étude de traits morpho-physio-phénotypiques, de la métatranscriptomique ainsi qu'une méthodologie basée sur l'isolement et la caractérisation de couples hôte-parasites (séquençage et hybridation in situ), ont été réalisés à partir d'échantillons lacustres (Pavin, méromictique ; Aydat, dimictique). Ces analyses ont révélé l'importante diversité des photo-osmo-phago-mixotrophes et des parasites tout en mettant en évidence les fortes variations saisonnières qu'ils subissent dans le mixolimnion du lac Pavin. Il semblerait, par exemple, que les périodes de brassage profitant aux communautés hôtes photosynthétiques favorisent le développement et la dissémination de champignons parasites notamment par la surexpression de gènes impliqués dans la phototaxie des zoospores et dans les métabolismes lipidiques. Parmi ces champignons parasites, les microsporidies sont des acteurs nouvellement identifiés dans les réseaux trophiques aquatiques. Nous avons en effet découvert avec une forte prévalence (42,5%) dans le lac d'Aydat, une association hôte-parasites entre une potentielle nouvelle espèce de microsporidie et une espèce de rotifère.Une importante biosphère rare a également été mise en évidence dans le monimolimnion anoxique du lac Pavin, caractérisée par de nombreux saprotrophes surexprimant des gènes liés aux métabolismes du soufre, du nitrate et de dégradation de la matière organique. Les métabolismes caractéristiques d'organismes de différents modes trophiques ont également été étudiés en réalisant une étude basée sur la construction de réseaux de similarité de séquences protéiques. Tout en caractérisant pour la première fois une majorité de séquences inconnues (>40%), nous avons révélé la proximité génétique de protéines entre microorganismes hétérotrophes et photo-osmo-phago-mixotrophes et entre saprotrophes et parasites, ainsi qu'une redondance fonctionnelle relative des métabolismes primaires. En revanche, nous avons identifié près d'un million de protéines caractéristiques d'un seul groupe fonctionnel qui, pour certaines, représentent de réelles perspectives d'étude des voies métaboliques impliquées dans les interactions hôte-parasitesOver the last few decades, our understanding of microbial diversity in the environment has advanced considerably, particularly with the advent of next-generation sequencing methods and -omics approaches. These methods have allowed for a more comprehensive evaluation of microbial diversity compared to traditional culture-based approaches. The most commonly used method for analyzing diversity is metabarcoding, which is based on the study of a unique and ubiquitous marker. This method has revealed a considerable and unsuspected diversity of microbial eukaryotes in aquatic environments. However, this approach is mainly descriptive and does not allow for the determination of the physiology or understanding of the role of these microorganisms in ecosystems. Other methods, such as metatranscriptomics, offer the possibility of studying their metabolic potential in relation to environmental parameters. Nevertheless, these high-throughput sequencing approaches lead to the production of a vast quantity of environmental sequences, most of which remain unknown. To better understand the diversity-function link within microbial eukaryotes and their role in lacustrine trophic networks, several approaches have been used.Metabarcoding coupled with a study of morpho-physio-phenotypic traits, metatranscriptomics and a methodology based on the isolation and characterization of host-parasite pairs (sequencing and in situ hybridization), were carried out on lake samples (Pavin, meromictic; Aydat, dimictic). These analyses revealed the high diversity of photo-osmo-phago-mixotrophs and parasites, while also highlighting the strong seasonal variations they undergo in the mixolimnion of lake Pavin. For example, periods of mixing benefiting photosynthetic host communities favor the development and dissemination of parasitic fungi, notably through the overexpression of genes involved in zoospore phototaxis and lipid metabolism. Among these parasitic fungi, Microsporidia are newly identified players in aquatic food webs. Indeed, we discovered a high prevalence (42.5%) host-parasite association between a potential new species of Microsporidia and a species of rotifer in lake Aydat. An important rare biosphere has also been highlighted in the anoxic monimolimnion of Lake Pavin, characterized by numerous saprotrophs overexpressing genes related to sulfur, nitrate, and organic matter degradation metabolisms. The characteristic metabolisms of organisms of different trophic modes have also been studied by constructing protein sequences similarity networks.While characterizing the majority of unknown sequences for the first time (>40%), we have revealed the genetic proximity of proteins between heterotrophic and photo-osmo-phago- mixotrophic microorganisms and between saprotrophs and parasites, as well as a relative functional redundancy of primary metabolisms. On the other hand, we have identified nearly one million proteins characteristic of a single functional group, which, for some, represent real prospects for studying the metabolic pathways involved in host-parasite interactions
28
Wei, Yulong. "Microbes Carry Distinct Genomic Signatures in Adaptation to Their Translation Machinery and Host Environments." Thesis, Université d'Ottawa / University of Ottawa, 2021. http://hdl.handle.net/10393/42422.
