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Find video protocols related to scientific articles indexed in Pubmed.
Effectiveness of Telemedicine for Controlling Asthma Symptoms: A Systematic Review and Meta-analysis.
Telemed J E Health
PUBLISHED: 11-14-2014
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Abstract Background: The effectiveness of telemedicine for the management of chronic diseases is unclear. This study examined the effectiveness of telemedicine in relieving asthma symptoms. Materials and Methods: A systematic review of the Medline, Cochrane, EMBASE, and Google Scholar databases was conducted until December 31, 2013 using the following key words: "asthma," "telemedicine," "telehealth," "e-health," "mobile health," "Internet," "telecommunication," "telemanagement," "remote," and "short message service." Inclusion criteria were randomized controlled trial, a diagnosis of asthma, the majority of the patients were ?18 years of age, and intervention involved any format of telemedicine. A meta-analysis of eligible studies was conducted with the primary outcome being change of asthma symptoms. Results: Of 813 articles identified, 11 were included in the qualitative synthesis, and 6 were included in the meta-analysis. Among the 11 studies, there were 1,460 patients in the intervention groups and 1,349 in the control groups, and the total numbers of participants ranged from 12 to 481 in the intervention groups and from 12 to 487 in the control groups. The mean age of patients ranged in the intervention groups from 34.4 to 54.6 years and in the control groups from 30.7 to 56.4 years. The treatment duration ranged from 0.5 to 12 months. The meta-analysis of six eligible studies revealed no significant difference in asthma symptom score change between the telemedicine and control groups (pooled Hedges's g=0.34, 95% confidence interval=-0.05 to 0.74, Z=1.69, p=0.090). Conclusions: Telemedicine interventions do not appear to improve asthma function scores, but other benefits may be present.
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DL-PRO: A Novel Deep Learning Method for Protein Model Quality Assessment.
Proc Int Jt Conf Neural Netw
PUBLISHED: 11-14-2014
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Computational protein structure prediction is very important for many applications in bioinformatics. In the process of predicting protein structures, it is essential to accurately assess the quality of generated models. Although many single-model quality assessment (QA) methods have been developed, their accuracy is not high enough for most real applications. In this paper, a new approach based on C-? atoms distance matrix and machine learning methods is proposed for single-model QA and the identification of native-like models. Different from existing energy/scoring functions and consensus approaches, this new approach is purely geometry based. Furthermore, a novel algorithm based on deep learning techniques, called DL-Pro, is proposed. For a protein model, DL-Pro uses its distance matrix that contains pairwise distances between two residues' C-? atoms in the model, which sometimes is also called contact map, as an orientation-independent representation. From training examples of distance matrices corresponding to good and bad models, DL-Pro learns a stacked autoencoder network as a classifier. In experiments on selected targets from the Critical Assessment of Structure Prediction (CASP) competition, DL-Pro obtained promising results, outperforming state-of-the-art energy/scoring functions, including OPUS-CA, DOPE, DFIRE, and RW.
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[Surgical treatment of lumbar spondylolisthesis by transforaminal lumbar interbody fusion].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 11-14-2014
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To explore the clinical outcomes of transforminal lumbar interbody fusion (TLIF) technique in treatment of lumbar spondylolisthesis.
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Impact of removing iodised salt on children's goitre status in areas with excessive iodine in drinking-water.
Br. J. Nutr.
PUBLISHED: 11-05-2014
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The impact of removing iodised salt on children's goitre status in a high-iodine area (HIA) remains unclear. The aim of the present study was to explore the changes in the prevalence of goitre in children after removing iodised salt from their diet. For this purpose, three towns with the median water iodine content of 150-300 ?g/l were selected randomly in Hengshui City, Hebei Province, China. A total of 452 and 459 children were randomly selected from the three towns in order to measure thyroid volume by ultrasound before and after removing iodised salt, respectively. Their goitre status was judged using the criteria of age-specific thyroid volume recommended by the WHO. After removing iodised salt, the overall median urinary iodine content (MUIC) of children decreased from 518 (interquartile range (IQR) 347-735) to 416 (IQR 274-609) ?g/l. The MUIC of children across sex and age group decreased significantly except for the age group of 9 years. The overall prevalence of goitre in the three towns significantly decreased from 24·56 % (n 111/452) to 5·88 % (n 27/459) (P< 0·001). Goitre prevalence in children aged 8-10 years decreased from 33·70 % (n 31/92), 23·32 % (n 45/193) and 20·96 % (n 35/167) to 6·10 % (n 10/164), 5·52 % (n 9/163) and 6·06 % (n 8/132), respectively. Goitre prevalence in boys and girls decreased from 27·05 % (n 66/244) and 21·63 % (n 45/208) to 6·66 % (n 15/226) and 5·15 % (n 12/233), respectively. The decreases in the prevalence of goitre in children across sex and age group were all statistically significant. The present study revealed that goitre prevalence in children decreased significantly after removing iodised salt from their diet for about 1·5 years in the HIA in Hebei Province.
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Genetic variants of interleukin-4 gene in autoimmune thyroid diseases: An updated meta-analysis.
Autoimmunity
PUBLISHED: 10-07-2014
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Abstract Autoimmune thyroid diseases (AITDs) including Graves' disease (GD) and Hashimoto's thyroiditis (HT) are common autoimmune endocrine disorders. Interleukin-4 (IL-4), a cytokine secreted by T cells, plays a critical role in antigen-specific Th2 responses. The IL-4 gene is highly polymorphic and it has been reported that the polymorphism at -590 (T/C, rs2243250) in the promoter region of IL-4 may contribute to the development of AITDs. Recently, several case-control studies have examined the association of genetic variants of IL-4 with AITDs. However, the results of these studies remain conflicting. To systematically study the role of IL-4 in the pathogenesis of AITDs, we conducted a meta-analysis including 11 eligible studies (1847 cases and 2068 healthy controls). Fixed-effect or random-effect models were used to calculate pooled odds ratios (ORs) with corresponding 95% confidence intervals (CIs). Our results revealed a significant association between the IL-4 genetic variant (-590, T/C, rs2243250) and the risk of developing AITDs (TC?+?TT versus TT genotype: OR?=?1.83, 95% CI?=?1.083-3.091, p?=?0.024). These findings demonstrate that the IL-4 rs2243250 genetic variant might play a key role in the development of AITDs.
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The complete sequence of the mitochondrial genome of Sandu black pig (Sus Scrofa).
Mitochondrial DNA
PUBLISHED: 09-27-2014
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Abstract Sandu black pig is one of the native breed in Guizhou province in China. The total length of mitochondrial genome of Sandu black pig is 16,741?bp. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Sandu black pig. The mitochondrial genome data of Sandu black pig presented is useful novel markers for further studying the population genetics of sus scrofa.
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[Evaluation of left ventricular myocardial function in coronary atherosclerosis patients with type 2 diabetes mellitus by speckle tracking echocardiography].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 09-26-2014
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To evaluate the left ventricular (LV) myocardial function in coronary atherosclerosis patients with type 2 diabetes mellitus (DM) by two-dimensional speckle tracking echocardiography (2D STE).
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Profiling the Metabolism of Astragaloside IV by Ultra Performance Liquid Chromatography Coupled with Quadrupole/Time-of-Flight Mass Spectrometry.
Molecules
PUBLISHED: 09-24-2014
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Astragaloside IV is a compound isolated from the Traditional Chinese Medicine Astragalus membranaceus, that has been reported to have bioactivities against cardiovascular disease and kidney disease. There is limited information on the metabolism of astragaloside IV, which impedes comprehension of its biological actions and pharmacology. In the present study, an ultra-performance liquid chromatography coupled with quadrupole/time-of-flight mass spectrometry (UPLC-Q-TOF-MS/MS)-based approach was developed to profile the metabolites of astragaloside IV in rat plasma, bile, urine and feces samples. Twenty-two major metabolites were detected. The major components found in plasma, bile, urine and feces included the parent chemical and phases I and II metabolites. The major metabolic reactions of astragaloside IV were hydrolysis, glucuronidation, sulfation and dehydrogenation. These results will help to improve understanding the metabolism and reveal the biotransformation profiling of astragaloside IV in vivo. The metabolic information obtained from our study will guide studies into the pharmacological activity and clinical safety of astragaloside IV.
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Primary biliary cirrhosis-autoimmune hepatitis overlap syndrome: Simplified criteria may be effective in the diagnosis of Chinese patients.
J Dig Dis
PUBLISHED: 09-16-2014
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The aim of this study was to evaluate the performances of three criteria, the Paris criteria, the revised diagnostic criteria and the simplified diagnostic scoring system for the diagnosis of primary biliary cirrhosis (PBC)-autoimmune hepatitis (AIH) overlap syndrome in Chinese patients.
