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Find video protocols related to scientific articles indexed in Pubmed.
Genome sequencing of 15 clinical Vibrio isolates, including 13 non-o1/non-o139 serogroup strains.
Genome Announc
PUBLISHED: 09-13-2014
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We present draft genome sequences of 15 clinical Vibrio isolates of various serogroups. These are valuable data for use in studying Vibrio cholerae genetic diversity, epidemic potential, and strain attribution.
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Draft Genome Assembly of Acinetobacter baumannii ATCC 19606.
Genome Announc
PUBLISHED: 08-21-2014
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Acinetobacter baumannii is an emerging nosocomial pathogen, and therefore high-quality genome assemblies for this organism are needed to aid in detection, diagnostic, and treatment technologies. Here we present the improved draft assembly of A. baumannii ATCC 19606 in two scaffolds. This 3,953,621-bp genome contains 3,750 coding regions and has a 39.1% G+C content.
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Genome Sequences of Two Carbapenemase-Resistant Klebsiella pneumoniae ST258 Isolates.
Genome Announc
PUBLISHED: 06-21-2014
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Klebsiella pneumoniae, an ESKAPE group (Enterococcus faecium, Staphylococcus aureus, Klebsiella pneumoniae, Acinetobacter baumannii, Pseudomonas aeruginosa, and Enterobacter species) pathogen, has acquired multiple antibiotic resistance genes and is becoming a serious public health threat. Here, we report the genome sequences of two representative strains of K. pneumoniae from the emerging K. pneumoniae carbapenemase (KPC) outbreak in northeast Ohio belonging to sequence type 258 (ST258) (isolates Kb140 and Kb677, which were isolated from blood and urine, respectively). Both isolates harbor a blaKPC gene, and strain Kb140 carries blaKPC-2, while Kb677 carries blaKPC-3.
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Larvae from deep-sea methane seeps disperse in surface waters.
Proc. Biol. Sci.
PUBLISHED: 05-16-2014
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Many species endemic to deep-sea methane seeps have broad geographical distributions, suggesting that they produce larvae with at least episodic long-distance dispersal. Cold-seep communities on both sides of the Atlantic share species or species complexes, yet larval dispersal across the Atlantic is expected to take prohibitively long at adult depths. Here, we provide direct evidence that the long-lived larvae of two cold-seep molluscs migrate hundreds of metres above the ocean floor, allowing them to take advantage of faster surface currents that may facilitate long-distance dispersal. We collected larvae of the ubiquitous seep mussel "Bathymodiolus" childressi and an associated gastropod, Bathynerita naticoidea, using remote-control plankton nets towed in the euphotic zone of the Gulf of Mexico. The timing of collections suggested that the larvae might disperse in the water column for more than a year, where they feed and grow to more than triple their original sizes. Ontogenetic vertical migration during a long larval life suggests teleplanic dispersal, a plausible explanation for the amphi-Atlantic distribution of "B." mauritanicus and the broad western Atlantic distribution of B. naticoidea. These are the first empirical data to demonstrate a biological mechanism that might explain the genetic similarities between eastern and western Atlantic seep fauna.
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The path to triacylglyceride obesity in the sta6 strain of Chlamydomonas reinhardtii.
Eukaryotic Cell
PUBLISHED: 02-28-2014
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When the sta6 (starch-null) strain of the green microalga Chlamydomonas reinhardtii is nitrogen starved in acetate and then "boosted" after 2 days with additional acetate, the cells become "obese" after 8 days, with triacylglyceride (TAG)-filled lipid bodies filling their cytoplasm and chloroplasts. To assess the transcriptional correlates of this response, the sta6 strain and the starch-forming cw15 strain were subjected to RNA-Seq analysis during the 2 days prior and 2 days after the boost, and the data were compared with published reports using other strains and growth conditions. During the 2 h after the boost, ?425 genes are upregulated ?2-fold and ?875 genes are downregulated ?2-fold in each strain. Expression of a small subset of "sensitive" genes, encoding enzymes involved in the glyoxylate and Calvin-Benson cycles, gluconeogenesis, and the pentose phosphate pathway, is responsive to culture conditions and genetic background as well as to boosting. Four genes-encoding a diacylglycerol acyltransferase (DGTT2), a glycerol-3-P dehydrogenase (GPD3), and two candidate lipases (Cre03.g155250 and Cre17.g735600)-are selectively upregulated in the sta6 strain. Although the bulk rate of acetate depletion from the medium is not boost enhanced, three candidate acetate permease-encoding genes in the GPR1/FUN34/YaaH superfamily are boost upregulated, and 13 of the "sensitive" genes are strongly responsive to the cell's acetate status. A cohort of 64 autophagy-related genes is downregulated by the boost. Our results indicate that the boost serves both to avert an autophagy program and to prolong the operation of key pathways that shuttle carbon from acetate into storage lipid, the combined outcome being enhanced TAG accumulation, notably in the sta6 strain.
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Characterization of the Asian Citrus Psyllid Transcriptome.
