JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
VER-246608, a novel pan-isoform ATP competitive inhibitor of pyruvate dehydrogenase kinase, disrupts warburg metabolism and induces context-dependent cytostasis in cancer cells.
Oncotarget
PUBLISHED: 09-24-2014
Show Abstract
Hide Abstract
Pyruvate dehydrogenase kinase (PDK) is a pivotal enzyme in cellular energy metabolism that has previously been implicated in cancer through both RNAi based studies and clinical correlations with poor prognosis in several cancer types. Here, we report the discovery of a novel and selective ATP competitive pan-isoform inhibitor of PDK, VER-246608. Consistent with a PDK mediated MOA, VER-246608 increased pyruvate dehydrogenase complex (PDC) activity, oxygen consumption and attenuated glycolytic activity. However, these effects were only observed under D-glucose-depleted conditions and required almost complete ablation of PDC E1? subunit phosphorylation. VER-246608 was weakly anti-proliferative to cancer cells in standard culture media; however, depletion of either serum or combined D-glucose/L-glutamine resulted in enhanced cellular potency. Furthermore, this condition-selective cytostatic effect correlated with reduced intracellular pyruvate levels and an attenuated compensatory response involving deamination of L-alanine. In addition, VER-246608 was found to potentiate the activity of doxorubicin. In contrast, the lipoamide site inhibitor, Nov3r, demonstrated sub-maximal inhibition of PDK activity and no evidence of cellular activity. These studies suggest that PDK inhibition may be effective under the nutrient-depleted conditions found in the tumour microenvironment and that combination treatments should be explored to reveal the full potential of this therapeutic strategy. 
Related JoVE Video
Formal synthesis of kingianin A based upon a novel electrochemically-induced radical cation Diels-Alder reaction.
Chem. Commun. (Camb.)
PUBLISHED: 09-09-2014
Show Abstract
Hide Abstract
The application of electrochemical reactions in natural product synthesis has burgeoned in recent years. We herein report a formal synthesis of the complex and dimeric natural product kingianin A, which employs an electrochemically-mediated radical cation Diels-Alder cycloaddition as the key step.
Related JoVE Video
Squamous cell carcinoma of the suprapubic tract: A rare presentation in patients with chronic indwelling urinary catheters.
Can Urol Assoc J
PUBLISHED: 08-19-2014
Show Abstract
Hide Abstract
Squamous cell carcinoma (SCC) of the bladder is uncommon, but can arise in the setting of long-term bladder catheterization and chronic inflammation. SCC can arise primarily from the suprapubic catheter tract, but fewer than 10 such cases have been reported. We document 2 cases of SCC arising from the suprapubic tract associated with chronic indwelling urinary catheters. SCC must be differentiated from granulomatous conditions, which are quite common in patients with suprapubic catheters.
Related JoVE Video
Decidualization induces a secretome switch in perivascular niche cells of the human endometrium.
Endocrinology
PUBLISHED: 08-13-2014
Show Abstract
Hide Abstract
The endometrial perivascular microenvironment is rich in mesenchymal stem-like cells that express type 1 integral membrane protein Sushi domain containing 2 (SUSD2) but the role of these cells in the decidual transformation of this tissue in pregnancy is unknown. We used an antibody directed against SUSD2 (W5C5) to isolate perivascular (W5C5(+)) and nonperivascular (W5C5(-)) fibroblasts from mid-luteal biopsies. We show that SUSD2 expression, and hence the ratio of W5C5(+):W5C5(-) cells, changes in culture depending on cell-cell contact and activation of the Notch signaling pathway. RNA sequencing revealed that cultures derived from W5C5(+) progenitor cells remain phenotypically distinct by the enrichment of novel and established endometrial perivascular signature genes. In an undifferentiated state, W5C5(+)-derived cells produced lower levels of various chemokines and inflammatory modulators when compared with their W5C5(-) counterparts. This divergence in secretomes was switched and became more pronounced upon decidualization, which transformed perivascular W5C5(+) cells into the dominant source of a range of chemokines and cytokines, including leukemia inhibitory factor and chemokine (C-C motif) ligand 7. Our findings suggest that the decidual response is spatially organized at the embryo-maternal interface with differentiating perivascular cells establishing distinct cytokine and chemokine profiles that could potentially direct trophoblast toward maternal vessels and govern local immune responses in pregnancy.
Related JoVE Video
MosaicSolver: a tool for determining recombinants of viral genomes from pileup data.
Nucleic Acids Res.
PUBLISHED: 08-12-2014
Show Abstract
Hide Abstract
Viral recombination is a key evolutionary mechanism, aiding escape from host immunity, contributing to changes in tropism and possibly assisting transmission across species barriers. The ability to determine whether recombination has occurred and to locate associated specific recombination junctions is thus of major importance in understanding emerging diseases and pathogenesis. This paper describes a method for determining recombinant mosaics (and their proportions) originating from two parent genomes, using high-throughput sequence data. The method involves setting the problem geometrically and the use of appropriately constrained quadratic programming. Recombinants of the honeybee deformed wing virus and the Varroa destructor virus-1 are inferred to illustrate the method from both siRNAs and reads sampling the viral genome population (cDNA library); our results are confirmed experimentally. Matlab software (MosaicSolver) is available.
Related JoVE Video
A virulent strain of deformed wing virus (DWV) of honeybees (Apis mellifera) prevails after Varroa destructor-mediated, or in vitro, transmission.
PLoS Pathog.
PUBLISHED: 06-01-2014
Show Abstract
Hide Abstract
The globally distributed ectoparasite Varroa destructor is a vector for viral pathogens of the Western honeybee (Apis mellifera), in particular the Iflavirus Deformed Wing Virus (DWV). In the absence of Varroa low levels DWV occur, generally causing asymptomatic infections. Conversely, Varroa-infested colonies show markedly elevated virus levels, increased overwintering colony losses, with impairment of pupal development and symptomatic workers. To determine whether changes in the virus population were due Varroa amplifying and introducing virulent virus strains and/or suppressing the host immune responses, we exposed Varroa-naïve larvae to oral and Varroa-transmitted DWV. We monitored virus levels and diversity in developing pupae and associated Varroa, the resulting RNAi response and transcriptome changes in the host. Exposed pupae were stratified by Varroa association (presence/absence) and virus levels (low/high) into three groups. Varroa-free pupae all exhibited low levels of a highly diverse DWV population, with those exposed per os (group NV) exhibiting changes in the population composition. Varroa-associated pupae exhibited either low levels of a diverse DWV population (group VL) or high levels of a near-clonal virulent variant of DWV (group VH). These groups and unexposed controls (C) could be also discriminated by principal component analysis of the transcriptome changes observed, which included several genes involved in development and the immune response. All Varroa tested contained a diverse replicating DWV population implying the virulent variant present in group VH, and predominating in RNA-seq analysis of temporally and geographically separate Varroa-infested colonies, was selected upon transmission from Varroa, a conclusion supported by direct injection of pupae in vitro with mixed virus populations. Identification of a virulent variant of DWV, the role of Varroa in its transmission and the resulting host transcriptome changes furthers our understanding of this important viral pathogen of honeybees.
Related JoVE Video
The effect of physical training on heart rate variability in healthy children: a systematic review with meta-analysis.
Pediatr Exerc Sci
PUBLISHED: 04-10-2014
Show Abstract
Hide Abstract
The positive effects of physical training on heart rate variability (HRV) in healthy adults are widely recognized; however, the responsiveness to training in healthy children has not yet been established. The aim of this study was to determine the influence of physical training on HRV in prepubertal healthy children. Systematic computerized searches were performed from 1950 to 2012 in the following databases: Medline, Embase, Cinahl, Lilacs, Scielo, SportDiscus, ProQuest; Web of Science; PEDro; Academic Search Premier and the Cochrane Library. The key words used were: heart rate variability, autonomic nervous system, exercise training, physical activity, continuous exercise, intermittent exercise, children, prepubescent, adolescents, and healthy. Although the database search initially identified 6,164 studies, after removing duplicates and excluding by title the number was 148, however, only 2 studies were included in this systematic review. The meta-analysis compared the experimental group (n = 29) with the control group (n = 28) for the HRV parameters: RR intervals, SDNN, RMSSD, pNN50, LF (log), HF (log), LF/HF and Total Power (log). The meta-analysis demonstrated similar HRV indices between both the experimental and control groups. In conclusion, the available results from randomized controlled trials do not support the hypothesis that physical training improves HRV in healthy children[AUQ2].
