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Find video protocols related to scientific articles indexed in Pubmed.
Phosphatase-Inert Glucosamine 6-Phosphate Mimics Serve as Actuators of the glmS Riboswitch.
ACS Chem. Biol.
PUBLISHED: 09-26-2014
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The glmS riboswitch is unique among gene-regulating riboswitches and catalytic RNAs. This is because its own metabolite, glucosamine-6-phosphate (GlcN6P), binds to the riboswitch and catalytically participates in the RNA self-cleavage reaction, thereby providing a novel negative feedback mechanism. Given that a number of pathogens harbor the glmS riboswitch, artificial actuators of this potential RNA target are of great interest. Structural/kinetic studies point to the 2-amino and 6-phosphate ester functionalities in GlcN6P as being crucial for this actuation. As a first step toward developing artificial actuators, we have synthesized a series of nine GlcN6P analogs bearing phosphatase-inert surrogates in place of the natural phosphate ester. Self-cleavage assays with the Bacillus cereus glmS riboswitch give a broad SAR. Two analogs display significant activity, namely, the 6-deoxy-6-phosphonomethyl analog (5) and the 6-O-malonyl ether (13). Kinetic profiles show a 22-fold and a 27-fold higher catalytic efficiency, respectively, for these analogs vs glucosamine (GlcN). Given their nonhydrolyzable phosphate surrogate functionalities, these analogs are arguably the most robust artificial glmS riboswitch actuators yet reported. Interestingly, the malonyl ether (13, extra O atom) is much more effective than the simple malonate (17), and the "sterically true" phosphonate (5) is far superior to the chain-truncated (7) or chain-extended (11) analogs, suggesting that positioning via Mg coordination is important for activity. Docking results are consistent with this view. Indeed, the viability of the phosphonate and 6-O-malonyl ether mimics of GlcN6P points to a potential new strategy for artificial actuation of the glmS riboswitch in a biological setting, wherein phosphatase-resistance is paramount.
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Can acute dermal systemic toxicity tests be replaced with oral tests? A comparison of route-specific systemic toxicity and hazard classifications under the Globally Harmonized System of Classification and Labelling of Chemicals (GHS).
Regul. Toxicol. Pharmacol.
PUBLISHED: 01-10-2013
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Acute systemic toxicity data (LD50 values) and hazard classifications derived in the rat following oral administration and dermal application have been analysed to examine whether or not orally-derived hazard classification or LD50 values can be used to determine dermal hazard classification. Comparing the oral and dermal classifications for 335 substances derived from oral and dermal LD50 values respectively revealed 17% concordance, and indicated that 7% of substances would be classified less severely while 76% would be classified more severely if oral classifications were applied directly to the dermal route. In contrast, applying the oral LD50 values within the dermal classification criteria to determine the dermal classification reduced the concordance to 15% and the relative under-classification to 1%, but increased the relative over-classification to 84%. Both under- and over-classification are undesirable, and mitigation strategies are discussed. Finally, no substance with an oral LD50 of >2000mg/kg was classified for acute systemic toxicity by the dermal route, suggesting that dermal testing for acute systemic toxicity of such substances adds nothing to the hazard characterisation and should be removed from routine regulatory data requirements.
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Regional particle size dependent deposition of inhaled aerosols in rats and mice.
Inhal Toxicol
PUBLISHED: 12-07-2011
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The current data analysis tools in nuclear medicine have not been used to evaluate intra organ regional deposition patterns of pharmaceutical aerosols in preclinical species.
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Economic impacts of non-native forest insects in the continental United States.
