The Evolution of Reduced Microbial Killing

Bacteria engage in a never-ending arms race in which they compete for limited resources and niche space. The outcome of this intense interaction is the evolution of a powerful arsenal of biological weapons. Perhaps the most studied of these are colicins, plasmid-based toxins produced by and active against Escherichia coli. The present study was designed to explore the molecular responses of a colicin-producing strain during serial transfer evolution. What evolutionary changes occur when colicins are produced with no target present? Can killing ability be maintained in the absence of a target? To address these, and other, questions, colicinogenic strains and a noncolicinogenic ancestor were evolved for 253 generations. Samples were taken throughout the experiment and tested for killing ability. By the 38th transfer, a decreased killing ability and an increase in fitness were observed in the colicin-producing strains. Surprisingly, DNA sequence determination of the colicin plasmids revealed no changes in plasmid sequences. However, a set of chromosomally encoded loci experienced changes in gene expression that were positively associated with the reduction in killing. The most significant expression changes were observed in DNA repair genes (which were downregulated in the evolved strains), Mg ion uptake genes (which were upregulated), and late prophage genes (which were upregulated). These results indicate a fine-tuned response to the evolutionary pressures of colicin production, with far more genes involved than had been anticipated

Ecological Impacts of Nitrogen Deposition, Drought and Nonnative Plant Invasion on Coastal Sage Scrub of the Santa Monica Mountains

Multiple drivers of global environmental change increasingly threaten native ecosystems, including atmospheric pollution and resulting changes in climate and nutrient cycling, and the globalization of species. These factors may also have complex and interactive ecological effects. Nitrogen (N) deposition, the input of reactive N from the atmosphere to the earth’s surface, is increasing dramatically worldwide due to anthropogenic air pollution, with the potential to negatively impact terrestrial plant diversity. Elevated N deposition may also interact with other drivers of environmental change, for example by promoting the invasion of nonnative plant species, or increasing plant susceptibility to drought or other secondary stressors. Perhaps nowhere in the U.S. is this of more immediate environmental concern than in southern California, which is a global hotspot of biodiversity and one of the most air-polluted and populous parts of the country. High levels of N deposition have been implicated in the widespread conversion of coastal sage scrub (CSS) to annual grasslands dominated by nonnative grasses and forbs. The Santa Monica Mountains National Recreation Area of southern California protects a substantial area of remaining CSS, but due to the park’s proximity to the City of Los Angeles, stands of CSS nearest urban areas may be subject to high levels of N deposition. The state of California is also in the midst of a record-breaking drought, beginning in 2011, and this may exacerbate the negative impacts of N deposition and nonnative plant species. The objective of this work is to explore the effects of N deposition, drought and nonnative plant invasion on CSS of the Santa Monica Mountains at multiple ecologically relevant scales. I explored relationships of atmospheric N pollution and N deposition with native plant richness and cover of nonnative species at the landscape level, finding N deposition reduces richness of native herbaceous species and is associated with higher nonnative cover. I also investigated the impact of multiple realistic levels of N addition on CSS in a field fertilization experiment on the low end of the N deposition gradient during a period that coincided with the California drought. Through this experiment, I demonstrated increased N availability may reduce water-use efficiency and drought tolerance of native shrubs, resulting in increased dieback, while concomitantly favoring nonnative annual species. Finally, I explored the role of the soil microbial community in mediating impacts of these factors on native and nonnative plant species, finding that N-impacted soil communities may provide less protection against drought in native shrub seedlings and increase growth of invasive plant species. Collectively, these results illustrate the significant ecological threat of increased N deposition on the severely threated CSS of southern California, and potential interactions with other drivers of global change such as extreme drought, and nonnative plant invasion

Exploring the effects of proteorhodopsin on the physiology of native and heterologous hosts