Related JoVE Video
Prolonged (9 h) poikilocapnic hypoxia (12% O2) augments cutaneous thermal hyperaemia in healthy humans.
Exp. Physiol.
PUBLISHED: 04-04-2014
Show Abstract
Hide Abstract
The primary aim of this study was to investigate the effect of systemic poikilocapnic hypoxia on forearm cutaneous thermal hyperaemia. A secondary aim was to examine the relationship between the individual susceptibility to oxygen desaturation and cutaneous vasodilator capacity. Twelve healthy participants (seven male) were exposed to 9 h of normoxia and 12% poikilocapnic hypoxia in a temperature- and humidity-controlled environmental chamber. Skin blood flow was assessed at the ventral forearm using laser Doppler flowmetry combined with rapid local heating. After 6 min at baseline (skin temperature clamped at 33°C), local skin temperature was elevated at a rate of 0.5°C every 5 s up to 42°C to elicit a sensory axon response and then held constant for 30 min to cause a plateau. Skin blood flow was calculated as cutaneous vascular conductance [CVC; in perfusion units/mean arterial blood pressure (APU mmHg(-1))] and expressed in raw format and relative to heating at 44°C in normoxia (%CVC44). During hypoxaemia, vasodilatation was greater during the initial peak (raw, ?0.35 APU mmHg(-1), P = 0.09; %CVC44, ?18%, P = 0.05) and the plateau phase (raw, ?0.55 APU mmHg(-1), P = 0.03; %CVC44, ?26%, P = 0.02). The rate of rise in cutaneous blood flow during the initial peak was significantly greater during poikilocapnic hypoxia (P < 0.01). We observed a negative relationship between oxygen saturation in poikilocapnic hypoxia and the change in baseline (P = 0.06), initial peak (P = 0.01) and plateau phase of thermal hyperaemia (P = 0.01). Prolonged poikilocapnic hypoxia causes robust increases in CVC during both phases of thermal hyperaemia that are dependent on the oxygen saturation of the individual.
Related JoVE Video
Brown and white adipose tissues: intrinsic differences in gene expression and response to cold exposure in mice.
Am. J. Physiol. Endocrinol. Metab.
PUBLISHED: 02-18-2014
Show Abstract
Hide Abstract
Brown adipocytes dissipate energy, whereas white adipocytes are an energy storage site. We explored the plasticity of different white adipose tissue depots in acquiring a brown phenotype by cold exposure. By comparing cold-induced genes in white fat to those enriched in brown compared with white fat, at thermoneutrality we defined a "brite" transcription signature. We identified the genes, pathways, and promoter regulatory motifs associated with "browning," as these represent novel targets for understanding this process. For example, neuregulin 4 was more highly expressed in brown adipose tissue and upregulated in white fat upon cold exposure, and cell studies showed that it is a neurite outgrowth-promoting adipokine, indicative of a role in increasing adipose tissue innervation in response to cold. A cell culture system that allows us to reproduce the differential properties of the discrete adipose depots was developed to study depot-specific differences at an in vitro level. The key transcriptional events underpinning white adipose tissue to brown transition are important, as they represent an attractive proposition to overcome the detrimental effects associated with metabolic disorders, including obesity and type 2 diabetes.
Related JoVE Video
Control of data quality for population-based cancer survival analysis.
Cancer Epidemiol
PUBLISHED: 02-14-2014
Show Abstract
Hide Abstract
Population-based cancer survival is an important measure of the overall effectiveness of cancer care in a population. Population-based cancer registries collect data that enable the estimation of cancer survival. To ensure accurate, consistent and comparable survival estimates, strict control of data quality is required before the survival analyses are carried out. In this paper, we present a basis for data quality control for cancer survival.
Related JoVE Video
Life-history diversity and its importance to population stability and persistence of a migratory fish: steelhead in two large North American watersheds.
J Anim Ecol
PUBLISHED: 02-03-2014
Show Abstract
Hide Abstract
1.Life-history strategies can buffer individuals and populations from environmental variability. For instance, it is possible that asynchronous dynamics among different life-histories can stabilize populations through portfolio effects. 2.Here we examine life-history diversity and its importance to stability for an iconic migratory fish species. In particular, we examined steelhead (Oncorhynchus mykiss), an anadromous and iteroparous salmonid, in two large, relatively pristine, watersheds, the Skeena and Nass, in northwestern British Columbia, Canada. We synthesized life-history information derived from scales collected from adult steelhead (N = 7227) in these watersheds across a decade. 3.These migratory fishes expressed 36 different manifestations of the anadromous life-history strategy, with 16 different combinations of freshwater and marine ages, 7.6% of fish performing multiple spawning migrations, and up to 4 spawning migrations. Furthermore, in the Nass watershed, different life-histories were differently prevalent through time-three different life-histories were the most prevalent in a given year and no life-history ever represented more than 45% of the population. These asynchronous dynamics among life-histories decreased the variability of numerical abundance and biomass of the aggregated population so that it was more than 20% more stable than the stability of the weighted average of specific life-histories, evidence of a substantial portfolio effect. Year of ocean entry was a key driver of dynamics; the median correlation coefficient of abundance of life-histories that entered the ocean the same year was 2.5 times higher than the median pairwise coefficient of life-histories that entered the ocean at different times. Simulations illustrated how different elements of life-history diversity contribute to stability and persistence of populations. 4.This study provides evidence that life-history diversity can dampen fluctuations in population abundances and biomass via portfolio effects. Conserving genetic integrity and habitat diversity in this and other large watersheds can enable a diversity of life-histories that increases stability to environmental variability. This article is protected by copyright. All rights reserved.
Related JoVE Video
Glycosylated yellow laccases of the basidiomycete Stropharia aeruginosa.
Enzyme Microb. Technol.
PUBLISHED: 01-29-2014
Show Abstract
Hide Abstract
Here we describe the identification, purification and characterisation of glycosylated yellow laccase proteins from the basidiomycete fungus Stropharia aeruginosa. Biochemical characterisation of two yellow laccases, Yel1p and Yel3p, show that they are both secreted, monomeric, N-glycosylated proteins of molecular weight around 55kDa with substrate specificities typical of laccases, but lacking the absorption band at 612nm typical of the blue laccase proteins. Low coverage, high throughput 454 transcriptome sequencing in combination with inverse-PCR was used to identify cDNA sequences. One of the cDNA sequences has been assigned to the Yel1p protein on the basis of identity between the translated protein sequence and the peptide data from the purified protein, and the full length gene sequence has been obtained. Biochemical properties, substrate specificities and protein sequence data have been used to discuss the unusual spectroscopic properties of S. aeruginosa proteins in the context of recent theories about the differences between yellow and blue laccases.
Related JoVE Video
Transcriptome and methylome profiling reveals relics of genome dominance in the mesopolyploid Brassica oleracea.
Genome Biol.
PUBLISHED: 01-27-2014
Show Abstract
Hide Abstract
Brassica oleracea is a valuable vegetable species that has contributed to human health and nutrition for hundreds of years and comprises multiple distinct cultivar groups with diverse morphological and phytochemical attributes. In addition to this phenotypic wealth, B. oleracea offers unique insights into polyploid evolution, as it results from multiple ancestral polyploidy events and a final Brassiceae-specific triplication event. Further, B. oleracea represents one of the diploid genomes that formed the economically important allopolyploid oilseed, Brassica napus. A deeper understanding of B. oleracea genome architecture provides a foundation for crop improvement strategies throughout the Brassica genus.
Related JoVE Video
Identification of potent CNS-penetrant thiazolidinones as novel CGRP receptor antagonists.
Bioorg. Med. Chem. Lett.
