New techniques for the remote sensing of foliar nitrogen concentration in forest ecosystems.

During my Doctoral study I researched about the remote detection of canopy N concentration in forest stands, its potentials and problems, under many overlapping perspectives. The study consisted of three parts. In S. Rossore 2000 dataset analysis, I tested regressions between N concentration and NIR reflectances derived from different sources (field samples, airborne and satellite sensors). The analysis was further expanded using a larger dataset acquired in year 2009 as part of a new campaign funded by the ESA. In both cases, a good correlation was observed between Landsat NIR, using both TM (2009) and ETM+ (2000) imagery, and N concentration measured by a CHN elemental analyzer. Concerning airborne sensors I did not obtain the same good results, mainly because of the large FOV of the two instruments, and to the anisotropy of vegetation reflectance. We also tested the relation between ground based ASD measures and nitrogen concentration, obtaining really good results. Thus, I decided to expand my study to the regional level, focusing only on field and satellite measures. I analyzed a large dataset for the whole of Catalonia, Spain; MODIS imagery was used, in consideration of its spectral characteristics and despite its rather poor spatial resolution. Also in this case a regression between nitrogen concentration and reflectances was found, but not so good as in previous experiences. Moreover, vegetation type was found to play an important role in the observed relationship. We concluded that MODIS is not the most suitable satellite sensor in realities like Italy and Catalonia, which present a patchy and inhomogeneous vegetation cover; so it could be utilized for the parameterization of eco-physiological and biogeochemical models, but not for really local nitrogen estimate. Thus multispectral sensors similar to Landsat Thematic Mapper, with better spatial resolution, could be the most appropriate sensors to estimate N concentration.

Entwicklung einer Thermodesorptionseinheit für die GC/MS zur Bestimmung hochreaktiver, biogener Kohlenwasserstoffe und deren Anwendung im Rahmen von Labor- und Feldstudien

Flüchtige organische Verbindungen (volatile organic compounds, VOCs), besonders rnTerpene, gelten als Vorläufer des sekundären organischen Aerosols (secondary rnorganic aerosols, SOA). Terpene werden von Pflanzen zur Abwehr oder zur rnAttraktion von Bestäubern emittiert. Ungesättigten Verbindungen, wie Sesquiterpene, rnsind sehr ozonolyseempfindlich und weisen nur geringe Konzentrationen in der rnAtmosphäre auf. Zudem lassen sie sich mit handelsüblichen rnThermodesorptionseinheiten meist nicht ohne Artefakte nachweisen, da sie eine hohe rnReaktivität mit vielen Oberflächen zeigen. rnDiese Arbeit präsentiert Forschungsergebnisse der qualitativen und rn(semi)quantitativen Auswertungen flüchtiger organischer Verbindungen in rnLaborstudien und biogenen Emissionsproben (Feldmessungen) mittels rnThermodesorption-Gaschromatographie-Massenspektrometrie (TD-GC/MS). Speziell rnzur Analyse hochreaktiver Verbindungen wurde eine Thermodesorptionseinheit für die rnGC/MS entwickelt. Diese besteht aus einer Kryofokussierung, einem Desorptionsofen rnund einer Heizung. Die Steuerung erfolgt über eine eigens dafür geschaffene rnBedienoberf läche von Labview® an einem PC über eine nachgeschaltete SPS rn(speicherprogrammierbare Steuerung). Das komplette Desorptionsprogramm und der rnStart der GC/MS-Analyse wurden automatisiert. rnDie Quantifizierung alle Proben wurde über Diffusionsquellen und rnVergleichsmessungen durch auf Adsorptionsröhrchen aufgebrachte rnVerdünnungsreihen realisiert. Um Informationen über die mutmaßlichen Vorläufer des rnsekundären organischen Aerosols zu erhalten, wurde zudem eine Ozon-Scrubber-rnMethode basierend auf Propen entwickelt. Diese wurde anhand von Standards in einer rnReaktionskammer getestet und in Feldmessungen erfolgreich angewendet. rnQuantitative Analysen zeigen, dass die meisten Terpene so vollständig vor der rnOzonolyse bewahrt werden können. Für hochreaktive Analyte wie α-Humulen oder rnβ-Caryophyllen wurden Wiederfindungsraten von über 80 % erreicht. So konnte die rnTemperaturabhängigkeit der Terpen-Emissionen der Fichte (Picea abies) in rnFeldmessungen nachgewiesen werden. rnEine weitere Anwendungsmöglichkeit wurde mit der Unterscheidung verschiedener rnArten der gleichen Gattung anhand der Emissionsmuster und der möglichen rnAbgrenzung verschiedener Bestäubertypen am Beispiel der Gattung Salvia untersucht. rnDie Emissionsanalysen zeigen, dass eine Zuordnung der Verwandtschaftsverhältnisse rnzusätzlich zu anderen Vergleichen möglich ist. Das gleiche gilt für die Differenzierung rnvon Bestäubertypen. Die Ergebnisse der Feldmessungen wurden durch rnMethodenvergleich zwischen biogenen Emissionsmessungen mit anschließender rnTD-GC/MS-Analyse und Extraktionen der jeweiligen Blüten/Blätter mit rnanschließender GC/MS-Messung bestätigt.

