Natural Selection For Disease Resistance In Hybrid Poplars Targets Stomatal Patterning Traits And Regulatory Genes.

The evolution of disease resistance in plants occurs within a framework of interacting phenotypes, balancing natural selection for life-history traits along a continuum of fast-growing and poorly defended, or slow-growing and well-defended lifestyles. Plant populations connected by gene flow are physiologically limited to evolving along a single axis of the spectrum of the growth-defense trade-off, and strong local selection can purge phenotypic variance from a population or species, making it difficult to detect variation linked to the trade-off. Hybridization between two species that have evolved different growth-defense trade-off optima can reveal trade-offs hidden in either species by introducing phenotypic and genetic variance. Here, I investigated the phenotypic and genetic basis for variation of disease resistance in a set of naturally formed hybrid poplars. The focal species of this dissertation were the balsam poplar (Populus balsamifera), black balsam poplar (P. trichocarpa), narrowleaf cottonwood (P. angustifolia), and eastern cottonwood (P. deltoides). Vegetative cuttings of samples were collected from natural populations and clonally replicated in a common garden. Ecophysiology and stomata traits, and the severity of poplar leaf rust disease (Melampsora medusae) were collected. To overcome the methodological bottleneck of manually phenotyping stomata density for thousands of cuticle micrographs, I developed a publicly available tool to automatically identify and count stomata. To identify stomata, a deep con- volutional neural network was trained on over 4,000 cuticle images of over 700 plant species. The neural network had an accuracy of 94.2% when applied to new cuticle images and phenotyped hundreds of micrographs in a matter of minutes. To understand how disease severity, stomata, and ecophysiology traits changed as a result of hybridization, statistical models were fit that included the expected proportion of the genome from either parental species in a hybrid. These models in- dicated that the ratio of stomata on the upper surface of the leaf to the total number of stomata was strongly linked to disease, was highly heritable, and wass sensitive to hybridization. I further investigated the genomic basis of stomata-linked disease variation by performing an association genetic analysis that explicitly incorporated admixture. Positive selection in genes involved in guard cell regulation, immune sys- tem negative regulation, detoxification, lipid biosynthesis, and cell wall homeostasis were identified. Together, my dissertation incorporated advances in image-based phenotyping with evolutionary theory, directed at understanding how disease frequency changes when hybridization alters the genomes of a population

The influence of hypoxia in erythropoiesis and morphology of red blood cells in sickle cell disease and hereditary spherocytosis.

