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.
GPKOW is essential for pre-mRNA splicing in vitro and suppresses splicing defect caused by dominant-negative DHX16 mutation in vivo.
Biosci. Rep.
PUBLISHED: 09-18-2014
Show Abstract
Hide Abstract
Human GPKOW protein contains a G-patch domain and two KOW domains, and is a homologue of Arabidopsis MOS2 and Saccharomyces Spp2 protein. GPKOW is found in the human spliceosome, but its role in pre-mRNA splicing remains to be elucidated. In this report, we showed that GPKOW interacted directly with the DHX16/hPRP2 and with RNA. Immuno-depletion of GPKOW from HeLa nuclear extracts resulted in an inactive spliceosome that still bound DHX16. Adding back recombinant GPKOW restored splicing to the depleted extract. In vivo, overexpression of GPKOW partially suppressed the splicing defect observed in dominant-negative DHX16 mutant expressing cells. Mutations at the G-patch domain greatly diminished the GPKOW-DHX16 interaction; however, the mutant was active in splicing and was able to suppress splicing defect. Mutations at the KOW1 domain slightly altered the GPKOW-RNA interaction, but the mutant was less functional in vitro and in vivo. Our results indicated that GPKOW can functionally impact DHX16 but that interaction between the proteins is not required for this activity.
Related JoVE Video
Impacts of different exposure scenarios on transcript abundances in Danio rerio embryos when investigating the toxicological burden of riverine sediments.
PLoS ONE
PUBLISHED: 09-04-2014
Show Abstract
Hide Abstract
Recently, a proof-of-concept study revealed the suitability of transcriptome analyses to obtain and assess changes in the abundance of transcripts in zebrafish (Danio rerio) embryos after exposure to organic sediment extracts. The present study investigated changes in the transcript abundance in zebrafish embryos exposed to whole sediment samples and corresponding organic extracts in order to identify the impact of different exposure pathways on sediment toxicity.
Related JoVE Video
Multi-contrast atherosclerosis characterization (MATCH) of carotid plaque with a single 5-min scan: technical development and clinical feasibility.
J Cardiovasc Magn Reson
PUBLISHED: 07-25-2014
Show Abstract
Hide Abstract
Multi-contrast weighted imaging is a commonly used cardiovascular magnetic resonance (CMR) protocol for characterization of carotid plaque composition. However, this approach is limited in several aspects including low slice resolution, long scan time, image mis-registration, and complex image interpretation. In this work, a 3D CMR technique, named Multi-contrast Atherosclerosis Characterization (MATCH), was developed to mitigate the above limitations.
Related JoVE Video
[Ocuurence of organophosphorus pesticides in animal foods and their diet exposure assessment].
Zhonghua Yu Fang Yi Xue Za Zhi
PUBLISHED: 07-03-2014
Show Abstract
Hide Abstract
To investigate the levels of organophosphorus pesticides (OPPs) in animal foods and to assess the diet exposure risk of OPPs to Chinese population.
Related JoVE Video
Tumor suppressor FOXO3 regulates ribonucleotide reductase subunit RRM2B and impacts on survival of cancer patients.
Oncotarget
PUBLISHED: 06-21-2014
Show Abstract
Hide Abstract
The role of Ribonucleotide reductase (RR) subunits in different cancers has been intensively studied in our laboratory. RRM2B was identified as a p53-inducible RR subunit that involves in various critical cellular mechanisms such as cell cycle regulation, DNA repair and replication, and mitochondrial homeostasis, etc. However, little is known about the p53-independent regulation of RRM2B in cancer pathology. In this study, we discovered tumor suppressor FOXO3 as the novel regulator of RRM2B. FOXO3 directly bound to and transcriptionally activated the promoter of RRM2B, and induced the expression of RRM2B at RNA and protein levels. Moreover, Overexpression of RRM2B and/or FOXO3 inhibited the proliferation of cancer cells. The cancer tissue microarray data also demonstrated a strong correlation between the co-expression of FOXO3 plus RRM2B and increased disease survival and reduced recurrence or metastasis in lung cancer patients. Our results suggest a novel regulatory control of RRM2B function, and imply the importance of FOXO signaling pathway in DNA replication modulation. This study provides the first time evidence that RRM2B is transcriptionally and functionally regulated independent of p53 pathway by FOXO3, and it establishes that FOXO3 and RRM2B could be used as predictive biomarkers for cancer progression.
Related JoVE Video
Reciprocal regulation of autophagy and dNTP pools in human cancer cells.
Autophagy
PUBLISHED: 05-16-2014
Show Abstract
Hide Abstract
Ribonucleotide reductase (RNR) plays a critical role in catalyzing the biosynthesis and maintaining the intracellular concentration of 4 deoxyribonucleoside triphosphates (dNTPs). Unbalanced or deficient dNTP pools cause serious genotoxic consequences. Autophagy is the process by which cytoplasmic constituents are degraded in lysosomes to maintain cellular homeostasis and bioenergetics. However, the role of autophagy in regulating dNTP pools is not well understood. Herein, we reported that starvation- or rapamycin-induced autophagy was accompanied by a decrease in RNR activity and dNTP pools in human cancer cells. Furthermore, downregulation of the small subunit of RNR (RRM2) by siRNA or treatment with the RNR inhibitor hydroxyurea substantially induced autophagy. Conversely, cancer cells with abundant endogenous intracellular dNTPs or treated with dNTP precursors were less responsive to autophagy induction by rapamycin, suggesting that autophagy and dNTP pool levels are regulated through a negative feedback loop. Lastly, treatment with si-RRM2 caused an increase in MAP1LC3B, ATG5, BECN1, and ATG12 transcript abundance in xenografted Tu212 tumors in vivo. Together, our results revealed a previously unrecognized reciprocal regulation between dNTP pools and autophagy in cancer cells.
Related JoVE Video
Wnt modulates MCL1 to control cell survival in triple negative breast cancer.
