Vegetation-Climate Interactions Along A Transition From Tundra To Boreal Forest In Alaska

Thesis (Ph.D.) University of Alaska Fairbanks, 2005The climate of the Alaskan Arctic is warming more rapidly than at any time in the last 400 years. Climate changes of the magnitude occurring in high latitudes have the potential to alter both the structure and function of arctic ecosystems. Structural responses reflect changes in community composition, which may also influence ecosystem function. Functional responses change the biogeochemical cycling of carbon and nutrients. We examined the structural and functional interactions between vegetation and climate across a gradient of vegetation types from arctic tundra to boreal forest. Canopy complexity combines vegetation structural properties such as biomass, cover, height, leaf area index (LAI) and stem area index (SAI). Canopy complexity determines the amount of the energy that will be available in an ecosystem and will also greatly influence the partitioning of that energy into different land surface processes such as heating the air, evaporating water and warming the ground. Across a gradient of sites in Western Alaska, we found that increasing canopy complexity was linked to increased sensible heating. Thus, vegetation structural changes could represent an important positive feedback to warming. Structural changes in ecosystems are linked to changes in ecosystem function. High latitude ecosystems play an important role in the earth's climate system because they contain nearly 40% of the world's reactive soil carbon. We examined Net Ecosystem Production (NEP) in major community types of Northern Alaska using a combination of field-based measurements and modeling. Modeled NEP decreased in both warmer and drier and warmer and wetter conditions. However, in colder and wetter conditions, NEP increased. The net effect for the region was a slight gain in ecosystem carbon; however, our research highlights the importance of climate variability in the carbon balance of the study region during the last two decades. The next step forward with this research will be to incorporate these results into coupled models of the land-atmosphere system. Improved representations of ecosystem structure and function will improve our ability to predict future responses of vegetation composition, carbon storage, and climate and will allow us to better examine the interactions between vegetation and the atmosphere in the context of a changing climate

Sight Words

What are sight words? Sight words are common words that a reader should recognize on sight. These are often referred to as “high frequency words” or “instant words.” Research indicates interventions used to teach sight words to students with disabilities, especially students with moderate to severe disabilities are beneficial. Multiple methods can be utilized to teach sight words to students with disabilities. These methods include: games, sight word recognition, and memorization. Research that catered specially to students with moderate to severe disabilities indicated that choosing between multiple methods is most effective way to teach sight words. This approach provides students with moderate to severe disabilities more generalization and independence

Drill Pipe Corrosion Control Using an Inert Drilling Fluid

The results of a geothermal drill pipe corrosion field test are presented. When a low-density drilling fluid was required for drilling a geothermal well because of an underpressured, fractured formation, two drilling fluids were alternately used to compare drill pipe corrosion rates. The first fluid was an air-water mist with corrosion control chemicals. The other fluid was a nitrogen-water mist without added chemicals. The test was conducted during November 1980 at the Baca location in northern New Mexico. Data from corrosion rings, corrosion probes, fluid samples and flow line instrumentation are plotted for the ten day test period. it is shown that the inert drilling fluid, nitrogen, reduced corrosion rates by more than an order of magnitude. Test setup and procedures are also discussed

