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Find video protocols related to scientific articles indexed in Pubmed.
In vitro pharmacological screening of three newly synthesised pyrimidine derivatives.
Nat. Prod. Res.
PUBLISHED: 10-04-2014
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The antibacterial and antifungal activities of three new pyrimidine derivatives, namely, 2,6-bis(4,6-dimethylpyrimidin-2-ylthio)benzene-1,4-diol (1),3,5-bis(4,6-dimethylpyrimidin-2-ylthio)-2-methylbenzene-1,4-diol (2) and 3,5-bis(4,6-dimethylpyrimidin-2-ylthio)-2-methoxybenzene-1,4-diol (3), synthesised by electrochemical method are presented here. The compounds were screened for their activities against Gram-positive and Gram-negative bacteria, Bacillus subtilis, Staphylococcusaureus, Escherichia coli and a pathogenic fungus Aspergillus niger. The results show that these compounds have significant activity against these bacteria and fungus. The minimum inhibitory concentration of compound 1 was determined as 62.5 ?g/mL against B. subtilis, 125 ?g/mL against E. coli and 250 ?g/mL against S. aureus establishing its promising activities higher than susceptible ranges.
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Quantitative 4D analyses of epithelial folding during Drosophila gastrulation.
Development
PUBLISHED: 06-19-2014
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Understanding the cellular and mechanical processes that underlie the shape changes of individual cells and their collective behaviors in a tissue during dynamic and complex morphogenetic events is currently one of the major frontiers in developmental biology. The advent of high-speed time-lapse microscopy and its use in monitoring the cellular events in fluorescently labeled developing organisms demonstrate tremendous promise in establishing detailed descriptions of these events and could potentially provide a foundation for subsequent hypothesis-driven research strategies. However, obtaining quantitative measurements of dynamic shapes and behaviors of cells and tissues in a rapidly developing metazoan embryo using time-lapse 3D microscopy remains technically challenging, with the main hurdle being the shortage of robust imaging processing and analysis tools. We have developed EDGE4D, a software tool for segmenting and tracking membrane-labeled cells using multi-photon microscopy data. Our results demonstrate that EDGE4D enables quantification of the dynamics of cell shape changes, cell interfaces and neighbor relations at single-cell resolution during a complex epithelial folding event in the early Drosophila embryo. We expect this tool to be broadly useful for the analysis of epithelial cell geometries and movements in a wide variety of developmental contexts.
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Stoichiometry of site-specific lysine acetylation in an entire proteome.
J. Biol. Chem.
PUBLISHED: 06-10-2014
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Acetylation of lysine ?-amino groups influences many cellular processes and has been mapped to thousands of sites across many organisms. Stoichiometric information of acetylation is essential to accurately interpret biological significance. Here, we developed and employed a novel method for directly quantifying stoichiometry of site-specific acetylation in the entire proteome of Escherichia coli. By coupling isotopic labeling and a novel pairing algorithm, our approach performs an in silico enrichment of acetyl peptides, circumventing the need for immunoenrichment. We investigated the function of the sole NAD(+)-dependent protein deacetylase, CobB, on both site-specific and global acetylation. We quantified 2206 peptides from 899 proteins and observed a wide distribution of acetyl stoichiometry, ranging from less than 1% up to 98%. Bioinformatic analysis revealed that metabolic enzymes, which either utilize or generate acetyl-CoA, and proteins involved in transcriptional and translational processes displayed the highest degree of acetylation. Loss of CobB led to increased global acetylation at low stoichiometry sites and induced site-specific changes at high stoichiometry sites, and biochemical analysis revealed altered acetyl-CoA metabolism. Thus, this study demonstrates that sirtuin deacetylase deficiency leads to both site-specific and global changes in protein acetylation stoichiometry, affecting central metabolism.
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Impact of brief and sequential exposure to nystatin, amphotericin B, ketoconazole, and fluconazole in modulating adhesion traits of oral Candida dubliniensis isolates.
J Investig Clin Dent
PUBLISHED: 04-08-2014
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Candida adherence is implicated in the pathogenesis of oral candidosis. Adhesion to buccal epithelial cells (BEC), germ tube (GT) formation, and relative cell surface hydrophobicity (CSH) are colonization attributes of candidal pathogenicity. Candida dubliniensis (C. dubliniensis) is allied with recurrent oral candidosis, which can be treated with nystatin, amphotericin B, ketoconazole, and fluconazole. Due to the diluent effect of saliva and the cleansing effect of the oral musculature in the oral cavity C. dubliniensis isolates undergo brief and sequential exposure to antifungal agents during therapy. Thus, in the present study, we evaluated the adhesion to BEC, GT formation, and the CSH of oral isolates of C. dubliniensis following brief and sequential exposure to nystatin, amphotericin B, ketoconazole, and fluconazole.
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Effects of high hydrostatic pressure on emulsifying properties of sweet potato protein in model protein-hydrocolloids system.
Food Chem
PUBLISHED: 03-28-2014
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The effects of high hydrostatic pressure (HHP) on emulsifying properties of sweet potato protein (SPP) in presence of 0.1%, 0.3% and 0.5% (w/v) of guar gum (GG) and glycerol monostearate (GMS) were investigated. Emulsifying stability index (ESI) of the SPP with GG revealed significant increase (P<0.05) in ESI value at 600MPa treatment, while the stability of SPP-GMS emulsions significantly decreased with increase in GMS concentrations and HHP treatments (200-600MPa). HHP treatment considerably reduced the creaming rate for SPP-GG model while such case was not observed for SPP-GMS model. The flow index for SPP-GG emulsion model was found to decrease with increase in HHP treatment and had non-Newtonian behaviour. The SPP-GMS emulsion models with HHP treatments showed comparatively lower viscosities but had more Newtonian flow character.
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Stable isotope labeling of phosphoproteins for large-scale phosphorylation rate determination.