BMC Cancer
PUBLISHED: 02-13-2014
Show Abstract
Hide Abstract
Triple negative breast cancer (TNBC) has higher rates of recurrence and distant metastasis, and poorer outcome as compared to non-TNBC. Aberrant activation of WNT signaling has been detected in TNBC, which might be important for triggering oncogenic conversion of breast epithelial cell. Therefore, we directed our focus on identifying the WNT ligand and its underlying mechanism in TNBC cells.
Related JoVE Video
Mutants TP53 p.R273H and p.R273C but not p.R273G enhance cancer cell malignancy.
Hum. Mutat.
PUBLISHED: 02-03-2014
Show Abstract
Hide Abstract
Mutation of the tumor suppressor TP53 gene occurs in greater than half of all human cancers. In addition to loss of tumor suppressor function of wild-type TP53, gain-of-function mutations endow cancer cells with more malignant properties. R273 is a mutation hotspot with the p.R273H, p.R273C, and p.R273G variants occurring most commonly in patient samples. To better understand the consequences of these R273 mutations, we constructed cancer cell lines expressing TP53 p.R273H, p.R273C, or p.R273G and explored their characteristics. We found that p.R273H and p.R273C, but not p.R273G, enhanced proliferation, invasion, and drug resistance in vitro. Furthermore, breast cancer susceptibility protein 1 was upregulated by mutant TP53 p.R273H and p.R273C in response to DNA damage and repair. Transcriptional analysis of the TP53-R273 mutants by RNA-seq confirmed that the apoptosis pathway was less active in p.R273H and p.R273C, compared with R273G. Molecular dynamics simulation further revealed that TP53-R273G binds more tightly to DNA than TP53-R273H or TP53-R273C. These findings indicate that mutation of TP53 at a single codon has different effects, and likely clinical implications. p.R273H and p.R273C lead to a more aggressive phenotype than p.R273G. These findings may contribute to future diagnosis and therapy in TP53 mutant cancers.
Related JoVE Video
Snapback primer mediated clamping PCR for detection of EGFR and KRAS mutations in NSCLC patients by high resolution melting analysis.
Biomed Res Int
PUBLISHED: 01-18-2014
Show Abstract
Hide Abstract
Assays for detecting somatic mutations are requested with higher sensitivity and more convenience. Here, we describe snapback primer mediated allele clamping enrichment polymerase chain reaction (SPACE-PCR), a novel form of PCR that amplifies minority alleles selectively from mixtures. We replaced regular PCR with SPACE-PCR before sequencing or genotyping assays to improve mutation detection sensitivity by up to 100-fold in detecting EGFR and KRAS somatic mutations. Combined SPACE-PCR with analysis of snapback primer by high resolution melting (SPACE-HRM), the high sensitive system that enables a closed-tube detection of mutations after isolating mutants has been established, as low as 1/10(5)-1/1000 mutant samples can be diagnosed. And finally, in a double-blind experiment of 150 cases of non-small-cell lung cancer (NSCLC) patients, compared with direct DNA sequencing and ADX-EGFR/KRAS mutation detection kit, up to 25% of the PCR-direct sequencing negative cases turned out to be positive in SPACE-HRM mutation tests; the specificity is 100%. Results demonstrated that the SPACE-HRM system we set up is a high sensitive assay that can be used for EGFR and KRAS allele enrichment and reliable detection. We anticipate that the method will be employed in multiple applications in the clinic, including diagnosis, scanner recurrence monitoring, and treatment management.
Related JoVE Video
Comparative homegarden medical ethnobotany of Naxi healers and farmers in Northwestern Yunnan, China.
J Ethnobiol Ethnomed
PUBLISHED: 01-10-2014
Show Abstract
Hide Abstract
Homegardens are ecologically and culturally important systems for cultivating medicinal plants for wellbeing by healers and farmers in Naxi communities of the Sino Himalayan region. The cultivation of medicinal plants in Naxi communities and associated ethnomedical knowledge base for maintaining and utilizing these resources is at risk with expanded commercialization of natural resources, development policies and rapid socio-economic change in China. Research is needed to understand the medicinal plant species maintained in Naxi homegardens, their use and contribution to community wellbeing, and how these practices and knowledge base varies between Naxi healers and farmers in order to develop plans for biodiversity conservation and preservation of ethnomedical practices. The main objective of this study is to document and compare medicinal plant species in Naxi homegardens and associated ethnomedical knowledge between Naxi healers and farmers.
Related JoVE Video
A functional MiR-124 binding-site polymorphism in IQGAP1 affects human cognitive performance.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
As a product of the unique evolution of the human brain, human cognitive performance is largely a collection of heritable traits. Rather surprisingly, to date there have been no reported cases to highlight genes that underwent adaptive evolution in humans and which carry polymorphisms that have a marked effect on cognitive performance. IQ motif containing GTPase activating protein 1 (IQGAP1), a scaffold protein, affects learning and memory in a dose-dependent manner. Its expression is regulated by miR-124 through the binding sites in the 3'UTR, where a SNP (rs1042538) exists in the core-binding motif. Here we showed that this SNP can influence the miR-target interaction both in vitro and in vivo. Individuals carrying the derived T alleles have higher IQGAP1 expression in the brain as compared to the ancestral A allele carriers. We observed a significant and male-specific association between rs1042538 and tactile performances in two independent cohorts. Males with the derived allele displayed higher tactual performances as compared to those with the ancestral allele. Furthermore, we found a highly diverged allele-frequency distribution of rs1042538 among world human populations, likely caused by natural selection and/or recent population expansion. These results suggest that current human populations still carry sequence variations that affect cognitive performances and that these genetic variants may likely have been subject to comparatively recent natural selection.
Related JoVE Video
Detection of Alternatively Spliced or Processed RNAs in Cancer Using Oligonucleotide Microarray.
Cancer Treat. Res.