PLoS ONE
PUBLISHED: 02-24-2011
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Reliable estimates of the impacts and costs of biological invasions are critical to developing credible management, trade and regulatory policies. Worldwide, forests and urban trees provide important ecosystem services as well as economic and social benefits, but are threatened by non-native insects. More than 450 non-native forest insects are established in the United States but estimates of broad-scale economic impacts associated with these species are largely unavailable. We developed a novel modeling approach that maximizes the use of available data, accounts for multiple sources of uncertainty, and provides cost estimates for three major feeding guilds of non-native forest insects. For each guild, we calculated the economic damages for five cost categories and we estimated the probability of future introductions of damaging pests. We found that costs are largely borne by homeowners and municipal governments. Wood- and phloem-boring insects are anticipated to cause the largest economic impacts by annually inducing nearly $1.7 billion in local government expenditures and approximately $830 million in lost residential property values. Given observations of new species, there is a 32% chance that another highly destructive borer species will invade the U.S. in the next 10 years. Our damage estimates provide a crucial but previously missing component of cost-benefit analyses to evaluate policies and management options intended to reduce species introductions. The modeling approach we developed is highly flexible and could be similarly employed to estimate damages in other countries or natural resource sectors.
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Habitat associations of juvenile fish at Ningaloo Reef, Western Australia: the importance of coral and algae.
PLoS ONE
PUBLISHED: 09-14-2010
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Habitat specificity plays a pivotal role in forming community patterns in coral reef fishes, yet considerable uncertainty remains as to the extent of this selectivity, particularly among newly settled recruits. Here we quantified habitat specificity of juvenile coral reef fish at three ecological levels; algal meadows vs. coral reefs, live vs. dead coral and among different coral morphologies. In total, 6979 individuals from 11 families and 56 species were censused along Ningaloo Reef, Western Australia. Juvenile fishes exhibited divergence in habitat use and specialization among species and at all study scales. Despite the close proximity of coral reef and algal meadows (10s of metres) 25 species were unique to coral reef habitats, and seven to algal meadows. Of the seven unique to algal meadows, several species are known to occupy coral reef habitat as adults, suggesting possible ontogenetic shifts in habitat use. Selectivity between live and dead coral was found to be species-specific. In particular, juvenile scarids were found predominantly on the skeletons of dead coral whereas many damsel and butterfly fishes were closely associated with live coral habitat. Among the coral dependent species, coral morphology played a key role in juvenile distribution. Corymbose corals supported a disproportionate number of coral species and individuals relative to their availability, whereas less complex shapes (i.e. massive & encrusting) were rarely used by juvenile fish. Habitat specialisation by juvenile species of ecological and fisheries importance, for a variety of habitat types, argues strongly for the careful conservation and management of multiple habitat types within marine parks, and indicates that the current emphasis on planning conservation using representative habitat areas is warranted. Furthermore, the close association of many juvenile fish with corals susceptible to climate change related disturbances suggests that identifying and protecting reefs resilient to this should be a conservation priority.
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Fomepizole fails to prevent progression of acidosis in 2-butoxyethanol and ethanol coingestion.
Clin Toxicol (Phila)
PUBLISHED: 06-22-2010
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2-butoxyethanol (2BE) is a solvent commonly incorporated into household and industrial cleaning products. Its ingestion causes rapid central nervous system depression, hypotension, and metabolic acidosis attributable to metabolism of the parent compound to butoxyacetic acid (BAA) by alcohol dehydrogenase. Lactic acidosis is also reported to develop in some cases. Published treatment strategies include the use of ethanol infusion, ethanol with concomitant dialysis, dialysis alone, and fomepizole.
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Smell, learn and live: the role of chemical alarm cues in predator learning during early life history in a marine fish.
Behav. Processes
PUBLISHED: 01-01-2010
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The speed with which individuals can learn to identify and react appropriately to predation threats when transitioning to new life history stages and habitats will influence their survival. This study investigated the role of chemical alarm cues in both anti-predator responses and predator identification during a transitional period in a newly settled coral reef damselfish, Pomacentrus amboinensis. Individuals were tested for changes in seven behavioural traits in response to conspecific and heterospecific skin extracts. Additionally, we tested whether fish could learn to associate a previously novel chemical cue (i.e. simulated predator scent) with danger, after previously being exposed to a paired cue combining the conspecific skin extract with the novel scent. Fish exposed to conspecific skin extracts were found to significantly decreased their feeding rate whilst those exposed to heterospecific and control cues showed no change. Individuals were also able to associate a previously novel scent with danger after only a single previous exposure to the paired conspecific skin extract/novel scent cue. Our results indicate that chemical alarm cues play a large role in both threat detection and learned predator recognition during the early post-settlement period in coral reef fishes.