Mol. Cell Proteomics
PUBLISHED: 02-16-2014
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Signals that control responses to stimuli and cellular function are transmitted through the dynamic phosphorylation of thousands of proteins by protein kinases. Many techniques have been developed to study phosphorylation dynamics, including several mass spectrometry (MS)-based methods. Over the past few decades, substantial developments have been made in MS techniques for the large-scale identification of proteins and their post-translational modifications. Nevertheless, all of the current MS-based techniques for quantifying protein phosphorylation dynamics rely on the measurement of changes in peptide abundance levels, and many methods suffer from low confidence in phosphopeptide identification due to poor fragmentation. Here we have optimized an approach for the stable isotope labeling of amino acids by phosphate using [?-¹?O?]ATP in nucleo to determine global site-specific phosphorylation rates. The advantages of this metabolic labeling technique are increased confidence in phosphorylated peptide identification, direct labeling of phosphorylation sites, measurement phosphorylation rates, and the identification of actively phosphorylated sites in a cell-like environment. In this study we calculated approximate rate constants for over 1,000 phosphorylation sites based on labeling progress curves. We measured a wide range of phosphorylation rate constants from 0.34 min?¹ to 0.001 min?¹. Finally, we applied stable isotope labeling of amino acids by phosphate to identify sites that have different phosphorylation kinetics during G1/S and M phase. We found that most sites had very similar phosphorylation rates under both conditions; however, a small subset of sites on proteins involved in the mitotic spindle were more actively phosphorylated during M phase, whereas proteins involved in DNA replication and transcription were more actively phosphorylated during G1/S phase. The data have been deposited to the ProteomeXchange with the identifier PXD000680.
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Post-antifungal effect and adhesion to buccal epithelial cells of oral Candida dubliniensis isolates subsequent to limited exposure to amphotericin B, ketoconazole and fluconazole.
J Investig Clin Dent
PUBLISHED: 01-29-2014
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The post-antifungal effect (PAFE) of Candida and its adherence to oral mucosal surfaces are important determinants of candidal pathogenicity. Candida dubliniensis is allied with recurrent oral candidosis. Oral candidosis can be treated with amphotericin B, ketoconazole and fluconazole. There is no information on the PAFE and its impact on adhesion to oral buccal epithelial cells (BEC) of oral C. dubliniensis isolates. Therefore, the main objective was to reconnoiter the PAFE and adhesion to BEC of 20 C. dubliniensis isolates following brief exposure to aforementioned antimycotics.
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Switch from canonical to noncanonical Wnt signaling mediates high glucose-induced adipogenesis.
Stem Cells
PUBLISHED: 01-11-2014
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Human bone marrow mesenchymal progenitor cells (MPCs) are multipotent cells that play an essential role in endogenous repair and the maintenance of the stem cell niche. We have recently shown that high levels of glucose, conditions mimicking diabetes, cause impairment of MPCs, resulting in enhanced adipogenesis and suppression of osteogenesis. This implies that diabetes may lead to reduced endogenous repair mechanisms through altering the differentiation potential of MPCs and, consequently, disrupting the stem cell niche. Phenotypic alterations in the bone marrow of long-term diabetic patients closely resemble this observation. Here, we show that high levels of glucose selectively enhance autogenous Wnt11 expression in MPCs to stimulate adipogenesis through the Wnt/protein kinase C noncanonical pathway. This novel mechanism may account for increased bone marrow adipogenesis, severe bone loss, and reduced vascular stem cells leading to chronic secondary complications of diabetes.
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Primate transcript and protein expression levels evolve under compensatory selection pressures.
Science
PUBLISHED: 10-17-2013
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Changes in gene regulation have likely played an important role in the evolution of primates. Differences in messenger RNA (mRNA) expression levels across primates have often been documented; however, it is not yet known to what extent measurements of divergence in mRNA levels reflect divergence in protein expression levels, which are probably more important in determining phenotypic differences. We used high-resolution, quantitative mass spectrometry to collect protein expression measurements from human, chimpanzee, and rhesus macaque lymphoblastoid cell lines and compared them to transcript expression data from the same samples. We found dozens of genes with significant expression differences between species at the mRNA level yet little or no difference in protein expression. Overall, our data suggest that protein expression levels evolve under stronger evolutionary constraint than mRNA levels.
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Semi-metallic polymers.
Nat Mater
PUBLISHED: 05-21-2013
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Polymers are lightweight, flexible, solution-processable materials that are promising for low-cost printed electronics as well as for mass-produced and large-area applications. Previous studies demonstrated that they can possess insulating, semiconducting or metallic properties; here we report that polymers can also be semi-metallic. Semi-metals, exemplified by bismuth, graphite and telluride alloys, have no energy bandgap and a very low density of states at the Fermi level. Furthermore, they typically have a higher Seebeck coefficient and lower thermal conductivities compared with metals, thus being suitable for thermoelectric applications. We measure the thermoelectric properties of various poly(3,4-ethylenedioxythiophene) samples, and observe a marked increase in the Seebeck coefficient when the electrical conductivity is enhanced through molecular organization. This initiates the transition from a Fermi glass to a semi-metal. The high Seebeck value, the metallic conductivity at room temperature and the absence of unpaired electron spins makes polymer semi-metals attractive for thermoelectrics and spintronics.
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Propranolol inhibits growth of hemangioma-initiating cells but does not induce apoptosis.
Pediatr. Res.
PUBLISHED: 04-05-2013
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Background:Infantile hemangioma (IH) is the most common tumor of infancy. The first-line therapy for IH is propranolol, a non-selective ?-adrenergic receptor antagonist. However, mechanisms for the therapeutic effect of propranolol and regrowth of IH following cessation of treatment in some cases are not clear. We have recently shown that IH arises from multipotent stem cells. Whether IH stem cells are responsive to propranolol and are selectively targeted is unknown, and is the focus of this study.Methods:IH stem cells were exposed to propranolol and assayed for cellular and molecular alterations. We used endothelial cells (ECs) as controls and bone marrow-mesenchymal progenitor cells (bm-MPCs) as normal stem/progenitor counterparts to determine selectivity.Results:Our results show that propranolol significantly reduced IH stem cell growth but failed to induce caspase-3 activation. Normal bm-MPCs and mature ECs showed maintained or increased caspase-3 activation and significantly reduced cyclin-D1 levels. We further show that IH stem cells may escape apoptosis by inducing anti-apoptotic pathways.Conclusions:This study reveals that propranolol does not induce apoptosis in IH stem cells, which is in contrast to ECs. Escape from apoptosis in IH stem cells may involve induction of anti-apoptoticpathways.Pediatric Research (2013); doi:10.1038/pr.2013.231.
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Distinct Rap1 activity states control the extent of epithelial invagination via ?-catenin.