J Genomics
PUBLISHED: 02-11-2014
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The Asian citrus psyllid, Diaphorina citri Kuwayama (Hemiptera: Psyllidae) is a vector for the causative agents of Huanglongbing, which threatens citrus production worldwide. This study reports and discusses the first D. citri transcriptomes, encompassing the three main life stages of D. citri, egg, nymph and adult. The transcriptomes were annotated using Gene Ontology (GO) and insecticide-related genes within each life stage were identified to aid the development of future D. citri insecticides. Transcriptome assemblies and other sequence data are available for download at the International Asian Citrus Psyllid Genome Consortium website [http://psyllid.org/download] and at NCBI [http://www.ncbi.nlm.nih.gov/bioproject/29447].
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Draft Genome Sequence of Pseudomonas putida Strain S610, a Seed-Borne Bacterium of Wheat.
Genome Announc
PUBLISHED: 12-28-2013
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We report the genome sequence of a seed-borne bacterium, Pseudomonas putida strain S610. The size of the draft genome sequence is approximately 4.6 Mb, which is the smallest among all P. putida strains sequenced to date.
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Draft Genome Sequences of Two Alginate-Overproducing Variants of Pseudomonas aeruginosa, PAO1-VE2 and PAO1-VE13.
Genome Announc
PUBLISHED: 12-17-2013
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The small envelope protein MucE and the sensor kinase KinB are a positive and negative alginate regulator, respectively. Here, we announce the draft genome sequences of the alginate-overproducing variants Pseudomonas aeruginosa PAO1-VE2 (PAO1 with constitutive expression of mucE) and PAO1-VE13 (PAO1 with kinB inactivated). Both mutants were generated from a transposon mutagenesis screen.
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Complete Genome Sequence of Bacillus thuringiensis Serovar Israelensis Strain HD-789.
Genome Announc
PUBLISHED: 12-07-2013
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Bacillus thuringiensis is an important microbial insecticide for controlling agricultural pests. We report the finished genome sequence of Bacillus thuringiensis serovar israelensis strain HD-789, which contains genes encoding 7 parasporal crystals consisting of Cry4Aa3, Cry4Ba5 (2 genes), Cry10Aa3, Cry11Aa3, Cry60Ba3, and Cry60Aa3, plus 3 Cyt toxin genes and 1 hemagglutinin gene.
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Systems-Level Analysis of Nitrogen Starvation-Induced Modifications of Carbon Metabolism in a Chlamydomonas reinhardtii Starchless Mutant.
Plant Cell
PUBLISHED: 11-26-2013
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To understand the molecular basis underlying increased triacylglycerol (TAG) accumulation in starchless (sta) Chlamydomonas reinhardtii mutants, we undertook comparative time-course transcriptomics of strains CC-4348 (sta6 mutant), CC-4349, a cell wall-deficient (cw) strain purported to represent the parental STA6 strain, and three independent STA6 strains generated by complementation of sta6 (CC-4565/STA6-C2, CC-4566/STA6-C4, and CC-4567/STA6-C6) in the context of N deprivation. Despite N starvation-induced dramatic remodeling of the transcriptome, there were relatively few differences (5 × 10(2)) observed between sta6 and STA6, the most dramatic of which were increased abundance of transcripts encoding key regulated or rate-limiting steps in central carbon metabolism, specifically isocitrate lyase, malate synthase, transaldolase, fructose bisphosphatase and phosphoenolpyruvate carboxykinase (encoded by ICL1, MAS1, TAL1, FBP1, and PCK1 respectively), suggestive of increased carbon movement toward hexose-phosphate in sta6 by upregulation of the glyoxylate pathway and gluconeogenesis. Enzyme assays validated the increase in isocitrate lyase and malate synthase activities. Targeted metabolite analysis indicated increased succinate, malate, and Glc-6-P and decreased Fru-1,6-bisphosphate, illustrating the effect of these changes. Comparisons of independent data sets in multiple strains allowed the delineation of a sequence of events in the global N starvation response in C. reinhardtii, starting within minutes with the upregulation of alternative N assimilation routes and carbohydrate synthesis and subsequently a more gradual upregulation of genes encoding enzymes of TAG synthesis. Finally, genome resequencing analysis indicated that (1) the deletion in sta6 extends into the neighboring gene encoding respiratory burst oxidase, and (2) a commonly used STA6 strain (CC-4349) as well as the sequenced reference (CC-503) are not congenic with respect to sta6 (CC-4348), underscoring the importance of using complemented strains for more rigorous assignment of phenotype to genotype.
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Draft Genome Sequence of a Mucoid Isolate of Pseudomonas aeruginosa Strain C7447m from a Patient with Cystic Fibrosis.
Genome Announc
PUBLISHED: 10-12-2013
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Alginate overproduction by Pseudomonas aeruginosa, or mucoidy, plays an important role in the pathogenesis of chronic lung infections in cystic fibrosis (CF) patients. Here we report the draft genome sequence of a clinical isolate of mucoid P. aeruginosa strain C7447m from a CF patient with chronic lung infection.