Die Lebensfahigkeit menschlicher Zellen h ¨ angt in hohem Maße vom Sauerstoff ab, der von den roten ¨ Blutkorperchen transportiert und zur Verf ¨ ugung gestellt wird. In dieser Arbeit wird untersucht, wie ¨ Sauerstoff die Physiologie und Pathophysiologie jener roten Blutkorperchen beeinflusst. Die Arbeit ¨ ist in zwei wesentliche Teile gegliedert. Zunachst werden Ergebnisse einer gr ¨ oßeren Studie mit Probanden vorgestellt, die in großer H ¨ ohe ¨ (3450 m) durchgefuhrt wurde. In dieser H ¨ ohe sorgt der reduzierte Luftdruck f ¨ ur eine Abnahme ¨ der Sauerstoffsattigung im Blut und f ¨ uhrt so zu einer erh ¨ ohten Produktion an roten Blutk ¨ orperchen ¨ (Erythropoese). Nach der Ruckkehr aus großer H ¨ ohe f ¨ allt die Zahl an roten Blutk ¨ orperchen nach ¨ kurzer Zeit wieder auf das vorherige Niveau Es ist bislang nicht verstanden, ob die neugebildeten roten Blutzellen dazu abgebaut werden. Der hyptothetische Mechanismus der Neozytolyse (engl. Neocytolisis) geht davon aus, dass ausgerechnet die neu gebildeten, roten Blutzellen als erste wieder abgebaut werden, wenn die Ruckkehr auf Meeresniveau erfolgt. Die wissenschaftliche Fragestellung, ¨ die im Rahmen dieser Studie beantwortet wurde, ist, ob und in welchem Maß Neocytolyse nach einem 3-wochigen Aufenthalt in großer H ¨ ohe stattfindet. Dazu wurden zun ¨ achst Untersuchungen an aller ¨ Probanden mittels in-vitro Zellkulturen durchgefuhrt, um sowohl die Erythropoese als auch (neu ent- ¨ standende) Retikulozyten zu charakterisieren. Die Ergebnisse zeigen eine beschleunigte Reifung der Vorlauferzellen in Zellkulturen bei niedrigerem Sauerstoffgehalt (3%) verglichen mit normaler Atmo- ¨ sphare (20%) und eine unerwartet verbesserte ¨ Uberlebensrate der Retikulozyten. Dies stimmt mit dem ¨ Ergebnis der Studie uberein, dass nach der R ¨ uckkehr von der gew ¨ ahlten H ¨ ohe keine Neozytolyse, d.h. ¨ kein bevorzugter Abbau von neu gebildeten roten Blutzellen, auftrat, was die Hypothese eines selektiven, vorzeitigen Abbaus von unreifen roten Blutzellen widerlegt. Weiterhin wurde in der Zellkultur unter verringerter Sauerstoffgabe eine erhohte Zahl bikonkaver Zellen beobachtet, was eine typische ¨ Gestalt fur einen fortgeschrittenen Reifegrad ist. Diese Beobachtung k ¨ onnte ein Anhaltspunkt daf ¨ ur¨ sein, dass der Reifeprozess von roten Blutzellen durch die Reduzierung des atmospharischen Sauer- ¨ stoffgehaltes begunstigt werden kann. Im Rahmen dieser Arbeit wurde zus ¨ atzlich ein Protokoll zur ¨ Isolation der Retikulozyten vom Vollblut der Probanden entwickelt, um die pure Zell-RNA jeweils vor und in großer Hohe zu sequenzieren. Jedoch muss die Ausbeute an RNA weiter optimiert werden, ¨ um einen detaillierten Vergleich der Gen-Expressions-Niveaus anstellen zu konnen. ¨ Der zweite Teil der Arbeit konzentriert sich auf die Untersuchung der Morphologie der roten Blutkor- ¨ perchen bei zwei Arten von Anamie. Aufgrund der hohen Empfindlichkeit der roten Blutk ¨ orperchen ¨ gegenuber Formvariationen, mussten die Proben vor jeder experimentellen Manipulation fixiert wer- ¨ den. Dazu musste ein angemessenes Verfahren entwicklelt werden, das im Rahmen dieser Arbeit vorgestellt wird. Zunachst wird auf die Sichelzellenan ¨ amie eingegangen, bei der es unter Desoxy- ¨ genierung des Hamoglobins zur starken Verformung der roten Blutk ¨ orperchen (Sichelzellen) kommt. ¨ Dies beintrachtigt sowohl deren Funktion als auch Lebensdauer. Eine quantitative Analyse von Zell- ¨ Projektionsbildern aus konfokalen Mikroskopieaufnahmen wurde mit Hilfe eines maßgeschneiderten Computerprogramms im Rahmen einer klinischen Pilotstudie der Phase II zur Therapie der Sichelzellanamie durchgef ¨ uhrt. Es konnte gezeigt werden, dass diese Methode in Kombination mit anderen ¨ experimentellen Verfahren ein wirkungsvolles Instrument zur Beurteilung des Zellhydratationszustands von Sichelzellenpatienten ist. Daher kann diese Technik zur Beurteilung der Wirksamkeit von Sichelzellen-Therapien oder zur Beurteilung des Zustands der roten Blutkorperchen eines Pa- ¨ tienten verwendet werden. Da die roten Blutkorperchen bei verschiedenen Arten von An ¨ amie auch ¨ verschiedene Formvariationen aufweisen, wurde eine weitere Blutkrankheit, die hereditare Sph ¨ arozy- ¨ tose, untersucht. In diesem Fall lag der Schwerpunkt auf der automatisierten Formerkennung der roten Blutkorperchen, die in der Regel manuell durchgef ¨ uhrt wird und daher einer Bewertungsinkonsistenz ¨ unterliegt. Die Untersuchung nutzt die 3D-Rekonstruktion der Zellen aus konfokalen Mikroskopieaufnahmen und die anschließende Formerkennung mittels kunstlicher neuronaler Netze. Die Beurteilung ¨ dieses Systems zeigte sowohl eine sehr gute Erkennungsrate, hohe Prazision, eine schnelle Prozesszeit, ¨ als auch ein objektives Ergebnis verglichen mit der manuellen