Dev. Cell
PUBLISHED: 03-08-2013
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Localized cell shape change initiates epithelial folding, while neighboring cell invagination determines the final depth of an epithelial fold. The mechanism that controls the extent of invagination remains unknown. During Drosophila gastrulation, a higher number of cells undergo invagination to form the deep posterior dorsal fold, whereas far fewer cells become incorporated into the initially very similar anterior dorsal fold. We find that a decrease in ?-catenin activity causes the anterior fold to invaginate as extensively as the posterior fold. In contrast, constitutive activation of the small GTPase Rap1 restricts invagination of both dorsal folds in an ?-catenin-dependent manner. Rap1 activity appears spatially modulated by Rapgap1, whose expression levels are high in the cells that flank the posterior fold but low in the anterior fold. We propose a model whereby distinct activity states of Rap1 modulate ?-catenin-dependent coupling between junctions and actin to control the extent of epithelial invagination.
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Isolation of Lodderomyces elongisporus from the Catheter Tip of a Fungemia Patient in the Middle East.
Case Rep Med
PUBLISHED: 01-27-2013
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Lodderomyces elongisporus is phenotypically closely related to Candida parapsilosis and has recently been identified as an infrequent cause of bloodstream infections in patients from Asia and Mexico. We report here the isolation of Lodderomyces elongisporus from the catheter of a suspected case of fungemia. The identity of the isolate was confirmed by phenotypic characteristics and ribosomal DNA sequencing.
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Factors associated with low hepatitis B vaccination; a user and provider perspective study in Peshawar.
J Pak Med Assoc
PUBLISHED: 12-01-2011
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Hepatitis B is a major burden in Pakistan. A cross-sectional study was conducted in Peshawar, from 9th June to 19th June 2010. Cluster random sampling was done. Confidence level of 95% and confidence interval of 5 was used to derive sample size. Parents of 506 children were asked about their hepatitis B immunization status who were aged 4 years or under. Questions on demographics, income, education, accessibility and occupation, knowledge and views on immunization were asked. Forty health personnel were interviewed for their views. In all, 62.2% children were completely vaccinated. Reasons for not being immunized included unawareness, busy schedule, long distance to the centre and various misconceptions. Education, mothers knowledge and views on immunization, income, closer accessibility, were the main factors associated with immunization. Health personnel thought lack of awareness among people, low accessibility and poor incentives as the shortcomings in immunization. It is recommended that effective steps should be taken to ensure better coverage.
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A computational statistics approach for estimating the spatial range of morphogen gradients.
Development
PUBLISHED: 10-17-2011
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A crucial issue in studies of morphogen gradients relates to their range: the distance over which they can act as direct regulators of cell signaling, gene expression and cell differentiation. To address this, we present a straightforward statistical framework that can be used in multiple developmental systems. We illustrate the developed approach by providing a point estimate and confidence interval for the spatial range of the graded distribution of nuclear Dorsal, a transcription factor that controls the dorsoventral pattern of the Drosophila embryo.
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A comparative study of antioxidant vitamins and simvastatin in hypercholesterolimic rabbits.
Pak J Pharm Sci
PUBLISHED: 10-01-2011
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The anti-lipidemic effects of orally administered antioxidant vitamins (vitamin A, vitamin C and vitamin E) individually and in combination were studied in cholesterol-fed rabbits and compared to the group of hypercholesterolemic animals that were treated with simvastatin. All treatment groups exhibited a decrease in serum total cholesterol, low density lipoprotein-cholesterol (LDL-C) and triglycerides concentrations, whilst vitamin C, vitamin E, the combination and simvastatin showed a more profound decrease in the lipid profile than vitamin A at different time intervals. The order of increase in high density lipoprotein-cholesterol (HDL-C) levels remained in favour of simvastatin, as none of the antioxidant vitamins treated group could exhibit a profound increase in the HDL-C.
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Coverage and causes of missed oral polio vaccine in urban and rural areas of Peshawar.
J Ayub Med Coll Abbottabad
PUBLISHED: 10-01-2011
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Poliomyelitis mainly affects children under five years of age. Pakistan is one of the few countries where wild polio is still endemic. The purpose of this study was to find out the coverage rate and factors associated with the failure of OPV in urban and rural areas of Peshawar.
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Genotypic heterogeneity and molecular basis of 5-flucytosine resistance among Candida dubliniensis isolates recovered from clinical specimens in Kuwait.
Med. Mycol.
PUBLISHED: 09-06-2011
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There is a paucity of information about genotypic heterogeneity among Candida dubliniensis isolates recovered from different geographic regions. This study explored genotypic heterogeneity among 103 C. dubliniensis strains obtained over a six-year period from clinical specimens in Kuwait. Genotype assignment was based on amplification with genotype-specific primers and sequencing of rDNA. Susceptibility to 5-flucytosine was determined by means of the Etest. DNA sequencing of cytosine deaminase was performed to determine the molecular basis of resistance to 5-flucytosine. DNA sequencing of rDNA identified seven different genotypes, i.e., 68 (66%) isolates were found to belong to genotype 1, 25 to genotype 4, six to genotype 5 and one each to genotypes 6-9. Strains of genotype 2 or genotype 3 were not detected. All isolates of genotype 4 but none of other genotypes were resistant to 5-flucytosine and the resistant strains all contained S29L mutation. Isolates of all other genotypes contained wild-type codon 29 in cytosine deaminase. A simple, PCR-RFLP-based method has been developed to facilitate rapid detection of S29L mutation in cytosine deaminase. A noteworthy observation of our study is the identification of five new genotypes of C. dubliniensis isolates, recovered from oral/respiratory specimens from patients of Middle Eastern origin. Furthermore, all 5-flucytosine resistant C. dubliniensis isolates in Kuwait belonged to genotype 4 only.
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Accurate proteome-wide protein quantification from high-resolution 15N mass spectra.
Genome Biol.
PUBLISHED: 07-11-2011
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In quantitative mass spectrometry-based proteomics, the metabolic incorporation of a single source of 15N-labeled nitrogen has many advantages over using stable isotope-labeled amino acids. However, the lack of a robust computational framework for analyzing the resulting spectra has impeded wide use of this approach. We have addressed this challenge by introducing a new computational methodology for analyzing 15N spectra in which quantification is integrated with identification. Application of this method to an Escherichia coli growth transition reveals significant improvement in quantification accuracy over previous methods.
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Phytochemical analysis, antioxidant and antibacterial effects of sea buckthorn berries.
Pak J Pharm Sci
PUBLISHED: 07-01-2011
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Sea buckthorn berries are therapeutically used as folk medicine for a variety of diseases, however, the scientific evidence is hardly available to support their role. This study explored their chemical constituents and their role as antioxidant and antibacterial agents. Three common solvents such as petroleum ether (40° - 60°C), chloroform and methanol were successively used for the extraction of active principles from sea buckthorn berries. Five major fractions (F1-F5) were isolated from the active methanol extract by column and thin layer chromatography. An attempt was made to identify the chemical nature of pooled fractions by available spectral means. Antioxidant potential of methanol extract and its fractions was measured by DPPH, formation of phosphomolybdenum complex and TBA methods. The hole-plate diffussion method was used to find out the antibacterial activity. A very brief structure-activity relationship of the potent antioxidant and antimicrobial compounds is discussed. Methanolic extract and its fractions contain numerous phenolic compounds such as flavonoids, which may be responsible for antioxidant and antibacterial effects.
