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Find video protocols related to scientific articles indexed in Pubmed.
Quantitative detection of trace explosive vapors by programmed temperature desorption gas chromatography-electron capture detector.
J Vis Exp
PUBLISHED: 07-25-2014
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The direct liquid deposition of solution standards onto sorbent-filled thermal desorption tubes is used for the quantitative analysis of trace explosive vapor samples. The direct liquid deposition method yields a higher fidelity between the analysis of vapor samples and the analysis of solution standards than using separate injection methods for vapors and solutions, i.e., samples collected on vapor collection tubes and standards prepared in solution vials. Additionally, the method can account for instrumentation losses, which makes it ideal for minimizing variability and quantitative trace chemical detection. Gas chromatography with an electron capture detector is an instrumentation configuration sensitive to nitro-energetics, such as TNT and RDX, due to their relatively high electron affinity. However, vapor quantitation of these compounds is difficult without viable vapor standards. Thus, we eliminate the requirement for vapor standards by combining the sensitivity of the instrumentation with a direct liquid deposition protocol to analyze trace explosive vapor samples.
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Tradeoffs and Synergies between biofuel production and large solar infrastructure in deserts.
Environ. Sci. Technol.
PUBLISHED: 02-18-2014
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Solar energy installations in deserts are on the rise, fueled by technological advances and policy changes. Deserts, with a combination of high solar radiation and availability of large areas unusable for crop production are ideal locations for large solar installations. However, for efficient power generation, solar infrastructures use large amounts of water for construction and operation. We investigated the water use and greenhouse gas (GHG) emissions associated with solar installations in North American deserts in comparison to agave-based biofuel production, another widely promoted potential energy source from arid systems. We determined the uncertainty in our analysis by a Monte Carlo approach that varied the most important parameters, as determined by sensitivity analysis. We considered the uncertainty in our estimates as a result of variations in the number of solar modules ha(-1), module efficiency, number of agave plants ha(-1), and overall sugar conversion efficiency for agave. Further, we considered the uncertainty in revenue and returns as a result of variations in the wholesale price of electricity and installation cost of solar photovoltaic (PV), wholesale price of agave ethanol, and cost of agave cultivation and ethanol processing. The life-cycle analyses show that energy outputs and GHG offsets from solar PV systems, mean energy output of 2405 GJ ha(-1) year(-1) (5 and 95% quantile values of 1940-2920) and mean GHG offsets of 464 Mg of CO2 equiv ha(-1) year(-1) (375-562), are much larger than agave, mean energy output from 206 (171-243) to 61 (50-71) GJ ha(-1) year(-1) and mean GHG offsets from 18 (14-22) to 4.6 (3.7-5.5) Mg of CO2 equiv ha(-1) year(-1), depending upon the yield scenario of agave. Importantly though, water inputs for cleaning solar panels and dust suppression are similar to amounts required for annual agave growth, suggesting the possibility of integrating the two systems to maximize the efficiency of land and water use to produce both electricity and liquid fuel. A life-cycle analysis of a hypothetical colocation indicated higher returns per m(3) of water used than either system alone. Water requirements for energy production were 0.22 L MJ(-1) (0.28-0.19) and 0.42 L MJ(-1) (0.52-0.35) for solar PV-agave (baseline yield) and solar PV-agave (high yield), respectively. Even though colocation may not be practical in all locations, in some water-limited areas, colocated solar PV-agave systems may provide attractive economic incentives in addition to efficient land and water use.
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Dynamic headspace generation and quantitation of triacetone triperoxide vapor.
J Chromatogr A
PUBLISHED: 01-14-2014
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Two methods for quantitation of triacetone triperoxide (TATP) vapor using a programmable temperature vaporization (PTV) inlet coupled to a gas chromatography/mass spectrometer (GC/MS) have been demonstrated. The dynamic headspace of bulk TATP was mixed with clean humid air to produce a TATP vapor stream. Sampling via a heated transfer line to a PTV inlet with a Tenax-TA™ filled liner allowed for direct injection of the vapor stream to a GC/MS for vapor quantitation. TATP was extracted from the vapor stream and subsequently desorbed from the PTV liner for splitless injection on the GC column. Calibration curves were prepared using solution standards with a standard split/splitless GC inlet for quantitation of the TATP vapor. Alternatively, vapor was sampled onto a Tenax-TA™ sample tube and placed into a thermal desorption system. In this instance, vapor was desorbed from the tube and subsequently trapped on a liquid nitrogen cooled PTV inlet. Calibration curves for this method were prepared from direct liquid injection of standards onto samples tube with the caveat that a vacuum is applied to the tube during deposition to ensure that the volatile TATP penetrates into the tube. Vapor concentration measurements, as determined by either GC/MS analysis or mass gravimetry of the bulk TATP, were statistically indistinguishable. Different approaches to broaden the TATP vapor dynamic range, including diluent air flow, sample chamber temperature, sample vial orifice size, and sample size are discussed. Vapor concentrations between 50 and 5400ngL(-1) are reported, with stable vapor generation observed for as long as 60 consecutive hours.
