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Find video protocols related to scientific articles indexed in Pubmed.
Phylotranscriptomic analysis of the origin and early diversification of land plants.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 10-29-2014
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Reconstructing the origin and evolution of land plants and their algal relatives is a fundamental problem in plant phylogenetics, and is essential for understanding how critical adaptations arose, including the embryo, vascular tissue, seeds, and flowers. Despite advances in molecular systematics, some hypotheses of relationships remain weakly resolved. Inferring deep phylogenies with bouts of rapid diversification can be problematic; however, genome-scale data should significantly increase the number of informative characters for analyses. Recent phylogenomic reconstructions focused on the major divergences of plants have resulted in promising but inconsistent results. One limitation is sparse taxon sampling, likely resulting from the difficulty and cost of data generation. To address this limitation, transcriptome data for 92 streptophyte taxa were generated and analyzed along with 11 published plant genome sequences. Phylogenetic reconstructions were conducted using up to 852 nuclear genes and 1,701,170 aligned sites. Sixty-nine analyses were performed to test the robustness of phylogenetic inferences to permutations of the data matrix or to phylogenetic method, including supermatrix, supertree, and coalescent-based approaches, maximum-likelihood and Bayesian methods, partitioned and unpartitioned analyses, and amino acid versus DNA alignments. Among other results, we find robust support for a sister-group relationship between land plants and one group of streptophyte green algae, the Zygnematophyceae. Strong and robust support for a clade comprising liverworts and mosses is inconsistent with a widely accepted view of early land plant evolution, and suggests that phylogenetic hypotheses used to understand the evolution of fundamental plant traits should be reevaluated.
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A 28-day Gavage Toxicity Study in Fischer 344 Rats with 3-methylfuran.
Toxicol Pathol
PUBLISHED: 06-08-2014
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3-Methylfuran is produced in foods during food processing and preservation techniques that involve heat treatment such as cooking, jarring, canning, and pasteurization. Currently, there are no studies available on the toxicity of 3-methylfuran. We conducted a 28-day gavage toxicity study (7 days per week) using doses of 0.0, 0.1, 0.3, 1.5, 3.0, 6.0, 12.0, and 25.0 mg/kg bw/day in order to determine the dose range needed to establish a no observed adverse effect level and to better characterize nonneoplastic effects including those affecting hematology, clinical biochemistry, gross morphology, and histopathology. Histological changes of the liver were noted in all treated animals and gross changes were noted beginning at 3.0 mg/kg bw/kg. Alterations in the activity of serum enzymes indicative of effects on the liver were observed, including increases in levels of alanine transaminase and alkaline phosphatase at the highest dose. There was a significant increase in serum thyroxine (T4) and triiodothyronine (T3), which was not accompanied by histological changes in the thyroid. For the most part, statistically significant changes were seen only at the highest dose for hematology and at the 2 highest doses for clinical chemistry parameters. In contrast, mild histological lesions in the liver were observed even at the lowest dose of 0.1 mg/kg bw/day.
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Parent Stress and Perceptions of Language Development: Comparing Down Syndrome and Other Developmental Disabilities.
Fam Relat
PUBLISHED: 04-23-2014
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This study extended research on the Down syndrome advantage by examining differences in parent stress and parent perceptions of language development between 29 parents of young children with Down syndrome and 82 parents of children with other developmental disabilities. Parents of children with Down syndrome reported lower levels of total stress, child-related stress, and stress surrounding the parent-child interaction. Parents of children in both groups reported that they felt successful in their ability to impact their children's communication development but did differ on perceptions of difficulty such that parents of children with Down syndrome perceived their children's communication difficulties as less severe despite the children exhibiting similar language skills. Finally, after accounting for potential explanatory confounding variables, child diagnosis remained a significant predictor of parent stress and perceptions of language development. Results highlight the importance of considering etiology when assisting families raising a child with a disability.
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Validity of a Non-Speech Dynamic Assessment of Phonemic Awareness via the Alphabetic Principle.
Augment Altern Commun
PUBLISHED: 02-26-2014
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Most assessments of phonemic awareness require speech responses and cannot be used with individuals with severe speech impairments who may use augmentative and alternative communication (AAC). This study investigated the reliability and construct validity of the Dynamic Assessment of Phonemic Awareness via the Alphabetic Principle (DAPA-AP), which does not require speech. In all, 17 adults with mild to moderate intellectual disabilities completed the DAPA-AP, a letter-sound knowledge task, four measures of phonological awareness, and two reading assessments. Results indicated the DAPA-AP was both a reliable and valid assessment of phonemic awareness for this sample. Consequently, the DAPA-AP represents an important step in developing phonemic awareness assessments that have the potential to be suitable for use with a wide range of individuals, including those with SSI.
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Between two fern genomes.