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Inequity in childhood immunization between urban and rural areas of Peshawar.
J Ayub Med Coll Abbottabad
PUBLISHED: 07-01-2011
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Purpose of this study was to find coverage of vaccines in EPI and compare the factors related to vaccine failure or missed vaccination in urban and rural areas of Peshawar.
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Direct targeting of Sec23a by miR-200s influences cancer cell secretome and promotes metastatic colonization.
Nat. Med.
PUBLISHED: 05-18-2011
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Although the role of miR-200s in regulating E-cadherin expression and epithelial-to-mesenchymal transition is well established, their influence on metastatic colonization remains controversial. Here we have used clinical and experimental models of breast cancer metastasis to discover a pro-metastatic role of miR-200s that goes beyond their regulation of E-cadherin and epithelial phenotype. Overexpression of miR-200s is associated with increased risk of metastasis in breast cancer and promotes metastatic colonization in mouse models, phenotypes that cannot be recapitulated by E-cadherin expression alone. Genomic and proteomic analyses revealed global shifts in gene expression upon miR-200 overexpression toward that of highly metastatic cells. miR-200s promote metastatic colonization partly through direct targeting of Sec23a, which mediates secretion of metastasis-suppressive proteins, including Igfbp4 and Tinagl1, as validated by functional and clinical correlation studies. Overall, these findings suggest a pleiotropic role of miR-200s in promoting metastatic colonization by influencing E-cadherin-dependent epithelial traits and Sec23a-mediated tumor cell secretome.
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Prevalence of Candida dubliniensis among oral Candida isolates in patients attending the Kuwait University Dental Clinic.
Med Princ Pract
PUBLISHED: 03-29-2011
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The aim of this study was to determine the oral candidal carriage of patients seeking dental treatment at the Kuwait University Dental Clinic and to ascertain the Candida species composition among them.
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Kodamaea ohmeri as an emerging pathogen: a case report and review of the literature.
Med. Mycol.
PUBLISHED: 03-28-2011
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Kodamaea (Pichia) ohmeri is a yeast-like fungus that has recently emerged as an important etiologic agent of fungemia in immunocompromised patients. We report such a case in a premature neonate born at 29 weeks of gestation. Prior to developing fungemia, she had two episodes of bacterial sepsis on day 13 and day 32 due to Enterobacter cloacae and Staphylococcus epidermidis, respectively. Kodamaea ohmeri was repeatedly isolated from blood cultures and its identity was determined by phenotypic characteristics and sequencing of the ITS and D1/D2 regions of rDNA. The neonate was successfully treated with amphotericin B. The published cases of K. ohmeri fungemia reported in pediatric patients are reviewed highlighting its increasing importance as a bloodstream pathogen.
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Optimization of the thermoelectric figure of merit in the conducting polymer poly(3,4-ethylenedioxythiophene).
Nat Mater
PUBLISHED: 03-23-2011
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Thermoelectric generators (TEGs) transform a heat flow into electricity. Thermoelectric materials are being investigated for electricity production from waste heat (co-generation) and natural heat sources. For temperatures below 200 °C, the best commercially available inorganic semiconductors are bismuth telluride (Bi(2)Te(3))-based alloys, which possess a figure of merit ZT close to one. Most of the recently discovered thermoelectric materials with ZT>2 exhibit one common property, namely their low lattice thermal conductivities. Nevertheless, a high ZT value is not enough to create a viable technology platform for energy harvesting. To generate electricity from large volumes of warm fluids, heat exchangers must be functionalized with TEGs. This requires thermoelectric materials that are readily synthesized, air stable, environmentally friendly and solution processable to create patterns on large areas. Here we show that conducting polymers might be capable of meeting these demands. The accurate control of the oxidation level in poly(3,4-ethylenedioxythiophene) (PEDOT) combined with its low intrinsic thermal conductivity (?=0.37 W m(-1) K(-1)) yields a ZT=0.25 at room temperature that approaches the values required for efficient devices.
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A comparison of the antifungal activity of herbal toothpastes against other brands of toothpastes on clinical isolates of Candida albicans and Candida dubliniensis.
Med Princ Pract
PUBLISHED: 01-20-2011
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To evaluate the anti-Candida activity on Candida albicans and Candida dubliniensis species of 2 herbal and 7 other brands of toothpastes commonly used in Kuwait.
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Coverage and causes of missed Haemophilus influenzae type B vaccination in urban and rural areas of Peshawar.
J Ayub Med Coll Abbottabad
PUBLISHED: 01-01-2011
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Haemophilus influenza type b (Hib) is a major cause of morbidity and mortality in Pakistan. Hib vaccine was introduced in 2009 in EPI programme. The purpose of this study was to find out the coverage and factors associated with non-immunization of Hib in urban and rural areas of Peshawar.
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Modification of an expression vector for efficient recombinant production and purification of mitogillin of Aspergillus fumigatus expressed in Escherichia coli.
Protein Expr. Purif.
PUBLISHED: 08-18-2010
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The diagnostic potential of secretory proteins of Aspergillus fumigatus is limited by their availability in pure form. We have constructed a vector (pGES-PH-1) to express genes encoding secretory proteins of A. fumigatus as fusion proteins with glutathione S-transferase (GST) in Escherichia coli. The mitogillin, a secretary protein of A. fumigatus, was expressed and purified to homogeneity by using pGES-PH-1. Mitogillin gene was PCR amplified from A. fumigatus DNA, cloned in pGES-PH-1 and expressed in E. coli as fusion protein with GST at N-terminal and 6xHis tag at C-terminal end. Pure mitogillin was obtained by purification on glutathione-Sepharose, cleavage of column-bound fusion protein by PreScission protease and by further purification on Ni-NTA-agarose. Polyclonal anti-mitogillin antibodies were raised in rabbits and were used to study its secretion during in vitro growth of A. fumigatus. The mitogillin was detectable in culture filtrate after 24 h of A. fumigatus growth and thereafter its amount increased progressively until 96 h in both, Sabouraud dextrose broth and potato dextrose broth. However, the secretion of mitogillin in culture medium was slightly delayed when A. fumigatus was grown in a minimal medium as mitogillin was detected only after 36 h of growth. Our results demonstrate the utility of the newly constructed expression vector with two affinity tags and PreScission protease cleavage site for high-level expression and efficient purification of a recombinant A. fumigatus secretory protein expressed in E. coli, which could be used for further studies.