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Loss of whole-tree hydraulic conductance during severe drought and multi-year forest die-off.
Oecologia
PUBLISHED: 01-07-2014
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Understanding the pathways through which drought stress kills woody vegetation can improve projections of the impacts of climate change on ecosystems and carbon-cycle feedbacks. Continuous in situ measurements of whole trees during drought and as trees die hold promise to illuminate physiological pathways but are relatively rare. We monitored leaf characteristics, water use efficiency, water potentials, branch hydraulic conductivity, soil moisture, meteorological variables, and sap flux on mature healthy and sudden aspen decline-affected (SAD) trembling aspen (Populus tremuloides) ramets over two growing seasons, including a severe summer drought. We calculated daily estimates of whole-ramet hydraulic conductance and modeled whole-ramet assimilation. Healthy ramets experienced rapid declines of whole-ramet conductance during the severe drought, providing an analog for what likely occurred during the previous drought that induced SAD. Even in wetter periods, SAD-affected ramets exhibited fivefold lower whole-ramet hydraulic conductance and sevenfold lower assimilation than counterpart healthy ramets, mediated by changes in leaf area, water use efficiency, and embolism. Extant differences between healthy and SAD ramets reveal that ongoing multi-year forest die-off is primarily driven by loss of whole-ramet hydraulic capability, which in turn limits assimilation capacity. Branch-level measurements largely captured whole-plant hydraulic limitations during drought and mortality, but whole-plant measurements revealed a potential role of other losses in the hydraulic continuum. Our results highlight the importance of a whole-tree perspective in assessing physiological pathways to tree mortality and indicate that the effects of mortality on these forests' assimilation and productivity are larger than expected based on canopy leaf area differences.
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Integrating stand and soil properties to understand foliar nutrient dynamics during forest succession following slash-and-burn agriculture in the Bolivian Amazon.
PLoS ONE
PUBLISHED: 01-01-2014
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Secondary forests cover large areas of the tropics and play an important role in the global carbon cycle. During secondary forest succession, simultaneous changes occur among stand structural attributes, soil properties, and species composition. Most studies classify tree species into categories based on their regeneration requirements. We use a high-resolution secondary forest chronosequence to assign trees to a continuous gradient in species successional status assigned according to their distribution across the chronosequence. Species successional status, not stand age or differences in stand structure or soil properties, was found to be the best predictor of leaf trait variation. Foliar ?(13)C had a significant positive relationship with species successional status, indicating changes in foliar physiology related to growth and competitive strategy, but was not correlated with stand age, whereas soil ?(13)C dynamics were largely constrained by plant species composition. Foliar ?(15)N had a significant negative correlation with both stand age and species successional status, - most likely resulting from a large initial biomass-burning enrichment in soil (15)N and (13)C and not closure of the nitrogen cycle. Foliar %C was neither correlated with stand age nor species successional status but was found to display significant phylogenetic signal. Results from this study are relevant to understanding the dynamics of tree species growth and competition during forest succession and highlight possibilities of, and potentially confounding signals affecting, the utility of leaf traits to understand community and species dynamics during secondary forest succession.
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Changes in ecologically critical terrestrial climate conditions.
Science
PUBLISHED: 08-03-2013
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Terrestrial ecosystems have encountered substantial warming over the past century, with temperatures increasing about twice as rapidly over land as over the oceans. Here, we review the likelihood of continued changes in terrestrial climate, including analyses of the Coupled Model Intercomparison Project global climate model ensemble. Inertia toward continued emissions creates potential 21st-century global warming that is comparable in magnitude to that of the largest global changes in the past 65 million years but is orders of magnitude more rapid. The rate of warming implies a velocity of climate change and required range shifts of up to several kilometers per year, raising the prospect of daunting challenges for ecosystems, especially in the context of extensive land use and degradation, changes in frequency and severity of extreme events, and interactions with other stresses.