Анотація:
How do bacteria grow and replicate rapidly? How do viruses and phages adapt to their host environments? Bacteria require efficient translation to grow and replicate rapidly, and translation is often rate-limited by initiation. A feature that is conserved across bacterial lineages is the Shine-Dalgarno (SD) sequence at the mRNA 5’ UTR, which pairs with the anti-SD sequence located at the 3’ end of mature 16S rRNA. Nonetheless, much about this interaction remains unclear. Chapter 2 reveals evolutionary differences between Cyanobacteria and chloroplast translation initiation using a new model (DtoStart) that better define optimal SD sequence and an RNA-Seq-based approach that reliably characterize the 3’ end of mature 16S rRNAs. Efficacy of translation elongation depends much on tRNA-mediated codon adaptation. In Escherichia coli, selection favours major codons because they are rapidly decoded by abundantly available cognate tRNAs. Nonetheless, the degree codon bias correlates with tRNA availability is unclear in many bacterial species because tRNA abundance is often inadequately approximated by gene copy numbers. To better understand tRNA-mediated codon bias, Chapter 3 describes an RNA-Seq-based approach to robustly quantify tRNA abundance. Finally, Chapter 4 evaluates the degree optimal translation initiation and elongation signals affect ribosome dynamics. The emergence of COVID-19 pandemic poses a serious global health emergency. To establish infection during cell entry, the coronavirus Spike protein binds to the host ACE2 receptor, and a high binding potential between these two players is key to infectivity. While SARS-CoV-2 transmits efficiently in humans, it is less clear which other mammals are at risk of being infected. Chapter 5 investigates the host range of SARS-CoV-2 through comparative sequence analyses at the ACE2 receptors and the Spike proteins. As obligate parasites, coronaviruses regularly infect host tissues that express antiviral proteins (AVPs) in abundance and must evade or adapt to the host cellular environments post-entry. Two AVPs that shape viral genomes are ZAP that binds to CpG dinucleotides to facilitate viral transcript degradation, and APOBEC3 which deaminates C into U leading to dysfunctional transcripts. Chapter 6 shows that coronavirus genomes are CpG deficient to evade ZAP and are subjected to constant C to U deamination by APOBEC3. This thesis examines two key concepts of microbial genome evolution: 1) coevolution between gene features and the translation machinery in bacteria, and 2) adaptation of viruses to the hosts they infect. Chapters 2, 3, and 4 are aimed at improving our understanding in bacterial gene expression in the applications of transgenic biosynthesis and phage therapy. Chapters 5 and 6 are aimed at improving our understanding in the origin and evolution of SARS-CoV-2 and our ability to control the spread of infection.
29
Lucio, Lorena Mendes de Carvalho. "Determinação das concentrações de resíduos de gases anestésicos e avaliação genômica e de estresse oxidativo em profissionais recém-expostos." Botucatu, 2016. http://hdl.handle.net/11449/143874.
Анотація:
Orientador: Leandro Gobbo BrazResumo: O presente estudo objetivou determinar as concentrações dos resíduos de gases anestésicos (RGA) em salas de operação (SO) e o impacto dessa exposição ocupacional em relação aos danos genômicos e estresse oxidativo em profissionais recém-expostos. O estudo foi conduzido no Hospital das Clínicas, Faculdade de Medicina de Botucatu-UNESP. As concentrações de isoflurano, sevoflurano e óxido nitroso (N2O) foram medidas nas SO por espectrofotometria infravermelha, com equipamento portátil. Sessenta e três médicos residentes, ao final de três anos do Programa de Residência Médica, foram alocados em dois grupos: exposto (Anestesiologia e Cirurgia, n=32) e controle (Clínica Médica, n=31). Amostras de sangue periférico e células bucais foram coletadas e protegidas da luz. Avaliaram-se danos no material genético (teste do cometa - danos basais, purinas e pirimidinas oxidadas em linfócitos; 8-hidroxi-2’-desoxiguanosina no plasma), micronúcleo (MN) em células bucais, proteínas carboniladas, marcadores de lipoperoxidação (malonaldeído e 4-hidroxinonenal) e capacidade antioxidante plasmática (ferric reducing antioxidant power, oxygen radical absorbance capacity e total antioxidant performance). As concentrações médias dos RGA foram superiores aos limites internacionalmente recomendados (2,7 vezes: isoflurano; 4,9 vezes: sevoflurano; 7,2 vezes: N2O). Os grupos não diferiram quanto aos dados demográficos (p>0,05). Detectou-se aumento significativo de danos basais no DNA (p=0,01) e maior frequê... (Resumo completo, clicar acesso eletrônico abaixo)
Abstract: This study determined the waste anesthetic gases (WAG) in operating rooms (OR) and evaluated the impact of the occupational exposure in genetic damage and oxidative stress in medical residents. The study was performed at “Hospital das Clínicas, Faculdade de Medicina de Botucatu-UNESP”. The concentrations of isoflurane, sevoflurane and nitrous oxide (N2O) were measured in ORs. Sixty-three medical residents completing their three-year Medical Residency Program were recruited for the study and were assigned to two groups: exposed group (n=32) of Anesthesiology and Surgery areas and control group (n=31) of Internal Medicine area. Blood and buccal cells were concomitantly collected from both groups and protected from light to measure genetic instability by buccal micronucleus (MN), basal and oxidized DNA damage (comet assay and 8-hydroxy-2′-deoxyguanosine), biomarkers of protein and lipid oxidation, and three different assays for plasma antioxidant activity. Mean WAG concentrations were above international thresholds (2.7-fold: isoflurane; 4.9-fold: sevoflurane; 7.2-fold: N2O). There was no significant difference between groups regarding demographic data. Basal DNA damage (p=0.01) and buccal MN frequency (by 2.3-fold; p=0.07) were increased in the exposed group compared to the control group. Results showed no significant difference for oxidative stress biomarkers between groups. In conclusion, this study shows that medical residents exposed to high WAG concentrations have increase... (Complete abstract click electronic access below)
Doutor
30
Lucio, Lorena Mendes de Carvalho [UNESP]. "Determinação das concentrações de resíduos de gases anestésicos e avaliação genômica e de estresse oxidativo em profissionais recém-expostos." Universidade Estadual Paulista (UNESP), 2016. http://hdl.handle.net/11449/143874.
