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.
[Analysis of mature T-cell and NK-cell lymphoma with CD30 expression based on latest WHO classification].
Zhonghua Bing Li Xue Za Zhi
PUBLISHED: 10-28-2014
Show Abstract
Hide Abstract
To investigate the frequency of different types of mature T- and NK-cell lymphomas diagnosed in a 4-year period at Sun Yat-sen University Cancer Center, and to study baseline CD30 for potential anti-CD30 targeted therapy in mature T- and NK-cell lymphoma.
Related JoVE Video
Spatial and Temporal Emergence Pattern of Lyme Disease in Virginia.
Am. J. Trop. Med. Hyg.
PUBLISHED: 10-22-2014
Show Abstract
Hide Abstract
The emergence of infectious diseases over the past several decades has highlighted the need to better understand epidemics and prepare for the spread of diseases into new areas. As these diseases expand their geographic range, cases are recorded at different geographic locations over time, making the analysis and prediction of this expansion complicated. In this study, we analyze spatial patterns of the disease using a statistical smoothing analysis based on areal (census tract level) count data of Lyme disease cases in Virginia from 1998 to 2011. We also use space and space-time scan statistics to reveal the presence of clusters in the spatial and spatiotemporal distribution of Lyme disease. Our results confirm and quantify the continued emergence of Lyme disease to the south and west in states along the eastern coast of the United States. The results also highlight areas where education and surveillance needs are highest.
Related JoVE Video
Use of an acidophilic yeast strain to enable the growth of leaching bacteria on solid media.
Arch. Microbiol.
PUBLISHED: 10-18-2014
Show Abstract
Hide Abstract
In this study, a Candida digboiensis strain was isolated from a heap leaching plant in Zambia and used in double-layer agar plate to efficiently isolate and purify leaching bacteria. Unlike Acidiphilium sp., the yeast strain was tetrathionate tolerant and could metabolize a great range of organic compounds including organic acids. These properties allowed the yeast strain to enable and fasten the growth of iron and sulfur oxidizers on double-layer agar plate. The isolates were identified as Acidithiobacillus ferrooxidans FOX1, Leptospirillun ferriphilum BN, and Acidithiobacillus thiooxidans ZMB. These three leaching bacteria were inhibited by organic acids such as acetic and propionic acids; however, their activities were enhanced by Candida digboiensis NB under dissolved organic matter stress.
Related JoVE Video
Doxorubicin attenuates serotonin-induced long-term synaptic facilitation by phosphorylation of p38 mitogen-activated protein kinase.
J. Neurosci.
PUBLISHED: 10-03-2014
Show Abstract
Hide Abstract
Doxorubicin (DOX) is an anthracycline used widely for cancer chemotherapy. Its primary mode of action appears to be topoisomerase II inhibition, DNA cleavage, and free radical generation. However, in non-neuronal cells, DOX also inhibits the expression of dual-specificity phosphatases (also referred to as MAPK phosphatases) and thereby inhibits the dephosphorylation of extracellular signal-regulated kinase (ERK) and p38 mitogen-activated protein kinase (p38 MAPK), two MAPK isoforms important for long-term memory (LTM) formation. Activation of these kinases by DOX in neurons, if present, could have secondary effects on cognitive functions, such as learning and memory. The present study used cultures of rat cortical neurons and sensory neurons (SNs) of Aplysia to examine the effects of DOX on levels of phosphorylated ERK (pERK) and phosphorylated p38 (p-p38) MAPK. In addition, Aplysia neurons were used to examine the effects of DOX on long-term enhanced excitability, long-term synaptic facilitation (LTF), and long-term synaptic depression (LTD). DOX treatment led to elevated levels of pERK and p-p38 MAPK in SNs and cortical neurons. In addition, it increased phosphorylation of the downstream transcriptional repressor cAMP response element-binding protein 2 in SNs. DOX treatment blocked serotonin-induced LTF and enhanced LTD induced by the neuropeptide Phe-Met-Arg-Phe-NH2. The block of LTF appeared to be attributable to overriding inhibitory effects of p-p38 MAPK, because LTF was rescued in the presence of an inhibitor (SB203580 [4-(4-fluorophenyl)-2-(4-methylsulfinylphenyl)-5-(4-pyridyl)-1H-imidazole]) of p38 MAPK. These results suggest that acute application of DOX might impair the formation of LTM via the p38 MAPK pathway.
Related JoVE Video
Epilithonimonas xixisoli sp. nov., isolated from bank side soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 09-27-2014
Show Abstract
Hide Abstract
A novel Gram-staining-negative, non-motile and rod-shaped bacterial strain containing flexirubin-type pigments, designated S31T, was isolated from bank side soil of the Xixi wetland in Zhejiang province, China. Growth occurred at 10-37°C (optimum, 32°C), pH 6-8 (optimum, pH 7) and with 0-2% (w/v) NaCl (optimum, 1%). Stain S31T had highest 16S rRNA gene similarities with the type stain of Epilithonimonas lactis H1T (96.2%), and Chryseobacterium molle DW3T (96.4%). Phylogenetic analysis suggested that strain S31T was a member of the genus Epilithonimonas. The dominant respiratory quinone was MK-6 and the G+C content was 33.3 mol%. The major fatty acids were iso-C15:0, summed feature 3 (iso-C15:0 2-OH and/or C16:1?7c) and anteiso-C15:0. The major polar lipids of strain S31T were phosphatidylethanolamine (PE), three unidentified aminolipids and four unidentified polar lipids. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S31T represents a novel species of the genus Epilithonimonas, for which the name Epilithonimonas xixisoli sp. nov. (type strain S31T =CGMCC 1.12802T=NBRC 110387T) is proposed.
Related JoVE Video
Cloning and characterization of 3-hydroxy-3-methylglutaryl-CoA reductase (HMGR) gene from Paris fargesii Franch.
Indian J. Biochem. Biophys.
PUBLISHED: 09-11-2014
Show Abstract
Hide Abstract
3-Hydroxy-3-methylglutaryl-coenzyme A reductase (HMGR) plays an important role in catalyzing the first committed step of isoprenoids biosynthesis in mevalonic acid (MVA) pathway. Here, we cloned a full-length transcript of Paris fargesii Franch. The full-length cDNA of P. fargesii HMGR (Pf-HMGR, GenBank accession no. JX508638) was 1,973 bp and contained a 1,728 bp ORF encoding 576 amino acids. Sequence analysis revealed that the deduced Pf-HMGR had high similarity with HMGRs from other plants, including Ricinus communis (77%), Litchi chinensis (76%), Michelia chapensis (75%) and Panax quinquefolius (72%). It had a calculated molecular mass of about 62.13 kDa and an isoelectric point (pI) of 8.47. It contained two transmembrane domains, two putative HMGR binding sites and two NADP(H)-binding sites. The predicted 3-D structure revealed that Pf-HMGR had a similar spatial structure with other plant HMGRs. Three catalytic regions, including L-domain, N-domain and S-domain were detected by structural modeling of HMGR. Tissue expression analysis revealed that Pf-HMGR was strongly expressed in roots and stems than in leaves. Taken together, our data laid a foundation for further investigation of HMGR's functions and regulatory mechanisms in plants.
Related JoVE Video
The role of +TIPs in directional tip expansion.
Mol. Microbiol.
PUBLISHED: 09-07-2014
Show Abstract
Hide Abstract
Aspergillus nidulans is an ideal model to study nuclear migration and intracellular transport by dynein and kinesin owing to its long neuron-like hyphae, conserved transport mechanisms, and powerful genetics. In this organism, as in other filamentous fungi, microtubules have been implicated in patterning cell shape through polarized tip growth - the hallmark mode of growth that generates the elongated hyphae. Exactly how microtubules regulate tip growth is incompletely understood and remains a fascinating question for various cell types, such as pollen tubes and root hairs. Zeng et?al. (2014) describe important new findings in A. nidulans regarding the role of EBA, the master regulator of microtubule plus end-tracking proteins, in specifying microtubule dynamics required for directional tip growth at the hyphal tip.
Related JoVE Video
Macronutrients intake and risk of Parkinson's disease: A meta-analysis.
Geriatr Gerontol Int
PUBLISHED: 08-28-2014
Show Abstract
Hide Abstract
We carried out a meta-analysis to summarize the evidence from published studies on macronutrients intake and risk of Parkinson's disease (PD).
Related JoVE Video
Homogenate extraction of gardenia yellow pigment from Gardenia Jasminoides Ellis fruit using response surface methodology.
J Food Sci Technol
PUBLISHED: 08-13-2014
Show Abstract
Hide Abstract
Homogenate extraction technology was developed for extraction of gardenia yellow pigment from Gardenia jasminoides Ellis fruit. The operating parameters affecting the color value of gardenia yellow pigment were studied on the basis of a Box-Behnken design and response surface methodology. Results showed that the optimum extraction conditions were as follows: extraction time 41 s, ethanol concentration 50 %, ratio of liquid to material 15:1 (mL:g) and particle size 1.7 mm. Under the optimum condition, the experimental color value was 52.37 g(-1), which was in keeping with the predicted one. Compared with the heat extraction method, the color value of gardenia yellow pigment of homogenate extraction was higher and the extraction time was shorter. Homogenate extraction method is an ideal means for extraction of gardenia yellow pigment from Gardenia jasminoides Ellis fruit.
Related JoVE Video
Upregulation of human PINK1 gene expression by NF?B signalling.
Mol Brain
PUBLISHED: 08-11-2014
Show Abstract
Hide Abstract
Parkinson's disease (PD) is one of the major neurodegenerative disorders. Mitochondrial malfunction is implicated in PD pathogenesis. Phosphatase and tensin homolog deleted on chromosome 10 (PTEN)-induced putative kinase 1 (PINK1), a serine/threonine kinase, plays an important role in the quality control of mitochondria and more than 70 PINK1 mutations have been identified to cause early-onset PD. However, the regulation of PINK1 gene expression remains elusive. In the present study, we identified the transcription start site (TSS) of the human PINK1 gene using switching mechanism at 5'end of RNA transcription (SMART RACE) assay. The TSS is located at 91 bp upstream of the translation start site ATG. The region with 104 bp was identified as the minimal promoter region by deletion analysis followed by dual luciferase assay. Four functional cis-acting nuclear factor kappa-light-chain-enhancer of activated B cells (NF?B)-binding sites within the PINK1 promoter were identified. NF?B overexpression led to the up-regulation of PINK1 expression in both HEK293 cells and SH-SY5Y cells. Consistently, lipopolysaccharide (LPS), a strong activator of NF?B, significantly increased PINK1 expression in SH-SY5Y cells. Taken together, our results clearly suggested that PINK1 expression is tightly regulated at its transcription level and NF?B is a positive regulator for PINK1 expression.
