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Find video protocols related to scientific articles indexed in Pubmed.
Phylogenomics resolves the timing and pattern of insect evolution.
Bernhard Misof, Shanlin Liu, Karen Meusemann, Ralph S Peters, Alexander Donath, Christoph Mayer, Paul B Frandsen, Jessica Ware, Tomáš Flouri, Rolf G Beutel, Oliver Niehuis, Malte Petersen, Fernando Izquierdo-Carrasco, Torsten Wappler, Jes Rust, Andre J Aberer, Ulrike Aspöck, Horst Aspöck, Daniela Bartel, Alexander Blanke, Simon Berger, Alexander Böhm, Thomas R Buckley, Brett Calcott, Junqing Chen, Frank Friedrich, Makiko Fukui, Mari Fujita, Carola Greve, Peter Grobe, Shengchang Gu, Ying Huang, Lars S Jermiin, Akito Y Kawahara, Lars Krogmann, Martin Kubiak, Robert Lanfear, Harald Letsch, Yiyuan Li, Zhenyu Li, Jiguang Li, Haorong Lu, Ryuichiro Machida, Yuta Mashimo, Pashalia Kapli, Duane D McKenna, Guanliang Meng, Yasutaka Nakagaki, José Luis Navarrete-Heredia, Michael Ott, Yanxiang Ou, Günther Pass, Lars Podsiadlowski, Hans Pohl, Björn M von Reumont, Kai Schütte, Kaoru Sekiya, Shota Shimizu, Adam Slipinski, Alexandros Stamatakis, Wenhui Song, Xu Su, Nikolaus U Szucsich, Meihua Tan, Xuemei Tan, Min Tang, Jingbo Tang, Gerald Timelthaler, Shigekazu Tomizuka, Michelle Trautwein, Xiaoli Tong, Toshiki Uchifune, Manfred G Walzl, Brian M Wiegmann, Jeanne Wilbrandt, Benjamin Wipfler, Thomas K F Wong, Qiong Wu, Gengxiong Wu, Yinlong Xie, Shenzhou Yang, Qing Yang, David K Yeates, Kazunori Yoshizawa, Qing Zhang, Rui Zhang, Wenwei Zhang, Yunhui Zhang, Jing Zhao, Chengran Zhou, Lili Zhou, Tanja Ziesmann, Shijie Zou, Yingrui Li, Xun Xu, Yong Zhang, Huanming Yang, Jian Wang, Jun Wang, Karl M Kjer, Xin Zhou.
Science
PUBLISHED: 11-06-2014
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Insects are the most speciose group of animals, but the phylogenetic relationships of many major lineages remain unresolved. We inferred the phylogeny of insects from 1478 protein-coding genes. Phylogenomic analyses of nucleotide and amino acid sequences, with site-specific nucleotide or domain-specific amino acid substitution models, produced statistically robust and congruent results resolving previously controversial phylogenetic relations hips. We dated the origin of insects to the Early Ordovician [~479 million years ago (Ma)], of insect flight to the Early Devonian (~406 Ma), of major extant lineages to the Mississippian (~345 Ma), and the major diversification of holometabolous insects to the Early Cretaceous. Our phylogenomic study provides a comprehensive reliable scaffold for future comparative analyses of evolutionary innovations among insects.
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ACPA positivity correlates with cartilage damage and proteoglycan levels in patients with rheumatoid arthritis in the hand joints.
PUBLISHED: 09-03-2014
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Objective: To investigate the factors associated with cartilage proteoglycan content in patients with rheumatoid arthritis (RA) Methods: 32 RA patients received high-field 3 Tesla Gadolinium-Enhanced MRI of Cartilage (dGEMRIC) for determining cartilage proteoglycan content. Measurements were performed in three individual cartilage regions (medial, central, lateral) of the metacarpophalangeal joints 2 and 3. dGEMRIC values were then related to disease duration, disease activity, anti-citrullinated protein antibody (ACPA) status, rheumatoid factor status and C-reactive protein level. Results: dGEMRIC values were not significantly different between the MCP2 and MCP3 joint. Inter-class correlations were high (>0.92) for all three (medial, central and lateral) cartilage compartments. dGEMRIC values were significantly lower in RA patients with longer disease duration (?3years) and those with ACPA positivity than those with a short disease duration (<3 years)(p=0.034) or negative ACPA (p=0.0002), respectively. In contrast, no association between cartilage proteoglycan content and disease activity, C-reactive protein level and rheumatoid factor status was found. Conclusion: Decreased cartilage proteoglycan content in RA patients is associated with disease duration and ACPA positivity but not with the actual disease activity, CRP level or rheumatoid factor status. These data suggest that the cumulative burden of inflammation as well as ACPA are the determinants for cartilage damage in RA. © 2014 American College of Rheumatology.
