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Find video protocols related to scientific articles indexed in Pubmed.
Antioxidant and Tyrosinase Inhibitory Effects of Neolignan Glycosides from Crataegus pinnatifida Seeds.
Planta Med.
PUBLISHED: 11-06-2014
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In our efforts to find an inhibitor of melanin formation and develop potential depigmenting agents for skin-protecting cosmetics and medicinal products from natural resources, we focused on the seeds of Crataegus pinnatifida which showed antioxidant and tyrosinase-inhibiting activities. By activity-guided fractionation of an extract of C. pinnatifida seeds, four new neolignan glycosides, pinnatifidaninsides A-D (1-4), along with two known compounds (5-6), were isolated. Their structures were elucidated by spectroscopic analyses, especially 1D, 2D?NMR and CD spectra. The antioxidant and tyrosinase-inhibiting activities of all isolates were assayed. Compound 6 showed good activity against 2,2-diphenyl-1-pikrylhydrazyl, while compounds 1, 2, 5, and 6 exhibited strong 2,2'-azino-bis (3-ethylbenzothiazoline-6-sulphonic acid) free radical scavenging activity, being as effective as, or even more effective than the positive control Trolox. Moreover, compounds 5 and 6 displayed a moderate mushroom tyrosinase inhibitory activity.
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Melatonin attenuates inflammatory response-induced brain edema in early brain injury following a subarachnoid hemorrhage: a possible role for the regulation of pro-inflammatory cytokines.
J. Pineal Res.
PUBLISHED: 09-15-2014
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Melatonin is a strong anti-oxidant that has beneficial effects against early brain injury (EBI) following a subarachnoid hemorrhage (SAH) in rats; protection includes the reduction of both mortality and neurological deficits. The molecular mechanisms underlying these clinical effects in the SAH model have not been clearly identified. This study examined the influence of melatonin on brain edema secondary to disruption of the blood-brain barrier (BBB) and the relationship between these effects and pro-inflammatory cytokines in EBI following SAH using the filament perforation model of SAH in male Sprague-Dawley rats. Melatonin (150 mg/kg) or vehicle was given via an intraperitoneal injection 2 hr after SAH induction. Brain samples were extracted 24 hr after SAH. Melatonin treatment markedly attenuated brain edema secondary to BBB dysfunctions by preventing the disruption of tight junction protein expression (ZO-1, occludin, and claudin-5). Melatonin treatment also repressed cortical levels of pro-inflammatory cytokines (IL-1?, IL-6, and TNF-?), which were increased in EBI 24 hr after SAH. To further identify the mechanism of this protection, we demonstrated that administration of melatonin attenuated matrix metallopeptidase 9 expression/activity and vascular endothelial growth factor expression, which are related to the inflammatory response and BBB disruption in EBI after SAH. Taken together, this report shows that melatonin prevents disruption of tight junction proteins which might play a role in attenuating brain edema secondary to BBB dysfunctions by repressing the inflammatory response in EBI after SAH, possibly associated with regulation of pro-inflammatory cytokines.
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Development of new potato virus X-based vectors for gene over-expression and gene silencing assay.
Virus Res.
PUBLISHED: 04-16-2014
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Multiple plant viruses, including potato virus X (PVX), have been modified as vectors for expressing heterologous genes or silencing endogenous genes in plants. PVX-based vectors facilitate the functional analysis of genes in plant. However, they can only express one protein in a time. In this paper we report the construction of new vectors based on a 35S promoter-driven PVX infectious clone, pCaPVX100. Vector pCaPVX440 contains two additional subgenomic promoters and can be utilized to express two foreign genes at the same time. Plasmid pCaPVX760 is a CP minus vector and can be used to express foreign proteins through the gene substitution strategy. In addition, plasmid pCaPVX100 was engineered into a gene silencing vector (pCaPVX440-LIC) by introducing a ligation independent cloning (LIC) site into the vector. These results indicate that the newly developed PVX vectors are competent for multiple research purposes.
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A new Hermeuptychia (Lepidoptera, Nymphalidae, Satyrinae) is sympatric and synchronic with H. sosybius in southeast US coastal plains, while another new Hermeuptychia species - not hermes - inhabits south Texas and northeast Mexico.