Related JoVE Video
Pedobacter xixiisoli sp. nov., isolated from bank soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-08-2014
Show Abstract
Hide Abstract
A Gram-stain-negative, rod-shaped, yellow, non-motile, aerobic bacterium (strain S27(T)) was isolated from bank soil of the Xixi wetland in Zhejiang province, PR China. Phylogenetic analysis, based on its 16S rRNA gene sequence, revealed that strain S27(T) could represent a novel species of the genus Pedobacter showing highest similarity to Pedobacter koreensis WPCB189(T) (95.45?%), followed by 'Pedobacter zeaxanthinifaciens' TDMA-5 (95.22?%). The temperature, pH and NaCl concentration ranges for growth were 6-37 °C (optimum 28 °C), pH 5.0-9.0 (optimum pH 7.5) and 0-3?% (w/v) [optimum 0.5?% (w/v)], respectively. The DNA G+C content was 36.1 mol%, MK-7 was the only respiratory quinone, and iso-C15?:?0, iso-C17?:?0 3-OH and summed feature 3 (C16?:?1?7c and/or iso-C15?:?0 2-OH) were the major fatty acids. These data all support the affiliation of strain S27(T) to the genus Pedobacter. The polar lipids of strain S27(T) comprised phosphatidylethanolamine, one unidentified aminophospholipid, four unidentified aminolipids and three unidentified lipids. However, strain S27(T) could be distinguished from other members of the genus Pedobacter due to its physiological and biochemical characteristics. Therefore, strain S27(T) represents a novel species of the genus Pedobacter, for which the name Pedobacter xixiisoli sp. nov. is proposed; the type strain is S27(T) (?=?CGMCC 1.12803(T)?=?NBRC 110388(T)).
Related JoVE Video
Sphingobacterium paludis sp. nov., isolated from wetland soil.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 07-21-2014
Show Abstract
Hide Abstract
A novel Gram-stain-negative bacteria, designated S37(T), was isolated from soil of the Xixi wetland, Zhejiang province, China. Cells of strain S37(T) were aerobic, non-motile rods. Growth occurred at 10-37 °C (optimum, 25 °C), pH 5.0-9.7 (optimum, pH 7.5) and with 0-6% (w/v) NaCl (optimum, 0.5%). Based on 16S rRNA gene sequence analysis, strain S37(T) was found to be a member of the genus Sphingobacterium and shared highest similarity with Sphingobacterium composti 4M24(T) (95.78%). The major fatty acids were summed feature 3 (iso-C15:0 2-OH and/or C16:1?7c), iso-C15:0 and iso-C17:0 3-OH, and the DNA G+C content was 43.8 mol%. The predominant respiratory quinone was MK-7. Based on its phenotypic and chemotaxonomic characteristics and phylogenetic data, strain S37(T) represents a novel species of the genus Sphingobacterium, for which the name Sphingobacterium paludis sp. nov. (type strain S37(T) = CGMCC 1.12801(T) = NBRC 110386(T)) is proposed.
Related JoVE Video
A randomized study of H3 antagonist ABT-288 in mild-to-moderate Alzheimer's dementia.
J. Alzheimers Dis.
PUBLISHED: 07-16-2014
Show Abstract
Hide Abstract
ABT-288, a highly selective histamine-3 receptor antagonist, demonstrated efficacy across several preclinical cognitive domains, and safety in healthy subjects and elderly volunteers.
Related JoVE Video
Down-regulation of MIF by NF?B under hypoxia accelerated neuronal loss during stroke.
FASEB J.
PUBLISHED: 06-26-2014
Show Abstract
Hide Abstract
Neuronal apoptosis is one of the major causes of poststroke neurological deficits. Inflammation during the acute phase of stroke results in nuclear translocation of NF?B in affected cells in the infarct area. Macrophage migration inhibitory factor (MIF) promotes cardiomyocyte survival in mice following heart ischemia. However, the role of MIF during stroke remains limited. In this study, we showed that MIF expression is down-regulated by 0.75 ± 0.10-fold of the control in the infarct area in the mouse brains. Two functional cis-acing NF?B response elements were identified in the human MIF promoter. Dual activation of hypoxia and NF?B signaling resulted in significant reduction of MIF promoter activity to 0.86 ± 0.01-fold of the control. Furthermore, MIF reduced caspase-3 activation and protected neurons from oxidative stress- and in vitro ischemia/reperfusion-induced apoptosis. H2O2 significantly induced cell death with 12.81 ± 0.58-fold increase of TUNEL-positive cells, and overexpression of MIF blocked the H2O2-induced cell death. Disruption of the MIF gene in MIF-knockout mice resulted in caspase-3 activation, neuronal loss, and increased infarct development during stroke in vivo. The infarct volume was increased from 6.51 ± 0.74% in the wild-type mice to 9.07 ± 0.66% in the MIF-knockout mice. Our study demonstrates that MIF exerts a neuronal protective effect and that down-regulation of MIF by NF?B-mediated signaling under hypoxia accelerates neuronal loss during stroke. Our results suggest that MIF is an important molecule for preserving a longer time window for stroke treatment, and strategies to maintain MIF expression at physiological level could have beneficial effects for stroke patients.
Related JoVE Video
Amyloid-? precursor protein facilitates the regulator of calcineurin 1-mediated apoptosis by downregulating proteasome subunit ? type-5 and proteasome subunit ? type-7.
Neurobiol. Aging
PUBLISHED: 06-05-2014
Show Abstract
Hide Abstract
Individuals with Down syndrome (DS), caused by trisomy of chromosome 21, inevitably develop characteristic Alzheimer's disease (AD) neuropathology, including neuritic plaques, neurofibrillary tangles, and neuronal loss. Amyloid-? protein, the major component of neuritic plaques, is the proteolytic product of amyloid-? precursor protein (APP). APP and the regulator of calcineurin 1 (RCAN1) genes on chromosome 21 play a pivotal role in promoting plaque formation and neuronal apoptosis. However, the mechanism underlying AD pathogenesis in DS is not well defined. In this study, we demonstrated that APP significantly increased RCAN1 level in both cells and transgenic mice. Overexpression of APP significantly reduced the expression of 2 proteasome subunits, proteasome subunit ? type-5 and proteasome subunit ? type-7, leading to the inhibition of proteasomal degradation of RCAN1. Furthermore, knockdown of RCAN1 expression attenuated APP-induced neuronal apoptosis. Taken together, the results clearly showed that APP has a previously unknown function in regulating RCAN1-mediated neuronal apoptosis through the proteasome pathway. Our study demonstrates a novel mechanism by which overexpression of APP and RCAN1 causes neurodegeneration and AD pathogenesis in DS, and it provides new insights into the potential of targeting APP-induced proteasomal impairment and RCAN1 accumulation for AD and DS treatment.
Related JoVE Video
Prognostic value of poorly differentiated clusters in invasive breast cancer.
World J Surg Oncol
PUBLISHED: 04-14-2014
Show Abstract
Hide Abstract
Our study aimed to assess the prognostic value of poorly differentiated clusters (PDCs) in invasive breast cancer.
Related JoVE Video
The endothelin antagonist atrasentan lowers residual albuminuria in patients with type 2 diabetic nephropathy.
J. Am. Soc. Nephrol.
PUBLISHED: 04-10-2014
Show Abstract
Hide Abstract
Despite optimal treatment, including renin-angiotensin system (RAS) inhibitors, patients with type 2 diabetic nephropathy have high cardiorenal morbidity and mortality related to residual albuminuria. We evaluated whether or not atrasentan, a selective endothelin A receptor antagonist, further reduces albuminuria when administered concomitantly with maximum tolerated labeled doses of RAS inhibitors. We enrolled 211 patients with type 2 diabetes, urine albumin/creatinine ratios of 300-3500 mg/g, and eGFRs of 30-75 ml/min per 1.73 m(2) in two identically designed, parallel, multinational, double-blind studies. Participants were randomized to placebo (n=50) or to 0.75 mg/d (n=78) or 1.25 mg/d (n=83) atrasentan for 12 weeks. Compared with placebo, 0.75 mg and 1.25 mg atrasentan reduced urine albumin/creatinine ratios by an average of 35% and 38% (95% confidence intervals of 24 to 45 and 28 to 47, respectively) and reduced albuminuria?30% in 51% and 55% of participants, respectively. eGFR and office BP measurements did not change, whereas 24-hour systolic and diastolic BP, LDL cholesterol, and triglyceride levels decreased significantly in both treatment groups. Use of atrasentan was associated with a significant increase in weight and a reduction in hemoglobin, but rates of peripheral edema, heart failure, or other side effects did not differ between groups. However, more patients treated with 1.25 mg/d atrasentan discontinued due to adverse events. After stopping atrasentan for 30 days, measured parameters returned to pretreatment levels. In conclusion, atrasentan reduced albuminuria and improved BP and lipid spectrum with manageable fluid overload-related adverse events in patients with type 2 diabetic nephropathy receiving RAS inhibitors.
Related JoVE Video
Draft Genome Sequence of the Extremophile Acidithiobacillus thiooxidans A01, Isolated from the Wastewater of a Coal Dump.
Genome Announc
PUBLISHED: 04-05-2014
Show Abstract
Hide Abstract
The draft genome of Acidithiobacillus thiooxidans A01 contains 3,820,158 bp, with a G+C content of 53.08% and 3,660 predicted coding sequences (CDSs). The bacterium contains a series of specific genes involved in the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs).
Related JoVE Video
Overexpression of c-Met increases the tumor invasion of human prostate LNCaP cancer cells in vitro and in vivo.