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Environmental and community controls on plant canopy chemistry in a Mediterranean-type ecosystem.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 04-08-2013
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Understanding how and why plant communities vary across space has long been a goal of ecology, yet parsing the relative importance of different influences has remained a challenge. Species-specific models are not generalizable, whereas broad plant functional type models lack important detail. Here we consider plant trait patterns at the local scale and ask whether plant chemical traits are more closely linked to environmental gradients or to changes in species composition. We used the visible-to-shortwave infrared (VSWIR) spectrometer of the Carnegie Airborne Observatory to develop maps of four plant chemical traits--leaf nitrogen per mass, leaf carbon per mass, leaf water concentration, and canopy water content--across a diverse Mediterranean-type ecosystem (Jasper Ridge Biological Preserve, CA). For all four traits, plant community alone was the strongest predictor of trait variation (explaining 46-61% of the heterogeneity), whereas environmental gradients accounted for just one fourth of the variation in the traits. This result emphasizes the critical role that species composition plays in mediating nutrient and carbon cycling within and among different communities. Environmental filtering and limits to similarity can act strongly, simultaneously, in a spatially heterogeneous environment, but the local-scale environmental gradients alone cannot account for the variation across this landscape.
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Droughts legacy: multiyear hydraulic deterioration underlies widespread aspen forest die-off and portends increased future risk.
Glob Chang Biol
PUBLISHED: 01-10-2013
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Forest mortality constitutes a major uncertainty in projections of climate impacts on terrestrial ecosystems and carbon-cycle feedbacks. Recent drought-induced, widespread forest die-offs highlight that climate change could accelerate forest mortality with its diverse and potentially severe consequences for the global carbon cycle, ecosystem services, and biodiversity. How trees die during drought over multiple years remains largely unknown and precludes mechanistic modeling and prediction of forest die-off with climate change. Here, we examine the physiological basis of a recent multiyear widespread die-off of trembling aspen (Populus tremuloides) across much of western North America. Using observations from both native trees while they are dying and a rainfall exclusion experiment on mature trees, we measure hydraulic performance over multiple seasons and years and assess pathways of accumulated hydraulic damage. We test whether accumulated hydraulic damage can predict the probability of tree survival over 2 years. We find that hydraulic damage persisted and increased in dying trees over multiple years and exhibited few signs of repair. This accumulated hydraulic deterioration is largely mediated by increased vulnerability to cavitation, a process known as cavitation fatigue. Furthermore, this hydraulic damage predicts the probability of interyear stem mortality. Contrary to the expectation that surviving trees have weathered severe drought, the hydraulic deterioration demonstrated here reveals that surviving regions of these forests are actually more vulnerable to future droughts due to accumulated xylem damage. As the most widespread tree species in North America, increasing vulnerability to drought in these forests has important ramifications for ecosystem stability, biodiversity, and ecosystem carbon balance. Our results provide a foundation for incorporating accumulated drought impacts into climate-vegetation models. Finally, our findings highlight the critical role of drought stress accumulation and repair of stress-induced damage for avoiding plant mortality, presenting a dynamic and contingent framework for drought impacts on forest ecosystems.
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Direct liquid deposition calibration method for trace cyclotrimethylenetrinitramine using thermal desorption instrumentation.
J Chromatogr A
PUBLISHED: 01-08-2013
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A simple method for establishing calibration curves with sorbent-filled thermal desorption tubes has been demonstrated for nitroaromatic and nitramine vapor samples using a thermal desorption system with a cooled inlet system (TDS-CIS), which was coupled to a gas chromatograph (GC) with an electron capture detector (ECD). The method relies upon the direct liquid deposition of standard solutions onto the glass frit at the head of sorbent-filled thermal desorption tubes. Linear calibration results and ideal system conditions for the TDS-CIS-GC-ECD were established for mixtures containing both cyclotrimethylenetrinitramine, a.k.a. RDX, and 2,4,6-trinitrotoluene (TNT). Because of the chemical characteristics of RDX, a higher TDS-CIS flow rate relative to the optimized approach for TNT was required for efficient RDX desorption. Simultaneous quantitation of TNT and RDX using the direct liquid deposition method with optimized instrumentation parameters for RDX were compared to results from a standard split/splitless GC inlet and a CIS.
