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Find video protocols related to scientific articles indexed in Pubmed.
Collection and extraction of saliva DNA for next generation sequencing.
J Vis Exp
PUBLISHED: 09-17-2014
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The preferred source of DNA in human genetics research is blood, or cell lines derived from blood, as these sources yield large quantities of high quality DNA. However, DNA extraction from saliva can yield high quality DNA with little to no degradation/fragmentation that is suitable for a variety of DNA assays without the expense of a phlebotomist and can even be acquired through the mail. However, at present, no saliva DNA collection/extraction protocols for next generation sequencing have been presented in the literature. This protocol optimizes parameters of saliva collection/storage and DNA extraction to be of sufficient quality and quantity for DNA assays with the highest standards, including microarray genotyping and next generation sequencing.
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Do the symptoms of language disorder align with treatment goals? An exploratory study of primary-grade students' IEPs.
J Commun Disord
PUBLISHED: 06-09-2014
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Individual Education Plans (IEPs) are legal documents that guide the treatment of students with language disorder (LD). This exploratory study investigated the extent to which students' symptoms of LD align with goals on their IEPs. A total of 99 kindergarten and first-grade students receiving treatment for LD in the public schools participated. IEPs were collected and coded for each student and norm-referenced measures were used to assess students' grammar, vocabulary, listening comprehension, and literacy skills in the fall of the academic year. Results showed there to be alignment between students' symptoms and IEP goals only in the area of vocabulary, such that students who had an IEP goal for vocabulary had lower scores on a vocabulary assessment than those without a goal. In general, there is limited alignment between observed symptoms of LD and treated symptoms as identified on students' IEPs. The limited alignment found in this study suggests more investigation is needed to understand the extent to which IEP goals, as potential indicators of treatment foci, should map on to students' symptoms. Learning outcomes: Readers will be able to: (1) explain the theoretical and practical relevance of treatment goals aligning to symptoms for children with language impairment; (2) identify three analytic methods used to investigate alignment between treatment goals and symptoms; and (3) describe the extent to which IEP goals align to children's symptoms in a sample of children receiving services in the public schools.
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Addressing the unmet need for visualizing conditional random fields in biological data.
BMC Bioinformatics
PUBLISHED: 04-24-2014
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The biological world is replete with phenomena that appear to be ideally modeled and analyzed by one archetypal statistical framework - the Graphical Probabilistic Model (GPM). The structure of GPMs is a uniquely good match for biological problems that range from aligning sequences to modeling the genome-to-phenome relationship. The fundamental questions that GPMs address involve making decisions based on a complex web of interacting factors. Unfortunately, while GPMs ideally fit many questions in biology, they are not an easy solution to apply. Building a GPM is not a simple task for an end user. Moreover, applying GPMs is also impeded by the insidious fact that the "complex web of interacting factors" inherent to a problem might be easy to define and also intractable to compute upon.
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Prevalence of psoriasis among adults in the U.S.: 2003-2006 and 2009-2010 National Health and Nutrition Examination Surveys.
Am J Prev Med
PUBLISHED: 02-05-2014
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A 2010 CDC-sponsored consultation of psoriasis, psoriatic arthritis, and public health experts developed a public health agenda for psoriasis and psoriatic arthritis indicating that additional population-based research is needed to better characterize psoriasis in the population.
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Who is afraid of math? Two sources of genetic variance for mathematical anxiety.
J Child Psychol Psychiatry
PUBLISHED: 01-27-2014
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Emerging work suggests that academic achievement may be influenced by the management of affect as well as through efficient information processing of task demands. In particular, mathematical anxiety has attracted recent attention because of its damaging psychological effects and potential associations with mathematical problem solving and achievement. This study investigated the genetic and environmental factors contributing to the observed differences in the anxiety people feel when confronted with mathematical tasks. In addition, the genetic and environmental mechanisms that link mathematical anxiety with math cognition and general anxiety were also explored.
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Gene silencing associated with SWI/SNF complex loss during NSCLC development.
Mol. Cancer Res.