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Draft Genome Sequence of a Stable Mucoid Strain of Pseudomonas aeruginosa PAO581 with a mucA25 Mutation.
Genome Announc
PUBLISHED: 10-12-2013
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A mutation in the mucA gene, which encodes a negative regulator of alginate production in Pseudomonas aeruginosa, is the main mechanism underlying the conversion to mucoidy in clinical isolates from patients with cystic fibrosis (CF). Here, we announce the draft genome sequence of the stable alginate-overproducing mucoid strain P. aeruginosa PAO581 with a mucA25 mutation, a derivative from the nonmucoid strains P. aeruginosa PAO381 and PAO1.
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Complete Genome Sequence of the Encephalomyelitic Burkholderia pseudomallei Strain MSHR305.
Genome Announc
PUBLISHED: 08-24-2013
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We describe the complete genome sequence of Burkholderia pseudomallei MSHR305, a clinical isolate taken from a fatal encephalomyelitis case, a rare form of melioidosis. This sequence will be used for comparisons to identify the genes that are involved in neurological cases.
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Characterization of TEM-1 ?-lactamase producing Kingella kingae clinical isolates.
Antimicrob. Agents Chemother.
PUBLISHED: 06-26-2013
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Kingella kingae is a human pathogen that causes pediatric osteoarticular infections and infective endocarditis in children and adults. The bacterium is usually susceptible to ?-lactam antibiotics, although ?-lactam resistance has been reported in rare isolates. This study was conducted to identify ?-lactam resistant strains and characterize the resistance mechanism. Screening of a set of 90 K. kingae clinical isolates obtained from different geographic locations revealed high level resistance to penicillins among 25% of the strains isolated from Minnesota (USA) and Iceland. These strains produced TEM-1 ?-lactamase and were shown to contain additional ? 50kb plasmids. Ion Torrent sequencing of extrachromosomal DNA from ?-lactamase producing strain confirmed plasmid location of the blatem gene. An identical plasmid pattern was demonstrated by multiplex PCR in all ?-lactamase producers. The porin genes fragments were analyzed to investigate relatedness of bacterial strains. Phylogenetic analysis revealed 27 single nucleotide polymorphisms (SNPs) in the por gene fragment, resulting in two major clusters with 11 allele types forming bacterial strains sub-clusters. ?-lactamase producers grouped together based on por genotyping. Our results suggest that the ?-lactamase producing strains likely originate from a single plasmid bearing K. kingae isolate that traveled from Europe to the USA or vice versa. This study highlights the abundance of penicillin resistance among K. kingae strains in some regions and emphasizes the importance of surveillance for antibiotic resistance of the pathogen.
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Genome Sequences of Two Klebsiella pneumoniae Isolates from Different Geographical Regions, Argentina (Strain JHCK1) and the United States (Strain VA360).
Genome Announc
PUBLISHED: 05-04-2013
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We report the sequences of two Klebsiella pneumoniae clinical isolates, strains JHCK1 and VA360, from a newborn with meningitis in Buenos Aires, Argentina, and from a tertiary care medical center in Cleveland, OH, respectively. Both isolates contain one chromosome and at least five plasmids; isolate VA360 contains the Klebsiella pneumoniae carbapenemase (KPC) gene.
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Nearly finished genomes produced using gel microdroplet culturing reveal substantial intraspecies genomic diversity within the human microbiome.
Genome Res.
PUBLISHED: 03-14-2013
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The majority of microbial genomic diversity remains unexplored. This is largely due to our inability to culture most microorganisms in isolation, which is a prerequisite for traditional genome sequencing. Single-cell sequencing has allowed researchers to circumvent this limitation. DNA is amplified directly from a single cell using the whole-genome amplification technique of multiple displacement amplification (MDA). However, MDA from a single chromosome copy suffers from amplification bias and a large loss of specificity from even very small amounts of DNA contamination, which makes assembling a genome difficult and completely finishing a genome impossible except in extraordinary circumstances. Gel microdrop cultivation allows culturing of a diverse microbial community and provides hundreds to thousands of genetically identical cells as input for an MDA reaction. We demonstrate the utility of this approach by comparing sequencing results of gel microdroplets and single cells following MDA. Bias is reduced in the MDA reaction and genome sequencing, and assembly is greatly improved when using gel microdroplets. We acquired multiple near-complete genomes for two bacterial species from human oral and stool microbiome samples. A significant amount of genome diversity, including single nucleotide polymorphisms and genome recombination, is discovered. Gel microdroplets offer a powerful and high-throughput technology for assembling whole genomes from complex samples and for probing the pan-genome of naturally occurring populations.
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The role of gaze direction in face memory in autism spectrum disorder.