Thesis: Ph. D. in Environmental Biology, Massachusetts Institute of Technology, Department of Civil and Environmental Engineering, 2016.Cataloged from PDF version of thesis.Includes bibliographical references (pages 131-145).Photoheterotrophic microbes use proteorhodopsin (PR) and other types of microbial rhodopsin photosystems to harness energy directly from sunlight. This thesis explores the photophysiology of PR in the context of a natural marine isolate, Dokdonia sp. strain MED 134, and by establishing Escherichia coli as a heterologous host to experimentally determine conditions under which the PR photosystem is capable of enhancing growth rate and yield. In Dokdonia sp. MED 134, PR and 11 other genes were discovered to be significantly induced by light but the induction of these genes increased growth rate and yield in an extremely carbon-limited environment; in richer media the induction of the genes by light had an inhibitory effect on growth. In E. coli, various genetic backgrounds were tested with PR expression, and one was discovered to exhibit slightly higher cell yields presumably as a result of light-driven proton pumping by PR. This work illustrates that PR is part of orchestrated response to light in a PR-containing isolate, but can also influence the growth of a heterologous host on its own. Further refinement of the genetic background of E. coli should unlock the full potential of PR as a cellular energy source for biotechnological applications-at least within this organism.by Michael Valliere.Ph. D. in Environmental Biolog

Ecological Impacts of Nitrogen Deposition, Drought and Nonnative Plant Invasion on Coastal Sage Scrub of the Santa Monica Mountains

Multiple drivers of global environmental change increasingly threaten native ecosystems, including atmospheric pollution and resulting changes in climate and nutrient cycling, and the globalization of species. These factors may also have complex and interactive ecological effects. Nitrogen (N) deposition, the input of reactive N from the atmosphere to the earth’s surface, is increasing dramatically worldwide due to anthropogenic air pollution, with the potential to negatively impact terrestrial plant diversity. Elevated N deposition may also interact with other drivers of environmental change, for example by promoting the invasion of nonnative plant species, or increasing plant susceptibility to drought or other secondary stressors. Perhaps nowhere in the U.S. is this of more immediate environmental concern than in southern California, which is a global hotspot of biodiversity and one of the most air-polluted and populous parts of the country. High levels of N deposition have been implicated in the widespread conversion of coastal sage scrub (CSS) to annual grasslands dominated by nonnative grasses and forbs. The Santa Monica Mountains National Recreation Area of southern California protects a substantial area of remaining CSS, but due to the park’s proximity to the City of Los Angeles, stands of CSS nearest urban areas may be subject to high levels of N deposition. The state of California is also in the midst of a record-breaking drought, beginning in 2011, and this may exacerbate the negative impacts of N deposition and nonnative plant species. The objective of this work is to explore the effects of N deposition, drought and nonnative plant invasion on CSS of the Santa Monica Mountains at multiple ecologically relevant scales. I explored relationships of atmospheric N pollution and N deposition with native plant richness and cover of nonnative species at the landscape level, finding N deposition reduces richness of native herbaceous species and is associated with higher nonnative cover. I also investigated the impact of multiple realistic levels of N addition on CSS in a field fertilization experiment on the low end of the N deposition gradient during a period that coincided with the California drought. Through this experiment, I demonstrated increased N availability may reduce water-use efficiency and drought tolerance of native shrubs, resulting in increased dieback, while concomitantly favoring nonnative annual species. Finally, I explored the role of the soil microbial community in mediating impacts of these factors on native and nonnative plant species, finding that N-impacted soil communities may provide less protection against drought in native shrub seedlings and increase growth of invasive plant species. Collectively, these results illustrate the significant ecological threat of increased N deposition on the severely threated CSS of southern California, and potential interactions with other drivers of global change such as extreme drought, and nonnative plant invasion