PUBLISHED: 01-11-2014
Show Abstract
Hide Abstract
Calcitonin gene-related peptide (CGRP) has been implicated in acute migraine pathogenesis. In an effort to identify novel CGRP receptor antagonists for the treatment of migraine, we have discovered thiazolidinone 49, a potent (Ki=30 pM, IC50=1 nM), orally bioavailable, CNS-penetrant CGRP antagonist with good pharmacokinetic properties.
Related JoVE Video
Uterine selection of human embryos at implantation.
Sci Rep
PUBLISHED: 01-08-2014
Show Abstract
Hide Abstract
Human embryos frequently harbor large-scale complex chromosomal errors that impede normal development. Affected embryos may fail to implant although many first breach the endometrial epithelium and embed in the decidualizing stroma before being rejected via mechanisms that are poorly understood. Here we show that developmentally impaired human embryos elicit an endoplasmic stress response in human decidual cells. A stress response was also evident upon in vivo exposure of mouse uteri to culture medium conditioned by low-quality human embryos. By contrast, signals emanating from developmentally competent embryos activated a focused gene network enriched in metabolic enzymes and implantation factors. We further show that trypsin, a serine protease released by pre-implantation embryos, elicits Ca(2+) signaling in endometrial epithelial cells. Competent human embryos triggered short-lived oscillatory Ca(2+) fluxes whereas low-quality embryos caused a heightened and prolonged Ca(2+) response. Thus, distinct positive and negative mechanisms contribute to active selection of human embryos at implantation.
Related JoVE Video
Protection of corneal epithelial stem cells prevents ultraviolet A damage during corneal collagen cross-linking treatment for keratoconus.
Br J Ophthalmol
PUBLISHED: 11-28-2013
Show Abstract
Hide Abstract
Cross-linking of the cornea is usually carried out at a young age as a treatment to manage ectasia. The corneal limbal region contains delicate long-lived stem cells, which could potentially be deleteriously affected by Ultraviolet A (UV-A) radiation. Damage to these stem cells may not demonstrate as a clinical problem for many years subsequent to cross-linking treatment. UV-A radiation is known to have potential mutagenic effects upon mammalian DNA and can result in cancer.
Related JoVE Video
Assessment of Myometrial Transcriptome Changes Associated with Spontaneous Human Labour by High Throughput RNA-seq.
Exp. Physiol.
PUBLISHED: 11-22-2013
Show Abstract
Hide Abstract
The transition of the human uterus from a quiescent to contractile state takes place over a number of weeks. On such biological timescales cellular phenotype is modified by changes in the transcriptome, which in turn, is under the control of the underlying endocrine, paracrine and biophysical processes resulting from the ongoing pregnancy. In this study we characterise the transition of the human myometrial transcriptome at term from not in labour (NIL) to in labour (LAB) using RNA-seq. mRNA was isolated from the myometrium of uterine biopsies from patients at term not in labour (n=5) and at term in spontaneous labour (n=5) without augmentation. 143.6 million separate reads were sequenced achieving a mean of ~13x coverage of the expressed human transcriptome per sample. Principal component analysis indicated that the NIL and LAB transcriptomes could be distinguished as two distinct clusters. A comparison of the NIL and LAB groups utilising 3 different statistical approaches (baySeq, edgeR and DESeq), demonstrated an overlap of 779 differentially expressed genes. A comparison with currently available microarray data indicated only a partial overlap in differentially expressed genes. We conclude that the described RNA-seq data sets represent the first fully annotated catalogue of expressed mRNAs in human myometrium. When considered together, the full expression repertoire and the differentially expressed gene sets should provide an excellent resource for stimulating new hypotheses of physiological function and discovery of novel therapeutic targets.
Related JoVE Video
Making open data work for plant scientists.
J. Exp. Bot.
PUBLISHED: 09-16-2013
Show Abstract
Hide Abstract
Despite the clear demand for open data sharing, its implementation within plant science is still limited. This is, at least in part, because open data-sharing raises several unanswered questions and challenges to current research practices. In this commentary, some of the challenges encountered by plant researchers at the bench when generating, interpreting, and attempting to disseminate their data have been highlighted. The difficulties involved in sharing sequencing, transcriptomics, proteomics, and metabolomics data are reviewed. The benefits and drawbacks of three data-sharing venues currently available to plant scientists are identified and assessed: (i) journal publication; (ii) university repositories; and (iii) community and project-specific databases. It is concluded that community and project-specific databases are the most useful to researchers interested in effective data sharing, since these databases are explicitly created to meet the researchers needs, support extensive curation, and embody a heightened awareness of what it takes to make data reuseable by others. Such bottom-up and community-driven approaches need to be valued by the research community, supported by publishers, and provided with long-term sustainable support by funding bodies and government. At the same time, these databases need to be linked to generic databases where possible, in order to be discoverable to the majority of researchers and thus promote effective and efficient data sharing. As we look forward to a future that embraces open access to data and publications, it is essential that data policies, data curation, data integration, data infrastructure, and data funding are linked together so as to foster data access and research productivity.
Related JoVE Video
BAI3, CDX2 and VIL1: a panel of three antibodies to distinguish small cell from large cell neuroendocrine lung carcinomas.
Histopathology
PUBLISHED: 07-02-2013
Show Abstract
Hide Abstract
Discriminating small-cell lung carcinoma (SCLC) from large-cell neuroendocrine carcinoma (LCNEC) rests on morphological criteria, and reproducibility has been shown to be poor. We aimed to identify immunohistochemical markers to assist this diagnosis.
Related JoVE Video
Fragment screening by weak affinity chromatography: comparison with established techniques for screening against HSP90.
Anal. Chem.
PUBLISHED: 06-27-2013
Show Abstract
Hide Abstract
The increasing use of fragment-based lead discovery (FBLD) in industry as well as in academia creates a high demand for sensitive and reliable methods to detect the binding of fragments to act as starting points in drug discovery programs. Nuclear magnetic resonance (NMR), surface plasmon resonance (SPR), and X-ray crystallography are well-established methods for fragment finding, and thermal shift and fluorescence polarization (FP) assays are used to a lesser extent. Weak affinity chromatography (WAC) was recently introduced as a new technology for fragment screening. The study presented here compares screening of 111 fragments against the ATPase domain of HSP90 by all of these methods, with isothermal titration calorimetry (ITC) used to confirm the most potent hits. The study demonstrates that WAC is comparable to the established methods of ligand-based NMR and SPR as a hit-id method, with hit correlations of 88% and 83%, respectively. The stability of HSP90 WAC columns was also evaluated and found to give 90% reproducibility even after 207 days of storage. A good correlation was obtained between the various technologies, validating WAC as an effective technology for fragment screening.
Related JoVE Video
Multiple copies of eukaryotic translation initiation factors in Brassica rapa facilitate redundancy, enabling diversification through variation in splicing and broad-spectrum virus resistance.
Plant J.
PUBLISHED: 06-05-2013
Show Abstract
Hide Abstract
Recessive strain-specific resistance to a number of plant viruses in the Potyvirus genus has been found to be based on mutations in the eukaryotic translation initiation factor 4E (eIF4E) and its isoform, eIF(iso)4E. We identified three copies of eIF(iso)4E in a number of Brassica rapa lines. Here we report broad-spectrum resistance to the potyvirus Turnip mosaic virus (TuMV) due to a natural mechanism based on the mis-splicing of the eIF(iso)4E allele in some TuMV-resistant B. rapa var. pekinensis lines. Of the splice variants, the most common results in a stop codon in intron 1 and a much truncated, non-functional protein. The existence of multiple copies has enabled redundancy in the host plants translational machinery, resulting in diversification and emergence of the resistance. Deployment of the resistance is complicated by the presence of multiple copies of the gene. Our data suggest that in the B. rapa subspecies trilocularis, TuMV appears to be able to use copies of eIF(iso)4E at two loci. Transformation of different copies of eIF(iso)4E from a resistant B. rapa line into an eIF(iso)4E knockout line of Arabidopsis thaliana proved misleading because it showed that, when expressed ectopically, TuMV could use multiple copies which was not the case in the resistant B. rapa line. The inability of TuMV to access multiple copies of eIF(iso)4E in B. rapa and the broad spectrum of the resistance suggest it may be durable.
Related JoVE Video
MEME-LaB: motif analysis in clusters.