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Improving evolutionary models for mitochondrial protein data with site-class specific amino acid exchangeability matrices.
PLoS ONE
PUBLISHED: 01-02-2013
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Adequate modeling of mitochondrial sequence evolution is an essential component of mitochondrial phylogenomics (comparative mitogenomics). There is wide recognition within the field that lineage-specific aspects of mitochondrial evolution should be accommodated through lineage-specific amino-acid exchangeability matrices (e.g., mtMam for mammalian data). However, such a matrix must be applied to all sites and this implies that all sites are subject to the same, or largely similar, evolutionary constraints. This assumption is unjustified. Indeed, substantial differences are expected to arise from three-dimensional structures that impose different physiochemical environments on individual amino acid residues. The objectives of this paper are (1) to investigate the extent to which amino acid evolution varies among sites of mitochondrial proteins, and (2) to assess the potential benefits of explicitly modeling such variability. To achieve this, we developed a novel method for partitioning sites based on amino acid physiochemical properties. We apply this method to two datasets derived from complete mitochondrial genomes of mammals and fish, and use maximum likelihood to estimate amino acid exchangeabilities for the different groups of sites. Using this approach we identified large groups of sites evolving under unique physiochemical constraints. Estimates of amino acid exchangeabilities differed significantly among such groups. Moreover, we found that joint estimates of amino acid exchangeabilities do not adequately represent the natural variability in evolutionary processes among sites of mitochondrial proteins. Significant improvements in likelihood are obtained when the new matrices are employed. We also find that maximum likelihood estimates of branch lengths can be strongly impacted. We provide sets of matrices suitable for groups of sites subject to similar physiochemical constraints, and discuss how they might be used to analyze real data. We also discuss how the general approach might be employed to improve a variety of mitogenomic-based research activities.
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Nitrogen deposition reduces plant diversity and alters ecosystem functioning: field-scale evidence from a nationwide survey of UK heathlands.
PLoS ONE
PUBLISHED: 01-01-2013
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Findings from nitrogen (N) manipulation studies have provided strong evidence of the detrimental impacts of elevated N deposition on the structure and functioning of heathland ecosystems. Few studies, however, have sought to establish whether experimentally observed responses are also apparent under natural, field conditions. This paper presents the findings of a nationwide field-scale evaluation of British heathlands, across broad geographical, climatic and pollution gradients. Fifty two heathlands were selected across an N deposition gradient of 5.9 to 32.4 kg ha(-1) yr(-1). The diversity and abundance of higher and lower plants and a suite of biogeochemical measures were evaluated in relation to climate and N deposition indices. Plant species richness declined with increasing temperature and N deposition, and the abundance of nitrophilous species increased with increasing N. Relationships were broadly similar between upland and lowland sites, with the biggest reductions in species number associated with increasing N inputs at the low end of the deposition range. Both oxidised and reduced forms of N were associated with species declines, although reduced N appears to be a stronger driver of species loss at the functional group level. Plant and soil biochemical indices were related to temperature, rainfall and N deposition. Litter C:N ratios and enzyme (phenol-oxidase and phosphomonoesterase) activities had the strongest relationships with site N inputs and appear to represent reliable field indicators of N deposition. This study provides strong, field-scale evidence of links between N deposition--in both oxidised and reduced forms--and widespread changes in the composition, diversity and functioning of British heathlands. The similarity of relationships between upland and lowland environments, across broad spatial and climatic gradients, highlights the ubiquity of relationships with N, and suggests that N deposition is contributing to biodiversity loss and changes in ecosystem functioning across European heathlands.
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The roles of hydraulic and carbon stress in a widespread climate-induced forest die-off.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 12-13-2011
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Forest ecosystems store approximately 45% of the carbon found in terrestrial ecosystems, but they are sensitive to climate-induced dieback. Forest die-off constitutes a large uncertainty in projections of climate impacts on terrestrial ecosystems, climate-ecosystem interactions, and carbon-cycle feedbacks. Current understanding of the physiological mechanisms mediating climate-induced forest mortality limits the ability to model or project these threshold events. We report here a direct and in situ study of the mechanisms underlying recent widespread and climate-induced trembling aspen (Populus tremuloides) forest mortality in western North America. We find substantial evidence of hydraulic failure of roots and branches linked to landscape patterns of canopy and root mortality in this species. On the contrary, we find no evidence that drought stress led to depletion of carbohydrate reserves. Our results illuminate proximate mechanisms underpinning recent aspen forest mortality and provide guidance for understanding and projecting forest die-offs under climate change.
