DENITRIFICATION IN SOILS: FROM GENES TO ENVIRONMENTAL OUTCOMES

Denitrification is an important process of global nitrogen cycle as it removes reactive nitrogen from the biosphere, and acts as the primary source of nitrous oxide (N2O). This thesis seeks to gain better understanding of the biogeochemistry of denitrification by investigating the process from four different aspects: genetic basis, enzymatic kinetics, environmental interactions, and environmental consequences. Laboratory and field experiments were combined with modeling efforts to unravel the complexity of denitrification process under microbiological and environmental controls. Dynamics of denitrification products observed in laboratory experiments revealed an important role of constitutive denitrification enzymes, whose presence were further confirmed with quantitative analysis of functional genes encoding nitrite reductase and nitrous oxide reductase. A metabolic model of denitrification developed with explicit denitrification enzyme kinetics and representation of constitutive enzymes successfully reproduced the dynamics of N2O and N2 accumulation observed in the incubation experiments, revealing important regulatory effect of denitrification enzyme kinetics on the accumulation of denitrification products. Field studies demonstrated complex interaction of belowground N2O production, consumption and transport, resulting in two pulse pattern in the surface flux. Coupled soil gas diffusion/denitrification model showed great potential in simulating the dynamics of N2O below ground, with explicit representation of the activity of constitutive denitrification enzymes. A complete survey of environmental variables showed distinct regulation regimes on the denitrification activity from constitutive enzymes and new synthesized enzymes. Uncertainties in N2O estimation with current biogeochemical models may be reduced as accurate simulation of the dynamics of N2O in soil and surface fluxes is possible with a coupled diffusion/denitrification model that includes explicit representation of denitrification enzyme kinetics. In conclusion, denitrification is a complex ecological function regulated at cellular level. To assess the environmental consequences of denitrification and develop useful tools to mitigate N2O emissions require a comprehensive understanding of the regulatory network of denitrification with respect to microbial physiology and environmental interactions.

Lessons from Two Decades of Hanta Virus Research

Dr. Richard J. Douglass has been conducting small mammal field studies since 1968. For the past 19 years he has been conducting field studies on the ecology of deer mice and hantavirus in Montana, Panama, and Argentina. He has published papers on mammals from rodents to large ungulates. He has been conducting student field trips at Montana Tech since 1983.

A Geological Report on South Boulder Canyon and The Mayflower Mine-Renova Areas

The purpose of this report is to serve as a written explanation of the accompanying geologic maps and columnar sec­tion. Each year the senior students in mining and geological engineering at the Montana School of Mines spend two weeks in the field where they learn the fundamentals of geologic mapping and related field studies. An additional week is spent at the school where maps are assembled, prints made, end other work is done in preparation for the writing of the report.

Landmark-based augmented reality system for paranasal and transnasal endoscopic surgeries

BACKGROUND: In this paper we present a landmark-based augmented reality (AR) endoscope system for endoscopic paranasal and transnasal surgeries along with fast and automatic calibration and registration procedures for the endoscope. METHODS: Preoperatively the surgeon selects natural landmarks or can define new landmarks in CT volume. These landmarks are overlaid, after proper registration of preoperative CT to the patient, on the endoscopic video stream. The specified name of the landmark, along with selected colour and its distance from the endoscope tip, is also augmented. The endoscope optics are calibrated and registered by fast and automatic methods. Accuracy of the system is evaluated in a metallic grid and cadaver set-up. RESULTS: Root mean square (RMS) error of the system is 0.8 mm in a controlled laboratory set-up (metallic grid) and was 2.25 mm during cadaver studies. CONCLUSIONS: A novel landmark-based AR endoscope system is implemented and its accuracy is evaluated. Augmented landmarks will help the surgeon to orientate and navigate the surgical field. Studies prove the capability of the system for the proposed application. Further clinical studies are planned in near future.

Induction of lucid dreams: A systematic review of evidence

In lucid dreams the dreamer is aware of dreaming and often able to influence the ongoing dream content. Lucid dreaming is a learnable skill and a variety of techniques is suggested for lucid dreaming induction. This systematic review evaluated the evidence for the effectiveness of induction techniques. A comprehensive literature search was carried out in biomedical databases and specific resources. Thirty-five studies were included in the analysis (11 sleep laboratory and 24 field studies), of which 26 employed cognitive techniques, 11 external stimulation and one drug application. The methodological quality of the included studies was relatively low. None of the induction techniques were verified to induce lucid dreams reliably and consistently, although some of them look promising. On the basis of the reviewed studies, a taxonomy of lucid dream induction methods is presented. Several methodological issues are discussed and further directions for future studies are proposed.

