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Find video protocols related to scientific articles indexed in Pubmed.
Impact of Park Renovations on Park Use and Park-Based Physical Activity.
J Phys Act Health
PUBLISHED: 06-24-2014
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Given the concerns about low rates of physical activity among low-income minority youth, many community based organizations are investing in the creation or renovation of public parks, in order to encourage youth to become more physically active. To what degree park renovations accomplish this goal is not known.
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Microbial community assembly and succession on lake sturgeon egg surfaces as a function of simulated spawning stream flow rate.
Microb. Ecol.
PUBLISHED: 06-07-2013
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We investigated microbial succession on lake sturgeon (Acipenser fulvescens) egg surfaces over the course of their incubation period as a function of simulated stream flow rate. The primary objective was to characterize the microbial community assembly during succession and to examine how simulated stream flow rate affect the successional process. Sturgeon eggs were reared under three flow regimes; high (0.55 m/s), low (0.18 m/s), and variable (0.35 and 0.11 m/s alternating 12 h intervals). Eggs were collected from each flow regime at different egg developmental stages. Microbial community DNA was extracted from egg surface and the communities were examined using 16S rRNA gene-based terminal restriction fragment length polymorphism and 454 pyrosequencing. Analysis of these datasets using principal component analysis revealed that microbial communities were clustered by egg developmental stages (early, middle, and late) regardless of flow regimes. 454 pyrosequencing data suggested that 90-98 % of the microbial communities were composed of the phyla Proteobacteria and Bacteroidetes throughout succession. ?-Protebacteria was more dominant in the early stage, Bacteroidetes became more dominant in the middle stage, and ?-Proteobacteria became dominant in the late stage. A total of 360 genera and 5,826 OTUs at 97 % similarity cutoff were associated with the eggs. Midway through egg development, the egg-associated communities of the low flow regime had a higher diversity than those communities developed under high or variable flow regimes. Results show that microbial community turnover occurred during embryogenesis, and stream flow rate influenced the microbial succession processes on the sturgeon egg surfaces.
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Dynamics of microbial community composition and function during in situ bioremediation of a uranium-contaminated aquifer.
Appl. Environ. Microbiol.
PUBLISHED: 04-15-2011
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A pilot-scale system was established to examine the feasibility of in situ U(VI) immobilization at a highly contaminated aquifer (U.S. DOE Integrated Field Research Challenge site, Oak Ridge, TN). Ethanol was injected intermittently as an electron donor to stimulate microbial U(VI) reduction, and U(VI) concentrations fell to below the Environmental Protection Agency drinking water standard (0.03 mg liter(-1)). Microbial communities from three monitoring wells were examined during active U(VI) reduction and maintenance phases with GeoChip, a high-density, comprehensive functional gene array. The overall microbial community structure exhibited a considerable shift over the remediation phases examined. GeoChip-based analysis revealed that Fe(III)-reducing bacterial (FeRB), nitrate-reducing bacterial (NRB), and sulfate-reducing bacterial (SRB) functional populations reached their highest levels during the active U(VI) reduction phase (days 137 to 370), in which denitrification and Fe(III) and sulfate reduction occurred sequentially. A gradual decrease in these functional populations occurred when reduction reactions stabilized, suggesting that these functional populations could play an important role in both active U(VI) reduction and maintenance of the stability of reduced U(IV). These results suggest that addition of electron donors stimulated the microbial community to create biogeochemical conditions favorable to U(VI) reduction and prevent the reduced U(IV) from reoxidation and that functional FeRB, SRB, and NRB populations within this system played key roles in this process.
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Use of primer selection and restriction enzymes to assess bacterial community diversity in an agricultural soil used for potato production via terminal restriction fragment length polymorphism.
Appl. Microbiol. Biotechnol.