Bioinformatics
PUBLISHED: 05-16-2013
Show Abstract
Hide Abstract
Genome-wide expression analysis can result in large numbers of clusters of co-expressed genes. Although there are tools for ab initio discovery of transcription factor-binding sites, most do not provide a quick and easy way to study large numbers of clusters. To address this, we introduce a web tool called MEME-LaB. The tool wraps MEME (an ab initio motif finder), providing an interface for users to input multiple gene clusters, retrieve promoter sequences, run motif finding and then easily browse and condense the results, facilitating better interpretation of the results from large-scale datasets.
Related JoVE Video
Mutational spectrum of the ZEB1 gene in corneal dystrophies supports a genotype-phenotype correlation.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 04-20-2013
Show Abstract
Hide Abstract
Mutations in ZEB1 have been reported in posterior polymorphous corneal dystrophy (PPCD3; MIM #609141) and Fuchs endothelial corneal dystrophy (FECD6; MIM #613270). Although PPCD and keratoconus are clinically and pathologically distinct, PPCD has been associated with keratoconus, suggesting a common genetic basis. The purpose of our study was to perform mutational screening of the ZEB1 gene in patients affected with keratoconus or PPCD.
Related JoVE Video
Pin1 inhibitors: Pitfalls, progress and cellular pharmacology.
Bioorg. Med. Chem. Lett.
PUBLISHED: 04-12-2013
Show Abstract
Hide Abstract
Compelling data supports the hypothesis that Pin1 inhibitors will be useful for the therapy of cancer: Pin1 deficient mice resist the induction of breast cancers normally evoked by expression of MMTV-driven Ras or Erb2 alleles. While Pin1 poses challenges for drug discovery, several groups have identified potent antagonists by structure based drug design, significant progress has been made designing peptidic inhibitors and a number of natural products have been found that blockade Pin1, notably epigallocatchechin gallate (EGCG), a major flavonoid in green tea. Here we critically discuss the modes of action and likely specificity of these compounds, concluding that a suitable chemical biology tool for probing the function of Pin1 has yet to be found. We conclude by outlining some open questions regarding the target validation of Pin1 and the prospects for identification of improved inhibitors in the future.
Related JoVE Video
Allele-specific siRNA silencing for the common keratin 12 founder mutation in Meesmann epithelial corneal dystrophy.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 03-21-2013
Show Abstract
Hide Abstract
To identify an allele-specific short interfering RNA (siRNA), against the common KRT12 mutation Arg135Thr in Meesmann epithelial corneal dystrophy (MECD) as a personalized approach to treatment.
Related JoVE Video
Three nights of sleep deprivation does not alter thermal strain during exercise in the heat.
Eur. J. Appl. Physiol.
PUBLISHED: 03-19-2013
Show Abstract
Hide Abstract
Individuals exposed to total sleep deprivation may experience an increased risk of impaired thermoregulation and physiological strain during prolonged physical activity in the heat. However, little is known of the impact of more relevant partial sleep deprivation (PSD). This randomized counterbalanced study investigated the effect of PSD on thermal strain during an exercise-heat stress.
Related JoVE Video
The effectiveness of evidence-based treatments for personality disorders when comparing treatment-as-usual and bona fide treatments.
Clin Psychol Rev
PUBLISHED: 03-03-2013
Show Abstract
Hide Abstract
The purpose of Study 1 was to examine the relative efficacy of evidence-based treatments (EBTs) when compared to treatment-as-usual (TAU) for adults diagnosed with a personality disorder (PD). The purpose of Study 2 was to investigate the strength of the differences between bona fide psychotherapeutic treatments for PDs.
Related JoVE Video
A local regulatory network around three NAC transcription factors in stress responses and senescence in Arabidopsis leaves.
Plant J.
PUBLISHED: 02-14-2013
Show Abstract
Hide Abstract
A model is presented describing the gene regulatory network surrounding three similar NAC transcription factors that have roles in Arabidopsis leaf senescence and stress responses. ANAC019, ANAC055 and ANAC072 belong to the same clade of NAC domain genes and have overlapping expression patterns. A combination of promoter DNA/protein interactions identified using yeast 1-hybrid analysis and modelling using gene expression time course data has been applied to predict the regulatory network upstream of these genes. Similarities and divergence in regulation during a variety of stress responses are predicted by different combinations of upstream transcription factors binding and also by the modelling. Mutant analysis with potential upstream genes was used to test and confirm some of the predicted interactions. Gene expression analysis in mutants of ANAC019 and ANAC055 at different times during leaf senescence has revealed a distinctly different role for each of these genes. Yeast 1-hybrid analysis is shown to be a valuable tool that can distinguish clades of binding proteins and be used to test and quantify protein binding to predicted promoter motifs.
Related JoVE Video
Genetic regulation of glucoraphanin accumulation in Beneforté broccoli.
New Phytol.
PUBLISHED: 02-09-2013
Show Abstract
Hide Abstract
· Diets rich in broccoli (Brassica oleracea var italica) have been associated with maintenance of cardiovascular health and reduction in risk of cancer. These health benefits have been attributed to glucoraphanin that specifically accumulates in broccoli. The development of broccoli with enhanced concentrations of glucoraphanin may deliver greater health benefits. · Three high-glucoraphanin F1 broccoli hybrids were developed in independent programmes through genome introgression from the wild species Brassica villosa. Glucoraphanin and other metabolites were quantified in experimental field trials. Global SNP analyses quantified the differential extent of B. villosa introgression · The high-glucoraphanin broccoli hybrids contained 2.5-3 times the glucoraphanin content of standard hybrids due to enhanced sulphate assimilation and modifications in sulphur partitioning between sulphur-containing metabolites. All of the high-glucoraphanin hybrids possessed an introgressed B. villosa segment which contained a B. villosa Myb28 allele. Myb28 expression was increased in all of the high-glucoraphanin hybrids. Two high-glucoraphanin hybrids have been commercialised as Beneforté broccoli. · The study illustrates the translation of research on glucosinolate genetics from Arabidopsis to broccoli, the use of wild Brassica species to develop cultivars with potential consumer benefits, and the development of cultivars with contrasting concentrations of glucoraphanin for use in blinded human intervention studies.
Related JoVE Video
In the wrong place at the wrong time: does cyclin mislocalization drive oncogenic transformation?
Nat. Rev. Cancer
PUBLISHED: 02-07-2013
Show Abstract
Hide Abstract
Cyclin-dependent kinases (CDKs) are regulated by both cyclin abundance and cyclin localization. Increased cyclin expression in cancer was first observed two decades ago, and its role in pathogenesis has been investigated in great depth. This Opinion article focuses on the spatial deregulation of cyclin expression and its potential link to oncogenesis. It describes the contexts in which particular cyclins have been reported to be mislocalized in neoplasia, reviews the mechanisms underlying the dynamic subcellular localization of CDK-cyclin complexes in normal cells, and discusses how these controls can be disrupted in cancer. It also outlines the mechanisms by which cyclin mislocalization might disrupt cell cycle control and interfere with faithful chromosome segregation. Finally, it discusses the extent to which cyclin mislocalization might facilitate tumorigenesis in human cancer.
Related JoVE Video
Staphylococcus aureus activates the NLRP3 inflammasome in human and rat conjunctival goblet cells.
PLoS ONE
PUBLISHED: 01-01-2013
Show Abstract
Hide Abstract
The conjunctiva is a moist mucosal membrane that is constantly exposed to an array of potential pathogens and triggers of inflammation. The NACHT, leucine rich repeat (LRR), and pyrin domain-containing protein 3 (NLRP3) is a Nod-like receptor that can sense pathogens or other triggers, and is highly expressed in wet mucosal membranes. NLRP3 is a member of the multi-protein complex termed the NLRP3 inflammasome that activates the caspase 1 pathway, inducing the secretion of biologically active IL-1?, a major initiator and promoter of inflammation. The purpose of this study was to: (1) determine whether NLRP3 is expressed in the conjunctiva and (2) determine whether goblet cells specifically contribute to innate mediated inflammation via secretion of IL-1?. We report that the receptors known to be involved in the priming and activation of the NLRP3 inflammasome, the purinergic receptors P2X4 and P2X7 and the bacterial Toll-like receptor 2 are present and functional in conjunctival goblet cells. Toxin-containing Staphylococcus aureus (S. aureus), which activates the NLRP3 inflammasome, increased the expression of the inflammasome proteins NLRP3, ASC and pro- and mature caspase 1 in conjunctival goblet cells. The biologically active form of IL-1? was detected in goblet cell culture supernatants in response to S. aureus, which was reduced when the cells were treated with the caspase 1 inhibitor Z-YVAD. We conclude that the NLRP3 inflammasome components are present in conjunctival goblet cells. The NRLP3 inflammasome appears to be activated in conjunctival goblet cells by toxin-containing S. aureus via the caspase 1 pathway to secrete mature IL1-?. Thus goblet cells contribute to the innate immune response in the conjunctiva by activation of the NLRP3 inflammasome.