Oncol Lett
PUBLISHED: 03-15-2014
Show Abstract
Hide Abstract
c-Met is a transmembrane tyrosine kinase receptor that may be activated by hepatocyte growth factor, an inducer of epithelial-mesenchymal transition (EMT), to regulate the associated downstream gene expression. This process is critical to cell migration in normal and pathological conditions. In the present study, the function of c-Met in the process of EMT was investigated in prostate cancer. Initially, a c-Met stable expression cell line was constructed using EMT- and c-Met-negative LNCaP prostate cancer cells. Following the identification of c-Met in the transfected cells, the changes in EMT, phosphatidylinositol 3-kinase (PI3K) and extracellular signal-regulated kinase pathway biomarkers were determined by western blot analysis. MTT, soft agar and Transwell assays, and xenograft studies were used to investigate the effects of c-Met on the proliferation, migration and tumorigenicity of LNCaP cells. The results of the present study revealed downregulation of E-cadherin and upregulation of vimentin in LNCaP-Met cells. The results demonstrated that c-Met enhanced proliferation, migration and tumorigenicity capacity when compared with LNCaP and LNCaP-pcDNA3.1 cells. Furthermore, these EMT-like changes were mediated via the PI3K and mitogen-activated protein kinase signaling pathways. The present study clearly demonstrates a crucial function for c-Met in EMT development in prostate cancer. c-Met-targeted treatment may be an effective adjuvant therapy for improving survival rates in patients with prostate cancer.
Related JoVE Video
Upregulation of SET Expression by BACE1 and its Implications in Down Syndrome.
Mol. Neurobiol.
PUBLISHED: 03-12-2014
Show Abstract
Hide Abstract
Down syndrome (DS) is one of the most common genetic diseases. Patients with DS display growth delay and intellectual disabilities and develop Alzheimer's disease (AD) neuropathology after middle age, including neuritic plaques and neurofibrillary tangles. Beta-site amyloid ? precursor protein (APP) cleaving enzyme 1 (BACE1), essential for A? production and neuritic plaque formation, is elevated in DS patients. However, its homolog, ?-site APP cleaving enzyme 2 (BACE2), functions as ?-secretase and plays a differential role in plaque formation. In this study, by using Two-dimensional sodium dodecyl sulfate polyacrylamide gel electrophoresis (2D SDS-PAGE) and LC-MS/MS proteomic profiling analysis, we found that the SET oncogene protein (SET) expression was associated with BACE1 but not BACE2. SET protein was increased in BACE1 overexpressing cells and was markedly reduced in the BACE1 knockout mice. We found that the overexpression of BACE1 or SET significantly inhibited cell proliferation. Moreover, knockdown of SET in BACE1 overexpression cells significantly rescued BACE1-induced cell growth suppression. Furthermore, both BACE1 and SET protein levels were increased in Down syndrome patients. It suggests that BACE1 overexpression-induced SET upregulation may contribute to growth delay and cognitive impairment in DS patients. Our work provides a new insight that BACE1 overexpression not only promotes neuritic plaque formation but may also potentiate neurodegeneration mediated by SET elevation in Alzheimer-associated dementia in DS.
Related JoVE Video
A network biology approach to discover the molecular biomarker associated with hepatocellular carcinoma.
Biomed Res Int
PUBLISHED: 03-06-2014
Show Abstract
Hide Abstract
In recent years, high throughput technologies such as microarray platform have provided a new avenue for hepatocellular carcinoma (HCC) investigation. Traditionally, gene sets enrichment analysis of survival related genes is commonly used to reveal the underlying functional mechanisms. However, this approach usually produces too many candidate genes and cannot discover detailed signaling transduction cascades, which greatly limits their clinical application such as biomarker development. In this study, we have proposed a network biology approach to discover novel biomarkers from multidimensional omics data. This approach effectively combines clinical survival data with topological characteristics of human protein interaction networks and patients expression profiling data. It can produce novel network based biomarkers together with biological understanding of molecular mechanism. We have analyzed eighty HCC expression profiling arrays and identified that extracellular matrix and programmed cell death are the main themes related to HCC progression. Compared with traditional enrichment analysis, this approach can provide concrete and testable hypothesis on functional mechanism. Furthermore, the identified subnetworks can potentially be used as suitable targets for therapeutic intervention in HCC.
Related JoVE Video
Computational analyses of synergism in small molecular network motifs.
PLoS Comput. Biol.
PUBLISHED: 03-01-2014
Show Abstract
Hide Abstract
Cellular functions and responses to stimuli are controlled by complex regulatory networks that comprise a large diversity of molecular components and their interactions. However, achieving an intuitive understanding of the dynamical properties and responses to stimuli of these networks is hampered by their large scale and complexity. To address this issue, analyses of regulatory networks often focus on reduced models that depict distinct, reoccurring connectivity patterns referred to as motifs. Previous modeling studies have begun to characterize the dynamics of small motifs, and to describe ways in which variations in parameters affect their responses to stimuli. The present study investigates how variations in pairs of parameters affect responses in a series of ten common network motifs, identifying concurrent variations that act synergistically (or antagonistically) to alter the responses of the motifs to stimuli. Synergism (or antagonism) was quantified using degrees of nonlinear blending and additive synergism. Simulations identified concurrent variations that maximized synergism, and examined the ways in which it was affected by stimulus protocols and the architecture of a motif. Only a subset of architectures exhibited synergism following paired changes in parameters. The approach was then applied to a model describing interlocked feedback loops governing the synthesis of the CREB1 and CREB2 transcription factors. The effects of motifs on synergism for this biologically realistic model were consistent with those for the abstract models of single motifs. These results have implications for the rational design of combination drug therapies with the potential for synergistic interactions.
Related JoVE Video
Whole-genome sequencing reveals novel insights into sulfur oxidation in the extremophile Acidithiobacillus thiooxidans.
BMC Microbiol.
PUBLISHED: 02-14-2014
Show Abstract
Hide Abstract
Acidithiobacillus thiooxidans (A. thiooxidans), a chemolithoautotrophic extremophile, is widely used in the industrial recovery of copper (bioleaching or biomining). The organism grows and survives by autotrophically utilizing energy derived from the oxidation of elemental sulfur and reduced inorganic sulfur compounds (RISCs). However, the lack of genetic manipulation systems has restricted our exploration of its physiology. With the development of high-throughput sequencing technology, the whole genome sequence analysis of A. thiooxidans has allowed preliminary models to be built for genes/enzymes involved in key energy pathways like sulfur oxidation.
Related JoVE Video
Towards the introduction of the 'Immunoscore' in the classification of malignant tumours.
J. Pathol.
PUBLISHED: 02-08-2014
Show Abstract
Hide Abstract
The American Joint Committee on Cancer/Union Internationale Contre le Cancer (AJCC/UICC) TNM staging system provides the most reliable guidelines for the routine prognostication and treatment of colorectal carcinoma. This traditional tumour staging summarizes data on tumour burden (T), the presence of cancer cells in draining and regional lymph nodes (N) and evidence for distant metastases (M). However, it is now recognized that the clinical outcome can vary significantly among patients within the same stage. The current classification provides limited prognostic information and does not predict response to therapy. Multiple ways to classify cancer and to distinguish different subtypes of colorectal cancer have been proposed, including morphology, cell origin, molecular pathways, mutation status and gene expression-based stratification. These parameters rely on tumour-cell characteristics. Extensive literature has investigated the host immune response against cancer and demonstrated the prognostic impact of the in situ immune cell infiltrate in tumours. A methodology named 'Immunoscore' has been defined to quantify the in situ immune infiltrate. In colorectal cancer, the Immunoscore may add to the significance of the current AJCC/UICC TNM classification, since it has been demonstrated to be a prognostic factor superior to the AJCC/UICC TNM classification. An international consortium has been initiated to validate and promote the Immunoscore in routine clinical settings. The results of this international consortium may result in the implementation of the Immunoscore as a new component for the classification of cancer, designated TNM-I (TNM-Immune).
Related JoVE Video
Intimate terrorism and situational couple violence in general surveys: ex-spouses required.
Violence Against Women
PUBLISHED: 02-06-2014
Show Abstract
Hide Abstract
In this article, we argue that past efforts to distinguish among types of intimate partner violence in general survey data have committed a critical error--using data on current spouses to develop operationalizations of intimate terrorism and situational couple violence. We use ex-spouse data from the National Violence Against Women Survey (NVAWS) to develop new operationalizations. We then demonstrate that NVAWS current spouse data contain little intimate terrorism; we argue that this is likely to be the case for all general surveys. In addition, the ex-spouse data confirm past findings regarding a variety of differences between intimate terrorism and situational couple violence, including those predicted by feminist theories.
Related JoVE Video
Association analysis between MTHFR genetic polymorphisms and the risk of congenital heart diseases in Chinese Han population.
J. Pharm. Pharmacol.
PUBLISHED: 02-03-2014
Show Abstract
Hide Abstract
Congenital heart diseases (CHD) are common birth defects in the world. The methylenetetrahydrofolate reductase (MTHFR) gene is one of the most important candidate genes for the development of CHD. This case-control study aimed to evaluate the effect of MTHFR c.382A>G and c.1129C>T genetic polymorphisms as risk factors for the development of CHD.
Related JoVE Video
Inhibition of hepatitis C virus replication by GS-6620, a potent C-nucleoside monophosphate prodrug.
Antimicrob. Agents Chemother.
PUBLISHED: 01-13-2014
Show Abstract
Hide Abstract
As a class, nucleotide inhibitors (NIs) of the hepatitis C virus (HCV) nonstructural protein 5B (NS5B) RNA-dependent RNA polymerase offer advantages over other direct-acting antivirals, including properties, such as pangenotype activity, a high barrier to resistance, and reduced potential for drug-drug interactions. We studied the in vitro pharmacology of a novel C-nucleoside adenosine analog monophosphate prodrug, GS-6620. It was found to be a potent and selective HCV inhibitor against HCV replicons of genotypes 1 to 6 and against an infectious genotype 2a virus (50% effective concentration [EC50], 0.048 to 0.68 ?M). GS-6620 showed limited activities against other viruses, maintaining only some of its activity against the closely related bovine viral diarrhea virus (EC50, 1.5 ?M). The active 5'-triphosphate metabolite of GS-6620 is a chain terminator of viral RNA synthesis and a competitive inhibitor of NS5B-catalyzed ATP incorporation, with Ki/Km values of 0.23 and 0.18 for HCV NS5B genotypes 1b and 2a, respectively. With its unique dual substitutions of 1'-CN and 2'-C-Me on the ribose ring, the active triphosphate metabolite was found to have enhanced selectivity for the HCV NS5B polymerase over host RNA polymerases. GS-6620 demonstrated a high barrier to resistance in vitro. Prolonged passaging resulted in the selection of the S282T mutation in NS5B that was found to be resistant in both cellular and enzymatic assays (>30-fold). Consistent with its in vitro profile, GS-6620 exhibited the potential for potent anti-HCV activity in a proof-of-concept clinical trial, but its utility was limited by the requirement of high dose levels and pharmacokinetic and pharmacodynamic variability.