PUBLISHED: 01-30-2011
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Terminal restriction fragment length polymorphism (T-RFLP) can be used to assess how land use management changes the dominant members of bacterial communities. We compared T-RFLP profiles obtained via amplification with forward primers (27, 63F) each coupled with the fluorescently labeled reverse primer (1392R) and multiple restriction enzymes to determine the best combination for interrogating soil bacterial populations in an agricultural soil used for potato production. Both primer pairs provide nearly universal recognition of a 1,400-bp sequence of the bacterial domain in the V(1)-V(3) region of the 16S ribosomal RNA (rRNA) gene relative to known sequences. Labeling the reverse primer allowed for direct comparison of each forward primer and the terminal restriction fragments relative migration units obtained with each primer pair and restriction enzyme. Redundancy analysis (RDA) and nested multivariate analysis of variance (MANOVA) were used to assess the effects of primer pair and choice of restriction enzyme on the measured relative migration units. Our research indicates that the 63F-1392R amplimer pair provides a more complete description with respect to the bacterial communities present in this potato (Solanum tuberosum L.)-barley (Hordeum vulgare L.) rotation over seeded to crimson clover (Trifolium praense L.). Domain-specific 16S rRNA gene primers are rigorously tested to determine their ability to amplify across a target region of the gene. Yet, variability within or between T-RFLP profiles can result from factors independent of the primer pair. Therefore, researchers should use RDA and MANOVA analyses to evaluate the effects that additional laboratory and environmental variables have on bacterial diversity.
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Significant association between sulfate-reducing bacteria and uranium-reducing microbial communities as revealed by a combined massively parallel sequencing-indicator species approach.
Appl. Environ. Microbiol.
PUBLISHED: 08-20-2010
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Massively parallel sequencing has provided a more affordable and high-throughput method to study microbial communities, although it has mostly been used in an exploratory fashion. We combined pyrosequencing with a strict indicator species statistical analysis to test if bacteria specifically responded to ethanol injection that successfully promoted dissimilatory uranium(VI) reduction in the subsurface of a uranium contamination plume at the Oak Ridge Field Research Center in Tennessee. Remediation was achieved with a hydraulic flow control consisting of an inner loop, where ethanol was injected, and an outer loop for flow-field protection. This strategy reduced uranium concentrations in groundwater to levels below 0.126 ?M and created geochemical gradients in electron donors from the inner-loop injection well toward the outer loop and downgradient flow path. Our analysis with 15 sediment samples from the entire test area found significant indicator species that showed a high degree of adaptation to the three different hydrochemical-created conditions. Castellaniella and Rhodanobacter characterized areas with low pH, heavy metals, and low bioactivity, while sulfate-, Fe(III)-, and U(VI)-reducing bacteria (Desulfovibrio, Anaeromyxobacter, and Desulfosporosinus) were indicators of areas where U(VI) reduction occurred. The abundance of these bacteria, as well as the Fe(III) and U(VI) reducer Geobacter, correlated with the hydraulic connectivity to the substrate injection site, suggesting that the selected populations were a direct response to electron donor addition by the groundwater flow path. A false-discovery-rate approach was implemented to discard false-positive results by chance, given the large amount of data compared.
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Biosequestration via cooperative binding of copper by Ralstonia pickettii.
Environ Technol
PUBLISHED: 07-29-2010
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Ralstonia pickettii isolated from copper-contaminated lake sediment are adapted to high levels of copper after 100 years of selective pressure. Two R. pickettii strains (12D and 12J) were selected for the studies reported herein due to their distinct differences in genomic structure, different metal resistance patterns and carriage of a filamentous phage. Copper sequestration studies revealed that these strains could bind up to 27.44 (12D) and 38.19 (12J) mg copper per g dry weight of cells and that viable cells sequestered more copper than heat-killed cells. Viable cells and heat-killed cells had significantly different saturation binding curves, indicating that one or more unique copper sequestration mechanism(s) was involved in binding by viable cells. Electron microscopy showed alteration of cell outer envelope after cells were grown in the presence of copper, suggesting that the accumulation of copper was membrane associated. X-ray Absorption Near Edge Structure and Extended X-ray Absorption Fine Structure revealed that the copper sequestered was present as Cu(II) and bound to oxygen and/or nitrogen. Recent completion of the genome sequence revealed that an approximately 220 kb region was enriched with metal resistance and transporter genes found in multiple copies. Comparative sequence analysis revealed that several genes may have been derived from horizontal transfer. Hence, rapid adaptation of R. pickettii to high concentrations of metal appears due to robust gene duplication and importation of several types of resistance determinants.