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Influence of prey body characteristics and performance on predator selection.
Oecologia
PUBLISHED: 07-15-2009
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At the time of settlement to the reef environment, coral reef fishes differ in a number of characteristics that may influence their survival during a predatory encounter. This study investigated the selective nature of predation by both a multi-species predator pool, and a single common predator (Pseudochromis fuscus), on the reef fish, Pomacentrus amboinensis. The study focused on the early post-settlement period of P. amboinensis, when mortality, and hence selection, is known to be highest. Correlations between nine different measures of body condition/performance were examined at the time of settlement, in order to elucidate the relationships between different traits. Single-predator (P. fuscus) choice trials were conducted in 57.4-l aquaria with respect to three different prey characteristics [standard length (SL), body weight and burst swimming speed], whilst multi-species trials were conducted on open patch reefs, manipulating prey body weight only. Relationships between the nine measures of condition/performance were generally poor, with the strongest correlations occurring between the morphological measures and within the performance measures. During aquaria trials, P. fuscus was found to be selective with respect to prey SL only, with larger individuals being selected significantly more often. Multi-species predator communities, however, were selective with respect to prey body weight, with heavier individuals being selected significantly more often than their lighter counterparts. Our results suggest that under controlled conditions, body length may be the most important prey characteristic influencing prey survival during predatory encounters with P. fuscus. In such cases, larger prey size may actually be a distinct disadvantage to survival. However, these relationships appear to be more complex under natural conditions, where the expression of prey characteristics, the selectivity fields of a number of different predators, their relative abundance, and the action of external environmental characteristics, may all influence which individuals survive.
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Economic impacts of invasive species in forests: past, present, and future.
Ann. N. Y. Acad. Sci.
PUBLISHED: 05-13-2009
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Biological invasions by nonnative species are a by-product of economic activities, with the vast majority of nonnative species introduced by trade and transport of products and people. Although most introduced species are relatively innocuous, a few species ultimately cause irreversible economic and ecological impacts, such as the chestnut blight that functionally eradicated the American chestnut across eastern North America. Assessments of the economic costs and losses induced by nonnative forest pests are required for policy development and need to adequately account for all of the economic impacts induced by rare, highly damaging pests. To date, countrywide economic evaluations of forest-invasive species have proceeded by multiplying a unit value (price) by a physical quantity (volume of forest products damaged) to arrive at aggregate estimates of economic impacts. This approach is inadequate for policy development because (1) it ignores the dynamic impacts of biological invasions on the evolution of prices, quantities, and market behavior, and (2) it fails to account for the loss in the economic value of nonmarket ecosystem services, such as landscape aesthetics, outdoor recreation, and the knowledge that healthy forest ecosystems exist. A review of the literature leads one to anticipate that the greatest economic impacts of invasive species in forests are due to the loss of nonmarket values. We proposed that new methods for evaluating aggregate economic damages from forest-invasive species need to be developed that quantify market and nonmarket impacts at microscales that are then extended using spatially explicit models to provide aggregate estimates of impacts. Finally, policies that shift the burden of economic impacts from taxpayers and forest landowners onto parties responsible for introducing or spreading invasives, whether through the imposition of tariffs on products suspected of imposing unacceptable risks on native forest ecosystems or by requiring standards on the processing of trade products before they cross international boundaries, may be most effective at reducing their impacts.
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Aerosol sampling system for collection of Capstone depleted uranium particles in a high-energy environment.