Related JoVE Video
E-cadherin gene promoter hypermethylation may contribute to the risk of bladder cancer among Asian populations.
Gene
PUBLISHED: 01-10-2014
Show Abstract
Hide Abstract
There are increasing scientific evidences suggesting that E-cadherin gene promoter hypermethylation may contribute to the development and progression of bladder cancer, but existing studies have yielded inconclusive results. This meta-analysis aims to assess the role of E-cadherin promoter hypermethylation in bladder carcinogenesis. We conducted an extensive literature search for relevant studies on PubMed, Embase, Web of Science, Cochrane Library, and CBM databases from their inception through May 1st, 2013. This meta-analysis was performed using the STATA 12.0 software. Crude risk ratio (RR) with 95% confidence interval (CI) was calculated. Ten clinical studies were included in this meta-analysis with a total of 620 bladder cancer samples,199 normal adjacent samples and 131 normal urothelium tissue. Our meta-analysis revealed that the methylation frequencies in bladder cancer tissues were obviously higher than those in normal control tissues (RR = 2.02, 95%CI: 1.00–4.12, P = 0.050). Subgroup analysis by ethnicity indicated that higher methylation frequencies were observed in bladder cancer tissues among Asian populations (RR = 2.35, 95%CI: 1.11–4.95, P = 0.025), but not among Caucasian populations (RR = 1.62, 95%CI: 0.48–5.53, P = 0.439). Univariate and multivariate meta-regression analyses showed that ethnicity may be the major source of heterogeneity (Pb0.05).No publication bias was detected in this meta-analysis (P=0.358). The present meta-analysis indicates that E-cadherin gene promoter hypermethylation may contribute to increased risk of bladder cancer among Asian populations.
Related JoVE Video
?-Elemene against human lung cancer via up-regulation of P53 protein expression to promote the release of exosome.
Lung Cancer
PUBLISHED: 01-09-2014
Show Abstract
Hide Abstract
?-Elemene, a novel antitumor plant drug extracted from the traditional Chinese medicinal herb Zedoary, has been shown to be effective against a wide variety of tumors. Recent studies have indicated that ?-elemene can inhibit the growth of lung cancer cells; however, the exact mechanism of ?-element's action in lung cancer remains largely unknown. In the present study, the antitumor effect of ?-elemene on human lung cancer cells and the mechanism involved has been investigated.
Related JoVE Video
Aberrant Expression of RCAN1 in Alzheimer's Pathogenesis: A New Molecular Mechanism and a Novel Drug Target.
Mol. Neurobiol.
PUBLISHED: 01-06-2014
Show Abstract
Hide Abstract
AD, a devastating neurodegenerative disorder, is the most common cause of dementia in the elderly. Patients with AD are characterized by three hallmarks of neuropathology including neuritic plaque deposition, neurofibrillary tangle formation, and neuronal loss. Growing evidences indicate that dysregulation of regulator of calcineurin 1 (RCAN1) plays an important role in the pathogenesis of AD. Aberrant RCAN1 expression facilitates neuronal apoptosis and Tau hyperphosphorylation, leading to neuronal loss and neurofibrillary tangle formation. This review aims to describe the recent advances of the regulation of RCAN1 expression and its physiological functions. Moreover, the AD risk factors-induced RCAN1 dysregulation and its role in promoting neuronal loss, synaptic impairments and neurofibrillary tangle formation are summarized. Furthermore, we provide an outlook into the effects of RCAN1 dysregulation on APP processing, A? generation and neuritic plaque formation, and the possible underlying mechanisms, as well as the potential of targeting RCAN1 as a new therapeutic approach.
Related JoVE Video
Surface display of the HPV L1 capsid protein by the autotransporter Shigella IcsA.
J. Microbiol.
PUBLISHED: 01-04-2014
Show Abstract
Hide Abstract
Autotransporters have become attractive tools for surface expression of foreign proteins in Gram-negative bacteria. In this study, the Shigella autotransporter IcsA, has been exploited to express the human papillomavirus (HPV) type 16 L1 capsid protein in Shigella sonnei and Escherichia coli. The L1 gene was fused in-frame to replace the coding sequence of the IcsA passenger domain that is responsible for actin-based motility. The resultant hybrid protein could be detected by an anti-L1 antibody on the surface of S. sonnei and E. coli. In E. coli, the protein was expressed on the entire surface of the bacterium. In contrast, the protein was detected mainly at one pole of the Shigella bacterium. However, the protein became evenly distributed on the surface of the Shigella bacterium when the icsP gene was removed. Our study demonstrated the possibility of exploiting autotransporters for surface expression of large, heterologous viral proteins, which may be a useful strategy for vaccine development.
Related JoVE Video
Comparative genome analysis reveals metabolic versatility and environmental adaptations of Sulfobacillus thermosulfidooxidans strain ST.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
The genus Sulfobacillus is a cohort of mildly thermophilic or thermotolerant acidophiles within the phylum Firmicutes and requires extremely acidic environments and hypersalinity for optimal growth. However, our understanding of them is still preliminary partly because few genome sequences are available. Here, the draft genome of Sulfobacillus thermosulfidooxidans strain ST was deciphered to obtain a comprehensive insight into the genetic content and to understand the cellular mechanisms necessary for its survival. Furthermore, the expressions of key genes related with iron and sulfur oxidation were verified by semi-quantitative RT-PCR analysis. The draft genome sequence of Sulfobacillus thermosulfidooxidans strain ST, which encodes 3225 predicted coding genes on a total length of 3,333,554 bp and a 48.35% G+C, revealed the high degree of heterogeneity with other Sulfobacillus species. The presence of numerous transposases, genomic islands and complete CRISPR/Cas defence systems testifies to its dynamic evolution consistent with the genome heterogeneity. As expected, S. thermosulfidooxidans encodes a suit of conserved enzymes required for the oxidation of inorganic sulfur compounds (ISCs). The model of sulfur oxidation in S. thermosulfidooxidans was proposed, which showed some different characteristics from the sulfur oxidation of Gram-negative A. ferrooxidans. Sulfur oxygenase reductase and heterodisulfide reductase were suggested to play important roles in the sulfur oxidation. Although the iron oxidation ability was observed, some key proteins cannot be identified in S. thermosulfidooxidans. Unexpectedly, a predicted sulfocyanin is proposed to transfer electrons in the iron oxidation. Furthermore, its carbon metabolism is rather flexible, can perform the transformation of pentose through the oxidative and non-oxidative pentose phosphate pathways and has the ability to take up small organic compounds. It encodes a multitude of heavy metal resistance systems to adapt the heavy metal-containing environments.
Related JoVE Video
Species associations in a species-rich subtropical forest were not well-explained by stochastic geometry of biodiversity.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
The stochastic dilution hypothesis has been proposed to explain species coexistence in species-rich communities. The relative importance of the stochastic dilution effects with respect to other effects such as competition and habitat filtering required to be tested. In this study, using data from a 25-ha species-rich subtropical forest plot with a strong topographic structure at Badagongshan in central China, we analyzed overall species associations and fine-scale species interactions between 2,550 species pairs. The result showed that: (1) the proportion of segregation in overall species association analysis at 2 m neighborhood in this plot followed the prediction of the stochastic dilution hypothesis that segregations should decrease with species richness but that at 10 m neighborhood was higher than the prediction. (2) The proportion of no association type was lower than the expectation of stochastic dilution hypothesis. (3) Fine-scale species interaction analyses using Heterogeneous Poisson processes as null models revealed a high proportion (47%) of significant species effects. However, the assumption of separation of scale of this method was not fully met in this plot with a strong fine-scale topographic structure. We also found that for species within the same families, fine-scale positive species interactions occurred more frequently and negative ones occurred less frequently than expected by chance. These results suggested effects of environmental filtering other than species interaction in this forest. (4) We also found that arbor species showed a much higher proportion of significant fine-scale species interactions (66%) than shrub species (18%). We concluded that the stochastic dilution hypothesis only be partly supported and environmental filtering left discernible spatial signals in the spatial associations between species in this species-rich subtropical forest with a strong topographic structure.
Related JoVE Video
RCAN1 overexpression exacerbates calcium overloading-induced neuronal apoptosis.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Down Syndrome (DS) patients develop characteristic Alzheimer's Disease (AD) neuropathology after their middle age. Prominent neuronal loss has been observed in the cortical regions of AD brains. However, the underlying mechanism leading to this neuronal loss in both DS and AD remains to be elucidated. Calcium overloading and oxidative stress have been implicated in AD pathogenesis. Two major isoforms of regulator of calcineurin 1 (RCAN1), RCAN1.1 and RCAN1.4, are detected in human brains. In this report we defined the transcriptional regulation of RCAN1.1 and RCAN1.4 by two alternative promoters. Calcium overloading upregulated RCAN1.4 expression by activating RCAN1.4 promoter through calcineurin-NFAT signaling pathway, thus forming a negative feedback loop in isoform 4 regulation. Furthermore, RCAN1.4 overexpression exacerbated calcium overloading-induced neuronal apoptosis, which was mediated by caspase-3 apoptotic pathway. Our results suggest that downregulating RCAN1.4 expression in neurons could be beneficial to AD patients.
Related JoVE Video
Identification of nitrogen-fixing genes and gene clusters from metagenomic library of acid mine drainage.