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Responses of microbial community functional structures to pilot-scale uranium in situ bioremediation.
ISME J
PUBLISHED: 03-18-2010
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A pilot-scale field test system with an inner loop nested within an outer loop was constructed for in situ U(VI) bioremediation at a US Department of Energy site, Oak Ridge, TN. The outer loop was used for hydrological protection of the inner loop where ethanol was injected for biostimulation of microorganisms for U(VI) reduction/immobilization. After 2 years of biostimulation with ethanol, U(VI) levels were reduced to below drinking water standard (<30 microg l(-1)) in the inner loop monitoring wells. To elucidate the microbial community structure and functions under in situ uranium bioremediation conditions, we used a comprehensive functional gene array (GeoChip) to examine the microbial functional gene composition of the sediment samples collected from both inner and outer loop wells. Our study results showed that distinct microbial communities were established in the inner loop wells. Also, higher microbial functional gene number, diversity and abundance were observed in the inner loop wells than the outer loop wells. In addition, metal-reducing bacteria, such as Desulfovibrio, Geobacter, Anaeromyxobacter and Shewanella, and other bacteria, for example, Rhodopseudomonas and Pseudomonas, are highly abundant in the inner loop wells. Finally, the richness and abundance of microbial functional genes were highly correlated with the mean travel time of groundwater from the inner loop injection well, pH and sulfate concentration in groundwater. These results suggest that the indigenous microbial communities can be successfully stimulated for U bioremediation in the groundwater ecosystem, and their structure and performance can be manipulated or optimized by adjusting geochemical and hydrological conditions.
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Microbial communities in the tonsils of healthy pigs.
Vet. Microbiol.
PUBLISHED: 02-23-2010
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The tonsils of mammals such as humans and pigs are colonized with an extensive microbiota and are frequently the site for asymptomatic carriage of bacterial pathogens. The goal of this study was to determine the composition of the microbial community of the tonsils in healthy pigs. Tonsils were collected from eight pigs from two different healthy herds. Samples of the tonsils from each pig were used for culture dependent and culture independent identification of the microbial community. Aerobic cultivation identified Pasteurella multocida, Actinobacillus spp., Staphylococcus aureus, Staphylococcus epidermidis, Streptococcus suis, Streptococcus dysgalactiae, and Escherichia coli from ? 50% of the pigs in both herds. For culture independent studies, microbial community members were identified by 16S rRNA sequences using the Ribosomal Database Project Pipeline programs developed at Michigan State University. Dominant genera identified by 16S rRNA analysis in pigs from both herds included Actinobacillus, Haemophilus, Pasteurella, Porphyromonas, Fusobacterium, Bacteroides, and Prevotella. These genera were detected in nearly every pig regardless of herd. In contrast, there was an asymmetric distribution of minor genera between the two herds, suggesting herd-specific differences in the microbial communities. In addition, we demonstrated primer bias between two frequently used forward primers when targeting the tonsillar community. Our results suggest that the major bacterial community members found in porcine tonsils are the same regardless of herd, while the minor species are unique to each herd. This is the first analysis using 16S rRNA sequence libraries of the composition of microbial communities in the porcine upper respiratory tract.
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Fecal bacterial diversity of human-habituated wild chimpanzees (Pan troglodytes schweinfurthii) at Mahale Mountains National Park, Western Tanzania.
Am. J. Primatol.