Klassifikation. Verglichen mit der Analyse von 2D Mikroskopieaufnahmen von Blutabstrichen, konnten durch die Auswertung korrespondierender 3D Aufnahmen außerdem andere Formspektren abgeleitet werden. Dies legt die Empfehlung nahe, die manuelle Klassifizierung von Zellformen (Stand der Technik) im Kontext von hereditarer Sph ¨ arozytose zu ¨ uberdenken.Human cell viability highly depends on oxygen, which is carried and provided by red blood cells. This thesis aimed to investigate how oxygen influences physiology and pathophysiology of red blood cells and is divided in two main parts. The first one presents results that are part of a larger study performed at high altitude (3450 m). Here, the reduced air pressure causes a decrease in blood oxygenation, which is balanced by an increase in red blood cells production (erythropoiesis). Upon return from high altitude, the amount of red blood cells is restored to the original levels within a few days, which is in contrast with the average red blood cell lifespan of 120 days. The reasons leading to such red blood cells premature clearance are not well understood. A hypothetical mechanism previously proposed is defined as neocytolisis, i.e. the selective clearance of the red blood cells formed at high altitude upon return to sea level. The scientific question of the study was therefore to assess if and how neocytolisis occurs after a 3-week stay at high altitude. The investigations performed in this thesis involved in vitro culture of erythroid precursors of the donors participating in the study to characterize both erythropoiesis and the obtained immature red blood cells, namely reticulocytes. Results highlighted an accelerated maturation of erythroid precursors in cultures performed at lower oxygen (3%) compared to atmospheric oxygen (20%) ones and an unexpected improved cell survival of the obtained reticulocytes. This was in accordance with the finding that after the stay at the chosen altitude no neocytolisis occurred, denying the hypothesis of a higher fragility of cells formed at low oxygen causing their selective premature clearance upon return from high altitude. Moreover, cultures performed at low oxygen resulted in the formation of more biconcave cells, the typical shape of mature red blood cells. This suggests that reducing oxygen levels in cultures may contribute to advance their maturation in vitro. In addition to cell cultures, another objective was to perform RNA sequencing of isolated reticulocytes from whole blood of the donors to compare pre- and high altitude conditions. A protocol for the isolation of a pure fraction of reticulocytes and their RNA was developed. However, total RNA yield needs to be increased to perform an accurate comparison of gene expression levels. The second part of the thesis focused on studying red blood cell morphology in two types of anemia. Because of the high sensitivity of red blood cells to shape variation, samples were always fixed before any experimental manipulation. A thorough study describing how to perform red blood cell fixation is presented. The first blood disease of study was sickle cell anemia. In this pathology, deoxygenation of hemoglobin causes the deformation of red blood cells to the shape of a sickle that impairs their functions and lifespan. The quantitative analysis of cell projections from confocal images by means of a customized computer program was employed within a pilot phase II clinical trial for the therapy of sickle cell disease. The obtained results combined with other experimental evaluations showed that red blood cell shape analysis of sickle cell disease patients is a simple but powerful tool to evaluate cell hydration state. Therefore, this technique may be used for the assessment of the efficacy of sickle cell disease therapies or to evaluate the state of red blood cells of a patient. Since red blood cells display shape variations in different types of anemia, a second blood disease was investigated, namely hereditary spherocytosis. In this case, the focus was the automation of red blood cells shape recognition, which is usually performed manually and therefore subjected to evaluation inconsistency. The investigation made use of 3D cell reconstructions from confocal images and automated shape recognition by means of artificial neural networks. System benchmarks showed a good recognition performance, high accuracy, fast processing time as well unbiased results compared to the manual classification. Moreover, the application of 3D imaging in contrast to the traditional 2D-microscopy typically employed in blood smear analysis revealed a different red blood cell shapes spectrum. These results therefore suggest to revise the state-of-the art manual shape classification applied in hereditary spherocytosis