Gigascience
PUBLISHED: 01-01-2014
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Ferns are the only major lineage of vascular plants not represented by a sequenced nuclear genome. This lack of genome sequence information significantly impedes our ability to understand and reconstruct genome evolution not only in ferns, but across all land plants. Azolla and Ceratopteris are ideal and complementary candidates to be the first ferns to have their nuclear genomes sequenced. They differ dramatically in genome size, life history, and habit, and thus represent the immense diversity of extant ferns. Together, this pair of genomes will facilitate myriad large-scale comparative analyses across ferns and all land plants. Here we review the unique biological characteristics of ferns and describe a number of outstanding questions in plant biology that will benefit from the addition of ferns to the set of taxa with sequenced nuclear genomes. We explain why the fern clade is pivotal for understanding genome evolution across land plants, and we provide a rationale for how knowledge of fern genomes will enable progress in research beyond the ferns themselves.
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A model of phonological processing, language, and reading for students with mild intellectual disability.
Am J Intellect Dev Disabil
PUBLISHED: 11-20-2013
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Little is known about the relationships between phonological processing, language, and reading in children with intellectual disability (ID). We examined the structure of phonological processing in 294 school-age children with mild ID and the relationships between its components and expressive and receptive language and reading skills using structural equation modeling. Phonological processing consisted of two distinct but correlated latent abilities: phonological awareness and naming speed. Phonological awareness had strong relationships with expressive and receptive language and reading skills. Naming speed had moderate relationships with these variables. Results suggest that children with ID bring the same skills to the task of learning to read as children with typical development, highlighting the fact that phonologically based reading instruction should be considered a viable approach.
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Support for AAC use in preschool, and growth in language skills, for young children with developmental disabilities.
Augment Altern Commun
PUBLISHED: 11-16-2013
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Little is known about how AAC use in preschool may impact language development for children with complex communication needs (e.g., children with autism, cerebral palsy, Down syndrome, and other developmental disabilities). We developed two surveys (a) to describe childrens use of AAC in preschool classrooms, as well as the use of prompts and question asking, and augmented input by their communication partners; and (b) to describe teachers experience, training, and perceived support in providing AAC. We then examined the relationship between childrens experience of AAC, including the use of prompts, question asking, and augmented input by their partners, and the growth of receptive and expressive language for 71 children with developmental disabilities over a two-year period. The use of AAC by peers to provide augmented input was associated with stronger language growth; the use of prompting and question asking by teachers was associated with weaker language growth. Teachers reported that they received little training regarding ways to support a childs use of AAC. Results suggest the need for further research on promoting AAC use at the preschool level, including research to promote peer interactions for AAC users.
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Change Detection and Change Blindness in Pigeons (Columba livia).
J Comp Psychol
PUBLISHED: 11-04-2013
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Change blindness is a phenomenon in which even obvious details in a visual scene change without being noticed. Although change blindness has been studied extensively in humans, we do not yet know if it is a phenomenon that also occurs in other animals. Thus, investigation of change blindness in a nonhuman species may prove to be valuable by beginning to provide some insight into its ultimate causes. Pigeons learned a change detection task in which pecks to the location of a change in a sequence of stimulus displays were reinforced. They were worse at detecting changes if the stimulus displays were separated by a brief interstimulus interval, during which the display was blank, and this primary result matches the general pattern seen in previous studies of change blindness in humans. A second experiment attempted to identify specific stimulus characteristics that most reliably produced a failure to detect changes. Change detection was more difficult when interstimulus intervals were longer and when the change was iterated fewer times. (PsycINFO Database Record (c) 2013 APA, all rights reserved).
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A peptide derived from TIMP-3 inhibits multiple angiogenic growth factor receptors and tumour growth and inflammatory arthritis in mice.
Angiogenesis
PUBLISHED: 09-23-2013
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The binding of vascular endothelial growth factor (VEGF) to VEGF receptor-2 (VEGFR-2) on the surface of vascular endothelial cells stimulates many steps in the angiogenic pathway. Inhibition of this interaction is proving of value in moderating the neovascularization accompanying age-related macular degeneration and in the treatment of cancer. Tissue inhibitor of metalloproteinases-3 (TIMP-3) has been shown to be a natural VEGFR-2 specific antagonist-an activity that is independent of its ability to inhibit metalloproteinases. In this investigation we localize this activity to the C-terminal domain of the TIMP-3 molecule and characterize a short peptide, corresponding to part of this domain, that not only inhibits all three VEGF-family receptors, but also fibroblast growth factor and platelet-derived growth factor receptors. This multiple-receptor inhibition may explain why the peptide was also seen to be a powerful inhibitor of tumour growth and also a partial inhibitor of arthritic joint inflammation in vivo.
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A total evidence approach to understanding phylogenetic relationships and ecological diversity in Selaginella subg. Tetragonostachys.
Am. J. Bot.
PUBLISHED: 08-08-2013
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Several members of Selaginella are renowned for their ability to survive extreme drought and "resurrect" when conditions improve. Many of these belong to subgenus Tetragonostachys, a group of ?45 species primarily found in North and Central America, with substantial diversity in the Sonoran and Chihuahuan Deserts. We evaluated the monophyly and the age of subgenus Tetragonostachys and assess how drought tolerance contributed to the evolution of this clade.
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Genomics of Compositae crops: reference transcriptome assemblies and evidence of hybridization with wild relatives.