Related JoVE Video
Metabolic switches and adaptations deduced from the proteomes of Streptomyces coelicolor wild type and phoP mutant grown in batch culture.
Mol. Cell Proteomics
PUBLISHED: 12-06-2011
Show Abstract
Hide Abstract
Bacteria in the genus Streptomyces are soil-dwelling oligotrophs and important producers of secondary metabolites. Previously, we showed that global messenger RNA expression was subject to a series of metabolic and regulatory switches during the lifetime of a fermentor batch culture of Streptomyces coelicolor M145. Here we analyze the proteome from eight time points from the same fermentor culture and, because phosphate availability is an important regulator of secondary metabolite production, compare this to the proteome of a similar time course from an S. coelicolor mutant, INB201 (?phoP), defective in the control of phosphate utilization. The proteomes provide a detailed view of enzymes involved in central carbon and nitrogen metabolism. Trends in protein expression over the time courses were deduced from a protein abundance index, which also revealed the importance of stress pathway proteins in both cultures. As expected, the ?phoP mutant was deficient in expression of PhoP-dependent genes, and several putatively compensatory metabolic and regulatory pathways for phosphate scavenging were detected. Notably there is a succession of switches that coordinately induce the production of enzymes for five different secondary metabolite biosynthesis pathways over the course of the batch cultures.
Related JoVE Video
Development of allele-specific therapeutic siRNA in Meesmann epithelial corneal dystrophy.
PLoS ONE
PUBLISHED: 10-01-2011
Show Abstract
Hide Abstract
Meesmann epithelial corneal dystrophy (MECD) is an inherited eye disorder caused by dominant-negative mutations in either keratins K3 or K12, leading to mechanical fragility of the anterior corneal epithelium, the outermost covering of the eye. Typically, patients suffer from lifelong irritation of the eye and/or photophobia but rarely lose visual acuity; however, some individuals are severely affected, with corneal scarring requiring transplant surgery. At present no treatment exists which addresses the underlying pathology of corneal dystrophy. The aim of this study was to design and assess the efficacy and potency of an allele-specific siRNA approach as a future treatment for MECD.
Related JoVE Video
Independently evolved virulence effectors converge onto hubs in a plant immune system network.
Science
PUBLISHED: 07-30-2011
Show Abstract
Hide Abstract
Plants generate effective responses to infection by recognizing both conserved and variable pathogen-encoded molecules. Pathogens deploy virulence effector proteins into host cells, where they interact physically with host proteins to modulate defense. We generated an interaction network of plant-pathogen effectors from two pathogens spanning the eukaryote-eubacteria divergence, three classes of Arabidopsis immune system proteins, and ~8000 other Arabidopsis proteins. We noted convergence of effectors onto highly interconnected host proteins and indirect, rather than direct, connections between effectors and plant immune receptors. We demonstrated plant immune system functions for 15 of 17 tested host proteins that interact with effectors from both pathogens. Thus, pathogens from different kingdoms deploy independently evolved virulence proteins that interact with a limited set of highly connected cellular hubs to facilitate their diverse life-cycle strategies.
Related JoVE Video
Reflexes from pulmonary arterial baroreceptors in dogs: interaction with carotid sinus baroreceptors.
J. Physiol. (Lond.)
PUBLISHED: 06-20-2011
Show Abstract
Hide Abstract
In contrast to the reflex vasodilatation occurring in response to stimulation of baroreceptors in the aortic arch, carotid sinuses and coronary arteries, stimulation of receptors in the wall of pulmonary arteries results in reflex systemic vasoconstriction. It is rare for interventions to activate only one reflexogenic region, therefore we investigated how these two types of reflexes interact. In anaesthetized dogs connected to cardiopulmonary bypass, reflexogenic areas of the carotid sinuses, aortic arch and coronary arteries and the pulmonary artery were subjected to independently controlled pressures. Systemic perfusion pressure (SPP) measured in the descending aorta (constant flow) provided an index of systemic vascular resistance. In other experiments, sympathetic efferent neural activity was recorded in fibres dissected from the renal nerve (RSNA). Physiological increases in pulmonary arterial pressure (PAP) induced significant increases in SPP (+39.1 ± 10.4 mmHg) and RSNA (+17.6 ± 2.2 impulses s(?1)) whereas increases in carotid sinus pressure (CSP) induced significant decreases in SPP (?42.6 ± 10.8 mmHg) and RSNA (?42.8 ± 18.2 impulses s(?1)) (P < 0.05 for each comparison; paired t test). To examine possible interactions, PAP was changed at different levels of CSP in both studies. With CSP controlled at 124 ± 2 mmHg, the threshold, set point and saturation pressures of the PAP–SPP relationship were higher than those with CSP at 60 ± 1 mmHg; this rightward shift was associated with a significant decrease in the reflex gain. Similarly, increasing CSP produced a rightward shift of the PAP–RSNA relationship, although the effect on reflex gain was inconsistent. Furthermore, the responses to changes in CSP were influenced by setting PAP at different levels; increasing the level of PAP from 5 ± 1 to 33 ± 3 mmHg significantly increased the set point and threshold pressures of the CSP–SPP relationship; the reflex gain was not affected. These results indicate the existence of interaction between pulmonary arterial and carotid sinus baroreceptor reflexes; physiological and pathological states that alter the stimulus to one may alter the reflex responses from the other.
Related JoVE Video
Viscosity of concentrated therapeutic protein compositions.
Adv. Drug Deliv. Rev.
PUBLISHED: 05-19-2011
Show Abstract
Hide Abstract
The use of monoclonal antibodies as therapeutic agents has been increasing steadily over the last decade for the treatment of various conditions. There is often a need to deliver a large dose of the protein, so there is a trend toward developing commercially viable liquid formulations of highly concentrated antibodies. Such concentrated solutions are associated with a number of challenges, including optimization of production processes, plus chemical and physical stability of the final product where solution viscosity becomes a critical quality attribute. Assessment of the rheological characteristics of concentrated compositions is essential as are development strategies to reduce the viscosity. This review covers the state-of-the-art rheology measurement techniques, focusing particularly on concentrated protein solutions. Current understanding of the mechanisms leading to high viscosity and control by formulation parameters is discussed.
Related JoVE Video
Policy implications of first-dollar coverage: a qualitative examination from the payer perspective.
Public Health Rep
PUBLISHED: 05-11-2011
Show Abstract
Hide Abstract
Immunization against potentially life-threatening illnesses for children and adults has proved to be one of the great public health successes of the 20th century and is extremely cost-effective. The Patient Protection and Affordable Care Act includes a number of provisions to increase coverage and access to immunizations for the consumer, including a provision for health plans to cover all Advisory Committee on Immunization Practices-recommended vaccines at first dollar, or without cost sharing. In this study, we examined payers perspectives on first-dollar coverage of vaccines and strategies to improve vaccination rates.
Related JoVE Video
Mathematics of Zernike polynomials: a review.
Clin. Experiment. Ophthalmol.
PUBLISHED: 04-27-2011
Show Abstract
Hide Abstract
Monochromatic aberrations of the eye principally originate from the cornea and the crystalline lens. Aberrometers operate via differing principles but function by either analysing the reflected wavefront from the retina or by analysing an image on the retina. Aberrations may be described as lower order or higher order aberrations with Zernike polynomials being the most commonly employed fitting method. The complex mathematical aspects with regards the Zernike polynomial expansion series are detailed in this review. Refractive surgery has been a key clinical application of aberrometers; however, more recently aberrometers have been used in a range of other areas ophthalmology including corneal diseases, cataract and retinal imaging.
