Detection of Bacillus anthracis from spores and cells by loop-mediated isothermal amplification without sample preparation

Loop-mediated isothermal amplification (LAMP) is a technique capable of rapidly amplifying specific nucleic acid sequences without specialized thermal cycling equipment. In addition, several detection methods that include dye fluorescence, gel electrophoresis, turbidity and colorimetric change, can be used to measure or otherwise detect target amplification. To date, publications have described the requirement for some form of sample nucleic acid extraction (boiling, lysis, DNA purification, etc.) prior to initiating a LAMP reaction. We demonstrate here, the first LAMP positive results obtained from vegetative cells and spores of Bacillus anthracis without nucleic acid extraction. Our data show that the simple addition of cells or spores to the reaction mixture, followed by heating at 63°C is all that is required to reproducibly amplify and detect target plasmid and chromosomal DNA via colorimetric change. The use of three primer sets targeting both plasmids and the chromosome of B. anthracis allows for the rapid discrimination of non-pathogenic bacteria from pathogenic bacteria within 30 min of sampling. Our results indicate that direct testing of B. anthracis spores and cells via LAMP assay will greatly simplify and shorten the detection process by eliminating nucleic acid purification. These results may allow more rapid detection of DNA from pathogenic organisms present in field and environmental samples.     

An adaptable spectroelectrochemical titrator: the midpoint reduction potential of the iron-sulfur center in lysine 2,3-aminomutase

Elaborations to an earlier design of an electron paramagnetic resonance (EPR) spectroelectrochemical titrator are described. While maintaining the anaerobic capabilities of the original design, a number of modifications and revisions have been introduced. The most significant modification is the use of a detachable spectral cell, making the apparatus modular and adaptable for multiple forms of spectroscopy. Additional modifications include removable reference, auxiliary, and working electrodes; modifications to facilitate sample transfer; and adaptations for operation within an anaerobic chamber. This apparatus has been used successfully in the coulometric titration of a [4Fe-4S] enzyme, as measured by EPR spectroscopy. The midpoint reduction potential for the 2+/1+ couple in the [4Fe-4S] cluster of lysine 2,3-aminomutase is -479+/-5mV, a value that falls within the range typical of ferredoxin-like iron-sulfur clusters.     

Stomatal response of hybrid poplar to incident light, sudden darkening and leaf excision

Responses of abaxial and adaxial stomata of Populus trichocarpa Torr. & Gray. × P. deltoides Bartr. (ex Marsh.) cv. Unal to incident light, sudden darkening and leaf excision in the light and in the dark were studied on 5-year-old trees in the field using diffusion porometry. Stomatal closure in the dark was found to be incomplete in most cases studies. Stomata closed after leaf excision in the dark within 90 min. Stomatal closure after darkening of an entire tree or an entire branch (white the rest of the tree was in the light) was slower, and complete stomatal closure was noticed only for adaxial stomata after 3 h. Adaxial stomata were more reactive and sensitive than abaxial stomata to sudden darkening and leaf excision in the light and the dark. In all treatments, stomatal response was more responsive in mature leaves than in young, still expanding leaves.     

Acclimation responses of mature Abies amabilis sun foliage to shading

This paper addresses two main questions. First, can evergreen foliage that has been structurally determined as sun foliage acclimate physiologically when it is shaded? Second, is this acclimation independent of the foliage ageing process and source-sink relations? To investigate these questions, a shading and debudding experiment was established using paired branches on opengrown Abies amabilis trees. For each tree, one branch was either shaded, debudded, or both, from before budbreak until the end of summer, while the other branch functioned as a control. Foliage samples were measured both prior to and during treatment for photosynthesis at light saturation (A _max), dark respiration, nitrogen content, chlorophyll content, chlorophyll-to-nitrogen ratio and chlorophyll a:b ratio. All age classes of foliage responded similarly during the treatment, although pre-treatment values differed between age classes. Within 1 month after the treatment began, A _max was lower in shaded foliage and remained lower throughout the treatment period. For debudded branches, A _max was lower than the controls only during active shoot elongation. At the end of the treatments in September, A _max in shade-treated sun foliage matched the rates in the true shade-formed foliage, but nitrogen remained significantly higher. By 1.5 months after treatment, chlorophyll content in shaded foliage was higher than in controls, and the chlorophyll a:b ratio was lower for the shaded foliage. On debudded branches, chlorophyll content and chlorophyll a:b ratio were similar to the values in control samples. Shading lowered the rate of nitrogen accumulation within a branch, while removing debudding decreased the amount of sequestered N that was exported from the older foliage to supply new growth. By September, chlorophyll content in shade-treated foliage was higher than that in the control sun foliage or in true shade foliage. The chlorophyll increase as a result of shading was unexpected. However, the chlorophyll-to-nitrogen ratio was identical for the shade-treated sun foliage and the true shade foliage while being significantly lower than the control sun foliage. It appears that acclimation to shading in mature foliage involves a reallocation of nitrogen within the leaf into thylakoid proteins. A redistribution of resources (nitrogen) among leaves is secondary and appears to function on a slower time scale than reallocation within the leaf. Thus, A. amabilis foliage that is structurally determined as sun foliage can acclimate to shade within a few months; this process is most likely independent of ageing and is only slightly affected by source-sink relations within a branch.     

