Eddy covariance and environmental data of boreal bogs plant species

In boreal bogs plant species are low in number, but they differ greatly in their growth forms and photosynthetic properties. We assessed how ecosystem carbon (C) sink dynamics were affected by seasonal variations in photosynthetic rate and leaf area of different species. Photosynthetic properties (light-response parameters), leaf area development and areal cover (abundance) of the species were used to quantify species-specific net and gross photosynthesis rates (PN and PG, respectively), which were summed to express ecosystem-level PN and PG. The ecosystem-level PG was compared with a gross primary production (GPP) estimate derived from eddy covariance measurements (EC). Species areal cover rather than differences in photosynthetic properties determined the species with the highest PG of both vascular plants and Sphagna. Species-specific contributions to the ecosystem PG varied over the growing season, which in turn determined the seasonal variation in ecosystem PG. The upscaled growing-season PG estimate, 230 g C/m**2, agreed well with the GPP estimated by the EC, 243 g C/m**2. Sphagna were superior to vascular plants in ecosystem-level PG throughout the growing season but had a lower PN. PN results indicated that areal cover of the species together with their differences in photosynthetic parameters shape the ecosystem-level C balance. Species with low areal cover but high photosynthetic efficiency appear to be potentially important for the ecosystem C sink. Results imply that functional diversity may increase the stability of C sink of boreal bogs.

Marine mammal species detection and classification

Thesis (Ph.D.)--University of Washington, 2016-04

Predator species identification from saliva at kill sites with limited remains

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

Detection and differentiation of Plasmodium species by polymerase chain reaction and colorimetric detection in blood samples of patients with suspected malaria

Polymerase chain reaction (PCR) is now recognized as a sensitive and specific method for detecting Plasmodium species in blood. In this Study. we tested 279 blood samples, from patients with Suspected malaria, by a PCR assay utilizing species-specific colorimetric detection. and compared the results to light microscopy. Overall, both assays were in agreement for 270 of the 279 specimens. P. vivax was detected in 131 (47.0%) specimens. P. falciparum in 64 (22.9%) specimens, P. ovale in 6 (2.1%) specimens, and P. malariae in 5 (1.8%) specimens. Both P. falciparum and P. vivax were detected in a further 10 (3.6%) specimens, and 54 (19.3%) specimens were negative by both assays. In the remaining nine specimens, microscopy either failed to detect the parasite or incorrectly identified the species present. In summary, the sensitivity, specificity and simplicity of the PCR assay makes it particularly suitable for use in a diagnostic laboratory. (C) 2004 Elsevier Inc. All rights reserved.

Design, development, and use of molecular primers and probes for the detection of Gluconacetobacter species in the pink sugarcane mealybug

Molecular tools for the species-specific detection of Gluconacetobacter sacchari, Gluconacetobacter diazotrophicus, and Gluconacetobacter liquefaciens from the pink sugarcane mealybug (PSMB) Saccharicoccus sacchari Cockerell (Homiptera: Pseudococcidae) were developed and used in polymerase chain reactions (PCR) and in fluorescence in situ hybridizations (FISH) to better understand the microbial diversity and the numerical significance of the acetic acid bacteria in the PSMB microenvironment. The presence of these species in the PSMB occurred over a wide range of sites, but not in all sites in sugarcane-growing areas of Queensland, Australia, and was variable over time. Molecular probes for use in FISH were also designed for the three acetic acid bacterial species, and shown to be specific only for the target species. Use of these probes in FISH of squashed whole mealybugs indicated that these acetic acid bacteria species represent only a small proportion of the microbial population of the PSMB. Despite the detection of Glac. sacchari, Glac. diazotrophicus, and Glac. liquefaciens by PCR from different mealybugs isolated at various times and from various sugarcane-growing areas in Queensland, Australia, these bacteria do not appear to be significant commensals in the PSMB environment.