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Indole inhibition of ColE1 replication contributes to stable plasmid maintenance.
Plasmid
PUBLISHED: 11-07-2011
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In the absence of active partitioning, strict control of plasmid copy number is required to minimise the possibility of plasmid loss at bacterial cell division. An important cause of multicopy plasmid instability is the formation of plasmid dimers by recombination and their subsequent proliferation by over-replication in a process known as the dimer catastrophe. This leads to the formation of dimer-only cells in which plasmid copy number is substantially lower than in cells containing only monomers, and which have a greatly increased probability of plasmid loss at division. The accumulation of dimers triggers the synthesis of the regulatory small RNA, Rcd, which stimulates tryptophanase and increases the production of indole. This, in turn, inhibits Escherichia coli cell division. The Rcd checkpoint hypothesis proposes that delaying cell division allows time for the relatively slow conversion of plasmid dimers to monomers by Xer-cer site-specific recombination. In the present work we have re-evaluated this hypothesis and concluded that a cell division block is insufficient to prevent the dimer catastrophe. Plasmid replication must also be inhibited. In vivo experiments have shown that indole, when added exogenously to a broth culture of E. coli does indeed stop plasmid replication as well as cell division. We have also shown that indole inhibits the activity of DNA gyrase in vitro and propose that this is the mechanism by which plasmid replication is blocked. The simultaneous effects of upon growth, cell division and DNA replication in E. coli suggest that indole acts as a true cell cycle regulator.
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Strong response of an invasive plant species (Centaurea solstitialis L.) to global environmental changes.
Ecol Appl
PUBLISHED: 09-24-2011
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Global environmental changes are altering interactions among plant species, sometimes favoring invasive species. Here, we examine how a suite of five environmental factors, singly and in combination, can affect the success of a highly invasive plant. We introduced Centaurea solstitialis L. (yellow starthistle), which is considered by many to be Californias most troublesome wildland weed, to grassland plots in the San Francisco Bay Area. These plots experienced ambient or elevated levels of warming, atmospheric CO2, precipitation, and nitrate deposition, and an accidental fire in the previous year created an additional treatment. Centaurea grew more than six times larger in response to elevated CO2, and, outside of the burned area, grew more than three times larger in response to nitrate deposition. In contrast, resident plants in the community responded less strongly (or did not respond) to these treatments. Interactive effects among treatments were rarely significant. Results from a parallel mesocosm experiment, while less dramatic, supported the pattern of results observed in the field. Taken together, our results suggest that ongoing environmental changes may dramatically increase Centaureas prevalence in western North America.
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Allometric growth and allocation in forests: a perspective from FLUXNET.
Ecol Appl
PUBLISHED: 08-12-2011
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To develop a scheme for partitioning the products of photosynthesis toward different biomass components in land-surface models, a database on component mass and net primary productivity (NPP), collected from FLUXNET sites, was examined to determine allometric patterns of allocation. We found that NPP per individual of foliage (Gfol), stem and branches (Gstem), coarse roots (Gcroot) and fine roots (Gfroot) in individual trees is largely explained (r2 = 67-91%) by the magnitude of total NPP per individual (G). Gfol scales with G isometrically, meaning it is a fixed fraction of G ( 25%). Root-shoot trade-offs were manifest as a slow decline in Gfroot, as a fraction of G, from 50% to 25% as stands increased in biomass, with Gstem and Gcroot increasing as a consequence. These results indicate that a functional trade-off between aboveground and belowground allocation is essentially captured by variations in G, which itself is largely governed by stand biomass and only secondarily by site-specific resource availability. We argue that forests are characterized by strong competition for light, observed as a race for individual trees to ascend by increasing partitioning toward wood, rather than by growing more leaves, and that this competition stronglyconstrains the allocational plasticity that trees may be capable of. The residual variation in partitioning was not related to climatic or edaphic factors, nor did plots with nutrient or water additions show a pattern of partitioning distinct from that predicted by G alone. These findings leverage short-term process studies of the terrestrial carbon cycle to improve decade-scale predictions of biomass accumulation in forests. An algorithm for calculating partitioning in land-surface models is presented.