PUBLISHED: 11-14-2013
Show Abstract
Hide Abstract
Deregulation of gene expression plays a pivotal role in tumorigenesis, so the ability to detect RNA alterations is of great value in cancer diagnosis and management. DNA microarrays have been used to measure changes in mRNA or microRNA level, but less often the change of RNA isoforms. Here we appraise the utilization of microarray in detecting alternatively processed RNAs, which have alternative splice forms, retained introns, or altered 3 untranslated regions. We cover the methodology and focus on cancer studies. Recent development in parallel or deep sequencing used in transcriptome analysis is also discussed.
Related JoVE Video
Gene transcription in the zebrafish embryo: regulators and networks.
Brief Funct Genomics
PUBLISHED: 10-22-2013
Show Abstract
Hide Abstract
The precise spatial and temporal control of gene expression is a key process in the development, maintenance and regeneration of the vertebrate body. A substantial proportion of vertebrate genomes encode genes that control the transcription of the genetic information into mRNA. The zebrafish is particularly well suited to investigate gene regulatory networks underlying the control of gene expression during development due to the external development of its transparent embryos and the increasingly sophisticated tools for genetic manipulation available for this model system. We review here recent data on the analysis of cis-regulatory modules, transcriptional regulators and their integration into gene regulatory networks in the zebrafish, using the developing spinal cord as example.
Related JoVE Video
Automated prior knowledge-based quantification of neuronal patterns in the spinal cord of zebrafish.
Bioinformatics
PUBLISHED: 10-17-2013
Show Abstract
Hide Abstract
To reliably assess the effects of unknown chemicals on the development of fluorescently labeled sensory-, moto- and interneuron populations in the spinal cord of zebrafish, automated data analysis is essential.
Related JoVE Video
Video assistant thoracoscopic (VATS) lobectomy: right lower lobe.
J Thorac Dis
PUBLISHED: 06-18-2013
Show Abstract
Hide Abstract
The 60-year-old female had a nodule in the right lower lobe of the lung, which was identified as a tumor by CT and PET-CT. Then the right lower lobectomy was performed. The posterior trocar placement, different from other surgery, is in the 5th intercostals space in the anterior latissimus dorsi, which can be built by a small incision when operation is needed. There is a vessel heteromorphosis that the inferior pulmonary vein and the mid pulmonary vein share the same stem. Also, this patient has many intumescentia lymph nodes. We can see, the lymph nodes can be ablated completely by VATS.
Related JoVE Video
Genome-wide, whole mount in situ analysis of transcriptional regulators in zebrafish embryos.
Dev. Biol.
PUBLISHED: 04-29-2013
Show Abstract
Hide Abstract
Transcription is the primary step in the retrieval of genetic information. A substantial proportion of the protein repertoire of each organism consists of transcriptional regulators (TRs). It is believed that the differential expression and combinatorial action of these TRs is essential for vertebrate development and body homeostasis. We mined the zebrafish genome exhaustively for genes encoding TRs and determined their expression in the zebrafish embryo by sequencing to saturation and in situ hybridisation. At the evolutionary conserved phylotypic stage, 75% of the 3302 TR genes encoded in the genome are already expressed. The number of expressed TR genes increases only marginally in subsequent stages and is maintained during adulthood suggesting important roles of the TR genes in body homeostasis. Fewer than half of the TR genes (45%, n=1711 genes) are expressed in a tissue-restricted manner in the embryo. Transcripts of 207 genes were detected in a single tissue in the 24h embryo, potentially acting as regulators of specific processes. Other TR genes were expressed in multiple tissues. However, with the exception of certain territories in the nervous system, we did not find significant synexpression suggesting that most tissue-restricted TRs act in a freely combinatorial fashion. Our data indicate that elaboration of body pattern and function from the phylotypic stage onward relies mostly on redeployment of TRs and post-transcriptional processes.
Related JoVE Video
MicroRNA-657 promotes tumorigenesis in hepatocellular carcinoma by targeting transducin-like enhancer protein 1 through nuclear factor kappa B pathways.
Hepatology
PUBLISHED: 04-05-2013
Show Abstract
Hide Abstract
Growing evidence indicates that deregulation of microRNAs (miRNAs) contributes to tumorigenesis. Dysregulation of miR-657 has been observed in several types of cancers, but its biological function is still largely unknown. Our results showed that miR-657 expression can be induced by hepatitis viral proteins and is significantly increased in hepatocellular carcinoma (HCC) tissues. Moreover, introduction of miR-657 dramatically increases proliferation and colony formation of HCC cells in vitro and induces tumor development in immunodeficient mice. Further studies showed that miR-657 directly targets the transducin-like enhancer protein 1 (TLE1) 3 untranslated region (UTR) and activates nuclear factor kappa B (NF-?B) pathways that contribute to hepatocarcinogenesis. Conclusion: This study identified a mechanism whereby miRNA-657 contributed to HCC through novel cancer pathways and provides new insights into the potential molecular mechanisms of hepatic carcinogenesis.
Related JoVE Video
Gene responses in the central nervous system of zebrafish embryos exposed to the neurotoxicant methyl mercury.
Environ. Sci. Technol.
PUBLISHED: 03-14-2013
Show Abstract
Hide Abstract
Methyl mercury (MeHg) is a neurotoxicant with adverse effects on the development of the nervous system from fish to man. Despite a detailed understanding of the molecular mechanisms by which MeHg affects cellular homeostasis, it is still not clear how MeHg causes developmental neurotoxicity. We performed here a genome-wide transcriptional analysis of MeHg-exposed zebrafish embryos and combined this with a whole-mount in situ expression analysis of 88 MeHg-affected genes. The majority of the analyzed genes showed tissue- and region-restricted responses in various organs and tissues. The genes were linked to gene ontology terms like oxidative stress, transport and cell protection. Areas even within the central nervous system (CNS) are affected differently resulting in distinct cellular stress responses. Our study revealed an unexpected heterogeneity in gene responses to MeHg exposure in different tissues and neuronal subregions, even though the known molecular action of MeHg would predict a similar burden of exposed cells. The overall structure of the developing brain of MeHg-exposed embryos appeared normal, suggesting that the mechanism leading to differentiation of the CNS is not overtly affected by exposure to MeHg. We propose that MeHg disturbs the function of the CNS by disturbing the cellular homeostasis. As these cellular stress responses comprise genes that are also involved in normal neuronal activity and learning, MeHg may affect the developing CNS in a subtle manner that manifests itself in behavioral deficits.