Autism Res
PUBLISHED: 02-15-2013
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We tested the hypothesis that the direction of gaze of target faces may play a role in reported face recognition deficits in those with an autism spectrum disorder (ASD). In previous studies, typically developing children and adults better remembered faces in which the eyes were gazing directly at them compared with faces in which the eyes were averted. In the current study, high-functioning children and adolescents with an ASD and age- and IQ-matched typically developing controls were shown a series of pictures of faces in a study phase. These pictures were of individuals whose gaze was either directed straight ahead or whose gaze was averted to one side. We tested the memory for these study faces in a recognition task in which the faces were shown with their eyes closed. The typically developing group better remembered the direct-gaze faces, whereas the ASD participants did not show this effect. These results imply that there may be an important link between gaze direction and face recognition abilities in ASD.
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A hybrid zone between Bathymodiolus mussel lineages from eastern Pacific hydrothermal vents.
BMC Evol. Biol.
PUBLISHED: 01-11-2013
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The inhabitants of deep-sea hydrothermal vents occupy ephemeral island-like habitats distributed sporadically along tectonic spreading-centers, back-arc basins, and volcanically active seamounts. The majority of vent taxa undergo a pelagic larval phase, and thus varying degrees of geographical subdivision, ranging from no impedance of dispersal to complete isolation, often exist among taxa that span common geomorphological boundaries. Two lineages of Bathymodiolus mussels segregate on either side of the Easter Microplate, a boundary that separates the East Pacific Rise from spreading centers connected to the Pacific-Antarctic Ridge.
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Response and resilience of soil biocrust bacterial communities to chronic physical disturbance in arid shrublands.
ISME J
PUBLISHED: 11-24-2011
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The impact of 10 years of annual foot trampling on soil biocrusts was examined in replicated field experiments at three cold desert sites of the Colorado Plateau, USA. Trampling detrimentally impacted lichens and mosses, and the keystone cyanobacterium, Microcoleus vaginatus, resulting in increased soil erosion and reduced C and N concentrations in surface soils. Trampled biocrusts contained approximately half as much extractable DNA and 20-52% less chlorophyll a when compared with intact biocrusts at each site. Two of the three sites also showed a decline in scytonemin-containing, diazotrophic cyanobacteria in trampled biocrusts. 16S rRNA gene sequence and terminal restriction fragment length polymorphism (T-RFLP) analyses of soil bacteria from untrampled and trampled biocrusts demonstrated a reduced proportion (23-65% reduction) of M. vaginatus and other Cyanobacteria in trampled plots. In parallel, other soil bacterial species that are natural residents of biocrusts, specifically members of the Actinobacteria, Chloroflexi and Bacteroidetes, became more readily detected in trampled than in untrampled biocrusts. Replicate 16S rRNA T-RFLP profiles from trampled biocrusts at all three sites contained significantly more fragments (n = 17) than those of untrampled biocrusts (n?6) and exhibited much higher variability among field replicates, indicating transition to an unstable disturbed state. Despite the dramatic negative impacts of trampling on biocrust physical structure and composition, M. vaginatus could still be detected in surface soils after 10 years of annual trampling, suggesting the potential for biocrust re-formation over time. Physical damage of biocrusts, in concert with changing temperature and precipitation patterns, has potential to alter performance of dryland ecosystems for decades.
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Influence of religiosity on 12-step participation and treatment response among substance-dependent adolescents.
J Stud Alcohol Drugs
PUBLISHED: 11-05-2011
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Religious practices among adults are associated with more 12-step participation which, in turn, is linked to better treatment outcomes. Despite recommendations for adolescents to participate in mutual-help groups, little is known about how religious practices influence youth 12-step engagement and outcomes. This study examined the relationships among lifetime religiosity, during-treatment 12-step participation, and outcomes among adolescents, and tested whether any observed beneficial relation between higher religiosity and outcome could be explained by increased 12-step participation.
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Genome of the cyanobacterium Microcoleus vaginatus FGP-2, a photosynthetic ecosystem engineer of arid land soil biocrusts worldwide.
J. Bacteriol.
PUBLISHED: 06-24-2011
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The filamentous cyanobacterium Microcoleus vaginatusis found in arid land soils worldwide. The genome of M. vaginatus strain FGP-2 allows exploration of genes involved in photosynthesis, desiccation tolerance, alkane production, and other features contributing to this organisms ability to function as a major component of biological soil crusts in arid lands.
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Estimating premorbid IQ in the prodromal phase of a neurodegenerative disease.
Clin Neuropsychol
PUBLISHED: 06-11-2011
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Estimates of premorbid intellect are often used in neuropsychological assessment to make inferences about cognitive decline. To optimize the method of controlling for premorbid intellect in assessments of prodromal neurodegenerative disease, we examined performance on the American National Adult Reading Test (ANART; administered during Years 1 and 3) and the two-subtest version of the Wechsler Abbreviated Scale of Intelligence (WASI; administered in Years 2 and 4) in an ongoing prospective longitudinal study of 371 participants with prodromal Huntington disease and 51 participants with normal CAG repeats. Although both measures performed similarly, the ANART demonstrated slightly lower variability in performance over a 2-year period and had slightly higher test-retest reliability than the WASI.
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Neurocognitive signs in prodromal Huntington disease.