PLoS ONE
PUBLISHED: 01-01-2014
Show Abstract
Hide Abstract
Biological nitrogen fixation is an essential function of acid mine drainage (AMD) microbial communities. However, most acidophiles in AMD environments are uncultured microorganisms and little is known about the diversity of nitrogen-fixing genes and structure of nif gene cluster in AMD microbial communities. In this study, we used metagenomic sequencing to isolate nif genes in the AMD microbial community from Dexing Copper Mine, China. Meanwhile, a metagenome microarray containing 7,776 large-insertion fosmids was constructed to screen novel nif gene clusters. Metagenomic analyses revealed that 742 sequences were identified as nif genes including structural subunit genes nifH, nifD, nifK and various additional genes. The AMD community is massively dominated by the genus Acidithiobacillus. However, the phylogenetic diversity of nitrogen-fixing microorganisms is much higher than previously thought in the AMD community. Furthermore, a 32.5-kb genomic sequence harboring nif, fix and associated genes was screened by metagenome microarray. Comparative genome analysis indicated that most nif genes in this cluster are most similar to those of Herbaspirillum seropedicae, but the organization of the nif gene cluster had significant differences from H. seropedicae. Sequence analysis and reverse transcription PCR also suggested that distinct transcription units of nif genes exist in this gene cluster. nifQ gene falls into the same transcription unit with fixABCX genes, which have not been reported in other diazotrophs before. All of these results indicated that more novel diazotrophs survive in the AMD community.
Related JoVE Video
Womens Decisions to Not Seek Formal Help for Partner Violence: A Comparison of Intimate Terrorism and Situational Couple Violence.
J Interpers Violence
PUBLISHED: 12-22-2013
Show Abstract
Hide Abstract
This study examined the help-seeking decisions of low-income women (n = 389) in two types of physically violent heterosexual relationships-intimate terrorism (i.e., physical violence used within a general pattern of coercive control) and situationally violent (i.e., physical violence that is not part of a general pattern of coercive control). Intimate terrorism victims were significantly more likely than situational couple violence victims to cite fear as a reason for not seeking help from the police, medical centers, and counselors/agencies. In contrast, situational couple violence victims more often said that they did not need help. Regression analyses also indicate that additional violence-related factors predict womens help-seeking. Findings emphasize the importance of distinguishing between types of male partner violence and recognizing womens exertions of personal choice and perceptions of dangerousness when examining their decisions about seeking help from service providers.
Related JoVE Video
Continuous intrajejunal infusion of levodopa-carbidopa intestinal gel for patients with advanced Parkinsons disease: a randomised, controlled, double-blind, double-dummy study.
Lancet Neurol
PUBLISHED: 12-20-2013
Show Abstract
Hide Abstract
Levodopa is the most effective therapy for Parkinsons disease, but chronic treatment is associated with the development of potentially disabling motor complications. Experimental studies suggest that motor complications are due to non-physiological, intermittent administration of the drug, and can be reduced with continuous delivery. We aimed to assess efficacy and safety of levodopa-carbidopa intestinal gel delivered continuously through an intrajejunal percutaneous tube.
Related JoVE Video
Black tea, green tea and risk of breast cancer: an update.
Springerplus
PUBLISHED: 12-01-2013
Show Abstract
Hide Abstract
Previous meta-analysis indicated conflicting results in case-control versus cohort studies on the association of green tea with breast cancer risk, and conflicting results were also found in case-control versus cohort studies in another meta-analysis on the association of black tea with breast cancer risk. Many studies were published after the previous meta-analysis. Besides, the dose-response relationship of tea consumption with breast cancer risk is unclear. Thus the association of tea consumption with breast cancer risk was assessed incorporating new publications. Summary relative risk (RR) for highest versus lowest level of tea consumption was calculated based on fixed or random effect models. Dose-response relationship was assessed by restricted cubic spline model and multivariate random-effect meta-regression. The combined results from 9 studies suggested no significant association between green tea consumption and breast cancer risk (RR = 0.82, 95% CI = 0.64-1.04). No significant association was found among cohort studies and case-control studies after sensitivity analysis, respectively. A linear but not significant dose-response association was found between green tea consumption and breast cancer risk. The combined results from 25 studies demonstrated no significant association between black tea consumption and breast cancer risk (RR = 0.98, 95% CI = 0.93-1.03), and no significant association was found in subgroup analysis. A linear but not significant dose-response association was found between black tea consumption and breast cancer risk. Based on the current evidence, black tea and green tea might not contribute significantly to breast cancer risk, respectively.
Related JoVE Video
Transcriptional regulation of human USP24 gene expression by NF-kappa B.
J. Neurochem.
PUBLISHED: 11-18-2013
Show Abstract
Hide Abstract
Impairment of the ubiquitin proteasome pathway is believed to play an important role in the pathogenesis of Parkinsons disease. This process is carried out under tight regulation by deubiquitinating enzymes. Genetic linkage studies indicated that the region of the human ubiquitin-specific protease 24 (USP24) gene is significantly correlated with Parkinsons disease. In this study, we cloned a 1648 bp 5 flanking region of the human USP24 gene coding sequence and a series of nested deletions into the pGL3-Basic vector. We analyzed promoter activities of these regions with a luciferase-based reporter assay system. A 64-bp region was identified to contain the transcription initiation site and a minimum promoter sequence for transcriptional activation of the USP24 gene expression. Expression of USP24 is controlled by a TATA-box-less promoter with several putative cis-acting elements. Transcriptional activation and gel-shift assay demonstrated that the USP24 gene promoter contains a functional NF?B-binding site. Over-expression of nuclear factor kappa-light-chain-enhancer of activated B cells (NF?B) and tumor-necrosis factor alpha (TNF?) treatment significantly increased the USP24 promoter activity, mRNA expression and protein level in human HEK293 cells, mouse N2a cells and human neuroblastoma SH-SY5Y cells. Deletion and mutation of the binding site abolished the regulatory effect of NF?B on human USP24 gene transcription. These results suggested that USP24 expression is tightly regulated at its transcription level and NF?B plays an important role in this process. Impairment of the ubiquitin proteasome system (UPS) has been implicated in neurodegenerative disorders. This report showed that the expression of human ubiquitin-specific protease 24 (USP24), a deubiquitinating enzyme of UPS, is tightly regulated by NF?B. The results suggest that dysregulation of NF?B-mediated USP24 expression may play a role in PD pathogenesis and modulating this process could have therapeutic potential.
Related JoVE Video
Differences in rheological and fractal properties of conditioned and raw sewage sludge.
J Environ Sci (China)
PUBLISHED: 11-07-2013
Show Abstract
Hide Abstract
Rheological tests for raw and conditioned activated sludge (AS) or anaerobic digested sludge (ADS) show that power-law relationships can be used to describe the evolution of several theological parameters, i.e., limiting viscosity (eta(infinity)), yield stress (tau(y)), cohesion energy of the sludge network (Ec), and storage modulus (G), with total suspended solid (TSS) content in raw and conditioned sludge. A gel-like structure that behaves similar to weak-link flocs/aggregates was observed in AS and ADS. As derived from the double-logarithmic plots of G-TSS content, the mass fractal dimensions of the raw and conditioned AS or ADS flocs/aggregates were 2.70 and 2.53 or 2.85 and 2.79, respectively. The rheological tests also indicate that both polymer conditioning and increased TSS content led to improved elastic behavior, cohesion energy, and yield stress of the sludge network, as well as expanded the corresponding linear viscoelastic range. The porosity of AS or ADS flocs/aggregates will be improved by polymer conditioning.
Related JoVE Video
Removal of Pb(II) from aqueous solution by hydrous manganese dioxide: adsorption behavior and mechanism.
J Environ Sci (China)
PUBLISHED: 08-08-2013
Show Abstract
Hide Abstract
Hydrous manganese dioxide (HMO) synthesized by redox of potassium permanganate and hydrogen peroxide was used as an adsorbent for Pb(II) removal. The specific surface area, pore volume and BJH pore diameter of the HMO were 79.31 m2/g, 0.07 cm3/g and 3.38 nm, respectively. The adsorption equilibrium at 298 K could be well described by the Langmuir isotherm equation with qmax value of 352.55 mg/g. The negative values of deltaG and the positive values of deltaH and deltaS indicated the adsorption process was spontaneous and endothermic. The pseudo second-order equation could best fit the adsorption data. The value of the calculated activation energy for Pb(II) adsorption onto the HMO was 38.23 kJ/mol. The uptake of Pb(II) by HMO was correlated with increasing surface hydroxyl group content and the main adsorbed speciation was PbOH+. The final chemical state of Pb(II) on the surface of HMO was similar to PbO. HMO was a promising candidate for Pb(II) removal from aqueous solution.
Related JoVE Video
Fusion of HPV L1 into Shigella surface IcsA: A new approach in developing live attenuated Shigella-HPV vaccine.
Antiviral Res.
PUBLISHED: 08-03-2013
Show Abstract
Hide Abstract
Despite the success of L1 virus-like particles (VLPs) vaccines in prevention of high-risk human papillomavirus (HPV) infection and cervical cancer, extraordinary high cost for the complete vaccination has impeded widespread use of the vaccine in resource-poor countries, where cervical cancers impose greater challenge. Presentation of HPV L1 protein by attenuated pathogenic bacteria through natural infection provides a promising low-cost and convenient alternative. Here, we describe the construction and characterization of attenuated L1-expressing Shigella vaccine candidate, by fusion of L1 into the autotransporter of Shigella sonnei, IcsA, an essential virulence factor responsible for actin-based motility. The functional ? domain of IcsA was replaced by codon-optimized L1 gene with independent open reading frames (ORFs) facilitated by suicide vector pJCB12. The L1 gene was stabilized in the genome of recombinant S. sonnei with protein expression and assembly of VLPs in the bacterial cytoplasm. Through conjunctival route vaccination in guinea pigs, L1-containing S. sonnei was able to elicit specific immune response to HPV16 L1 VLP as well as bacterial antigens. The results demonstrated the feasibility of the novel stratagem to develop prophylactic Shigella-HPV vaccines.
Related JoVE Video
Cells susceptible to epithelial-mesenchymal transition are enriched in stem-like side population cells from prostate cancer.
Oncol. Rep.