Related JoVE Video
Endometriosis of the lung: report of a case and literature review.
Eur. J. Med. Res.
PUBLISHED: 02-24-2013
Show Abstract
Hide Abstract
This paper reports a case of endometriosis of the lung in a 29-year-old woman with long-term periodic catamenial hemoptysis. A chest computed tomography image obtained during menstruation revealed a radiographic opaque lesion in the lingular segment of the left superior lobe. During bronchoscopy, bleeding in the mucosa of the distal bronchus of the lingular segment of the left superior lobe was observed. Histopathology subsequent to an exploratory thoracotomy confirmed the diagnosis of endometriosis of the left lung. The 2-year follow-up after lingular lobectomy of the left superior lobe showed no recurrence or complications.
Related JoVE Video
Glutathione S-transferase M1 null genotype contributes to increased risk of esophageal carcinoma in Chinese population.
Tumour Biol.
PUBLISHED: 02-22-2013
Show Abstract
Hide Abstract
Glutathione S-transferases (GSTs) play important roles in the detoxification of electrophilic carcinogens, and GSTM1 null genotype is associated with the dysfunction of GSTs. Previous studies investigating the association between GSTM1 null genotype and risk of esophageal carcinoma in Chinese provided inconsistent findings. To provide a more precise estimation on the association between GSTM1 null genotype and risk of esophageal carcinoma in Chinese population, a meta-analysis was performed. Eligible studies were searched in PubMed, Embase, and China National Knowledge Infrastructure databases. Odds ratio (OR) with the corresponding 95 % confidence interval (95 %CI) was used to assess the association. A total of 18 case-control studies involving 1,947 cases and 3,506 controls were finally included in the meta-analysis. Meta-analysis of those 18 studies showed that GSTM1 null genotype was associated with an increased risk of esophageal carcinoma in Chinese (random effect model OR = 1.49, 95 %CI = 1.11-2.00, P = 0.008). The findings from cumulative meta-analysis showed that the association was more obvious as the data increased by publication year. There was no risk of publication bias in the meta-analysis. Therefore, the findings from our meta-analysis provide a strong evidence for the association between GSTM1 null genotype and risk of esophageal carcinoma in Chinese population, and GSTM1 null genotype contributes to increased risk of esophageal carcinoma in Chinese.
Related JoVE Video
ppENK Gene Methylation Status in the Development of Pancreatic Carcinoma.
Gastroenterol Res Pract
PUBLISHED: 02-11-2013
Show Abstract
Hide Abstract
Objective. To explore the association of hypermethylation of the proenkephalin gene (ppENK) with pancreatic carcinoma and to identify the effects of a demethylating agent on pancreatic cell lines. Method. Human pancreatic cancer tissues and five pancreatic carcinoma cell lines, as well as normal pancreatic tissue, were used. ppENK methylation status was detected by MS-PCR (methylation-specific PCR). Results. Methylation of ppENK was detected in 90.3% (28/31) of the human pancreatic carcinoma tissues but was not seen in normal pancreatic tissue. There was no correlation between the extent of methylation of ppENK and the clinicopathological features of the pancreatic carcinomas. Methylated ppENK was detected in all the pancreatic cancer cell lines and was associated with loss of mRNA expression in the pancreatic carcinoma cell lines and normal pancreatic tissue. After treatment with 5-aza-dC, methylated ppENK was not detected and the inhibition of ppENK mRNA expression was reversed. Conclusions. Inhibition of ppENK expression by a change in its methylation status plays an important role in pancreatic carcinogenesis. ppENK methylation is thus an important molecular event that distinguishes pancreatic carcinoma tissue from normal pancreatic tissue. Effects on cell growth, apoptosis, and the cell cycle may contribute to changes of ppENK methylation status.
Related JoVE Video
Significant association of 5p15.33 (TERT-CLPTM1L genes) with lung cancer in Chinese Han population.
Exp. Lung Res.
PUBLISHED: 01-31-2013
Show Abstract
Hide Abstract
Lung cancer is a leading cause of cancer-related deaths throughout the world. Recent genome-wide association studies and consecutive validation supported that the 5p15.33 region containing telomerase reverse transcriptase gene (TERT) and cleft lip and palate transmembrane protein 1-like (CLPTM1L) gene showed significant association with lung cancer in multiple populations. Here we studied a large Chinese Han cohort consisting of 1759 cases and 1804 controls. In the 1st stage (784 cases versus 782 controls) we genotyped 13 tag SNPs within 5p15.33 region to further investigate the association. After the 2nd stage validation (975 cases versus 1022 controls), the study clarified the association that rs2736100 of the TERT gene conferred the highest significant risk of lung cancer (P=4×10(-3) in the 1st stage association, P=4×10(-4) in the 2nd stage validation, and P=1×10(-5), odds ratio=1.24 in the combined population). The results provided the evidence of a cross-race susceptibility of the lung cancer locus.
Related JoVE Video
[High throuput analysis of organophosphorus pesticide residues and their metabolites in animal original foods by dual gas chromatography-dual pulse flame photometric detection].
