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1281. [Article] Linking greater sage-grouse habitat use and suitability across spatiotemporal scales in central Oregon
Greater Sage-grouse (Centrocercus urophasianus) habitat research has historically focused on fine-scale (0.007 - 0.032 ha) vegetation structure and composition immediately surrounding sites selected by ...Citation Citation
- Title:
- Linking greater sage-grouse habitat use and suitability across spatiotemporal scales in central Oregon
- Author:
- Freese, Mark T.
Greater Sage-grouse (Centrocercus urophasianus) habitat research has historically focused on fine-scale (0.007 - 0.032 ha) vegetation structure and composition immediately surrounding sites selected by birds. However, little work has evaluated vegetation attributes important for Greater Sage-grouse at a landscape-scale or identified landscape attributes that influence habitat use patterns. Habitat use patterns by Greater Sage-grouse are complex and can occur across relatively large heterogeneous landscapes. This creates a major challenge for managers to interpret and predict habitat use patterns as well as to evaluate habitat suitability and prioritize habitats that are in need of ecological restoration. The goals of this research were to evaluate plot-level habitat characteristics found to be important in sustaining Greater Sage-grouse populations at a landscape-level and to identify landscape-level attributes associated with bird occurrence. Specific questions this research addressed were: 1) what is the variation in vegetation composition and structure at the plot versus landscape-level, 2) how does topography influence the distribution of vegetation composition and structure, and 3) what attributes at the landscape-level are most closely associated with Greater Sage-grouse habitat use? To address these questions we selected a 31,416 ha area in central Oregon surrounding a Greater Sage-grouse lek with a population that has been relatively stable since 1987. In February 2006, 50 Greater Sage-grouse were trapped, radio collared, and then tracked for two consecutive years. Four-hundred eighty bird UTM (Universal Transverse Mercator) coordinate location points were recorded for the entire population of birds during the duration of this study. Each collared Greater Sage-grouse was located on average every 15 ± 0.56 (mean ± SE) days, ranging from 1 to 154 days. Vegetation for the entire study area was mapped by cover types, which were defined by the dominant shrub species. When shrubs were not present in the plant community, cover types were separated by other surface characteristics such as bare ground, water, meadow, etc. A total of 23 cover types were delineated. Cover types were mapped using 0.5-m NAIP (National Agricultural Imagery Program) imagery. In addition to cover type, a set of biophysical predictor variables were created for the entire study area in a GIS (Geographic Information System) to evaluate the association with Greater Sage-grouse location points. These variables included elevation, slope, aspect, curvature, solar radiation, ruggedness index, northing, easting, and distance from roads, leks, and mesic habitats. A stratified random sample with cover types serving as the stratum was used to select random locations for sampling plot-level habitat variables. A total of 352 plots were sampled from 18 cover types across the study area with a minimum of 15 plots per cover type. Vegetation measurements collected were similar to those reported in the habitat guidelines developed by Connelly et al. (2000) and the Bureau of Land Management et al. (2000). Measurements included vegetation cover, height, and density of forbs recognized as important Greater Sage-grouse food species. Plot elevation, slope, aspect, curvature and landscape position were also recorded. Summary statistics were used to describe means and ranges within and between cover types. A combination of multiple linear regression and analysis of variance (ANOVA) were used to evaluate the effects of topographic attributes on the distribution of vegetation composition and structure. To address the third question, maximum entropy software was used to develop models that predict Greater Sage-grouse seasonal habitat use, generate maps from those models, and describe the shapes of the response curves as it relates Greater Sage-grouse habitat preference to individual landscape predictor variables. Total shrub canopy cover across all cover types averaged 19.4%, ranging from 11.6 to 27.7%. Big (mountain and Wyoming) and low sagebrush canopy cover commonly varied between 2.6 and 16 fold within cover types. Deep-rooted perennial tussock grass cover averaged across all upland plots, was 26.7%, ranging from less than 1% to over 50%. Vegetation cover, Greater Sage-grouse food forb density, and sagebrush and grass height were significantly (P < 0.05) correlated with topographic attributes. Cover for the different plant life forms and food forb density increased with elevation. Cover for most of the herbaceous life forms was also greater on north than south aspects. Compared to Connelly et al. (2000) and the BLM et al. (2000) habitat guidelines, < 1% of the study area satisfied breeding and nesting guideline criteria, while < 31% satisfied the brood-rearing guideline criteria. Although most of the study area did not meet habitat recommendations presented in the guidelines, patches imbedded throughout the study area did and most areas satisfied many but not all of the guideline requirements. These results suggests that evaluating only mean values of community structure, both within and among cover types across the study area, limited the ability to fully identify patch variability and landscape heterogeneity as it relates to habitat suitability across large areas. Maximum entropy results suggest Greater Sage-grouse habitat use during the breeding season increases near leks and within cover types of low sagebrush and low sagebrush/mountain big sagebrush complexes. Preferred summer habitat includes areas relatively high in elevation, distances that are close to leks, and within or a close proximity to habitats that harbor succulent vegetation through much of the summer. With Greater Sage-grouse utilizing resources within expansive landscapes, understanding the attributes that can be applied at a landscape-scale that attract disproportionate levels of habitat use can help managers predict where birds are likely to occur across the landscape. With the ability to discriminate between areas that Greater Sage-grouse are likely to use or avoid, managers can allocate limited resources to more effectively create, manipulate, and administer habitat conservation efforts where bird use is predicted and prioritize areas across the landscape in need of ecological restoration.