PUBLISHED: 07-31-2013
Show Abstract
Hide Abstract
Accumulating evidence suggests that epithelial-mesenchymal transition (EMT) acts as an important factor for the promotion of tumor progression. Strategies for suppressing EMT remain the subject of ongoing research. In the present study, fluorescence-activated cell sorting (FACS) was used to isolate side population (SP) cells from human prostate cancer (PCa) cell lines and xenograft tissues. After identifying their molecular and functional stem-like characteristics, stem-like SP cells from a cell line and from xenograft tissue were transfected with hypoxia inducible factor-1? (HIF-1?). The potential of the prostate stem-like SP cells to undergo EMT was compared with that in their bulk counterparts after HIF-1? introduction. Stem-like SP cells acquired more complete EMT molecular features and exhibited stronger aggressive capability than the homologous bulk population cells both in vitro (proliferation and invasion) and in vivo (tumorigenesis and metastasis formation). We, therefore, concluded that EMT is closely associated with tumor heterogeneity, and that PCa cells susceptible to EMT are enriched in stem-like SP cells. These findings disclose a new approach, targeting the cellular basis of the EMT process that may help to identify effective and accurate methods for suppressing tumor growth and preventing distant dissemination.
Related JoVE Video
In silico and experimental methods revealed highly diverse bacteria with quorum sensing and aromatics biodegradation systems--a potential broad application on bioremediation.
Bioresour. Technol.
PUBLISHED: 07-27-2013
Show Abstract
Hide Abstract
Phylogenetic overlaps between aromatics-degrading bacteria and acyl-homoserine-lactone (AHL) or autoinducer (AI) based quorum-sensing (QS) bacteria were evident in literatures; however, the diversity of bacteria with both activities had never been finely described. In-silico searching in NCBI genome database revealed that more than 11% of investigated population harbored both aromatic ring-hydroxylating-dioxygenase (RHD) gene and AHL/AI-synthetase gene. These bacteria were distributed in 10 orders, 15 families, 42 genus and 78 species. Horizontal transfers of both genes were common among them. Using enrichment and culture dependent method, 6 Sphingomonadales and 4 Rhizobiales with phenanthrene- or pyrene-degrading ability and AHL-production were isolated from marine, wetland and soil samples. Thin-layer-chromatography and gas-chromatography-mass-spectrum revealed that these Sphingomonads produced various AHL molecules. This is the first report of highly diverse bacteria that harbored both aromatics-degrading and QS systems. QS regulation may have broad impacts on aromatics biodegradation, and would be a new angle for developing bioremediation technology.
Related JoVE Video
Endoscopic realignment in the management of complete transected ureter.
Int Urol Nephrol
PUBLISHED: 07-08-2013
Show Abstract
Hide Abstract
To present experience and feasibility of endoscopic realignment for treatment of delayed recognized iatrogenic complete transected ureteral injuries.
Related JoVE Video
The use of multidimensional data to identify the molecular biomarker for pancreatic ductal adenocarcinoma.
Biomed Res Int
PUBLISHED: 06-28-2013
Show Abstract
Hide Abstract
Pancreatic ductal adenocarcinoma (PDAC) is a lethal disease, and the patient has an extremely poor overall survival with a less than 5% 5-year survival rate. Development of potential biomarkers provides a critical foundation for the diagnosis of PDAC. In this project, we have adopted an integrative approach to simultaneously identify biomarker and generate testable hypothesis from multidimensional omics data. We first examine genes for which expression levels are correlated with survival data. The gene list was screened with TF regulation, predicted miRNA targets information, and KEGG pathways. We identified that 273 candidate genes are correlated with patient survival data. 12 TF regulation gene sets, 11 miRNAs targets gene sets, and 15 KEGG pathways are enriched with these survival genes. Notably, CEBPA/miRNA32/PER2 signaling to the clock rhythm qualifies this pathway as a suitable target for therapeutic intervention in PDAC. PER2 expression was highly associated with survival data, thus representing a novel biomarker for earlier detection of PDAC.
Related JoVE Video
Combined genomics and experimental analyses of respiratory characteristics of Shewanella putrefaciens W3-18-1.
Appl. Environ. Microbiol.
PUBLISHED: 06-28-2013
Show Abstract
Hide Abstract
It has previously been shown that the Shewanella putrefaciens W3-18-1 strain produces remarkably high current in microbial fuel cells (MFCs) and can form magnetite at 0°C. To explore the underlying mechanisms, we developed a genetic manipulation method by deleting the restriction-modification system genes of the SGI1 (Salmonella genome island 1)-like prophage and analyzed the key genes involved in bacterial respiration. W3-18-1 has less respiratory flexibility than the well-characterized S. oneidensis MR-1 strain, as it possesses fewer cytochrome c genes and lacks the ability to oxidize sulfite or reduce dimethyl sulfoxide (DMSO) and timethylamine oxide (TMAO). W3-18-1 lacks the hydrogen-producing Fe-only hydrogenase, and the hydrogen-oxidizing Ni-Fe hydrogenase genes were split into two separate clusters. Two periplasmic nitrate reductases (NapDAGHB and NapDABC) were functionally redundant in anaerobic growth of W3-18-1 with nitrate as the electron acceptor, though napDABC was not regulated by Crp. Moreover, nitrate respiration started earlier in W3-18-1 than in MR-1 (with NapDAGHB only) under microoxic conditions. These results indicate that Shewanella putrefaciens W3-18-1 is well adapted to habitats with higher oxygen levels. Taken together, the results of this study provide valuable insights into bacterial genome evolution.
Related JoVE Video
Combination of Culture-Dependent and -Independent Methods Reveals Diverse Acyl Homoserine Lactone-Producers from Rhizosphere of Wetland Plants.
Curr. Microbiol.
PUBLISHED: 05-05-2013
Show Abstract
Hide Abstract
The culture-dependent method and a degenerate primer-based culture-independent method were combined in an effort to identify N-acyl homoserine lactone (AHL) producers in rhizosphere of wetland plants, Salix babylonica (willow) and Phragmites australis (reed). Overall, eight potential AHL-producing genera were found, which were Aeromonas, Pseudomonas, Polymorphum, Agrobacterium, Rhizobium, Sinorhizobium, Ensifer, and Pectobacterium. Thin layer chromatograph assay revealed various AHL profiles from cultivable AHL-producers. The degenerate primer pair RAHL352F and RAHL461R was found to cover AHL synthetase genes from families Rhizobiaceae and Rhodobacteraceae. Little overlap was found in taxa of potential AHL-producers obtained by the two methods, indicating that they were well complement to each other. This is the first survey for AHL-producers that employed combined culture-dependent and -independent methods.
Related JoVE Video
Concurrent processing of vehicle lane keeping and speech comprehension tasks.
Accid Anal Prev
PUBLISHED: 04-26-2013
Show Abstract
Hide Abstract
With the growing prevalence of using in-vehicle devices and mobile devices while driving, a major concern is their impact on driving performance and safety. However, the effects of cognitive load such as conversation on driving performance are still controversial and not well understood. In this study, an experiment was conducted to investigate the concurrent performance of vehicle lane keeping and speech comprehension tasks with improved experimental control of the confounding factors identified in previous studies. The results showed that the standard deviation of lane position (SDLP) was increased when the driving speed was faster (0.30 m at 36 km/h; 0.36 m at 72 km/h). The concurrent comprehension task had no significant effect on SDLP (0.34 m on average) or the standard deviation of steering wheel angle (SDSWA; 5.20° on average). The correct rate of the comprehension task was reduced in the dual-task condition (from 93.4% to 91.3%) compared with the comprehension single-task condition. Mental workload was significantly higher in the dual-task condition compared with the single-task conditions. Implications for driving safety were discussed.
Related JoVE Video
Deficit in long-term synaptic plasticity is rescued by a computationally predicted stimulus protocol.
J. Neurosci.
PUBLISHED: 04-19-2013
Show Abstract
Hide Abstract
Mutations in the gene encoding CREB-binding protein (CBP) cause deficits in long-term plasticity, learning, and memory. Here, long-term synaptic facilitation (LTF) at Aplysia sensorimotor synapses in cell culture was used as a model system to investigate methods for overcoming deficits in LTF produced by a CBP knockdown. Injecting CBP-siRNA into individual sensory neurons reduced CBP levels and impaired LTF produced by a standard protocol of five 5-min pulses of serotonin (5-HT) delivered at 20 min interstimulus intervals. A computational model, which simulated molecular processes underlying LTF induction, predicted a rescue protocol of five pulses of 5-HT at non-uniform interstimulus intervals that overcame the consequences of reduced CBP and restored LTF. These results suggest that complementary empirical and computational studies can identify methods for ameliorating impairments of learning attributable to molecular lesions.
Related JoVE Video
Effects of solution conditions on the physicochemical properties of stratification components of extracellular polymeric substances in anaerobic digested sludge.
J Environ Sci (China)
PUBLISHED: 04-17-2013
Show Abstract
Hide Abstract
The composition and effects of solution conditions on the physicochemical properties of the stratification components of extracellular polymeric substances (EPS) in anaerobic digested sludge were determined. The total EPS in anaerobic digested sludge were extracted by the cation exchange resin method. Another EPS extraction method, the centrifugation and sonication technique was employed to stratify the EPS into three fractions: slime, loosely bound (LB)-EPS, and tightly bound (TB)-EPS from the outside to the inside of the anaerobic digested sludge. Proteins and polysaccharides were dispersed uniformly across the different EPS fractions, and humic-like substances were mainly partitioned in the slime, with TB-EPS second. Protein was the major constituent of the LB-EPS and TB-EPS, and the corresponding ratios ranged from 54.0% to 65.6%. The hydrophobic part in the EPS chemical components was primarily comprised of protein and DNA, while the hydrophilic part was mainly composed of polysaccharide. In the slime, the hydrophobic values of several EPS chemical components (protein, polysaccharide, humic-like substances and DNA) were all below 50%. The protein/polysaccharide ratio had a significant influence on the Zeta potentials and isoelectric point values of the EPS: the greater the protein/polysaccharide ratio of the EPS was, the greater the Zeta potential and the higher the isoelectric point value were. All Zeta potentials of the EPS showed a decreasing trend with increasing pH. The corresponding isoelectric point values (pH) were 2.8 for total EPS, 2.2 for slime, 2.7 for LB-EPS, and 2.6 for TB-EPS. As the ionic strength increased, the Zeta potentials sharply increased and then gradually became constant without charge reversal. In addition, as the temperature increased (< 40 degrees C), the apparent viscosity of the EPS decreased monotonically and then gradually became stable between 40 and 60 degrees C.