Zookeys
PUBLISHED: 01-01-2014
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Hermeuptychia intricata Grishin, sp. n. is described from the Brazos Bend State Park in Texas, United States, where it flies synchronously with Hermeuptychia sosybius (Fabricius, 1793). The two species differ strongly in both male and female genitalia and exhibit 3.5% difference in the COI barcode sequence of mitochondrial DNA. Setting such significant genitalic and genotypic differences aside, we were not able to find reliable wing pattern characters to tell a difference between the two species. This superficial similarity may explain why H. intricata, only distantly related to H. sosybius, has remained unnoticed until now, despite being widely distributed in the coastal plains from South Carolina to Texas, USA (and possibly to Costa Rica). Obscuring the presence of a cryptic species even further, wing patterns are variable in both butterflies and ventral eyespots vary from large to almost absent. To avoid confusion with the new species, neotype for Papilio sosybius Fabricius, 1793, a common butterfly that occurs across northeast US, is designated from Savannah, Georgia, USA. It secures the universally accepted traditional usage of this name. Furthermore, we find that DNA barcodes of Hermeuptychia specimens from the US, even those from extreme south Texas, are at least 4% different from those of H. hermes (Fabricius, 1775)-type locality Brazil: Rio de Janeiro-and suggest that the name H. hermes should not be used for USA populations, but rather reserved for the South American species. This conclusion is further supported by comparison of male genitalia. However, facies, genitalia and 2.1% different DNA barcodes set Hermeuptychia populations in the lower Rio Grande Valley of Texas apart from H. sosybius. These southern populations, also found in northeastern Mexico, are described here as Hermeuptychia hermybius Grishin, sp. n. (type locality Texas: Cameron County). While being phylogenetically closer to H. sosybius than to any other Hermeuptychia species, H. hermybius can usually be recognized by wing patterns, such as the size of eyespots and the shape of brown lines on hindwing. "Intricate Satyr" and "South Texas Satyr" are proposed as the English names for H. intricata and H. hermybius, respectively.
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M2SG: mapping human disease-related genetic variants to protein sequences and genomic loci.
Bioinformatics
PUBLISHED: 09-03-2013
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Online Mendelian Inheritance in Man (OMIM) is a manually curated compendium of human genetic variants and the corresponding phenotypes, mostly human diseases. Instead of directly documenting the native sequences for gene entries, OMIM links its entries to protein and DNA sequences in other databases. However, because of the existence of gene isoforms and errors in OMIM records, mapping a specific OMIM mutation to its corresponding protein sequence is not trivial. Combining computer programs and extensive manual curation of OMIM full-text descriptions and original literature, we mapped 98% of OMIM amino acid substitutions (AASs) and all SwissProt Variant (SwissVar) disease-related AASs to reference sequences and confidently mapped 99.96% of all AASs to the genomic loci. Based on the results, we developed an online database and interactive web server (M2SG) to (i) retrieve the mapped OMIM and SwissVar variants for a given protein sequence; and (ii) obtain related proteins and mutations for an input disease phenotype. This database will be useful for analyzing sequences, understanding the effect of mutations, identifying important genetic variations and designing experiments on a protein of interest. Availability and implementation: The database and web server are freely available at http://prodata.swmed.edu/M2S/mut2seq.cgi.
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LRIG1 dictates the chemo-sensitivity of temozolomide (TMZ) in U251 glioblastoma cells via down-regulation of EGFR/topoisomerase-2/Bcl-2.
Biochem. Biophys. Res. Commun.