Neuropsychology
PUBLISHED: 05-04-2011
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PREDICT-HD is a large-scale international study of people with the Huntington disease (HD) CAG-repeat expansion who are not yet diagnosed with HD. The objective of this study was to determine the stage in the HD prodrome at which cognitive differences from CAG-normal controls can be reliably detected.
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Not whale-fall specialists, Osedax worms also consume fishbones.
Biol. Lett.
PUBLISHED: 04-13-2011
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Marine annelid worms of the genus Osedax exploit sunken vertebrate bones for food. To date, the named species occur on whale or other mammalian bones, and it is argued that Osedax is a whale-fall specialist. To assess whether extant Osedax species could obtain nutrition from non-mammalian resources, we deployed teleost bones and calcified shark cartilage at approximately 1000 m depth for five months. Although the evidence from shark cartilage was inconclusive, the teleost bones hosted three species of Osedax, each of which also lives off whalebones. This suggests that rather than being a whale-fall specialist, Osedax has exploited and continues to exploit a variety of food sources. The ability of Osedax to colonize and to grow on fishbone lends credibility to a hypothesis that it might have split from its siboglinid relatives to assume the bone-eating lifestyle during the Cretaceous, well before the origin of marine mammals.
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Genetic diversity and demographic instability in Riftia pachyptila tubeworms from eastern Pacific hydrothermal vents.
BMC Evol. Biol.
PUBLISHED: 04-13-2011
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Deep-sea hydrothermal vent animals occupy patchy and ephemeral habitats supported by chemosynthetic primary production. Volcanic and tectonic activities controlling the turnover of these habitats contribute to demographic instability that erodes genetic variation within and among colonies of these animals. We examined DNA sequences from one mitochondrial and three nuclear gene loci to assess genetic diversity in the siboglinid tubeworm, Riftia pachyptila, a widely distributed constituent of vents along the East Pacific Rise and Galápagos Rift.
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Genomic signatures of strain selection and enhancement in Bacillus atrophaeus var. globigii, a historical biowarfare simulant.
PLoS ONE
PUBLISHED: 02-15-2011
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Despite the decades-long use of Bacillus atrophaeus var. globigii (BG) as a simulant for biological warfare (BW) agents, knowledge of its genome composition is limited. Furthermore, the ability to differentiate signatures of deliberate adaptation and selection from natural variation is lacking for most bacterial agents. We characterized a lineage of BGwith a long history of use as a simulant for BW operations, focusing on classical bacteriological markers, metabolic profiling and whole-genome shotgun sequencing (WGS).
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Fabrication of biodegradable nano test tubes by template synthesis.
Nanomedicine (Lond)
PUBLISHED: 11-03-2010
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Recent publications have suggested that cylindrically shaped drug-delivery carriers have an advantage over carriers based on spherical particles in both blood circulation and cell internalization rates. For this reason, this article introduces a method to fabricate hollow, uniform, biodegradable chitosan nano test tubes for applications in drug delivery.
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Systems Factorial Technology provides new insights on global-local information processing in autism spectrum disorders.
J Math Psychol
PUBLISHED: 02-01-2010
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Previous studies of global-local processing in autism spectrum disorders (ASDs) have indicated mixed findings, with some evidence of a local processing bias, or preference for detail-level information, and other results suggesting typical global advantage, or preference for the whole or gestalt. Findings resulting from this paradigm have been used to argue for or against a detail focused processing bias in ASDs, and thus have important theoretical implications. We applied Systems Factorial Technology, and the associated Double Factorial Paradigm (both defined in the text), to examine information processing characteristics during a divided attention global-local task in high-functioning individuals with an ASD and typically developing controls. Group data revealed global advantage for both groups, contrary to some current theories of ASDs. Information processing models applied to each participant revealed that task performance, although showing no differences at the group level, was supported by different cognitive mechanisms in ASD participants compared to controls. All control participants demonstrated inhibitory parallel processing and the majority demonstrated a minimum-time stopping rule. In contrast, ASD participants showed exhaustive parallel processing with mild facilitatory interactions between global and local information. Thus our results indicate fundamental differences in the stopping rules and channel dependencies in individuals with an ASD.
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Discrepancies between self- and parent-perceptions of autistic traits and empathy in high functioning children and adolescents on the autism spectrum.
J Autism Dev Disord
PUBLISHED: 07-24-2009
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Self-perception in high-functioning children and adolescents with Autism Spectrum Disorder (ASD) was examined by comparing parent- and self-reports on the Autism Spectrum, Empathy, and Systemizing Quotients (AQ, EQ and SQ). Participants were 20 youths with ASD and 22 typically developing controls. Both parents and participants in the ASD group reported more autistic traits (higher AQ) and less empathy (lower EQ) than the control group. SQ ratings did not differ between groups. Comparisons of self- and parent-reports indicated that youths with ASD reported significantly fewer autistic traits and more empathic features than their parents attributed to them. There were no discrepancies between parent- and self-reports in the control group. Implications regarding the use of self-report in ASD are discussed.
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A remarkable diversity of bone-eating worms (Osedax; Siboglinidae; Annelida).
BMC Biol.