Related JoVE Video
Interference control in 6-11 year-old children with and without ADHD: behavioral and ERP study.
Int. J. Dev. Neurosci.
PUBLISHED: 04-10-2013
Show Abstract
Hide Abstract
Event-related potentials (ERPs) were recorded during a hybrid Simon-spatial Stroop task. We compared interference control and conflict monitoring in children with and without attention-deficit/hyperactivity disorder (ADHD), to examine developmental functional patterns. We found that children with ADHD exhibited lower accuracy rates and longer and more variable reaction time (RT) in both tasks, especially in the incongruent condition. In both controls and ADHD children, the accuracy rate increased and RT decreased with age. Major development in interference control occurred from 6-7 to 8 years in ADHD children and controls, yet only occurred from 9 to 10-11 years in normal children. The ERP results revealed that the N2 potentials were not significantly different from age-matched controls in the two tasks and that the development pattern of conflict monitoring was not different in school age children with and without ADHD. Children with ADHD had normal conflict monitoring ability.
Related JoVE Video
Association of endothelial nitric oxide synthase gene polymorphisms with type 2 diabetes mellitus: a meta-analysis.
Endocr. J.
PUBLISHED: 04-07-2013
Show Abstract
Hide Abstract
A meta-analysis was performed to assess the association of endothelial nitric oxide synthase (NOS3) gene polymorphisms [4b4a VNTR and G894T (rs1799983)] with type 2 diabetes mellitus (T2DM). A comprehensive search was conducted to identify all eligible articles. Fixed or random effect pooled measure was selected based on homogeneity test. Heterogeneity among studies was evaluated using the I2. Meta-regression was used to explore potential sources of between-study heterogeneity. Publication bias was estimated using Eggers linear regression test. 19 articles involving 8,009 subjects for 4b4a VNTR and 19 articles involving 8,600 subjects for G894T were included. After excluding articles that deviated from Hardy-Weinberg equilibrium in controls and sensitivity analysis, significant association was found between 4a and increased risk of T2DM considering dominant model [OR (95% CI)=1.32 (1.17-1.48)], a vs. b [OR (95% CI)=1.34 (1.21-1.48)], and aa vs. bb [OR (95% CI)=1.52 (1.05-2.22)]. The 894T allele was also found associated with increased risk of T2DM considering dominant model [OR (95% CI)=1.14 (1.03-1.26)], recessive model [OR (95%CI)=1.28 (1.06-1.54)], T vs. G [OR (95% CI)=1.18 (1.09-1.27)], and TT vs. GG [OR (95% CI)=1.33 (1.09-1.62)]. The findings were consistent in Asian population. The meta-analysis indicated that NOS3 gene 4b4a VNTR and G894T polymorphisms might be associated with T2DM risk.
Related JoVE Video
Association of the A1298C polymorphism in MTHFR gene with ischemic stroke.
J Clin Neurosci
PUBLISHED: 04-01-2013
Show Abstract
Hide Abstract
A meta-analysis was performed to assess the association between the methylenetetrahydrofolate reductase (MTHFR) A1298C genetic polymorphism and ischemic stroke. A comprehensive search was conducted to identify all case-control or cohort studies. The fixed or random effect pooled measure was selected based on the homogeneity between studies, as assessed by I(2). Meta-regression was used to explore the potential sources of between-study heterogeneity. Publication bias was estimated using Eggers linear regression test. Thirteen case-control studies corresponded to the inclusion criteria comprising 2133 patients and 2572 controls which were included in the present meta-analysis. After excluding articles that deviated from Hardy-Weinberg equilibrium in controls and the key contributors to between-study heterogeneity, significant associations between MTHFR A1298C genetic polymorphism and risk of ischemic stroke were observed in dominant (odds ratio [OR] 1.227, 95% confidence interval [CI] 1.062-1.416) and codominant (OR 1.138, 95% CI 1.007-1.286) inheritance models. Moreover, in the subgroup analysis based on region (Asia and Europe), significant associations were observed in most genetic models in Asia but not in Europe. This meta-analysis suggests that MTHFR A1298C genetic polymorphism is associated with increased risk of ischemic stroke, and the C allele may be an important risk factor for ischemic stroke.
Related JoVE Video
Bifurcation stenting in patients with ST-segment elevation myocardial infarction: an analysis from dkcrush II randomized study.
Catheter Cardiovasc Interv
PUBLISHED: 03-26-2013
Show Abstract
Hide Abstract
We sought to study the clinical outcomes of bifurcation stenting in patients who presented with stent thrombosis segment elevation myocardial infarction (STEMI).
Related JoVE Video
Transulnar catheterization in patients with ipsilateral radial artery occlusion.
Catheter Cardiovasc Interv
PUBLISHED: 03-14-2013
Show Abstract
Hide Abstract
The transradial approach to percutaneous coronary intervention (PCI) has recently gained popularity among interventionalists. However, radial artery occlusion (RAO) limits the ability for repeat catheterization. In current practice, transulnar catheterization is thought to be a contraindication in patients with ipsilateral RAO.
Related JoVE Video
Zerumbone induces apoptosis in human renal cell carcinoma via Gli-1/Bcl-2 pathway.
Pharmazie
PUBLISHED: 03-09-2013
Show Abstract
Hide Abstract
Renal cell carcinoma (RCC) is a malignant disease insensitive to conventional treatments such as radiochemotherapy and immunotherapy. Search for new approaches to induce cancer cell apoptosis will improve the management of RCC. Here, we reported that zerumbone, a monosesquiterpine, shows anticancer effects on human RCC cells via induction of apoptosis in vitro. Human renal clear cell carcinoma 786-0 and 769-P cell lines were used as the model system. Exposure of RCC cells to zerumbone resulted in cell viability inhibition, accompanied by DNA fragmentation and increased apoptotic index. Mechanically, treatment of RCC cells with zerumbone activated caspase-3 and caspase-9, and finally led to cleavage of PARR In addition, downregulation of Gli-1 and Bcl-2, which were closely related to the chemoresistance of RCC, was observed in zerumbone-treated RCC cells. Taken together, our study provided the first evidence that zerumbone imparted strong inhibitory and apoptotic effects on human RCC cells. The zerumbone-induced apoptosis might be related to the activation of the caspase cascade and deregulation of the Gli-1/Bcl-2 pathway. Our results suggest that zerumbone merit further investigation as an apoptosis inducer as well as a novel RCC chemotherapeutic agent in the clinical setting.
Related JoVE Video
Serum uric acid levels and incidence of impaired fasting glucose and type 2 diabetes mellitus: A meta-analysis of cohort studies.
Diabetes Res. Clin. Pract.
PUBLISHED: 03-03-2013
Show Abstract
Hide Abstract
AIMS: A meta-analysis of cohort studies was conducted to assess the association between serum uric acid (SUA) levels and incidence of impaired fasting glucose (IFG) and type 2 diabetes mellitus (T2DM). METHODS: A comprehensive search was conducted to identify eligible studies. The fixed or random effect pooled measure was selected based on between-study heterogeneity. Dose-response relationship was assessed by restricted cubic spline model and multivariate random-effect meta-regression. RESULTS: Twelve studies with fifteen results were included involving 6340 cases and 62,834 participants. The pooled multivariate-adjusted relative risk (RR) (95%CI) of IFG and T2DM for the highest vs. lowest level of SUA was 1.54 (1.41-1.68), I(2)=42.2%. The association was consistent and significant across subgroup analysis. A nonlinear relationship was found of SUA levels with incidence of IFG and T2DM (P<0.01), and the multivariate-adjusted RRs (95%CI) of IFG and T2DM were 1.02 (0.95-1.10), 1.04 (0.94-1.15), 1.10 (0.99-1.22), 1.25 (1.16-1.35), 1.43 (1.31-1.55), 1.50 (1.38-1.63) and 1.49 (1.34-1.67) for 2.5, 3.5, 4.5, 5.5, 6.5, 7.5 and 8.5mg/dl of SUA. The RR (95%CI) of T2DM for the highest vs. lowest level of SUA was 1.67 (1.51-1.86), and a nonlinear relationship was also found between SUA levels and incidence of T2DM. CONCLUSIONS: SUA levels are positively associated with incidence of IFG and T2DM, and the association might be nonlinear.
Related JoVE Video
A novel degenerated primer pair detects diverse genes of acyl homoserine lactone synthetase in Rhizobiaceae family.
Curr. Microbiol.
PUBLISHED: 02-22-2013
Show Abstract
Hide Abstract
A novel degenerated primer set was designed to amplify acyl homoserine lactone (AHL) synthetase genes from members of the family Rhizobiaceae. The primer set successfully amplified AHL synthetase genes from pure cultures of AHL producers from Rhizobiaceae, but not from AHL producers out of the Rhizobiaceae family, indicating the specificity of this primer set to the Rhizobiaceae family. An inoculation experiment showed that the minimal detectable concentration of AHL producers from the soil was around 2.5 × 10(7) CFU/g soil. When applying to environmental samples, 7 and 14 different genotypes of AHL synthetase genes were identified in the rhizosphere of Glycine max and Vigna unguiculata, respectively, which revealed complicated and unknown AHL-based quorum-sensing networks in the rhizosphere. This is the first primer set that covers diverse AHL synthetase genes from different genera. It will be a useful culture-independent approach for better understanding of the ecological significance of QS in natural habitats.
Related JoVE Video
BACE2 degradation mediated by the macroautophagy-lysosome pathway.
Eur. J. Neurosci.
PUBLISHED: 02-14-2013
Show Abstract
Hide Abstract
Neuritic plaque is the pathological hallmark in Alzheimers disease (AD). Amyloid-? protein (A?), the central component of neuritic plaques, is generated from amyloid-? precursor protein (APP) by ?-site APP cleaving enzyme 1 (BACE1) and ?-secretase. ?-site APP cleaving enzyme 2 (BACE2), a homolog of BACE1, functions differently from BACE1 in APP processing. BACE1 is the ?-secretase essential for A? production, and BACE2, a ?-secretase, cleaves APP within the A? domain, preventing A? production. Elucidation of the mechanism underlying BACE2 degradation is important for defining its biological features and its potential role in Alzheimers disease drug development. In this report we first showed that the half-life of BACE2 is approximately 20 h. Lysosomal inhibition increased BACE2 protein levels whereas proteasomal inhibition had no effect on BACE2 protein expression. Furthermore, we identified that macroautophagy mediated BACE2 degradation. Finally, we showed that lysosomal inhibition increased BACE2 cleavage of APP. Taken together, our in vitro study showed that BACE2 is degraded through the macrophagy-lysosome pathway and that lysosomal inhibition affects BACE2 processing of APP. Modulation of BACE2 degradation via the lysosomal pathway could be a new target for AD drug development.