PUBLISHED: 06-28-2013
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In the current study, we aimed to understand the potential role of leucine-rich repeats and immunoglobulin-like domains 1 (LRIG1) in TMZ-resistance of U251 glioma cells. We established TMZ-resistant U251 clones (U251/TMZ cells), which expressed low level of LRIG1, but high levels of epidermal growth factor receptor (EGFR), topoisomerase-2 (Topo-2) and Bcl-2. Depletion of LRIG1 by the targeted RNA interference (RNAi) upregulated EGFR/Topo-2/Bcl-2 in U251 cells, and the cells were resistant to TMZ. Reversely, over-expression of LRIG1 in U251 cells downregulated EGFR/Topo-2/Bcl-2 expressions, and cells were hyper-sensitive to TMZ. Our data suggested EGFR-dependent mammalian target of rapamycin (mTOR) activation was important for Topo-2 and Bcl-2 expressions in U251/TMZ cells. The EGFR inhibitor and the mTOR inhibitor downregulated Topo-2/Bcl-2 expressions, both inhibitors also restored TMZ sensitivity in U251/TMZ cells. Finally, inhibition of Topo-2 or Bcl-2 by targeted RNAi(s) knockdown or by the corresponding inhibitor re-sensitized U251/TMZ cells to TMZ, indicating that both Topo-2 and Bcl-2 were important for TMZ resistance in the resistant U251 cells. Based on these results, we concluded that LRIG1 inhibits EGFR expression and the downstream signaling activation, interferes with Bcl-2/Topo-2 expressions and eventually sensitizes glioma cells to TMZ.
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The comparison between dissociate bone flap cranioplasty and traditional cranioplasty in the treatment of depressed skull fractures.
J Craniofac Surg
PUBLISHED: 03-26-2013
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Depressed skull fractures (DSF) with operation indications should be paid with enough attention because they have several complications and can influence esthetics. The optimal surgical method for DSF remains unclear. We explored the merits of dissociate bone flap cranioplasty.
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Glioblastoma mimicking a cerebral contusion: A case report.
Oncol Lett
PUBLISHED: 03-09-2013
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A 61-year-old male presented with a rare case of glioblastoma mimicking a cerebral contusion subsequent to collapsing. The patient had been medicated for hypertension for seven years and diabetes for eight years prior to hospitalization. Brain computed tomography (CT) revealed a cerebral contusion and intracerebral hemorrhage (ICH) in the left temporal region. The patient was initially administered intravenous drugs to reduce the intracranial pressure following the diagnosis of a cerebral contusion. Serial CT revealed ICH resorption. However, the patient was again admitted due to a headache and vomiting two months later. Magnetic resonance imaging (MRI) demonstrated an enhanced ring-shaped mass around the cyst cavity within the left temporal region, with surrounding edema. The patient underwent cyst puncture drainage in the temporal region. No tumor cells were identified in the cyst fluid and the culture was also negative. The patient was admitted for a headache and vomiting for the third time one month after being discharged. A cyst, tumor and meningoencephalitis were suspected following an MRI scan. The patient was treated with a left temporal craniotomy for a mass resection and biopsy. The histological diagnosis of the biopsy specimen was that of a glioblastoma. Two months later, MRI revealed a recurrence of the glioblastoma. In the present case, a brain tumor should have initially been suspected as the cause of the ICH, despite the history of craniocerebral trauma and hypertension. Early awareness of this potential cause of ICH may facilitate a more prompt diagnosis and treatment.
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miR-92b controls glioma proliferation and invasion through regulating Wnt/beta-catenin signaling via Nemo-like kinase.
Neuro-oncology
PUBLISHED: 02-14-2013
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Nemo-like kinase (NLK) is an evolutionarily conserved protein kinase involved in Wnt/beta-catenin signaling, which has been reported to be associated with gliomagenesis. In the present study, we aimed to identify a concrete mechanism of Wnt/beta-catenin pathway regulation by microRNAs (miRNAs) in glioma.
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Seq2Ref: a web server to facilitate functional interpretation.
BMC Bioinformatics
PUBLISHED: 01-15-2013
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The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines inevitably introduce errors, making the annotations unreliable. Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of reference proteins that have been experimentally characterized or manually curated.
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An automatic method for CASP9 free modeling structure prediction assessment.
Bioinformatics
PUBLISHED: 10-12-2011
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Manual inspection has been applied to and is well accepted for assessing critical assessment of protein structure prediction (CASP) free modeling (FM) category predictions over the years. Such manual assessment requires expertise and significant time investment, yet has the problems of being subjective and unable to differentiate models of similar quality. It is beneficial to incorporate the ideas behind manual inspection to an automatic score system, which could provide objective and reproducible assessment of structure models.