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Coverage and factors associated with tetanus toxoid vaccination among married women of reproductive age: a cross sectional study in Peshawar.
J Ayub Med Coll Abbottabad
PUBLISHED: 07-01-2010
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Pakistan has one of the highest maternal mortality rates in the world, with widely prevalent maternal and neonatal tetanus. The purpose of this study was to estimate the coverage and determine the factors associated with tetanus toxoid vaccination status among females of reproductive age in Peshawar.
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Levels of (1?3)-?-D-glucan, Candida mannan and Candida DNA in serum samples of pediatric cancer patients colonized with Candida species.
BMC Infect. Dis.
PUBLISHED: 01-20-2010
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Surveillance cultures may be helpful in identifying patients at increased risk of developing invasive candidiasis. However, only scant information exists on the effect of Candida colonization on serum levels of diagnostic biomarkers. This prospective surveillance study determined the extent of Candida colonization among pediatric cancer patients and its possible impact on serum levels of (1-3)-?-D-glucan (BDG), Candida mannan and Candida DNA.
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Prevalence of Candida dubliniensis among cancer patients in Kuwait: a 5-year retrospective study.
Mycoses
PUBLISHED: 12-11-2009
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Despite close genetic and phenotypic relationship of Candida dubliniensis with Candida albicans, its role in human disease is mostly restricted to oral colonisation, particularly among HIV-infected patients. The prevalence of C. dubliniensis in association with other disease conditions has been infrequently reported. In this study, we present data on the prevalence of C. dubliniensis among yeast species isolated from cancer patients over a 5-year period. A total of 1445 yeast isolates recovered from respiratory specimens, blood, urine and oral swabs were analysed. Candida dubliniensis isolates were provisionally identified by phenotypic methods and their identity was further confirmed by species-specific amplification and/or sequencing of internally transcribed spacer region of rDNA. Antifungal susceptibility for fluconazole was determined by Etest. The number of isolates identified as C. dubliniensis, C. albicans and other yeast species were 71 (4.9%), 862 (59.6%) and 512 (35%) respectively. All the C. dubliniensis isolates originated from respiratory (5.9%) or oral (3.2%) specimens with an overall prevalence of 4.9%, and were found to be susceptible to fluconazole. The isolation of C. dubliniensis from respiratory or oral specimens and not from blood or urine specimens suggests that this species has preference to colonise these sites of human body.
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Development of a nested PCR assay for the detection of Fusarium solani DNA and its evaluation in the diagnosis of invasive fusariosis using an experimental mouse model.
Mycoses
PUBLISHED: 12-09-2009
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Fusarium infections are increasingly being encountered in immunocompromised patients. Fusarium solani accounts for nearly half of these infections. A specific nested PCR (nPCR) assay has been developed by using DNA isolated from several Fusarium species and other common fungi. Furthermore, DNA samples isolated from bronchoalveolar lavage (BAL) and serum samples from mice infected intravenously with F. solani conidia and sacrificed on every third day post infection were used for the evaluation of the established nPCR protocol. The lung homogenate, BAL and blood from infected animals were also cultured. The nPCR assay was specific for F. solani and detected 450 fg of DNA corresponding roughly to 11 F. solani cells. Cultures of lung homogenate of infected animals up to day 16 yielded F. solani with decreasing fungal load and were negative thereafter. The nPCR positivity in BAL was 100% concordant with lung tissue culture results. Although detection of F. solani DNA in serum was less sensitive than in BAL, it remained positive for longer duration. Our data from an experimental mouse model show that detection of DNA in BAL and to a lesser extent in serum by nPCR offers a sensitive and specific diagnostic approach to invasive F. solani infection.
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Cryptococcus randhawai sp. nov., a novel anamorphic basidiomycetous yeast isolated from tree trunk hollow of Ficus religiosa (peepal tree) from New Delhi, India.
Antonie Van Leeuwenhoek
PUBLISHED: 09-16-2009
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A novel anamorphic Cryptococcus species is described, which was isolated in New Delhi (India) from decaying wood of a tree trunk hollow of Ficus religiosa. On the basis of sequence analysis of the D1/D2 domains of the 26S rRNA gene and the internally transcribed spacer (ITS)-1 and ITS-2 region sequences, the isolate belonged to the Cryptococcus albidus cluster (Filobasidiales, Tremellomycetes) and was closely related to Cryptococcus saitoi, Cryptococcus cerealis and Cryptococcus friedmannii with 98% sequence identity. Phenotypically, the species differed from C. saitoi with respect to growth temperature (up to 37degrees C), presence of a thin capsule, ability to grow in the absence of vitamins, and inability to assimilate citrate and ethylamine. With respect to C. friedmannii, it differed in growth temperature, ability to assimilate lactose, raffinose, L: -rhamnose, myo-inositol, and inability to utilize citrate. Furthermore, our isolate also differed from C. cerealis in growth temperature, presence of capsule and inability to assimilate L: -sorbose. In view of the above phenotypic differences and unique rDNA sequences, we consider that our isolate represents a new species of Cryptococcus, and therefore, a new species, Cryptococcus randhawai is proposed for this taxon. The type strain J11/2002 has been deposited in the culture collection of the Centraalbureau voor Schimmelcultures (CBS10160) and CABI Biosciences (IMI 393306).
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Protein quantification across hundreds of experimental conditions.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 08-26-2009
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Quantitative studies of protein abundance rarely span more than a small number of experimental conditions and replicates. In contrast, quantitative studies of transcript abundance often span hundreds of experimental conditions and replicates. This situation exists, in part, because extracting quantitative data from large proteomics datasets is significantly more difficult than reading quantitative data from a gene expression microarray. To address this problem, we introduce two algorithmic advances in the processing of quantitative proteomics data. First, we use space-partitioning data structures to handle the large size of these datasets. Second, we introduce techniques that combine graph-theoretic algorithms with space-partitioning data structures to collect relative protein abundance data across hundreds of experimental conditions and replicates. We validate these algorithmic techniques by analyzing several datasets and computing both internal and external measures of quantification accuracy. We demonstrate the scalability of these techniques by applying them to a large dataset that comprises a total of 472 experimental conditions and replicates.