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Tranzschelia in the Americas revisited: two new species and notes on the Tranzschelia thalictri complex.
Mycologia
PUBLISHED: 05-28-2014
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Two new species of Tranzschelia (Pucciniales) are described from the Americas. Tranzschelia pseudofusca is a microcyclic species on Anemone spp. (Ranunculaceae) with North American distribution. T. mexicana on Prunus salicifolia (Rosaceae) is found in Colombia, Ecuador and Mexico. It is assumed that T. mexicana is a macrocyclic host-alternating species. T. thalictri, a holarctic microcyclic species, has variable morphology and probably is an aggregate of related species. Specimens are documented with scanning electron microscopy (ESEM) and light microscopy including a simple new technique to illuminate urediniospore germ pores. Results are discussed with respect to similar species, distribution and life-cycle characters. A key for American species on telial hosts is provided.
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The evolutionary history of holometabolous insects inferred from transcriptome-based phylogeny and comprehensive morphological data.
BMC Evol. Biol.
PUBLISHED: 03-04-2014
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Despite considerable progress in systematics, a comprehensive scenario of the evolution of phenotypic characters in the mega-diverse Holometabola based on a solid phylogenetic hypothesis was still missing. We addressed this issue by de novo sequencing transcriptome libraries of representatives of all orders of holometabolan insects (13 species in total) and by using a previously published extensive morphological dataset. We tested competing phylogenetic hypotheses by analyzing various specifically designed sets of amino acid sequence data, using maximum likelihood (ML) based tree inference and Four-cluster Likelihood Mapping (FcLM). By maximum parsimony-based mapping of the morphological data on the phylogenetic relationships we traced evolutionary transformations at the phenotypic level and reconstructed the groundplan of Holometabola and of selected subgroups.
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Drinking water biofilms on copper and stainless steel exhibit specific molecular responses towards different disinfection regimes at waterworks.
Biofouling
PUBLISHED: 07-22-2013
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Biofilms growing on copper and stainless steel substrata in natural drinking water were investigated. A modular pilot-scale distribution facility was installed at four waterworks using different raw waters and disinfection regimes. Three-month-old biofilms were analysed using molecular biology and microscopy methods. High total cell numbers, low counts of actively respiring cells and low numbers of cultivable bacteria indicated the high abundance of viable but not cultivable bacteria in the biofilms. The expression of the recA SOS responsive gene was detected and underlined the presence of transcriptionally active bacteria within the biofilms. This effect was most evident after UV disinfection, UV oxidation and UV disinfection with increased turbidity at waterworks compared to chemically treated and non-disinfected systems. Furthermore, live/dead staining techniques and environmental scanning electron microscopy imaging revealed the presence of living and intact bacteria in biofilms on copper substrata. Cluster analyses of DGGE profiles demonstrated differences in the composition of biofilms on copper and steel materials.
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The Pax gene eyegone facilitates repression of eye development in Tribolium.
Evodevo
PUBLISHED: 01-13-2011
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The Pax transcription factor gene eyegone (eyg) participates in many developmental processes in Drosophila, including the Notch signaling activated postembryonic growth of the eye primordium, global development of the adult head and the development of the antenna. In contrast to other Pax genes, the functional conservation of eyg in species other than Drosophila has not yet been explored.
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Contact pressure effects on vibrational bands of kaolinite during infrared spectroscopic measurements in a diamond attenuated total reflection cell.