A Preliminary Study of the Ostracoda of the Big Snowy Group, Mississippian, of Montana.

In the field, samples were taken vertically and horizon­tally along the various outcrops in different sections of central and south-central Montana. At important localities the samples were taken about every half-foot verti­cally; in other sections they were taken every few feet.

Continuous monitoring of bovine spongiform encephalopathy rapid test performance by weak positive tissue controls and quality control charts

Bovine spongiform encephalopathy (BSE) rapid tests and routine BSE-testing laboratories underlie strict regulations for approval. Due to the lack of BSE-positive control samples, however, full assay validation at the level of individual test runs and continuous monitoring of test performance on-site is difficult. Most rapid tests use synthetic prion protein peptides, but it is not known to which extend they reflect the assay performance on field samples, and whether they are sufficient to indicate on-site assay quality problems. To address this question we compared the test scores of the provided kit peptide controls to those of standardized weak BSE-positive tissue samples in individual test runs as well as continuously over time by quality control charts in two widely used BSE rapid tests. Our results reveal only a weak correlation between the weak positive tissue control and the peptide control scores. We identified kit-lot related shifts in the assay performances that were not reflected by the peptide control scores. Vice versa, not all shifts indicated by the peptide control scores indeed reflected a shift in the assay performance. In conclusion these data highlight that the use of the kit peptide controls for continuous quality control purposes may result in unjustified rejection or acceptance of test runs. However, standardized weak positive tissue controls in combination with Shewhart-CUSUM control charts appear to be reliable in continuously monitoring assay performance on-site to identify undesired deviations.

Multilocus sequence typing (MLST) of Mycoplasma hyopneumoniae: a diverse pathogen with limited clonality

A multilocus sequence typing (MLST) scheme was established and evaluated for Mycoplasma hyopneumoniae, the etiologic agent of enzootic pneumonia in swine with the aim of defining strains. Putative target genes were selected by genome sequence comparisons. Out of 12 housekeeping genes chosen and experimentally validated, the 7 genes efp, metG, pgiB, recA, adk, rpoB, and tpiA were finally used to establish the MLST scheme. Their usefulness was assessed individually and in combination using a set of well-defined field samples and strains of M. hyopneumoniae. A reduction to the three targets showing highest variation (adk, rpoB, and tpiA) was possible resulting in the same number of sequence types as using the seven targets. The established MLST approach was compared with the recently described typing method using the serine-rich repeat motif-encoding region of the p146 gene. There was coherence between the two methods, but MLST resulted in a slightly higher resolution. Farms recognized to be affected by enzootic pneumonia were always associated with a single M. hyopneumoniae clone, which in most cases differed from farm to farm. However, farms in close geographic or operational contact showed identical clones as defined by MLST typing. Population analysis showed that recombination in M. hyopneumoniae occurs and that strains are very diverse with only limited clonality observed. Elaborate classical MLST schemes using multiple targets for M. hyopneumoniae might therefore be of limited value. In contrast, MLST typing of M. hyopneumoniae using the three genes adk, rpoB, and tpiA seems to be sufficient for epidemiological investigations by direct amplification of target genes from lysate of clinical material without prior cultivation.

El sector nororiental de la Cuenca de Antepaís del Guadalquivir (Cordillera Bética, Mioceno Superior): estratigrafía, cronología y evolución sedimentaria