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Measuring differential gene expression by short read sequencing: quantitative comparison to 2-channel gene expression microarrays.
BMC Genomics
PUBLISHED: 05-12-2009
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High-throughput cDNA synthesis and sequencing of poly(A)-enriched RNA is rapidly emerging as a technology competing to replace microarrays as a quantitative platform for measuring gene expression.
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Rapid molecular differentiation and genotypic heterogeneity among Candida parapsilosis and Candida orthopsilosis strains isolated from clinical specimens in Kuwait.
J. Med. Microbiol.
PUBLISHED: 05-12-2009
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Recent molecular studies have led to the recognition of three distinct species within the Candida parapsilosis complex, namely Candida parapsilosis, Candida orthopsilosis and Candida metapsilosis. As currently available yeast identification systems fail to differentiate these species, there is a paucity of information on their occurrence in different geographical regions. This study describes a simple PCR-based protocol for rapid discrimination among C. parapsilosis, C. orthopsilosis and C. metapsilosis strains by using primers derived from unique sequences within the internally transcribed spacer 1 (ITS1)-5.8 rRNA-ITS2 region. Retrospective analysis of 114 C. parapsilosis-complex isolates recovered from clinical specimens in Kuwait identified 109 as C. parapsilosis, five as C. orthopsilosis and none as C. metapsilosis. The results were further validated by PCR-RFLP patterns of the secondary alcohol dehydrogenase gene fragment. DNA sequencing of the ITS region and the D1/D2 regions of the 28S rRNA gene confirmed the species-specific identification of all five C. orthopsilosis strains. The amplicon length of the intergenic spacer between the 28S and 5S rRNA genes (IGS1) was also species-specific, and PCR-RFLP analyses of the IGS1 region identified two distinct genotypes among the five C. orthopsilosis strains, which corresponded with the ITS region sequence data. The three bloodstream C. orthopsilosis strains were confined to a single genotype. Among 81 randomly selected C. parapsilosis strains, two genotypes were detected by IGS1 region analyses, indicating limited genotypic heterogeneity among C. parapsilosis sensu stricto strains. As far as is known, this is the first report on the identification of C. orthopsilosis from a bloodstream infection in the Arabian Gulf region.
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A practical algorithm for finding maximal exact matches in large sequence datasets using sparse suffix arrays.
Bioinformatics
PUBLISHED: 04-23-2009
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High-throughput sequencing technologies place ever increasing demands on existing algorithms for sequence analysis. Algorithms for computing maximal exact matches (MEMs) between sequences appear in two contexts where high-throughput sequencing will vastly increase the volume of sequence data: (i) seeding alignments of high-throughput reads for genome assembly and (ii) designating anchor points for genome-genome comparisons.
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Curcumin prevents diabetes-associated abnormalities in the kidneys by inhibiting p300 and nuclear factor-kappaB.
Nutrition
PUBLISHED: 03-05-2009
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Diabetic nephropathy is a debilitating disease that leads to end-stage renal failure in the Western world. Hyperglycemia is the initiating factor in several chronic diabetic complications which mediates increased oxidative stress and eventually the increased production of vasoactive factors and extracellular matrix proteins. We hypothesized that curcumin, a potent antioxidant, might be beneficial in preventing the development of diabetic nephropathy because this compound has been shown to inhibit p300, a histone acetyltransferase that plays a role in regulating gene expression through its interaction with the transcription factor nuclear factor-kappaB.
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Mucor circinelloides as a cause of invasive maxillofacial zygomycosis: an emerging dimorphic pathogen with reduced susceptibility to posaconazole.
J. Clin. Microbiol.
PUBLISHED: 01-26-2009
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A case of maxillofacial zygomycosis caused by Mucor circinelloides, identified by phenotypic and molecular methods and treated successfully with liposomal amphotericin B (AmBisome) and surgical debridement, is described. The isolate was resistant to posaconazole. This report underscores the importance of prior susceptibility testing of zygomycetes to guide therapy with the most effective antifungal agent for an improved prognosis.
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Effects of metformin-diet intervention before and throughout pregnancy on obstetric and neonatal outcomes in patients with polycystic ovary syndrome.
Curr Med Res Opin
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Prospectively assess whether metformin/diet pre-conception and throughout pregnancy would safely reduce first trimester miscarriage and improve pregnancy outcomes in women with polycystic ovary syndrome (PCOS). Research design and methods: In 76 PCOS women, first pregnancy miscarriage and live birth were compared before and on metformin/diet, started 6.8 months (median) before conception, continued throughout pregnancy. On metformin 2-2.55?g/day, low glycemic index diet, first pregnancy outcomes in PCOS were compared with 156 community obstetric practice women (controls).
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Regulation of vascular endothelial growth factor expression by extra domain B segment of fibronectin in endothelial cells.
Invest. Ophthalmol. Vis. Sci.
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Diabetic retinopathy entails proliferation of vascular endothelial cells (ECs) and unregulated angiogenesis. We have previously shown that ECs increase the expression of an embryonic variant of fibronectin (FN), called extra domain-B FN (ED-B FN) in response to high glucose. We also showed that ED-B FN regulates EC tube morphogenesis, possibly through vascular endothelial growth factor (VEGF). In the present study, we have attempted to decipher the mechanisms by which ED-B FN may modulate EC phenotype.
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Titrating lovaza from 4 to 8 to 12 grams/day in patients with primary hypertriglyceridemia who had triglyceride levels >500?mg/dl despite conventional triglyceride lowering therapy.
Lipids Health Dis
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Omega-3 fatty acids are important in treatment of severe primary hypertriglyceridemia (HTG). In 15 patients with severe primary HTG (TG >500?mg/dl despite conventional TG lowering therapy), we assessed efficacy-safety of sequential monthly treatment with Lovaza, 4 to 8 to 12?g/day.
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Elevated IGF2 prevents leptin induction and terminal adipocyte differentiation in hemangioma stem cells.
Exp. Mol. Pathol.
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Infantile hemangioma is a benign vascular tumor that exhibits a unique yet predictable lifecycle of rapid proliferation followed by spontaneous regression. Recent studies have identified that insulin-like growth factor-2 (IGF2), a fetal mitogen, is highly expressed during the proliferative phase of hemangioma growth. Since hemangiomas arise from CD133+ stem cells, high levels of IGF2 may regulate the activity of the stem cells and therefore, hemangioma growth. The aim of this study was to understand the functional significance of elevated IGF2 in hemangiomas. We show that IGF2 localizes to the CD133+ cells in hemangioma specimens. We, therefore, hypothesized that IGF2 may be regulating the plasticity of hemangioma stem cells. To test our hypothesis, we used CD133-selected cells from hemangiomas to knockdown the expression of IGF2. We found that IGF2 is a mitogen for hemangioma stem cells and prevents leptin induction and full terminal differentiation of hemangioma stem cells into adipocytes. We also show that IGF2 does not alter the initial commitment phase. These findings implicate an important role of IGF2 in expanding hemangioma stem cells and preventing terminal adipocyte differentiation.