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1282. [Article] Carbon Nanodots as Biolabels for Fluorescence Immunoassays
There has been a tremendous growth in interest in carbon nanodots (C-dots) in the past several years. As a nascent nanomaterial, C-dots have shown great promise in applications that benefit from their ...Citation Citation
- Title:
- Carbon Nanodots as Biolabels for Fluorescence Immunoassays
- Author:
- Wu, Yuanyuan
There has been a tremendous growth in interest in carbon nanodots (C-dots) in the past several years. As a nascent nanomaterial, C-dots have shown great promise in applications that benefit from their superior water dispersibility, low toxicity, non-blinking fluorescent output, chemical and biological compatibility, ease of functionalization and resistance to photobleaching. With this positive outlook, however, challenges remain for the practical application of these fluorophores in specific biolabeling processes and bioassays. The goal of this effort has been to combine C-dots with biorecognition units for quantitative biomolecule determinations; specifically, the development of novel fluorescent immunoassays is presented here. These studies largely focused on the use of C-dot-labeled antibodies to target a protein disease biomarker, human alpha-fetoprotein (AFP). The research effort began with C-dot synthesis, followed by the application of capillary electrophoresis (CE) as an analysis tool for C-dot characterization and synthesis optimization. In addition, the CE work facilitated optimization of ensuing C-dot biolabeling reactions. C-dots were hydrothermally synthesized from citric acid (CA) and ethylene diamine (EDA) with a quantum yield as high as 99%. A novel CE method utilizing an alkaline working buffer was developed for rapid and reliable analysis of C-dots. A calibration curve was established over a broad concentration range (0.5-10 mg/mL) with excellent linearity (R²=0.9989). Then, the C-dots were used to label antibodies via amine-amine coupling using glutaraldehyde. All of the components in the conjugation reaction were baseline separated using the newly developed CE method. One peak in the electropherogram, having a migration time between that of the unlabeled antibody and that for the unmodified C-dots, was identified as representing the C-dot labeled antibodies. In summary, a novel, simple and rapid CE method was developed for: (1) quantitation of C-dots and (2) analysis of a C-dot-antibody bioconjugate, thus providing a method for optimization of conditions for acquiring the desired C-dot bioconjugate. The research continued with the development of a sensitive, selective, environmentally-friendly, high throughput, well plate based immunosorbent assay for human AFP using C-dots. The capture anti-AFP (Ab₁) was coated onto polystyrene well plates and bovine serum albumin (BSA) was used to block unsaturated binding sites. The C-dots were used to label the other member of the anti-AFP pair (Ab₂) via amine-amine coupling using glutaraldehyde. AFP was incubated to form a sandwich immunocomplex between Ab₁ and Ab₂ in the well plates, with unbound AFP and Ab₂ washed away with Tween-20. The fluorescence intensities detected from the C-dots in these immunocomplexes positively correlated to the concentrations of AFP antigen. A 5-parameter logistic regression curve was established between fluorescence and clinically important AFP concentrations (range: 0-350 ng/mL with an R-squared value of 0.995). The results were in agreement with those from two more traditional immunoassays which used horseradish peroxidase (HRP, R²=0.964) and fluorescein isothiocyanate (FITC, R²=0.973) as biolabels. This demonstration was the first example of a C-dot linked immunosorbent (solid phase) assay. To enable convenient separation by centrifugation and straightforward surface chemistry, in the next stage of the research described here, C-dots were encapsulated into a stable suspension of 45 nm silica nanoparticles through a reverse microemulsion method. A novel ratiometric immunoassay was developed to target human AFP, based on C-dot doped silica nanoparticles (CD-SNPs) and fluorescein isothiocyanate (FITC). CD-SNPs (Ab₁-CD-SNPs) capped with capture antibodies together with FITC labeled secondary antibodies (Ab₂-FITC) constituted a ratiometric immunoassay pair, in which CD-SNPs functioned as both a solid support enabling separation and washing, and as a built-in source of correction to account for inconsistent environmental effects and experimental errors. A linear calibration curve was established between ratio of FITC to C-dot fluorescent signals ("F/C") and a broad range of AFP concentrations (0-280 μg/dL with an R-squared value of 0.9977) with a low detection limit (0.317 μg/dL or 3.17 ng/mL) and acceptable recoveries. This is the first application of carbon nanodot doped silica nanoparticles to quantitative immunoassays for protein disease biomarkers. Moreover, the demonstration that these