An identification tool for the Australian weedy Sporobolus species based on random amplified polymorphic DNA (RAPD) profiles

Based on morphological features alone, there is considerable difficulty in identifying the 5 most economically damaging weed species of Sporobolus [ viz. S. pyramidalis P. Beauv., S. natalensis ( Steud.) Dur and Schinz, S. fertilis ( Steud.) Clayton, S. africanus (Poir.) Robyns and Tourney, and S. jacquemontii Kunth.] found in Australia. A polymerase chain reaction (PCR)-based random amplified polymorphic DNA ( RAPD) technique was used to create a series of genetic markers that could positively identify the 5 major weeds from the other less damaging weedy and native Sporobolus species. In the initial RAPD pro. ling experiment, using arbitrarily selected primers and involving 12 species of Sporobolus, 12 genetic markers were found that, when used in combination, could consistently identify the 5 weedy species from all others. Of these 12 markers, the most diagnostic were UBC51(490) for S. pyramidalis and S. natalensis; UBC43(310,2000,2100) for S. fertilis and S. africanus; and OPA20(850) and UBC43(470) for S. jacquemontii. Species-specific markers could be found only for S. jacquemontii. In an effort to understand why there was difficulty in obtaining species-specific markers for some of the weedy species, a RAPD data matrix was created using 40 RAPD products. These 40 products amplified by 6 random primers from 45 individuals belonging to 12 species, were then subjected to numerical taxonomy and multivariate system (NTSYS pc version 1.70) analysis. The RAPD similarity matrix generated from the analysis indicated that S. pyramidalis was genetically more similar to S. natalensis than to other species of the 'S. indicus complex'. Similarly, S. jacquemontii was more similar to S. pyramidalis, and S. fertilis was more similar to S. africanus than to other species of the complex. Sporobolus pyramidalis, S. jacquemontii, S. africanus, and S. creber exhibited a low within-species genetic diversity, whereas high genetic diversity was observed within S. natalensis, S. fertilis, S. sessilis, S. elongates, and S. laxus. Cluster analysis placed all of the introduced species ( major and minor weedy species) into one major cluster, with S. pyramidalis and S. natalensis in one distinct subcluster and S. fertilis and S. africanus in another. The native species formed separate clusters in the phenograms. The close genetic similarity of S. pyramidalis to S. natalensis, and S. fertilis to S. africanus may explain the difficulty in obtaining RAPD species-specific markers. The importance of these results will be within the Australian dairy and beef industries and will aid in the development of integrated management strategy for these weeds.

Unicellular pheromone glands of the pentatomid bug Nezara viridula (Heteroptera : Insecta): Ultrastructure, classification, and proposed function

Male Nezara viridula produce sex pheromones from many independent single cells, each with a duct that opens onto the ventral abdominal surface. Despite the presence of along duct and an associated end complex (in the form of a cupule and microvillus saccule), the structural organization of the cells that comprise the gland conform to Class 1 epidermal gland cell classification : a single cell surrounds the entire secretory complex. Each cuticular cupule contains a central bed of filaments and opens into a narrow tubular ductule that leads from the base of the cupule through the epidermis to the cuticle to open externally as a pore. The cuticle of the cupule is continuous with that of the ductule and has the appearance of three layers, although the inner (middle) layer may be a gap formed during construction of the complex. In young adult males, just molted, the ultrastructure of the cells and their inclusions indicate that they are not active. The region of the cell that is distal to the abdominal cuticle is reduced and the proximal region, surrounding the duct, is enlarged when compared with sexually mature (3-4 weeks old) adult males. At maturity the pheromone cells are enlarged distally around the cupule, but are reduced to a narrow sleeve proximally, around the ductule. Two characteristic cell profiles are evident, based on the shape of the cupule and the organelle content. Type A shows a broad opening to the cupule, an abundance of mitochondria, and few vesicular bodies. Type B has an elongated, narrow, vase-like opening to the cupule, few mitochondria, and numerous vesicular bodies. Type B cells are smaller and more abundant than Type A. Distribution within the epidermal layer also differs. It is likely that the different types represent cells producing different secretion profiles. However, the secretions retained by the standard fixation protocol within mature cells of both types look similar and appear to collect as crystalline bodies within the lumen. This may represent a common storage mechanism.