Mol Ecol Resour
PUBLISHED: 05-22-2013
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Although the Compositae harbours only two major food crops, sunflower and lettuce, many other species in this family are utilized by humans and have experienced various levels of domestication. Here, we have used next-generation sequencing technology to develop 15 reference transcriptome assemblies for Compositae crops or their wild relatives. These data allow us to gain insight into the evolutionary and genomic consequences of plant domestication. Specifically, we performed Illumina sequencing of Cichorium endivia, Cichorium intybus, Echinacea angustifolia, Iva annua, Helianthus tuberosus, Dahlia hybrida, Leontodon taraxacoides and Glebionis segetum, as well 454 sequencing of Guizotia scabra, Stevia rebaudiana, Parthenium argentatum and Smallanthus sonchifolius. Illumina reads were assembled using Trinity, and 454 reads were assembled using MIRA and CAP3. We evaluated the coverage of the transcriptomes using BLASTX analysis of a set of ultra-conserved orthologs (UCOs) and recovered most of these genes (88-98%). We found a correlation between contig length and read length for the 454 assemblies, and greater contig lengths for the 454 compared with the Illumina assemblies. This suggests that longer reads can aid in the assembly of more complete transcripts. Finally, we compared the divergence of orthologs at synonymous sites (Ks) between Compositae crops and their wild relatives and found greater divergence when the progenitors were self-incompatible. We also found greater divergence between pairs of taxa that had some evidence of postzygotic isolation. For several more distantly related congeners, such as chicory and endive, we identified a signature of introgression in the distribution of Ks values.
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A 28-day Gavage Toxicity Study in Male Fischer 344 Rats with 2-methylfuran.
Toxicol Pathol
PUBLISHED: 04-18-2013
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In most thermally treated products, a series of alkylated furan derivatives have been found, in particular 2-substituted alkylfurans such as 2-methylfuran. These methyl analogs are metabolically activated in a similar fashion as the parent furan, yielding highly reactive unsaturated dialdehydes. There is currently limited toxicological data available for 2-methyl furan exposure by any route that makes conducting a risk assessment difficult. In this pilot study, we report the general toxicology findings affecting tissue morphology, histopathology, clinical biochemistry, and hematology in a 28-day gavage study. The liver was the primary target organ that developed dose-dependent toxicity. Relative liver weights were increased by 42% at 25.0 mg/kg/body weight (bw)/day. Histological changes in the liver were observed at 0.4, 1.5, 3.0, 6.0, 12.0, and 25.0 mg/kg bw/day. These changes were not accompanied by clinical changes in the serum enzyme markers such as alanine transaminase, alkaline phosphatase, and aspartate transaminase. Clinical biochemistry markers for kidney were altered, but these were not accompanied by histological changes. The prostate was significantly decreased in size at the 25.0 mg/kg bw/day dose of 2-methyfuran. Some hematological parameters were also altered.
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How to deploy online guidance during a major incident.
J Bus Contin Emer Plan
PUBLISHED: 12-02-2011
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The experience of users of the web resource developed by the Health Protection Agency, following the arrival of H1N1 influenza, can be used to formulate criteria for web communication of up-to-date guidance in any incident management. Users participated in an online questionnaire survey. Responses were analysed quantitatively and qualitatively. Seventy-four per cent (95 per cent CI 67-81) of respondents rated the online content as excellent or good, with higher levels of satisfaction among healthcare professionals. Across all respondent categories there was demand for information more specific to their circumstances, alongside implementation of mechanisms such as text and e-mail to alert users to updates of web content. Based on the study findings, several recommendations were made on the use of similar web-based resources in future. With consideration of these recommendations, this strategy of web-based communication can be employed in other high profile incidents requiring a national response.
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Genomics of Compositae weeds: EST libraries, microarrays, and evidence of introgression.
Am. J. Bot.
PUBLISHED: 11-04-2011
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Weeds cause considerable environmental and economic damage. However, genomic characterization of weeds has lagged behind that of model plants and crop species. Here we describe the development of genomic tools and resources for 11 weeds from the Compositae family that will serve as a basis for subsequent population and comparative genomic analyses. Because hybridization has been suggested as a stimulus for the evolution of invasiveness, we also analyze these genomic data for evidence of hybridization.
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Recently formed polyploid plants diversify at lower rates.
Science
PUBLISHED: 08-18-2011
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Polyploidy, the doubling of genomic content, is a widespread feature, especially among plants, yet its macroevolutionary impacts are contentious. Traditionally, polyploidy has been considered an evolutionary dead end, whereas recent genomic studies suggest that polyploidy has been a key driver of macroevolutionary success. We examined the consequences of polyploidy on the time scale of genera across a diverse set of vascular plants, encompassing hundreds of inferred polyploidization events. Likelihood-based analyses indicate that polyploids generally exhibit lower speciation rates and higher extinction rates than diploids, providing the first quantitative corroboration of the dead-end hypothesis. The increased speciation rates of diploids can, in part, be ascribed to their capacity to speciate via polyploidy. Only particularly fit lineages of polyploids may persist to enjoy longer-term evolutionary success.
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Molecular evolution across the Asteraceae: micro- and macroevolutionary processes.
Mol. Biol. Evol.