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Folate and vitamin B12 in idiopathic male infertility.
Asian J. Androl.
PUBLISHED: 08-22-2011
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Although methylenetetrahydrofolate reductase, a folate enzyme gene, has been associated with idiopathic male infertility, few studies have examined other folate-related metabolites and genes. We investigated whether idiopathic male infertility is associated with variants in folate, vitamin B(12) (B12) and total homocysteine (tHcy)-related genes and measured these metabolites in blood. We conducted a case-control study that included 153 men with idiopathic infertility and 184 fertile male controls recruited at the Fertility Center and Antenatal Care Center, University Hospital, Malmö and Lund, Sweden. Serum folate, red cell folate (RCF), serum B12, plasma tHcy and semen quality were measured. Subjects were genotyped for 20 common variants in 12 genes related to folate/B12/homocysteine metabolism. Metabolite concentrations and genotype distributions were compared between cases and controls using linear and logistic regression with adjustment for covariates. The phosphatidylethanolamine N-methyltransferase (PEMT) M175V and TCblR rs173665 polymorphisms were significantly associated with infertility (P=0.01 and P=0.009, respectively), but not with semen quality. Among non-users of supplements, infertile men had lower serum folate concentrations than fertile men (12.89 vs. 14.73 nmol l(-1); P=0.02), but there were no significant differences in RCF, B12 or tHcy. Folate, B12 and tHcy concentrations were not correlated with any semen parameters. This study provides little support for low folate or B12 status in the pathogenesis of idiopathic male infertility. Although additional data are needed to confirm these initial findings, our results suggest that PEMT and TCblR, genes involved in choline and B12 metabolism, merit further investigation in idiopathic male infertility.
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The origin of natural tetraploid loach Misgurnus anguillicaudatus (Teleostei: Cobitidae) inferred from meiotic chromosome configurations.
Genetica
PUBLISHED: 05-25-2011
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In the loach, or Oriental weatherfish Misgurnus anguillicaudatus (Teleostei: Cobitidae), diploid (2n = 50) and tetraploid individuals (4n = 100) are often sympatric in central China. The evolutionary mechanism of this tetraploidization was analyzed with the observation of meiotic behavior of chromosomes in both the germinal vesicles of mature oocytes and the primary spermatocytes in diploid and tetraploid loaches. Whereas diploid specimens usually showed 25 bivalents in meiotic cells, tetraploid loaches exhibited 0-6 quadrivalents and 38-50 bivalents in both sexes, with the modal number of quadrivalents as three in females and four in males. In the diploid specimens, the two largest metacentric chromosomes bearing nucleolar organizing regions (NORs) identified by chromomycin A(3) staining and fluorescence in situ hybridization with a 5.8S + 28S rDNA probe formed one bivalent with terminal association. In the tetraploids, four NOR-bearing chromosomes never formed a quadrivalent, but were organized into two terminally-associated bivalents. These findings suggest an autotetraploid origin of the natural tetraploid loach and subsequent rediploidization of whole genome. The latter process, however, seems still in progress as inferred from the concurrence of up-to several quadrivalents and the majority of bivalents.
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[Preliminary comparison on the time-effect rule of pain-relieving in the treatment of moderate dysmenorrhea between acupuncture on single-point and acupuncture on multi-point].
Zhongguo Zhen Jiu
PUBLISHED: 05-03-2011
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To compare the time-effect rule of pain-relieving in moderate dysmenorrhea in the treatment between acupuncture on single-point and acupuncture on multi-point so as to determine the best time of needle retaining on single-point and multi-point as well as provide the reference evidences of acupuncture frequency in the treatment.
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CASP9 target classification.