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[Research thoughts and technology system framework of jinfukang oral liquid secondary exploitation].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 09-11-2014
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Most Chinese medicine has good clinical efficacy and application. However, the material basis is vague for the lack of basic research, the value of Chinese medicine is hard to reflect for the low technology level and product quality is difficult to maintain for the quality control indicator selection is incorrect. Chinese medicine Jinfukang oral liquid is a typical product of Chinese medicines. Jinfukang oral liquid was selected as a model drug in this article. Based on the overall concept and systems theory of traditional Chinese medicine, the research idea and technology system for modern Chinese medicine secondary exploitation was formed. The system includes three parts, for the first, basic research to make clear the components structure and their action mechanism, for the second, technology upgraded to optimize process and improve the product quality, for the last, exploring the associated industry to form the industrial chain. The research ideas and technology system based on the material basis research and development of modern Chinese medicine, guided with component structure in Chinese medicine and aimed clinical needs. This research ideas and technology system provides strategies and methods for the development of modern Chinese medicine secondary exploitation.
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Site-specific recombination of nitrogen-fixation genes in cyanobacteria by XisF-XisH-XisI complex: Structures and models.
Proteins
PUBLISHED: 09-01-2014
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Nitrogen fixation is an important process that converts atmospheric gaseous nitrogen, a form plants cannot utilize, into ammonia that can be easily assimilated. Large serine recombinase XisF (fdxN element site-specific recombinase), together with controlling factors XisH and XisI, plays a critical role in the expression of nitrogen fixation genes of certain Anabaena and Nostoc species of cyanobacteria. All three proteins are required to excise the fdxN DNA element from the chromosome in differentiating heterocysts for the expression of nitrogen fixation related genes. We report the first crystal structures of XisH and XisI proteins, both adopting novel protein folds. Based on the analysis of their sequences and structures, we propose that XisH and XisI proteins function as endonucleases and recombination directionality factors (RDFs), respectively. © Proteins 2014;. © 2014 Wiley Periodicals, Inc.
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Clinical analysis of 56 patients with rhupus syndrome: manifestations and comparisons with systemic lupus erythematosus: a retrospective case-control study.
Medicine (Baltimore)
PUBLISHED: 08-30-2014
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To investigate the clinical features of Rhupus syndrome, we retrospectively reviewed the medical records of 56 patients with Rhupus who were hospitalized at the Peking Union Medical College Hospital, Beijing, China, between January 2000 and March 2013. We analyzed the clinical manifestations of Rhupus syndrome and compared these with a control group of 160 randomly selected systemic lupus erythematosus (SLE) patients without coexisting rheumatoid arthritis (RA). In our center, 1.30% (56/4301) of hospitalized SLE patients had Rhupus syndrome. The median disease duration was 8.0 years and 83.9% had RA onset. All Rhupus patients showed radiological erosion in the joints. Compared with the control group, Rhupus patients had a longer disease duration, higher prevalence of anticyclic citrullinated peptide antibody and rheumatoid factor, higher incidence of symmetrical polyarthritis with more joint deformities and rheumatic nodules, and increased erythrocyte sediment rate and c-reactive protein levels (P < 0.005). In addition, a lower SLE disease activity index and incidences of malar rash, hemolytic anemia, renal and neurological involvement (P < 0.005), and hypocomplementemia (P < 0.05) was observed in the Rhupus group.Rhupus syndrome is rare in SLE patients. Most Rhupus patients had RA onset and a distinctive clinical profile characterized by more severe RA-associated and mild SLE-associated damage. Specific autoantibodies and imaging findings could be helpful for making accurate Rhupus diagnoses.
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[The prevalence and clinical significance of arthritis in patients with systemic sclerosis].
Zhonghua Nei Ke Za Zhi
PUBLISHED: 08-23-2014
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To explore the prevalence and independent influencing factors of arthritis in Chinese patients with systemic sclerosis (SSc).
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DAX-1 inhibits hepatocellular carcinoma proliferation by inhibiting ?-catenin transcriptional activity.
Cell. Physiol. Biochem.
PUBLISHED: 08-19-2014
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Hepatocellular carcinoma (HCC) represents the most common type of liver cancer. DAX1 (dosage-sensitive sex reversal adrenal hypoplasia congenital critical region on X chromosome, gene 1), an atypical member of the nuclear receptor family due to lack of classical DNA-binding domains, has been known for its fundamental roles in the development, especially in the sex determination and steroidogenesis. Previous studies also showed that DAX-1 played a critical role in endocrine and sex steroid-dependent neoplasms such as adrenocortical, pituitary, endometrial, and ovarian tumors. However, its biological roles in the development of HCC remain largely unexplored.
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[Cardioprotective effect and mechanism of intensive lipid modulation on patients with coronary artery disease undergoing noncardiac surgery].
Beijing Da Xue Xue Bao
PUBLISHED: 08-19-2014
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To explore the protective effect and possible mechanism of intensive lipid modulation on the perioperative period of patients with stable coronary artery disease undergoing noncardiac surgery.
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ATO/ATRA/anthracycline-chemotherapy sequential consolidation achieves long-term efficacy in primary acute promyelocytic leukemia.
PLoS ONE
PUBLISHED: 08-14-2014
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The combination of all-trans retinoic acid (ATRA) and arsenic trioxide (As2O3, ATO) has been effective in obtaining high clinical complete remission (CR) rates in acute promyelocytic leukemia (APL), but the long-term efficacy and safety among newly diagnosed APL patients are unclear. In this retrospective study, total 45 newly diagnosed APL patients received ATRA/chemotherapy combination regimen to induce remission. Among them, 43 patients (95.6%) achieved complete remission (CR) after induction therapy, followed by ATO/ATRA/anthracycline-based chemotherapy sequential consolidation treatment with a median follow-up of 55 months. In these patients, the estimated overall survival (OS) and the relapse-free survival (RFS) were 94.4% ± 3.9% and 94.6 ± 3.7%, respectively. The toxicity profile was mild and reversible. No secondary carcinoma was observed. These results demonstrated the high efficacy and minimal toxicity of ATO/ATRA/anthracycline-based chemotherapy sequential consolidation treatment for newly diagnosed APL in long-term follow-up, suggesting a potential frontline therapy for APL.
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Pregnancy-related systemic lupus erythematosus: clinical features, outcome and risk factors of disease flares--a case control study.
PLoS ONE
PUBLISHED: 08-13-2014
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To investigate the clinical features, outcome, and risk factors of disease flares in patients with pregnancy-related lupus (PRL).
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The complete mitochondrial genome sequence of Diannan small-ear pig (Sus Scrofa).
Mitochondrial DNA
PUBLISHED: 08-05-2014
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Abstract In this study, the complete mitochondrial genome sequence of Diannan small-ear pig in Yunnan Province was firstly reported, which was determined through polymerase chain reaction (PCR) method. The total length of mitochondrial genome of Diannan small-ear pig was 16720?bp, including 34.77% A, 26.18% C, 25.81% T and 13.24% G, and in the order A?>?C?>?T?>?G. Mitochondrial genome contained a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. The mitochondrial genome of Diannan small-ear pig provides an important data set for the study on genetic mechanism.
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The complete sequence of the mitochondrial genome of Rongchang pig (Sus Scrofa).
Mitochondrial DNA
PUBLISHED: 08-05-2014
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Abstract Rongchang pig is one of the native breeds in Sichuan province in China. The total length of mitochondrial genome of Rongchang pig is 16,710?bp, including 34.67% A, 26.18% C, 25.82% T and 13.33% G, and in the order A?>?C?>?T?>?G. Mitochondrial genome contains a major non-coding control region (D-Loop region), 2 ribosomal RNA genes, 13 protein-coding genes (PCGs) and 22 transfer RNA genes. This is the first report of the complete mitochondrial genome sequence about Rongchang pig. The mitochondrial genome of Rongchang pig subsequently provides an important information in genetic mechanism and the evolution genomes.
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Characterization of a biopharmaceutical protein and evaluation of its purification process using automated capillary Western blot.
Electrophoresis
PUBLISHED: 08-01-2014
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This paper describes the application of an automated size-based capillary Western blot system (Sally instrument) from ProteinSimple, Inc., for biopharmaceutical Fusion-Fc protein characterization and evaluation of its purification process. The Fusion-Fc protein column purification from an excess of single chain Fc polypeptide and removal of an enzyme co-expressed for protein maturation have been demonstrated using an automated capillary Western system. The clearance of a selected host cell protein (HCP) present in cell culture of Fusion-Fc protein was also quantitatively monitored throughout the protein purification process. Additionally, the low levels of Fusion-Fc product-related impurities detected by traditional slab gel Western blot were confirmed by the automated capillary Western system. Compared to the manual approach, the automated capillary Western blot provides the advantages of ease of operation, higher sample throughput, greater linearity range and higher precision for protein quantitation. This article is protected by copyright. All rights reserved.