PUBLISHED: 06-20-2011
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The Asteraceae (Compositae) is a large family of over 20,000 wild, weedy, and domesticated species that comprise approximately 10% of all angiosperms, including annual and perennial herbs, shrubs and trees, and species on every continent except Antarctica. As a result, the Asteraceae provide a unique opportunity to understand the evolutionary genomics of lineage radiation and diversification at numerous phylogenetic scales. Using publicly available expressed sequence tags from 22 species representing four of the major Asteraceae lineages, we assessed neutral and nonneutral evolutionary processes across this diverse plant family. We used bioinformatic tools to identify candidate genes under selection in each species. Evolution at silent and coding sites were assessed for different Gene Ontology functional categories to compare rates of evolution over both short and long evolutionary timescales. Our results indicate that patterns of molecular change across the family are surprisingly consistent on a macroevolutionary timescale and much more so more than would be predicted from the analysis of one (or many) examples of microevolution. These analyses also point to particular classes of genes that may be crucial in shaping the radiation of this diverse plant family. Similar analyses of nuclear and chloroplast genes in six other plant families confirm that many of these patterns are common features of the plant kingdom.
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Discovery of GSK143, a highly potent, selective and orally efficacious spleen tyrosine kinase inhibitor.
Bioorg. Med. Chem. Lett.
PUBLISHED: 06-17-2011
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The lead optimisation of the diaminopyrimidine carboxamide series of spleen tyrosine kinase inhibitors is described. The medicinal chemistry strategy was focused on optimising the human whole blood activity whilst achieving a sufficient margin over liability kinases and hERG activity. GSK143 is a potent and highly selective SYK inhibitor showing good efficacy in the rat Arthus model.
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The Selaginella genome identifies genetic changes associated with the evolution of vascular plants.
Jo Ann Banks, Tomoaki Nishiyama, Mitsuyasu Hasebe, John L Bowman, Michael Gribskov, Claude dePamphilis, Victor A Albert, Naoki Aono, Tsuyoshi Aoyama, Barbara A Ambrose, Neil W Ashton, Michael J Axtell, Elizabeth Barker, Michael S Barker, Jeffrey L Bennetzen, Nicholas D Bonawitz, Clint Chapple, Chaoyang Cheng, Luiz Gustavo Guedes Corrêa, Michael Dacre, Jeremy DeBarry, Ingo Dreyer, Marek Eliáš, Eric M Engstrom, Mark Estelle, Liang Feng, Cédric Finet, Sandra K Floyd, Wolf B Frommer, Tomomichi Fujita, Lydia Gramzow, Michael Gutensohn, Jesper Harholt, Mitsuru Hattori, Alexander Heyl, Tadayoshi Hirai, Yuji Hiwatashi, Masaki Ishikawa, Mineko Iwata, Kenneth G Karol, Barbara Koehler, Uener Kolukisaoglu, Minoru Kubo, Tetsuya Kurata, Sylvie Lalonde, Kejie Li, Ying Li, Amy Litt, Eric Lyons, Gerard Manning, Takeshi Maruyama, Todd P Michael, Koji Mikami, Saori Miyazaki, Shin-Ichi Morinaga, Takashi Murata, Bernd Mueller-Roeber, David R Nelson, Mari Obara, Yasuko Oguri, Richard G Olmstead, Naoko Onodera, Bent Larsen Petersen, Birgit Pils, Michael Prigge, Stefan A Rensing, Diego Mauricio Riaño-Pachón, Alison W Roberts, Yoshikatsu Sato, Henrik Vibe Scheller, Burkhard Schulz, Christian Schulz, Eugene V Shakirov, Nakako Shibagaki, Naoki Shinohara, Dorothy E Shippen, Iben Sørensen, Ryo Sotooka, Nagisa Sugimoto, Mamoru Sugita, Naomi Sumikawa, Milos Tanurdzic, Günter Theißen, Peter Ulvskov, Sachiko Wakazuki, Jing-Ke Weng, William W G T Willats, Daniel Wipf, Paul G Wolf, Lixing Yang, Andreas D Zimmer, Qihui Zhu, Therese Mitros, Uffe Hellsten, Dominique Loqué, Robert Otillar, Asaf Salamov, Jeremy Schmutz, Harris Shapiro, Erika Lindquist, Susan Lucas, Daniel Rokhsar, Igor V Grigoriev.
Science
PUBLISHED: 05-05-2011
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Vascular plants appeared ~410 million years ago, then diverged into several lineages of which only two survive: the euphyllophytes (ferns and seed plants) and the lycophytes. We report here the genome sequence of the lycophyte Selaginella moellendorffii (Selaginella), the first nonseed vascular plant genome reported. By comparing gene content in evolutionarily diverse taxa, we found that the transition from a gametophyte- to a sporophyte-dominated life cycle required far fewer new genes than the transition from a nonseed vascular to a flowering plant, whereas secondary metabolic genes expanded extensively and in parallel in the lycophyte and angiosperm lineages. Selaginella differs in posttranscriptional gene regulation, including small RNA regulation of repetitive elements, an absence of the trans-acting small interfering RNA pathway, and extensive RNA editing of organellar genes.