Components and Controls of Water Flux in an Old-growth Douglas-fir–Western Hemlock Ecosystem

We report measurements of rates of sap flow in dominant trees, changes in soil moisture, and evaporation from coarse woody debris in an old-growth Douglas-fir–western hemlock ecosystem at Wind River, Washington, USA, during dry periods in summer. The measurements are compared with eddy-covariance measurements of water-vapor fluxes above the forest (E_e) and at the forest floor (E_u) to examine the components of ecosystem water loss and the factors controlling them. Daily values of E_u were about 10% of E_e. Evaporation from coarse woody debris was only about 2% of E_e. Transpiration (E_t), estimated by scaling sap-flow measurements accounted for about 70% of (E_e– E_u); transpiration from subdominant trees may account for the remainder. The daily total change in soil moisture (E_s) in the top 30 cm was larger than the net change, probably because of hydraulic redistribution of soil water by roots. Observed differences between E_s and E_e were probably because roots also extract water from greater depth, and/or because the measuring systems sample at different spatial scales. The ratio of E_t to E_s decreased with decreasing soil water content, suggesting that partitioning in water use between understory and overstory changed during the season. The rate of soil drying exceeded E_e early in the day, probably because water vapor was being stored in canopy air space and condensed or adsorbed on tree stems, lichens, and mosses. The daily variation of E_e with vapor-pressure deficit showed strong hysteresis, most likely associated with transpiration of water stored in tree stems and branches.     

A CRITICAL REVIEW OF THE REGIME SHIFT-"JUNK FOOD"-NUTRITIONAL STRESS HYPOTHESIS FOR THE DECLINE OF THE WESTERN STOCK OF STELLER SEA LION

Steller sea lions ( Eumetopias jubatus ) in the central and western Gulf of Alaska, Aleutian Islands, and Bering Sea have declined by 80% in the last 30 yr. One hypothesis for the decline in this western Steller sea lion population is that a climate regime shift in 1976–1977 changed the species composition of the fish community and reduced the nutritional quality (energy density) of the sea lion prey field. This in turn led to nutritional stress and reduced individual fitness, survival, and reproduction of sea lions. Implications of this regime shift-"junk food" hypothesis are that (1) the recruitment and abundance of supposed high quality species ( e.g. , Pacific herring, Clupea pallasi ) decreased while those of supposed low quality ( e.g. , species in the family Gadidae) increased following the regime shift, (2) Steller sea lion diets shifted in response to this change in fish community structure, and (3) a diet composed principally of gadids ( e.g. , walleye pollock, Theragra chalcogramma ) is detrimental to sea lion fitness and survival. We examine data relating to each of these implications and find little support for the hypothesis that increases in the availability and consumption of gadids following the regime shift are primarily responsible for the decline of the western population of Steller sea lion.     

The “Reservation Effect”: Implications for Background Comparisons

A difficult challenge in ecological risk assessment can be determining what constitutes the “background” or ground-state condition for a site. This is because off-site conditions may not reflect to any relevant degree the history of the site itself and may therefore not be appropriate as benchmarks. One of the more important concerns is that underestimates may be made regarding contaminant-related impacts on-site because observations may indicate that community or population quality on-site equals or surpasses that observed off-site. In other cases, overestimates of the degree of contaminant impact may be made if environmental resources on-site are highly managed or devoid of natural communities. As such, management decisions may be confounded by artifacts of non-toxicant-related human influence and will not necessarily appropriately address the contaminant-related issues. Examples of these conditions are discussed herein.     

Experimental removal and addition of leaf litter inputs reduces nitrate production and loss in a lowland tropical forest

Environmental perturbations such as changes in land use, climate, and atmospheric carbon dioxide concentrations may alter organic matter inputs to surface soils. While the carbon (C) cycle response to such perturbations has received considerable attention, potential responses of the soil nitrogen (N) cycle to changing organic matter inputs have been less well characterized. Changing litter inputs to surface to soils may alter the soil N cycle directly, by controlling N substrate availability, or indirectly, via interactions with soil C biogeochemistry. We investigated soil N-cycling responses to a leaf litter manipulation in a lowland tropical forest using isotopic and molecular techniques. Both removing and doubling leaf litter inputs decreased the size of the soil nitrate pool, gross nitrification rates, and the relative abundance of ammonia-oxidizing microorganisms. Gross nitrification rates were correlated with the relative abundance of ammonia-oxidizing archaea, and shifts in the N-cycling microbial community composition correlated with concurrent changes in edaphic properties, notably pH and C:N ratios. These results highlight the importance of understanding coupled biogeochemical cycles in global change scenarios and suggest that environmental perturbations that alter organic matter inputs in tropical forests could reduce inorganic N losses to surface waters and the atmosphere by limiting nitrate production.