PUBLISHED: 02-11-2010
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Although the intestinal flora of chimpanzees has not been studied, insight into this dynamic environment can be obtained through studies on their feces. We analyzed fecal samples from human-habituated, wild chimpanzees at Mahale Mountains National Park, Tanzania, and compared microbial community profiles to determine if members of the same social group were similar. Between July and December 2007, we collected fresh fecal samples from 12 individuals: four juveniles, four adolescents, and four adults, including three parent-offspring pairs. Each sample was analyzed using Terminal-Restriction Fragment Length Polymorphism of amplified 16S rRNA genes. Twelve different profiles were generated, having between 1 and 15 Terminal-Restriction Fragments (T-RFs). Overall, a total of 23 different T-RFs were produced. Putative assignments of T-RFs corresponded to the phyla Firmicutes (Clostridia, Bacilli, and Lactobacilli), Bacteroidetes, Tenericutes (Mollicutes Class), Actinobacteria, and Proteobacteria, as well as to uncultured or unidentified organisms. Firmicutes and Bacteroidetes phyla and Mollicutes Class were the most commonly assigned in 11, 8, and 8 of the samples, respectively, with this being the first report of Mollicutes in wild chimpanzees. Principal Components Analysis (PCA) revealed clustering of nine samples, and 80.5% of the diversity was accounted for by three samples. Morisita indices of community similarity ranged between 0.00 and 0.89, with dissimiliarity (<0.5) between most samples when compared two at a time. Our findings suggest that, although phylotypes are common among individuals, profiles among members of the same social group are host-specific. We conclude that factors other than social group, such as kinship and age, may influence fecal bacterial profiles of wild chimpanzees, and recommend that additional studies be conducted.
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GeoChip-based analysis of functional microbial communities during the reoxidation of a bioreduced uranium-contaminated aquifer.
Environ. Microbiol.
PUBLISHED: 07-14-2009
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A pilot-scale system was established for in situ biostimulation of U(VI) reduction by ethanol addition at the US Department of Energys (DOEs) Field Research Center (Oak Ridge, TN). After achieving U(VI) reduction, stability of the bioreduced U(IV) was evaluated under conditions of (i) resting (no ethanol injection), (ii) reoxidation by introducing dissolved oxygen (DO), and (iii) reinjection of ethanol. GeoChip, a functional gene array with probes for N, S and C cycling, metal resistance and contaminant degradation genes, was used for monitoring groundwater microbial communities. High diversity of all major functional groups was observed during all experimental phases. The microbial community was extremely responsive to ethanol, showing a substantial change in community structure with increased gene number and diversity after ethanol injections resumed. While gene numbers showed considerable variations, the relative abundance (i.e. percentage of each gene category) of most gene groups changed little. During the reoxidation period, U(VI) increased, suggesting reoxidation of reduced U(IV). However, when introduction of DO was stopped, U(VI) reduction resumed and returned to pre-reoxidation levels. These findings suggest that the community in this system can be stimulated and that the ability to reduce U(VI) can be maintained by the addition of electron donors. This biostimulation approach may potentially offer an effective means for the bioremediation of U(VI)-contaminated sites.
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Bacterial and archaeal phylogenetic diversity of a cold sulfur-rich spring on the shoreline of Lake Erie, Michigan.
Appl. Environ. Microbiol.
PUBLISHED: 06-19-2009
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Studies of sulfidic springs have provided new insights into microbial metabolism, groundwater biogeochemistry, and geologic processes. We investigated Great Sulphur Spring on the western shore of Lake Erie and evaluated the phylogenetic affiliations of 189 bacterial and 77 archaeal 16S rRNA gene sequences from three habitats: the spring origin (11-m depth), bacterial-algal mats on the spring pond surface, and whitish filamentous materials from the spring drain. Water from the spring origin water was cold, pH 6.3, and anoxic (H(2), 5.4 nM; CH(4), 2.70 microM) with concentrations of S(2-) (0.03 mM), SO(4)(2-) (14.8 mM), Ca(2+) (15.7 mM), and HCO(3)(-) (4.1 mM) similar to those in groundwater from the local aquifer. No archaeal and few bacterial sequences were >95% similar to sequences of cultivated organisms. Bacterial sequences were largely affiliated with sulfur-metabolizing or chemolithotrophic taxa in Beta-, Gamma-, Delta-, and Epsilonproteobacteria. Epsilonproteobacteria sequences similar to those obtained from other sulfidic environments and a new clade of Cyanobacteria sequences were particularly abundant (16% and 40%, respectively) in the spring origin clone library. Crenarchaeota sequences associated with archaeal-bacterial consortia in whitish filaments at a German sulfidic spring were detected only in a similar habitat at Great Sulphur Spring. This study expands the geographic distribution of many uncultured Archaea and Bacteria sequences to the Laurentian Great Lakes, indicates possible roles for epsilonproteobacteria in local aquifer chemistry and karst formation, documents new oscillatorioid Cyanobacteria lineages, and shows that uncultured, cold-adapted Crenarchaeota sequences may comprise a significant part of the microbial community of some sulfidic environments.