Appl Spectrosc
PUBLISHED: 05-21-2010
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Over the last decades infrared spectroscopy has become a frequently used method to investigate the structure and bonding properties of clay minerals. Along with classic transmission techniques, attenuated total reflection (ATR) spectroscopy has been applied as a very fast and easy method. In this study we compared transmission spectra of kaolinite with ATR spectra obtained by a single-reflection diamond ATR accessory (Golden Gate Mark II). The ATR spectra showed anomalous band positions that were obviously affected by the applied contact pressure of the sapphire anvil. Most of these vibrations can be assigned to basal Si-O bonds and all of them shifted their positions to lower wavenumbers. It is suggested that these peak shifts are due to changes in the Si-O-Si bond angle Theta. They are caused by distortions and rotations of SiO(4) units within the tetrahedral sheet, due to shear forces perpendicular to the uniaxial pressure applied by the anvil. Furthermore, the intensity of a normally very weak transversal optical mode (TO mode) of the inner surface hydroxyls (3684 cm(-1)) remarkably increased with increasing contact pressure, while the longitudinal optical mode (LO mode) at 3694 cm(-1) strongly decreased its intensity. This possibly is determined by a strong alignment of the platy kaolinite particles along their ab-planes due to the applied pressure.
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Charles Darwin, beetles and phylogenetics.
Naturwissenschaften
PUBLISHED: 03-13-2009
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Here, we review Charles Darwins relation to beetles and developments in coleopteran systematics in the last two centuries. Darwin was an enthusiastic beetle collector. He used beetles to illustrate different evolutionary phenomena in his major works, and astonishingly, an entire sub-chapter is dedicated to beetles in "The Descent of Man". During his voyage on the Beagle, Darwin was impressed by the high diversity of beetles in the tropics, and he remarked that, to his surprise, the majority of species were small and inconspicuous. However, despite his obvious interest in the group, he did not get involved in beetle taxonomy, and his theoretical work had little immediate impact on beetle classification. The development of taxonomy and classification in the late nineteenth and earlier twentieth century was mainly characterised by the exploration of new character systems (e.g. larval features and wing venation). In the mid-twentieth century, Hennigs new methodology to group lineages by derived characters revolutionised systematics of Coleoptera and other organisms. As envisioned by Darwin and Ernst Haeckel, the new Hennigian approach enabled systematists to establish classifications truly reflecting evolution. Roy A. Crowson and Howard E. Hinton, who both made tremendous contributions to coleopterology, had an ambivalent attitude towards the Hennigian ideas. The Mickoleit school combined detailed anatomical work with a classical Hennigian character evaluation, with stepwise tree building, comparatively few characters and a priori polarity assessment without explicit use of the outgroup comparison method. The rise of cladistic methods in the 1970s had a strong impact on beetle systematics. Cladistic computer programs facilitated parsimony analyses of large data matrices, mostly morphological characters not requiring detailed anatomical investigations. Molecular studies on beetle phylogeny started in the 1990s with modest taxon sampling and limited DNA data. This has changed dramatically. With very large data sets and high throughput sampling, phylogenetic questions can be addressed without prior knowledge of morphological characters. Nevertheless, molecular studies have not lead to the great breakthrough in beetle systematics--yet. Especially the phylogeny of the extremely species rich suborder Polyphaga remains incompletely resolved. Coordinated efforts of molecular workers and of morphologists using innovative techniques may lead to more profound insights in the near future. The final aim is to develop a well-founded phylogeny, which truly reflects the evolution of this immensely species rich group of organisms.
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Combined use of molecular biology taxonomy, Raman spectrometry, and ESEM imaging to study natural biofilms grown on filter materials at waterworks.
Chemosphere
PUBLISHED: 03-13-2009
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DNA-based population analysis was applied in combination with Raman spectrometry and Environmental Scanning Electron Microscopy for the characterisation of natural biofilms from sand and activated carbon filters operated for a long term at a municipal waterworks. Whereas the molecular biology polymerase chain reaction combined with denaturing gradient gel electrophoresis approach provides a deeper insight into the bacterial biofilm diversities, Raman spectrometry analyses the chemical composition of the extracellular polymer substances (EPS), microorganisms embedded in EPS as well as other substances inside biofilm (inorganic compounds and humic substances). Microscopy images the spatial distribution of biofilms on the two different filter materials. In addition, bacterial bulk water populations were compared with biofilm consortia using the molecular fingerprint technique mentioned. Population analysis demonstrated the presence of more diverse bacterial species embedded in a matrix of EPS (polysaccharides, peptides, and nucleic acids) on the sand filter materials. In contrast to this, activated carbon granules were colonised by reduced numbers of bacterial species in biofilms. Besides alpha-, beta-, and gamma-Proteobacteria, a noticeable specific colonisation with Actinobacteria was found on activated carbon particles. Here, the reduced biofilm formation came along with a decreased EPS synthesis. The taxonomy profiles of the different biofilms revealed up to 60% similarity on the same filter materials and 32% similarity of different materials. Similarity of adherent communities from filter materials and bulk water populations from the filter effluent varied between 36% and 58% in sand filters and 6-40% in granular activated carbon filters. The biofilm investigation protocols are most crucial to subsequent acquisition of knowledge on biofilm dynamics and bacterial contributions to transformation or adsorption processes in waterworks facilities.