Species differential regulation of COX2 can be described by an NFκB-dependent logic AND gate

Cyclooxygenase 2 (COX2), a key regulatory enzyme of the prostaglandin/eicosanoid pathway, is an important target for anti-inflammatory therapy. It is highly induced by pro-inflammatory cytokines in a Nuclear factor kappa B (NFκB)-dependent manner. However, the mechanisms determining the amplitude and dynamics of this important pro-inflammatory event are poorly understood. Furthermore, there is significant difference between human and mouse COX2 expression in response to the inflammatory stimulus tumor necrosis factor alpha (TNFα). Here, we report the presence of a molecular logic AND gate composed of two NFκB response elements (NREs) which controls the expression of human COX2 in a switch-like manner. Combining quantitative kinetic modeling and thermostatistical analysis followed by experimental validation in iterative cycles, we show that the human COX2 expression machinery regulated by NFκB displays features of a logic AND gate. We propose that this provides a digital, noise-filtering mechanism for a tighter control of expression in response to TNFα, such that a threshold level of NFκB activation is required before the promoter becomes active and initiates transcription. This NFκB-regulated AND gate is absent in the mouse COX2 promoter, most likely contributing to its differential graded response in promoter activity and protein expression to TNFα. Our data suggest that the NFκB-regulated AND gate acts as a novel mechanism for controlling the expression of human COX2 to TNFα, and its absence in the mouse COX2 provides the foundation for further studies on understanding species-specific differential gene regulation.

Morphometrics of seagrasses at species level, Moreton Bay, Australia determined from core samples collected in 2012-2013

Seagrass meadows are important marine carbon sinks, yet they are threatened and declining worldwide. Seagrass management and conservation requires adequate understanding of the physical and biological factors determining carbon content in seagrass sediments. Here, we identified key factors that influence carbon content in seagrass meadows across several environmental gradients in Moreton Bay, SE Queensland. Sampling was conducted in two regions: (1) Canopy Complexity, 98 sites on the Eastern Banks, where seagrass canopy structure and species composition varied while turbidity was consistently low; and (2) Turbidity Gradient, 11 locations across the entire bay, where turbidity varied among sampling locations. Sediment organic carbon content and seagrass structural complexity (shoot density, leaf area, and species specific characteristics) were measured from shallow sediment and seagrass biomass cores at each location, respectively. Environmental data were obtained from empirical measurements (water quality) and models (wave height). The key factors influencing carbon content in seagrass sediments were seagrass structural complexity, turbidity, water depth, and wave height. In the Canopy Complexity region, carbon content was higher for shallower sites and those with higher seagrass structural complexity. When turbidity varied along the Turbidity Gradient, carbon content was higher at sites with high turbidity. In both regions carbon content was consistently higher in sheltered areas with lower wave height. Seagrass canopy structure, water depth, turbidity, and hydrodynamic setting of seagrass meadows should therefore be considered in conservation and management strategies that aim to maximize sediment carbon content.

Seawater carbonate chemistry and growth, carbon acquisition, and species interaction of Antarctic phytoplankton species in a laboratory experiment

Despite the fact that ocean acidification is considered to be especially pronounced in the Southern Ocean, little is known about CO2-dependent physiological processes and the interactions of Antarctic phytoplankton key species. We therefore studied the effects of CO2 partial pressure (PCO2) (16.2, 39.5, and 101.3 Pa) on growth and photosynthetic carbon acquisition in the bloom-forming species Chaetoceros debilis, Pseudo-nitzschia subcurvata, Fragilariopsis kerguelensis, and Phaeocystis antarctica. Using membrane-inlet mass spectrometry, photosynthetic O2 evolution and inorganic carbon (Ci) fluxes were determined as a function of CO2 concentration. Only the growth of C. debilis was enhanced under high PCO2. Analysis of the carbon concentrating mechanism (CCM) revealed the operation of very efficient CCMs (i.e., high Ci affinities) in all species, but there were species-specific differences in CO2-dependent regulation of individual CCM components (i.e., CO2 and uptake kinetics, carbonic anhydrase activities). Gross CO2 uptake rates appear to increase with the cell surface area to volume ratios. Species competition experiments with C. debilis and P. subcurvata under different PCO2 levels confirmed the CO2-stimulated growth of C. debilis observed in monospecific incubations, also in the presence of P. subcurvata. Independent of PCO2, high initial cell abundances of P. subcurvata led to reduced growth rates of C. debilis. For a better understanding of future changes in phytoplankton communities, CO2-sensitive physiological processes need to be identified, but also species interactions must be taken into account because their interplay determines the success of a species.