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Periodically porous top electrodes on vertical nanowire arrays for highly sensitive gas detection.
Nanotechnology
PUBLISHED: 08-05-2011
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Nanowires of various materials and configurations have been shown to be highly effective in the detection of chemical and biological species. In this paper, we report a novel, nanosphere-enabled approach to fabricating highly sensitive gas sensors based on ordered arrays of vertically aligned silicon nanowires topped with a periodically porous top electrode. The vertical array configuration helps to greatly increase the sensitivity of the sensor while the pores in the top electrode layer significantly improve sensing response times by allowing analyte gases to pass through freely. Herein, we show highly sensitive detection to both nitrogen dioxide (NO(2)) and ammonia (NH(3)) in humidified air. NO(2) detection down to 10 parts per billion (ppb) is demonstrated and an order-of-magnitude improvement in sensor response time is shown in the detection of NH(3).
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Fast carbon nanotube detectors for micro gas chromatographs.
Nanoscale
PUBLISHED: 07-15-2011
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Highly sensitive and completely reversible chemiresistor detectors based on carbon nanotubes (CNTs) were fabricated for multi-component chemical analysis. CNT detectors were used in a series configuration with a gas chromatography column and exposed to a mixture of nine different compounds. It is shown that CNT detectors were able to show parts per billion (pbb) sensitivity responses to each individual component of the mixture and detect nine distinct chemical compounds in roughly 210 s when the detector operates in current stimulated desorption (CSD) mode. This is the first demonstration of an uncoated CNT detector to analyze multi-component chemical mixtures providing an alternative yet simple sensing approach for online air quality control and health monitoring applications.
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Vapor detection performance of vertically aligned, ordered arrays of silicon nanowires with a porous electrode.
Anal. Chem.
PUBLISHED: 05-17-2011
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Vertically aligned, ordered arrays of silicon nanowires capped with a porous top electrode are used to detect gas phase ammonia and nitrogen dioxide in humidified air. The sensors had very fast response times and large signal-to-noise ratios. Calibration curves were created using both an initial slope method and a fixed-time point method. The initial-slope method had a power law dependence that correlates well with concentration, demonstrating a viable alternative for eventual quantitative vapor detection and enabling shorter sampling and regeneration times.
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Global change could amplify fire effects on soil greenhouse gas emissions.
PLoS ONE
PUBLISHED: 04-25-2011
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Little is known about the combined impacts of global environmental changes and ecological disturbances on ecosystem functioning, even though such combined impacts might play critical roles in shaping ecosystem processes that can in turn feed back to climate change, such as soil emissions of greenhouse gases.
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Direct climate effects of perennial bioenergy crops in the United States.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 02-28-2011
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Biomass-derived energy offers the potential to increase energy security while mitigating anthropogenic climate change, but a successful path toward increased production requires a thorough accounting of costs and benefits. Until recently, the efficacy of biomass-derived energy has focused primarily on biogeochemical consequences. Here we show that the biogeophysical effects that result from hypothetical conversion of annual to perennial bioenergy crops across the central United States impart a significant local to regional cooling with considerable implications for the reservoir of stored soil water. This cooling effect is related mainly to local increases in transpiration, but also to higher albedo. The reduction in radiative forcing from albedo alone is equivalent to a carbon emissions reduction of , which is six times larger than the annual biogeochemical effects that arise from offsetting fossil fuel use. Thus, in the near-term, the biogeophysical effects are an important aspect of climate impacts of biofuels, even at the global scale. Locally, the simulated cooling is sufficiently large to partially offset projected warming due to increasing greenhouse gases over the next few decades. These results demonstrate that a thorough evaluation of costs and benefits of bioenergy-related land-use change must include potential impacts on the surface energy and water balance to comprehensively address important concerns for local, regional, and global climate change.
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Nonthermal current-stimulated desorption of gases from carbon nanotubes.
Science
PUBLISHED: 09-11-2010
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The desorption of gases from carbon nanotubes is usually a slow process that limits the nanotubes utility as sensors or as memristors. Here, we demonstrate that flow in the nanotube above the Poole-Frenkel conduction threshold can stimulate adsorbates to desorb without heating the sensor substantially. The method is general: alcohols, aromatics, amines, and phosphonates were all found to desorb. We postulate that the process is analogous to electron-stimulated desorption, but with an internally conducted rather than externally applied source of electrons.
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Hierarchical state-space estimation of leatherback turtle navigation ability.