Related JoVE Video
Quality of vision after myopic and hyperopic laser-assisted subepithelial keratectomy.
J Cataract Refract Surg
PUBLISHED: 04-15-2011
Show Abstract
Hide Abstract
To assess quality of vision after laser-assisted subepithelial keratectomy (LASEK).
Related JoVE Video
High-resolution temporal profiling of transcripts during Arabidopsis leaf senescence reveals a distinct chronology of processes and regulation.
Plant Cell
PUBLISHED: 03-29-2011
Show Abstract
Hide Abstract
Leaf senescence is an essential developmental process that impacts dramatically on crop yields and involves altered regulation of thousands of genes and many metabolic and signaling pathways, resulting in major changes in the leaf. The regulation of senescence is complex, and although senescence regulatory genes have been characterized, there is little information on how these function in the global control of the process. We used microarray analysis to obtain a high-resolution time-course profile of gene expression during development of a single leaf over a 3-week period to senescence. A complex experimental design approach and a combination of methods were used to extract high-quality replicated data and to identify differentially expressed genes. The multiple time points enable the use of highly informative clustering to reveal distinct time points at which signaling and metabolic pathways change. Analysis of motif enrichment, as well as comparison of transcription factor (TF) families showing altered expression over the time course, identify clear groups of TFs active at different stages of leaf development and senescence. These data enable connection of metabolic processes, signaling pathways, and specific TF activity, which will underpin the development of network models to elucidate the process of senescence.
Related JoVE Video
Visual and refractive outcomes following myopic laser-assisted subepithelial keratectomy with a flying-spot excimer laser.
J Cataract Refract Surg
PUBLISHED: 03-15-2011
Show Abstract
Hide Abstract
To investigate the visual and refractive outcomes following laser-assisted subepithelial keratectomy (LASEK) surgery with a flying-spot excimer laser.
Related JoVE Video
Merging resource availability with isotope mixing models: the role of neutral interaction assumptions.
PLoS ONE
PUBLISHED: 03-04-2011
Show Abstract
Hide Abstract
Bayesian mixing models have allowed for the inclusion of uncertainty and prior information in the analysis of trophic interactions using stable isotopes. Formulating prior distributions is relatively straightforward when incorporating dietary data. However, the use of data that are related, but not directly proportional, to diet (such as prey availability data) is often problematic because such information is not necessarily predictive of diet, and the information required to build a reliable prior distribution for all prey species is often unavailable. Omitting prey availability data impacts the estimation of a predators diet and introduces the strong assumption of consumer ultrageneralism (where all prey are consumed in equal proportions), particularly when multiple prey have similar isotope values.
Related JoVE Video
Multifocal intraocular lens with a surface-embedded near section: Short-term clinical outcomes.
J Cataract Refract Surg
PUBLISHED: 02-22-2011
Show Abstract
Hide Abstract
To evaluate the visual and refractive outcomes and quality of life after implantation of a multifocal intraocular lens (IOL) with a surface-embedded near section.
Related JoVE Video
Benefits of exercise in rheumatoid arthritis.
J Aging Res
PUBLISHED: 02-13-2011
Show Abstract
Hide Abstract
This paper aims to highlight the importance of exercise in patients with rheumatoid arthritis (RA) and to demonstrate the multitude of beneficial effects that properly designed exercise training has in this population. RA is a chronic, systemic, autoimmune disease characterised by decrements to joint health including joint pain and inflammation, fatigue, increased incidence and progression of cardiovascular disease, and accelerated loss of muscle mass, that is, "rheumatoid cachexia". These factors contribute to functional limitation, disability, comorbidities, and reduced quality of life. Exercise training for RA patients has been shown to be efficacious in reversing cachexia and substantially improving function without exacerbating disease activity and is likely to reduce cardiovascular risk. Thus, all RA patients should be encouraged to include aerobic and resistance exercise training as part of routine care. Understanding the perceptions of RA patients and health professionals to exercise is key to patients initiating and adhering to effective exercise training.
Related JoVE Video
Laser-assisted subepithelial keratectomy retreatment surgery.
J Cataract Refract Surg
PUBLISHED: 01-19-2011
Show Abstract
Hide Abstract
To evaluate the outcomes of laser-assisted subepithelial keratectomy (LASEK) retreatment surgery after prior LASEK surgery.
Related JoVE Video
Subscale assessment of the NEI-RQL-42 questionnaire with Rasch analysis.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 01-01-2011
Show Abstract
Hide Abstract
To explore the psychometric properties of the 13 subscales of the NEI-RQL-42 questionnaire using Rasch analysis.
Related JoVE Video
Effect of tear hyperosmolarity and signs of clinical ocular surface pathology upon conjunctival goblet cell function in the human ocular surface.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 01-01-2011
Show Abstract
Hide Abstract
To investigate the effect of tear hyperosmolarity and signs of clinical ocular surface pathology on conjunctival goblet cell population.
Related JoVE Video
Evaluating antimicrobial efficacy and cost of 3 dressings containing silver versus a novel antimicrobial hydrogel impregnated gauze dressing containing Oakin, an oak extract.
Adv Skin Wound Care
PUBLISHED: 11-19-2010
Show Abstract
Hide Abstract
Antimicrobial wound dressings are becoming more popular and are routinely used in the treatment of chronic and problematic wounds. Despite the ever-growing number and types of these antimicrobial products, many practitioners often do not report significant clinical differences between various common antimicrobial wound dressings despite wide variations in cost. Although these dressings use different active ingredients or different presentations of a particular active ingredient, all attempt to protect the wound from bacterial colonization and promote wound repair. With so many topical antimicrobial dressings to choose from in the clinical setting (many having already fallen into disfavor due to their cytotoxic characteristics) it was of prime interest to determine if there was a substantial difference between some of the more commonly used antimicrobial dressings, with silver versus an antimicrobial wound dressing using Oakin (oak extract [Amerx Health Care Corporation, Clearwater, Florida]) as the active ingredient.
Related JoVE Video
Recombinants between Deformed wing virus and Varroa destructor virus-1 may prevail in Varroa destructor-infested honeybee colonies.
J. Gen. Virol.
PUBLISHED: 10-06-2010
Show Abstract
Hide Abstract
We have used high-throughput Illumina sequencing to identify novel recombinants between Deformed wing virus (DWV) and Varroa destructor virus-1 (VDV-1), which accumulate to higher levels than DWV in both honeybees and Varroa destructor mites. The recombinants, VDV-1(VVD) and VDV-1(DVD), exhibit crossovers between the 5-UTR and the regions encoding the structural (capsid) and non-structural viral proteins. This implies that the genomes are modular and that each region may evolve independently, as demonstrated in human enteroviruses. Individual honeybee pupae were infected with a mixture of observed recombinants and DWV. A strong correlation was observed between VDV-1(DVD) levels in honeybee pupae and associated mites, suggesting that this recombinant, with a DWV-derived 5-UTR and non-structural protein region flanking a VDV-1-derived capsid-encoding region, is better adapted to transmission between V. destructor and honeybees than the parental DWV or a recombinant bearing the VDV-1-derived 5-UTR (VDV-1(VVD)).
Related JoVE Video
Chemical and biological characterisation of a sensor surface for bioprocess monitoring.
Biosens Bioelectron
PUBLISHED: 09-21-2010
Show Abstract
Hide Abstract
This paper describes the step-wise fabrication and characterisation of a multi-layer dual polarization interferometry (DPI) based biosensor utilising Protein G (ProG) as the bio-recognition layer for the detection of a fragment antibody (Fab). The biosensor is capable of monitoring the concentration of Fab product within the extracellular medium of a fed-batch fermentation after leakage from Escherichia coli (E.coli). The activity, stability and functionality of each sensor layer were analysed in situ using DPI, whilst the chemical identity and homogeneity of the chemical layers were assessed ex situ using X-ray photoelectron spectroscopy (XPS) and secondary ion mass spectrometry (SIMS). Two different biotin linkers were found to produce hugely differing surfaces after the capture of NeutrAvidin™ (NA) and biotinylated Protein G (b-ProG). The hydrophilic (PEG)(4)-biotin linker resulted in a surface where the b-ProG layer was deposited and organised above the NA layer producing an active and stable surface, whilst the hydrophobic LC-biotin linker generated a surface where the b-ProG layer was buried within the NA layer leading to variable surfaces and poor binding of the Fab target. The biosensor has a detection limit of 1.7 ?g/ml with a dynamic range covering two orders of magnitude. The sensor can detect the onset of Fab leakage as early as 2h following product induction, with high signal-to-noise ratios and little interference from extracellular components. Leakage of Fab followed a biphasic profile, switching to a more rapid rate 20 h after induction, indicating accelerated product loss and the need for cultivation harvest.