PUBLISHED: 01-20-2014
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The SWI/SNF chromatin-remodeling complex regulates gene expression and alters chromatin structures in an ATP-dependent manner. Recent sequencing efforts have shown mutations in BRG1 (SMARCA4), one of two mutually exclusive ATPase subunits in the complex, in a significant number of human lung tumor cell lines and primary non-small cell lung carcinoma (NSCLC) clinical specimens. To determine how BRG1 loss fuels tumor progression in NSCLC, molecular profiling was performed after restoration of BRG1 expression or treatment with a histone deacetylase inhibitor or a DNA methyltransferase (DNMT) inhibitor in a BRG1-deficient NSCLC cells. Importantly, validation studies from multiple cell lines revealed that BRG1 reexpression led to substantial changes in the expression of CDH1, CDH3, EHF, and RRAD that commonly undergo silencing by other epigenetic mechanisms during NSCLC development. Furthermore, treatment with DNMT inhibitors did not restore expression of these transcripts, indicating that this common mechanism of gene silencing did not account for their loss of expression. Collectively, BRG1 loss is an important mechanism for the epigenetic silencing of target genes during NSCLC development.
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Understanding the sequence requirements of protein families: insights from the BioVis 2013 contests.
BMC Proc
PUBLISHED: 01-01-2014
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In 2011, the BioVis symposium of the IEEE VisWeek conferences inaugurated a new variety of data analysis contest. Aimed at fostering collaborations between computational scientists and biologists, the BioVis contest provided real data from biological domains with emerging visualization needs, in the hope that novel approaches would result in powerful new tools for the community. In 2011 and 2012 the theme of these contests was expression Quantitative Trait Locus analysis, within and across tissues respectively. In 2013 the topic was updated to protein sequence and mutation visualization.
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Empirically Based Profiles of the Early Literacy Skills of Children With Language Impairment in Early Childhood Special Education.
J Learn Disabil
PUBLISHED: 11-16-2013
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The purpose of this study was to empirically determine whether specific profiles characterize preschool-aged children with language impairment (LI) with respect to their early literacy skills (print awareness, name-writing ability, phonological awareness, alphabet knowledge); the primary interest was to determine if one or more profiles suggested vulnerability for future reading problems. Participants were 218 children enrolled in early childhood special education classrooms, 95% of whom received speech-language services. Children were administered an assessment of early literacy skills in the fall of the academic year. Based on results of latent profile analysis, four distinct literacy profiles were identified, with the single largest profile (55% of children) representing children with generally poor literacy skills across all areas examined. Children in the two low-risk categories had higher oral language skills than those in the high-risk and moderate-risk profiles. Across three of the four early literacy measures, children with language as their primary disability had higher scores than those with LI concomitant with other disabilities. These findings indicate that there are specific profiles of early literacy skills among children with LI, with about one half of children exhibiting a profile indicating potential susceptibility for future reading problems.
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Gene-environment interplay in child psychology and psychiatry - challenges and ways forward.
J Child Psychol Psychiatry
PUBLISHED: 09-07-2013
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This special issue in the Journal of Child Psychology and Psychiatry presents several invited articles examining gene-environment interplay in child development and psychopathology. Models of gene-environment interplay have been exhaustively discussed in the literature, including an important contribution by Rutter, Moffitt and Caspi (2006) published in this journal.
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Gene × smoking interactions on human brain gene expression: finding common mechanisms in adolescents and adults.
J Child Psychol Psychiatry
PUBLISHED: 06-04-2013
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Numerous studies have examined gene × environment interactions (G × E) in cognitive and behavioral domains. However, these studies have been limited in that they have not been able to directly assess differential patterns of gene expression in the human brain. Here, we assessed G × E interactions using two publically available datasets to assess if DNA variation is associated with post-mortem brain gene expression changes based on smoking behavior, a biobehavioral construct that is part of a complex system of genetic and environmental influences.
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Enantioselective total synthesis of (+)-scuteflorin A using organocatalytic asymmetric epoxidation.
J. Org. Chem.
PUBLISHED: 12-13-2011
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We report the first enantioselective total synthesis of (+)-scuteflorin A in 14% overall yield, employing a chiral iminium salt to effect an organocatalytic asymmetric epoxidation of xanthyletin in >99% ee as the key step.
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Surveillance and control of communicable diseases related to passenger ships in Europe.
Int Marit Health
PUBLISHED: 09-13-2011
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This study was conducted within the European SHIPSAN (ship sanitation) project and aims at exploring the legislative framework and current practices related to surveillance of communicable diseases and response aboard passenger ships in Europe. A detailed questionnaire was disseminated and completed by 59 competent authorities in 27 European countries. The majority of competent authorities used national legislation without special provisions for passenger ships. Only 20% had specific provisions for ships regarding quarantine, while a smaller proportion of new Member States (MS) have specific legislation in comparison with old MS (p = 0.01). The Maritime Declaration of Health (MDH) was the main reporting tool used. About 30.5% of the competent authorities declared that they require submission of MDH by all arriving ships, but 28.8% only from affected areas, and 11.9% never require MDH. A total of 45 outbreaks or incidents (36 gastrointestinal, 1 incident of legionellosis, 3 respiratory, and 1 influenza-like illness outbreak, occupational tuberculosis, varicella, scabies, and meningitis) were reported to EU competent authorities during 2006. About 75% of the responders stated that there are gaps in the surveillance and control of communicable diseases. A diversity of approaches in EU countries, and gaps regarding surveillance and response and training needs of personnel were identified.