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Toxicologic and immunologic effects of perinatal exposure to the brominated diphenyl ether (BDE) mixture DE-71 in the Sprague-Dawley rat.
Environ. Toxicol.
PUBLISHED: 02-24-2011
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Brominated diphenyl ethers (BDEs) are persistent environmental contaminants found in human blood, tissues, and milk. To assess the impact of the commercial BDE mixture DE-71 on the developing immune system in relation to hepatic and thyroid changes, adult (F0) rats were exposed to DE-71 by gavage at doses of 0, 0.5, 5, or 25 mg/kg body weight (bw)/d for 21 weeks. F0 rats were bred and exposure continued through gestation, lactation and postweaning. F1 pups were weaned and exposed to DE-71 by gavage from postnatal day (PND) 22 to 42. On PND 42, half of the F1 rats were assessed for toxicologic changes. The remaining F1 rats were challenged with the T-dependent antigen keyhole limpet hemocyanin (KLH) and immune function was assessed on PND 56. Dose-dependent increases in total BDE concentrations were detected in the liver and adipose of all F0 and F1 rats. In F0 rats, increased liver weight, hepatocellular hypertrophy, and decreased serum thyroxine (T4) were characteristic of DE-71 exposure. In F1 rats perinatal DE-71 exposure caused a nondose-dependent increase in body weight and dose-dependent increases in liver weight and hepatocellular hypertrophy. Serum T3 and T4 levels were decreased. In spleen from DE-71 exposed rats the area occupied by B cells declined while the area occupied by T cells increased; however, cellular and humoral immune responses to KLH challenge were not altered. Thus hepatic and thyroid changes in rats exposed perinatally to DE-71 were associated with altered splenic lymphocyte populations, an effect which has been linked to hypothyroidism.
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Genetic modification of chondrocytes using viral vectors.
Methods Mol. Biol.
PUBLISHED: 02-09-2011
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The use of isolated cells to construct engineered tissues provides the opportunity to genetically modify those cells prior to the formation of tissue. This should make it possible to create transgenic human model tissues that can be used to determine gene function as well as to identify or validate potential therapeutic targets. As proof of principle, we have used RNA interference to selectively suppress the expression of aggrecanase genes in human chondrocytes, in an attempt to determine which of these key enzymes have roles in arthritic cartilage destruction. This combination of gene targeting and tissue engineering we are using should be equally applicable to the identification of gene function in other biological systems.
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De novo characterization of the gametophyte transcriptome in bracken fern, Pteridium aquilinum.
BMC Genomics
PUBLISHED: 02-08-2011
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Because of their phylogenetic position and unique characteristics of their biology and life cycle, ferns represent an important lineage for studying the evolution of land plants. Large and complex genomes in ferns combined with the absence of economically important species have been a barrier to the development of genomic resources. However, high throughput sequencing technologies are now being widely applied to non-model species. We leveraged the Roche 454 GS-FLX Titanium pyrosequencing platform in sequencing the gametophyte transcriptome of bracken fern (Pteridium aquilinum) to develop genomic resources for evolutionary studies.
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EvoPipes.net: Bioinformatic Tools for Ecological and Evolutionary Genomics.
Evol. Bioinform. Online
PUBLISHED: 10-20-2010
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Recent increases in the production of genomic data are yielding new opportunities and challenges for biologists. Among the chief problems posed by next-generation sequencing are assembly and analyses of these large data sets. Here we present an online server, http://EvoPipes.net, that provides access to a wide range of tools for bioinformatic analyses of genomic data oriented for ecological and evolutionary biologists. The EvoPipes.net server includes a basic tool kit for analyses of genomic data including a next-generation sequence cleaning pipeline (SnoWhite), scaffolded assembly software (SCARF), a reciprocal best-blast hit ortholog pipeline (RBH Orthologs), a pipeline for reference protein-based translation and identification of reading frame in transcriptome and genomic DNA (TransPipe), a pipeline to identify gene families and summarize the history of gene duplications (DupPipe), and a tool for developing SSRs or microsatellites from a transcriptome or genomic coding sequence collection (findSSR). EvoPipes.net also provides links to other software developed for evolutionary and ecological genomics, including chromEvol and NU-IN, as well as a forum for discussions of issues relating to genomic analyses and interpretation of results. Overall, these applications provide a basic bioinformatic tool kit that will enable ecologists and evolutionary biologists with relatively little experience and computational resources to take advantage of the opportunities provided by next-generation sequencing in their systems.
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Maximal flow at functional residual capacity in healthy children from birth to 7 years, and beyond.
Chest
PUBLISHED: 10-07-2010
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Reference values for maximal expiratory flows throughout childhood have been developed for each age group, but it remains a challenge to find a single outcome measure that can be tracked from birth to childhood. We believe that maximal flow at functional residual capacity (FRC) (VmaxFRC) may be a good candidate. The aim of this article was to explore the possible use of VmaxFRC as a continuous measure in healthy infants and children of preschool age.
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Palladium-catalyzed [1,3]-O-to-C rearrangement of pyrans toward functionalized cyclohexanones.