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Executive function and postural instability in people with Parkinson's disease.
Parkinsons Dis
PUBLISHED: 07-17-2014
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The specific aspects of cognition contributing to balance and gait have not been clarified in people with Parkinson's disease (PD). Twenty PD participants and twenty age- and gender-matched healthy controls were assessed on cognition and clinical mobility tests. General cognition was assessed with the Mini Mental State Exam and Addenbrooke's Cognitive Exam. Executive function was evaluated using the Trail Making Tests (TMT-A and TMT-B) and a computerized cognitive battery which included a series of choice reaction time (CRT) tests. Clinical gait and balance measures included the Tinetti, Timed Up & Go, Berg Balance, and Functional Reach tests. PD participants performed significantly worse than the controls on the tests of cognitive and executive function, balance, and gait. PD participants took longer on Trail Making Tests, CRT-Location, and CRT-Colour (inhibition response). Furthermore, executive function, particularly longer times on CRT-Distracter and greater errors on the TMT-B, was associated with worse balance and gait performance in the PD group. Measures of general cognition were not associated with balance and gait measures in either group. For PD participants, attention and executive function were impaired. Components of executive function, particularly those involving inhibition response and distracters, were associated with poorer balance and gait performance in PD.
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Allogeneic Bone Marrow Mesenchymal Stem Cell Transplantation in Patients with UDCA-Resistant Primary Biliary Cirrhosis.
Stem Cells Dev.
PUBLISHED: 07-16-2014
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The objective of this study was to evaluate the safety and efficacy of allogeneic bone marrow mesenchymal stromal/stem cell transplantation (BM-MSCT) for patients with ursodeoxycholic acid (UDCA)-resistant primary biliary cirrhosis (PBC). Ten patients were enrolled in this trial of BM-MSCT. All patients were permitted to concurrently continue their previous UDCA treatment. The efficacy of BM-MSCT in UDCA-resistant PBC was assessed at various time points throughout the 12-month follow up. No transplantation-related side effects were observed. The life quality of the patients was improved after BM-MSCT as demonstrated by responses to the PBC-40 questionnaire. Serum levels of ALT, AST, ?-GT, and IgM significantly decreased from baseline after BM-MSCT. In addition, the percentage of CD8(+) T cells was reduced, while that of CD4(+)CD25(+)Foxp3(+) T cells was increased in peripheral lymphocytic subsets. Serum levels of IL-10 were also elevated. Notably, the optimal therapeutic outcome was acquired in 3 to 6 months and could be maintained for 12 months after BM-MSCT. In conclusion, allogeneic BM-MSCT in UDCA-resistant PBC is safe and appears to be effective.
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BridgeDb app: unifying identifier mapping services for Cytoscape.
F1000Res
PUBLISHED: 07-01-2014
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The BridgeDb app for Cytoscape allows users to map and annotate identifiers of genes, proteins and metabolites in the context of biological networks. The app greatly simplifies the identifier mapping process in Cytoscape by providing a unified interface to different mapping resources and services. The app also provides a programming interface via Cytoscape Commands that can be utilized for identifier mapping by other Cytoscape apps. In this article we provide a technical guide to the BridgeDb app for mapping identifiers in Cytoscape.
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Image Classification with Densely Sampled Image Windows and Generalized Adaptive Multiple Kernel Learning.
IEEE Trans Cybern
PUBLISHED: 06-27-2014
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We present a framework for image classification that extends beyond the window sampling of fixed spatial pyramids and is supported by a new learning algorithm. Based on the observation that fixed spatial pyramids sample a rather limited subset of the possible image windows, we propose a method that accounts for a comprehensive set of windows densely sampled over location, size, and aspect ratio. A concise high-level image feature is derived to effectively deal with this large set of windows, and this higher level of abstraction offers both efficient handling of the dense samples and reduced sensitivity to misalignment. In addition to dense window sampling, we introduce generalized adaptive ?p-norm multiple kernel learning (GA-MKL) to learn a robust classifier based on multiple base kernels constructed from the new image features and multiple sets of prelearned classifiers from other classes. With GA-MKL, multiple levels of image features are effectively fused, and information is shared among different classifiers. Extensive evaluation on benchmark datasets for object recognition (Caltech256 and Caltech101) and scene recognition (15Scenes) demonstrate that the proposed method outperforms the state-of-the-art under a broad range of settings.
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Spectral embedded hashing for scalable image retrieval.
IEEE Trans Cybern
PUBLISHED: 06-22-2014
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We propose a new graph based hashing method called spectral embedded hashing (SEH) for large-scale image retrieval. We first introduce a new regularizer into the objective function of the recent work spectral hashing to control the mismatch between the resultant hamming embedding and the low-dimensional data representation, which is obtained by using a linear regression function. This linear regression function can be employed to effectively handle the out-of-sample data, and the introduction of the new regularizer makes SEH better cope with the data sampled from a nonlinear manifold. Considering that SEH cannot efficiently cope with the high dimensional data, we further extend SEH to kernel SEH (KSEH) to improve the efficiency and effectiveness, in which a nonlinear regression function can also be employed to obtain the low dimensional data representation. We also develop a new method to efficiently solve the approximate solution for the eigenvalue decomposition problem in SEH and KSEH. Moreover, we show that some existing hashing methods are special cases of our KSEH. Our comprehensive experiments on CIFAR, Tiny-580K, NUS-WIDE, and Caltech-256 datasets clearly demonstrate the effectiveness of our methods.
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[Construction of research system for processing mechanism of traditional Chinese medicine based on chemical composition transformation combined with intestinal absorption barrier].
Zhongguo Zhong Yao Za Zhi
PUBLISHED: 06-21-2014
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Based on practice of Epimedium processing mechanism for many years and integrated multidisciplinary theory and technology, this paper initially constructs the research system for processing mechanism of traditional Chinese medicine based on chemical composition transformation combined with intestinal absorption barrier, which to form an innovative research mode of the " chemical composition changes-biological transformation-metabolism in vitro and in vivo-intestinal absorption-pharmacokinetic combined pharmacodynamic-pharmacodynamic mechanism". Combined with specific examples of Epimedium and other Chinese herbal medicine processing mechanism, this paper also discusses the academic thoughts, research methods and key technologies of this research system, which will be conducive to systematically reveal the modem scientific connotation of traditional Chinese medicine processing, and enrich the theory of Chinese herbal medicine processing.
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Long-term experiment on physiological responses to synergetic effects of ocean acidification and photoperiod in the Antarctic sea ice algae Chlamydomonas sp. ICE-L.
Environ. Sci. Technol.
PUBLISHED: 06-20-2014
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Studies on ocean acidification have mostly been based on short-term experiments of low latitude with few investigations of the long-term influence on sea ice communities. Here, the combined effects of ocean acidification and photoperiod on the physiological response of the Antarctic sea ice microalgae Chlamydomonas sp. ICE-L were examined. There was a general increase in growth, PSII photosynthetic parameters, and N and P uptake in continuous light, compared to those exposed to regular dark and light cycles. Elevated pCO2 showed no consistent effect on growth rate (p=0.8) and N uptake (p=0.38) during exponential phrase, depending on the photoperiod but had a positive effect on PSII photosynthetic capacity and P uptake. Continuous dark reduced growth, photosynthesis, and nutrient uptake. Moreover, intracellular lipid, mainly in the form of PUFA, was consumed at 80% and 63% in low and high pCO2 in darkness. However, long-term culture under high pCO2 gave a more significant inhibition of growth and Fv/Fm to high light stress. In summary, ocean acidification may have significant effects on Chlamydomonas sp. ICE-L survival in polar winter. The current study contributes to an understanding of how a sea ice algae-based community may respond to global climate change at high latitudes.
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Diverse and divergent protein post-translational modifications in two growth stages of a natural microbial community.
Nat Commun
PUBLISHED: 06-16-2014
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Detailed characterization of post-translational modifications (PTMs) of proteins in microbial communities remains a significant challenge. Here we directly identify and quantify a broad range of PTMs (hydroxylation, methylation, citrullination, acetylation, phosphorylation, methylthiolation, S-nitrosylation and nitration) in a natural microbial community from an acid mine drainage site. Approximately 29% of the identified proteins of the dominant Leptospirillum group II bacteria are modified, and 43% of modified proteins carry multiple PTM types. Most PTM events, except S-nitrosylations, have low fractional occupancy. Notably, PTM events are detected on Cas proteins involved in antiviral defense, an aspect of Cas biochemistry not considered previously. Further, Cas PTM profiles from Leptospirillum group II differ in early versus mature biofilms. PTM patterns are divergent on orthologues of two closely related, but ecologically differentiated, Leptospirillum group II bacteria. Our results highlight the prevalence and dynamics of PTMs of proteins, with potential significance for ecological adaptation and microbial evolution.