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Heritability across the distribution: an application of quantile regression.
Behav. Genet.
PUBLISHED: 08-11-2011
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We introduce a new method for analyzing twin data called quantile regression. Through the application presented here, quantile regression is able to assess the genetic and environmental etiology of any skill or ability, at multiple points in the distribution of that skill or ability. This method is compared to the Cherny et al. (Behav Genet 22:153-162, 1992) method in an application to four different reading-related outcomes in 304 pairs of first-grade same sex twins enrolled in the Western Reserve Reading Project. Findings across the two methods were similar; both indicated some variation across the distribution of the genetic and shared environmental influences on non-word reading. However, quantile regression provides more details about the location and size of the measured effect. Applications of the technique are discussed.
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BRG1 mutations found in human cancer cell lines inactivate Rb-mediated cell-cycle arrest.
J. Cell. Physiol.
PUBLISHED: 04-27-2011
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Eukaryotic organisms package DNA into chromatin for compact storage in the cell nucleus. However, this process promotes transcriptional repression of genes. To overcome the transcriptional repression, chromatin remodeling complexes have evolved that alter the configuration of chromatin packaging of DNA into nucleosomes by histones. The SWI/SNF chromatin remodeling complex uses energy from ATP hydrolysis to reposition nucleosomes and make DNA accessible to transcription factors. Recent studies showing mutations of BRG1, one of two mutually exclusive ATPase subunits, in human tumor cell lines and primary tissue samples have implicated a role for its loss in cancer development. While most of the mutations lead to complete loss of BRG1 protein expression, others result in single amino acid substitutions. To better understand the role of these BRG1 point mutations in cancer development, we characterized SWI/SNF function in human tumor cell lines with these mutations in the absence of BRM expression, the other ATPase component. We found that the mutant BRG1 proteins still interacted with the core complex members and appeared at the promoters of target genes. However, while these mutations did not affect CD44 and CDH1 expression, known targets of the SWI/SNF complex, they did abrogate Rb-mediated cell-cycle arrest. Therefore, our results implicate that these mutations disrupt the de novo chromatin remodeling activity of the complex without affecting the status of existing nucleosome positioning.
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Validation of a cost-efficient multi-purpose SNP panel for disease based research.
PLoS ONE
PUBLISHED: 04-13-2011
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Here we present convergent methodologies using theoretical calculations, empirical assessment on in-house and publicly available datasets as well as in silico simulations, that validate a panel of SNPs for a variety of necessary tasks in human genetics disease research before resources are committed to larger-scale genotyping studies on those samples. While large-scale well-funded human genetic studies routinely have up to a million SNP genotypes, samples in a human genetics laboratory that are not yet part of such studies may be productively utilized in pilot projects or as part of targeted follow-up work though such smaller scale applications require at least some genome-wide genotype data for quality control purposes such as DNA "barcoding" to detect swaps or contamination issues, determining familial relationships between samples and correcting biases due to population effects such as population stratification in pilot studies.
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Genetic covariation underlying reading, language and related measures in a sample selected for specific language impairment.
Behav. Genet.
PUBLISHED: 01-04-2011
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Specific language impairment is a developmental language disorder characterized by failure to develop language normally in the absence of a specific cause. Previous twin studies have documented the heritability of reading and language measures as well as the genetic correlation between those measures. This paper presents results from an alternative to the classical twin designs by estimating heritability from extended pedigrees. These pedigrees were previously studied as part of series of molecular genetic studies of specific language impairment where the strongest genetic findings were with reading phenotypes rather than language despite selecting pedigrees based on language impairments. To explore the relationship between reading and language in these pedigrees, variance components estimates of heritability of reading and language measures were conducted showing general agreement with the twin literature, as were genetics correlations between reading and language. Phonological short-term memory, phonological awareness and auditory processing were evaluated as candidate mediators of the reading-language genetic correlations. Only phonological awareness showed significant genetic correlations with all reading measures and several language measures while phonological short-term memory and auditory processing did not.