Related JoVE Video
Comparative study of nickel resistance of pure culture and co-culture of Acidithiobacillus thiooxidans and Leptospirillum ferriphilum.
Arch. Microbiol.
PUBLISHED: 02-13-2013
Show Abstract
Hide Abstract
The effect of Ni²? on the growth and functional gene expression of the pure culture and co-culture of Acidithiobacillus thiooxidans and Leptospirillum ferriphilum has been studied. Compared with the pure culture, the co-culture showed a stronger sulfur and ferrous ion oxidation activity. At 100 mM, A. thiooxidans in co-culture grew faster and had 48 h shorter lag phases. The cell number of A. thiooxidans in co-culture was about 5 times higher than that in pure culture. The existence of A. thiooxidans in co-culture activated the expression of some metal resistance genes in L. ferriphilum at least 16 h in advance. A. thiooxidans in co-culture tends to chose more efficient pathways to transport nickel ion, ensuring the export of heavy metal was faster and more effective than that in pure culture. All the data indicated that there were synergetic interactions between iron- and sulfur-oxidizing bacteria under the stress of Ni²?.
Related JoVE Video
Coffee and caffeine intake and breast cancer risk: an updated dose-response meta-analysis of 37 published studies.
Gynecol. Oncol.
PUBLISHED: 02-01-2013
Show Abstract
Hide Abstract
We conducted an updated meta-analysis to summarize the evidence from published studies regarding the association of coffee and caffeine intake with breast cancer risk.
Related JoVE Video
Evaluation of the application potential of bentonites in phenanthrene bioremediation by characterizing the biofilm community.
Bioresour. Technol.
PUBLISHED: 01-30-2013
Show Abstract
Hide Abstract
Application of clay minerals in bioremediation has emerged as a new and promising research field. In this study, the application of calcinated bentonite (CB) and calcinated organobentonite (COB) in phenanthrene (Phe) bioremediation showed high Phe removal efficiency. Clone libraries based on 16S rRNA gene and scanning electronic microscopy showed that diverse taxa of bacteria formed biofilms on both COB and CB particles. The family Sphingomonadaceae was the major group and made up 18% and 23% of the COB and CB biofilm composition, respectively. All and 80% of dioxygenase genes from COB and CB biofilms were closely related to that of Sphingomonas sp., and others matched to that of Comamonas and Mycobacterium. The selective effect of COB on bacterial community was also evident. This study characterized for the first time the bacterial diversity of biofilm community and functional Phe degrading groups on bentonites particles, and provided useful information for future applications.
Related JoVE Video
Delayed recovery of spontaneous circulation following cessation of cardiopulmonary resuscitation in an older patient: a case report.
J Med Case Rep
PUBLISHED: 01-28-2013
Show Abstract
Hide Abstract
This report describes the apparent resurrection of a patient in an emergency department setting. Befittingly named the Lazarus phenomenon, the recovery of spontaneous circulation after cessation of cardiopulmonary resuscitation is an extremely rare occurrence that was first described in 1982 and has been mentioned only 38 times in the medical literature. Our patients case is remarkable in that it helps illustrate many of the mechanisms of this rare phenomenon. It also serves as a reminder of our limitations in determining when to terminate cardiopulmonary resuscitation and suggests that cessation of cardiopulmonary resuscitation should be approached with more care.
Related JoVE Video
The prognostic value of tumor budding in invasive breast cancer.
Pathol. Res. Pract.
PUBLISHED: 01-27-2013
Show Abstract
Hide Abstract
We investigated the prognostic value of tumor budding in 160 cases of operable invasive ductal carcinoma, not otherwise specified (IDC-NOS). The number of buds was counted in H&E slides with a maximal invasive margin in a 0.950mm(2) field of vision (200×). According to a cut-off score selected by ROC analysis, the cohort was dichotomized into a low (0-7 budding foci, 107 cases, 66.9%) and a high-grade budding group (8 or more budding foci, 53 cases, 33.1%). The inter-observer test showed a good reproducibility with 0.717 as the ? value. High-grade budding was significantly associated with the presence of lymphovascular invasion (LVI) (P=0.001), larger tumor size (P=0.014), and worse clinical outcome (P<0.001). By immunohistochemical staining, budded cells at the margin displayed epithelial mesenchymal transition (EMT)-like molecular phenotype and decreased proliferative activity. Survival analyses revealed that tumor budding (HR 4.275, P<0.001) together with tumor size (HR 2.468, P=0.002), node status (HR 2.362, P<0.001), and LVI status (HR 1.910, P=0.035) was the independent prognostic factor in IDC-NOS. In conclusion, tumor budding is a reproducible, significant, and independent histopathological prognostic factor in IDC-NOS.
Related JoVE Video
Differential gene expression and bioinformatics analysis of copper resistance gene afe_1073 in Acidithiobacillus ferrooxidans.
Biol Trace Elem Res
PUBLISHED: 01-24-2013
Show Abstract
Hide Abstract
Copper resistance of acidophilic bacteria is very significant in bioleaching of copper ore since high concentration of copper are harmful to the growth of organisms. Copper resistance gene afe_1073 was putatively considered to be involved in copper homeostasis in Acidithiobacillus ferrooxidans ATCC23270. In the present study, differential expression of afe_1073 in A. ferrooxidans strain DY26 and DC was assessed with quantitative reverse transcription polymerase chain reaction. The results showed the expression of afe_1073 in two strains increased with the increment of copper concentrations. The expression of DY26 was lower than that of DC at the same copper concentration although A. ferrooxidans strain DY26 possessed higher copper resistance than strain DC. In addition, bioinformatics analysis showed AFE_1073 was a typical transmembrane protein P1b1-ATPase, which could reduce the harm of Cu(+) by pumping it out from the cell. There were two mutation sites in AFE_1073 between DY26 and DC and one may change the hydrophobicity of AFE_1073, which could enhance the ability of DY26 to pump out Cu(+). Therefore, DY26 needed less gene expression of afe_1073 for resisting copper toxicity than that of DC at the same copper stress. Our study will be beneficial to understanding the copper resistance mechanism of A. ferrooxidans.
Related JoVE Video
RubisCO gene clusters found in a metagenome microarray from acid mine drainage.
Appl. Environ. Microbiol.
PUBLISHED: 01-18-2013
Show Abstract
Hide Abstract
The enzyme responsible for carbon dioxide fixation in the Calvin cycle, ribulose-1,5-bisphosphate carboxylase/oxygenase (RubisCO), is always detected as a phylogenetic marker to analyze the distribution and activity of autotrophic bacteria. However, such an approach provides no indication as to the significance of genomic content and organization. Horizontal transfers of RubisCO genes occurring in eubacteria and plastids may seriously affect the credibility of this approach. Here, we presented a new method to analyze the diversity and genomic content of RubisCO genes in acid mine drainage (AMD). A metagenome microarray containing 7,776 large-insertion fosmids was constructed to quickly screen genome fragments containing RubisCO form I large-subunit genes (cbbL). Forty-six cbbL-containing fosmids were detected, and six fosmids were fully sequenced. To evaluate the reliability of the metagenome microarray and understand the microbial community in AMD, the diversities of cbbL and the 16S rRNA gene were analyzed. Fosmid sequences revealed that the form I RubisCO gene cluster could be subdivided into form IA and IB RubisCO gene clusters in AMD, because of significant divergences in molecular phylogenetics and conservative genomic organization. Interestingly, the form I RubisCO gene cluster coexisted with the form II RubisCO gene cluster in one fosmid genomic fragment. Phylogenetic analyses revealed that horizontal transfers of RubisCO genes may occur widely in AMD, which makes the evolutionary history of RubisCO difficult to reconcile with organismal phylogeny.
Related JoVE Video
Confidence interval procedures for system reliability and applications to competing risks models.
Lifetime Data Anal
PUBLISHED: 01-15-2013
Show Abstract
Hide Abstract
System reliability depends on the reliability of the systems components and the structure of the system. For example, in a competing risks model, the system fails when the weakest component fails. The reliability function and the quantile function of a complicated system are two important metrics for characterizing the systems reliability. When there are data available at the component level, the system reliability can be estimated by using the component level information. Confidence intervals (CIs) are needed to quantify the statistical uncertainty in the estimation. Obtaining system reliability CI procedures with good properties is not straightforward, especially when the system structure is complicated. In this paper, we develop a general procedure for constructing a CI for the system failure-time quantile function by using the implicit delta method. We also develop general procedures for constructing a CI for the cumulative distribution function (cdf) of the system. We show that the recommended procedures are asymptotically valid and have good statistical properties. We conduct simulations to study the finite-sample coverage properties of the proposed procedures and compare them with existing procedures. We apply the proposed procedures to three applications; two applications in competing risks models and an application with a [Formula: see text] system. The paper concludes with some discussion and an outline of areas for future research.
Related JoVE Video
Thermally induced phase transformation of pearl powder.
Mater Sci Eng C Mater Biol Appl
PUBLISHED: 01-11-2013
Show Abstract
Hide Abstract
The polymorphic phase transformation of thermally treated pearl powder was investigated by X-ray diffraction and thermoanalytical techniques. The phase transformation was based on quantification of the calcite content at various temperatures using Rietveld refinement analysis. The results show that the phase transformation of pearl aragonite occurred within a temperature range of 360-410 °C, which is 50-100 °C lower than the range for non-biomineralized aragonite. These thermoanalytical results suggest that the phase transformation of pearl aragonite may occur immediately after the thermal decomposition of the organic matrix in the pearl powder. An important finding is that decomposition of the organic matrix may greatly facilitate such transformation by releasing additional space for an easier structural reconstruction during the phase transformation process.
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.