low-cost, simply-obtained and highly- fluorescent C-dots can be simply encapsulated into silica nanoparticles for specific biolabeling may expand future applications of C-dots into areas of in-vivo cellular imaging, drug delivery, and in-vitro cell labeling and biomolecule sensing. In the last part of the research effort described here, an alternative colorimetric detection platform, where an Apple iPhone 4 camera equipped with a color analysis application (ColorAssist) was combined with Vitros® blood urea nitrogen (BUN) colorimetric assays, was examined as a model for rapid and inexpensive clinical diagnostic testing. Color images of assay slides at various concentrations of urea were collected with the smartphone camera and quantified in three spectral ranges (red/green/blue or RGB) using the color analysis application. Absorbance values were converted from these diffuse reflectance data to quantitate BUN over its clinically important concentration range (2-190 mg/dL) with good linearity (R² = 0.9996 [n = 5]). This method was also applied to canine serum samples, the urea concentrations obtained were in good agreement with those from the instrumental "gold standard" (Beckman Coulter AU480) and a commercial colorimetric dry slide analyzer (HeskaTM Element DC)). This effort demonstrated that smart phones have the potential to be used as simple, effective colorimetric detectors for quantitative diagnostic tests. Furthermore, many additional demonstrations of the use of C-dots for sensitive detection of ions showed discernible color changes as well. This in turn suggests a valuable direction for future research: to explore combinations of these simple and effective colorimetric C-dot assays for both point-of-care applications in the developed world and field deployment in developing nations.
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Stratigraphic measurement of the 1,238-rn thick Cowlitz Formation in the southwest Washington type section along Olequa and Stillwater creeks reveals complex facies succession of wave- to tide-dominated ...
Citation Citation
- Title:
- Lithofacies, stratiography, and geology of the middle eocene type cowlitz formation and associated volcanic and sedimentary units, Eastern Willapa Hills, southwest Washington
- Author:
- Payne, Charles William
Stratigraphic measurement of the 1,238-rn thick Cowlitz Formation in the southwest Washington type section along Olequa and Stillwater creeks reveals complex facies succession of wave- to tide-dominated deltaic sequences. The underlying, 625-rn thick upper member of the McIntosh Formation (as mapped by Wells, 1981) is composed of two units: a basal 130-m thick prograding offshore to marginal marine coal-bearing, lithic-arkosic sandstone facies succession (upper McIntosh sandstone) and a thicker, 500- m thick bathyal foraminilera-rich siltstone facies that is, in part, in fault contact with the overlying Cowlitz Formation. The lower member of the McIntosh Formation is 375 rn thick in Stillwater Creek, with the base not exposed in the study area. The Cowlitz Formation is subdivided into five informal units. The basal 558-m thick unit consists of (1) multiple prograding, wave-dominated shoreface hummocky stratified lithic arkosic sandstone successions (unit 1A) that comprise several thickeningand coarsening-upwards parasequences and (2) coal-bearing delta plain facies associations (unit 1B). The 205-m thick second unit is composed of five coarsening-up stormdominated, hummocky-bedded shelf to delta-front arkosic sandstone parasequences. Fining-upwards subtidal, intertidal, and supratidal facies associations constitute the 170-m thick third member. Tidal-estuarine facies in unit 3 include: (1) nested subtidal micaceous lithic-arkosic sandstone channels, (2) cross-bedded subtidal sandstone ridges with brackish water mollusc hash, (3) sandy and muddy accretionary-bank, and (4) coalbearing marsh-swamp deposits. Thin basaltic volcaniclastic interbeds occur within units one, two, and three. A 155-m thick fourth unit, consists of wave-dominated, arkosic sandstone, shoreface to offshore bioturbated mudstone facies successions; these successions form 10 coarsening-upward parasequences that overall define a retrogradational parasequence set. Thick, transgressive, bioturbated outer shelfal molluscbearing sandy siltstone and glauconitic mudstone in the Big Bend type locality along the Cowlitz River can be correlated to this unit in the type section in Olequa Creek. The uppermost unit consists of 150 m of deeper marine laminated siltstone, subordinate finegrained and thin-bedded turbidites, thick amalgamated submarine-channel sandstone and chaotic mudstone conglomerate, and slump-folded and soft-sediment deformed laminated siltstone intervals. Petrography of lithic-arkosic micaceous sandstones of the McIntosh and Cowlitz formations indicates there was a distant eastern, extrabasinal acid plutonic-metamorphic source for the arkosic component of these