PLoS ONE
PUBLISHED: 06-10-2010
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Remotely sensed tracking technology has revealed remarkable migration patterns that were previously unknown; however, models to optimally use such data have developed more slowly. Here, we present a hierarchical Bayes state-space framework that allows us to combine tracking data from a collection of animals and make inferences at both individual and broader levels. We formulate models that allow the navigation ability of animals to be estimated and demonstrate how information can be combined over many animals to allow improved estimation. We also show how formal hypothesis testing regarding navigation ability can easily be accomplished in this framework. Using Argos satellite tracking data from 14 leatherback turtles, 7 males and 7 females, during their southward migration from Nova Scotia, Canada, we find that the circle of confusion (the radius around an animals location within which it is unable to determine its location precisely) is approximately 96 km. This estimate suggests that the turtles navigation does not need to be highly accurate, especially if they are able to use more reliable cues as they near their destination. Moreover, for the 14 turtles examined, there is little evidence to suggest that male and female navigation abilities differ. Because of the minimal assumptions made about the movement process, our approach can be used to estimate and compare navigation ability for many migratory species that are able to carry electronic tracking devices.
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Sample handling and chemical kinetics in an acoustically levitated drop microreactor.
Anal. Chem.
PUBLISHED: 09-23-2009
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Accurate measurement of enzyme kinetics is an essential part of understanding the mechanisms of biochemical reactions. The typical means of studying such systems use stirred cuvettes, stopped-flow apparatus, microfluidic systems, or other small sample containers. These methods may prove to be problematic if reactants or products adsorb to or react with the containers surface. As an alternative approach, we have developed an acoustically-levitated drop reactor eventually intended to study enzyme-catalyzed reaction kinetics related to free radical and oxidative stress chemistry. Microliter-scale droplet generation, reactant introduction, maintenance, and fluid removal are all important aspects in conducting reactions in a levitated drop. A three capillary bundle system has been developed to address these needs. We report kinetic measurements for both luminol chemiluminescence and the reaction of pyruvate with nicotinamide adenine dinucleotide, catalyzed by lactate dehydrogenase, to demonstrate the feasibility of using a levitated drop in conjunction with the developed capillary sample handling system as a microreactor.
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The velocity of climate change.
Nature
PUBLISHED: 08-27-2009
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The ranges of plants and animals are moving in response to recent changes in climate. As temperatures rise, ecosystems with nowhere to go, such as mountains, are considered to be more threatened. However, species survival may depend as much on keeping pace with moving climates as the climates ultimate persistence. Here we present a new index of the velocity of temperature change (km yr(-1)), derived from spatial gradients ( degrees C km(-1)) and multimodel ensemble forecasts of rates of temperature increase ( degrees C yr(-1)) in the twenty-first century. This index represents the instantaneous local velocity along Earths surface needed to maintain constant temperatures, and has a global mean of 0.42 km yr(-1) (A1B emission scenario). Owing to topographic effects, the velocity of temperature change is lowest in mountainous biomes such as tropical and subtropical coniferous forests (0.08 km yr(-1)), temperate coniferous forest, and montane grasslands. Velocities are highest in flooded grasslands (1.26 km yr(-1)), mangroves and deserts. High velocities suggest that the climates of only 8% of global protected areas have residence times exceeding 100 years. Small protected areas exacerbate the problem in Mediterranean-type and temperate coniferous forest biomes. Large protected areas may mitigate the problem in desert biomes. These results indicate management strategies for minimizing biodiversity loss from climate change. Montane landscapes may effectively shelter many species into the next century. Elsewhere, reduced emissions, a much expanded network of protected areas, or efforts to increase species movement may be necessary.
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Linking definitions, mechanisms, and modeling of drought-induced tree death.
Trends Plant Sci.
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Tree death from drought and heat stress is a critical and uncertain component in forest ecosystem responses to a changing climate. Recent research has illuminated how tree mortality is a complex cascade of changes involving interconnected plant systems over multiple timescales. Explicit consideration of the definitions, dynamics, and temporal and biological scales of tree mortality research can guide experimental and modeling approaches. In this review, we draw on the medical literature concerning human death to propose a water resource-based approach to tree mortality that considers the tree as a complex organism with a distinct growth strategy. This approach provides insight into mortality mechanisms at the tree and landscape scales and presents promising avenues into modeling tree death from drought and temperature stress.