PUBLISHED: 06-29-2009
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Bone-eating Osedax worms have proved to be surprisingly diverse and widespread. Including the initial description of this genus in 2004, five species that live at depths between 25 and 3,000 m in the eastern and western Pacific and in the north Atlantic have been named to date. Here, we provide molecular and morphological evidence for 12 additional evolutionary lineages from Monterey Bay, California. To assess their phylogenetic relationships and possible status as new undescribed species, we examined DNA sequences from two mitochondrial (COI and 16S rRNA) and three nuclear genes (H3, 18S and 28S rRNA).
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Loblolly pine (Pinus taeda) female gametophyte and embryo pH changes during seed development.
Tree Physiol.
PUBLISHED: 04-08-2009
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Stage-specific measurements of female gametophyte (FG) and embryo pH (hydrogen ion concentration) were made through the sequence of loblolly pine (Pinus taeda L.) seed development. The FG tissue from two open-pollinated trees showed similar pH profiles starting at 5.5 shortly after fertilization, increasing to about 6.1 at stage 7, levelling off at 6.3-6.5 towards the end of development and dropping to 6.0 just before cone opening. Measurements of the chalazal end were 0.05-0.2 pH units less than the micropylar end through early-to-mid-development. In contrast, embryo pH maintained a nearly constant value near 7.0 through development. Profiles of pH through seed development were similar whether portrayed by date or stage of embryo present in the seed. The pH profiles assisted in the development of improved embryogenic tissue initiation techniques. When post-autoclaving maturation medium pH was raised from about 5.3 in control medium to 5.7 or 5.5-5.7 with 2(n-morpholino)ethanesulphonic acid, cotyledonary embryo yields increased.
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Osmotic measurements in whole megagametophytes and embryos of loblolly pine (Pinus taeda) during seed development.
Tree Physiol.
PUBLISHED: 03-25-2009
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Water potential (Psi) and osmotic potential (Psis) were measured weekly through the sequence of seed development in megagametophytes of loblolly pine (Pinus taeda L.). A Wescor 5500XRS vapor pressure osmometer, modified with a cycle hold switch, was used to measure Psi for whole megagametophytes containing embryos. The Psi measurements for megagametophytes with embryos removed were also attempted but readings were distorted due to cell lysates from the cut surfaces. Six seasonal sets of megagametophyte Psi profiles were generated. Megagametophytes from most of the trees examined showed a consistent Psi pattern: low measurements of -1.0 to -0.75 MPa during early embryo development in late June to early July when embryo Stages 1-2 occur; an increase for one to several weeks to levels of -0.5 to -0.75 MPa, beginning at Stages 3-5 when apical dome formation occurs; followed by a steady drop from -0.85 to -1.7 to -2.0 MPa from Stage 6 onward from late August until just before cone seed release. The Psis was measured for supernatant from centrifuged frozen-thawed megagametophyte tissue (embryos removed). Megagametophyte Psis profiles were similar for seeds analyzed from two trees and resembled Psi observations starting low, rising around Stages 4-7 and then undergoing a major reduction indicating a strong solute accumulation beginning at Stages 7-9.1. Somatic embryos stop growth prematurely in vitro at Stages 8-9.1. The major change in the accumulation of megagametophyte solutes at Stages 8-9.1 correlates with the halt in somatic embryo maturation and suggests that identifying, quantifying and using the major natural soluble compounds that accumulate during mid- to late-stage seed development may be important to improve conifer somatic embryo maturation.
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Guide for mass prophylaxis of hospital employees in preparation for a bioterrorist attack.
Am J Health Syst Pharm
PUBLISHED: 03-07-2009
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The key elements required for the health-system pharmacist to prepare and implement a hospital-based mass prophylaxis distribution effort for hospital employees are described.
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Alveolar hydatid disease (Echinococcus multilocularis) in the liver of a Canadian dog in British Columbia, a newly endemic region.
Can. Vet. J.
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An adult dog that lived in central British Columbia was examined because of a history of lethargy and vomiting. Histology, immunohistochemistry, and polymerase chain reaction (PCR) examination of a hepatic mass confirmed the presence of an alveolar hydatid cyst, the first description of Echinococcus multilocularis in British Columbia. We provide recommendations for case management and remind practitioners in endemic areas of western Canada that dogs can serve as definitive and, rarely, intermediate hosts for E. multilocularis.
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?X216, a P2-like bacteriophage with broad Burkholderia pseudomallei and B. mallei strain infectivity.
BMC Microbiol.
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Burkholderia pseudomallei and B. mallei are closely related Category B Select Agents of bioterrorism and the causative agents of the diseases melioidosis and glanders, respectively. Rapid phage-based diagnostic tools would greatly benefit early recognition and treatment of these diseases. There is extensive strain-to-strain variation in B. pseudomallei genome content due in part to the presence or absence of integrated prophages. Several phages have previously been isolated from B. pseudomallei lysogens, for example ?K96243, ?1026b and ?52237.
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Draft genome sequence for Pseudomonas aeruginosa strain PAO579, a mucoid derivative of PAO381.