Анотація:
Submitted by LORENA MENDES DE CARVALHO LUCIO null (limcarvalho@yahoo.com.br) on 2016-09-12T13:56:26Z
No. of bitstreams: 1
TESE FINAL LORENA POS BANCA Repositorio UNESP 12.09.16.pdf: 1673690 bytes, checksum: 578ad77e846c1bc6a83776f9b4d1b8bf (MD5)Approved for entry into archive by Felipe Augusto Arakaki (arakaki@reitoria.unesp.br) on 2016-09-14T18:44:12Z (GMT) No. of bitstreams: 1 lucio_lmc_dr_bot.pdf: 1673690 bytes, checksum: 578ad77e846c1bc6a83776f9b4d1b8bf (MD5)
Made available in DSpace on 2016-09-14T18:44:12Z (GMT). No. of bitstreams: 1 lucio_lmc_dr_bot.pdf: 1673690 bytes, checksum: 578ad77e846c1bc6a83776f9b4d1b8bf (MD5) Previous issue date: 2016-08-25
Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)
Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)
Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)
O presente estudo objetivou determinar as concentrações dos resíduos de gases anestésicos (RGA) em salas de operação (SO) e o impacto dessa exposição ocupacional em relação aos danos genômicos e estresse oxidativo em profissionais recém-expostos. O estudo foi conduzido no Hospital das Clínicas, Faculdade de Medicina de Botucatu-UNESP. As concentrações de isoflurano, sevoflurano e óxido nitroso (N2O) foram medidas nas SO por espectrofotometria infravermelha, com equipamento portátil. Sessenta e três médicos residentes, ao final de três anos do Programa de Residência Médica, foram alocados em dois grupos: exposto (Anestesiologia e Cirurgia, n=32) e controle (Clínica Médica, n=31). Amostras de sangue periférico e células bucais foram coletadas e protegidas da luz. Avaliaram-se danos no material genético (teste do cometa - danos basais, purinas e pirimidinas oxidadas em linfócitos; 8-hidroxi-2’-desoxiguanosina no plasma), micronúcleo (MN) em células bucais, proteínas carboniladas, marcadores de lipoperoxidação (malonaldeído e 4-hidroxinonenal) e capacidade antioxidante plasmática (ferric reducing antioxidant power, oxygen radical absorbance capacity e total antioxidant performance). As concentrações médias dos RGA foram superiores aos limites internacionalmente recomendados (2,7 vezes: isoflurano; 4,9 vezes: sevoflurano; 7,2 vezes: N2O). Os grupos não diferiram quanto aos dados demográficos (p>0,05). Detectou-se aumento significativo de danos basais no DNA (p=0,01) e maior frequência de MN em células bucais (2,3 vezes; p=0,07) no grupo exposto em relação ao grupo controle, mas não houve diferença (p>0,05) entre os grupos em relação a todos os marcadores de estresse oxidativo. Em conclusão, o estudo mostra que médicos residentes expostos a altas concentrações de RGA apresentam aumento significativo de danos sistêmicos no DNA e frequência aumentada de instabilidade genômica (MN bucais), mas não de estresse oxidativo. Portanto, este estudo mostra que jovens profissionais já apresentam alterações genômicas, o que reforça a importância do biomonitoramento e da diminuição da exposição aos RGA.
This study determined the waste anesthetic gases (WAG) in operating rooms (OR) and evaluated the impact of the occupational exposure in genetic damage and oxidative stress in medical residents. The study was performed at “Hospital das Clínicas, Faculdade de Medicina de Botucatu-UNESP”. The concentrations of isoflurane, sevoflurane and nitrous oxide (N2O) were measured in ORs. Sixty-three medical residents completing their three-year Medical Residency Program were recruited for the study and were assigned to two groups: exposed group (n=32) of Anesthesiology and Surgery areas and control group (n=31) of Internal Medicine area. Blood and buccal cells were concomitantly collected from both groups and protected from light to measure genetic instability by buccal micronucleus (MN), basal and oxidized DNA damage (comet assay and 8-hydroxy-2′-deoxyguanosine), biomarkers of protein and lipid oxidation, and three different assays for plasma antioxidant activity. Mean WAG concentrations were above international thresholds (2.7-fold: isoflurane; 4.9-fold: sevoflurane; 7.2-fold: N2O). There was no significant difference between groups regarding demographic data. Basal DNA damage (p=0.01) and buccal MN frequency (by 2.3-fold; p=0.07) were increased in the exposed group compared to the control group. Results showed no significant difference for oxidative stress biomarkers between groups. In conclusion, this study shows that medical residents exposed to high WAG concentrations have increased systemic DNA damage and genomic instability (buccal MN), but not oxidative stress. Thus, these young professionals already have genetic damage in the beginning of their career. Our results reinforce the importance of the biomonitoring and also the adequate measures to decrease ambient air pollution in the OR.
FAPESP: 2013/21130-0
CNPq: 472453/2013-0
CAPES/PGCI: 14527-13-8
31
Guerin, Nina. "Acclimatation du pico-eucaryote photosynthétique Pelagomonas calceolata aux changements environnementaux." Electronic Thesis or Diss., université Paris-Saclay, 2023. https://www.biblio.univ-evry.fr/theses/2023/interne/2023UPASL138.pdf.