Prehospital Systolic Blood Pressure Thresholds: A Community‐based Outcomes Study

Objectives Emergency medical services (EMS) personnel commonly use systolic blood pressure ( sBP ) to triage and treat acutely ill patients. The definition of prehospital hypotension and its associated outcomes are poorly defined. The authors sought to determine the discrimination of prehospital sBP thresholds for 30‐day mortality and to compare patient classification by best‐performing thresholds to traditional cutoffs. Methods In a community‐based cohort of adult, nontrauma, noncardiac arrest patients transported by EMS between 2002 and 2006, entries to state hospital discharge data and death certificates were linked. Prehospital sBP thresholds between 40 and 140 mm Hg in derivation ( n =  132,624) and validation ( n =  22,020) cohorts and their discrimination for 30‐day mortality, were examined. Cutoffs were evaluated using the 0/1 distance, Youden index, and adjusted Z‐statistics from multivariable logistic regression models. Results In the derivation cohort, 1,594 (1.2%) died within 24 hours, 7,404 (6%) were critically ill during hospitalization, and 6,888 (5%) died within 30 days. The area under the receiver operating characteristic (ROC) curve for sBP was 0.60 (95% confidence interval [CI] = 0.59, 0.61) for 30‐day mortality and 0.64 (95% CI = 0.62 0.66) for 24‐hour mortality. The 0/1 distance, Youden index, and adjusted Z‐statistics found best‐performing sBP thresholds between 110 and 120 mm Hg. When compared to an sBP ≤ 90 mm Hg, a cutoff of 110 mm Hg would identify 17% ( n =  137) more deaths at 30 days, while overtriaging four times as many survivors. Conclusions Prehospital sBP is a modest discriminator of clinical outcomes, yet no threshold avoids substantial misclassification of 30‐day mortality among noninjured patients. Resumen Los Umbrales de la Presión Arterial Sistólica Prehospitalaria: Un Estudio de Base Comunitaria Acerca de la Evolución de los Pacientes Objetivos El personal de los sistemas de emergencias médicas ( SEM ) usa frecuentemente la presión arterial sistólica ( PAS ) para clasificar y tratar a los pacientes agudos. Las definiciones de hipotensión prehospitalaria y sus resultados asociados están pobremente definidos. Se determinó la discriminación de los umbrales de PAS prehospitalaria para la mortalidad a los 30 días, y se comparó la clasificación del paciente por los mejores umbrales con los puntos de corte tradicionales. Metodología Estudio de cohorte de base comunitaria de pacientes adultos no traumatológicos ni con paradas cardiorrespiratorias transportados por los SEM entre 2002 y 2006, cuyas historias estaban vinculadas con los datos de alta hospitalaria y los certificados de mortalidad. Se examinaron los umbrales de PAS prehospitalaria entre 40 mm Hg y 140 mm Hg en las cohortes de derivación ( n =  132.624), y validación ( n =  22,020), y su discriminación para la mortalidad a los 30 días. Los puntos de corte se evaluaron usando la distancia 0/1, el índice de Youden y los estadísticos Z ajustados de los modelos de regresión logística multivariable. Resultados: En la cohorte de derivación, 1.594 (1,2%) fallecieron en las primeras 24 horas, 7.404 (6%) estuvieron críticamente enfermos durante el ingreso y 6.888 (5%) fallecieron en los 30 primeros días. El área bajo la curva de la ROC para PAS fue 0,60 ( IC 95% = 0,59–0,61) para la mortalidad a los 30 días y 0,64 ( IC 95% = 0,62–0,66) para la mortalidad a las 24 horas. La distancia 0/1, el índice de Youden y las estadísticas Z ajustadas hallaronque los mejores umbrales de PAS estaban entre 110 y 120 mm Hg. Cuando se comparó con una PAS ≤ 90 mm Hg, un punto de corte de 110 mm Hg identificaría un 17% ( n =  137) más de muertes a los 30 días, mientras que sobreclasificaría cuatro veces más a los supervivientes. Conclusiones La presión arterial sistólica es un discriminador modesto de resultados clínicos. No obstante, ningún umbral evita una mala clasificación de la mortalidad a los 30 días entre los pacientes no traumatológicos.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/1/acem12142-sup-0002-DataSupplementS2_FigS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/2/acem12142-sup-0007-DataSupplementS7_FigS4.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/3/acem12142-sup-0006-DataSupplementS6_FigS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/4/acem12142-sup-0009-DataSupplementS9_TableS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/5/acem12142-sup-0003-DataSupplementS3.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/6/acem12142-sup-0008-DataSupplementS8_TableS2.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/7/acem12142-sup-0004-DataSupplementS4_TableS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/8/acem12142-sup-0001-DataSupplementS1.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/98303/9/acem12142.pd

Attribution of disturbance change agent from Landsat time-series in support of habitat monitoring in the Puget Sound region, USA

To understand causes and consequences of landscape change, it is often not enough to simply detect change. Rather, the agent causing the change must also be determined. Here, we describe and test a method of change agent attribution built on four tenets: agents operate on patches rather than pixels; temporal context can provide insight into the agent of change; human interpretation is critical because agent labels are inherently human-defined; and statistical modeling must be flexible and non-parametric. In the Puget Sound, USA, we used LandTrendr Landsat time-series-based algorithms to identify abrupt disturbances, and then applied spatial rules to aggregate these to patches. We then derived a suite of spectral, patch-shape, and landscape position variables for each patch. These were then linked to patch-level training labels determined by interpreters at 1198 training patches, and modeled statistically using the Random Forest machine-learning algorithm. Labeled agents of change included urbanization, forest management, and natural change (largely fire), as well as labels associated with spectral change that was non-informative (false change). The success of the method was evaluated using both out-of-bag (OOB) error and a small, fully-independent validation interpretation dataset. Overall OOB accuracy was above 80%, but most successful in the numerically well-represented forest management class. Validation with the independent data was generally lower than that estimated with the OOB approach, but comparable when either first or second voting scores were used for prediction. Spatial and temporal patterns within the study area followed expectations well, with most urbanization occurring in the lower elevation regions around Seattle–Tacoma, most forest management occurring in mid-slope managed forests, and most natural disturbance occurring in protected areas. Temporal patterns of change agent aggregated to the watershed level suggest substantial year-over-year variability that could be used to examine year-over-year variability in fish species populations.Keywords: Disturbance, Change attribution, Puget Sound, Salmon, LandTrendr, Time series, Change detection, Landsa

The Generation of Successive Unmarked Mutations and Chromosomal Insertion of Heterologous Genes in Actinobacillus pleuropneumoniae Using Natural Transformation