J. Bacteriol.
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Pseudomonas aeruginosa is an opportunistic pathogen that establishes a chronic lung infection in individuals afflicted with cystic fibrosis. Here, we announce the draft genome of P. aeruginosa strain PAO579, an alginate-overproducing derivative of strain PAO381.
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Genomic comparison of Escherichia coli O104:H4 isolates from 2009 and 2011 reveals plasmid, and prophage heterogeneity, including shiga toxin encoding phage stx2.
PLoS ONE
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In May of 2011, an enteroaggregative Escherichia coli O104:H4 strain that had acquired a Shiga toxin 2-converting phage caused a large outbreak of bloody diarrhea in Europe which was notable for its high prevalence of hemolytic uremic syndrome cases. Several studies have described the genomic inventory and phylogenies of strains associated with the outbreak and a collection of historical E. coli O104:H4 isolates using draft genome assemblies. We present the complete, closed genome sequences of an isolate from the 2011 outbreak (2011C-3493) and two isolates from cases of bloody diarrhea that occurred in the Republic of Georgia in 2009 (2009EL-2050 and 2009EL-2071). Comparative genome analysis indicates that, while the Georgian strains are the nearest neighbors to the 2011 outbreak isolates sequenced to date, structural and nucleotide-level differences are evident in the Stx2 phage genomes, the mer/tet antibiotic resistance island, and in the prophage and plasmid profiles of the strains, including a previously undescribed plasmid with homology to the pMT virulence plasmid of Yersinia pestis. In addition, multiphenotype analysis showed that 2009EL-2071 possessed higher resistance to polymyxin and membrane-disrupting agents. Finally, we show evidence by electron microscopy of the presence of a common phage morphotype among the European and Georgian strains and a second phage morphotype among the Georgian strains. The presence of at least two stx2 phage genotypes in host genetic backgrounds that may derive from a recent common ancestor of the 2011 outbreak isolates indicates that the emergence of stx2 phage-containing E. coli O104:H4 strains probably occurred more than once, or that the current outbreak isolates may be the result of a recent transfer of a new stx2 phage element into a pre-existing stx2-positive genetic background.
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Response of biological soil crust diazotrophs to season, altered summer precipitation, and year-round increased temperature in an arid grassland of the colorado plateau, USA.
Front Microbiol
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Biological soil crusts (biocrusts), which supply significant amounts of fixed nitrogen into terrestrial ecosystems worldwide (?33?Tg y(-1)), are likely to respond to changes in temperature and precipitation associated with climate change. Using nifH gene-based surveys, we explored variation in the diazotrophic community of biocrusts of the Colorado Plateau, USA in response to season (autumn vs. spring), as well as field manipulations that increased the frequency of small volume precipitation events and year-round soil temperature. Abundance of nifH genes in biocrusts ranged from 3?×?10(6) to 1?×?10(8)?g(-1) soil, and nifH from heterocystous cyanobacteria closely related to Scytonema hyalinum, Spirirestis rafaelensis, and Nostoc commune comprised >98% of the total. Although there was no apparent seasonal effect on total nifH gene abundance in the biocrusts, T-RFLP analysis revealed a strong seasonal pattern in nifH composition. SpirirestisnifH abundance was estimated to oscillate 1 to >2 orders of magnitude between autumn (low) and spring (high). A year-round increase of soil temperature (2-3°C) had little effect on the diazotroph community structure over 2?years. Altered summer precipitation had little impact on diazotroph community structure over the first 1.5?years of the study, when natural background patterns across years and seasons superseded any treatment effects. However, after the second summer of treatments, nifH abundance was 2.6-fold lower in biocrusts receiving altered precipitation. Heterocystous cyanobacteria were apparently more resilient to altered precipitation than other cyanobacteria. The results demonstrate that diazotrophic community composition of biocrusts in this semi-arid grassland undergoes strong seasonal shifts and that the abundance of its dominant members decreased in response to more frequent, small volume precipitation events.
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Assessing an intervention to improve clinical trial perceptions among predominately African-American communities in South Carolina.
Prog Community Health Partnersh
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African Americans (AA) are not well-represented in cancer clinical trials despite having significantly higher cancer mortality rates than their European-American (EA) counterparts.
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The Role of Religiousness on Substance-Use Disorder Treatment Outcomes: A Comparison of Black and White Adolescents.
J Soc Social Work Res
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This study compares 41 Black and 124 White adolescents at intake and discharge from a residential treatment program for substance-use disorders. Study data were obtained as part of a larger study (N = 195) that sought to assess the relationship of helping behavior and addiction recovery. This post-hoc analysis aims to identify cultural strengths that may be associated with recovery from substance-use disorders among Black adolescents. Using regression analyses and controlling for the severity of substance use and background variables that distinguish racial groups, religious practices and behaviors at intake were examined. Specifically, Black youth and White youth were compared on treatment outcomes, including alcohol or drug use during treatment, drug craving, 12-Step work, and 12-Step helping. The burden of health and socioeconomic disparities at intake did not disproportionately disfavor Black adolescents. Outcomes related to 12-Step measures were similar between Black and White youth. White adolescents reported higher craving scores at discharge, and Black adolescents were more likely to use drugs during treatment. High levels of religiousness at treatment intake were linked to greater 12-Step work and greater 12-Step helping at discharge. High levels of religiousness at intake were not related to drug use during treatment or to craving scores at discharge. The relationship between intake levels of religiousness and treatment-related outcomes did not differ by race.