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Increasing genotype-phenotype model determinism: application to bivariate reading/language traits and epistatic interactions in language-impaired families.
Hum. Hered.
PUBLISHED: 05-14-2010
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While advances in network and pathway analysis have flourished in the era of genome-wide association analysis, understanding the genetic mechanism of individual loci on phenotypes is still readily accomplished using genetic modeling approaches. Here, we demonstrate two novel genotype-phenotype models implemented in a flexible genetic modeling platform. The examples come from analysis of families with specific language impairment (SLI), a failure to develop normal language without explanatory factors such as low IQ or inadequate environment. In previous genome-wide studies, we observed strong evidence for linkage to 13q21 with a reading phenotype in language-impaired families. First, we elucidate the genetic architecture of reading impairment and quantitative language variation in our samples using a bivariate analysis of reading impairment in affected individuals jointly with language quantitative phenotypes in unaffected individuals. This analysis largely recapitulates the baseline analysis using the categorical trait data (posterior probability of linkage (PPL) = 80%), indicating that our reading impairment phenotype captured poor readers who also have low language ability. Second, we performed epistasis analysis using a functional coding variant in the brain-derived neurotrophic factor (BDNF) gene previously associated with reduced performance on working memory tasks. Modeling epistasis doubled the evidence on 13q21 and raised the PPL to 99.9%, indicating that BDNF and 13q21 susceptibility alleles are jointly part of the genetic architecture of SLI. These analyses provide possible mechanistic insights for further cognitive neuroscience studies based on the models developed herein.
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Hygiene inspections on passenger ships in Europe - an overview.
BMC Public Health
PUBLISHED: 03-10-2010
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Hygiene inspections on passenger ships are important for the prevention of communicable diseases. The European Union (EU) countries conduct hygiene inspections on passenger ships in order to ensure that appropriate measures have been taken to eliminate potential sources of contamination which could lead to the spread of communicable diseases. This study was implemented within the framework of the EU SHIPSAN project and it investigates the legislation applied and practices of hygiene inspections of passenger ships in the EU Member States (MS) and European Free Trade Association countries.
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Occupational health legislation and practices related to seafarers on passenger ships focused on communicable diseases: results from a European cross-sectional study (EU SHIPSAN PROJECT).
J Occup Med Toxicol
PUBLISHED: 02-10-2010
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Seafarers play an important role in the transmission of communicable diseases. The aim of the present study is to draw information and identify possible gaps on occupational health practices related to seafarers sailing on ships within the European Union Member States (EU MS) with focus on communicable diseases.
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Evaluation of a bayesian model integration-based method for censored data.
Hum. Hered.
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Non-random missing data can adversely affect family-based linkage detection through loss of power and possible introduction of bias depending on how censoring is modeled. We examined the statistical properties of a previously proposed quantitative trait threshold (QTT) model developed for when censored data can be reasonably inferred to be beyond an unknown threshold.
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Asymmetric epoxidation using iminium salt organocatalysts featuring dynamically controlled atropoisomerism.
J. Org. Chem.
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Introduction of a pseudoaxial substituent at a stereogenic center adjacent to the nitrogen atom in binaphthyl- and biphenyl-derived azepinium salt organocatalysts affords improved enantioselectivities and yields in the epoxidation of unfunctionalized alkenes. In the biphenyl-derived catalysts, the atropoisomerism at the biphenyl axis is controlled by the interaction of this substituent with the chiral substituent at nitrogen.
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Gene × gene interaction in shared etiology of autism and specific language impairment.
Biol. Psychiatry
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To examine the relationship between autism spectrum disorders (ASD) and specific language impairment (SLI), family studies typically take a comparative approach where families with one disease are examined for traits of the other disease. In contrast, the present report is the first study with both disorders required to be present in each family to provide a more direct test of the hypothesis of shared genetic etiology.
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An eQTL biological data visualization challenge and approaches from the visualization community.
