Predicting chemical environments of bacteria from receptor signaling

Sensory systems have evolved to respond to input stimuli of certain statistical properties, and to reliably transmit this information through biochemical pathways. Hence, for an experimentally well-characterized sensory system, one ought to be able to extract valuable information about the statistics of the stimuli. Based on dose-response curves from in vivo fluorescence resonance energy transfer (FRET) experiments of the bacterial chemotaxis sensory system, we predict the chemical gradients chemotactic Escherichia coli cells typically encounter in their natural environment. To predict average gradients cells experience, we revaluate the phenomenological Weber's law and its generalizations to the Weber-Fechner law and fold-change detection. To obtain full distributions of gradients we use information theory and simulations, considering limitations of information transmission from both cell-external and internal noise. We identify broad distributions of exponential gradients, which lead to log-normal stimuli and maximal drift velocity. Our results thus provide a first step towards deciphering the chemical nature of complex, experimentally inaccessible cellular microenvironments, such as the human intestine.Comment: DG and GM contributed equally to this wor

Biotic and abiotic factors contributing to the invasion success of microstegium vimineum in eastern deciduous forests.

Forest managers face multiple challenges in maintaining woodland systems, including climate change, habitat destruction and fragmentation, and the invasion of novel species. Invaders can change microclimates, alter nutrient cycling and understory habitat, and outcompete native species, leading to native species population declines and reduction in species richness. To effectively combat plant invasions it is necessary to first understand factors contributing to invasive species spread, including the complex interactions between invaders and native biota. This dissertation investigates the abiotic conditions and biotic interactions associated with invasion success of the non-native grass Microstegium vimineum, which is a species of great concern for forest managers throughout the eastern US. My initial study identified the most important abiotic elements associated with Microstegium presence. I found light availability and soil moisture to be the strongest predictors of Microstegium cover, followed by soil nitrogen and soil phosphorous. In this study I also examined the relationship between Microstegium and soil arbuscular mycorrhizae. I found no differences in abundance of soil mycorrhizae between invaded and noninvaded areas, and no difference in root colonization of Microstegium across abiotic gradients. My second study analyzed the germination and growth of Microstegium, native grasses, and native woody species in field soils associated with Microstegium invasion. I found that Microstegium-associated soils enhanced Microstegium seed germination, while inhibiting the germination of native grass species. Surprisingly, I found greater aboveground biomass and stem height of native woody species in Microstegium-associated soils; however, I also found increased seedling mortality in Microstegium-associated soils. For my final study, I surveyed Microstegium invasion at the landscape scale in seven local nature reserves to create a habitat suitability analysis using Geographic Information System (GIS) processing. I combined various habitat variables indicative of Microstegium presence to identify areas of greatest habitat suitability. These findings can inform best practices for prevention and eradication of Microstegium. For example, the creation of a habitat suitability analysis for a nature reserve, coupled with the knowledge of the importance of various abiotic factors to Microstegium presence, can assist land managers to direct limited resources to areas of highest susceptibility to invasion or to mitigate population spread

Evolution of chemotaxis in stochastic environments

Most of our understanding of bacterial chemotaxis comes from studies of Escherichia coli. However, recent evidence suggests significant departures from the E. coli paradigm in other bacterial species. In the first part of this work, we argue that the observed departures may stem from different species inhabiting distinct environments and thus adapting differently to specific environmental pressures. We therefore study the performance of various chemotactic strate¬gies under a range of stochastic time- and space-varying attractant distributions in silico. We describe a novel type of response in which the bacterium tumbles more when attractant concen¬tration is increasing, in contrast to the “adaptive” response of E. coli, and demonstrate how this response explains the behavior of aerobically-grown Rhodobacter sphaeroides. In this “specu¬lator” response, bacteria compare the current attractant concentration to the long-term average. By tumbling persistently when the current concentration is higher than the average, bacteria maintain their position in regions of high attractant concentration. If the current concentration is lower than the average, or is declining, bacteria swim away in search of more favorable con¬ditions. When the attractant distribution is spatially complex but slowly-changing, this response is as effective as that of E. coli. In the latter part of this work, we show that optimal response sensitivity is high for both adaptive and speculator responses. We argue that response sensi¬tivity would increase over long evolutionary timescales and show that increases in response sensitivity could drive the evolution of adaptive and speculator responses

Science-based restoration monitoring of coastal habitats, Volume Two: Tools for monitoring coastal habitats

Healthy coastal habitats are not only important ecologically; they also support healthy coastal communities and improve the quality of people’s lives. Despite their many benefits and values, coastal habitats have been systematically modified, degraded, and destroyed throughout the United States and its protectorates beginning with European colonization in the 1600’s (Dahl 1990). As a result, many coastal habitats around the United States are in desperate need of restoration. The monitoring of restoration projects, the focus of this document, is necessary to ensure that restoration efforts are successful, to further the science, and to increase the efficiency of future restoration efforts

Beneath the Bottom Line: Agricultural Approaches To Reduce Agrichemical Contamination of Groundwater

The report discusses contamination of the hydrogeological system (a primer), technologies to improve nutrient and pest management, farmer decision-making and technical assistance to reduce agrichemical contamination of groundwater, and public influences on agrichemical contamination of groundwater

Precision Agriculture Technology for Crop Farming

This book provides a review of precision agriculture technology development, followed by a presentation of the state-of-the-art and future requirements of precision agriculture technology. It presents different styles of precision agriculture technologies suitable for large scale mechanized farming; highly automated community-based mechanized production; and fully mechanized farming practices commonly seen in emerging economic regions. The book emphasizes the introduction of core technical features of sensing, data processing and interpretation technologies, crop modeling and production control theory, intelligent machinery and field robots for precision agriculture production

Fish behavior and its use in the capture and culture of fishes

Fishery management, Behaviour, Food fish, Fish culture, Conferences

Precision Agriculture Technology for Crop Farming

This book provides a review of precision agriculture technology development, followed by a presentation of the state-of-the-art and future requirements of precision agriculture technology. It presents different styles of precision agriculture technologies suitable for large scale mechanized farming; highly automated community-based mechanized production; and fully mechanized farming practices commonly seen in emerging economic regions. The book emphasizes the introduction of core technical features of sensing, data processing and interpretation technologies, crop modeling and production control theory, intelligent machinery and field robots for precision agriculture production