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Hemangioblastoma stromal cells show committed stem cell phenotype.
Can J Neurol Sci
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Hemangioblastomas are benign vascular tumors of the central nervous system that occur sporadically or in association with von Hippel-Lindau disease. These tumors are characteristically composed of a dense capillary network with intervening stromal/interstitial cells. To date, the histogenesis of hemangioblastoma remains unclear. We hypothesize that hemangioblastomas arise from a defective mesodermal stem cell, which gives rise to the atypical vasculature.
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Comparing the effects of salts of diclofenac and alminoprofen with aspirin on serum electrolytes, creatinine and urea levels in rabbits.
Pak J Pharm Sci
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The effects of diclofenac sodium, diclofenac potassium, alminoprofen and aspirin on serum electrolytes (serum Na(+) and K(+)), urea and creatinine were compared in rabbits in acute and chronic phases of treatment. The data suggested that all the four drugs markedly increased the serum electrolytes, urea and creatinine levels in both post-treatment phases. In conclusion, present study does not present any advantage of diclofenac sodium over diclofenac potassium at electrolyte levels on short and long term treatment. Nevertheless, current data support the evidence of renal function impairment by all the four drug therapies used in the present study, which is generally caused by NSAIDS.
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Thrombophilia and retinal vascular occlusion.
Clin Ophthalmol
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The purpose of this research was to assess associations of thrombophilia with central retinal vein occlusion (CRVO), central retinal artery occlusion (CRAO), and amaurosis fugax (AF); to evaluate outcomes of normalizing high homocysteine; and to study CRVO, CRAO, and AF developing in estrogens/estrogen agonists in women subsequently shown to have thrombophilia.
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Quantitative measurement of allele-specific protein expression in a diploid yeast hybrid by LC-MS.
Mol. Syst. Biol.
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Understanding the genetic basis of gene regulatory variation is a key goal of evolutionary and medical genetics. Regulatory variation can act in an allele-specific manner (cis-acting) or it can affect both alleles of a gene (trans-acting). Differential allele-specific expression (ASE), in which the expression of one allele differs from another in a diploid, implies the presence of cis-acting regulatory variation. While microarrays and high-throughput sequencing have enabled genome-wide measurements of transcriptional ASE, methods for measurement of protein ASE (pASE) have lagged far behind. We describe a flexible, accurate, and scalable strategy for measurement of pASE by liquid chromatography-coupled mass spectrometry (LC-MS). We apply this approach to a hybrid between the yeast species Saccharomyces cerevisiae and Saccharomyces bayanus. Our results provide the first analysis of the relative contribution of cis-acting and trans-acting regulatory differences to protein expression divergence between yeast species.
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Cataract: trends in surgical procedures and visual outcomes; a study in a tertiary care hospital.
J Pak Med Assoc
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To determine the current procedures in practice and visual outcome following a cataract surgery.
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Unique responses of stem cell-derived vascular endothelial and mesenchymal cells to high levels of glucose.
PLoS ONE
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Diabetes leads to complications in selected organ systems, and vascular endothelial cell (EC) dysfunction and loss is the key initiating and perpetuating step in the development of these complications. Experimental and clinical studies have shown that hyperglycemia leads to EC dysfunction in diabetes. Vascular stem cells that give rise to endothelial progenitor cells (EPCs) and mesenchymal progenitor cells (MPCs) represent an attractive target for cell therapy for diabetic patients. Whether these vascular stem/progenitor cells succumb to the adverse effects of high glucose remains unknown. We sought to determine whether adult vascular stem/progenitor cells display cellular activation and dysfunction upon exposure to high levels of glucose as seen in diabetic complications. Mononuclear cell fraction was prepared from adult blood and bone marrow. EPCs and MPCs were derived, characterized, and exposed to either normal glucose (5 mmol/L) or high glucose levels (25 mmol/L). We then assayed for cell activity and molecular changes following both acute and chronic exposure to high glucose. Our results show that high levels of glucose do not alter the derivation of either EPCs or MPCs. The adult blood-derived EPCs were also resistant to the effects of glucose in terms of growth. Acute exposure to high glucose levels increased caspase-3 activity in EPCs (1.4x increase) and mature ECs (2.3x increase). Interestingly, MPCs showed a transient reduction in growth upon glucose challenge. Our results also show that glucose skews the differentiation of MPCs towards the adipocyte lineage while suppressing other mesenchymal lineages. In summary, our studies show that EPCs are resistant to the effects of high levels of glucose, even following chronic exposure. The findings further show that hyperglycemia may have detrimental effects on the MPCs, causing reduced growth and altering the differentiation potential.
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The role of the factor V leiden mutation in osteonecrosis of the hip.
Clin. Appl. Thromb. Hemost.
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We examined the hypothesis that the factor V Leiden (FVL) and G20101A prothrombin gene mutations are commonly associated with hip osteonecrosis. We prospectively evaluated 244 consecutively referred adults with osteonecrosis (ON), 161 idiopathic and 83 secondary. Cases (n = 244) did not differ from 104 normal controls by race. Of the 244 patients, 23 (9.4%) were FVL heterozygotes versus 2 of 104 controls (1.9%), P = .013, risk ratio (RR) = 4.90, 95% confidence interval (CI) 1.18 to 20.4. Of the 161 patients with idiopathic ON, 15 (9.3%) were FVL heterozygotes versus 2 of 104 normal controls (1.9%), P = .017, RR = 4.84, 95% CI 1.13 to 20.8. Of the 83 patients with secondary ON, 8 (9.6%) FVL heterozygotes versus 2 of 104 normal controls (1.9%), P = .024, RR = 5.01, 95% CI 1.09 to 23.0. Prothrombin gene heterozygosity in normal controls (2.9%) did not differ from ON cases (3.4%), P = 1.0. The thrombophilic FVL mutation is commonly associated with and may be pathoetiologic for hip osteonecrosis.
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Global secretome analysis identifies novel mediators of bone metastasis.
Cell Res.