Анотація:
Les picoeucaryotes photosynthétiques (PPE) sont abondants dans tous les océans et constituent une part importante de la biomasse et de la production primaire. Les modèles climatiques prédisent une extension des zones oligotrophes dans les prochaines décennies ce qui pourrait fortement augmenter l'abondance et l'impact écologique des PPE. Parmi eux, la microalgue Pelagomonas calceolata (Stramenopiles/Pelagophyceae) est très largement répandue dans les océans (Worden et al., 2012) mais son rôle dans le cycle du carbone et son impact sur la chaine trophique restent méconnus (Dupont et al., 2015). Des analyses in situ et in vitro suggèrent que P. calceolata peut s'adapter aux variations environnementales grâce à une importante capacité de modulation de l'expression des gènes (Carradec et al., 2018 ; Dimier et al., 2009). L'objectif de cette thèse est de comprendre comment P. calceolata s'adapte aux variations environnementales des nombreux milieux qu'elle occupe. Dans le premier chapitre, le génome de P. calceolata est assemblé annoté puis comparé à ceux des autres PPEs. Grâce aux données de métagénomiques et métatranscriptomiques issues de l'expédition Tara Oceans, la biogéographie et de l'activité transcriptomique de P. calceolata dans les différentes conditions environnementales a permis de mieux comprendre la distribution présente et future de cette algue, et les gènes impliqués dans son succès écologique (Guérin et al 2022). Dans le deuxième chapitre, nous nous sommes particulièrement intéressés aux capacités d'acclimatation de P. calceolata face aux changements de quantité et de source d'azote. Les gènes différentiellement exprimés (DEG) chez P. calceolata en fonction de la concentration en nitrate dans les échantillons Tara Oceans ont été comparés avec ceux identifiés lors d'expériences de croissance en conditions contrôlées. P. calceolata a été cultivé dans des milieux déplétés en nitrate ou dans lesquelles le nitrate a été remplacé par de l'ammonium, de l'urée ou du cyanate. La comparaison des DEG issus du laboratoire avec ceux issus des données environnementales permet de mieux comprendre le métabolisme de cette microalgue face au manque de nitrate, quels mécanismes sont mis en place dans l'environnement pour faire face à la variabilité de la disponibilité du nitrate, notamment par sa capacité à utiliser des sources d'azote organique. Dans le troisième chapitre, nous avons voulu mieux comprendre comment la profondeur impacte la physiologie de P. calceolata. En effet, on retrouve P. calceolata dans des échantillons d'eaux provenant de la surface et au moins jusqu'à 200m de profondeur. Nous avons constaté que la profondeur d'échantillonnage impactait fortement l'expression des gènes de P. calceolata impliqués dans la photorespiration et dans les mécanismes de concentration du carbone. Lors de cette thèse de doctorat, la caractérisation des capacités d'adaptation de P. calceolata a permis de mieux comprendre comment la régulation transcriptomique lui permet d'être cosmopolite, et montre que cette microalgue peut servir d'organisme modèle grâce à la possibilité de l'étudier simultanément en laboratoire et dans des données multi-omiques environnementalesPhotosynthetic picoeukaryotes (PPE) are abundant in all oceans and represent a significant proportion of biomass and primary production. Climate models predict an extension of oligotrophic areas in the following decades, which could greatly increase the abundance and ecological impact of PPEs. Among them, the microalga Pelagomonas calceolata (Stramenopiles/Pelagophyceae) is widely distributed in the oceans (Worden et al., 2012) but its role in the carbon cycle and its impact on the trophic chain remain poorly characterised (Dupont et al., 2015). In situ and in vitro analyses suggest that P. calceolata can adapt to environmental variations thanks to a significant capacity to modulate gene expression (Carradec et al., 2018; Dimier et al., 2009). The aim of this thesis is to understand how P. calceolata adapts to environmental variations in the many environments it lives in. In the first chapter, the P. calceolata genome is assembled, annotated and compared with those of other PPEs. Thanks to metagenomic and metatranscriptomic data from the Tara Oceans expedition, the biogeography and transcriptomic activity of P. calceolata under different environmental conditions has provided a better understanding of the present and future distribution of this alga, and the genes involved in its ecological success (Guérin et al 2022). In the second chapter, we focused on the acclimatisation habilites of P. calceolata to changing nitrogen quantities and sources. Differentially expressed genes (DEGs) in P. calceolata as a function of nitrate concentration in Tara Oceans samples were compared with those identified during growth experiments under controlled conditions. P. calceolata was grown in media depleted in nitrate or in which nitrate was replaced by ammonium, urea or cyanate. The comparison of DEGs obtained in the laboratory with those obtained from environmental data provides a better understanding of the metabolism of this microalga in the face of nitrate shortage, and of the mechanisms put in place in the environment to cope with variability in nitrate availability, in particular through its ability to use organic nitrogen sources. In the third chapter, we aimed to better understand how depth affects the physiology of P. calceolata. P. calceolata is found in water samples from the surface down to a depth of at least 200m. We found that sampling depth had a strong impact on the expression of P. calceolata genes involved in photorespiration and carbon concentration mechanisms. During this PhD thesis, the characterisation of the adaptive capacities of P. calceolata led to a better understanding of how transcriptomic regulation enables it to be cosmopolitan, and shows that this microalga can be used as a model organism thanks to the possibility of studying it simultaneously in the laboratory and in environmental multi-omics data
32
Ly, Delphine. "Prédictions génomiques des interactions Génotype x Environnement à l'aide d'indicateurs agro-climatiques chez le blé tendre (Triticum aestivum L.)." Thesis, Clermont-Ferrand 2, 2016. http://www.theses.fr/2016CLF22669/document.
Анотація:
Un des principaux enjeux de l’amélioration des plantes consiste aujourd’hui à faire face au changement climatique, en assurant un rendement élevé et plus stable dans des systèmes agricoles économes en intrants (eau, fertilisants) et respectueux de l’environnement. Les nouvelles variétés de blé devront non seulement être tolérantes aux stress hydriques et aux fortes températures, mais aussi continuer à être productives avec des apports limités en fertilisation, tout en maintenant une qualité du grain adaptés aux différents usages. De nouvelles méthodes de prédiction des réponses des blés à ces stress sont indispensables pour avancer dans cette direction. Dans ce travail, nous avons tout d’abord identifié les stress qui régissaient les interactions entre génotypes et les environnements (GxE) dans les essais considérés, puis développé un modèle génomique de l’adaptation à un stress environnemental (Factorial Regression genomic Best Linear Unbiased Prediction ou FR-gBLUP), en particulier pour le stress hydrique. En émettant l’hypothèse que plus des variétés de blés sont génétiquement proches, plus elles répondront de façon similaire à un stress environnemental donné, nous avons mesuré par validation croisée des gains de précision de prédiction par rapport à un modèle additif variant entre 3.5% et 15.4%. Des simulations complètent l’étude en démontrant que plus la part de variance expliquée par les réponses au stress considéré est importante, plus le modèle FR-gBLUP apporte un gain de précision. Pour prédire les réponses variétales à un stress particulier, les environnements doivent être finement caractérisés pour les stress limitant le développement des plantes. En nous intéressant plus particulièrement au stress azoté en France, nous avons établi des indicateurs de stress à partir d’un modèle de culture, et les avons comparés à des indicateurs classiques, tels que le type de conduite azotée ou l’azote disponible. Nous avons ainsi mis en évidence l’intérêt des modèles de culture pour caractériser les interactions GxE et pour prédire la réponse génomique au stress azoté, à condition que le signal d’interaction soit assez fort. Au-delà de l’application potentielle de ces méthodes pour la sélection ou la recommandation de variétés de blés plus adaptées ou plus résistantes au changement climatique, les résultats de ce travail démontrent aussi l’intérêt de la complémentarité des approches éco-physiologiques et génétiquesIn a climate change context, assuring high and stable yield in more sustainable agricultural systems is a major challenge for plant breeding. We are aiming for future wheat varieties which will be heat and drought tolerant, and also productive in limited fertilization input environments. New prediction methods of the response to these stresses are needed to move forward. In this study, we first identified stresses that generated interactions between genotypes and environments (GxE) in our experimental trials and then developed a genomic model for adaptation to a particular environmental stress (Factorial Regression genomic Best Linear Unbiased Prediction ou FR-gBLUP), in our case drought. This model hypothesizes that the more individuals are genetically close, the more their response to a stress will resemble. We used cross-validations to measure prediction accuracy gains compared to an additive model and observed gains between 3.5% and 15.4%. Besides, simulation studies showed that the more the variance explained by the responses to the stress is important, the more the FR-gBLUP model will improve the additive model. Furthermore, fine characterization of the stresses limiting the plants’ growth is required to predict varietal responses to a particular stress. We focused on the particular case of nitrogen stress in France. By establishing crop model based stress indicators and comparing them to classical indicators, such as the management system or the available nitrogen, we pointed out the interest of crop model to characterize GxE interactions and to predict the genomic response to nitrogen stress, as long as the GxE interaction signal is strong enough. Beyond the potential applications of these methods for breeding or recommendation for varieties more adapted or tolerant to environmental stresses, this study also raises the interest of coupling eco-physiological and genetics approaches
33
Sofer, Tamar. "Statistical Methods for High Dimensional Data in Environmental Genomics." Thesis, Harvard University, 2012. http://dissertations.umi.com/gsas.harvard:10403.