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Changes in land use alter the structure of bacterial communities in Western Amazon soils.
ISME J
PUBLISHED: 05-14-2009
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Here we show how agricultural practices by indigenous peoples as well as forest recovery relate to the structure and composition of Amazon soil bacterial communities. Soil samples were collected in different land use systems and bacterial community composition and diversity were explored by T-RFLP, cloning and sequencing, and data were analyzed with multivariate techniques. The main differences in bacterial community structure were related to changes in the soil attributes that, in turn, were correlated to land use. Community structure changed significantly along gradients of base saturation, [Al3+] and pH. The relationship with soil attributes accounted for about 31% of the variation of the studied communities. Clear differences were observed in community composition as shown by the differential distribution of Proteobacteria, Bacteroidetes, Firmicutes, Acidobacteria and Actinobacteria. Similarity between primary and secondary forest communities indicates the recovery of bacterial community structure during succession. Pasture and crop soil communities were among the most diverse, showing that these land use types did not deplete bacterial diversity under the conditions found in our sites.
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Temporal Shifts in Microbial Communities in Nonpregnant African-American Women with and without Bacterial Vaginosis.
Interdiscip Perspect Infect Dis
PUBLISHED: 01-27-2009
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Bacterial vaginosis (BV) has been described as an increase in the number of anaerobic and facultatively anaerobic bacteria relative to lactobacilli in the vaginal tract. Several undesirable consequences of this community shift can include irritation, white discharge, an elevated pH, and increased susceptibility to sexually transmitted infections. While the etiology of the condition remains ill defined, BV has been associated with adverse reproductive and pregnancy outcomes. In order to describe the structure of vaginal communities over time we determined the phylogenetic composition of vaginal communities from seven women sampled at multiple points using 16S rRNA gene sequencing. We found that women with no evidence of BV had communities dominated by lactobacilli that appeared stable over our sampling periods while those with BV had greater diversity and decreased stability overtime. In addition, only Lactobacillus iners was found in BV positive communities.
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Effects of dairy manure and corn stover co-digestion on anaerobic microbes and corresponding digestion performance.
Bioresour. Technol.
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This study investigated the effects of corn stover as a supplemental feed on anaerobic digestion of dairy manure under different hydraulic retention times (HRT). The results elucidated that both HRT and corn stover supplement significantly influenced microbial community and corresponding anaerobic digestion performance. The highest biogas production of 497 mL per gram total solid loading per day was observed at a HRT of 40 days from digestion of manure supplemented with corn stover. Biogas production was closely correlated with the populations of Bacteroidetes, Clostridia and methanogens. Composition of the solid digestate (AD fiber) from the co-digestion of corn stover and dairy manure was similar to the digestion of dairy manure. However, the hydrolysis of AD fiber was significantly (P < 0.05) different among the different digestions. Both HRT and feed composition influenced the hydrolyzability of AD fiber via shifting the composition of microbial community.
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Genome sequence of Desulfitobacterium hafniense DCB-2, a Gram-positive anaerobe capable of dehalogenation and metal reduction.
BMC Microbiol.
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The genome of the Gram-positive, metal-reducing, dehalorespiring Desulfitobacterium hafniense DCB-2 was sequenced in order to gain insights into its metabolic capacities, adaptive physiology, and regulatory machineries, and to compare with that of Desulfitobacterium hafniense Y51, the phylogenetically closest strain among the species with a sequenced genome.
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Defining the "core microbiome" of the microbial communities in the tonsils of healthy pigs.
BMC Microbiol.
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Porcine tonsils are the colonization site for many pathogenic as well as commensal microorganisms and are the primary lymphoid tissue encountered by organisms entering through the mouth or nares. The goal of this study was to provide an in-depth characterization of the composition and structure of the tonsillar microbial communities and to define the core microbiome in the tonsils of healthy pigs, using high throughput bar-coded 454-FLX pyrosequencing.
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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.

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.