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Find video protocols related to scientific articles indexed in Pubmed.
Ena/VASP proteins cooperate with the WAVE complex to regulate the actin cytoskeleton.
Dev. Cell
PUBLISHED: 07-21-2014
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Ena/VASP proteins and the WAVE regulatory complex (WRC) regulate cell motility by virtue of their ability to independently promote actin polymerization. We demonstrate that Ena/VASP and the WRC control actin polymerization in a cooperative manner through the interaction of the Ena/VASP EVH1 domain with an extended proline rich motif in Abi. This interaction increases cell migration and enables VASP to cooperatively enhance WRC stimulation of Arp2/3 complex-mediated actin assembly in vitro in the presence of Rac. Loss of this interaction in Drosophila macrophages results in defects in lamellipodia formation, cell spreading, and redistribution of Ena to the tips of filopodia-like extensions. Rescue experiments of abi mutants also reveals a physiological requirement for the Abi:Ena interaction in photoreceptor axon targeting and oogenesis. Our data demonstrate that the activities of Ena/VASP and the WRC are intimately linked to ensure optimal control of actin polymerization during cell migration and development.
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Dual practice by doctors working in South and East Asia: a review of its origins, scope and impact, and the options for regulation.
Health Policy Plan
PUBLISHED: 10-21-2013
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Health professionals often undertake private work whilst also employed by government. Such dual practice (DP) is found in both high-income and lower- and middle-income countries (LMIC) around the world, with varying degrees of tolerance. This review focuses on DP in South and East Asia in the context of the rapidly expanding mixed health systems in this region. Although good data are lacking, health service uptake in South and East Asia is increasing, particularly in the private sector. Appropriately regulated, DP can improve health service access, the range of services offered and doctors satisfaction. By contrast, weakly regulated DP can negatively affect public health service access, quality, efficiency and equity, as doctors often pursue the balance of public and private work that maximizes their income and other benefits. The environment for regulation of DP is changing rapidly, with improved communications opportunities, increasing literacy and rising civil society, particularly in this region. Currently, the options for regulating DP include (1) those which restrict the opportunities for dual practitioners to prioritize income and other benefits over their responsibility to the public; these require a level of regulatory capacity often missing in LMIC governments; and (2) those which not only tolerate public-sector doctors private work but also encourage adequate health services for the general public. Growth of the private sector and weak regulation in South and East Asia increases the risk that dual practitioners will ignore the poor. Responsive and decentred regulation of doctors involving professional associations, civil society and other stakeholders is increasingly recommended. Moreover, as governments in LMIC strive for universal health coverage, market and financing opportunities for regulation of DP may arise, particularly involving insurers. This may also help to improve the current imbalance in the urban-rural distribution of doctors.
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Bacterial versus fungal laccase: potential for micropollutant degradation.
AMB Express
PUBLISHED: 10-11-2013
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Relatively high concentrations of micropollutants in municipal wastewater treatment plant (WWTP) effluents underscore the necessity to develop additional treatment steps prior to discharge of treated wastewater. Microorganisms that produce unspecific oxidative enzymes such as laccases are a potential means to improve biodegradation of these compounds. Four strains of the bacterial genus Streptomyces (S. cyaneus, S. ipomoea, S. griseus and S. psammoticus) and the white-rot fungus Trametes versicolor were studied for their ability to produce active extracellular laccase in biologically treated wastewater with different carbon sources. Among the Streptomyces strains evaluated, only S. cyaneus produced extracellular laccase with sufficient activity to envisage its potential use in WWTPs. Laccase activity produced by T. versicolor was more than 20 times greater, the highest activity being observed with ash branches as the sole carbon source. The laccase preparation of S. cyaneus (abbreviated LSc) and commercial laccase from T. versicolor (LTv) were further compared in terms of their activity at different pH and temperatures, their stability, their substrate range, and their micropollutant oxidation efficiency. LSc and LTv showed highest activities under acidic conditions (around pH 3 to 5), but LTv was active over wider pH and temperature ranges than LSc, especially at near-neutral pH and between 10 and 25[degree sign]C (typical conditions found in WWTPs). LTv was also less affected by pH inactivation. Both laccase preparations oxidized the three micropollutants tested, bisphenol A, diclofenac and mefenamic acid, with faster degradation kinetics observed for LTv. Overall, T. versicolor appeared to be the better candidate to remove micropollutants from wastewater in a dedicated post-treatment step.