Action crisis and cost–benefit thinking: A cognitive analysis of a goal-disengagement phase

The present research is based on the notion that disengagement from goals is not a discrete event but a process (Klinger, 1975). A critical phase in this process is when difficulties and setbacks in striving for a goal accumulate. This critical phase is termed here as an action crisis. Given the profound effects that people's thoughts have on their self-regulatory efficiency, it is essential to understand the cognitive correlates of an action crisis. In two experimental lab and two correlational field studies, the hypothesis that goal-related costs and benefits become cognitively highly accessible during an action crisis was tested and supported. Participants who were experiencing an action crisis in such diverse goal areas as intimate relationships, sports, and university studies, thought about goal-related costs and benefits more intensively and frequently in comparison to participants who were not in an action crisis. In an incidental learning task they recognized more of cost–benefit-items and less of implementation-items than the control group. Results are interpreted in terms of action phase specific mindsets (Gollwitzer, 1990, 2012).

The Struggle of Giving Up Personal Goals – Affective, Physiological, and Cognitive Consequences of an Action Crisis.

A critical phase in goal striving occurs when setbacks accumulate and goal disengagement becomes an issue. This critical phase is conceptualized as an action crisis and assumed to be characterized by an intrapsychic conflict in which the individual becomes torn between further goal pursuit and goal disengagement. Our theorizing converges with Klinger’s conceptualization of goal disengagement as a process, rather than a discrete event. Two longitudinal field studies tested and found support for the hypothesis that an action crisis not only compromises an individual’s psychological and physiological well-being, but also dampens the cognitive evaluation of the respective goal. In Study 3, marathon runners experiencing an action crisis in their goal of running marathons showed a stronger cortisol secretion and a lower performance in the race 2 weeks later. Results are interpreted in terms of action-phase–specific mindsets with a focus on self-regulatory processes in goal disengagement.

Strategies for reducing fumigant loss to the atmosphere

A model is developed to describe transport and loss of methyl bromide (MeBr) in soil following application as a soil fumigant. The model is used to investigate the effect of soil and management factors on MeBr volatilization. Factors studied include depth of injection, soil water content, presence or absence of tarp, depth to downward barrier, and irrigation after injection. Of these factors, the most important was irrigation after injection followed by covering with the tarp, which increased the diffusive resistance of the soil and prevented early loss of MeBr. The model offers an explanation for the apparently contradictory observations of earlier field studies of MeBr volatilization from soils under different conditions. The model was also used to calculate the concentration-time index for various management alternatives, showing that the irrigation application did not make the surface soil more difficult to fumigate, except at very early times. Therefore, irrigation shows promise for reducing fumigant loss while at the same time permitting control of target organisms during fumigation.

PCR-based assay using occult blood detection cards for detection of diarrheagenic Escherichia coli in specimens from U.S. travelers to Mexico with acute diarrhea.

Large field studies of travelers' diarrhea for multiple destinations are limited by the need to perform stool cultures on site in a timely manner. A method for the collection, transport, and storage of fecal specimens that does not require immediate processing and refrigeration and that is stable for months would be advantageous. This study was designed to determine if enterotoxigenic Escherichia coli (ETEC) and enteroaggregative E. coli (EAEC) DNA could be identified from cards that were processed for the evaluation of fecal occult blood. U.S. students traveling to Mexico during 2005 to 2007 were monitored for the occurrence of diarrheal illness. When ill, students provided a stool specimen for culture and occult blood by the standard methods. Cards then were stored at room temperature prior to DNA extraction. Fecal PCR was performed to identify ETEC and EAEC in DNA extracted from stools and from occult blood cards. Significantly more EAEC cases were identified by PCR that was performed on DNA that was extracted from cards (49%) or from frozen feces (40%) than from culture methods that used HEp-2 adherence assays (13%) (P < 0.001). Similarly, more ETEC cases were detected from card DNA (38%) than from fecal DNA (30%) or by culture that was followed by hybridization (10%) (P < 0.001). The sensitivity and specificity of the card test were 75 and 62%, respectively, compared to those for EAEC by culture and were 50 and 63%, respectively, compared to those for ETEC. DNA extracted from fecal cards that was used for the detection of occult blood is of use in identifying diarrheagenic E. coli.