Анотація:
In this dissertation, we propose methodology to analyze high dimensional genomics data, in which the observations have large number of outcome variables, in addition to exposure variables. In the Chapter 1, we investigate methods for genetic pathway analysis, where we have a small number of exposure variables. We propose two Canonical Correlation Analysis based methods, that select outcomes either sequentially or by screening, and show that the performance of the proposed methods depend on the correlation between the genes in the pathway. We also propose and investigate criterion for fixing the number of outcomes, and a powerful test for the exposure effect on the pathway. The methodology is applied to show that air pollution exposure affects gene methylation of a few genes from the asthma pathway. In Chapter 2, we study penalized multivariate regression as an efficient and flexible method to study the relationship between large number of covariates and multiple outcomes. We use penalized likelihood to shrink model parameters to zero and to select only the important effects. We use the Bayesian Information Criterion (BIC) to select tuning parameters for the employed penalty and show that it chooses the right tuning parameter with high probability. These are combined in the “two-stage procedure”, and asymptotic results show that it yields consistent, sparse and asymptotically normal estimator of the regression parameters. The method is illustrated on gene expression data in normal and diabetic patients. In Chapter 3 we propose a method for estimation of covariates-dependent principal components analysis (PCA) and covariance matrices. Covariates, such as smoking habits, can affect the variation in a set of gene methylation values. We develop a penalized regression method that incorporates covariates in the estimation of principal components. We show that the parameter estimates are consistent and sparse, and show that using the BIC to select the tuning parameter for the penalty functions yields good models. We also propose the scree plot residual variance criterion for selecting the number of principal components. The proposed procedure is implemented to show that the first three principal components of genes methylation in the asthma pathway are different in people who did not smoke, and people who did.
34
Kaplarevic, Mihailo. "Environmental genome informational utility system (EnGENIUS)." Access to citation, abstract and download form provided by ProQuest Information and Learning Company; downloadable PDF file, 126 p, 2007. http://proquest.umi.com/pqdweb?did=1362531681&sid=19&Fmt=2&clientId=8331&RQT=309&VName=PQD.
35
Baysal, Can. "Redesigning rice for environmental sustainability, enhanced productivity and specialty uses." Doctoral thesis, Universitat de Lleida, 2021. http://hdl.handle.net/10803/672397.
Анотація:
Vaig dirigir la proteïna verda fluorescent codificada en el nucli (eGFP) a les mitocòndries d'arròs utilitzant sis pre-seqüències mitocondrials amb divers origen filogenètic. Vaig investigar la seva efectivitat mitjançant anàlisi de immunotransferència, microscòpia confocal i electrònica tant en calls com en plantes regenerades. Vaig confirmar que els pèptids COX4, SEU9 dirigien eficaçment eGFP a les mitocòndries d'arròs independentment del seu origen. Vaig utilitzar aquesta metodologia per disseccionar i expressar la proteïna NifH nitrogenasa Fe, extremadament sensible a l'oxigen, i la seva maturasa NifM en les mitocòndries d'arròs, superant així el coll d'ampolla més desafiant de l'enginyeria de la fixació biològica de nitrogen en els cereals. Per tant, vaig poder expressar i purificar quantitats substancials de NifH a partir de calls d'arròs i vaig confirmar que la NifH aïllada exercia el paper fonamental de l'activitat emzimática de NifH necessària per dissenyar la fixació de nitrogen, inclosa la transferència d'electrons i la biosíntesi de FeMo-co. D'aquesta manera demostre, per primera vegada, l'expressió i activitat estables d'un component nitrogenasa en qualsevol cereal.