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Micropollutant dynamics in Vidy Bay-a coupled hydrodynamic-photolysis model to assess the spatial extent of ecotoxicological risk.
Environ. Sci. Technol.
PUBLISHED: 08-07-2013
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The direct discharge of effluent wastewater into Vidy Bay (Lake Geneva) results in the formation of an effluent plume with locally high concentrations of wastewater-derived micropollutants. The micropollutant hotspots above the wastewater outfall present a potential ecotoxicological risk, yet the spatial extent of the plume and the associated ecotoxicological risk zone remain unclear. This work combines the two main processes affecting the spreading of the plume, namely dilution of micropollutants due to mixing and degradation by photolysis, into a coupled hydrodynamic-photolysis model, with which we estimated the spatial extent of the risk zone in Vidy Bay. The concentration of micropollutants around the wastewater outfall was simulated for typical wind scenarios and seasons relevant to Vidy Bay, and the resulting ecotoxicological risk was evaluated. Specifically, we determined the direct and indirect photolysis rate constants for 24 wastewater-derived micropollutants and implemented these in a hydrodynamic particle tracking model, which tracked the movement of water parcels from the wastewater outfall. Simulations showed that owing to thermal stratification, the zone of ecotoxicological risk is largest in summer and extends horizontally over 300 m from the outfall. Photolysis processes contribute to reducing the plume extent mainly under unstratified conditions when the plume surfaces. Moreover, it was shown that only a few compounds, mainly antibiotics, dominate the total ecotoxicological risk.
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Predictors of neurobehavioral symptoms in a university population: a multivariate approach using a postconcussive symptom questionnaire.
J Int Neuropsychol Soc
PUBLISHED: 07-25-2013
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Several factors have been linked to severity of postconcussive-type (neurobehavioral) symptoms. In this study, predictors of neurobehavioral symptoms were examined using multivariate methods to determine the relative importance of each. Data regarding demographics, symptoms, current alcohol use, history of traumatic brain injury (TBI), orthopedic injuries, and psychiatric/developmental diagnoses were collected via questionnaire from 3027 university students. The most prominent predictors of symptoms were gender, history of depression or anxiety, history of attention-deficit/hyperactivity disorder or learning disability diagnosis, and frequency of alcohol use. Prior mild TBI was significantly related to overall symptoms, but this effect was small in comparison to other predictors. These results provide further evidence that neurobehavioral symptoms are multi-determined phenomena, and highlight the importance of psychiatric comorbidity, demographic factors, and health behaviors to neurobehavioral symptom presentation after mild TBI.
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Mosaic VSGs and the scale of Trypanosoma brucei antigenic variation.
PLoS Pathog.
PUBLISHED: 07-01-2013
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A main determinant of prolonged Trypanosoma brucei infection and transmission and success of the parasite is the interplay between host acquired immunity and antigenic variation of the parasite variant surface glycoprotein (VSG) coat. About 0.1% of trypanosome divisions produce a switch to a different VSG through differential expression of an archive of hundreds of silent VSG genes and pseudogenes, but the patterns and extent of the trypanosome diversity phenotype, particularly in chronic infection, are unclear. We applied longitudinal VSG cDNA sequencing to estimate variant richness and test whether pseudogenes contribute to antigenic variation. We show that individual growth peaks can contain at least 15 distinct variants, are estimated computationally to comprise many more, and that antigenically distinct mosaic VSGs arise from segmental gene conversion between donor VSG genes or pseudogenes. The potential for trypanosome antigenic variation is probably much greater than VSG archive size; mosaic VSGs are core to antigenic variation and chronic infection.
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Revisiting the diffusion approximation to estimate evolutionary rates of gene family diversification.