To boldly go: individual differences in boldness influence migratory tendency

Partial migration, whereby only a fraction of the population migrates, is thought to be the most common type of migration in the animal kingdom, and can have important ecological and evolutionary consequences. Despite this, the factors that influence which individuals migrate and which remain resident are poorly understood. Recent work has shown that consistent individual differences in personality traits in animals can be ecologically important, but field studies integrating personality traits with migratory behaviour are extremely rare. In this study, we investigate the influence of individual boldness, an important personality trait, upon the migratory propensity of roach, a freshwater fish, over two consecutive migration seasons. We assay and individually tag 460 roach and show that boldness influences migratory propensity, with bold individuals being more likely to migrate than shy fish. Our data suggest that an extremely widespread personality trait in animals can have significant ecological consequences via influencing individual-level migratory behaviour.

Investigating Peatland Stratigraphy and Hydrogeology Using Integrated Electrical Geophysics

Hydrology has been suggested as the mechanism controlling vegetation and related surficial pore-water chemistry in large peatlands. Peatland hydrology influences the carbon dynamics within these large carbon reservoirs and will influence their response to global warming. A geophysical survey was completed in Caribou Bog, a large peatland in Maine, to evaluate peatland stratigraphy and hydrology. Geophysical measurements were integrated with direct measurements of peat stratigraphy from probing, fluid chemistry, and vegetation patterns in the peatland. Consistent with previous field studies, ground-penetrating radar (GPR) was an excellent method for delineating peatland stratigraphy. Prominent reflectors from the peat-lake sediment and lake sediment-mineral soil contacts were precisely recorded up to 8 m deep. Two-dimensional resistivity and induced polarization imaging were used to investigate stratigraphy beneath the mineral soil, beyond the range of GPR. We observe that the peat is chargeable, and that IP imaging is an alternative method for defining peat thickness. The chargeability of peat is attributed to the high surface-charge density on partially decomposed organic matter. The electrical conductivity imaging resolved glaciomarine sediment thickness (a confining layer) and its variability across the basin. Comparison of the bulk conductivity images with peatland vegetation revealed a correlation between confining layer thickness and dominant vegetation type, suggesting that stratigraphy exerts a control on hydrogeology and vegetation distribution within this peatland. Terrain conductivity measured with a Geonics EM31 meter correlated with confining glaciomarine sediment thickness and was an effective method for estimating variability in glaciomarine sediment thickness over approximately 18 km(2). Our understanding of the hydrogeology, stratigraphy, and controls on vegetation growth in this peatland was much enhanced from the geophysical study.

Significant Contribution of Large Particles to Optical Backscattering in the Open Ocean

The light scattering properties of oceanic particles have been suggested as an alternative index of phytoplankton biomass than chlorophyll-a concentration (chl-a), with the benefit of being less sensitive to physiological forcings (e.g., light and nutrients) that alter the intracellular pigment concentrations. The drawback of particulate scattering is that it is not unique to phytoplankton. Nevertheless, field studies have demonstrated that, to first order, the particulate beam-attenuation coefficient (c(p)) can track phytoplankton biomass. The relationship between c(p) and the particulate backscattering coefficient (b(bp)), a property retrievable from space, has not been fully evaluated, largely due to a lack of open-ocean field observations. Here, we present extensive data on inherent optical properties from the Equatorial Pacific surface waters and demonstrate a remarkable coherence in b(bp) and c(p). Coincident measurements of particle size distributions (PSDs) and optical properties of size-fractionated samples indicate that this covariance is due to both the conserved nature of the PSD and a greater contribution of phytoplankton-sized particles to b(bp) than theoretically predicted. These findings suggest that satellite-derived b(bp)could provide similar information on phytoplankton biomass in the open ocean as c(p).