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[Prospective study of efficacy and safety of hydroxychloroquine in pregnant patients with systemic lupus erythematosus].
Zhonghua Yi Xue Za Zhi
PUBLISHED: 05-24-2014
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To evaluate the efficacy and safety of hydroxychloroquine (HCQ) in pregnant patients with systemic lupus erythematosus (SLE).
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RNA-protein distance patterns in ribosomes reveal the mechanism of translational attenuation.
Sci China Life Sci
PUBLISHED: 05-22-2014
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Elucidating protein translational regulation is crucial for understanding cellular function and drug development. A key molecule in protein translation is ribosome, which is a super-molecular complex extensively studied for more than a half century. The structure and dynamics of ribosome complexes were resolved recently thanks to the development of X-ray crystallography, Cryo-EM, and single molecule biophysics. Current studies of the ribosome have shown multiple functional states, each with a unique conformation. In this study, we analyzed the RNA-protein distances of ribosome (2.5 MDa) complexes and compared these changes among different ribosome complexes. We found that the RNA-protein distance is significantly correlated with the ribosomal functional state. Thus, the analysis of RNA-protein binding distances at important functional sites can distinguish ribosomal functional states and help understand ribosome functions. In particular, the mechanism of translational attenuation by nascent peptides and antibiotics was revealed by the conformational changes of local functional sites.
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Transmembrane protein 106A is silenced by promoter region hypermethylation and suppresses gastric cancer growth by inducing apoptosis.
J. Cell. Mol. Med.
PUBLISHED: 05-21-2014
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Inactivation of tumour suppressor genes by promoter methylation plays an important role in the initiation and progression of gastric cancer (GC). Transmembrane 106A gene (TMEM106A) encodes a novel protein of previously unknown function. This study analysed the biological functions, epigenetic changes and the clinical significance of TMEM106A in GC. Data from experiments indicate that TMEM106A is a type II membrane protein, which is localized to mitochondria and the plasma membrane. TMEM106A was down-regulated or silenced by promoter region hypermethylation in GC cell lines, but expressed in normal gastric tissues. Overexpression of TMEM106A suppressed cell growth and induced apoptosis in GC cell lines, and retarded the growth of xenografts in nude mice. These effects were associated with the activation of caspase-2, caspase-9, and caspase-3, cleavage of BID and inactivation of poly (ADP-ribose) polymerase (PARP). In primary GC samples, loss or reduction of TMEM106A expression was associated with promoter region hypermethylation. TMEM106A was methylated in 88.6% (93/105) of primary GC and 18.1% (2/11) in cancer adjacent normal tissue samples. Further analysis suggested that TMEM106A methylation in primary GCs was significantly correlated with smoking and tumour metastasis. In conclusion, TMEM106A is frequently methylated in human GC. The expression of TMEM106A is regulated by promoter hypermethylation. TMEM106A is a novel functional tumour suppressor in gastric carcinogenesis.
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Acute pleural and pericardial effusion induced by chemotherapy in treating chronic myelocytic leukemia.
Clin. Lab.
PUBLISHED: 05-21-2014
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Report of a rare and serious complication of chemotherapy with daunorubicin and cytarabine (DA regimen).
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Saltation of particles in turbulent channel flow.
Phys Rev E Stat Nonlin Soft Matter Phys
PUBLISHED: 05-07-2014
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This paper numerically investigates particle saltation in a turbulent channel flow having a rough bed consisting of two to three layers of densely packed spheres. The Shields function is 0.065 which is just above the sediment entrainment threshold to give a bed-load regime. The applied methodology is a combination of three technologies, i.e., the direct numerical simulation of turbulent flow; the combined finite-discrete element modeling of the deformation, movement, and collision of the particles; and the immersed boundary method for the fluid-solid interaction. It is shown that the presence of entrained particles significantly modifies the flow profiles of velocity, turbulent intensities, and shear stresses in the vicinity of a rough bed. The quasi-streamwise-aligned streaky structures are not observed in the near-wall region and the particles scatter on the rough bed owing to their large size. However, in the outer flow region, the turbulent coherent structures recover due to the weakening rough-bed effects and particle interferences. First- and second-order statistical features of particle translational and angular velocities, together with sediment concentration and volumetric flux density profiles, are presented. Several key parameters of the particle saltation trajectory are calculated and agree closely with published experimental data. Time histories of the hydrodynamic forces exerted upon a typical saltating particle, together with those of the particle's coordinates and velocities, are presented. A strong correlation is shown between the abruptly decreasing streamwise velocity and increasing vertical velocity at collision which indicates that the continuous saltation of large-grain-size particles is controlled by collision parameters such as particle incident angle, local bed packing arrangement, and particle density, etc.
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Differentiating enteric Escherichia coli from environmental bacteria through the putative glucosyltransferase gene (ycjM).
Water Res.
PUBLISHED: 05-04-2014
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This study is to tackle the challenge posed by the "naturalized" Escherichia coli population against the worldwide practice of E. coli-based water quality monitoring. In the literature, the putative glucosyltransferase gene (ycjM) of E. coli has been identified in silico to be one of the 114 genes specific to enteric E. coli. Based on the sequence of E. coli K-12 MG1655, a PCR assay (ycjPCR) targeting ycjM was developed in this study. As demonstrated by the ycjPCR assay using 367 E. coli strains isolated from animal feces, 97.2% of the isolates carried the ycjM with variations from 93.9% to 100% among nine different host sources, but none of the 17 strains of non-E. coli bacteria and only 23.0% of the environment-isolated cryptic Escherichia strains contained the ycjM. These data experimentally confirmed ycjM to be enteric specific. Our study also showed that the ycjPCR assay was superior to the commonly used tuf- or uidA-based PCR methods in differentiating enteric E. coli from ß-D-glucuronidase-positive environmental bacteria. Furthermore, study on 190 E. coli isolates from water samples, using EPA Method 1603 followed by bacterial identification with Biolog MicroStation™ and ycjPCR assay, indicated that the prevalence of ycjM in the E. coli water isolates had a significant (p < 0.05, odds ratio ) spatial variation from 69.6% to 93.8%. These data suggest that E. coli profile using EPA Method 1603 or other ß-D-glucuronidase-activity-based methods may need further analysis using the ycjM profile to accurately determinate fecal pollution in water.
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Is nationwide special campaign on antibiotic stewardship program effective on ameliorating irrational antibiotic use in China? Study on the antibiotic use of specialized hospitals in China in 2011-2012.
J. Huazhong Univ. Sci. Technol. Med. Sci.
PUBLISHED: 04-28-2014
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With dwindling number of new antibiotics and inappropriate use of antibiotics, the emergence and spread of antibiotics resistance occurs commonly in healthcare institutions worldwide. In China, antibiotics are commonly over prescribed and misused. This study is to assess the effect of the nationwide special campaign on antibiotic stewardship program (ASP) at specialized hospitals in China by investigating prescription information from 2011 to 2012. Data on the hospital consumption and prescription of systemic antibiotics were obtained from four specialized hospitals, including maternity, children's, stomatological and cancer hospitals. Systematic random sampling was used to select outpatient prescriptions and inpatient cases. A total of 105 specialized hospitals in 2011 and 121 specialized hospitals in 2012 were analysed. The defined daily doses (DDDs) per 100 inpatient days, the percentage of antibiotic use in outpatient prescriptions, and the percentage of antibiotic use in inpatient cases were used as measurements of antibiotic use. The overall antibiotic use density in the selected hospitals decreased between 2011 and 2012 from 39.37 to 26.54 DDD/100 inpatient days (P<0.001). The percentage of antibiotic use in outpatient prescriptions (range: 24.12%-18.71%, P=0.109) and inpatient cases (64.85%-60.10%, P=0.006) also decreased within the two years. Significant changes were observed among regions and different hospitals within the two years. And antibiotic consumption was correlated with the type and size of specialized hospital in 2012, but not with the regions. This analysis of antibiotic consumption of specialized hospitals allows relevant comparisons for benchmarking and shows that national ASP has improved antibiotic rational use in China. The data will assist policymakers in formulating effective strategies to decrease antibiotic overuse and identify areas that require further work.
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Clinical and laboratory characteristics of systemic sclerosis patients with pulmonary arterial hypertension in China.
Clin. Exp. Rheumatol.
PUBLISHED: 04-27-2014
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Pulmonary arterial hypertension (PAH) is associated with significant morbidity and mortality, especially in systemic sclerosis (SSc). Since there was no published study regarding PAH in the Chinese SSc population, we aimed to describe a cohort to provide some data for early diagnosis.
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Identification and evaluation of quantitative trait loci underlying resistance to multiple HG types of soybean cyst nematode in soybean PI 437655.
Theor. Appl. Genet.