Related JoVE Video
Discovery of cell-active phenyl-imidazole Pin1 inhibitors by structure-guided fragment evolution.
Bioorg. Med. Chem. Lett.
PUBLISHED: 07-28-2010
Show Abstract
Hide Abstract
Pin1 is an emerging oncology target strongly implicated in Ras and ErbB2-mediated tumourigenesis. Pin1 isomerizes bonds linking phospho-serine/threonine moieties to proline enabling it to play a key role in proline-directed kinase signalling. Here we report a novel series of Pin1 inhibitors based on a phenyl imidazole acid core that contains sub-?M inhibitors. Compounds have been identified that block prostate cancer cell growth under conditions where Pin1 is essential.
Related JoVE Video
Hyperopic LASEK treatments with mitomycin C using the SCHWIND AMARIS.
J Refract Surg
PUBLISHED: 06-24-2010
Show Abstract
Hide Abstract
To investigate the outcomes of hyperopic laser epithelial keratomileusis (LASEK) with mitomycin C (MMC) using the SCHWIND AMARIS platform.
Related JoVE Video
The development of an instrument to measure quality of vision: the Quality of Vision (QoV) questionnaire.
Invest. Ophthalmol. Vis. Sci.
PUBLISHED: 05-26-2010
Show Abstract
Hide Abstract
To develop an instrument to measure subjective quality of vision: the Quality of Vision (QoV) questionnaire.
Related JoVE Video
Increasing reports of non-tuberculous mycobacteria in England, Wales and Northern Ireland, 1995-2006.
BMC Public Health
PUBLISHED: 05-20-2010
Show Abstract
Hide Abstract
Non-tuberculous mycobacteria have long been identified as capable of causing human disease and the number at risk, due to immune-suppression, is rising. Several reports have suggested incidence to be increasing, yet routine surveillance-based evidence is lacking. We investigated recent trends in, and the epidemiology of, non-tuberculous mycobacterial infections in England, Wales and Northern Ireland, 1995-2006.
Related JoVE Video
Polymer- and colloid-mediated bioassays, sensors and diagnostics.
Trends Biotechnol.
PUBLISHED: 04-14-2010
Show Abstract
Hide Abstract
Synthetic polymers and colloids are increasingly being exploited in bioassays to help measure gene expression, sequence genomes, monitor metabolic disorders and detect the presence of disease. This can be attributed to their potential to reduce reaction scales, improve throughput, lower costs and improve the sensitivity, selectivity, stability and reproducibility of assays. This review highlights the newest application areas, including some of the strategies employed, as well as major technical challenges and future opportunities. The move away from conventional assay approaches is being driven by a desire to improve our basic understanding of human biology, to diagnose diseases earlier, and to manage healthcare resources more efficiently. These endeavors are important owing to a rising world population and an increasing average life span.
Related JoVE Video
Crystal structure of the ectodomain complex of the CGRP receptor, a class-B GPCR, reveals the site of drug antagonism.
Structure
PUBLISHED: 04-04-2010
Show Abstract
Hide Abstract
Dysregulation of the calcitonin gene-related peptide (CGRP), a potent vasodilator, is directly implicated in the pathogenesis of migraine. CGRP binds to and signals through the CGRP receptor (CGRP-R), a heterodimer containing the calcitonin receptor-like receptor (CLR), a class B GPCR, and RAMP1, a receptor activity-modifying protein. We have solved the crystal structure of the CLR/RAMP1 N-terminal ectodomain heterodimer, revealing how RAMPs bind to and potentially modulate the activities of the CLR GPCR subfamily. We also report the structures of CLR/RAMP1 in complex with the clinical receptor antagonists olcegepant (BIBN4096BS) and telcagepant (MK0974). Both drugs act by blocking access to the peptide-binding cleft at the interface of CLR and RAMP1. These structures illustrate, for the first time, how small molecules bind to and modulate the activity of a class B GPCR, and highlight the challenges of designing potent receptor antagonists for the treatment of migraine and other class B GPCR-related diseases.
Related JoVE Video
Comparison of higher order aberrations after LASIK and LASEK for myopia.
J Refract Surg
PUBLISHED: 03-05-2010
Show Abstract
Hide Abstract
To compare the change in higher order aberrations (HOAs) after LASIK and laser epithelial keratomileusis (LASEK).
Related JoVE Video
Higher order aberrations using the NIDEK OPD-Scan and AMO WaveScan.
J Refract Surg
PUBLISHED: 03-04-2010
Show Abstract
Hide Abstract
To compare higher order aberrations measured with the NIDEK OPD-Scan and AMO WaveScan.
Related JoVE Video
Enhancing data integration with text analysis to find proteins implicated in plant stress response.
J Integr Bioinform
PUBLISHED: 02-19-2010
Show Abstract
Hide Abstract
High throughput genomic studies can identify large numbers of potential candidate genes, which must be interpreted and filtered by investigators to select the best ones for further analysis. Prioritization is generally based on evidence that supports the role of a gene product in the biological process being investigated. The two most important bodies of information providing such evidence are bioinformatics databases and the scientific literature. In this paper we present an extension to the Ondex data integration framework that uses text mining techniques over Medline abstracts as a method for accessing both these bodies of evidence in a consistent way. In an example use case, we apply our method to create a knowledge base of Arabidopsis proteins implicated in plant stress response and use various scoring metrics to identify key protein-stress associations. In conclusion, we show that the additional text mining features are able to highlight proteins using the scientific literature that would not have been seen using data integration alone. Ondex is an open-source software project and can be downloaded, together with the text mining features described here, from www.ondex.org.
Related JoVE Video
Spawning salmon and the phenology of emergence in stream insects.
Proc. Biol. Sci.
PUBLISHED: 02-03-2010
Show Abstract
Hide Abstract
Phenological dynamics are controlled by environmental factors, disturbance regimes and species interactions that alter growth or mortality risk. Ecosystem engineers can be a key source of disturbance, yet their effects on the phenologies of co-occurring organisms are virtually unexplored. We investigated how the abundance of a dominant ecosystem engineer, spawning sockeye salmon (Oncorhynchus nerka), alters the emergence phenology of stream insects. In streams with high densities of salmon, peak insect emergence occurred in early July, immediately prior to salmon spawning. By contrast, peak insect emergence in streams with low densities of salmon was weeks later and more protracted. The emergence of specific taxa was also significantly related to salmon density. A common rearing experiment revealed that differences in emergence timing are maintained in the absence of spawning salmon. We hypothesize that these patterns are probably driven by predictable and severe disturbance from nest-digging salmon driving local adaptation and being a trait filter of insect emergence. Thus, salmon regulate the timing and duration of aquatic insect emergence, a cross-ecosystem flux from streams to riparian systems.
Related JoVE Video
Refolding and characterization of a soluble ectodomain complex of the calcitonin gene-related peptide receptor.