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Understanding advanced modes of mechanical ventilation.
Crit Care Nurs Clin North Am
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Approaches to mechanical ventilation (MV) are consistently changing and the level of ventilator sophistication provides opportunities to improve pulmonary support for critically ill patients. Advanced MV modes are used in the treatment of patients with complex pulmonary conditions. To achieve optimal patient outcomes MV modes that best meet the needs of patients evolving pulmonary conditions are necessary. Its essential for nurses to integrate pulmonary MV knowledge in the care of critically ill patients. The purpose of this article is to describe the evidence supporting lung protective modes of MV used in the care of critically ill adults.
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Self-reported and parent-reported pain for common painful events in high-functioning children and adolescents with autism spectrum disorder.
Clin J Pain
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Previous research suggests that children with autism spectrum disorders (ASD) are at a higher risk for painful experiences, but there is limited research examining pain in children with ASD.
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Genome sequence of Kingella kingae septic arthritis isolate PYKK081.
J. Bacteriol.
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Kingella kingae is a human oral bacterium that can cause infections of the skeletal system in children. The bacterium is also a cardiovascular pathogen causing infective endocarditis in children and adults. We report herein the draft genome sequence of septic arthritis K. kingae strain PYKK081.
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Addiction and "Generation Me:" Narcissistic and Prosocial Behaviors of Adolescents with Substance Dependency Disorder in Comparison to Normative Adolescents.
Alcohol Treat Q
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The purpose of this study is to explore narcissistic and prosocial behaviors as reported by adolescents with and without substance dependency disorder (SDD). This study employs a quasi-experimental design using SDD adolescents compared with two normative samples of adolescents. In comparison to normative adolescents, adolescents with SDD were strongly distinguished by overt narcissistic behaviors and less monetary giving. Levels of narcissistic and prosocial behaviors among adolescents with SDD suggest a connection between self-centeredness and addiction. Results also suggest volunteerism as a potential option to counter narcissism in substance dependent adolescents.
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Three acyltransferases and nitrogen-responsive regulator are implicated in nitrogen starvation-induced triacylglycerol accumulation in Chlamydomonas.
J. Biol. Chem.
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Algae have recently gained attention as a potential source for biodiesel; however, much is still unknown about the biological triggers that cause the production of triacylglycerols. We used RNA-Seq as a tool for discovering genes responsible for triacylglycerol (TAG) production in Chlamydomonas and for the regulatory components that activate the pathway. Three genes encoding acyltransferases, DGAT1, DGTT1, and PDAT1, are induced by nitrogen starvation and are likely to have a role in TAG accumulation based on their patterns of expression. DGAT1 and DGTT1 also show increased mRNA abundance in other TAG-accumulating conditions (minus sulfur, minus phosphorus, minus zinc, and minus iron). Insertional mutants, pdat1-1 and pdat1-2, accumulate 25% less TAG compared with the parent strain, CC-4425, which demonstrates the relevance of the trans-acylation pathway in Chlamydomonas. The biochemical functions of DGTT1 and PDAT1 were validated by rescue of oleic acid sensitivity and restoration of TAG accumulation in a yeast strain lacking all acyltransferase activity. Time course analyses suggest than a SQUAMOSA promoter-binding protein domain transcription factor, whose mRNA increases precede that of lipid biosynthesis genes like DGAT1, is a candidate regulator of the nitrogen deficiency responses. An insertional mutant, nrr1-1, accumulates only 50% of the TAG compared with the parental strain in nitrogen-starvation conditions and is unaffected by other nutrient stresses, suggesting the specificity of this regulator for nitrogen-deprivation conditions.
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Sex differences for the recognition of direct versus averted gaze faces.
Memory
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Gaze direction plays a central role in face recognition. Previous research suggests that faces with direct gaze are better remembered than faces with averted gaze. We compared recognition of faces with direct versus averted gaze in male versus female participants. A total of 52 adults (23 females, 29 males) and 46 children (25 females, 21 males) completed a computerised task that assessed their recognition of faces with direct gaze and faces with averted gaze. Adult male participants showed superior recognition of faces with direct gaze compared to faces with averted gaze. There was no difference between recognition of direct and averted gaze faces for the adult female participants. Children did not demonstrate this sex difference; rather, both male and female youth participants showed better recognition of faces with direct gaze compared to averted gaze. A large body of previous research has revealed superior recognition of faces with direct, compared to averted gaze. However, relatively few studies have examined sex differences. Our findings suggest that gaze direction has differential effects on face recognition for adult males and females, but not for children. These findings have implications for previous explanations of better recognition for direct versus averted gaze.
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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.