Org. Lett.
PUBLISHED: 10-05-2010
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Functionalized cyclohexanones are prepared from cyclic enol ethers via a Pd-catalyzed [1,3]-O-to-C rearrangement reaction. ?-Arylketones are generated with excellent diastereocontrol when basic phosphine ligands are used. In contrast, a Lewis acid is required to promote the rearrangement of the alkyl-substituted enol ether systems.
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Establishing genomic tools and resources for Guizotia abyssinica (L.f.) Cass.-the development of a library of expressed sequence tags, microsatellite loci, and the sequencing of its chloroplast genome.
Mol Ecol Resour
PUBLISHED: 09-26-2010
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We present an EST library, chloroplast genome sequence, and nuclear microsatellite markers that were developed for the semi-domesticated oilseed crop noug (Guizotia abyssinica) from Ethiopia. The EST library consists of 25?711 Sanger reads, assembled into 17?538 contigs and singletons, of which 4781 were functionally annotated using the Arabidopsis Information Resource (TAIR). The age distribution of duplicated genes in the EST library shows evidence of two paleopolyploidizations-a pattern that noug shares with several other species in the Heliantheae tribe (Compositae family). From the EST library, we selected 43 microsatellites and then designed and tested primers for their amplification. The number of microsatellite alleles varied between 2 and 10 (average 4.67), and the average observed and expected heterozygosities were 0.49 and 0.54, respectively. The chloroplast genome was sequenced de novo using Illuminas sequencing technology and completed with traditional Sanger sequencing. No large re-arrangements were found between the noug and sunflower chloroplast genomes, but 1.4% of sites have indels and 1.8% show sequence divergence between the two species. We identified 34 tRNAs, 4 rRNA sequences, and 80 coding sequences, including one region (trnH-psbA) with 15% sequence divergence between noug and sunflower that may be particularly useful for phylogeographic studies in noug and its wild relatives.
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Ancient genome duplications during the evolution of kiwifruit (Actinidia) and related Ericales.
Ann. Bot.
PUBLISHED: 06-24-2010
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To assess the number and phylogenetic distribution of large-scale genome duplications in the ancestry of Actinidia, publicly available expressed sequenced tags (ESTs) for members of the Actinidiaceae and related Ericales, including tea (Camellia sinensis), were analysed.
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Lentiviral shRNA knock-down of ADAMTS-5 and -9 restores matrix deposition in 3D chondrocyte culture.
J Tissue Eng Regen Med
PUBLISHED: 06-23-2010
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Aggrecan is one of the two major constituents of articular cartilage, and during diseases such as osteoarthritis (OA) it is subject to degradation by proteolytic enzymes. The primary proteases responsible for aggrecan cleavage are the aggrecanases, identified as members of the ADAMTS family of proteases, which are upregulated in response to inflammatory stimuli. It is uncertain which of the six aggrecanases (ADAMTS-1, -4, -5, -8, -9 and -15) are primarily responsible for the degradation of aggrecan in human cartilage. Here we show that four of the six aggrecanases are expressed in immortalized chondrocyte cell-lines and can be upregulated in response to inflammatory cytokines. Using RNA interference, we demonstrate robust knock-down of ADAMTS-5 and -9 expression in these cells and, by culturing them on three-dimensional (3D) scaffolds, show that reduction in expression of ADAMTS-5 enzyme results in an increase in matrix deposition. These data suggest that the quality of tissue-engineered cartilage matrix might be improved by targeted depletion of aggrecanase expression. Moreover, this work also provides further evidence that ADAMTS-5 may be a therapeutic target in the treatment of arthritic disease.
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NU-IN: Nucleotide evolution and input module for the EvolSimulator genome simulation platform.
BMC Res Notes
PUBLISHED: 04-24-2010
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There is increasing demand to test hypotheses that contrast the evolution of genes and gene families among genomes, using simulations that work across these levels of organization. The EvolSimulator program was developed recently to provide a highly flexible platform for forward simulations of amino acid evolution in multiple related lineages of haploid genomes, permitting copy number variation and lateral gene transfer. Synonymous nucleotide evolution is not currently supported, however, and would be highly advantageous for comparisons to full genome, transcriptome, and single nucleotide polymorphism (SNP) datasets. In addition, EvolSimulator creates new genomes for each simulation, and does not allow the input of user-specified sequences and gene family information, limiting the incorporation of further biological realism and/or user manipulations of the data.
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Randomized comparison of augmented and nonaugmented language interventions for toddlers with developmental delays and their parents.
J. Speech Lang. Hear. Res.
PUBLISHED: 04-03-2010
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This study compared the language performance of young children with developmental delays who were randomly assigned to 1 of 3 parent-coached language interventions. Differences in performance on augmented and spoken word size and use, vocabulary size, and communication interaction skills were examined.
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Probabilistic models of chromosome number evolution and the inference of polyploidy.
Syst. Biol.