BMC Bioinformatics
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In 2011, the IEEE VisWeek conferences inaugurated a symposium on Biological Data Visualization. Like other domain-oriented Vis symposia, this symposiums purpose was to explore the unique characteristics and requirements of visualization within the domain, and to enhance both the Visualization and Bio/Life-Sciences communities by pushing Biological data sets and domain understanding into the Visualization community, and well-informed Visualization solutions back to the Biological community. Amongst several other activities, the BioVis symposium created a data analysis and visualization contest. Unlike many contests in other venues, where the purpose is primarily to allow entrants to demonstrate tour-de-force programming skills on sample problems with known solutions, the BioVis contest was intended to whet the participants appetites for a tremendously challenging biological domain, and simultaneously produce viable tools for a biological grand challenge domain with no extant solutions. For this purpose expression Quantitative Trait Locus (eQTL) data analysis was selected. In the BioVis 2011 contest, we provided contestants with a synthetic eQTL data set containing real biological variation, as well as a spiked-in gene expression interaction network influenced by single nucleotide polymorphism (SNP) DNA variation and a hypothetical disease model. Contestants were asked to elucidate the pattern of SNPs and interactions that predicted an individuals disease state. 9 teams competed in the contest using a mixture of methods, some analytical and others through visual exploratory methods. Independent panels of visualization and biological experts judged entries. Awards were given for each panels favorite entry, and an overall best entry agreed upon by both panels. Three special mention awards were given for particularly innovative and useful aspects of those entries. And further recognition was given to entries that correctly answered a bonus question about how a proposed "gene therapy" change to a SNP might change an individuals disease status, which served as a calibration for each approaches applicability to a typical domain question. In the future, BioVis will continue the data analysis and visualization contest, maintaining the philosophy of providing new challenging questions in open-ended and dramatically underserved Bio/Life Sciences domains.
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Water Safety Plan on cruise ships: a promising tool to prevent waterborne diseases.
Sci. Total Environ.
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Legionella spp. and other waterborne pathogens have been isolated from various water systems on land based premises as well as on ships and cases of Legionnaires disease have been associated with both sites. Peculiarities of cruise ships water systems make the risk management a challenging process. The World Health Organization suggests a Water Safety Plan (WSP) as the best approach to mitigate risks and hazards such as Legionella spp. and others.
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Defining the genetic architecture of human developmental language impairment.
Life Sci.
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Language is a uniquely human trait, which poses limitations on animal models for discovering biological substrates and pathways. Despite this challenge, rapidly developing biotechnology in the field of genomics has made human genetics studies a viable alternative route for defining the molecular neuroscience of human language. This is accomplished by studying families that transmit both normal and disordered language across generations. The language disorder reviewed here is specific language impairment (SLI), a developmental deficiency in language acquisition despite adequate opportunity, normal intelligence, and without any apparent neurological etiology. Here, we describe disease gene discovery paradigms as applied to SLI families and review the progress this field has made. After review the evidence that genetic factors influence SLI, we discuss methods and findings from scans of the human chromosomes, including the main replicated regions on chromosomes 13, 16 and 19 and two identified genes, ATP2C2 and CMIP that appear to account for the language variation on chromosome 16. Additional work has been done on candidate genes, i.e., genes chosen a priori and not through a genome scanning studies, including several studies of CNTNAP2 and some recent work implicating BDNF as a gene x gene interaction partner of genetic variation on chromosome 13 that influences language. These recent developments may allow for better use of post-mortem human brain samples functional studies and animal models for circumscribed language subcomponents. In the future, the identification of genetic variation associated with language phenotypes will provide the molecular pathways to understanding human language.
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A Genome Scan for Loci Shared by Autism Spectrum Disorder and Language Impairment.
Am J Psychiatry
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OBJECTIVE The authors conducted a genetic linkage study of families that have both autism spectrum disorder (ASD) and language-impaired probands to find common communication impairment loci. The hypothesis was that these families have a high genetic loading for impairments in language ability, thus influencing the language and communication deficits of the family members with ASD. Comprehensive behavioral phenotyping of the families also enabled linkage analysis of quantitative measures, including normal, subclinical, and disordered variation in all family members for the three general autism symptom domains: social, communication, and compulsive behaviors. METHOD The primary linkage analysis coded persons with either ASD or specific language impairment as "affected." The secondary linkage analysis consisted of quantitative metrics of autism-associated behaviors capturing normal to clinically severe variation, measured in all family members. RESULTS Linkage to language phenotypes was established at two novel chromosomal loci, 15q23-26 and 16p12. The secondary analysis of normal and disordered quantitative variation in social and compulsive behaviors established linkage to two loci for social behaviors (at 14q and 15q) and one locus for repetitive behaviors (at 13q). CONCLUSION These data indicate shared etiology of ASD and specific language impairment at two novel loci. Additionally, nonlanguage phenotypes based on social aloofness and rigid personality traits showed compelling evidence for linkage in this study group. Further genetic mapping is warranted at these loci.
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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.