J. Theor. Biol.
PUBLISHED: 06-21-2013
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Genetic diversity in multigene families is shaped by multiple processes, including gene conversion and point mutation. Because multi-gene families are involved in crucial traits of organisms, quantifying the rates of their genetic diversification is important. With increasing availability of genomic data, there is a growing need for quantitative approaches that integrate the molecular evolution of gene families with their higher-scale function. In this study, we integrate a stochastic simulation framework with population genetics theory, namely the diffusion approximation, to investigate the dynamics of genetic diversification in a gene family. Duplicated genes can diverge and encode new functions as a result of point mutation, and become more similar through gene conversion. To model the evolution of pairwise identity in a multigene family, we first consider all conversion and mutation events in a discrete manner, keeping track of their details and times of occurrence; second we consider only the infinitesimal effect of these processes on pairwise identity accounting for random sampling of genes and positions. The purely stochastic approach is closer to biological reality and is based on many explicit parameters, such as conversion tract length and family size, but is more challenging analytically. The population genetics approach is an approximation accounting implicitly for point mutation and gene conversion, only in terms of per-site average probabilities. Comparison of these two approaches across a range of parameter combinations reveals that they are not entirely equivalent, but that for certain relevant regimes they do match. As an application of this modelling framework, we consider the distribution of nucleotide identity among VSG genes of African trypanosomes, representing the most prominent example of a multi-gene family mediating parasite antigenic variation and within-host immune evasion.
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Hypertriglyceridemia in patients with metastatic breast cancer and treatment with capecitabine.
J Chemother
PUBLISHED: 06-21-2013
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Several reports have described hypertriglyceridemia (HTG) in cancer patients, including breast cancer patients treated with capecitabine (CAP). However, the exact range of HTG in patients with metastatic breast cancer (MBC) treated with CAP has clearly not been defined. A retrospective analysis on 54 patients with MBC treated with CAP longer than 2 months was conducted. HTG was defined as triglyceride blood level above 150 mg/dl. Baseline data included age, body mass index (BMI), tumour characteristics, treatment duration, concomitant treatment with lapatinib, diagnosis of dyslipidemia, and diabetes mellitus, as well as antihyperlipidemic therapy. Clinically significant HTG (triglycerides >300 mg/dl) was found in 4/54 (7%) of patients. Post-treatment HTG was associated only with concomitant treatment with lapatinib (P<0·01). Three of the patients had dyslipidemia before treatment with CAP, and one patient also had diabetes-mellitus. No HTG-related complications occurred. Clinically significant HTG in MBC patients treated with CAP may be associated with pre-existing risk factors, such as dyslipidemia or diabetes-mellitus.
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Evolutionary dynamics and information hierarchies in biological systems.
Ann. N. Y. Acad. Sci.
PUBLISHED: 05-20-2013
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The study of evolution has entered a revolutionary new era, where quantitative and predictive methods are transforming the traditionally qualitative and retrospective approaches of the past. Genomic sequencing and modern computational techniques are permitting quantitative comparisons between variation in the natural world and predictions rooted in neo-Darwinian theory, revealing the shortcomings of current evolutionary theory, particularly with regard to large-scale phenomena like macroevolution. Current research spanning and uniting diverse fields and exploring the physical and chemical nature of organisms across temporal, spatial, and organizational scales is replacing the model of evolution as a passive filter selecting for random changes at the nucleotide level with a paradigm in which evolution is a dynamic process both constrained and driven by the informational architecture of organisms across scales, from DNA and chromatin regulation to interactions within and between species and the environment.
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A cell-surface phylome for African trypanosomes.
PLoS Negl Trop Dis
PUBLISHED: 02-04-2013
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The cell surface of Trypanosoma brucei, like many protistan blood parasites, is crucial for mediating host-parasite interactions and is instrumental to the initiation, maintenance and severity of infection. Previous comparisons with the related trypanosomatid parasites T. cruzi and Leishmania major suggest that the cell-surface proteome of T. brucei is largely taxon-specific. Here we compare genes predicted to encode cell surface proteins of T. brucei with those from two related African trypanosomes, T. congolense and T. vivax. We created a cell surface phylome (CSP) by estimating phylogenies for 79 gene families with putative surface functions to understand the more recent evolution of African trypanosome surface architecture. Our findings demonstrate that the transferrin receptor genes essential for bloodstream survival in T. brucei are conserved in T. congolense but absent from T. vivax and include an expanded gene family of insect stage-specific surface glycoproteins that includes many currently uncharacterized genes. We also identify species-specific features and innovations and confirm that these include most expression site-associated genes (ESAGs) in T. brucei, which are absent from T. congolense and T. vivax. The CSP presents the first global picture of the origins and dynamics of cell surface architecture in African trypanosomes, representing the principal differences in genomic repertoire between African trypanosome species and provides a basis from which to explore the developmental and pathological differences in surface architectures. All data can be accessed at: http://www.genedb.org/Page/trypanosoma_surface_phylome.