PUBLISHED: 03-04-2014
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We performed QTL analysis for SCN resistance in PI 437655 in two mapping populations, characterized CNV of Rhg1 through whole-genome resequencing and evaluated the effects of QTL pyramiding to enhance resistance. Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most serious pests of soybean worldwide. PI 437655 has broader resistance to SCN HG types than PI 88788. The objectives of this study were to identify quantitative trait loci (QTL) underlying SCN resistance in PI 437655, and to evaluate the QTL for their contribution to SCN resistance. Two F6:7 recombinant inbred line populations, derived from cv. Williams 82 × PI 437655 and cv. Hutcheson × PI 437655 crosses, were evaluated for resistance to SCN HG types 1.2.5.7 (PA2), 0 (PA3), 1.3.5.6.7 (PA14), and 1.2.3.4.5.6.7 (LY2). The 1,536 SNP array was used to genotype the mapping populations and construct genetic linkage maps. Two significant QTL were consistently mapped on chromosomes (Chr.) 18 and 20 in these two populations. One QTL on Chr. 18, which corresponds to the known Rhg1 locus, contributed resistance to SCN HG types 1.2.5.7, 0, 1.3.5.6.7, and 1.2.3.4.5.6.7 (PA2, PA3, PA14, and LY2, respectively). Copy number variation (CNV) analysis by whole-genome resequencing showed that PI 437655 and PI 88788 had similar CNV at the Rhg1 locus. The QTL on Chr. 20 contributed resistance to SCN HG types 1.3.5.6.7 (PA14) and 1.2.3.4.5.6.7 (LY2). Evaluation of both QTL showed that pyramiding of Rhg1 and the QTL on Chr. 20 significantly improved the resistance to SCN HG types 1.3.5.6.7 (PA14) and 1.2.3.4.5.6.7 (LY2) in both populations. Our studies provided useful information for deploying PI 437655 as a donor for SCN resistance in soybean breeding through marker-assisted selection.
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xMDFF: molecular dynamics flexible fitting of low-resolution X-ray structures.
Acta Crystallogr. D Biol. Crystallogr.
PUBLISHED: 02-14-2014
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X-ray crystallography remains the most dominant method for solving atomic structures. However, for relatively large systems, the availability of only medium-to-low-resolution diffraction data often limits the determination of all-atom details. A new molecular dynamics flexible fitting (MDFF)-based approach, xMDFF, for determining structures from such low-resolution crystallographic data is reported. xMDFF employs a real-space refinement scheme that flexibly fits atomic models into an iteratively updating electron-density map. It addresses significant large-scale deformations of the initial model to fit the low-resolution density, as tested with synthetic low-resolution maps of D-ribose-binding protein. xMDFF has been successfully applied to re-refine six low-resolution protein structures of varying sizes that had already been submitted to the Protein Data Bank. Finally, via systematic refinement of a series of data from 3.6 to 7?Å resolution, xMDFF refinements together with electrophysiology experiments were used to validate the first all-atom structure of the voltage-sensing protein Ci-VSP.
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Pregnenolone, a cholesterol metabolite, induces glioma cell apoptosis via activating extrinsic and intrinsic apoptotic pathways.
Oncol Lett
PUBLISHED: 02-07-2014
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Gliomas are one of the most common types of malignant tumors worldwide, however, an effective therapeutic strategy not yet been fully determined. The present study aimed to investigate the anti-glioma activity and underlying mechanisms of pregnenolone, which originates from cholesterol and is metabolized into important steroid hormones in the body. The results demonstrated that 100 ?M pregnenolone induced a significant loss of cell viability in various malignant glioma cell lines. In the U-87 MG, LN-18 and C6 cell lines, the loss of cell viability resulted from cell apoptosis, which was evidenced by apoptotic nuclear morphology changes and caspase 3 activation. Moreover, the increased activities of caspase 8 and 9 strongly indicated that pregnenolone activated the extrinsic and intrinsic pathways of apoptosis. Additionally, glioma cell apoptosis was prevented by the general caspase inhibitor, Z-VAD-FMK. In the C6 cells, upregulation of Fas and Fas ligand triggered the activation of the extrinsic pathway, whereas knockdown of Fas significantly abrogated the cell apoptosis that was induced by pregnenolone. Furthermore, downregulation of the anti-apoptotic protein, B-cell lymphoma 2 and upregulation of pro-apoptotic proteins, such as Bax and Bak, activated the intrinsic pathway. In conclusion, pregnenolone induced glioma cell apoptosis in a caspase-dependent manner, which was mediated by activation of the extrinsic and intrinsic apoptotic pathways.
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A randomized phase 2b study of peginterferon lambda-1a for the treatment of chronic HCV infection.
J. Hepatol.
PUBLISHED: 01-20-2014
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Peginterferon lambda-1a (Lambda) is a type-III interferon with similar antiviral activity to alfa interferons but with a diminished extrahepatic receptor distribution, reducing the risk for extrahepatic adverse events.
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New metabolite profiles of Danshensu in rats by ultraperformance liquid chromatography/quadrupole-time-of-flight mass spectrometry.
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
PUBLISHED: 01-11-2014
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In our research, ultraperformance liquid chromatography/quadrupole-time-of-flight mass spectrometry (U-HPLC/Q-TOF-MS) was established for analyzing the metabolite profiles of Danshensu (DSS) in rat feces, bile, urine, plasma and the possible metabolic pathways were subsequently proposed after the oral dose of 80mg/kg; rat biological samples were collected and pretreated by protein precipitation. Then, the samples were injected into an Acquity ultraperformance liquid chromatography BEHC column with mobile phase consisted of acetonitrile (solvent A)-0.1% formic acid-water (solvent B) with a linear gradient elution program. Totally, 17 metabolites of DSS were identified, including 4, 5, 4 and 4 metabolites in the feces, urine, blood, and bile samples respectively. Most of them were to our knowledge reported for the first time. The results indicated that DSS was metabolized via dehydrogenation, deoxygenation, methylation, glucuronidation, and sulfation pathways in vivo. Among these, methylation was considered as the main physiologic processes of it. This study revealed that U-HPLC/Q-TOF-MS was more accurate and sensitive to detect and identify the possible metabolites and to better understand the metabolism of DSS in vivo.
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The expression of a novel anti-inflammatory cytokine IL-35 and its possible significance in childhood asthma.
Immunol. Lett.
PUBLISHED: 01-07-2014
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Interleukin-35 (IL-35) is a novel anti-inflammatory cytokine and has been shown to play an important role in maintaining immune homeostasis. However, the effect of IL-35 on human asthma remains unclear. The present study is to investigate the expression and significance of IL-35 in childhood asthma. Forty-one asthmatic children and forty-two healthy controls were recruited in Qilu Children's Hospital of Shandong University. Serum total immunoglobulin E level was measured by radioimmunosorbent test. Peripheral blood eosinophils were counted using BC-5800 Automatic Blood Cell Analyzer. IL-35 mRNA in peripheral blood mononuclear cells was detected by quantitative real-time polymerase chain reaction. Serum IL-35, IL-4 and interferon-? levels were measured using enzyme-linked immunosorbent assay. The correlations among the above indexes were also analyzed using Pearson's method. Our results showed that serum total IgE, eosinophil count and serum IL-4 were significantly increased in asthmatic children compared with control children, and serum IFN-? level in asthmatic patients was obviously lower than that in healthy controls. We also found that there was an obviously positive correlation between serum IgE and IL-4 levels in asthmatic patients. In addition, significantly negative correlation was found between serum total IgE and IFN-? levels. More importantly, we found that the expression of IL-35 mRNA and protein was both down-regulated in asthmatic children, and serum IL-35 level was inversely related to serum IL-4 level. Moreover, significantly positive correlation was also found between serum IL-35 and IFN-? levels. The results suggest that the decreased expression of IL-35 could be involved in the pathogenesis of childhood asthma.
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Magnetic-luminescent YbPO4:Er,Dy microspheres designed for tumor theranostics with synergistic effect of photodynamic therapy and chemotherapy.
Int J Nanomedicine
PUBLISHED: 01-01-2014
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In this paper, magnetic and fluorescent bifunctional YbPO4:Er,Dy microspheres were synthesized via a simple solvothermal method. The prepared microspheres exposed to 980 nm near-infrared (NIR) laser light emitted bright upconversion fluorescence (450-570 nm) after calcination at high temperatures (>800°C). Results of magnetic resonance studies demonstrated that the YbPO4:Er,Dy microspheres are more suitable to be used as a transverse relaxation time (negative) contrast magnetic resonance imaging agent. The microspheres successfully entered the human hepatocellular carcinoma cells and presented low toxicity. A well-selected photodynamic therapy (PDT) drug, merocyanine 540 (MC540) with an ultraviolet-visible spectroscopy absorption maximum of 540 nm, was loaded onto the microspheres to obtain YbPO4:Er,Dy-MC540. Since the upconversion fluorescence emitting from the microspheres could be absorbed by MC540 with a small absorption/emission disparity, YbPO4:Er,Dy-MC540 could kill the hepatocellular carcinoma cells via PDT mechanism effectively. In other words, being upconverting particles, the prepared microspheres acted as light transducers in the NIR light-triggered PDT process. A chemotherapy drug, doxorubicin, was further loaded onto YbPO4:Er,Dy-MC540 to achieve enhanced antitumor effect based on synergistic therapeutic efficacy of PDT and chemotherapy. It is expected that the prepared YbPO4:Er,Dy microspheres have applications in tumor theranostics including magnetic-fluorescent bimodal imaging and NIR light-triggered PDT.