We have developed a simple method of generating scarless, unmarked mutations in Actinobacillus pleuropneumoniae by exploiting the ability of this bacterium to undergo natural transformation, and with no need to introduce plasmids encoding recombinases or resolvases. This method involves two successive rounds of natural transformation using linear DNA: the first introduces a cassette carrying cat (which allows selection by chloramphenicol) and sacB (which allows counter-selection using sucrose) flanked by sequences to either side of the target gene; the second transformation utilises the flanking sequences ligated directly to each other in order to remove the cat-sacB cassette. In order to ensure efficient uptake of the target DNA during transformation, A. pleuropneumoniae uptake sequences are added into the constructs used in both rounds of transformation. This method can be used to generate multiple successive deletions and can also be used to introduce targeted point mutations or insertions of heterologous genes into the A. pleuropneumoniae chromosome for development of live attenuated vaccine strains. So far, we have applied this method to highly transformable isolates of serovars 8 (MIDG2331), which is the most prevalent in the UK, and 15 (HS143). By screening clinical isolates of other serovars, it should be possible to identify other amenable strains

The Helicobacter pylori HpyAXII restriction–modification system limits exogenous DNA uptake by targeting GTAC sites but shows asymmetric conservation of the DNA methyltransferase and restriction endonuclease components

The naturally competent organism Helicobacter pylori encodes a large number of restriction–modification (R–M) systems that consist of a restriction endonuclease and a DNA methyltransferase. R–M systems are not only believed to limit DNA exchange among bacteria but may also have other cellular functions. We report a previously uncharacterized H. pylori type II R–M system, M.HpyAXII/R.HpyAXII. We show that this system targets GTAC sites, which are rare in the H. pylori chromosome but numerous in ribosomal RNA genes. As predicted, this type II R–M system showed attributes of a selfish element. Deletion of the methyltransferase M.HpyAXII is lethal when associated with an active endonuclease R.HpyAXII unless compensated by adaptive mutation or gene amplification. R.HpyAXII effectively restricted both unmethylated plasmid and chromosomal DNA during natural transformation and was predicted to belong to the novel ‘half pipe’ structural family of endonucleases. Analysis of a panel of clinical isolates revealed that R.HpyAXII was functional in a small number of H. pylori strains (18.9%, n = 37), whereas the activity of M.HpyAXII was highly conserved (92%, n = 50), suggesting that GTAC methylation confers a selective advantage to H. pylori. However, M.HpyAXII activity did not enhance H. pylori fitness during stomach colonization of a mouse infection model

A Single Nucleotide Change Affects Fur-Dependent Regulation of sodB in H. pylori

Helicobacter pylori is a significant human pathogen that has adapted to survive the many stresses found within the gastric environment. Superoxide Dismutase (SodB) is an important factor that helps H. pylori combat oxidative stress. sodB was previously shown to be repressed by the Ferric Uptake Regulator (Fur) in the absence of iron (apo-Fur regulation) [1]. Herein, we show that apo regulation is not fully conserved among all strains of H. pylori. apo-Fur dependent changes in sodB expression are not observed under iron deplete conditions in H. pylori strains G27, HPAG1, or J99. However, Fur regulation of pfr and amiE occurs as expected. Comparative analysis of the Fur coding sequence between G27 and 26695 revealed a single amino acid difference, which was not responsible for the altered sodB regulation. Comparison of the sodB promoters from G27 and 26695 also revealed a single nucleotide difference within the predicted Fur binding site. Alteration of this nucleotide in G27 to that of 26695 restored apo-Fur dependent sodB regulation, indicating that a single base difference is at least partially responsible for the difference in sodB regulation observed among these H. pylori strains. Fur binding studies revealed that alteration of this single nucleotide in G27 increased the affinity of Fur for the sodB promoter. Additionally, the single base change in G27 enabled the sodB promoter to bind to apo-Fur with affinities similar to the 26695 sodB promoter. Taken together these data indicate that this nucleotide residue is important for direct apo-Fur binding to the sodB promoter

Multiple Peptidoglycan Modification Networks Modulate Helicobacter pylori's Cell Shape, Motility, and Colonization Potential

Helical cell shape of the gastric pathogen Helicobacter pylori has been suggested to promote virulence through viscosity-dependent enhancement of swimming velocity. However, H. pylori csd1 mutants, which are curved but lack helical twist, show normal velocity in viscous polymer solutions and the reason for their deficiency in stomach colonization has remained unclear. Characterization of new rod shaped mutants identified Csd4, a DL-carboxypeptidase of peptidoglycan (PG) tripeptide monomers and Csd5, a putative scaffolding protein. Morphological and biochemical studies indicated Csd4 tripeptide cleavage and Csd1 crosslinking relaxation modify the PG sacculus through independent networks that coordinately generate helical shape. csd4 mutants show attenuation of stomach colonization, but no change in proinflammatory cytokine induction, despite four-fold higher levels of Nod1-agonist tripeptides in the PG sacculus. Motility analysis of similarly shaped mutants bearing distinct alterations in PG modifications revealed deficits associated with shape, but only in gel-like media and not viscous solutions. As gastric mucus displays viscoelastic gel-like properties, our results suggest enhanced penetration of the mucus barrier underlies the fitness advantage conferred by H. pylori's characteristic shape