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Chronic epigastric pain in a middle-aged man.
AJR Am J Roentgenol
PUBLISHED: 06-25-2011
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The objective of this article is to describe and show a number of imaging findings that are classical for an intussusception in an adult and discuss the clinical manifestations and associated findings. We also discuss the differential diagnosis of intussusception in an adult and the most likely causes.
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Angiogenesis and host immune response contribute to the aggressive character of non-melanoma skin cancers in renal transplant recipients.
Histopathology
PUBLISHED: 05-19-2011
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The aim of this study was to determine the contribution of tumour angiogenesis to the aggressive growth of non-melanoma skin cancers (NMSCs) in renal transplant recipients (RTRs).
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Predictive hydrogeochemical modelling of bauxite residue sand in field conditions.
J. Hazard. Mater.
PUBLISHED: 04-15-2011
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The suitability of residue sand (the coarse fraction remaining from Bayers process of bauxite refining) for constructing the surface cover of closed bauxite residue storage areas was investigated. Specifically, its properties as a medium for plant growth are of interest to ensure residue sand can support a sustainable ecosystem following site closure. The geochemical evolution of the residue sand under field conditions, its plant nutrient status and soil moisture retention were studied by integrated modelling of geochemical and hydrological processes. For the parameterization of mineral reactions, amounts and reaction kinetics of the mineral phases natron, calcite, tricalcium aluminate, sodalite, muscovite and analcime were derived from measured acid neutralization curves. The effective exchange capacity for ion adsorption was measured using three independent exchange methods. The geochemical model, which accounts for mineral reactions, cation exchange and activity corrected solution speciation, was formulated in the geochemical modelling framework PHREEQC, and partially validated in a saturated-flow column experiment. For the integration of variably saturated flow with multi-component solute transport in heterogeneous 2D domains, a coupling of PHREEQC with the multi-purpose finite-element solver COMSOL was established. The integrated hydrogeochemical model was applied to predict water availability and quality in a vertical flow lysimeter and a cover design for a storage facility using measured time series of rainfall and evaporation from southwest Western Australia. In both scenarios the sand was fertigated and gypsum-amended. Results show poor long-term retention of fertilizer ions and buffering of the pH around 10 for more than 5 y of leaching. It was concluded that fertigation, gypsum amendment and rainfall leaching alone were insufficient to render the geochemical conditions of residue sand suitable for optimal plant growth within the given timeframe. The surface cover simulation demonstrates that the soil moisture status in the residue sand can be ameliorated by an appropriate design of the cover layer with respect to thickness, slope and distance between lateral drains.
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Laryngopharyngeal reflux: More questions than answers.
Cleve Clin J Med
PUBLISHED: 05-05-2010
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Laryngopharyngeal reflux (LPR), an extraesophageal variant of gastroesophageal reflux disease, is associated with hoarseness, chronic cough, throat-clearing, sore throat, and dysphagia. But because these symptoms are nonspecific, laryngoscopy is often done and the diagnosis of LPR is considered if edema, erythema, ventricular obliteration, pseudosulcus, or postcricoid hyperplasia is noted. Most patients with suspected LPR are given a 2-month trial of a proton pump inhibitor. Yet there is still little or no solid evidence on which to base the diagnosis or the treatment of LPR. We review the current understanding of the pathophysiology and discuss current diagnostic tests and treatment regimens in patients with suspected LPR.
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The genome sequence of Trypanosoma brucei gambiense, causative agent of chronic human african trypanosomiasis.
PLoS Negl Trop Dis
PUBLISHED: 03-02-2010
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Trypanosoma brucei gambiense is the causative agent of chronic Human African Trypanosomiasis or sleeping sickness, a disease endemic across often poor and rural areas of Western and Central Africa. We have previously published the genome sequence of a T. b. brucei isolate, and have now employed a comparative genomics approach to understand the scale of genomic variation between T. b. gambiense and the reference genome. We sought to identify features that were uniquely associated with T. b. gambiense and its ability to infect humans.