Estudios estratigráficos y sedimentológicos de afloramiento y el análisis paleoecológico y bioestratigráfico mediante foraminíferos, han permitido realizar una reinterpretación sedimentaria de las unidades de margas y areniscas miocenas del sector nororiental de la Cuenca del Guadalquivir. El relleno sedimentario ha sido dividido en cuatro unidades litoestratigráficas (I-IV), todas ellas depositadas durante el Tortoniense, entre 10 y 7.89 Ma, aproximadamente. La Unidad I (Tortoniense antiguo no basal) está fomada por arenas y calizas de algas, y es interpretada como una unidad transgresiva y expansiva sobre el basamento que evoluciona desde ambientes marinos someros a rampa de carbonatos tipo rhodalgal. La Unidad II (Tortoniense inferior, biozona MMi11: entre 10 y 9.54 Ma) está caracterizada por una alternancia rítmica de margas arcillosas y silíceas, depositadas en ambientes pelágicos y profundos de aguas frías-eutróficas, si bien con repetidos cambios en la estratificación y distribución de nutrientes en la columna de agua. Esta unidad registra una importante somerización en su parte superior, dando paso gradual a la Unidad III. La Unidad III (Tortoniense inferior, biozonaMMi11: desde 9.54 Ma) está dominada por areniscas, aunque lateralmente aparecen brechas intraformacionales con estratos contorsionados. Está nutrida por deltas desde la costa y se interpreta como el depósito de bancos arenosos movilizados por la acción de corrientes mareales y el oleaje de tormentas en rampas. La Unidad IV (Tortoniense superior, biozona MMi12: desde 8.35 Ma) está representada por margas pelágicas similares a las de la Unidad II, de la que difiere por la presencia de intercalaciones arenosas genéticamente relacionadas con procesos mareales y de tormentas.

Method Validation for Bacterial and Viral Analysis of Geoducks

Thesis (Master's)--University of Washington, 2016-06

Particle tracking in a salinity gradient: A method for measuring sinking rate of individual phytoplankton in the laboratory

This paper presents a new method to measure the sinking rates of individual phytoplankton “particles” (cells, chains, colonies, and aggregates) in the laboratory. Conventional particle tracking and high resolution video imaging were used to measure particle sinking rates and particle size. The stabilizing force of a very mild linear salinity gradient (1 ppt over 15 cm) prevented the formation of convection currents in the laboratory settling chamber. Whereas bulk settling methods such as SETCOL provide a single value of sinking rate for a population, this method allows the measurement of sinking rate and particle size for a large number of individual particles or phytoplankton within a population. The method has applications where sinking rates vary within a population, or where sinking rate-size relationships are important. Preliminary data from experiments with both laboratory and field samples of marine phytoplankton are presented here to illustrate the use of the technique, its applications, and limitations. Whereas this paper deals only with sinking phytoplankton, the method is equally valid for positively buoyant species, as well as nonbiological particles.

Discovery of "Warm Dust" galaxies in clusters at z ~ 0.3: evidence for stripping of cool dust in the dense environment?

Using far-infrared imaging from the "Herschel Lensing Survey," we derive dust properties of spectroscopically confirmed cluster member galaxies within two massive systems at z ~ 0.3: the merging Bullet Cluster and the more relaxed MS2137.3-2353. Most star-forming cluster sources (~90%) have characteristic dust temperatures similar to local field galaxies of comparable infrared (IR) luminosity (T_dust ~ 30 K). Several sub-luminous infrared galaxy (LIRG; L_IR < 10^11 L_☉) Bullet Cluster members are much warmer (T_dust > 37 K) with far-infrared spectral energy distribution (SED) shapes resembling LIRG-type local templates. X-ray and mid-infrared data suggest that obscured active galactic nuclei do not contribute significantly to the infrared flux of these "warm dust" galaxies. Sources of comparable IR luminosity and dust temperature are not observed in the relaxed cluster MS2137, although the significance is too low to speculate on an origin involving recent cluster merging. "Warm dust" galaxies are, however, statistically rarer in field samples (>3σ), indicating that the responsible mechanism may relate to the dense environment. The spatial distribution of these sources is similar to the whole far-infrared bright population, i.e., preferentially located in the cluster periphery, although the galaxy hosts tend toward lower stellar masses (M_* < 10^10 M_☉). We propose dust stripping and heating processes which could be responsible for the unusually warm characteristic dust temperatures. A normal star-forming galaxy would need 30%-50% of its dust removed (preferentially stripped from the outer reaches, where dust is typically cooler) to recover an SED similar to a "warm dust" galaxy. These progenitors would not require a higher IR luminosity or dust mass than the currently observed normal star-forming population.