També vaig fer servir CRISPR / CAS9 per mutar el OsSBEIIb (que codifica l'enzim ramificadora de midó IIb), que es requereix per a la síntesi d'amilopectina densament ramificada en l'endosperma de l'arròs. Vaig investigar els efectes de la inactivació de l'enzim de biosíntesi de midó individual en el midó d'arròs i en el seu metabolisme general. Les plantes mutants homocigotas, en què OsSBEIIb estava completament inactivat, van produir llavors opaques amb reserves de midó esgotades el contingut d'amilosa va augmentar de 19.6 a 27.4% i el contingut de midó resistent (RS) va augmentar de 0.2 a 17.2%. A causa de la mutació, hi va haver un augment general en l'acumulació de sucres, àcids grassos, aminoàcids i fitosterols en l'endosperma mutant, el que suggereix que els intermediaris en la via de biosíntesi del midó van augmentar el flux a través de vies indirectes causant un profund impacte en l'acumulació de múltiples metabòlits primaris i secundaris.Conseguí dirigir la proteína verde fluorescente codificada en el núcleo (eGFP) a las mitocondrias de arroz utilizando seis pre-secuencias mitocondriales con diverso orígen filogenético. Investigué su efectividad mediante análisis de inmunotransferencia, microscopía confocal y electrónica tanto en callos como en plantas regeneradas. Confirmé que los péptidos COX4, SU9 dirigían eficazmente eGFP a las mitocondrias de arroz independientemente de su origen. Utilicé esta metodología para diseccionar y expresar la proteína NifH nitrogenasa Fe, extremadamente sensible al oxígeno, y su maturasa NifM en las mitocondrias de arroz, superando así el cuello de botella más desafiante de la ingeniería de la fijación biológica de nitrógeno en los cereales. Por lo tanto, pude expresar y purificar cantidades sustanciales de NifH a partir de callos de arroz y confirmé que la NifH aislada desempeñaba el papel fundamental de la actividad emzimática de NifH necesaria para diseñar la fijación de nitrógeno, incluida la transferencia de electrones y la biosíntesis de FeMo-co. De esta manera pude demostrar, por primera vez, la expresión y actividad estables de un componente nitrogenasa en cualquier cereal. También usé CRISPR / Cas9 para mutar el OsSBEIIb (que codifica la enzima ramificadora de almidón IIb), que se requiere para la síntesis de amilopectina densamente ramificada en el endospermo del arroz. Investigué los efectos de la inactivación de la enzima de biosíntesis de almidón individual en el almidón de arroz y en su metabolismo general. Las plantas mutantes homocigotas, en las que OsSBEIIb estaba completamente inactivado, produjeron semillas opacas con reservas de almidón agotadas cuyo contenido de amilosa aumentó de 19.6 a 27.4% y el contenido de almidón resistente (RS) aumentó de 0.2 a 17.2%. Debido a la mutación, hubo un aumento general en la acumulación de azúcares, ácidos grasos, aminoácidos y fitoesteroles en el endospermo mutante, lo que sugiere que los intermediarios en la vía de biosíntesis del almidón aumentaron el flujo a través de vías indirectas causando un profundo impacto en la acumulación de múltiples metabolitos primarios y secundarios.
I targeted nuclear-encoded green fluorescent protein (eGFP) to rice mitochondria using six mitochondrial pre-sequences with diverse phylogenetic origin. I investigated their effectiveness by immunoblot analysis, confocal and electron microscopy in callus and regenerated plants. I confirmed that COX4, SU9 targeting peptides effectively targeted eGFP to rice mitochondria regardless of their origin. I used this methodology to dissect and express extremely oxygen sensitive nitrogenase Fe Protein NifH and its maturase NifM in rice mitochondria to overcome the most challenging bottleneck of engineering biological nitrogen fixation in cereals. Therefore, I was able to express and purify substantial amounts of NifH from rice callus, and I confirmed that the isolated NifH carried out the fundamental role of NifH enzymatic activity required to engineer nitrogen fixation, including electron transfer, and FeMo-co biosynthesis. I was thus able to demonstrate for the first-time stable expression and activity of a nitrogenase component in any cereal. I have further used CRISPR/Cas9 to mutate the OsSBEIIb (encoding starch branching enzyme IIb), which is required for the synthesis of densely branched amylopectin in the rice endosperm. I investigated the effects of the inactivation of individual starch biosynthesis enzyme in rice starch and overall metabolism. Homozygous mutant plants, in which OsSBEIIb was completely inactivated, produced opaque seeds with depleted starch reserves whose amylose content increased from 19.6 to 27.4% and resistant starch (RS) content increased from 0.2 to 17.2%. Because of the mutation there was a general increase in the accumulation of sugars, fatty acids, amino acids, and phytosterols in the mutant endosperm, suggesting that intermediates in the starch biosynthesis pathway increased flux through spillover pathways causing a profound impact on the accumulation of multiple primary and secondary metabolites.
36
Ogburn, Emma. "The pneumococcal biofilm environment : impact of environment upon growth, the capsule locus and genomic instability." Thesis, University of Warwick, 2005. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.425557.
37
Vilo, Muñoz Claudia Andrea. "Understanding Microbial Biodegradation of Environmental Contaminants." Thesis, University of North Texas, 2015. https://digital.library.unt.edu/ark:/67531/metadc801956/.
Анотація:
The accumulation of industrial contaminants in the natural environments have rapidly become a serious threat for human and animal life. Fortunately, there are microorganisms capable of degrading or transforming environmental contaminants. The present dissertation work aimed to understand the genomic basis of microbial degradation and resistance. The focus was the genomic study of the following bacteria: a) Pseudomonas fluorescens NCIMB 11764, a unique bacterium with specific enzymes that allow cyanide adaptation features. Potential cyanide degradation mechanisms found in this strain included nit1C cluster, and CNO complex. Potential cyanide tolerance genes found included cyanide insensitive oxidases, nitric oxide producing gene, and iron metabolism genes. b) Cupriavidus sp. strain SK-3 and strain SK-4. The genome of both bacteria presented the bph operon for polychlorinated biphenyl (PCB) degradation, but we found differences in the sequences of the genes. Those differences might indicate their preferences for different PCB substrates. c) Arsenic resistant bacterial communities observed in the Atacama Desert. Specific bacteria were found to thrive depending on the arsenic concentration. Examples were Bacteroidetes and Spirochaetes phyla whose proportions increased in the river with high arsenic concentrations. Also, DNA repair and replication metabolic functions seem to be necessary for resistance to arsenic contaminated environments. Our research give us insights on how bacteria communities, not just individually, can adapt and become resistant to the contaminants. The present dissertation work showed specific genes and mechanisms for degradation and resistance of contaminants that could contribute to develop new bioremediation strategies.