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varDB: common ground for a shifting landscape.
Trends Parasitol.
PUBLISHED: 03-02-2009
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Antigenic variation is a phylogenetically widespread phenomenon thought to lead to survival benefits for the pathogen. Although governed by genetic mechanisms, antigenic variation is ultimately manifested in variant proteins. The varDB database is an attempt to gain an overview of common structures and functions of variant proteins related to enhanced survival. varDB provides a wealth of sequence data and several tools to facilitate their analysis, but current limitations preclude achievement of its full promise. A critique of this database and how it could serve the scientific community is provided here.
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Morphological quantification of filamentous fungal development using membrane immobilization and automatic image analysis.
J. Ind. Microbiol. Biotechnol.
PUBLISHED: 02-17-2009
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Mycelial morphology is a critically important process property in industrial fermentations of filamentous micro-organisms, as particular phenotypes are associated with maximum productivity. However, the accurate quantification of complex morphologies still represents a significant challenge in elucidating this relationship. A system has been developed for high-resolution characterisation of filamentous fungal growth on a solid substrate, using membrane immobilization and fully-automatic plug-ins developed for the public domain, Java-based, image-processing software, ImageJ. The system has been used to quantify the microscopic development of Aspergillus oryzae on malt agar, by measuring spore projected area and circularity, the total length of a hyphal element, the number of tips per element, and the hyphal growth unit. Two different stages of growth are described, from the swelling of a population of conidiospores up to fully developed, branched hyphae 24 h after inoculation. Spore swelling expressed as an increase in mean equivalent spore diameter was found to be approximately linear with time. Widespread germination of spores was observed by 8 h after inoculation. From approximately 12 h, the number of tips was found to increase exponentially. The specific growth rate of a population of hyphae was calculated as approximately 0.24-0.27 h(-1). A wide variation in growth kinetics was found within the population. The robustness of the image-analysis system was verified by testing the effect of small variations in the input data.
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Subcutaneous Crotaline Fab antivenom for the treatment of rattlesnake envenomation in a porcine model.
Clin Toxicol (Phila)
PUBLISHED: 01-21-2009
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This study was designed to investigate whether the local, subcutaneous injection of Crotaline Fab antivenom (CroFab) at the rattlesnake envenomation site would result in less extremity edema when compared to intravenous (i.v.) antivenom infusion alone.
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An anatomically comprehensive atlas of the adult human brain transcriptome.
Nature
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Neuroanatomically precise, genome-wide maps of transcript distributions are critical resources to complement genomic sequence data and to correlate functional and genetic brain architecture. Here we describe the generation and analysis of a transcriptional atlas of the adult human brain, comprising extensive histological analysis and comprehensive microarray profiling of ?900 neuroanatomically precise subdivisions in two individuals. Transcriptional regulation varies enormously by anatomical location, with different regions and their constituent cell types displaying robust molecular signatures that are highly conserved between individuals. Analysis of differential gene expression and gene co-expression relationships demonstrates that brain-wide variation strongly reflects the distributions of major cell classes such as neurons, oligodendrocytes, astrocytes and microglia. Local neighbourhood relationships between fine anatomical subdivisions are associated with discrete neuronal subtypes and genes involved with synaptic transmission. The neocortex displays a relatively homogeneous transcriptional pattern, but with distinct features associated selectively with primary sensorimotor cortices and with enriched frontal lobe expression. Notably, the spatial topography of the neocortex is strongly reflected in its molecular topography-the closer two cortical regions, the more similar their transcriptomes. This freely accessible online data resource forms a high-resolution transcriptional baseline for neurogenetic studies of normal and abnormal human brain function.
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Clathrin potentiates vaccinia-induced actin polymerization to facilitate viral spread.