Proteins
PUBLISHED: 04-11-2011
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The Critical assessment of protein structure prediction round 9 (CASP9) aimed to evaluate predictions for 129 experimentally determined protein structures. To assess tertiary structure predictions, these target structures were divided into domain-based evaluation units that were then classified into two assessment categories: template based modeling (TBM) and template free modeling (FM). CASP9 targets were split into domains of structurally compact evolutionary modules. For the targets with more than one defined domain, the decision to split structures into domains for evaluation was based on server performance. Target domains were categorized based on their evolutionary relatedness to existing templates as well as their difficulty levels indicated by server performance. Those target domains with sequence-related templates and high server prediction performance were classified as TMB, whereas those targets without identifiable templates and low server performance were classified as FM. However, using these generalizations for classification resulted in a blurred boundary between CASP9 assessment categories. Thus, the FM category included those domains without sequence detectable templates (25 target domains) as well as some domains with difficult to detect templates whose predictions were as poor as those without templates (five target domains). Several interesting examples are discussed, including targets with sequence related templates that exhibit unusual structural differences, targets with homologous or analogous structure templates that are not detectable by sequence, and targets with new folds.
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CASP9 assessment of free modeling target predictions.
Proteins
PUBLISHED: 04-11-2011
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We present an overview of the ninth round of Critical Assessment of Protein Structure Prediction (CASP9) "Template free modeling" category (FM). Prediction models were evaluated using a combination of established structural and sequence comparison measures and a novel automated method designed to mimic manual inspection by capturing both global and local structural features. These scores were compared to those assigned manually over a diverse subset of target domains. Scores were combined to compare overall performance of participating groups and to estimate rank significance. Moreover, we discuss a few examples of free modeling targets to highlight the progress and bottlenecks of current prediction methods. Notably, a server prediction model for a single target (T0581) improved significantly over the closest structure template (44% GDT increase). This accomplishment represents the "winner" of the CASP9 FM category. A number of human expert groups submitted slight variations of this model, highlighting a trend for human experts to act as "meta predictors" by correctly selecting among models produced by the top-performing automated servers. The details of evaluation are available at http://prodata.swmed.edu/CASP9/ .
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HangOut: generating clean PSI-BLAST profiles for domains with long insertions.
Bioinformatics
PUBLISHED: 04-22-2010
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Profile-based similarity search is an essential step in structure-function studies of proteins. However, inclusion of non-homologous sequence segments into a profile causes its corruption and results in false positives. Profile corruption is common in multidomain proteins, and single domains with long insertions are a significant source of errors. We developed a procedure (HangOut) that, for a single domain with specified insertion position, cleans erroneously extended PSI-BLAST alignments to generate better profiles.
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[Injection by near infrared diffuse reflectance spectroscopy].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 12-30-2009
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In the present study, a total of 47 levofloxacin hydrochloride injection samples were detected by near infrared (NIR) spectroscopy, and 37 samples were randomly selected to establish the quantitative models by partial least squares (PLS) and artificial neural network (ANN) technology, while other 12 samples were used for prediction. On the one hand, the model was established by PLS, the coefficient of determination (R2) of the prediction is 0.964, and the root mean squared error of prediction (RMSEP) is 0.2428. On the other hand, after the spectrum variables were highly effectively compressed using the wavelet transformation technology, the quantitative analysis model of levofloxacin hydrochloride was established through the ANN technology. The R2 and RMSEP of the model is 0.944 and 0.5722, respectively. In this work, we have a detailed comparison between the two technologies in the progress of two quantitative models and optimizing correlative parameter, and finally we got a satisfied result. The simulation experiment indicated that the above PLS model is more steady and precise than ANN model, which can get hold of a rapid and nondestructive quantitative analysis result of the injection. Thus, the research can provide powerful scientific basis and technical support for further analysis of levofloxacin hydrochloride injection.
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[Analysis of infrared spectroscopy of ginsengs by support vector machine and wavelet transform].