38
Gilley, Jonathan Nicholas. "An evolutionary analysis of the Surfeit genes and their genomic environments." Thesis, University College London (University of London), 1999. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.313024.
39
Haig, Sarah-Jane. "Characterising the functional ecology of slow sand filters through environmental genomics." Thesis, University of Glasgow, 2014. http://theses.gla.ac.uk/5523/.
Анотація:
Today the water industry faces a huge challenge in supplying a sustainable, energy efficient and safe supply of drinking water to an increasing world population. Slow sand filters (SSFs) have been used for hundreds of years to provide a safe and reliable source of potable drinking water, with minimal energy requirements. However, a lack of knowledge pertaining to the treatment mechanisms, particularly the biological processes, underpinning SSF operation, has meant SSFs are still operated as “black boxes”. This lack of knowledge pertaining to the underlying ecology and ecophysiology limits the design and optimisation of SSFs. This thesis represents the most comprehensive microbial community survey of full-scale SSFs to-date. Using traditional microbiological methods alongside up-to-date molecular techniques and extensive water quality analyses, specific taxa and community metrics are linked to changes in water quality production. Furthermore, it has been verified that laboratory scale SSFs can mimic the microbial community and water quality production of full-scale filters. This allowed rigorous experiments pertaining to operational differences, pathogen and novel contaminant removal to be performed. This has revealed, for the first time, that multiple trophic interactions within SSFs are integral to optimal performance. This thesis has shown that SSFs are phylogenetically and metabolically diverse systems capable of producing high quality water, with the ability to adapt to remove novel contaminants. Using the information gathered, improvements to filter maintenance and operation can be achieved. Future work will apply the microbial and macrobial community dynamics and impact of novel contaminants on filter performance discovered in this thesis into predictive models for water quality.
40
Coolon, Joseph. "Ecological genomics of nematode responses to different bacterial environments." Diss., Manhattan, Kan. : Kansas State University, 2008. http://hdl.handle.net/2097/2750.
41
Weber, Eva. "Ecological insights into unexplored Archaea through environmental ecophysiology, single-cell genomics and cultivation." Thesis, University of Aberdeen, 2017. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=231673.
42
Brown, Margaret M. "Application of genomic techniques to development of biomarkers for the aquatic environment." Thesis, Glasgow Caledonian University, 2004. http://ethos.bl.uk/OrderDetails.do?uin=uk.bl.ethos.443169.
43
Larsson, Magnus. "CapExBio : A Knowledge Capitalizing, Cooperative Environment for the Genomics Community." Thesis, Uppsala universitet, Institutionen för informationsteknologi, 2010. http://urn.kb.se/resolve?urn=urn:nbn:se:uu:diva-166153.
44
Liedke, Mônica Souza. "Proteção do genoma humano e socioambientalismo : aspectos bioéticos e jurídicos." reponame:Repositório Institucional da UCS, 2009. https://repositorio.ucs.br/handle/11338/445.
Анотація:
A construção do paradigma socioambiental é resultado da compreensão de que não é possível a proteção isolada, implicando o cuidado conjunto. O ser humano, ente integrante da biodiversidade, está amparado pelas legislações que lhe são próprias, assim como pelas legislações ambientais. O genoma humano é próprio de cada indivíduo e o distingue dos demais entes da mesma espécie. O desenvolvimento do Projeto Genoma Humano possibilitou o acesso e o uso das informações genéticas. A evolução da ciência deve ser regulamentada para evitar a utilização indevida das informações genéticas, assim como para que os benefícios proporcionados por essa evolução sejam acessíveis a toda população. O ser humano não pode sofrer discriminação em razão da sua carga genética. O acesso às informações contidas nos genes deve ocorrer unicamente para melhorar a saúde dos indivíduos. O consentimento informado é imprescindível para acesso e uso das informações genéticas. A bioinformática possibilita a descoberta das funções de cada gene específico. A farmacogenômica, por sua vez, proporciona o tratamento e a cura de doenças de acordo com a carga genética de cada indivíduo. Os biorepositórios e os biobancos são importantes para conservar o material genético destinado à pesquisa, bem como a ser utilizado no futuro tratamento médico do próprio doador. As pesquisas genéticas devem ser conduzidas de forma transparente e regulada a fim de evitar a detenção do biopoder. O acesso do genoma humano pode permitir a manipulação desse com finalidades bioterroristas de modo a atingir à população em geral ou a determinado grupo específico. Alguns países já estão patenteando os genes, muito embora sejam considerados descoberta e não invenção. A não permissão do patenteamento de genes no Brasil deixa o país em desvantagem quanto aos demais que permitem, pois futuramente, nosso país, poderá ter que pagar royalties pela utilização dos genes já patenteados no desenvolvimento de pesquisas genéticas. Todas essas situações demonstram a importância de proteger o genoma humano para que as atuais e futuras gerações não tenham sua carga genética alterada. A criação de uma legislação nacional e, principalmente, internacional é indispensável.Submitted by Marcelo Teixeira (mvteixeira@ucs.br) on 2014-05-29T18:15:58Z No. of bitstreams: 1 Dissertacao Monica Souza Liedke.pdf: 1347371 bytes, checksum: 041ecbd172b0c26294c008a919ffc003 (MD5)
Made available in DSpace on 2014-05-29T18:15:58Z (GMT). No. of bitstreams: 1 Dissertacao Monica Souza Liedke.pdf: 1347371 bytes, checksum: 041ecbd172b0c26294c008a919ffc003 (MD5)
The build of the socio-environment paradigm is resultant from the comprehension that isolated protection is not possible, implying collective care. The human being, as a biodiversity integrant, is supported by his laws, but also by environment laws. The human genome is unique for each individual and distinguishes itself from the others beings of the same species. The development of The Human Genome Project made possible the access to and the use of genetic information. Science evolution must be ruled to avoid improper use of genetic information, but also for granting universal access to it. The human being must not be discriminated by its genetic information. Genetic information access should only be for individual health improvement. Informed assent is essential for the access and the use of this information. Pharmacogenomics, in its turn, provides treatment and cure for diseases in agreement with every individual genetic information. The biorepositories and biobanks are important to preserve genetic material destined to research, such as future use in the medical treatment of the donor. Genetic researches must be lead in a clear and ruled form in order to avoid retention of biopower. The access to the human genome can permit its manipulation with bioterrorist intents of reaching general population or a specific group. Some countries are already patenting the genes, although they are considered findings and not inventions. The non permission of gene patenting in Brazil put the country in disadvantage with the others that permit, because, in the future, our country could pay royalties for the already patented in the development of genetic researches. All these situations show the importance of protecting human genome for this and future generations. The creation of national and, mainly, international laws is indispensable.