PUBLISHED: 12-10-2009
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Polyploidy, the genome wide duplication of chromosome number, is a key feature in eukaryote evolution. Polyploidy exists in diverse groups including animals, fungi, and invertebrates but is especially prevalent in plants with most, if not all, plant species having descended from a polyploidization event. Polyploids often differ markedly from their diploid progenitors in morphological, physiological, and life history characteristics as well as rates of adaptation. The altered characteristics displayed by polyploids may contribute to their success in novel ecological habitats. Clearly, a better understanding of the processes underlying changes in the number of chromosomes within genomes is a key goal in our understanding of speciation and adaptation for a wide range of families and genera. Despite the fundamental role of chromosome number change in eukaryotic evolution, probabilistic models describing the evolution of chromosome number along a phylogeny have not yet been formulated. We present a series of likelihood models, each representing a different hypothesis regarding the evolution of chromosome number along a given phylogeny. These models allow us to reconstruct ancestral chromosome numbers and to estimate the expected number of polyploidization events and single chromosome changes (dysploidy) that occurred along a phylogeny. We test, using simulations, the accuracy of this approach and its dependence on the number of taxa and tree length. We then demonstrate the application of the method for the study of chromosome number evolution in 4 plant genera: Aristolochia, Carex, Passiflora, and Helianthus. Considering the depth of the available cytological and phylogenetic data, formal models of chromosome number evolution are expected to advance significantly our understanding of the importance of polyploidy and dysploidy across different taxonomic groups.
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Paleopolyploidy in the Brassicales: analyses of the Cleome transcriptome elucidate the history of genome duplications in Arabidopsis and other Brassicales.
Genome Biol Evol
PUBLISHED: 10-01-2009
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The analysis of the Arabidopsis genome revealed evidence of three ancient polyploidy events in the evolution of the Brassicaceae, but the exact phylogenetic placement of these events is still not resolved. The most recent event is called the At-alpha (alpha) or 3R, the intermediate event is referred to as the At-beta (beta) or 2R, and the oldest is the At-gamma (gamma) or 1R. It has recently been established that At-gamma is shared with other Rosids, including papaya (Carica), poplar (Populus), and grape (Vitis), whereas data to date suggest that At-alpha is Brassicaceae specific. To address more precisely when the At-alpha and At-beta events occurred and which plant lineages share these paleopolyploidizations, we sequenced and analyzed over 4,700 normalized expressed sequence tag sequences from the Cleomaceae, the sister family to the Brassicaceae. Analysis of these Cleome data with homologous sequences from other Rosid genomes (Arabidopsis, Carica, Gossypium, Populus, and Vitis) yielded three major findings: 1) confirmation of a Cleome-specific paleopolyploidization (Cs-alpha) that is independent of the Brassicaceae At-alpha paleopolyploidization; 2) Cleome and Arabidopsis share the At-beta duplication, which is lacking from papaya within the Brassicales; and 3) rates of molecular evolution are faster for the herbaceous annual taxa Arabidopsis and Cleome than the other predominantly woody perennial Rosid lineages. These findings contribute to our understanding of the dynamics of genome duplication and evolution within one of the most comprehensively surveyed clades of plants, the Rosids, and clarify the complex history of the At-alpha, At-beta, and At-gamma duplications of Arabidopsis.
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The frequency of polyploid speciation in vascular plants.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 08-10-2009
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Since its discovery in 1907, polyploidy has been recognized as an important phenomenon in vascular plants, and several lines of evidence indicate that most, if not all, plant species ultimately have a polyploid ancestry. However, previous estimates of the frequency of polyploid speciation suggest that the formation and establishment of neopolyploid species is rare. By combining information from the botanical communitys vast cytogenetic and phylogenetic databases, we establish that 15% of angiosperm and 31% of fern speciation events are accompanied by ploidy increase. These frequency estimates are higher by a factor of four than earlier estimates and lead to a standing incidence of polyploid species within genera of 35% (n = 1,506). Despite this high incidence, we find no direct evidence that polyploid lines, once established, enjoy greater net species diversification. Thus, the widespread occurrence of polyploid taxa appears to result from the substantial contribution of polyploidy to cladogenesis, but not from subsequent increases in diversification rates of polyploid lines.
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Comparative genomic and population genetic analyses indicate highly porous genomes and high levels of gene flow between divergent helianthus species.
Evolution
PUBLISHED: 05-09-2009
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While speciation can be found in the presence of gene flow, it is not clear what impact this gene flow has on genome- and range-wide patterns of differentiation. Here we examine gene flow across the entire range of the common sunflower, H. annuus, its historically allopatric sister species H. argophyllus and a more distantly related, sympatric relative H. petiolaris. Analysis of genotypes at 26 microsatellite loci in 1015 individuals from across the range of the three species showed substantial introgression between geographically proximal populations of H. annuus and H. petiolaris, limited introgression between H. annuus and H. argophyllus, and essentially no gene flow between the allopatric pair, H. argophyllus and H. petiolaris. Analysis of sequence divergence levels among the three species in 1420 orthologs identified from EST databases identified a subset of loci showing extremely low divergence between H. annuus and H. petiolaris and extremely high divergence between the sister species H. annuus and H. argophyllus, consistent with introgression between H. annuus and H. petiolaris at these loci. Thus, at many loci, the allopatric sister species are more genetically divergent than the more distantly related sympatric species, which have exchanged genes across much of the genome while remaining morphologically and ecologically distinct.
