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Find video protocols related to scientific articles indexed in Pubmed.
[Characterization of recombinant L-isoleucine-4-hydroxylase from Bacillus thuringiensis and its application in 4hydroxyisoleucine biosynthesis].
Wei Sheng Wu Xue Bao
PUBLISHED: 10-28-2014
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L-isoleucine-4-hydroxylase (IDO) encoding gene ido from Bacillus thuringiensis TCCC 11826 was cloned and expressed, followed by enzyme characterization. In addition, recombinant strain was tested for its 4-Hydroxyisoleucine (4-HIL) biotransformation.
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Draft Genome Sequence of Halotolerant Polycyclic Aromatic Hydrocarbon-Degrading Pseudomonas bauzanensis Strain W13Z2.
Genome Announc
PUBLISHED: 10-18-2014
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Pseudomonas bauzanensis W13Z2 is a halotolerant polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from petroleum-contaminated drill cuttings in the Bohai Sea. Here, we report the 8.6-Mb draft genome sequence of this strain, which will provide insights into the diversity of Pseudomonas and the mechanism of PAHs degradation in drill cuttings.
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Feedback mechanisms in a mechanical model of cell polarization.
Phys Biol
PUBLISHED: 10-15-2014
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Directed cell migration requires a spatially polarized distribution of polymerized actin. We develop and treat a mechanical model of cell polarization based on polymerization and depolymerization of actin filaments at the two ends of a cell, modulated by forces at either end that are coupled by the cell membrane. We solve this model using both a simulation approach that treats filament nucleation, polymerization, and depolymerization stochastically, and a rate-equation approach based on key properties such as the number of filaments N and the number of polymerized subunits F at either end of the cell. The rate-equation approach agrees closely with the stochastic approach at steady state and, when appropriately generalized, also predicts the dynamic behavior accurately. The calculated transitions from symmetric to polarized states show that polarization is enhanced by a high free-actin concentration, a large pointed-end off-rate, a small barbed-end off-rate, and a small spontaneous nucleation rate. The rate-equation approach allows us to perform a linear-stability analysis to pin down the key interactions that drive the polarization. The polarization is driven by a positive-feedback loop having two interactions. First, an increase in F at one side of the cell lengthens the filaments and thus reduces the decay rate of N (increasing N); second, increasing N enhances F because the force per growing filament tip is reduced. We find that the transitions induced by changing system properties result from supercritical pitchfork bifurcations. The filament lifetime depends strongly on the average filament length, and this effect is crucial for obtaining polarization correctly.
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Draft Genome Sequence of Brachybacterium phenoliresistens Strain W13A50, a Halotolerant Hydrocarbon-Degrading Bacterium.
Genome Announc
PUBLISHED: 09-20-2014
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Brachybacterium phenoliresistens strain W13A50 was isolated from a petroleum-contaminated saline site, which could degrade hydrocarbon under high salinity conditions. Here, we present 4.2-Mb draft genome sequence of this strain, which will provide insights into the diversity of Brachybacterium and the mechanism of hydrocarbon degradation in saline environments.
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[Role of endoplasmic reticulum stress in D-GalN/LPS-induced acute liver failure].
Zhonghua Gan Zang Bing Za Zhi
PUBLISHED: 09-03-2014
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To study the role of endoplasmic reticulum stress (ERS) in acute liver failure (ALF) using a mouse model of D-Galactosamine/lipopolysaccharide (D-GalN/LPS)-induced ALF.
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Mst1 directs Myosin IIa partitioning of low and higher affinity integrins during T cell migration.
PLoS ONE
PUBLISHED: 08-18-2014
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Chemokines promote T cell migration by transmitting signals that induce T cell polarization and integrin activation and adhesion. Mst1 kinase is a key signal mediator required for both of these processes; however, its molecular mechanism remains unclear. Here, we present a mouse model in which Mst1 function is disrupted by a hypomorphic mutation. Microscopic analysis of Mst1-deficient CD4 T cells revealed a necessary role for Mst1 in controlling the localization and activity of Myosin IIa, a molecular motor that moves along actin filaments. Using affinity specific LFA-1 antibodies, we identified a requirement for Myosin IIa-dependent contraction in the precise spatial distribution of low and higher affinity LFA-1 on the membrane of migrating T cells. Mst1 deficiency or Myosin inhibition resulted in multipolar cells, difficulties in uropod detachment and mis-localization of low affinity LFA-1. Thus, Mst1 regulates Myosin IIa dynamics to organize high and low affinity LFA-1 to the anterior and posterior membrane during T cell migration.