Cell Host Microbe
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During their egress, newly assembled vaccinia virus particles fuse with the plasma membrane and enhance their spread by inducing Arp2/3-dependent actin polymerization. Investigating the events surrounding vaccinia virus fusion, we discovered that vaccinia transiently recruits clathrin in a manner dependent on the clathrin adaptor AP-2. The recruitment of clathrin to vaccinia dramatically enhances the ability of the virus to induce actin-based motility. We demonstrate that clathrin promotes clustering of the virus actin tail nucleator A36 and host N-WASP, which activates actin nucleation through the Arp2/3 complex. Increased clustering enhances N-WASP stability, leading to more efficient actin tail initiation and sustained actin polymerization. Our observations uncover an unexpected role for clathrin during virus spread and have important implications for the regulation of actin polymerization.
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Genome hyperevolution and the success of a parasite.
Ann. N. Y. Acad. Sci.
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The strategy of antigenic variation is to present a constantly changing population phenotype that enhances parasite transmission, through evasion of immunity arising within, or existing between, host animals. Trypanosome antigenic variation occurs through spontaneous switching among members of a silent archive of many hundreds of variant surface glycoprotein (VSG) antigen genes. As with such contingency systems in other pathogens, switching appears to be triggered through inherently unstable DNA sequences. The archive occupies subtelomeres, a genome partition that promotes hypermutagenesis and, through telomere position effects, singular expression of VSG. Trypanosome antigenic variation is augmented greatly by the formation of mosaic genes from segments of pseudo-VSG, an example of implicit genetic information. Hypermutation occurs apparently evenly across the whole archive, without direct selection on individual VSG, demonstrating second-order selection of the underlying mechanisms. Coordination of antigenic variation, and thereby transmission, occurs through networking of trypanosome traits expressed at different scales from molecules to host populations.
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Quantifying the branching frequency of virtual filamentous microbes using fractal analysis.
Biotechnol. Bioeng.
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The productivity of an industrial fermentation process involving a filamentous microbe is heavily dependent on the morphological form adopted by the organism. The development of systems capable of rapidly and accurately characterizing morphology within a given process represents a significant challenge, as the complex phenotypes that are manifested are not easily quantified. Conventional parameters employed in these analyses are often of limited value, as they reveal little about the branching behavior of the organism; an important consideration given the demonstrated link between branching frequency and metabolite production. In this study, the influence of branching behavior on the spatial distribution of mycelia grown in silico is examined through fractal analysis. It is demonstrated that fractal dimension, quantified based on the frequency distribution of parameterized boundary curves, and lacunarity act as robust estimators of branching behavior. The analysis can, in theory, be applied to any morphological form, providing universally applicable process parameters for more complete data acquisition.
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Genome-wide analysis reveals extensive functional interaction between DNA replication initiation and transcription in the genome of Trypanosoma brucei.
Cell Rep
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Identification of replication initiation sites, termed origins, is a crucial step in understanding genome transmission in any organism. Transcription of the Trypanosoma brucei genome is highly unusual, with each chromosome comprising a few discrete transcription units. To understand how DNA replication occurs in the context of such organization, we have performed genome-wide mapping of the binding sites of the replication initiator ORC1/CDC6 and have identified replication origins, revealing that both localize to the boundaries of the transcription units. A remarkably small number of active origins is seen, whose spacing is greater than in any other eukaryote. We show that replication and transcription in T. brucei have a profound functional overlap, as reducing ORC1/CDC6 levels leads to genome-wide increases in mRNA levels arising from the boundaries of the transcription units. In addition, ORC1/CDC6 loss causes derepression of silent Variant Surface Glycoprotein genes, which are critical for host immune evasion.
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Variable iodine intake persists in the context of universal salt iodization in China.
J. Nutr.
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Iodine deficiency disorders were prevalent in China until the introduction of universal salt iodization in 1995. Concerns have recently arisen about possible excess iodine intake in this context. To document iodine intake and the contribution from iodized salt in China, we surveyed dietary iodine intake during Chinas nationally representative 2007 total diet study (TDS) and during an additional TDS in 4 coastal provinces and Beijing in 2009. Iodine intake was broken down by age and sex in 2009. Mean daily iodine and salt intake and the contribution from different food and beverage groups (and in 2009, individual items) was measured. The iodine in food cooked with iodized and noniodized salt was also assessed. The mean calculated iodine intake of a standard male in China was 425 ?g/d in 2007 and 325 ?g/d in coastal areas in 2009, well below the upper limit (UL) in all provinces. In 2009, iodine intake was above the UL in only 1-7% of age-sex groups, except among children (18-19%). A concerning number of individuals consumed less than the WHO-recommended daily allowance, including 31.5% of adult women. Salt contributed 63.5% of food iodine, and 24.6% of salt iodine was lost in cooking. Overall salt consumption declined between the surveys. Salt iodization assures iodine nutrition in China where environmental iodine is widely lacking. The risk of iodine excess is low, but planned decreases in salt iodization levels may increase the existing risk of inadequate intake. Regular monitoring of urinary iodine and more research on the impact of excess iodine intake is recommended.