45
McDonagh, Andrew N. "Comparative genomics and systems biology of environmental stress responses relevant to fungal virulence." Thesis, Imperial College London, 2010. http://hdl.handle.net/10044/1/11825.
46
Curreem, Oi-ting Shirly, and 嘉藹庭. "The study of environmental adaptability of laribacter hongkongensis bygenomic and proteomic approach." Thesis, The University of Hong Kong (Pokfulam, Hong Kong), 2009. http://hub.hku.hk/bib/B43931686.
47
Teets, Nicholas Mario. "Cellular and Molecular Mechanisms of Environmental Stress Tolerance in Insects." The Ohio State University, 2012. http://rave.ohiolink.edu/etdc/view?acc_num=osu1354542991.
48
Viger, Maud. "Physiology, genetics and genomics of drought adaptation in Populus." Thesis, University of Southampton, 2011. https://eprints.soton.ac.uk/202473/.
Анотація:
As the demand for energy rises, Populus species are increasingly grown as bioenergy crops. Meanwhile, due to global change, predictions indicate that summer droughts will increase in frequency and intensity over Europe. This study was carried out to evaluate the adaptation to drought in Populus, at different levels: genetic, genomics and physiology. Forests trees such as poplar are very important ecologically and economically but the Populus genus is known to be drought sensitive. Consequently, it is essential to understand drought response and tolerance for those trees. Two populations of poplar were used for this study, a mapping population (Family 331) and a natural population of Populus nigra. The F2 mapping population obtained from a cross of Populus deltoides and Populus trichocarpa, showed differences in stomatal conductance and carbon isotope composition in both clones and the F2 progeny. It was also used to discover QTL related to water use efficiency highlighting interesting areas of the genome. Combining QTL discovery and microarray analysis of the two clones in response to drought, a list of candidate genes was defined for water use efficiency. The natural population of Populus nigra consisting of 500 genotypes of wild black poplar showed variation in numerous physiological measurements such as leaf development and carbon isotope discrimination in well-watered conditions depending on their latitude of origin. The drier genotypes (from Spain and South France) had the smallest leaf area which could be linked to an adaptation to drought. Physiological measurements of extreme genotypes in leaf size of this population revealed differences in response to water depending on their latitude of origin. Stomatal conductance rapidly decreased and water use efficiency improved for Spanish genotypes after a slow and moderate drought stress. Direct comparisons between the transcriptome of extreme genotypes from Spain and North Italy in well watered and drought conditions provided an insight into the genomic pathways induced during water deficit. Six candidate genes were selecting for further analysis using real-time PCR: two stomatal development genes (ERECTA and SPEECHLESS), two ABA related genes (ATHVA22A and CCD1), a second messenger (IP3) and a NAC transcription factor (RD26)
49
Payne, Bryony. "Genome duplication in a protein rich environment." Thesis, University of Aberdeen, 2006. http://digitool.abdn.ac.uk:80/webclient/DeliveryManager?pid=165723.
50
Eresjö, Cassandra, and Frida Hallgren. "En god arbetsmiljö genom ett effektivt systematiskt arbetsmiljöarbete." Thesis, Högskolan Dalarna, Personal och arbetsliv, 2017. http://urn.kb.se/resolve?urn=urn:nbn:se:du-25285.
Анотація:
Studiens syfte är att beskriva hur ett systematiskt arbetsmiljöarbete kan bedrivas effektivt så att det bidrar till en bra arbetsmiljö. Tidigare forskning lyfter bland annat ledarskapets betydelse och vikten av att involvera medarbetarna i arbetsmiljöarbetet. Forskningen visar också att det hårda och tekniska delarna ofta prioriteras före de psykosociala bitarna. Det empiriska materialet insamlades genom en metodtriangulering bestående av en fokusgruppsintervju och en enkätundersökning på ett företag i Sverige. Resultatet visar att respondenterna lyfter flera olika delar som viktiga för att kunna bedriva ett effektivt systematiskt arbetsmiljöarbete. Studien utmynnade i slutsatserna att SAM kan bedrivas effektivt om det finns ett helhetstänk där alla delar i arbetsmiljön är viktiga. Det har visat sig att den psykosociala arbetsmiljön är svårare att behandla än den fysiska arbetsmiljön. Ledarskapet är en del som har visat sig vara av betydelse för hur arbetsmiljöarbetet lyckas, dessutom lyfts den ekonomiska aspekten som viktig för möjligheten att kunna bedriva ett effektivt SAM.The purpose of this study is to describe how a systematic work environmental management can be conducted effectively to contribute to a good work environment. Prior research enhances the importance of leadership and the necessity of involving the co-workers in the work environmental management. Research also shows that the hard and technical parts are often prioritized before the psychosocial part. The empirical material was gathered through a mixed method consisting of interviews of a focus group and a survey on a corporation in Sweden. The result shows that respondents raise several different parts as important in order to conduct effective systematic work environmental management. The study gave the conclusions that systematic work environmental management can be conducted effectively if there is a thought-through plan and commitment where all parts of the work environment are covered and taken with importance. It has been shown that the psychosocial work environment is more difficult to treat than the physical environment. Leadership is a part that has shown to be of importance on how the work environmental management will succeed and that the economic aspect is regarded as important for an effective systematic work environmental management.