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Calmodulin and PI(3,4,5)P? cooperatively bind to the Itk pleckstrin homology domain to promote efficient calcium signaling and IL-17A production.
Sci Signal
PUBLISHED: 08-07-2014
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Precise regulation of the kinetics and magnitude of Ca(2+) signaling enables this signal to mediate diverse responses, such as cell migration, differentiation, vesicular trafficking, and cell death. We showed that the Ca(2+)-binding protein calmodulin (CaM) acted in a positive feedback loop to potentiate Ca(2+) signaling downstream of the Tec kinase family member Itk. Using NMR (nuclear magnetic resonance), we mapped CaM binding to two loops adjacent to the lipid-binding pocket within the Itk pleckstrin homology (PH) domain. The Itk PH domain bound synergistically to Ca(2+)/CaM and the lipid phosphatidylinositol 3,4,5-trisphosphate [PI(3,4,5)P3], such that binding to Ca(2+)/CaM enhanced the binding to PI(3,4,5)P3 and vice versa. Disruption of CaM binding attenuated Itk recruitment to the membrane and diminished release of Ca(2+) from the endoplasmic reticulum. Moreover, disruption of this feedback loop abrogated Itk-dependent production of the proinflammatory cytokine IL-17A (interleukin-17A) by CD4(+) T cells. Additionally, we found that CaM associated with PH domains from other proteins, indicating that CaM may regulate other PH domain-containing proteins.
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Chemokine treatment rescues profound T-lineage progenitor homing defect after bone marrow transplant conditioning in mice.
Blood
PUBLISHED: 05-29-2014
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Development of T cells in the thymus requires continuous importation of T-lineage progenitors from the bone marrow via the circulation. Following bone marrow transplant, recovery of a normal peripheral T-cell pool depends on production of naïve T cells in the thymus; however, delivery of progenitors to the thymus limits T-lineage reconstitution. Here, we examine homing of intravenously delivered progenitors to the thymus following irradiation and bone marrow reconstitution. Surprisingly, following host conditioning by irradiation, we find that homing of lymphoid-primed multipotent progenitors and common lymphoid progenitors to the thymus decreases more than 10-fold relative to unirradiated mice. The reduction in thymic homing in irradiated mice is accompanied by a significant reduction in CCL25, an important chemokine ligand for thymic homing. We show that pretreatment of bone marrow progenitors with CCL25 and CCL21 corrects the defect in thymic homing after irradiation and promotes thymic reconstitution. These data suggest new therapeutic approaches to promote T-cell regeneration.
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In vivo powering of pacemaker by breathing-driven implanted triboelectric nanogenerator.
Adv. Mater. Weinheim
PUBLISHED: 05-08-2014
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The first application of an implanted triboelectric nanogenerator (iTENG) that enables harvesting energy from in vivo mechanical movement in breathing to directly drive a pacemaker is reported. The energy harvested by iTENG from animal breathing is stored in a capacitor and successfully drives a pacemaker prototype to regulate the heart rate of a rat. This research shows a feasible approach to scavenge biomechanical energy, and presents a crucial step forward for lifetime-implantable self-powered medical devices.
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Evaluation of human health risks posed by carcinogenic and non-carcinogenic multiple contaminants associated with consumption of fish from Taihu Lake, China.
Food Chem. Toxicol.
PUBLISHED: 03-08-2014
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The present study estimated the human daily intake and uptake of organochlorine pesticides (OCPs), polychlorinated biphenyls (PCBs), polybrominated diphenyl ethers (PBDEs), polycyclic aromatic hydrocarbons (PAHs), and toxic trace elements [mercury (Hg), chromium (Cr), cadmium (Cd), and arsenic (As)] due to consumption of fish from Taihu Lake, China, and the associated potential health risks posed by these contaminants. The health risks posed by the contaminants were assessed using a risk quotient of the fish consumption rate to the maximum allowable fish consumption rate considering the contaminants for carcinogenic and non-carcinogenic effect endpoints. The results showed that fish consumption would not pose non-cancer risks. However, some species would cause a cancer risk. Relative risks of the contaminants were calculated to investigate the contaminant which posed the highest risk to humans. As a result, in view of the contaminants for carcinogenic effects, As was the contaminant which posed the highest risk to humans. However, when non-carcinogenic effects of the contaminants were considered, Hg posed the highest risk. The risk caused by PBDEs was negligible. The results demonstrated that traditional contaminants, such as As, Hg, DDTs (dichlorodiphenyltrichloroethane and its metabolites), and PCBs, require more attention in Taihu Lake than the other target contaminants.