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Feasibility of fine-needle aspiration biopsy and its applications in superficial cervical lesion biopsies.
Int J Clin Exp Pathol
PUBLISHED: 01-01-2014
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The aim of the study was to investigate the feasibility and value of clinical application of fine-needle aspiration histological biopsy via ultrasound-guided thyroid nodule and enlarged cervical lymph node fine-needle aspiration histological biopsy. Fine-needle aspiration cytological and histological biopsies and surgical treatments were performed on 982 patients with thyroid nodule and 1435 patients with enlarged cervical lymph nodes. A comparative study of the histological and cytological examination results and post-surgical etiology results was subsequently conducted. Among the 982 thyroid nodule patients, the acquisition rates were 89.8% (882/982) for fine-needle aspiration histological biopsy and 96.2% (945/982) for cytological biopsy, while among the 1435 patients with enlarged cervical lymph nodes, the acquisition rate for fine-needle aspiration cytological biopsy was slightly higher than that for histological biopsy, with values of 95.7% (1374/1435) and 91.4% (1312/1435), respectively. For the thyroid nodule patients, when the acquired histological and cytological biopsy results were compared with the post-surgical etiology results, the sensitivity, specificity, and accuracy of the histological results were 98.5%, 100%, and 98.9%, respectively, whereas those of the cytological results were 86.8%, 82.9%, and 85.6%, respectively; the differences between the 2 biopsy methods were statistically significant (P < 0.05). For the patients with enlarged cervical lymph nodes, when the acquired histological and cytological biopsy results were compared with the post-surgical etiology results, the sensitivity, specificity, and accuracy of the histological results were 96.3%, 99.8%, and 97.6%, respectively, whereas the those of the cytological results were 76.8%, 92.1%, and 82.2%, respectively; again, the differences between the 2 methods were statistically significant (P < 0.05). In conclusion, Fine-needle aspiration histological biopsy is a reliable and highly accurate examination method. It is simple and feasible, thus facilitating the discrimination of malignant and benign thyroid nodules and enlarged cervical lymph nodes and playing an important role in the establishment of reasonable clinical therapeutic regimens.
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Expression of Derlin-1 and its effect on expression of autophagy marker genes under endoplasmic reticulum stress in lung cancer cells.
Cancer Cell Int.
PUBLISHED: 01-01-2014
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Recent findings indicated that Derlin-1 has an important function in tumour progression. In this study, we aimed to determine whether Derlin-1 has an oncogene function as a cross-talk molecule with autophagy.
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Disrupting KATP channels diminishes the estrogen-mediated protection in female mutant mice during ischemia-reperfusion.
Clin Proteomics
PUBLISHED: 01-01-2014
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Estrogen has been shown to mediate protection in female hearts against ischemia-reperfusion (I-R) stress. Composed by a Kir6.2 pore and an SUR2 regulatory subunit, cardiac ATP-sensitive potassium channels (KATP) remain quiescent under normal physiological conditions but they are activated by stress stimuli to confer protection to the heart. It remains unclear whether KATP is a regulatory target of estrogen in the female-specific I-R signaling pathway. In this study, we aimed at delineating the molecular mechanism underlying estrogen modulation on KATP channel activity during I-R.
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Enhanced bioavailability of apigenin via preparation of a carbon nanopowder solid dispersion.
Int J Nanomedicine
PUBLISHED: 01-01-2014
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In this study, a novel carbon nanopowder (CNP) drug carrier was developed to improve the oral bioavailability of apigenin (AP). Solid dispersions (SDs) of AP with CNP were prepared, and their in vitro drug release and in vivo performance were evaluated. The physicochemical properties of the formulations were examined by differential scanning calorimetry, X-ray diffraction, and scanning electron microscopy. Drug release profiles showed that AP dissolution from the CNP-AP system (weight ratio, 6:1) after 60 minutes improved by 275% compared with that of pure AP. Moreover, the pharmacokinetic analysis of SD formulations in rats showed that the AP area under the curve0-t value was 1.83 times higher for the CNP-AP system than for pure AP, indicating that its bioavailability was significantly improved. In addition, compared with pure AP, SDs had a significantly higher peak and shorter time to peak. Preliminary intestinal toxicity tests indicated that there was no significant difference in the tissues of the rats treated with the CNP-AP system, rats treated with the CNP alone, and controls. In conclusion, CNP-based SDs could be used for enhancing the bioavailability of poorly water-soluble drugs while also improving drug safety.
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Downregulation of mTOR by lentivirus inhibits prostate cancer cell growth.
Int J Clin Exp Pathol
PUBLISHED: 01-01-2014
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Prostate cancer, one of the most lethal forms of urinary system cancer, remains resistant to currently available treatments. Therefore, novel mechanism and target-based approaches are needed for the management of this neoplasm. PI3K/AKT signaling pathway activation correlates with human prostate cancer progression and metastasis. However, the role of mTOR in prostate cancer is not well-established. Here, we demonstrate that mTOR is over-expressed in both clinical tissue specimens and cultured human prostate cancer cells when compared to normal prostate tissues, respectively. Further, mTOR gene knockdown via lentivirus mediated mTOR specific shRNA resulted in a significant decrease in the viability and growth of prostate cancer cells without affecting normal human prostate cells. In addition, mTOR inhibition resulted in a significant i) decrease in 4EBP1, S6K, PI3K and AKT protein, ii) increase in PARP protein of prostate cancer cells. Most importantly, mTOR inhibition triggered apoptosis and suppressed pancreatic carcinoma growth in vivo in a mouse xenograft model. We suggest that targeting of mTOR may be a viable approach for the treatment of prostate cancer.
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P3DB 3.0: From plant phosphorylation sites to protein networks.
Nucleic Acids Res.
PUBLISHED: 11-15-2013
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In the past few years, the Plant Protein Phosphorylation Database (P(3)DB, http://p3db.org) has become one of the most significant in vivo data resources for studying plant phosphoproteomics. We have substantially updated P(3)DB with respect to format, new datasets and analytic tools. In the P(3)DB 3.0, there are altogether 47 923 phosphosites in 16 477 phosphoproteins curated across nine plant organisms from 32 studies, which have met our multiple quality standards for acquisition of in vivo phosphorylation site data. Centralized by these phosphorylation data, multiple related data and annotations are provided, including protein-protein interaction (PPI), gene ontology, protein tertiary structures, orthologous sequences, kinase/phosphatase classification and Kinase Client Assay (KiC Assay) data-all of which provides context for the phosphorylation event. In addition, P(3)DB 3.0 incorporates multiple network viewers for the above features, such as PPI network, kinase-substrate network, phosphatase-substrate network, and domain co-occurrence network to help study phosphorylation from a systems point of view. Furthermore, the new P(3)DB reflects a community-based design through which users can share datasets and automate data depository processes for publication purposes. Each of these new features supports the goal of making P(3)DB a comprehensive, systematic and interactive platform for phosphoproteomics research.
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Soybean knowledge base (SoyKB): a web resource for integration of soybean translational genomics and molecular breeding.
Nucleic Acids Res.
PUBLISHED: 10-16-2013
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Soybean Knowledge Base (http://soykb.org) is a comprehensive web resource developed for bridging soybean translational genomics and molecular breeding research. It provides information for six entities including genes/proteins, microRNAs/sRNAs, metabolites, single nucleotide polymorphisms, plant introduction lines and traits. It also incorporates many multi-omics datasets including transcriptomics, proteomics, metabolomics and molecular breeding data, such as quantitative trait loci, traits and germplasm information. Soybean Knowledge Base has a new suite of tools such as In Silico Breeding Program for soybean breeding, which includes a graphical chromosome visualizer for ease of navigation. It integrates quantitative trait loci, traits and germplasm information along with genomic variation data, such as single nucleotide polymorphisms, insertions, deletions and genome-wide association studies data, from multiple soybean cultivars and Glycine soja.
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FFAS-3D: improving fold recognition by including optimized structural features and template re-ranking.