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Probing the Drosophila retinal determination gene network in Tribolium (II): The Pax6 genes eyeless and twin of eyeless.
Dev. Biol.
PUBLISHED: 02-26-2009
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The Pax6 genes eyeless (ey) and twin of eyeless (toy) are upstream regulators in the retinal determination gene network (RDGN), which instructs the formation of the adult eye primordium in Drosophila. Most animals possess a singleton Pax6 ortholog, but the dependence of eye development on Pax6 is widely conserved. A rare exception is given by the larval eyes of Drosophila, which develop independently of ey and toy. To obtain insight into the origin of differential larval and adult eye regulation, we studied the function of toy and ey in the red flour beetle Tribolium castaneum. We find that single and combinatorial knockdown of toy and ey affect larval eye development strongly but adult eye development only mildly in this primitive hemimetabolous species. Compound eye-loss, however, was provoked when ey and toy were RNAi-silenced in combination with the early retinal gene dachshund (dac). We propose that these data reflect a role of Pax6 during regional specification in the developing head and that the subsequent maintenance and growth of the adult eye primordium is regulated partly by redundant and partly by specific functions of toy, ey and dac in Tribolium. The results from embryonic knockdown and comparative protein sequence analysis lead us further to conclude that Tribolium represents an ancestral state of redundant control by ey and toy.
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The head of Merope tuber (Meropeidae) and the phylogeny of Mecoptera (Hexapoda).
Arthropod Struct Dev
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External and internal features of the head of adults of Merope tuber were examined and described in detail. The results were compared to conditions found in other members of Mecoptera and other antliophoran lineages. A list of characters of different body parts and life stages is presented. The parsimony analysis and a recent evaluation of thoracic features suggest a basal placement of Merope within monophyletic Pistillifera. The monophyly of Mecoptera was not supported by our data set. Nannochoristidae (Nannomecoptera) was placed as sistertaxon of a clade comprising Diptera and Siphonaptera. Cephalic features supporting this group are modifications of the mouthparts linked to feeding on liquid substrates. Considering recent results of extensive morphological and molecular investigations we consider this placement of Nannochoristidae and the implied mecopteran paraphyly as a possible artefact. Potential cephalic autapomorphies of Mecoptera are the presence of a tooth-like projection of the gena and a prepharyngeal tube, the absence of M. frontolabralis, and the origin of M. tentoriooralis on the middle region of the anterior tentorial arm. Despite of the conspicuous morphological differences between Caurinus and the other boreid genera the family forms a well supported clade. A sistergroup relationship between Boreidae and Pistillifera is confirmed. A unique synapomorphy is the presence of specialized dilator muscles of the salivary duct. The reconstruction of the relationships of the pistilliferan taxa is strongly impeded by a serious lack of morphological data. However, a group comprising Eomeropidae, Choristidae, Apteropanorpidae, Panorpidae and Panorpodidae is supported in our analyses. Further well documented anatomical data are needed for a reliable reconstruction of mecopteran relationships. The collecting and morphological study of larvae should also have high priority. Inherent problems are extreme secondary modifications of cephalic features of Caurinus and Nannochorista.
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The thoracic skeleto-muscular system of Mengenilla (Strepsiptera: Mengenillidae) and its phylogenetic implications.