Spacelab mission 1 experiment descriptions, third edition

Experiments and facilities selected for flight on the first Spacelab mission are described. Chosen from responses to the Announcement of Opportunity for the Spacelab 1 mission, the experiments cover five broad areas of investigation: atmospheric physics and Earth observations; space plasma physics; astronomy and solar physics; material sciences and technology; and life sciences. The name of the principal investigator and country is listed for each experiment

Fungal Nanotechnology

Fungal Nanotechnologies (FN) 1 and 2 provide updated and comprehensive information that deals with the green and sustainable production of metal- and organic-based nanostructures by various fungal species. Additionally, intracellular and extracellular mechanisms will be investigated, as well as fungal nanotechnology applications in the biomedical, environmental, and agri-food sectors. FN is still in its infant stage; therefore, many studies should be focused on this area. Plants, animal and humans will benefit greatly from this, and efficient and ecologically friendly approaches should be created

Factors affecting the identification of phytoplankton groups by means of remote sensing

A literature review was conducted on the state of the art as to whether or not information about communities and populations of phytoplankton in aquatic environments can be derived by remote sensing. In order to arrive at this goal, the spectral characteristics of various types of phytoplankton were compared to determine first, whether there are characteristic differences in pigmentation among the types and second, whether such differences can be detected remotely. In addition to the literature review, an extensive, but not exhaustive, annotated bibliography of the literature that bears on these questions is included as an appendix, since it constitutes a convenient resource for anyone wishing an overview of the field of ocean color. The review found some progress has already been made in remote sensing of assemblages such as coccolithophorid blooms, mats of cyanobacteria, and red tides. Much more information about the composition of algal groups is potentially available by remote sensing particularly in water bodies having higher phytoplankton concentrations, but it will be necessary to develop the remote sensing techniques required for working in so-called Case 2 waters. It is also clear that none of the satellite sensors presently available or soon to be launched is ideal from the point of view of what we might wish to know; it would seem wise to pursue instruments with the planned characteristics of the Moderate Resolution Imaging Spectrometer-Tilt (MODIS-T) or Medium Resolution Imaging Spectrometer (MERIS)

Remote Sensing of Plant Biodiversity

This Open Access volume aims to methodologically improve our understanding of biodiversity by linking disciplines that incorporate remote sensing, and uniting data and perspectives in the fields of biology, landscape ecology, and geography. The book provides a framework for how biodiversity can be detected and evaluated—focusing particularly on plants—using proximal and remotely sensed hyperspectral data and other tools such as LiDAR. The volume, whose chapters bring together a large cross-section of the biodiversity community engaged in these methods, attempts to establish a common language across disciplines for understanding and implementing remote sensing of biodiversity across scales. The first part of the book offers a potential basis for remote detection of biodiversity. An overview of the nature of biodiversity is described, along with ways for determining traits of plant biodiversity through spectral analyses across spatial scales and linking spectral data to the tree of life. The second part details what can be detected spectrally and remotely. Specific instrumentation and technologies are described, as well as the technical challenges of detection and data synthesis, collection and processing. The third part discusses spatial resolution and integration across scales and ends with a vision for developing a global biodiversity monitoring system. Topics include spectral and functional variation across habitats and biomes, biodiversity variables for global scale assessment, and the prospects and pitfalls in remote sensing of biodiversity at the global scale

Undergraduate catalog 2010-12, original

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