Long-Term Quantitative Microscopy: From Microbial Population Dynamics to Growth of Plant Roots

Quantitative optical measurements at the micron scale have been crucial to the study of multiple biological processes, including bacterial chemotaxis, eukaryotic gene expression and y development. Extending measurements to long time scales allows complete observation of processes that are otherwise studied piecemeal, such as development and evolution. This thesis describes the development of two types of microscope for making long term, quantitative measurements, and the tools for image analysis. The rst device is a digital holographic microscope for measuring microbial population dynamics. It allows three dimensional localization of hundreds of cells within a mm3 sized volume, at micron resolution and an acquisition period of minutes. The technique is simple and inexpensive, which enabled us to construct ten replicate devices for parallel measurements. Each device incorporates precise and programmable control of light and temperature for the microbial ecosystem. Experiments were performed with the green algae Chlamydomonas reinhardtii and the ciliate Tetrahymena reinhardtii, both together and in isolation, and continued for as long as 90 days. The population dynamics exhibited a striking degree of repeatability, despite the presence of added noise in the illumination, spatial gradients of cell density, convection currents and phenotypic changes of both species. The second device is a thin light sheet fluorescence microscope for tracking nuclei in growing roots of the flowering plant Arabidopsis thaliana. The device incorporates a chamber designed to maintain optical quality while providing conditions for root growth. Optical feedback to a translation stage is used to maintain the root tip in the fi eld of view as the root grows by centimeters over several days. Data from a three day experiment is presented to demonstrate the technique. Over 1,000 nuclei were tracked simultaneously, and hundreds of cell divisions were automatically identif ed. The device was also used to image the regeneration of a root tip after surgical excision. The data corroborate earlier investigations at a more detailed level than was previously possible

The diversity and interactions of fungi from the Paleozoic and Mesozoic of Antarctica

Fungi are ubiquitous in all ecosystems and are the driving force in many types of interactions, such as mutualists, saprotrophs, parasites, and necrotrophs. Fungi are equally as integral in extant ecosystems as they certainly were in paleoecosystems. Paleomycology, the study of fossil fungi, is an emerging field of paleontology. Most fossil fungi are found in or in close association with plants and thus, paleomycology is also considered a sub-discipline of paleobotany. Therefore when plants are well preserved there is the increase potential to examine their fungal associates. Permineralized material is a preservation type that offers the opportunity to study plants, fungi, and other microorganisms anatomically and morphologically. Prior research suggested that fungi were too fragile and delicate to be structurally preserved in the fossil record; however, fungi have been described in some early paleobotanical studies as dispersed fragments, spores, and other remnants. The taxonomic and ecological affinities of many of these fungi, however, were not described in great detail. The objective of this study is to investigate the fungal components and plant-fungal associations of the Permian, Triassic, and Jurassic of Antarctica. The Paleobotanical Collections at the University of Kansas (KU) house the largest collection of Antarctic permineralized peat deposits in the world. To date, the majority of reports on Antarctic fossil fungi are found in Triassic peat material, with fewer reports on Permian fungi, and are most sparse on Jurassic fungi. These contributions utilized the acetate peel technique, a traditional method of studying permineralized material in paleobotany, and provided a platform for the investigation of microorganisms in ancient Antarctic environments. It has been demonstrated that paleontological thin sections of permineralized peat yields more information on fossil microbes because the fine details of the microorganisms are not etched away as they would be in the acetate peel technique. This study will fully exploit the use of paleontological thin section techniques, as well as preliminary studies using analytical techniques, to discover and describe new fossil fungi and plant-fungal interactions from the Antarctic paleobotanical collections at KU. Despite the large number of fungal remains in the fossil record, including those that provide direct or indirect evidence of an association or interaction with land plants, the discipline of paleomycology is at a relatively early stage of development. As more information is obtained about fossil fungi, including those from Antarctic permineralized peat deports, it will be increasingly possible to present more detailed hypotheses that can be used in association with those described from modern communities, to more accurately depict the role of these organisms in the functioning of early continental ecosystems. Therefore, this study adds new information to our understanding of the diversity of fungi in the Permian, Triassic, and Jurassic of Antarctica, and thus contributes to a more focused concept of the complexity of late Paleozoic and Mesozoic ecosystems

Fossilisation processes in terrestrial environments and their impact on archaeological deposits.

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