Se Pu
PUBLISHED: 12-21-2011
Show Abstract
Hide Abstract
A method was established for the quantitative determination of 54 organophosphorus pesticide residues and their metabolites in foods of animal origin by dual gas chromatography-dual pulse flame photometric detection. Homogenized samples were extracted with acetone and methylene chloride, and cleaned-up by gel permeation chromatography (GPC). The response of each analyte showed a good linearity with a correlation coefficient not less than 0. 99. The recovery experiments were performed by a blank sample spiked at low, medium and high fortification levels. The recoveries for beef, mutton, pork, chicken were in the range of 50. 5% -128. 1% with the relative standard deviations (n = 6) of 1. 1% -25. 5%, which demonstrated the good precision and accuracy of the present method. The limits of detection for the analytes were in the range of 0. 001 -0. 170 mg/kg, and the limits of quantification were in the range of 0. 002 -0. 455 mg/kg. Animal food samples collected from markets such as meat, liver and kidney were analyzed, and the residues of dichlorovos and disulfoton-sulfoxide were found in the some samples. The established method is sensitive and selective enough to detect organophosphorus pesticide residues in animal foods.
Related JoVE Video
[GC-MS analysis on volatile components of wild Trogopterus faeces from Laishui county of Hebei province].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 12-05-2011
Show Abstract
Hide Abstract
To analysis the volatile components of Trogopterus faeces.
Related JoVE Video
Transcriptional response of zebrafish embryos exposed to neurotoxic compounds reveals a muscle activity dependent hspb11 expression.
PLoS ONE
PUBLISHED: 07-22-2011
Show Abstract
Hide Abstract
Acetylcholinesterase (AChE) inhibitors are widely used as pesticides and drugs. Their primary effect is the overstimulation of cholinergic receptors which results in an improper muscular function. During vertebrate embryonic development nerve activity and intracellular downstream events are critical for the regulation of muscle fiber formation. Whether AChE inhibitors and related neurotoxic compounds also provoke specific changes in gene transcription patterns during vertebrate development that allow them to establish a mechanistic link useful for identification of developmental toxicity pathways has, however, yet not been investigated. Therefore we examined the transcriptomic response of a known AChE inhibitor, the organophosphate azinphos-methyl (APM), in zebrafish embryos and compared the response with two non-AChE inhibiting unspecific control compounds, 1,4-dimethoxybenzene (DMB) and 2,4-dinitrophenol (DNP). A highly specific cluster of APM induced gene transcripts was identified and a subset of strongly regulated genes was analyzed in more detail. The small heat shock protein hspb11 was found to be the most sensitive induced gene in response to AChE inhibitors. Comparison of expression in wildtype, ache and sop(fixe) mutant embryos revealed that hspb11 expression was dependent on the nicotinic acetylcholine receptor (nAChR) activity. Furthermore, modulators of intracellular calcium levels within the whole embryo led to a transcriptional up-regulation of hspb11 which suggests that elevated intracellular calcium levels may regulate the expression of this gene. During early zebrafish development, hspb11 was specifically expressed in muscle pioneer cells and Hspb11 morpholino-knockdown resulted in effects on slow muscle myosin organization. Our findings imply that a comparative toxicogenomic approach and functional analysis can lead to the identification of molecular mechanisms and specific marker genes for potential neurotoxic compounds.
Related JoVE Video
Genome sequence and global sequence variation map with 5.5 million SNPs in Chinese rhesus macaque.
Genome Biol.
PUBLISHED: 05-01-2011
Show Abstract
Hide Abstract
Rhesus macaque (Macaca mulatta) is the most widely used nonhuman primate animal in biomedical research. A global map of genetic variations in rhesus macaque is valuable for both evolutionary and functional studies.
Related JoVE Video
Synthesis of OH-group-containing, biodegradable polyurethane and protein fixation on its surface.
Biomacromolecules
PUBLISHED: 04-29-2011
Show Abstract
Hide Abstract
A series of biodegradable polyurethanes containing free side hydroxyl groups (PUOH) were synthesized successfully in two steps: (1) PLA diol as soft segment, hexamethylene diisocyanate (HDI) as hard segment, and benzalpentaerythritol (BPO) as a chain extender were used to synthesize PUs with protected OH groups; (2) CF(3)COOH was used as a deprotection agent to remove the benzal groups on PU to prepare PUOH. The properties of PU and PUOH were characterized by Fourier transform infrared spectroscopy (FT-IR), nuclear magnetic resonance (NMR), differential scanning calorimetry (DSC), water contact angle measurement, and gel permeation chromatography (GPC). The benzal groups were removed completely in 15 min without detrimental effect on PU main chains to obtain PUOHs. 4-Azidobenzoic acid was conjugated to PUOH through its esterification with the free OH groups on PUOH. The results of immunofluorescence assay showed that the phenyl azide groups formed were capable of binding mouse IgG under UV (254 nm) irradiation in 3 min; the bound mouse IgG retained its own biological activity and could further bind the FITC-labeled anti(mouse IgG). Therefore, this material has a potential in immunofluorescence assay and related fields.
Related JoVE Video
Early finding of chest wall metastasis of hepatocellular carcinoma in a woman by fluorodeoxyglucose-positron emission tomography scan: a case report.
J Med Case Rep
PUBLISHED: 04-13-2011
Show Abstract
Hide Abstract
The use of fluorodeoxyglucose-positron emission tomography to evaluate well-differentiated hepatocellular carcinomas is facing critical problems. It is reported that the activity of fluorodeoxyglucose-6-phosphatase, which converts fluorodeoxyglucose-6-phosphatase to fluorodeoxyglucose, is high in normal liver cells. However, the enzyme-converting activity of glucose-6-phosphatase of well-differentiated hepatocellular carcinomas is similar to normal liver tissue. Thus, using fluorodeoxyglucose in diagnosing primary hepatocellular carcinomas is difficult. However, using fluorodeoxyglucose to detect extrahepatic metastasis of hepatocellular carcinomas is still possible.
Related JoVE Video
Multiple biomarker expression on circulating tumor cells in comparison to tumor tissues from primary and metastatic sites in patients with locally advanced/inflammatory, and stage IV breast cancer, using a novel detection technology.
Breast Cancer Res. Treat.