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Bone is the one of the most common sites of distant metastasis of solid tumors. Secreted proteins are known to influence pathological interactions between metastatic cancer cells and the bone stroma. To comprehensively profile secreted proteins associated with bone metastasis, we used quantitative and non-quantitative mass spectrometry to globally analyze the secretomes of nine cell lines of varying bone metastatic ability from multiple species and cancer types. By comparing the secretomes of parental cells and their bone metastatic derivatives, we identified the secreted proteins that were uniquely associated with bone metastasis in these cell lines. We then incorporated bioinformatic analyses of large clinical metastasis datasets to obtain a list of candidate novel bone metastasis proteins of several functional classes that were strongly associated with both clinical and experimental bone metastasis. Functional validation of selected proteins indicated that in vivo bone metastasis can be promoted by high expression of (1) the salivary cystatins CST1, CST2, and CST4; (2) the plasminogen activators PLAT and PLAU; or (3) the collagen functionality proteins PLOD2 and COL6A1. Overall, our study has uncovered several new secreted mediators of bone metastasis and therefore demonstrated that secretome analysis is a powerful method for identification of novel biomarkers and candidate therapeutic targets.
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BclAF1 restriction factor is neutralized by proteasomal degradation and microRNA repression during human cytomegalovirus infection.
Proc. Natl. Acad. Sci. U.S.A.
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Cell proteins can restrict the replication of viruses. Here, we identify the cellular BclAF1 protein as a human cytomegalovirus restriction factor and describe two independent mechanisms the virus uses to decrease its steady-state levels. Immediately following infection, the viral pp71 and UL35 proteins, which are delivered to cells within virions, direct the proteasomal degradation of BclAF1. Although BclAF1 reaccumulates through the middle stages of infection, it is subsequently down-regulated at late times by miR-UL112-1, a virus-encoded microRNA. In the absence of BclAF1 neutralization, viral gene expression and replication are inhibited. These data identify two temporally and mechanistically distinct functions used by human cytomegalovirus to down-regulate a cellular antiviral protein.
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Evolution of hemangioma endothelium.
Exp. Mol. Pathol.
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Infantile hemangioma is a benign vascular tumor, characterized by a unique life cycle consisting of rapid growth and spontaneous regression. Three distinct phases (proliferating, involuting, and involuted) take place over the course of approximately 5-8 years, with specific cell types defining each separate phase. The origin of the cells comprising hemangiomas has been deliberated over since the late 1800s. We have recently provided experimental evidence that hemangiomas arise from multipotent stem cells. These hemangioma stem cells that give rise to the endothelial cells are also the essential source of adipocytes during hemangioma involution. The molecular mechanisms that regulate the differentiation of the hemangioma stem cells remain unclear. Although recent studies have elucidated a number of signaling pathways underlying hemangioma pathogenesis, many unanswered questions remain. Herein, we review the unique cellular composition of infantile hemangioma, as well as some of the signaling pathways active within hemangioma-genesis. Understanding the mechanisms behind changes in cellular fate throughout the hemangioma growth pattern will not only provide insight into the stem cell population that resides within the tumor, but will help to establish more effective eradicating therapies.
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Vascular stem cells in diabetic complications: evidence for a role in the pathogenesis and the therapeutic promise.
Cardiovasc Diabetol
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Long standing diabetes leads to structural and functional alterations in both the micro- and the macro-vasculature. Vascular endothelial cells (ECs) are the primary target of the hyperglycemia-induced adverse effects. Vascular stem cells that give rise to endothelial progenitor cells (EPCs) and mesenchymal progenitor cells (MPCs) represent an attractive target for cell therapy for diabetic patients. A number of studies have reported EPC dysfunction as a novel participant in the culmination of the diabetic complications. The controversy behind the identity of EPCs and the similarity between these progenitor cells to hematopoietic cells has led to conflicting results. MPCs, on the other hand, have not been examined for a potential role in the pathogenesis of the complications. These multipotent cells, however, do show a therapeutic role. In this article, we summarize the vascular changes that occur in diabetic complications highlighting some of the common features, the key findings that illustrate an important role of vascular stem cells (VSCs) in the pathogenesis of chronic diabetic complications, and provide mechanisms by which these cells can be used for therapy.
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Differential positioning of adherens junctions is associated with initiation of epithelial folding.
Nature
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During tissue morphogenesis, simple epithelial sheets undergo folding to form complex structures. The prevailing model underlying epithelial folding involves cell shape changes driven by myosin-dependent apical constriction. Here we describe an alternative mechanism that requires differential positioning of adherens junctions controlled by modulation of epithelial apical-basal polarity. Using live embryo imaging, we show that before the initiation of dorsal transverse folds during Drosophila gastrulation, adherens junctions shift basally in the initiating cells, but maintain their original subapical positioning in the neighbouring cells. Junctional positioning in the dorsal epithelium depends on the polarity proteins Bazooka and Par-1. In particular, the basal shift that occurs in the initiating cells is associated with a progressive decrease in Par-1 levels. We show that uniform reduction of the activity of Bazooka or Par-1 results in uniform apical or lateral positioning of junctions and in each case dorsal fold initiation is abolished. In addition, an increase in the Bazooka/Par-1 ratio causes formation of ectopic dorsal folds. The basal shift of junctions not only alters the apical shape of the initiating cells, but also forces the lateral membrane of the adjacent cells to bend towards the initiating cells, thereby facilitating tissue deformation. Our data thus establish a direct link between modification of epithelial polarity and initiation of epithelial folding.
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Drosophila Src regulates anisotropic apical surface growth to control epithelial tube size.
Nat. Cell Biol.
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Networks of epithelial and endothelial tubes are essential for the function of organs such as the lung, kidney and vascular system. The sizes and shapes of these tubes are highly regulated to match their individual functions. Defects in tube size can cause debilitating diseases such as polycystic kidney disease and ischaemia. It is therefore critical to understand how tube dimensions are regulated. Here we identify the tyrosine kinase Src as an instructive regulator of epithelial-tube length in the Drosophila tracheal system. Loss-of-function Src42 mutations shorten tracheal tubes, whereas Src42 overexpression elongates them. Surprisingly, Src42 acts distinctly from known tube-size pathways and regulates both the amount of apical surface growth and, with the conserved formin dDaam, the direction of growth. Quantitative three-dimensional image analysis reveals that Src42- and dDaam-mutant tracheal cells expand more in the circumferential than the axial dimension, resulting in tubes that are shorter in length-but larger in diameter-than wild-type tubes. Thus, Src42 and dDaam control tube dimensions by regulating the direction of anisotropic growth, a mechanism that has not previously been described.
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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.

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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.