Enhanced Volatile Organic Compounds emissions and organic aerosol mass increase the oligomer content of atmospheric aerosols

Secondary organic aerosol (SOA) accounts for a dominant fraction of the submicron atmospheric particle mass, but knowledge of the formation, composition and climate effects of SOA is incomplete and limits our understanding of overall aerosol effects in the atmosphere. Organic oligomers were discovered as dominant components in SOA over a decade ago in laboratory experiments and have since been proposed to play a dominant role in many aerosol processes. However, it remains unclear whether oligomers are relevant under ambient atmospheric conditions because they are often not clearly observed in field samples. Here we resolve this long-standing discrepancy by showing that elevated SOA mass is one of the key drivers of oligomer formation in the ambient atmosphere and laboratory experiments. We show for the first time that a specific organic compound class in aerosols, oligomers, is strongly correlated with cloud condensation nuclei (CCN) activities of SOA particles. These findings might have important implications for future climate scenarios where increased temperatures cause higher biogenic volatile organic compound (VOC) emissions, which in turn lead to higher SOA mass formation and significant changes in SOA composition. Such processes would need to be considered in climate models for a realistic representation of future aerosol-climate-biosphere feedbacks.

Medição do transporte sólido por arrastamento através de sensores acústicos

A quantificação do material sólido transportado (transporte sólido) ao longo de um curso de água é extremamente importante nas mais variadas áreas da engenharia fluvial. O transporte sólido em rios de montanha dá-se maioritariamente por arrastamento no fundo, através de deslizamento, rolamento e saltação dos sedimentos. Ao longo dos tempos foram desenvolvidas várias fórmulas para estimar o transporte sólido por arrastamento, contudo, devido à complexidade dos processos de transporte de sedimentos, bem como a variabilidade espacial e temporal, a previsão de taxas de transporte não foi conseguida exclusivamente através de investigação teórica. Para obter um melhor conhecimento sobre os processos de transporte sólido por arrastamento em rios de montanha, torna-se necessário monitorizá-los com maior precisão possível. Com os avanços na electrónica, novos métodos tecnológicos foram desenvolvidos para resolver a problemática da quantificação do transporte sólido, em detrimento dos atuais métodos tradicionais, que se baseiam na recolha de amostras em campo, para posterior correlação. O objetivo principal da presente dissertação foi o desenvolvimento de um equipamento capaz de estimar/monitorizar continuamente o transporte sólido por arrastamento em rios de montanha, que utilizasse tecnologia de baixo custo. Este equipamento dispõe de um sensor piezolelétrico que realizará medições à vibração causada pelo embate dos sedimentos sobre uma chapa metálica. A energia do sinal resultante dos impactos reverterá em peso. A metodologia usada para a obtenção das medições foi a realização de ensaios laboratoriais, tendo sido dado especial destaque à influência da variação do caudal, bem como da forma dos sedimentos, na intensidade do sinal adquirido.

Dynamics of a large submersed plant bed in upper Chesapeake Bay

A large SAV bed in upper Chesapeake Bay has experienced several abrupt shifts over the past half-century, beginning with near-complete loss after a record-breaking flood in 1972, followed by an unexpected, rapid resurgence in the early 2000’s, then partial decline in 2011 following another major flood event. Together, these trends and events provide a unique opportunity to study a recovering SAV ecosystem from several different perspectives. First, I analyzed and synthesized existing time series datasets to make inferences about what factors prompted the recovery. Next, I analyzed existing datasets, together with field samples and a simple hydrodynamic model to investigate mechanisms of SAV bed loss and resilience to storm events. Finally, I conducted field deployments and experiments to explore how the bed affects internal physical and biogeochemical processes and what implications those effects have for the dynamics of the system. I found that modest reductions in nutrient loading, coupled with several consecutive dry years likely facilitated the SAV resurgence. Furthermore, positive feedback processes may have played a role in the sudden nature of the recovery because they could have reinforced the state of the bed before and after the abrupt shift. I also found that scour and poor water clarity associated with sediment deposition during the 2011 flood event were mechanisms of plant loss. However, interactions between the bed, water flow, and waves served as mechanisms of resilience because these processes created favorable growing conditions (i.e., clear water, low flow velocities) in the inner core of the bed. Finally, I found that that interactions between physical and biogeochemical processes led to low nutrient concentrations inside the bed relative to outside the bed, which created conditions that precluded algal growth and reinforced vascular plant dominance. This work demonstrates that positive feedbacks play a central role in SAV resilience to both chronic eutrophication as well as acute storm events. Furthermore, I show that analysis of long-term ecological monitoring data, together with field measurements and experiments, can be an effective approach for understanding the mechanisms underlying ecosystem dynamics.