Bioinformatics
PUBLISHED: 10-15-2013
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?Homology detection enables grouping proteins into families and prediction of their structure and function. The range of application of homology-based predictions can be significantly extended by using sequence profiles and incorporation of local structural features. However, incorporation of the latter terms varies a lot between existing methods, and together with many examples of distant relations not recognized even by the best methods, suggests that further improvements are still possible.
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Mitochondrial DNA sequence of the hybrid of Duroc (?)?×?[Landrace (?)?×?Yorshire (?)] pig.
Mitochondrial DNA
PUBLISHED: 10-10-2013
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Abstract Duroc (?)?×?[Landrace (?)?×?Yorshire (?)] (D?×?LY) pig is the popular hybrid pigs in order to make the most use of the heterosis in the world. In this study, the complete nucleotide sequence of D?×?LY pig mitochondrial genome was determined for the first time. Sequence analysis showed that the genome structure was in accordance with other pig breeds. It contained 22 tRNA genes, 2 ribosomal RNA genes, 13 protein-coding genes and 1 control region (D-loop region). The complete mitochondrial genome sequence of the D?×?LY pig provides an important data set for further study in genetic mechanism.
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Circles within circles: crosstalk between protein Ser/Thr/Tyr-phosphorylation and Met oxidation.
BMC Bioinformatics
PUBLISHED: 10-09-2013
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Reversible posttranslational protein modifications such as phosphorylation of Ser/Thr/Tyr and Met oxidation are critical for both metabolic regulation and cellular signalling. Although these modifications are typically studied individually, herein we describe the potential for cross-talk and hierarchical regulation.
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The complete mitochondrial genome of the Daweizi pig.
Mitochondrial DNA
PUBLISHED: 10-05-2013
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Abstract Daweizi pig is one of the famous native breed in China. In this work we reported the complete mitochondrial genome sequence of the Daweizi pig in Human Province for the first time. The total length of the mitogenome is 16,690?bp, with the base composition of 34.68% for A, 25.80% for T, 26.21% for C, 13.31% for G and an A?+?T (60.48%)-rich feature occurs in the Daweizi pig. It is made up of two ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and one non-coding control region (D-loop region). The arrangement of these genes was the same as that found in the Landrace pig. The complete mitochondrial genome sequence of the Daweizi pig provides an important data set for further study on the germplasm resources.
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The complete mitochondrial genome of the Ningxiang pig.
Mitochondrial DNA
PUBLISHED: 09-20-2013
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Abstract In this work, we reported the complete mitochondrial genome sequence of the Ningxiang pig (Human Province), which was determined through PCR-based method. The total length of the mitogenome is 16,690?bp. The overall composition of the mitogenome was estimated to be 34.70% for A, 25.81% for T, 26.18% for C, 13.30% for G, respectively, indicating that an A?+?T(60.52%)-rich feature occurs in the Ningxiang pig. It contains the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region). The arrangement of these genes was the same as that found in the Landrace pig. All the protein initiation codons are ATG, except for ND2. ND3 and ND5 are ATA, ND4L is GTG. The complete mitochondrial genome sequence of the Ningxiang pig in Human Province provides an important data for further study about genetic mechanism.
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The complete mitochondrial genome of the Shaziling pig.
Mitochondrial DNA
PUBLISHED: 09-20-2013
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Abstract In this study, the complete mitochondrial genome sequence of the Shaziling pig was reported in Human Province, which was determined through PCR-based method. The total length of the mitogenome is 16,690?bp. It contains the typical structure, including 2 ribosomal RNA genes, 13 protein-coding genes, 22 transfer RNA genes and 1 non-coding control region (D-loop region) as that of most other vertebrates. The overall composition of the mitogenome was estimated to be 34.67% for A, 25.84% for T, 26.17% for C and 13.32% for G, with an A?+?T (60.51%)-rich feature in the Shaziling pig. All the protein initiation codons are ATG, except for ND2, ND3 and ND5 are ATA, ND4L is GTG, ND6 is TTA. The complete mitochondrial genome sequence of the Shaziling pig in Human Province provides an important data set for the study in genetic mechanism.
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hsa-miR-141 downregulates TM4SF1 to inhibit pancreatic cancer cell invasion and migration.
Int. J. Oncol.
PUBLISHED: 09-04-2013
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Expression of the transmembrane-4-L-six-family-1 (TM4SF1) is high in human pancreatic cancer cells, but the underlying mechanism remains unclear. In this study, we aimed to identify and characterize microRNAs that regulate TM4SF1 expression in PC cells. Western blot analysis and quantitative polymerase chain reaction were used to detect TM4SF1 and hsa-miR-141 levels in four PC cell lines. SW1990 and BxPc-3 cells were transfected with the inhibitor miR-141, the inhibitor negative control, the miR-141 mimic and the mimic negative control; and cell invasion, migration, proliferation, cell cycle progression and apoptosis were detected by Transwell, MTT and flow cytometry assays, respectively. The miR-141 levels negatively correlated with the TM4SF1 protein levels in PC cells. The TM4SF1 protein levels were lower in the 141M group but higher in the 141I group, although the TM4SF1 mRNA levels had no significant changes, compared to the negative controls. Luciferase assays demonstrated that hsa-miR-141 directly targeted the 3-untranslated region of the TM4SF1 gene. In addition, miR-141 downregulated TM4SF1 expression to inhibit invasion and migration of PC cells but had no effects on cell proliferation, cell cycle progression or apoptosis. TM4SF1 is a direct target of miR-141. Our findings that TM4SF1 expression was inhibited by miR-141 provide new insights into the oncogenic mechanism of TM4SF1 and suggest that miR-141 represents a novel molecular target for PC therapy.
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Learning with Augmented Features for Supervised and Semi-supervised Heterogeneous Domain Adaptation.
IEEE Trans Pattern Anal Mach Intell
PUBLISHED: 09-04-2013
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In this paper, we study the heterogeneous domain adaptation (HDA) problem, in which the data from the source domain and the target domain are represented by heterogeneous features with different dimensions. By introducing two different projection matrices, we first transform the data from two domains into a common subspace such that the similarity between samples across different domains can be measured. We then develop two new feature mapping functions for two domains, which respectively augments the transformed source and target samples with their original features and padding zeros. Existing supervised learning methods (e.g., SVM and SVR) can be readily employed by incorporating our newly proposed augmented feature representations for supervised HDA. As a showcase, we propose a novel method called Heterogeneous Feature Augmentation (HFA) based on SVM. We show that the proposed formulation can be equivalently derived as a standard Multiple Kernel Learning (MKL) problem, which is convex and thus the global solution can be guaranteed. To additionally utilize the unlabeled data in the target domain, we further propose the semi-supervised HFA (SHFA) which can simultaneously learn the target classifier as well as infer the labels of unlabeled target samples. Comprehensive experiments on three different applications clearly demonstrate that our SHFA and HFA outperform the existing HDA methods.
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Protein depth calculation and the use for improving accuracy of protein fold recognition.
J. Comput. Biol.
PUBLISHED: 08-31-2013
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Protein structure and function are largely specified by the distribution of different atoms and residues relative to the core and surface of the molecule. Relative depths of atoms therefore are key attributions that have been widely used in protein structure modeling and function annotation. However, accurate calculation of depth is time consuming. Here, we developed an algorithm which uses Euclidean distance transform (EDT) to convert the target protein structure into a 3D gray-scale image, where depths of atoms in the protein can be conveniently and precisely derived from the minimum distance of the pixels to the surface of the protein. We tested the proposed EDT-based method on a set of 261 non-redundant protein structures, which shows that the method is 2.6 times faster than the widely used method proposed by Chakravarty and Varadarajan. Depth values by EDT method are highly accurate with a Pearsons correlation coefficient ?1 compared to the calculations from exhaustive search. To explore the usefulness of the method in protein structure prediction, we add the calculated residue depth to the scoring function of the state of the art, profile-profile alignment based fold-recognition program, which shows an additional 3% improvement in the TM-score of the alignments. The data demonstrate that the EDT-based depth calculation program can be used as an efficient tool to assist protein structure analysis and structure-based function annotation.
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Using an intervening sequence of Faecalibacterium 16S rDNA to identify poultry feces.
Water Res.
PUBLISHED: 08-06-2013
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This study was designed to identify poultry feces-specific marker(s) within sequences of Faecalibacterium 16S rDNA for detecting poultry fecal pollution in water. Bioinformatics tools were used in the comparative analysis of 7,458 sequences of Faecalibacterium 16S rDNA, reportedly associated with various poultry (chicken and turkey) and animal species. One intervening sequence (IVS) within between the hypervariable region 1 and the conserved region 2, designated as IVS-p, was found to be unique to poultry feces. Based on this sequence, a PCR assay (PCR-p) was developed. The PCR-p produced an amplicon of 132 bp only in the test when fecal or wastewater samples from poultry were used, but not when using fecal or wastewater samples from other sources. The non-poultry sources included feces of beef or dairy cattle, dog, horse, human, domestic or wild geese, seagull, sheep, swine, and wild turkey. These data indicate that IVS-p may prove to be a useful genetic marker for the specific identification of poultry fecal pollution in environmental waterways. Furthermore, results of data mining and PCR assay indicate that the IVS-p may have a broad geographic distribution. This report represents initial evidence of the potential utility of ribosomal intervening sequences as genetic markers for tracking host sources of fecal pollution in waterways.