PUBLISHED: 04-06-2011
Show Abstract
Hide Abstract
Patients with locally advanced/inflammatory breast cancer (LABC/IBC) face a high likelyhood of recurrence and prognosis for relapsed, or de novo stage IV metastatic breast cancer (MBC) remains poor. Estrogen (ER) and HER2 receptor expression on primary or MBC allow targeted therapies, but an estimated 10-18% of tumors do not exhibit these biomarkers and survival in these cases is even poorer. Variations in discordance rates for the expression of ER and HER2 receptors have been observed between primary and metastatic tumors and such discordances may lead to suboptimal treatment. Circulating tumor cells (CTCs) are considered the seeds of residual disease and distant metastases and their characterization could help guide treatment selection. To explore this possibility, we used multiple biomarker assessment of CTCs in comparison to primary and metastatic tumor sites. Thirty-six patients with LABC/IBC, or stage IV MBC were evaluated. Blood samples were procured prior to initiating or changing therapy. CTCs were identified based on presence of cytokeratin and nucleus staining, and the absence of CD45. A multimarker assay was developed to simultaneously quantify expression of HER2, ER, and ERCC1, a DNA excision repair protein. Novel fiber-optic array scanning technology (FAST) was used for sensitive location of CTCs. CTCs were detected in 82% of MBC and 62% LABC/IBC cases. Multiplex marker expression was successfully carried out in samples from18 patients with MBC and in 8 patients with LABC/IBC that contained CTCs. In MBC, we detected actionable discordance rates of 40 and 23%, respectively for ER and HER2 where a biomarker was negative in the primary or metastatic tumor and positive in the CTCs. In LABC/IBC, actionable discordances were 60 and 20% for ER and HER2, respectively. Pilot trials evaluating the effectiveness of treatment selections based on actionable discordances between biomarker expression patterns on CTCs and primary or metastatic tumor sites may allow for a prospective assessment of CTC-based individualized targeted therapies.
Related JoVE Video
Inhibitors of mTOR overcome drug resistance from topoisomerase II inhibitors in solid tumors.
Cancer Lett.
PUBLISHED: 03-28-2011
Show Abstract
Hide Abstract
The present study was performed to investigate the possible role of mTOR inhibitors in restoring chemosensitivity to adriamycin/cisplatin and elucidate the underlying mechanism. Combining adriamycin/cisplatin with torisel synergistically inhibited the cell proliferation in human oropharyngeal carcinoma cell line KB and its multidrug-resistant subclone KB/7D. Combining adriamycin and torisel inhibited the phosphorylation of 4EBP-1 and p70S6K, the proteins involved in mTOR pathway, increased expression of ?H2AX indicative of DNA damage, triggered cell cycle arrest at G2/M and apoptosis. We conclude that chromatin decondensation by DNA damage provided an easy access for torisel to block the translation of proteins essential for DNA repair thereby restoring the chemosensitivity.
Related JoVE Video
[Essential oil composition of three herbal medicines from Curcuma wenyujin by GC-MS].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 12-24-2010
Show Abstract
Hide Abstract
To compare the contents and composition of volatile oil of Wenyujin (steamed root of Curcuma wenyujin) Wenezhu (steamed rhieome of Curcuma wenyujin) and Pianjianghuang (rhizome of Curcuma wenyujin).
Related JoVE Video
[Determination of methyl nonyl ketone in volatile oil from herbs of Houttuynia cordata by GC-MS].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 10-12-2010
Show Abstract
Hide Abstract
To develop a GC-MS method for the determination of methyl nonyl ketone in the volatile oil from the herbs of Houttuynia cordata.
Related JoVE Video
Nuclear retention of unspliced pre-mRNAs by mutant DHX16/hPRP2, a spliceosomal DEAH-box protein.
J. Biol. Chem.
PUBLISHED: 09-14-2010
Show Abstract
Hide Abstract
Defective or imbalanced expression of spliceosomal factors has been linked to human disease; however, how a defective spliceosome affects intron-containing gene transcripts in human cells is largely unknown. DEAH-box protein DHX16 is a human orthologue of Saccharomyces cerevisiae spliceosomal protein Prp2, an RNA-dependent ATPase that activates the spliceosome before the first catalytic step of splicing. Yeast prp2 mutants accumulate unspliced RNAs from the vast majority of intron-containing genes. Here we used a genomic tiling microarray to screen transcripts from four chromosomes in human cells expressing a dominant negative DHX16 mutant and identified a number of gene transcripts that retained their introns. The mutant protein also affected gene transcripts that are sensitive to pladienolide, an SF3b inhibitor. The unspliced RNAs were retained in the nucleus, and block of nonsense-mediated decay did not affect their accumulation. Thus, a perturbation of human PRP2/DHX16 results in accumulation of unspliced transcripts, similar to the outcome in yeast prp2 mutants. The results further suggest that mutant DHX16/hPRP2 causes a defective spliceosome to retain unspliced gene transcripts in the nuclei of human cells.
Related JoVE Video
Regulatory interactions specifying Kolmer-Agduhr interneurons.
Development
PUBLISHED: 07-07-2010
Show Abstract
Hide Abstract
In the zebrafish spinal cord, two classes of neurons develop from the lateral floor plate: Kolmer-Agduhr (KA) and V3 interneurons. We show here that the differentiation of the correct number of KA cells depends on the activity of the homeobox transcription factor Nkx2.9. This factor acts in concert with Nkx2.2a and Nkx2.2b. These factors are also required for the expression of the zinc-finger transcription factor Gata2 in the lateral floor plate. In turn, Gata2 is necessary for expression of the basic helix-loop-helix transcription factor Tal2 that acts upstream of the GABA-synthesizing enzyme glutamic acid decarboxylase 67 gene (gad67) in KA cells. Expression of the transcription factor Sim1, which marks the V3 interneurons in the lateral floor plate, depends also on the three Nkx2 factors. sim1 expression does not require, however, gata2 and tal2. KA cells of the lateral floor plate and the KA cells located more dorsally in the spinal cord share expression of transcription factors. The functional connections between the different regulatory genes, however, differ in the two GABAergic cell types: although gata2 and tal2 are expressed in KA cells, they are dispensable for gad67 expression in these cells. Instead, olig2 and gata3 are required for the differentiation of gad67-expressing KA cells. This suggests that the layout of regulatory networks is crucially dependent on the lineage that differs between KA and KA cells.