Kelp Beds as Habitat for American Lobster Homarus Americanus

The American lobster Homarus americanus and kelp Laminaria longicruris and L. saccharina are prominent and often intimately associated members of the subtidal community in the western North Atlantic Ocean. However, no one has identified the nature of this relationship or specifically investigated whether kelp beds are a superior habitat for lobsters. We conducted field studies in 1990 and 1991 at a coastal site centrally located along the Gulf of Maine, USA, to determine how lobsters use kelp beds as habitat. Identically sized and spaced plots of live and artificial (plastic) kelp were established and monitored for lobster population densities. Adjacent featureless sediment plots of identical size served as controls. Lobster population density and biomass were significantly higher in both real and artificial kelp treatments than in non-kelp control plots (p < 0.0001). The change in lobster density was apparent the day following placement of the experiment, so a secondary trophic effect such as attracting prey into treatments is unlikely to have occurred. Thus, kelp beds can affect local lobster population densities by providing shelter for lobsters, thereby concentrating individuals and increasing the local carrying capacity of potential lobster habitats. The effect of kelp beds on the local carrying capacity of lobster habitats was further explored by testing how lobsters respond to differing patch sizes. A graded size series of circular patches of artificial kelp was established, in which kelp blade density and total area were held constant for each treatment. Treatments were subdivided into four 1 M2, two 2 M2, or one 4 m2 patches. Experiments were surveyed for lobster population density and size structure to determine ff statistical differences existed among treatments. Lobster density was significantly greater in the smallest patches (p < 0.001). Moreover, lobsters typically occupied the edges of kelp beds, and their abundance within kelp patches corresponded to the patch's perimeter-to-area relationship. This suggests that edge effects' influence the local carrying capacity for lobsters by influencing the lobsters' choice of kelp beds as habitat.

Satellite-Detected Fluorescence Reveals Global Physiology of Ocean Phytoplankton

Phytoplankton photosynthesis links global ocean biology and climate-driven fluctuations in the physical environment. These interactions are largely expressed through changes in phytoplankton physiology, but physiological status has proven extremely challenging to characterize globally. Phytoplankton fluorescence does provide a rich source of physiological information long exploited in laboratory and field studies, and is now observed from space. Here we evaluate the physiological underpinnings of global variations in satellite-based phytoplankton chlorophyll fluorescence. The three dominant factors influencing fluorescence distributions are chlorophyll concentration, pigment packaging effects on light absorption, and light-dependent energy-quenching processes. After accounting for these three factors, resultant global distributions of quenching-corrected fluorescence quantum yields reveal a striking consistency with anticipated patterns of iron availability. High fluorescence quantum yields are typically found in low iron waters, while low quantum yields dominate regions where other environmental factors are most limiting to phytoplankton growth. Specific properties of photosynthetic membranes are discussed that provide a mechanistic view linking iron stress to satellite-detected fluorescence. Our results present satellite-based fluorescence as a valuable tool for evaluating nutrient stress predictions in ocean ecosystem models and give the first synoptic observational evidence that iron plays an important role in seasonal phytoplankton dynamics of the Indian Ocean. Satellite fluorescence may also provide a path for monitoring climate-phytoplankton physiology interactions and improving descriptions of phytoplankton light use efficiencies in ocean productivity models.

Dynamic Activity-Related Incentives for Physical Activity.

The present studies adopted the theoretical framework of activity- and purpose-related incentives (Rheinberg, 2008) to explain the maintenance of physical activity. We hypothesized that activity-related incentives (e.g., “fun”) increase more than purpose-related incentives (e.g., “health”) between the initiation and maintenance phase of physical activity. Additionally, change in activity-related incentives was hypothesized to be a better predictor of maintenance of physical activity than change in purpose-related incentives. Two correlative field studies with rehabilitation patients (Study 1) and Nordic Walkers (Study 2) were conducted to test the hypotheses. Participants’ incentives of physical activity were measured at the beginning of exercising and two weeks (Study 1; T2) and three months (Study 2; T2) later. At T2, participants were asked for their current physical activity. Both studies showed a greater change of activity-related incentives than purpose-related incentives. Furthermore, change in activity-related incentives was more predictive of the maintenance of physical activity than change in purpose-related incentives. The results showed the important role of activity-related incentives in maintenance of physical activity. The theoretical contribution to physical activity maintenance research and practical implications for health promotion programs were discussed.