Health Phys
PUBLISHED: 02-11-2009
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The Capstone Depleted Uranium (DU) Aerosol Study was undertaken to obtain aerosol samples resulting from a large-caliber DU penetrator striking an Abrams or Bradley test vehicle. The sampling strategy was designed to (1) optimize the performance of the samplers and maintain their integrity in the extreme environment created during perforation of an armored vehicle by a DU penetrator, (2) collect aerosols as a function of time post perforation, and (3) obtain size-classified samples for analysis of chemical composition, particle morphology, and solubility in lung fluid. This paper describes the experimental setup and sampling methodologies used to achieve these objectives. Custom-designed arrays of sampling heads were secured to the inside of the target in locations approximating the breathing zones of the crew locations in the test vehicles. Each array was designed to support nine filter cassettes and nine cascade impactors mounted with quick-disconnect fittings. Shielding and sampler placement strategies were used to minimize sampler loss caused by the penetrator impact and the resulting fragments of eroded penetrator and perforated armor. A cyclone train was used to collect larger quantities of DU aerosol for measurement of chemical composition and solubility. A moving filter sample was used to obtain semicontinuous samples for DU concentration determination. Control for the air samplers was provided by five remotely located valve control and pressure monitoring units located inside and around the test vehicle. These units were connected to a computer interface chassis and controlled using a customized LabVIEW engineering computer control program. The aerosol sampling arrays and control systems for the Capstone study provided the needed aerosol samples for physicochemical analysis, and the resultant data were used for risk assessment of exposure to DU aerosol.
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Unprecedented mass bleaching and loss of coral across 12° of latitude in Western Australia in 2010-11.
PLoS ONE
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Globally, coral bleaching has been responsible for a significant decline in both coral cover and diversity over the past two decades. During the summer of 2010-11, anomalous large-scale ocean warming induced unprecedented levels of coral bleaching accompanied by substantial storminess across more than 12° of latitude and 1200 kilometers of coastline in Western Australia (WA).
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Relative and combined effects of habitat and fishing on reef fish communities across a limited fishing gradient at Ningaloo.
Mar. Environ. Res.
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Habitat degradation and fishing are major drivers of temporal and spatial changes in fish communities. The independent effects of these drivers are well documented, but the relative importance and interaction between fishing and habitat shifts is poorly understood, particularly in complex systems such as coral reefs. To assess the combined and relative effects of fishing and habitat we examined the composition of fish communities on patch reefs across a gradient of high to low structural complexity in fished and unfished areas of the Ningaloo Marine Park, Western Australia. Biomass and species richness of fish were positively correlated with structural complexity of reefs and negatively related to macroalgal cover. Total abundance of fish was also positively related to structural complexity, however this relationship was stronger on fished reefs than those where fishing is prohibited. The interaction between habitat condition and fishing pressure is primarily due to the high abundance of small bodied planktivorous fish on fished reefs. However, the influence of management zones on the abundance and biomass of predators and target species is small, implying spatial differences in fishing pressure are low and unlikely to be driving this interaction. Our results emphasise the importance of habitat in structuring reef fish communities on coral reefs especially when gradients in fishing pressure are low. The influence of fishing effort on this relationship may however become more important as fishing pressure increases.
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Molecular dynamics simulation for PBR pebble tracking simulation via a random walk approach using Monte Carlo simulation.
Appl Radiat Isot
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Using a Monte Carlo (MC) simulation, random walks were used for pebble tracking in a two-dimensional geometry in the presence of a biased gravity field. We investigated the effect of viscosity damping in the presence of random Gaussian fluctuations. The particle tracks were generated by Molecular Dynamics (MD) simulation for a Pebble Bed Reactor. The MD simulations were conducted in the interaction of noncohesive Hertz-Mindlin theory where the random walk MC simulation has a correlation with the MD simulation. This treatment can easily be extended to include the generation of transient gamma-ray spectra from a single pebble that contains a radioactive tracer. Then the inverse analysis thereof could be made to determine the uncertainty of the realistic measurement of transient positions of that pebble by any given radiation detection system designed for that purpose.
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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.

How does it work?

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

Video X seems to be unrelated to Abstract Y...

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.