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Environmental filtering and land-use history drive patterns in biomass accumulation in a mediterranean-type landscape.
Ecol Appl
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Aboveground biomass (AGB) reflects multiple and often undetermined ecological and land-use processes, yet detailed landscape-level studies of AGB are uncommon due to the difficulty in making consistent measurements at ecologically relevant scales. Working in a protected mediterranean-type landscape (Jasper Ridge Biological Preserve, California, USA), we combined field measurements with remotely sensed data from the Carnegie Airborne Observatorys light detection and ranging (lidar) system to create a detailed AGB map. We then developed a predictive model using a maximum of 56 explanatory variables derived from geologic and historic-ownership maps, a digital elevation model, and geographic coordinates to evaluate possible controls over currently observed AGB patterns. We tested both ordinary least-squares regression (OLS) and autoregressive approaches. OLS explained 44% of the variation in AGB, and simultaneous autoregression with a 100-m neighborhood improved the fit to an r2 = 0.72, while reducing the number of significant predictor variables from 27 variables in the OLS model to 11 variables in the autoregressive model. We also compared the results from these approaches to a more typical field-derived data set; we randomly sampled 5% of the data 1000 times and used the same OLS approach each time. Environmental filters including incident solar radiation, substrate type, and topographic position were significant predictors of AGB in all models. Past ownership was a minor but significant predictor, despite the long history of conservation at the site. The weak predictive power of these environmental variables, and the significant improvement when spatial autocorrelation was incorporated, highlight the importance of land-use history, disturbance regime, and population dynamics as controllers of AGB.
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Indole prevents Escherichia coli cell division by modulating membrane potential.
Biochim. Biophys. Acta
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Indole is a bacterial signalling molecule that blocks E. coli cell division at concentrations of 3-5 mM. We have shown that indole is a proton ionophore and that this activity is key to the inhibition of division. By reducing the electrochemical potential across the cytoplasmic membrane of E. coli, indole deactivates MinCD oscillation and prevents formation of the FtsZ ring that is a prerequisite for division. This is the first example of a natural ionophore regulating a key biological process. Our findings have implications for our understanding of membrane biology, bacterial cell cycle control and potentially for the design of antibiotics that target the cell membrane.
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Characterization of thermal desorption instrumentation with a direct liquid deposition calibration method for trace 2,4,6-trinitrotoluene quantitation.
J Chromatogr A
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The use of thermal desorption systems for the analysis of trace vapors typically requires establishing a calibration curve from vapors generated with a permeation tube. The slow equilibration time of permeation tubes causes such an approach to become laborious when covering a wide dynamic range. Furthermore, many analytes of interest, such as explosives, are not available as permeation tubes. A method for easily and effectively establishing calibration curves for explosive vapor samples via direct deposition of standard solutions on thermal desorption tubes was investigated. The various components of the thermal desorption system were compared to a standard split/splitless inlet. Calibration curves using the direct liquid deposition method with a thermal desorption unit coupled to a cryo-focusing inlet were compared to a standard split/splitless inlet, and a statistical difference was observed but does not eliminate or deter the use of the direct liquid deposition method for obtaining quantitative results for explosive vapors.
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The Land-Use Efficiency of Big Solar.
Environ. Sci. Technol.
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As utility-scale solar energy (USSE) systems increase in size and numbers globally, there is a growing interest in understanding environmental interactions between solar energy development and land-use decisions. Maximizing the efficient use of land for USSE is one of the major challenges in realizing the full potential of solar energy, however, the land-use efficiency (LUE; Wm-2) of USSE remains ambiguous. We quantified the capacity-based LUE of 183 USSE installations (> 20 MW; planned, under construction, and operating) using California as a case study. In California, USSE installations are concentrated in the Central Valley and interior regions of southern California and have a LUE of 35.0 Wm-2. The installations occupy approximately 86,000 hectares and more land is allocated for photovoltaic schemes (72,294 ha) than for concentrating solar power (13,604 ha). Photovoltaic installations are greater in abundance (93%) than concentrating solar power, but technology type and nameplate capacity has no impact on capacity-based LUE. More USSE installations are on private land (80%) and have a significantly greater LUE (35.8 Wm-2) than installations on public land (25.4 Wm-2). Our findings can be used to better understand and improve the LUE of USSE, thereby maximizing economic, energetic, and environmental returns on investments.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

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In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.