Related JoVE Video
Methyl mercury suppresses the formation of the tail primordium in developing zebrafish embryos.
Toxicol. Sci.
PUBLISHED: 02-24-2010
Show Abstract
Hide Abstract
The objective of this study was to characterize the mechanisms of action of the model environmental toxicant methyl mercury (MeHg) in the zebrafish embryo. Zebrafish embryos were exposed to MeHg, and the effective concentration and window of exposure were determined in wild-type and fluorescent reporter transgenic zebrafish embryos. Genes were systematically assessed for altered expression in response to MeHg by in situ hybridization. MeHg impairs development of the fin fold and the tail fin primordium. Alterations in transgene expression were noted at 6 microg/l MeHg, making this shh:gfp line the most sensitive biosensor of MeHg exposure. The matrix metalloproteases mmp9 and mmp13 and eight other genes are induced in the embryonic tail in response to MeHg. Our data suggest that MeHg impairs tail development at least partially by activation of the tissue remodeling proteases Mmp9 and Mmp13.
Related JoVE Video
Two new chalcones from leaves of Morus alba L.
Fitoterapia
PUBLISHED: 02-22-2010
Show Abstract
Hide Abstract
Two new chalcone derivatives named morachalcones B and C (1 and 2) were isolated from the leaves of Morus alba L. Their structures were elucidated by spectroscopic analysis. Morachalcones B (1) and C (2) represent two examples of chalcones having unusual furan rings which are formed by cyclization between C-alpha-OH and C-2-OH. Compounds 1 and 2 displayed only moderate cytotoxic activity against HCT-8 and BGC823 human cancer cell lines.
Related JoVE Video
[Effects of tree ages and geographic area on quality of bark of Magnolia officinalis and M. officinalis var. biloba].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 11-27-2009
Show Abstract
Hide Abstract
The effects of tree ages and geographic area on quality of bark of Magnolia officinalis (MO) and M. officinalis var. biloba (MOB) were studied. The volatile oils of samples extracted by a water stream distillation method were analyzed using a GC/MS method. The non-volatile ingredients of samples were determined by an HPLC method. Seven and twenty characteristic peaks were detected in the HPLC and GC fingerprint of MO, respectively, and the similar HPLC and GC fingerprint were showed in MOB. For samples collected in the same geographic area with different ages, the concentrations of active ingredients varied barely, whereas for those samples collected from different geographic area, differences on the concentrations of active ingredients were observed, for example, the concentrations of the amount of magnolol and honokiol in samples collected in Hubei province were higher than those collected in other areas. Big differences on the concentrations of active ingredients were found between MO and MOB, for MO, the ratio of honokiol/ magnolol was more than 0.7, whereas the ratio-was less than 0.7 in the case of MOB, and the concentrations of honokiol in MO were higher than those in MOB.
Related JoVE Video
Zebrafish embryos as models for embryotoxic and teratological effects of chemicals.
Reprod. Toxicol.
PUBLISHED: 03-02-2009
Show Abstract
Hide Abstract
The experimental virtues of the zebrafish embryo such as small size, development outside of the mother, cheap maintenance of the adult made the zebrafish an excellent model for phenotypic genetic and more recently also chemical screens. The availability of a genome sequence and several thousand mutants and transgenic lines together with gene arrays and a broad spectrum of techniques to manipulate gene functions add further to the experimental strength of this model. Pioneering studies suggest that chemicals can have in many cases very similar toxicological and teratological effects in zebrafish embryos and humans. In certain areas such as cardiotoxicity, the zebrafish appears to outplay the traditional rodent models of toxicity testing. Several pilot projects used zebrafish embryos to identify new chemical entities with specific biological functions. In combination with the establishment of transgenic sensor lines and the further development of existing and new automated imaging systems, the zebrafish embryos could therefore be used as cost-effective and ethically acceptable animal models for drug screening as well as toxicity testing.
Related JoVE Video
Prediction of lung cancer risk in a Chinese population using a multifactorial genetic model.
BMC Med. Genet.
Show Abstract
Hide Abstract
Lung cancer is a complex polygenic disease. Although recent genome-wide association (GWA) studies have identified multiple susceptibility loci for lung cancer, most of these variants have not been validated in a Chinese population. In this study, we investigated whether a genetic risk score combining multiple.
Related JoVE Video
Quality evaluation of semen oroxyli based on the determination of multiple components with a single reference standard.
J Chromatogr Sci
Show Abstract
Hide Abstract
The determination of multiple components is considered to be one of the key methods to control the quality of traditional Chinese medicine (TCM), because the clinical efficacy of TCM is derived from the synergistic action of multi-components. When simultaneously determining multi-components in TCM with multiple reference standards (MRS), the limited availability and high expense of various reference standards is a major obstacle. Currently, a practical method determining multi-components with a single reference standard (SRS) is needed to solve the problem, in which the contents of those components without reference standards can be calculated using relative conversion factor. In the present paper, both MRS and SRS methods were established for the simultaneous quantitative determination of seven bioactive flavonoids in Muhudie (MHD), the seed of Oroxylum indicum L., a traditional Chinese herb that has been used for centuries. Forty samples were assayed and data obtained from the two methods were compared, and no statistically significant difference was observed by a T-test (P > 0.05), thus, the SRS method can be applied for quality analysis of MHD. At the same time, a certain correlation was discovered between the contents of the bioactive components and the morphological character of MHD.
Related JoVE Video
A two-SNP IL-6 promoter haplotype is associated with increased lung cancer risk.
J. Cancer Res. Clin. Oncol.
Show Abstract
Hide Abstract
Aberrant expression of interleukin-6 (IL-6) may play an important role in lung carcinogenesis. Whether IL-6 promoter haplotypes are associated with lung cancer risk and their functions have not yet been studied. We tested the hypothesis that single-nucleotide polymorphism (SNP) and/or haplotypes of IL-6 promoter are associated with risk of lung cancer.