Biochemistry
PUBLISHED: 01-27-2010
Show Abstract
Hide Abstract
The calcitonin gene-related peptide (CGRP) receptor is a heterodimer of two membrane proteins: calcitonin receptor-like receptor (CLR) and receptor activity-modifying protein 1 (RAMP1). CLR is a class B G-protein-coupled receptor (GPCR), possessing a characteristic large amino-terminal extracellular domain (ECD) important for ligand recognition and binding. Dimerization of CLR with RAMP1 provides specificity for CGRP versus related agonists. Here we report the expression, purification, and refolding of a soluble form of the CGRP receptor comprising a heterodimer of the CLR and RAMP1 ECDs. The extracellular protein domains corresponding to residues 23-133 of CLR and residues 26-117 of RAMP1 were shown to be sufficient for formation of a stable, monodisperse complex. The binding affinity of the purified ECD complex for the CGRP peptide was significantly lower than that of the native receptor (IC(50) of 12 microM for the purified ECD complex vs 233 pM for membrane-bound CGRP receptor), indicating that other regions of CLR and/or RAMP1 are important for peptide agonist binding. However, high-affinity binding to known potent and specific nonpeptide antagonists of the CGRP receptor, including olcegepant and telcagepant (K(D) < 0.02 muM), as well as N-terminally truncated peptides and peptide analogues (140 nM to 1.62 microM) was observed.
Related JoVE Video
Metabolic engineering for production of biorenewable fuels and chemicals: contributions of synthetic biology.
J. Biomed. Biotechnol.
PUBLISHED: 01-13-2010
Show Abstract
Hide Abstract
Production of fuels and chemicals through microbial fermentation of plant material is a desirable alternative to petrochemical-based production. Fermentative production of biorenewable fuels and chemicals requires the engineering of biocatalysts that can quickly and efficiently convert sugars to target products at a cost that is competitive with existing petrochemical-based processes. It is also important that biocatalysts be robust to extreme fermentation conditions, biomass-derived inhibitors, and their target products. Traditional metabolic engineering has made great advances in this area, but synthetic biology has contributed and will continue to contribute to this field, particularly with next-generation biofuels. This work reviews the use of metabolic engineering and synthetic biology in biocatalyst engineering for biorenewable fuels and chemicals production, such as ethanol, butanol, acetate, lactate, succinate, alanine, and xylitol. We also examine the existing challenges in this area and discuss strategies for improving biocatalyst tolerance to chemical inhibitors.
Related JoVE Video
The dynamic architecture of the metabolic switch in Streptomyces coelicolor.
BMC Genomics
PUBLISHED: 01-06-2010
Show Abstract
Hide Abstract
During the lifetime of a fermenter culture, the soil bacterium S. coelicolor undergoes a major metabolic switch from exponential growth to antibiotic production. We have studied gene expression patterns during this switch, using a specifically designed Affymetrix genechip and a high-resolution time-series of fermenter-grown samples.
Related JoVE Video
Metabolic evolution of energy-conserving pathways for succinate production in Escherichia coli.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-16-2009
Show Abstract
Hide Abstract
During metabolic evolution to improve succinate production in Escherichia coli strains, significant changes in cellular metabolism were acquired that increased energy efficiency in two respects. The energy-conserving phosphoenolpyruvate (PEP) carboxykinase (pck), which normally functions in the reverse direction (gluconeogenesis; glucose repressed) during the oxidative metabolism of organic acids, evolved to become the major carboxylation pathway for succinate production. Both PCK enzyme activity and gene expression levels increased significantly in two stages because of several mutations during the metabolic evolution process. High-level expression of this enzyme-dominated CO(2) fixation and increased ATP yield (1 ATP per oxaloacetate). In addition, the native PEP-dependent phosphotransferase system for glucose uptake was inactivated by a mutation in ptsI. This glucose transport function was replaced by increased expression of the GalP permease (galP) and glucokinase (glk). Results of deleting individual transport genes confirmed that GalP served as the dominant glucose transporter in evolved strains. Using this alternative transport system would increase the pool of PEP available for redox balance. This change would also increase energy efficiency by eliminating the need to produce additional PEP from pyruvate, a reaction that requires two ATP equivalents. Together, these changes converted the wild-type E. coli fermentation pathway for succinate into a functional equivalent of the native pathway that nature evolved in succinate-producing rumen bacteria.
Related JoVE Video
Cooperation and individuality among man-eating lions.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 11-02-2009
Show Abstract
Hide Abstract
Cooperation is the cornerstone of lion social behavior. In a notorious case, a coalition of two adult male lions from Tsavo, southern Kenya, cooperatively killed dozens of railway workers in 1898. The "man-eaters of Tsavo" have since become the subject of numerous popular accounts, including three Hollywood films. Yet the full extent of the lions man-eating behavior is unknown; estimates range widely from 28 to 135 victims. Here we use stable isotope ratios to quantify increasing dietary specialization on novel prey during a time of food limitation. For one lion, the delta(13)C and delta(15)N values of bone collagen and hair keratin (which reflect dietary inputs over years and months, respectively) reveal isotopic changes that are consistent with a progressive dietary specialization on humans. These findings not only support the hypothesis that prey scarcity drives individual dietary specialization, but also demonstrate that sustained dietary individuality can exist within a cooperative framework. The intensity of human predation (up to 30% reliance during the final months of 1898) is also associated with severe craniodental infirmities, which may have further promoted the inclusion of unconventional prey under perturbed environmental conditions.
Related JoVE Video
Structure-guided design of alpha-amino acid-derived Pin1 inhibitors.
Bioorg. Med. Chem. Lett.
PUBLISHED: 10-21-2009
Show Abstract
Hide Abstract
The peptidyl prolyl cis/trans isomerase Pin1 is a promising molecular target for anti-cancer therapeutics. Here we report the structure-guided evolution of an indole 2-carboxylic acid fragment hit into a series of alpha-benzimidazolyl-substituted amino acids. Examples inhibited Pin1 activity with IC(50) <100nM, but were inactive on cells. Replacement of the benzimidazole ring with a naphthyl group resulted in a 10-50-fold loss in ligand potency, but these examples downregulated biomarkers of Pin1 activity and blocked proliferation of PC3 cells.
Related JoVE Video
Attitudes towards diagnostic tests and therapies for dry eye disease.
Ophthalmic Res.
PUBLISHED: 10-14-2009
Show Abstract
Hide Abstract
The purpose of this study was to survey the attitudes of optometrists and ophthalmologists, located in a number of different countries, towards diagnostic tests and therapies for dry eye disease.
Related JoVE Video
Normal human mammary epithelial cells proliferate rapidly in the presence of elevated levels of the tumor suppressors p53 and p21(WAF1/CIP1).
J. Cell. Sci.
PUBLISHED: 07-28-2009
Show Abstract
Hide Abstract
In normal cells, p53 protein is maintained at low levels, but the levels increase after stress or inappropriate growth signals to coordinate growth arrest or apoptosis. Human mammary epithelial cells (HMECs) are unusual in that they exhibit two phases of growth. The second growth phase, referred to as post-selection, follows a period of temporary growth arrest and is characterized by the absence of p16(INK4a) (also known as CDK4I and p16-INK4a) expression. Previously, we observed that post-selection HMECs have elevated levels of p53. Exogenous p16(INK4a) expression decreased levels of both p53 transcript and protein, and this effect was inhibited by nutlin-3a, indicating that p16(INK4a) can regulate p53 expression by affecting both p53 transcription and Mdm2-dependent degradation of p53. The p53 in post-selection HMECs was wild type and, as expected, increased p53 expression was associated with elevated p21(WAF1/CIP1) and Mdm2 levels; the p53 response to DNA damage seemed normal. Despite elevated levels of wild-type p53 and p21(WAF1/CIP1), post-selection cells grew more rapidly than their pre-selection HMEC precursors. We found that the post-selection HMECs contain a truncated Mdm2 protein (p60), which presumably lacks the p53 ubiquitylation domain. We propose that the increased levels of p53 in post-selection HMECs are due to the presence of an Mdm2 fragment that binds p53 but does not result in its degradation.
Related JoVE Video
Archaeogenetic evidence of ancient nubian barley evolution from six to two-row indicates local adaptation.
PLoS ONE
PUBLISHED: 05-20-2009
Show Abstract
Hide Abstract
Archaeobotanical samples of barley (Hordeum vulgare L.) found at Qasr Ibrim display a two-row phenotype that is unique to the region of archaeological sites upriver of the first cataract of the Nile, characterised by the development of distinctive lateral bracts. The phenotype occurs throughout all strata at Qasr Ibrim, which range in age from 3000 to a few hundred years.
Related JoVE Video

What is Visualize?

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

How does it work?

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

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

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