Arthropod Struct Dev
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The thorax of Mengenilla was examined using traditional morphological techniques and its features were documented in detail using scanning electron microscopy and computer-based 3D reconstructions. The results were compared to conditions found in other holometabolan insects. The implications for the systematic placement of Strepsiptera are discussed. The observations are interpreted in the light of the recently confirmed sistergroup relationship between Strepsiptera and Coleoptera (Coleopterida). The synapomorphies of the thorax of Strepsiptera and Coleoptera are partly related with posteromotorism (e.g., increased size of the metathorax), partly with a decreased intrathoracic flexibility (e.g., a fused pronotum and propleurum), and partly independent from these two character complexes (e.g., not connected profurca and propleuron). Strepsiptera are more derived than Coleoptera in some thoracic features (e.g., extremely enlarged metathorax) but have also preserved some plesiomorphic conditions (e.g., tegulae in both pterothoracic segments). All potential apomorphies of Mecopterida are missing in Strepsiptera. The last common ancestor of Coleopterida had already acquired posteromotorism but the wings were still largely unmodified. Several reductions in the mesothorax likely occurred independently.
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The larvae of Nymphomyiidae (Diptera, Insecta) - ancestral and highly derived?
Arthropod Struct Dev
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Larval head structures of Nymphomyia dolichopeza were examined and described in detail. The conditions are compared to those of other dipteran representatives. Our results support the monophyly of Nymphomyiidae. Potential apomorphies are dimorphic crochets on the abdominal prolegs and the complete loss of the tentorium. Possible synapomorphies of Nymphomyiidae and Deuterophlebiidae could be the rows of spatulate macrosetae covering the ventral surface of the labrum-epipharynx, the presence of distinct teeth along the anterior premento-hypopharyngeal margin, the absence of labral microtrichia and some other affinities concerning the life history of the two groups. A clade Blephariceromorpha is also supported by some larval features. Potential synapomorphies of Nymphomyiidae, Deuterophlebiidae and Blephariceridae are the vestigial M. labroepipharyngalis, the absence of a movable premandible, crochet-tipped prolegs, the complete loss of spiracles and non-retractable anal papillae. A clade Nymphomyiidae and Chironomidae is only weakly supported by characters of the larval head. The anteriorly serrate and posteriorly fused hypostoma is a potential apomorphic character. Our results support neither phylogenetic affinities between Nymphomyiidae and Axymyiidae nor a sistergroup relationship between Nymphomyiidae and the remaining Diptera. However, a comprehensive cladistic analysis is not presented in our study.
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On dorsal prothoracic appendages in treehoppers (Hemiptera: Membracidae) and the nature of morphological evidence.
PLoS ONE
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A spectacular hypothesis was published recently, which suggested that the "helmet" (a dorsal thoracic sclerite that obscures most of the body) of treehoppers (Insecta: Hemiptera: Membracidae) is connected to the 1st thoracic segment (T1; prothorax) via a jointed articulation and therefore was a true appendage. Furthermore, the "helmet" was interpreted to share multiple characteristics with wings, which in extant pterygote insects are present only on the 2nd (T2) and 3rd (T3) thoracic segments. In this context, the "helmet" could be considered an evolutionary novelty. Although multiple lines of morphological evidence putatively supported the "helmet"-wing homology, the relationship of the "helmet" to other thoracic sclerites and muscles remained unclear. Our observations of exemplar thoraces of 10 hemipteran families reveal multiple misinterpretations relevant to the "helmet"-wing homology hypothesis as originally conceived: 1) the "helmet" actually represents T1 (excluding the fore legs); 2) the "T1 tergum" is actually the anterior dorsal area of T2; 3) the putative articulation between the "helmet" and T1 is actually the articulation between T1 and T2. We conclude that there is no dorsal, articulated appendage on the membracid T1. Although the posterior, flattened, cuticular evagination (PFE) of the membracid T1 does share structural and genetic attributes with wings, the PFE is actually widely distributed across Hemiptera. Hence, the presence of this structure in Membracidae is not an evolutionary novelty for this clade. We discuss this new interpretation of the membracid T1 and the challenges of interpreting and representing morphological data more broadly. We acknowledge that the lack of data standards for morphology is a contributing factor to misinterpreted results and offer an example for how one can reduce ambiguity in morphology by referencing anatomical concepts in published ontologies.
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What is Visualize?

JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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

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

In developing our video relationships, we compare around 5 million PubMed articles to our library of over 4,500 methods videos. In some cases the language used in the PubMed abstracts makes matching that content to a JoVE video difficult. In other cases, there happens not to be any content in our video library that is relevant to the topic of a given abstract. In these cases, our algorithms are trying their best to display videos with relevant content, which can sometimes result in matched videos with only a slight relation.