Guang Pu Xue Yu Guang Pu Fen Xi
PUBLISHED: 05-22-2009
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In the present study, 40 samples of ginsengs (20 samples from Jian and 20 samples from Fushun) were surveyed by Fourier transform infrared (IR) spectroscopy. Meanwhile, in order to eliminate the spectral differences from the baseline drifts, the original ginseng spectra were processed using first derivative method. To avoid enhancing the noise resulting from the derivative the spectra were smoothed. This smoothing was done by using the Savitzky-Golay algorithm, a moving window averaging method. Artificial neural network (ANN), support vector machine (SVM) as the new pattern recognition technology, and wavelet transform (WT) were applied. Firstly, the spectrum variables of infrared spectroscopy were compressed through the WT technology before the models were established, in order to reduce the time in establishing models. Then, the identification models of cultivation area of ginsengs were studied comparatively by the use of ANN and SVM methods. The corresponding important parameters of models were also discussed in detail, including the parameters of wavelet compressing and training parameters of ANN and SVM models. The simulation experiment indicated that the ANN model can carry on the distinction among 40 samples of ginsengs from Jilin, and the accuracy rate of identification was 92.5%. The radial basis function (RBF) SVM classifiers and the polynomial SVM classifiers were studied comparatively in this experiment. The best experimental results were obtained using RBF SVM classifier with sigma = 0.6, and the accuracy rate of identification was 97.5%. Finally, compared with ANN approach, SVM algorithm showed its excellent generalization for identification results while the number of samples was smaller. The overall results show that IR spectroscopy combined with SVM and WT technology can be efficiently utilized for rapid and simple identification of the cultivation area of ginsengs, and thus provides the certain technology support and the foundation for further researching ginseng and other IR applications.
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Association between swimming lessons and drowning in childhood: a case-control study.
Arch Pediatr Adolesc Med
PUBLISHED: 03-04-2009
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To estimate the association between swimming lessons and the risk of drowning among children aged 1 to 19 years.
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Large-area unmodified superhydrophobic copper substrate can be prepared by an electroless replacement deposition.
J Colloid Interface Sci
PUBLISHED: 02-28-2009
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Using an electroless replacement deposition method, large-area superhydrophobic metal substrate could be obtained. The superhydrophobic surfaces were prepared via a replacement reaction between copper substrate and HAuCl(4) solution. The roughness of the copper substrate increased much after the replacement reaction. X-ray powder diffraction (XRD) pattern and energy dispersive X-ray (EDX) spectroscopy have proved that gold, CuCl and Cu(2)O formed on the surface of copper substrate after the replacement reaction. The surface showed remarkable superhydrophobic properties with a contact angle higher than 150 degrees without any modification with a self-assembled monolayer (SAM) of long chain thiol or perfluoro molecules.
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Circulating angiogenic factors in gestational proteinuria without hypertension.
Am. J. Obstet. Gynecol.
PUBLISHED: 01-24-2009
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Our goal was to determine whether obstetric outcomes and serum angiogenic factors are altered in women with gestational proteinuria without hypertension.
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MESSA: MEta-Server for protein Sequence Analysis.
BMC Biol.
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Computational sequence analysis, that is, prediction of local sequence properties, homologs, spatial structure and function from the sequence of a protein, offers an efficient way to obtain needed information about proteins under study. Since reliable prediction is usually based on the consensus of many computer programs, meta-severs have been developed to fit such needs. Most meta-servers focus on one aspect of sequence analysis, while others incorporate more information, such as PredictProtein for local sequence feature predictions, SMART for domain architecture and sequence motif annotation, and GeneSilico for secondary and spatial structure prediction. However, as predictions of local sequence properties, three-dimensional structure and function are usually intertwined, it is beneficial to address them together.
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A predicted miR-27a-mediated network identifies a signature of glioma.
Oncol. Rep.
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The dysregulation of physiological microRNA (miRNA) activity has been shown to play an important role in gliomagenesis. In a previous study, using microRNA arrays and glioma tissues found that miR-27a was upregulated, which was also identified in the glioma cell lines and samples by quantitative real-time polymerase chain reaction (qRT-PCR). In this study, in order to explore the potential roles of miR-27a in the progression of glioma, we first utilized text-mining of PubMed abstracts with natural language processing (NLP) to identify 1,168 glioma-related molecules. In addition, miR-27a targets predicted by computational methods were integrated with the results from NLP analysis, followed by Gene Ontology (GO), pathway and network analysis. We identified 33 hub genes by overlap calculation and demonstrated that miR-27a may be involved in the progression of glioma through adherens junction, focal adhesion, the neurotrophin signaling pathway, the MAPK signaling pathway, the transforming growth factor-? (TGF-?) signaling pathway, cytokine-cytokine receptor interactions, the p53 signaling pathway, the apoptotic signaling pathway, as well as others. Our data may provide researchers with a better understanding of the mechanisms of the miR-27a-target network in glioma initiation and progression.