sandstones. The predominant quartz, feldspar, and mica constituents of Cowlitz Formation were transported from a distant dissected arc (such as the Idaho Batholith and metamorphic core complexes to the east) through an ancestral Columbia River drainage system. A second, local and active intrabasinal basaltic source (Grays River volcanics) supplied basaltic scoria and lava rock fragments to form volcaniclastic interbeds. Some volcaniclastics were reworked and mixed with the arkosic extrabasinal sediments in the shallow marine and nonmarine environments of units 2 and 3 of the Cowlitz Formation. Explosive calc-alkaline volcanic activity (Northcraft Formation or Goble Volcanics) is also evident in the silicic and pumiceous tuff beds interbedded with coal marsh/swamp strata in units 1 and 3. Paleocurrent directions indicated by crossbedded tidal strata of unit 3 are to the north-northwest and south-southeast as a resultof shore parallel transport and deflection around a proposed growing volcanic edifice of Grays River volcanics to the south and southwest. A very high sedimentation rate of 1.6 m/1,000 years was calculated for the upper part of the Cowlitz Formation (units 3 to 5) using thickness measurement and 39Ar/40Ar age dates from the Cowlitz Formation (i. e., from tuff in unit 3) and the easternmost locality in the unconformably overlying Grays River volcanics at Bebe Mountain. The large influx of sediment deposited over a relatively short time period was accommodated by this rapidly subsiding forearc basin. In this study area, subaerial flows of the Grays River volcanics locally unconformably overlie the Cowlitz Formation. A 38.9± 0.1 Ma 39Ar/40Ar age date from a tuff bed in unit 3 of the underlying Cowlitz Formation (Irving et al., 1996) and three 39Ar/40Ar age dates of 38.640.40 (south Abernathy Mtn.), 37.44±0.45 (west Bebe Mtn.), and 36.85 ± 0.46 Ma (east Bebe Mtn.) from the overlying Grays River volcanics bracket the timing of this regional unconformity. Additionally, field mapping (this study) and drill hole data supplied by Weyerhaeuser Company (Pauli, written communications) show there is a valley-fill unit at the base of the Grays River volcanics exposed on the surface and in the subsurface, respectively. These data confirm the volcanic- and tectonically-controlled unconformable relationship of the Cowlitz Formation to the overlying the Grays River volcanics. The Cowlitz Formation is in disconformable contact (a tectonically forced sequence boundary) with an overlying second, younger lowstand valley-fill unit (Toutle Formation unit A) recognized in this study along Olequa Creek. The 265-m thick, newly discovered, Toutle Formation in this area is subdivided into three informal units: (1) a basal incised, non-marine valley-fill sequence (unit A), (2) a marginal marine (estuarine or nearshore) sequence (unit B), and (3) an upper fluvial sequence (unit C). A 31.9 ± 0.4Ma 39Ar/40Ar date from a homblende-bearing pumiceous lapilli tuff in unit A indicates that the Toutle Formation is a time equivalent of the upper fluvial member of the Oligocene type Toutle Formation and the middle part of the Lincoln Creek Formation far from the center of the forearc basin to the west. Unit C of the Toutle Formation grades upward into the overlying deeper marine tuffaceous siltstone of the Lincoln Creek Formation. Deformation in this area resulted from two plate tectonic events: (1) latest middle Eocene highly oblique subduction that resulted in short-lived, normal faulting and intrusion of Grays River basalt dikes along small faults and (2) rapid post mid-Miocene oblique subduction that formed northeast-trending dextral and northwest-trending sinistral conjugate faults and broad regional compressional folding throughout southwest Washington. The broad open Arkansas anticline that trends northwest-southeast between Bebe and Abernathy mountains is an eastward extension of the Willapa Hills basement uplift to the west and is extensively cut by northeast and northwest trending faults (Plate I). This compressional event deformed both the Cowlitz Formation and the overlying Grays River volcanics. A similar structural pattern recognized in regional field mapping by Wells (1981) indicates this folding event also deformed mid-Miocene volcanic and sedimentary unit (i.e., Astoria Formation and Columbia River basalts). Reservoir quality of the Cowlitz and upper McIntosh formations micaceous lithicarkosic sandstones is good. These sandstones are clean, highly friable and porous except where carbonate and smectite clay rim cements formed in the lithic arkose. Unit 5 siltstone could act as a cap rock in the subsurface and the 1- to 10-rn thick coals could be a source for natural gas. The McIntosh marine siltstone is another possible source for gas and the micaceous arkosic sandstone in the upper McIntosh is a potential reservoir. Stratigraphic pinchouts and normal and wrench fault traps are similar to the Mist gas field of northwest Oregon.