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The impact of mutation and gene conversion on the local diversification of antigen genes in African trypanosomes.
Mol. Biol. Evol.
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Patterns of genetic diversity in parasite antigen gene families hold important information about their potential to generate antigenic variation within and between hosts. The evolution of such gene families is typically driven by gene duplication, followed by point mutation and gene conversion. There is great interest in estimating the rates of these processes from molecular sequences for understanding the evolution of the pathogen and its significance for infection processes. In this study, a series of models are constructed to investigate hypotheses about the nucleotide diversity patterns between closely related gene sequences from the antigen gene archive of the African trypanosome, the protozoan parasite causative of human sleeping sickness in Equatorial Africa. We use a hidden Markov model approach to identify two scales of diversification: clustering of sequence mismatches, a putative indicator of gene conversion events with other lower-identity donor genes in the archive, and at a sparser scale, isolated mismatches, likely arising from independent point mutations. In addition to quantifying the respective probabilities of occurrence of these two processes, our approach yields estimates for the gene conversion tract length distribution and the average diversity contributed locally by conversion events. Model fitting is conducted using a Bayesian framework. We find that diversifying gene conversion events with lower-identity partners occur at least five times less frequently than point mutations on variant surface glycoprotein (VSG) pairs, and the average imported conversion tract is between 14 and 25 nucleotides long. However, because of the high diversity introduced by gene conversion, the two processes have almost equal impact on the per-nucleotide rate of sequence diversification between VSG subfamily members. We are able to disentangle the most likely locations of point mutations and conversions on each aligned gene pair.
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NUP-1 Is a large coiled-coil nucleoskeletal protein in trypanosomes with lamin-like functions.
PLoS Biol.
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A unifying feature of eukaryotic nuclear organization is genome segregation into transcriptionally active euchromatin and transcriptionally repressed heterochromatin. In metazoa, lamin proteins preserve nuclear integrity and higher order heterochromatin organization at the nuclear periphery, but no non-metazoan lamin orthologues have been identified, despite the likely presence of nucleoskeletal elements in many lineages. This suggests a metazoan-specific origin for lamins, and therefore that distinct protein elements must compose the nucleoskeleton in other lineages. The trypanosomatids are highly divergent organisms and possess well-documented but remarkably distinct mechanisms for control of gene expression, including polycistronic transcription and trans-splicing. NUP-1 is a large protein localizing to the nuclear periphery of Trypanosoma brucei and a candidate nucleoskeletal component. We sought to determine if NUP-1 mediates heterochromatin organization and gene regulation at the nuclear periphery by examining the influence of NUP-1 knockdown on morphology, chromatin positioning, and transcription. We demonstrate that NUP-1 is essential and part of a stable network at the inner face of the trypanosome nuclear envelope, since knockdown cells have abnormally shaped nuclei with compromised structural integrity. NUP-1 knockdown also disrupts organization of nuclear pore complexes and chromosomes. Most significantly, we find that NUP-1 is required to maintain the silenced state of developmentally regulated genes at the nuclear periphery; NUP-1 knockdown results in highly specific mis-regulation of telomere-proximal silenced variant surface glycoprotein (VSG) expression sites and procyclin loci, indicating a disruption to normal chromatin organization essential to life-cycle progression. Further, NUP-1 depletion leads to increased VSG switching and therefore appears to have a role in control of antigenic variation. Thus, analogous to vertebrate lamins, NUP-1 is a major component of the nucleoskeleton with key roles in organization of the nuclear periphery, heterochromatin, and epigenetic control of developmentally regulated loci.