A review of shellfish restoration and management projects in Rhode Island

Shellfish management and restoration efforts in Rhode Island date back to the late 19th century. From the late 1890s to the Second World War the Rhode Island Fisheries Commission operated a lobster hatchery in Wickford Harbor in response to a perceived decline in lobster catches in Narragansett Bay. Berried lobsters were collected, eggs hatched, larvae reared, and postlarval fifth stage juveniles were released to the bay. The project was discontinued primarily because of costs and a failure to demonstrate the efficacy of juvenile seeding in improving lobster catches. From the 1930s to the 1980s, there have been several similar efforts to establish hatcheries to produce juvenile bivalve mollusks for public and private reseeding efforts, but none of these efforts were economically sustainable. The longest running efforts to improve shellfisheries have been state programs to relay northern quahogs, Mercenaria mercenaria, from dense population assemblages in waters closed to shellfishing. Large-scale relays began in the 1950s in response to heavy fishing pressure but ended in the 1960s when commercial power dredging for shellfish was banned in Narragansett Bay. A small-scale state program existing since the late 1970s pays a modest fee to supervised shellfishers for hand digging quahogs in closed waters and planting them in management areas for depuration and eventual harvest. The amounts of shellfish relayed annually has varied widely since 1977, ranging between 7 and 322 metric tonnes, with an average of 98 metric tonnes per year. A new relay program has been underway since 1997. It involves assessing the shellfish stocks in the closed Providence River and hiring dredge boats to relay shellfish into down bay management areas. Based on maximum sustainable yield (MSY) considerations, annual relays should not exceed 10.3% of the standing crop (or 2721 metric tonnes) in the Providence River. An effort to restore lobsters onto monitored artificial reefs is underway using settlement funds from a 1989 oil spill in Narragansett Bay. Finally, the Rhode Island Public Benefit Aquaculture Project, a joint educational effort with commercial fisheries involvement, is involving secondary level students in the nursery culture of shellfish (though marina-based upwellers) for seeding of public shellfish beds

Rotational excitation of carbon dioxide due to collision with a liquid surface [abstract]

Abstract only availableTo improve our understanding of collisional energy transfer at a gas-liquid interface, we have investigated collisions of carbon dioxide molecules with a simple atomic liquid surface. Our particular focus here is on the transfer of the impinging molecules' initial kinetic energy to its rotational degrees of freedom. In these simulations, CO2 molecules are treated as rigid rotors, thus permitting unambiguous isolation of the fraction of the initial (purely translational) kinetic energy flowing into rotations. The first phase of this work involved modifying the molecular dynamics code to incorporate molecular species rather than atoms as impinging particles and the evaluation of the rotational state of the molecules after leaving the surface.DOD MURI grant managed by the Army Research Offic

Web-based inventory tracking system

The Technical Event Services (TES), which is the primary provider of equipment and services to support Sun's trade show presence, at Sun Microsystems was analyzed, and it was determined that the TES group needed a more efficient way of tracking their trade show equipment. Originally it was tracked by e-mail and paper documents. Our system is a Web Inventory Tracking System (WITS). The system replaces the current method of tracking equipment. The process and methodology used to develop this system are located in this document

Vorrichtung und Verfahren zur entfernungsaufgelösten Bestimmung eines physikalischen Parameters in einer Messumgebung

Beschrieben wird eine Vorrichtung sowie ein Verfahren zur entfernungsaufgelösten Bestimmung eines physikalischen Parameters in einer Messumgebung unter Nutzung einer zerstörungsfreien Prüftechnik mit wenigstens einem Mikrowellen-Sensor-Paar, das einen ersten und zweiten Mikrowellen-Sensor umfasst, die in einem ersten vorgegebenen Abstand zueinander längs einer gemeinsamen Messebene angeordnet sind und jeweils eine Sende- und Empfangsapertur aufweisen, die innerhalb eines der Messumgebung zugewandten Halbraumes überlappen, einem ortsauflösenden optischen Sensor mit einer zumindest teilweise den Bereich der überlappenden Sende- und Empfangsaperturen des wenigstens einen Mikrowellen-Sensor-Paars erfassenden Sensorapertur, einer Datenerfassungseinheit, die in einer Datenverbindung mit dem wenigstens einen Mikrowellen-Sensor-Paar sowie dem ortsauflösenden optischen Sensor steht, in der Mikrowellen-Sensor-Daten sowie optische Sensordaten erfassbar sind sowie einer Auswerteinheit, in der die erfassten Mikrowellen-Sensor-Daten auf der Grundlage der optischen Sensordaten zur entfernungsaufgelösten Bestimmung des physikalischen Parameters auswertbar sind