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The transcription factor Foxp1 is a critical negative regulator of the differentiation of follicular helper T cells.
Nat. Immunol.
PUBLISHED: 02-24-2014
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CD4(+) follicular helper T cells (T(FH) cells) are essential for germinal center (GC) responses and long-lived antibody responses. Here we report that naive CD4(+) T cells deficient in the transcription factor Foxp1 'preferentially' differentiated into T(FH) cells, which resulted in substantially enhanced GC and antibody responses. We found that Foxp1 used both constitutive Foxp1A and Foxp1D induced by stimulation of the T cell antigen receptor (TCR) to inhibit the generation of T(FH) cells. Mechanistically, Foxp1 directly and negatively regulated interleukin 21 (IL-21); Foxp1 also dampened expression of the costimulatory molecule ICOS and its downstream signaling at early stages of T cell activation, which rendered Foxp1-deficient CD4(+) T cells partially resistant to blockade of the ICOS ligand (ICOSL) during T(FH) cell development. Our findings demonstrate that Foxp1 is a critical negative regulator of T(FH) cell differentiation.
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Mn-Ni content-dependent structures and electrochemical behaviors of serial Li(1.2)Ni(0.13+x)Co(0.13)Mn(0.54-x)O(2) as lithium-ion battery cathodes.
ACS Appl Mater Interfaces
PUBLISHED: 02-07-2014
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In this paper, a citric acid-assisted sol-gel route has been successfully used for the nanofabrication of serial solid solutions in a chemical formula of Li1.2Ni0.13+xCo0.13Mn0.54-xO2 at the x value of -0.06, -0.03, 0, 0.03, or 0.06. Powdered X-ray diffraction (XRD) results indicate that all the solid solutions possess the well-established structural characteristics for a homogeneous solid solution of Li2MnO3 and LiNi1/3+xCo1/3Mn1/3-xO2 components with an increasing Li2MnO3 content along with the decrease of x value. Scanning electron microscope (SEM) observation and elemental analyses show that these samples are composed of polyhedral nanoparticles with a chemical composition similar to that of the corresponding raw materials. Applied as lithium-ion battery cathodes, the initial Coulombic efficiency, cycling stability, and rate capability of solid solutions are determined by their chemical compositions, giving an optimal x value within the range of -0.03 and 0.03. That is, the variation of x value in the formula Li1.2Ni0.13+xCo0.13Mn0.54-xO2 should exert a great influence on the electrochemical performances of these cathodes. Anyways, these suggest an effective strategy to understand the relationship between the Mn-Ni content-dependent crystal structures and electrochemical behaviors of solid solutions.
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Draft Genome Sequence of Gordonia alkanivorans Strain CGMCC6845, a Halotolerant Hydrocarbon-Degrading Bacterium.
Genome Announc
PUBLISHED: 02-01-2014
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Gordonia alkanivorans strain CGMCC6845 is a halotolerant hydrocarbon-degrading bacterium isolated from petroleum-contaminated saline soil. Here we present the 5.0-Mb draft genome sequence of this strain, which will improve our understanding of the diversity of G. alkanivorans and the mechanisms of microbial hydrocarbon degradation in saline environment.
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Draft Genome Sequence of Advenella kashmirensis Strain W13003, a Polycyclic Aromatic Hydrocarbon-Degrading Bacterium.
Genome Announc
PUBLISHED: 02-01-2014
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Advenella kashmirensis strain W13003 is a polycyclic aromatic hydrocarbon (PAH)-degrading bacterium isolated from PAH-contaminated marine sediments. Here, we report the 4.8-Mb draft genome sequence of this strain, which will provide insights into the diversity of A. kashmirensis and the mechanism of PAH degradation in the marine environment.
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Draft Genome Sequence of Brevibacillus panacihumi Strain W25, a Halotolerant Hydrocarbon-Degrading Bacterium.
Genome Announc
PUBLISHED: 01-25-2014
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Brevibacillus panacihumi strain W25 was isolated from hydrocarbon-contaminated saline soil. Here, we report the 5.5-Mb draft genome sequence of this strain, which may provide insights into the mechanism of microbial hydrocarbon degradation in saline environments.