Relative abundance of diatom species in surface samples from the Southern Ocean, Sea ice species

Diatoms from 228 Southern Ocean core-top sediment samples were examined to determine the geographic distributions of 32 major diatom species/taxa preserved in the sediments of three zonally-distinct regions; Sea Ice, Open Ocean and the Tropical/Subtropical. In the first of three papers, 14 species/taxa occurring in the region where sea ice covers the ocean surface on an annual basis are geographically documented. Comparisons are drawn between the diatom abundances on the sea floor, sea ice parameters (annual duration and concentration in February and September) and February sea-surface temperature. Such parameters are commonly used in reconstructing past oceanographic conditions in the Sea Ice and Open Ocean zones. Analysis of the geographic patterns and sea-surface parameter correlations reveals species-specific distributions regulated primarily by sea ice coverage and sea-surface temperature, which support the use of diatom remains for the estimation of these past sea-surface environmental parameters. Comparison with reliable accounts of the 14 species from the sediments or plankton also provides the first glimpses into species-specific ecology and habitat linkages.

Coccosphere geometry measurements from culture experiments on the coccolithophore species Calcidiscus leptoporus, Calcidiscus quadriperforatus and Helicosphaera carteri

Coccolithophores are a key phytoplankton group that exhibit remarkable diversity in their biology, ecology, and calcitic exoskeletons (coccospheres). An understanding of the physiological processes that underpin coccosphere architecture is essential for maximizing the information that can be retrieved from their extensive fossil record. Using culturing experiments on four modern species from three long-lived families, we investigate how coccosphere architecture responds to population shifts from rapid (exponential) to slowed (stationary) growth phases as nutrients become depleted. These experiments reveal statistical differences in cell size and the number of coccoliths per cell between these two growth phases, specifically that cells in exponential-phase growth are typically smaller with fewer coccoliths, whereas cells experiencing growth-limiting nutrient depletion have larger coccosphere sizes and greater numbers of coccoliths per cell. Although the exact numbers are species-specific, these growth-phase shifts in coccosphere geometry are common to four different coccolithophore families (Calcidiscaceae, Coccolithaceae, Isochrysidaceae, Helicosphaeraceae), demonstrating that this is a core physiological response to nutrient depletion across a representative diversity of this phytoplankton group. Polarised light microscopy was used for all coccosphere geometry measurements.

Relative abundance of diatom species in surface samples from the Southern Ocean, major open ocean species

Diatom assemblages from 228 core-top samples were investigated to determine the modern geographic distributions of 10 major open ocean species or species groups in the Atlantic and Indian sectors of the Southern Ocean. Our study gives a more comprehensive view of the relationships between diatom distribution and environmental pressures than previous studies, as our modern database covers a much wider area, and additionally highlights the relationships with sea ice cover and concentration. The 10 species or species categories can mainly be lumped into three groupings. First, a cool open ocean grouping composed of Rhizosolenia pointed group, Thalassiosira gracilis group and Trichotoxon reinboldii with maximum relative abundances occurring within the maximum winter sea-ice edge. Second, a pelagic open ocean grouping composed of Fragilariopsis kerguelensis, Thalassiosira lentiginosa, Thalassiosira oliverana and Thalassiothrix spp. group with maximum occurrences at the Antarctic Polar Front. Third, a warm open ocean grouping with maximum abundances observed within the Polar Front Zone and composed of the Rhizosolenia rounded group, the Thalassionema nitzschioides var. nitzschioides group and the Thalassionema nitzschioides var. lanceolata. Comparisons of the abovementioned 10 species or species groups with modern February sea-surface temperatures and sea-ice duration and concentration reveal species-specific sedimentary distributions regulated both by sea-surface temperatures and sea ice conditions that support the use of diatom remains to reconstruct past variations of these environmental parameters via qualitative and transfer function approaches.