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Identification of ORC1/CDC6-interacting factors in Trypanosoma brucei reveals critical features of origin recognition complex architecture.
PLoS ONE
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DNA replication initiates by formation of a pre-replication complex on sequences termed origins. In eukaryotes, the pre-replication complex is composed of the Origin Recognition Complex (ORC), Cdc6 and the MCM replicative helicase in conjunction with Cdt1. Eukaryotic ORC is considered to be composed of six subunits, named Orc1-6, and monomeric Cdc6 is closely related in sequence to Orc1. However, ORC has been little explored in protists, and only a single ORC protein, related to both Orc1 and Cdc6, has been shown to act in DNA replication in Trypanosoma brucei. Here we identify three highly diverged putative T. brucei ORC components that interact with ORC1/CDC6 and contribute to cell division. Two of these factors are so diverged that we cannot determine if they are eukaryotic ORC subunit orthologues, or are parasite-specific replication factors. The other we show to be a highly diverged Orc4 orthologue, demonstrating that this is one of the most widely conserved ORC subunits in protists and revealing it to be a key element of eukaryotic ORC architecture. Additionally, we have examined interactions amongst the T. brucei MCM subunits and show that this has the conventional eukaryotic heterohexameric structure, suggesting that divergence in the T. brucei replication machinery is limited to the earliest steps in origin licensing.
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Antigenic diversity is generated by distinct evolutionary mechanisms in African trypanosome species.
Proc. Natl. Acad. Sci. U.S.A.
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Antigenic variation enables pathogens to avoid the host immune response by continual switching of surface proteins. The protozoan blood parasite Trypanosoma brucei causes human African trypanosomiasis ("sleeping sickness") across sub-Saharan Africa and is a model system for antigenic variation, surviving by periodically replacing a monolayer of variant surface glycoproteins (VSG) that covers its cell surface. We compared the genome of Trypanosoma brucei with two closely related parasites Trypanosoma congolense and Trypanosoma vivax, to reveal how the variant antigen repertoire has evolved and how it might affect contemporary antigenic diversity. We reconstruct VSG diversification showing that Trypanosoma congolense uses variant antigens derived from multiple ancestral VSG lineages, whereas in Trypanosoma brucei VSG have recent origins, and ancestral gene lineages have been repeatedly co-opted to novel functions. These historical differences are reflected in fundamental differences between species in the scale and mechanism of recombination. Using phylogenetic incompatibility as a metric for genetic exchange, we show that the frequency of recombination is comparable between Trypanosoma congolense and Trypanosoma brucei but is much lower in Trypanosoma vivax. Furthermore, in showing that the C-terminal domain of Trypanosoma brucei VSG plays a crucial role in facilitating exchange, we reveal substantial species differences in the mechanism of VSG diversification. Our results demonstrate how past VSG evolution indirectly determines the ability of contemporary parasites to generate novel variant antigens through recombination and suggest that the current model for antigenic variation in Trypanosoma brucei is only one means by which these parasites maintain chronic infections.
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A comparison of long-term postconcussive symptoms between university students with and without a history of mild traumatic brain injury or orthopedic injury.
J Int Neuropsychol Soc
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Mild traumatic brain injury (mild TBI) is often associated with postconcussive symptoms such as headache, memory problems, and irritability. However, high rates of similar symptoms in groups without a history of TBI raise questions about the clinical validity of the postconcussive syndrome. This study was conducted to address these issues through systematic examination of symptoms reported by those with and without a history of mild TBI or orthopedic injury. Responses to the Postconcussion Syndrome Checklist (PCSC), demographic information, and medical history were collected via online questionnaire from 3027 non-referred university students (2280 without a history of mild TBI or orthopedic injury, 491 with a history of orthopedic injury, and 256 with post-acute mild TBI). Although the mild TBI group reported higher mean levels of symptoms, confirmatory factor analyses demonstrated that symptoms clustered into parallel cognitive, somatic, affective, and sensory factors in all three groups. Despite modestly higher mean symptoms among those with a history of mild TBI, symptom clusters did not differ from non-TBI groups. These findings cast doubts about the clinical validity of the "postconcussive syndrome" and raise questions about pathways by which mild TBI and other factors may influence the expression of chronic symptoms.
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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.