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A comparative assessment and analysis of 20 representative sequence alignment methods for protein structure prediction.
Sci Rep
PUBLISHED: 07-01-2013
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Protein sequence alignment is essential for template-based protein structure prediction and function annotation. We collect 20 sequence alignment algorithms, 10 published and 10 newly developed, which cover all representative sequence- and profile-based alignment approaches. These algorithms are benchmarked on 538 non-redundant proteins for protein fold-recognition on a uniform template library. Results demonstrate dominant advantage of profile-profile based methods, which generate models with average TM-score 26.5% higher than sequence-profile methods and 49.8% higher than sequence-sequence alignment methods. There is no obvious difference in results between methods with profiles generated from PSI-BLAST PSSM matrix and hidden Markov models. Accuracy of profile-profile alignments can be further improved by 9.6% or 21.4% when predicted or native structure features are incorporated. Nevertheless, TM-scores from profile-profile methods including experimental structural features are still 37.1% lower than that from TM-align, demonstrating that the fold-recognition problem cannot be solved solely by improving accuracy of structure feature predictions.
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A genome-wide association study in Han Chinese identifies a susceptibility locus for primary Sjögrens syndrome at 7q11.23.
Nat. Genet.
PUBLISHED: 06-19-2013
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Primary Sjögrens syndrome is one of the most common autoimmune diseases. So far, genetic studies of Sjögrens syndrome have relied mostly on candidate gene approaches. To identify new genetic susceptibility loci for primary Sjögrens syndrome, we performed a three-stage genome-wide association study in Han Chinese. In the discovery stage, we analyzed 556,134 autosomal SNPs in 542 cases and 1,050 controls. We then validated promising associations in 2 replication stages comprising 1,303 cases and 2,727 controls. The combined analysis identified GTF2I at 7q11.23 (rs117026326: Pcombined = 1.31 × 10(-53), combined odds ratio (ORcombined) = 2.20) as a new susceptibility locus for primary Sjögrens syndrome. Our analysis also confirmed previously reported associations in Europeans in the regions of STAT4, TNFAIP3 and the major histocompatibility complex (MHC). Fine mapping of the region around GTF2I showed that rs117026326 in GTF2I had the most significant association, with associated SNPs extending from GTF2I to GTF2IRD1-GTF2I.
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Antibody-directed Double Suicide Gene Therapy Targeting of MUC1- Positive Leukemia Cells In Vitro and In Vivo.
Curr Gene Ther
PUBLISHED: 05-17-2013
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Our aim was to specifically transfer the cytosine deaminase (CD) and thymidine kinase (TK) genes into mucin 1 (MUC1)-positive leukemia cells by anti-MUC1 antibody directed infection of replication-defective lentivirus and to evaluate the targeted cytotoxicity of double suicide genes to leukemia. The target gene vector (containing CD and TK) and envelope (containing GFP and anti-MUC1) and packaging plasmids were cotransfected into 293T cells to produce the recombinant lentivirus. Suicide genes in virus-infected leukemia cells (U937, Jurkat, and K562) were detected by western blot. The cytotoxicity and bystander effect in vitro and the therapeutic effect in vivo were detected after treatment with the prodrugs. The results revealed that combined treatment with prodrug 5-fluorocytosine (5-FC) and ganciclovir (GCV) inhibited leukemia cell growth and caused significant bystander effect than treatment with either prodrug alone. TK/GCV treatment alone induced degeneration and cell death while the effect of CD/5-FC alone mainly caused vacuolar degeneration and necrosis. The addictive effects of combinatorial use of GCV and 5-FC mainly induced swelling of the mitochondria followed by necrosis of the leukemia cells. In vivo experiments revealed that both single and combinatorial prodrug treatments could prolong the survival time of leukemic mice. In summary, anti-MUC1 antibody directed lentiviral vector successfully transduced dual suicide genes and exerted targeted cytotoxicity against MUC1 positive leukemia cells. This targeted lentiviral dual suicide gene delivering system provides a promising approach for clinical treatment of leukemia in future.
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[Application of electric detachable stent in the embolization therapy of intracranial aneurysms].
Zhonghua Wai Ke Za Zhi
PUBLISHED: 04-13-2013
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To evaluate the efficacy and safety of Solitaire(TM) AB neurovascular stenting-assisted coil embolization for patients with wide-necked or dissecting aneurysms.
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The characteristics of patients having ankylosing spondylitis associated with Takayasus arteritis.
Clin. Rheumatol.
PUBLISHED: 04-12-2013
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Both ankylosing spondylitis (AS) and Takayasus arteritis (TA) are infrequent, and their association is even more rare. Our objective was to assess their association and characteristics in our patients. We conducted retrospective analysis of our hospital inpatients from June 2000 to July 2011 who had both AS and TA. We used modified New York criteria for ankylosing spondylitis (1984) as AS diagnosis criterion and American College of Rheumatology Classification Criteria for Takayasus Arteritis as TA diagnosis criterion. All clinical data, lab data, and radiological data were collected. Six patients were included in our study because they fulfilled our AS and TA criteria, four males and 2 females, aged from 18 to 35 years old. Four patients were HLA-B27 positive and 2 were negative. All patients inflammatory markers such as erythrocyte sedimentation rate and C-reactive protein were high. The clinical characteristics of patients with both diseases did not seem to be different from that of patients with AS or TA alone in China. All patients were first diagnosed as AS, then found TA 3-20 years later. After diagnosed those patients having AS and TA, patients were given prednisone and cyclophosphamide and their symptoms improved gradually. Our study provides further evidence of the association of TA with AS. We should know that some AS patients can do have TA. To AS patients who have fever, bruit, or pulselessness, we should suspect that they have TA.
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The anti-inflammation effect of Moutan Cortex on advanced glycation end products-induced rat mesangial cells dysfunction and High-glucose-fat diet and streptozotocin-induced diabetic nephropathy rats.
J Ethnopharmacol
PUBLISHED: 03-14-2013
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Moutan Cortex (MC, family: Paeonia suffruticosa Andr.) is a well-known traditional herbal medicine that has been shown to hold a protective effect on inflammation in several diseases. However, its anti-inflammatory activity on diabetic nephropathy (DN) has been less reported. The present study was conducted to evaluate the potential attenuation activities of MC on inflammation in AGEs-induced rat mesangial cells dysfunction and high-glucose-fat diet and streptozotocin (STZ)-induced DN rats and explore the possible mechanism underlying its DN effect.
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Enhanced oral absorption of 20(S)-protopanaxadiol by self-assembled liquid crystalline nanoparticles containing piperine: in vitro and in vivo studies.
Int J Nanomedicine
PUBLISHED: 02-12-2013
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20(S)-protopanaxadiol (PPD), similar to several other anticancer agents, has low oral absorption and is extensively metabolized. These factors limit the use of PPD for treatment of human diseases.
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Prostate-targeted mTOR-shRNA inhibit prostate cancer cell growth in human tumor xenografts.
Int J Clin Exp Med
PUBLISHED: 01-26-2013
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To construct a recombinant lentivirus vector driven by the PSMA promoter carrying mTOR-shRNA, and to obtain the effect on the mTOR gene silencing in human prostate cancer xenografts.
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Protein structural model selection by combining consensus and single scoring methods.
PLoS ONE
PUBLISHED: 01-01-2013
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Quality assessment (QA) for predicted protein structural models is an important and challenging research problem in protein structure prediction. Consensus Global Distance Test (CGDT) methods assess each decoy (predicted structural model) based on its structural similarity to all others in a decoy set and has been proved to work well when good decoys are in a majority cluster. Scoring functions evaluate each single decoy based on its structural properties. Both methods have their merits and limitations. In this paper, we present a novel method called PWCom, which consists of two neural networks sequentially to combine CGDT and single model scoring methods such as RW, DDFire and OPUS-Ca. Specifically, for every pair of decoys, the difference of the corresponding feature vectors is input to the first neural network which enables one to predict whether the decoy-pair are significantly different in terms of their GDT scores to the native. If yes, the second neural network is used to decide which one of the two is closer to the native structure. The quality score for each decoy in the pool is based on the number of winning times during the pairwise comparisons. Test results on three benchmark datasets from different model generation methods showed that PWCom significantly improves over consensus GDT and single scoring methods. The QA server (MUFOLD-Server) applying this method in CASP 10 QA category was ranked the second place in terms of Pearson and Spearman correlation performance.
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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.