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Rodent herpesvirus peru encodes a secreted chemokine decoy receptor.
J. Virol.
PUBLISHED: 10-30-2013
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Viruses have long been studied not only for their pathology and associated disease but also as model systems for understanding cellular and immunological processes. Rodent herpesvirus Peru (RHVP) is a recently characterized rhadinovirus related to murine gammaherpesvirus 68 (MHV68) and Kaposis sarcoma-associated herpesvirus (KSHV) that establishes acute and latent infection in laboratory mice. RHVP encodes numerous unique proteins that we hypothesize might facilitate host immune evasion during infection. We report here that open reading frame (ORF) R17 encodes a high-affinity chemokine binding protein that broadly recognizes human and murine CC and C chemokines. The interaction of R17 with chemokines is generally characterized by rapid association kinetics, and in the case of CCL3, CCL4, CCL5, CCL24, and XCL1, extremely stable complexes are formed. Functionally, R17 potently inhibited CCL2-driven chemotaxis of the human monocytic cell line THP-1, CCL3-driven chemotaxis of peripheral blood mononuclear cells, and CCL2-mediated calcium flux. Our studies also reveal that R17 binds to glycosaminoglycans (GAGs) in a process dependent upon two BBXB motifs and that chemokine and GAG binding can occur simultaneously at distinct sites. Collectively, these studies suggest that R17 may play a role in RHVP immune evasion through the targeted sabotage of chemokine-mediated immune surveillance.
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[Applicating food frequency questionnaire to assess the relationship between dietary polyunsaturated fatty acid intake and hypertension, dyslipidemia of Pumi nationality].
Wei Sheng Yan Jiu
PUBLISHED: 09-13-2013
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The relationship between dietary polyunsaturated fatty acid intake and hypertension, dyslipidemia of Pumi nationality was studied,which provides a scientific basis of prevention and cure of hypertension and dyslipidemia.
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T cell development requires constraint of the myeloid regulator C/EBP-? by the Notch target and transcriptional repressor Hes1.
Nat. Immunol.
PUBLISHED: 08-18-2013
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Notch signaling induces gene expression of the T cell lineage and discourages alternative fate outcomes. Hematopoietic deficiency in the Notch target Hes1 results in severe T cell lineage defects; however, the underlying mechanism is unknown. We found here that Hes1 constrained myeloid gene-expression programs in T cell progenitor cells, as deletion of the myeloid regulator C/EBP-? restored the development of T cells from Hes1-deficient progenitor cells. Repression of Cebpa by Hes1 required its DNA-binding and Groucho-recruitment domains. Hes1-deficient multipotent progenitor cells showed a developmental bias toward myeloid cells and dendritic cells after Notch signaling, whereas Hes1-deficient lymphoid progenitor cells required additional cytokine signaling for diversion into the myeloid lineage. Our findings establish the importance of constraining developmental programs of the myeloid lineage early in T cell development.
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Factors influencing on the bioaccessibility of polybrominated diphenyl ethers in size-specific dust from air conditioner filters.
Chemosphere
PUBLISHED: 06-03-2013
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Size-specific concentrations and bioaccessibility of polybrominated diphenyl ethers (PBDEs) in dust from air conditioner filters were measured, and the factors influencing the PBDE bioaccessibility were determined. Generally, the PBDE concentrations increased with decreasing dust particle size, and BDE209 (deca-BDE) was generally the predominant congener. The bioaccessibility ranged from 20.3% to 50.8% for tri- to hepta-BDEs, and from 5.1% to 13.9% for BDE209 in dust fractions of varied particle size. The bioaccessibility of most PBDE congeners decreased with increasing dust particle size. The way of being of PBDE (adsorbed to dust surface or incorporated into polymers) in dust significantly influenced the bioaccessibility. There was a significant negative correlation between the tri- to hepta-BDE bioaccessibility and organic matter (OM) contents in dust. Furthermore, tri- to hepta-BDE bioaccessibility increased with increasing polarity of OMs, while with decreasing aromaticity of OMs. The tri- to hepta-BDE bioaccessibility significantly positively correlated with the surface areas and pore volumes of dust. Using multiple linear regression analysis, it was found that the OM contents and pore volumes of dust were the most important factors to influence the tri- to hepta-BDE bioaccessibility and they could be used to estimate the bioaccessibility of tri- to hepta-BDEs according to the following equation: bioaccessibility (%)=45.05-0.49 × OM%+1.79 × pore volume. However, BDE209 bioaccessibility did not correlate to any of these factors.