Related JoVE Video
Association between CASP8 and CASP10 polymorphisms and toxicity outcomes with platinum-based chemotherapy in Chinese patients with non-small cell lung cancer.
Oncologist
Show Abstract
Hide Abstract
Caspase-8 and caspase-10 play crucial roles in both cancer development and chemotherapy efficacy. In this study, we aimed to comprehensively assess single nucleotide polymorphisms (SNPs) of the caspase-8 (CASP8) and caspase-10 (CASP10) genes in relation to toxicity outcomes with first-line platinum-based chemotherapy in patients with advanced non-small cell lung cancer (NSCLC). We genotyped 13 tag SNPs of CASP8 and CASP10 in 663 patients with advanced NSCLC treated with platinum-based chemotherapy regimens. Associations between SNPs and chemotherapy toxicity outcomes were identified in a discovery set of 279 patients and then validated in an independent set of 384 patients. In both the discovery and validation sets, variant homozygotes of CASP8 rs12990906 and heterozygotes of CASP8 rs3769827 and CASP10 rs11674246 and rs3731714 had a significantly lower risk for severe toxicity overall. However, only the association with the rs12990906 variant was replicated in the validation set for hematological toxicity risk. In a stratified analysis, we found that some other SNPs, including rs3769821, rs3769825, rs7608692, and rs12613347, were significantly associated with severe toxicity risk in some subgroups, such as in nonsmoking patients, patients with adenocarcinoma, and patients treated with cisplatin combinations. Consistent results were also found in haplotype analyses. Our results provide novel evidence that polymorphisms in CASP8 and CASP10 may modulate toxicity outcomes in patients with advanced NSCLC treated with platinum-based chemotherapy. If validated, the findings will facilitate the genotype-based selection of platinum-based chemotherapy regimens.
Related JoVE Video
A combined DNA-microarray and mechanism-specific toxicity approach with zebrafish embryos to investigate the pollution of river sediments.
Reprod. Toxicol.
Show Abstract
Hide Abstract
The zebrafish embryo has repeatedly proved to be a useful model for the analysis of effects by environmental toxicants. This proof-of-concept study was performed to investigate if an approach combining mechanism-specific bioassays with microarray techniques can obtain more in-depth insights into the ecotoxicity of complex pollutant mixtures as present, e.g., in sediment extracts. For this end, altered gene expression was compared to data from established bioassays as well as to results from chemical analysis. Mechanism-specific biotests indicated a defined hazard potential of the sediment extracts, and microarray analysis revealed several classes of significantly regulated genes which could be related to the hazard potential. Results indicate that potential classes of contaminants can be assigned to sediment extracts by both classical biomarker genes and corresponding expression profile analyses of known substances. However, it is difficult to distinguish between specific responses and more universal detoxification of the organism.
Related JoVE Video
Determination of 49 organophosphorus pesticide residues and their metabolites in fish, egg, and milk by dual gas chromatography-dual pulse flame photometric detection with gel permeation chromatography cleanup.
J. Agric. Food Chem.
Show Abstract
Hide Abstract
A new method for the quantitative determination of 49 kinds of organophosphorus pesticide residues and their metabolites in fish, egg, and milk by dual gas chromatography-dual pulse flame photometric detection was developed. Homogenized samples were extracted with acetone and methylene chloride (1 + 1, v/v), and then the extracts were cleaned up by gel permeation chromatography (GPC). The response of each organophosphorus pesticide showed a good linearity with its concentration; the linearity correlation was not less than 0.99. The detection limits (S/N = 3) of pesticides were in the range of 0.001-0.025 mg kg?¹. The recovery experiments were performed by blank sample spiked at low, medium, and high fortification levels. The recoveries for fish, egg, and milk were 50.9-142.2, 53.3-137.2, and 50.3-139.4% with relative standard deviations (RSD, n = 6) of 2.3-24.9, 4.3-26.7, and 2.8-32.2%, respectively. The method was applied to detect organophosphorus pesticides in samples collected from the market, and satisfactory results were obtained. This quantitative method was highly sensitive and exact and could be applied to the accurate determination of organophosphorus contaminants in fish, egg, and milk.
Related JoVE Video
Identification of an AAA ATPase VPS4B-dependent pathway that modulates epidermal growth factor receptor abundance and signaling during hypoxia.
Mol. Cell. Biol.
Show Abstract
Hide Abstract
VPS4B, an AAA ATPase (ATPase associated with various cellular activities), participates in vesicular trafficking and autophagosome maturation in mammalian cells. In solid tumors, hypoxia is a common feature and an indicator of poor treatment outcome. Our studies demonstrate that exogenous or endogenous (assessed with anchorage-independent three-dimensional multicellular spheroid culture) hypoxia induces VPS4B downregulation by the ubiquitin-proteasome system. Inhibition of VPS4B function by short hairpin VPS4B (sh-VPS4B) or expression of dominant negative VPS4B(E235Q) promotes anchorage-independent breast cancer cell growth and resistance to gefitinib, U0126, and genotoxicity. Biochemically, hyperactivation of epidermal growth factor receptor (EGFR), a receptor tyrosine kinase essential for cell proliferation and survival, accompanied by increased EGFR accumulation and altered intracellular compartmentalization, is observed in cells with compromised VPS4B. Furthermore, enhanced FOS/JUN induction and AP-1 promoter activation are noted in EGF-treated cells with VPS4B knockdown. However, VPS4B depletion does not affect EGFRvIII stability or its associated signaling. An inverse correlation between VPS4B expression and EGFR abundance is observed in breast tumors, and high-grade or recurrent breast carcinomas exhibit lower VPS4B expression. Together, our findings highlight a potentially critical role of VPS4B downregulation or chronic-hypoxia-induced VPS4B degradation in promoting tumor progression, unveiling a nongenomic mechanism for EGFR overproduction in human breast cancer.
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.