Rapid detection and quantification of the marine toxic algae, Alexandrium minutum, using a super-paramagnetic immunochromatographic strip test

The dinoflagellates of Alexandrium genus are known to be producers of paralytic shellfish toxins that regularly impact the shellfish aquaculture industry and fisheries. Accurate detection of Alexandrium including A. minutum is crucial for environmental monitoring and sanitary issues. In this study, we firstly developed a quantitative lateral flow immunoassay (LFIA) using super-paramagnetic nanobeads for A. minutum whole cells. This dipstick assay relies on two distinct monoclonal antibodies used in a sandwich format and directed against surface antigens of this organism. No sample preparation is required. Either frozen or live cells can be detected and quantified. The specificity and sensitivity are assessed by using phytoplankton culture and field samples spiked with a known amount of cultured A. minutum cells. This LFIA is shown to be highly specific for A. minutum and able to detect reproducibly 105 cells/L within 30 min. The test is applied to environmental samples already characterized by light microscopy counting. No significant difference is observed between the cell densities obtained by these two methods. This handy super-paramagnetic lateral flow immnunoassay biosensor can greatly assist water quality monitoring programs as well as ecological research.

Influence of Soil Biogeochemical Properties on the Invasiveness of Old World Climbing Fern (Lygodium microphyllum)

The state of Florida has one of the most severe exotic species invasion problems in the United States, but little is known about their influence on soil biogeochemistry. My dissertation research includes a cross-continental field study in Australia, Florida, and greenhouse and growth chamber experiments, focused on the soil-plant interactions of one of the most problematic weeds introduced in south Florida, Lygodium microphyllum (Old World climbing fern). Analysis of field samples from the ferns introduced and their native range indicate that L microphyllum is highly dependent on arbuscular mycorrhizal fungi (AMF) for phosphorus uptake and biomass accumulation. Relationship with AMF is stronger in relatively dry conditions, which are commonly found in some Florida sites, compared to more common wet sites where the fern is found in its native Australia. In the field, L. microphyllum is found to thrive in a wide range of soil pH, texture, and nutrient conditions, with strongly acidic soils in Australia and slightly acidic soils in Florida. Soils with pH 5.5 - 6.5 provide the most optimal growth conditions for L. microphyllum, and the growth declines significantly at soil pH 8.0, indicating that further reduction could happen in more alkaline soils. Comparison of invaded and uninvaded soil characteristics demonstrates that L. microphyllum can change the belowground soil environment, with more conspicuous impact on nutrient-poor sandy soils, to its own benefit by enhancing the soil nutrient status. Additionally, the nitrogen concentration in the leaves, which has a significant influence in the relative growth rate and photosynthesis, was significantly higher in Florida plants compared to Australian plants. Given that L. microphyllum allocates up to 40% of the total biomass to rhizomes, which aid in rapid regeneration after burning, cutting or chemical spray, hence management techniques targeting the rhizomes look promising. Over all, my results reveal for the first time that soil pH, texture, and AMF are major factors facilitating the invasive success of L. mcirophyllum. Finally, herbicide treatments targeting rhizomes will most likely become the widely used technique to control invasiveness of L. microphyllum in the future. However, a complete understanding of the soil ecosystem is necessary before adding any chemicals to the soil to achieve a successful long-term invasive species management strategy.

Detection of African Swine Fever Virus Antibodies in Serum and Oral Fluid Specimens Using a Recombinant Protein 30 (p30) Dual Matrix Indirect ELISA

In the absence of effective vaccine(s), control of African swine fever caused by African swine fever virus (ASFV) must be based on early, efficient, cost-effective detection and strict control and elimination strategies. For this purpose, we developed an indirect ELISA capable of detecting ASFV antibodies in either serum or oral fluid specimens. The recombinant protein used in the ELISA was selected by comparing the early serum antibody response of ASFV-infected pigs (NHV-p68 isolate) to three major recombinant polypeptides (p30, p54, p72) using a multiplex fluorescent microbead-based immunoassay (FMIA). Non-hazardous (non-infectious) antibody-positive serum for use as plate positive controls and for the calculation of sample-to-positive (S:P) ratios was produced by inoculating pigs with a replicon particle (RP) vaccine expressing the ASFV p30 gene. The optimized ELISA detected anti-p30 antibodies in serum and/or oral fluid samples from pigs inoculated with ASFV under experimental conditions beginning 8 to 12 days post inoculation. Tests on serum (n = 200) and oral fluid (n = 200) field samples from an ASFV-free population demonstrated that the assay was highly diagnostically specific. The convenience and diagnostic utility of oral fluid sampling combined with the flexibility to test either serum or oral fluid on the same platform suggests that this assay will be highly useful under the conditions for which OIE recommends ASFV antibody surveillance, i.e., in ASFV-endemic areas and for the detection of infections with ASFV isolates of low virulence.