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Long non-coding RNA: a new player in cancer.
J Hematol Oncol
PUBLISHED: 05-08-2013
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Emerging evidence showed that long non-coding RNAs (lncRNAs) play important roles in a wide range of biological processes and dysregulated lncRNAs are involved in many complex human diseases, including cancer. Although a few lncRNAs functions in cancer have been characterized, the detailed regulatory mechanisms of majority of lncRNAs in cancer initiation and progression remain largely unknown. In this review, we summarized recent progress on the mechanisms and functions of lncRNAs in cancer, especially focusing on the oncogenic and tumor suppressive roles of the newly identified lncRNAs, and the pathways these novel molecules might be involved in. Their potentials as biomarkers for diagnosis and prognosis in cancer are also discussed in this paper.
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Analysis of synonymous codon usage patterns in the genus Rhizobium.
World J. Microbiol. Biotechnol.
PUBLISHED: 04-25-2013
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The codon usage patterns of rhizobia have received increasing attention. However, little information is available regarding the conserved features of the codon usage patterns in a typical rhizobial genus. The codon usage patterns of six completely sequenced strains belonging to the genus Rhizobium were analysed as model rhizobia in the present study. The relative neutrality plot showed that selection pressure played a role in codon usage in the genus Rhizobium. Spearmans rank correlation analysis combined with correspondence analysis (COA) showed that the codon adaptation index and the effective number of codons (ENC) had strong correlation with the first axis of the COA, which indicated the important role of gene expression level and the ENC in the codon usage patterns in this genus. The relative synonymous codon usage of Cys codons had the strongest correlation with the second axis of the COA. Accordingly, the usage of Cys codons was another important factor that shaped the codon usage patterns in Rhizobium genomes and was a conserved feature of the genus. Moreover, the comparison of codon usage between highly and lowly expressed genes showed that 20 unique preferred codons were shared among Rhizobium genomes, revealing another conserved feature of the genus. This is the first report of the codon usage patterns in the genus Rhizobium.
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Mycorrhizal responsiveness of maize (Zea mays L.) genotypes as related to releasing date and available P content in soil.
Mycorrhiza
PUBLISHED: 02-20-2013
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The aim of this study was to compare the mycorrhizal responsiveness among old and recent Chinese maize genotypes (released from 1950s to 2008) in low- and high-Olsen-P soils and to identify parameters that would indicate the relationships between the mycorrhizal responsiveness and the functional traits related to P uptake of maize. A greenhouse factorial experiment was conducted. The factors were maize genotype [Huangmaya (HMY), Zhongdan 2 (ZD2), Nongda 108 (ND108), and NE15], inoculation with or without arbuscular mycorrhizal fungi (AMF) (Rhizophagus irregularis), and Olsen-P levels (4, 9, 18, 36, or 60 mg P kg(-1)). Old and recently released genotypes differed in their response to AMF under low- and high-P supply. Three kinds of responses (in terms of shoot growth) were observed: the response was positive if the soil P content was low, but negative if the soil Olsen-P content was high (HMY and ND108); the response was neutral regardless of soil P content (ZD2); and the response was positive regardless of soil P content (NE15). Principle component (PC) analysis showed that the first PC comprised morphological and physiological traits of maize roots, and the second PC comprised mycorrhizal traits. The opposite was the case, however, in high-P soil. It is concluded that maize breeding selection from 1950s to 2000s is not always against the AM association and that AMF play positive roles in promoting the growth of some maize genotypes in high-P soil. The root length colonization by efficient AMF might be a useful parameter for breeding varieties with increased mycorrhizal responsiveness.
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Platypus TCR? provides insight into the origins and evolution of a uniquely mammalian TCR locus.
J. Immunol.
PUBLISHED: 10-05-2011
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TCR? is an unconventional TCR that was first discovered in marsupials and appears to be absent from placental mammals and nonmammals. In this study, we show that TCR? is also present in the duckbill platypus, an egg-laying monotreme, consistent with TCR? being ancient and present in the last common ancestor of all extant mammals. As in marsupials, platypus TCR? is expressed in a form containing double V domains. These V domains more closely resemble Ab V than that of conventional TCR. Platypus TCR? differs from its marsupial homolog by requiring two rounds of somatic DNA recombination to assemble both V exons and has a genomic organization resembling the likely ancestral form of the receptor genes. These results demonstrate that the ancestors of placental mammals would have had TCR? but it has been lost from this lineage.