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Quinolines as a novel structural class of potent and selective PDE4 inhibitors. Optimisation for inhaled administration.
Bioorg. Med. Chem. Lett.
PUBLISHED: 02-20-2009
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Crystallography driven optimisation of a lead derived from similarity searching of the GSK compound collection resulted in the discovery of quinoline-3-carboxamides as highly potent and selective inhibitors of phosphodiesterase 4B. This series has been optimized to GSK256066, a potent PDE4B inhibitor which also inhibits LPS induced production of TNF-alpha from isolated human peripheral blood mononuclear cells with a pIC(50) of 11.1. GSK256066 also has a suitable profile for inhaled dosing.
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4-Phenyl-7-azaindoles as potent and selective IKK2 inhibitors.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-26-2009
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The synthesis and SAR of a novel series of IKK2 inhibitors are described. Modification around the hinge binding region of the 7-azaindole led to a series of potent and selective inhibitors with good cellular activity.
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SCARF: maximizing next-generation EST assemblies for evolutionary and population genomic analyses.
Bioinformatics
PUBLISHED: 01-06-2009
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Scaffolded and Corrected Assembly of Roche 454 (SCARF) is a next-generation sequence assembly tool for evolutionary genomics that is designed especially for assembling 454 EST sequences against high-quality reference sequences from related species. The program was created to knit together 454 contigs that do not assemble during traditional de novo assembly, using a reference sequence library to orient the 454 sequences.
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Development of an ultra-dense genetic map of the sunflower genome based on single-feature polymorphisms.
PLoS ONE
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The development of ultra-dense genetic maps has the potential to facilitate detailed comparative genomic analyses and whole genome sequence assemblies. Here we describe the use of a custom Affymetrix GeneChip containing nearly 2.4 million features (25 bp sequences) targeting 86,023 unigenes from sunflower (Helianthus annuus L.) and related species to test for single-feature polymorphisms (SFPs) in a recombinant inbred line (RIL) mapping population derived from a cross between confectionery and oilseed sunflower lines (RHA280×RHA801). We then employed an existing genetic map derived from this same population to rigorously filter out low quality data and place 67,486 features corresponding to 22,481 unigenes on the sunflower genetic map. The resulting map contains a substantial fraction of all sunflower genes and will thus facilitate a number of downstream applications, including genome assembly and the identification of candidate genes underlying QTL or traits of interest.
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Quantitative visualization of biological data in Google Earth using R2G2, an R CRAN package.
Mol Ecol Resour
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We briefly introduce R2G2, an R CRAN package to visualize spatially explicit biological data within the Google Earth interface. Our package combines a collection of basic graph-editing features, including automated placement of dots, segments, polygons, images (including graphs produced with R), along with several complex three-dimensional (3D) representations such as phylogenies, histograms and pie charts. We briefly present some example data sets and show the immediate benefits in communication gained from using the Google Earth interface to visually explore biological results. The package is distributed with detailed help pages providing examples and annotated source scripts with the hope that users will have an easy time using and further developing this package. R2G2 is distributed on http://cran.r-project.org/web/packages.
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Reading instruction for children who use AAC: considerations in the pursuit of generalizable results.
Augment Altern Commun
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Our purpose was to review evidence-based literacy instruction for children with severe speech impairment (SSI) who communicate with AAC. This review focuses on three issues important to researchers in this area: participant heterogeneity, assessment and instruction tasks, and research design. We found eight articles that reported attempts to teach phonological awareness and individual-word reading to a total of 26 children with SSI who used AAC. We evaluated these studies based on reporting of participant characteristics, assessment and instruction modifications, and the strength of research designs. We conclude by highlighting the need for standard assessments that can be used across studies, discussing strategies for facilitating meta-analyses, and suggesting the creation of an online database for researchers to share results on literacy instruction for this population.
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4-Phenyl-7-azaindoles as potent, selective and bioavailable IKK2 inhibitors demonstrating good in vivo efficacy.
Bioorg. Med. Chem. Lett.
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The lead optimization of a series of potent azaindole IKK2 inhibitors is described. Optimization of the human whole blood activity and selectivity over IKK1 in parallel led to the discovery of 16, a potent and selective IKK2 inhibitor showing good efficacy in a rat model of neutrophil activation.
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Rarely successful polyploids and their legacy in plant genomes.
Curr. Opin. Plant Biol.
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Polyploidy, or whole genome duplication, is recognized as an important feature of eukaryotic genome evolution. Among eukaryotes, polyploidy has probably had the largest evolutionary impact on vascular plants where many contemporary species are of recent polyploid origin. Genomic analyses have uncovered evidence of at least one round of polyploidy in the ancestry of most plants, fueling speculation that genome duplications lead to increases in net diversity. In spite of the frequency of ancient polyploidy, recent analyses have found that recently formed polyploid species have higher extinction rates than their diploid relatives. These results suggest that despite leaving a substantial legacy in plant genomes, only rare polyploids survive over the long term and most are evolutionary dead-ends.
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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.