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miR-92a is a critical regulator of the apoptosis pathway in glioblastoma with inverse expression of BCL2L11.
Oncol. Rep.
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Recent studies have revealed that miR-92a is overexpressed in several types of malignancies and provides a protumorigenic effect. Our findings demonstrate that the high expression of miR-92a in human glioma specimens is significantly correlated with low levels of BCL2L11 (Bim) protein and high-grade glioma. Here, we present the first evidence that miR-92a antisense oligonucleotide (AS-miR-92a) provides a tumor suppressive effect via induction of apoptosis in human glioma cells. In addition, we show that Bim is a direct functional target of miR-92a. Introducing Bim cDNA without 3UTR abrogates miR-92a-induced cell survival. Further investigations will focus on the therapeutic use of AS-miR?92a-mediated antitumor effects in glioma.
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Predictive sequence analysis of the Candidatus Liberibacter asiaticus proteome.
PLoS ONE
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Candidatus Liberibacter asiaticus (Ca. L. asiaticus) is a parasitic gram-negative bacterium that is closely associated with Huanglongbing (HLB), a worldwide citrus disease. Given the difficulty in culturing the bacterium and thus in its experimental characterization, computational analyses of the whole Ca. L. asiaticus proteome can provide much needed insights into the mechanisms of the disease and guide the development of treatment strategies. In this study, we applied state-of-the-art sequence analysis tools to every Ca. L. asiaticus protein. Our results are available as a public website at http://prodata.swmed.edu/liberibacter_asiaticus/. In particular, we manually curated the results to predict the subcellular localization, spatial structure and function of all Ca. L. asiaticus proteins (http://prodata.swmed.edu/liberibacter_asiaticus/curated/). This extensive information should facilitate the study of Ca. L. asiaticus proteome function and its relationship to disease. Pilot studies based on the information from our website have revealed several potential virulence factors, discussed herein.
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The ABC transporters in Candidatus Liberibacter asiaticus.
Proteins
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Candidatus Liberibacter asiaticus (Ca. L. asiaticus) is a Gram-negative bacterium and the pathogen of Citrus Greening disease (Huanglongbing, HLB). As a parasitic bacterium, Ca. L. asiaticus harbors ABC transporters that play important roles in exchanging chemical compounds between Ca. L. asiaticus and its host. Here, we analyzed all the ABC transporter-related proteins in Ca. L. asiaticus. We identified 14 ABC transporter systems and predicted their structures and substrate specificities. In-depth sequence and structure analysis including multiple sequence alignment, phylogenetic tree reconstruction, and structure comparison further support their function predictions. Our study shows that this bacterium could use these ABC transporters to import metabolites (amino acids and phosphates) and enzyme cofactors (choline, thiamine, iron, manganese, and zinc), resist to organic solvent, heavy metal, and lipid-like drugs, maintain the composition of the outer membrane (OM), and secrete virulence factors. Although the features of most ABC systems could be deduced from the abundant experimental data on their orthologs, we reported several novel observations within ABC system proteins. Moreover, we identified seven nontransport ABC systems that are likely involved in virulence gene expression regulation, transposon excision regulation, and DNA repair. Our analysis reveals several candidates for further studies to understand and control the disease, including the type I virulence factor secretion system and its substrate that are likely related to Ca. L. asiaticus pathogenicity and the ABC transporter systems responsible for bacterial OM biosynthesis that are good drug targets.
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[The tumorigenicity of immortalized cells differentiated from mouse embryonic stem cells].
Zhonghua Zheng Xing Wai Ke Za Zhi
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To discuss the tumorigenicity of immortalized endothelial cells differentiated from embryonic stem cells.
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What is Visualize?

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

How does it work?

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

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

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