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Functional regulation of an immobilized redox protein on an oriented metal coordinated peptide monolayer as an electron mediator.
Langmuir
PUBLISHED: 09-15-2011
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We fabricated a vertically and unidirectionally oriented metal coordinated ?-helical peptide monolayer, Leu(2)Ala(Pyri)(Co(II))Leu(6)Ala(4-Pyri)(Co(II))Leu(6), by stepwise polymerization on a mixed self-assembled monolayer consisting of amino-alkanethiol, dialkyl disulfide, and ferrocenyl alkanethiol acted as a photoresponsive electron donor. Redox-active protein, nitrate reductase (NR), was fixed on the surface of the peptide monolayer. By contrast, we fixed NR on the mixed self-assembled monolayer directly. Upon photoirradiation, electron flow occurred from the excited ferrocenyl group on the substrate to the electron acceptor, NR, on the surface of the molecular layers. The activated NR on the molecular layers reduced the nitrate to nitrite. The amount of the bioelectrocatalytic product, nitrite, generated by the immobilized NR on the peptide monolayer was larger than that produced by the immobilized NR on the mixed self-assembled monolayer directly. That is to say, the NR on the peptide monolayer has been more activated rather than that on the peptide absent monolayer by photoirradiation. The effective activation of the NR on the peptide monolayer can be explained in terms of enhancement of the vectorial electron flow along the macro-dipole moment of the ?-helical peptide that arranged unidirectionally. It suggested that the ordered metal coordinated ?-helical peptide monolayer acted as an efficient electron mediator to achieve a communication between the electron donor and the redox-active moiety. Such a hybrid molecular system looks promising for novel nanodevices, such as nano-photoreactors.
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Inhibitory effect of endostatin combined with paclitaxel-cisplatin on breast cancer in xenograft-bearing mice.
Exp Ther Med
PUBLISHED: 08-31-2011
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In the present study, we aimed to investigate the tumor-inhibiting effects of recombinant human endostatin (rhES) combined with paclitaxel-cisplatin (TP regimen) on human breast cancer in xenograft-bearing nude mice. A total of 24 mice bearing human breast cancer xenografts were administered both rhES and TP, TP alone, rhES alone or saline. The tumor growth inhibition was observed. Serum vascular endothelial growth factor (VEGF) levels and microvessel density (MVD) were determined by ELISA and immunohistochemistry, respectively. Cell apoptosis was detected using terminal deoxynucleotidyl transferase dUTP nick end-labeling (TUNEL) staining. Survival time was observed in another 24 nude mice with the same treatment. MVD expression in the group administered rhES and TP was lower than that in the other groups (P<0.05); serum VEGF levels in the combined drug group were lower compared to the other groups; the apoptotic index increased in the combined drug group. We conclude that the effect of the TP regimen combined with rhES on breast cancer is better than that of the TP regimen alone.
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Analysis of bacterial community in bulking sludge using culture-dependent and -independent approaches.
J Environ Sci (China)
PUBLISHED: 01-01-2011
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The bacterial community of a bulking sludge from a municipal wastewater treatment plant with anoxic-anaerobic-oxic process was investigated by combination of cultivation and 16S rRNA gene clone library analysis for understanding the causes of bulking. A total of 28 species were obtained from 63 isolates collected from six culture media. The most cultivable species belonged to gamma-Proteobacteria including Klebsiella sp., Pseudomonas sp., Aeromonas sp. and Acinetobacter sp. Further analysis of these strains by repetitive sequence based on polymerase chain reaction (rep-PCR) technology showed that rep-PCR yielded discriminatory banding patterns within the same genus using REP and BOX primer sets. While the culture-independent assessment revealed that beta-Proteobacteria was the dominant group in the bulking sample. Sequence analysis revealed that the highest proportion (14.7%) of operational taxonomic units was 98% similar to Candidatus Accumulibacter phosphatis, which is used to remove phosphorous from wastewater. Our results indicated that combining different approaches can produce complementary information, thus generate a more accurate view of microbial community in bulking sludge.
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Archaeal community structure along a gradient of petroleum contamination in saline-alkali soil.
J Environ Sci (China)
PUBLISHED: 01-01-2011
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The response of archaeal communities to petroleum contamination in saline-alkali soil was characterized by analyses of three soil samples with different total petroleum hydrocarbon concentrations. Through the construction and screening of 16S rRNA gene clone libraries based on DNA extracts from these soils, nine distinct phylogenetic groups were identified. Statistical analyses showed that the distribution of archaeal community structures differ significantly along the gradient of petroleum contamination in these three saline-alkali soils. Five phylogenetic groups were dominant in the control soil, two of which were also abundant in the lightly contaminated soil. Four phylogenetic groups were dominant in heavily contaminated soil, one of which was also abundant in the lightly contaminated soil. The halophilic genus of Haloferax and the haloalkaliphilic genus of Natronomonas were more abundant in heavily contaminated soil. These results suggested that the genera of Haloferax and Natronomonas may have a role in the natural attenuation of petroleum-contaminated saline-alkali soil.
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[Determination of 16 polycyclic aromatic hydrocarbons in airborne particle samples using two-step thermal desorption and gas chromatography-mass spectrometry].
Se Pu
PUBLISHED: 12-22-2010
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A method for the determination of 16 polycyclic aromatic hydrocarbons (PAHs) in airborne particle samples was developed using two-step thermal desorption and gas chromatography-mass spectrometry (GC-MS). The thermal desorption conditions and GC-MS parameters were optimized. The results showed that the detection limits (LODs) of this method varied from 0.14 to 0.42 ng/m3. The average recoveries were ranged from 52.7% to 97.9%, and the relative standard deviations (RSD) were ranged from 8.0% to 18.4%. The method was applied to analyze 32 collected airborne particle samples. In comparison with the traditional method, this method can avoid the waste of organic solvents and also shorten the analysis time. It is a green method, and beneficial for the environment and the analysts.
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Adrenal and extra-adrenal nonfunctioning composite pheochromocytoma/paraganglioma with immunohistochemical ectopic hormone expression: comparison of two cases.
Urol. Int.
PUBLISHED: 01-18-2010
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Adrenal composite pheochromocytoma is rare, most of which is functional, and extra-adrenal composite paraganglioma is extremely rare. We describe and compare the clinicopathological and immunohistochemical features of a retroperitoneal extra-adrenal composite paraganglioma and an adrenal composite pheochromocytoma. Both tumors were nonfunctioning and laboratory tests revealed no biochemical abnormalities. Both tumors were composed of typical paraganglioma/pheochromocytoma closely admixed with ganglioneuroma component. In addition to typical immunohistochemical phenotypes characteristic of each component, both tumors showed focal staining of somatostatin, and the adrenal tumor was also regionally positive for insulin and prolactin. Despite this aberrant immunohistochemical expression, relevant clinical symptoms or laboratory abnormalities were absent. These tumors serve to exemplify the extremely rare occurrences of clinically silent, nonfunctioning composite pheochromocytoma or paraganglioma with aberrant expression of hormones.
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[Tolerant mechanisms of bacteria to organic solvents].
Sheng Wu Gong Cheng Xue Bao
PUBLISHED: 08-13-2009
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Organic solvents are usually toxic to microorganisms for destroying the physiological functions. Recently, some studies have revealed that some bacteria are capable of living in conditions with high concentration of solvents through tolerant and adaptive mechanisms. This discovery inspires the research on adaptation and alteration of industrial bacteria, especially for those producing solvents or degrading toxic organic compounds. For a deep understanding and a wide application of the tolerant mechanisms, we address here the recent discoveries on solvents toxicity to bacteria by the parameter logP, and tolerant mechanisms of solvent-tolerant-bacteria to solvents, such as changes in cell membrane including cis-trans isomerisation, the saturated-to-unsaturated fatty acids ratio and the phospholipids head-groups, changes in outer membrane and cell morphology, and other stress responses. Moreover, our experiences in screening novel solvent-tolerant-bacteria and methods in increasing solvent tolerance of industrial microbes are introduced to give a promising strategy for improving solvent production.
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The clinical outcomes of late preterm infants: a multi-center survey of Zhejiang, China.
J Perinat Med
PUBLISHED: 07-14-2009
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To explore birth rate, delivery mode, medical problems, requirement of respiratory support, and acute outcomes of late preterm infants in Zhejiang province in eastern China.
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On the genomics of immunoglobulins in the gray, short-tailed opossum Monodelphis domestica.
Immunogenetics
PUBLISHED: 04-27-2009
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Annotated maps of the IGH, IGK, and IGL loci in the gray, short-tailed opossum Monodelphis domestica were generated from analyses of the available whole genome sequence for this species. Analyses of their content and organization confirmed a number of previous conclusions based on characterization of complementary DNAs encoding opossum immunoglobulin heavy and light chains and limited genomic analysis, including (a) the predominance of a single immunoglobulin heavy chain variable region (IGHV) subgroup and clan, (b) the presence of a single immunoglobulin (Ig)G subclass, (c) the apparent absence of an IgD, and (d) the general organization and V gene complexity of the IGK and IGL light chain loci. In addition, several unexpected discoveries were made including the presence of a partial V to D, germline-joined IGHV segment, the first germline-joined Ig V gene to be found in a mammal. In addition was the presence of a larger number of IGKV subgroups than had been previously identified. With this report, annotated maps of the major histocompatibility complex, T-cell receptor, and immunoglobulin loci have been completed for M. domestica, the only non-eutherian mammalian species for which this has been accomplished, strengthening the utility of this species as a model organism.
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Electric-field-enhanced oriented cobalt coordinated peptide monolayer and its electrochemical properties.
J Colloid Interface Sci
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The monolayer composed of cobalt coordinated peptides having lipoic acid at the amino terminals was fabricated on gold substrate by a self-assembly method under the electric field. For comparison, the self-assembled peptide monolayer was also prepared without applying a voltage. A leucine-rich hexadecapeptide, Leu(2)HisLeu(6)HisLeu(6), was chosen as the cobalt coordinated peptide. Histidines, His, were introduced as metal ligands for cobalt to the sequential peptide. The complexation between the cobalt and imidazole groups of His residues formed a stable ?-helical peptide bundle, which oriented perpendicularly to the substrate surface. In the case of the self-assembled peptide monolayer (SAM), which was fabricated under the electric field, the peptide macro-dipole moments aligned unidirectionally along to the direction of the electric field, and the cobalt complexes were fixed in the monolayer to form the ordered arrangement. On the other hand, the SAM prepared without applying the voltage formed the mixture of parallel and antiparallel packing owing to the dipole-dipole interaction. As the result, the efficient non-linear electron flow through the SAM, which was fabricated under the electric field, was achieved by the regular alignment of the peptide macro-dipole moment and the cobalt complexes. This result implied that the self-assembly under the electric field is an efficient method to obtain stable oriented ?-helical peptide monolayers. This method may be useful for the fabrication of the nano-devices capable of transferring information.
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Early postnatal B cell ontogeny and antibody repertoire maturation in the opossum, Monodelphis domestica.
PLoS ONE
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Marsupials are a lineage of mammals noted for giving birth to highly altricial young, which complete much of their "fetal" development externally attached to a teat. Postnatal B cell ontogeny and diversity was investigated in a model marsupial species, the gray short-tailed opossum, Monodelphis domestica. The results support the initiation of B cell development late in gestation and progressing into the first two weeks of postnatal life. Transcription of CD79a and CD79b was detected in embryonic tissue prior to birth, while immunoglobulin heavy chain locus transcription was not detected until the first postnatal 24 hours. Transcription of the Ig light chains was not detected until postnatal day 7 at the earliest. The predicted timing of the earliest appearance of mature B cells and completion of gene rearrangements is consistent with previous analyses on the timing of endogenous antibody responses in newborn marsupials. The diversity of early B cell IgH chains is limited, as has been seen in fetal humans and mice, but lacks bias in the gene segments used to encode the variable domains. Newborn light chain diversity is, from the start, comparable to that of the adult, consistent with an earlier hypothesis that light chains contribute extensively to antibody diversity in this species.
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Terrimonas pekingensis sp. nov., isolated from bulking sludge, and emended descriptions of the genus Terrimonas, Terrimonas ferruginea, Terrimonas lutea and Terrimonas aquatica.
Int. J. Syst. Evol. Microbiol.
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A Gram-negative, strictly aerobic, non-motile and non-spore-forming rod that produced white, viscous colonies, designated QH(T), was isolated from bulking sludge collected from a municipal wastewater treatment plant in Beijing, China. Phylogenetic analysis based on 16S rRNA gene sequences showed that strain QH(T) belonged to the genus Terrimonas and shared 96.3?% sequence similarity with Terrimonas lutea DY(T), 94.1?% with Terrimonas ferruginea ATCC 13524(T) and 93.8?% with Terrimonas aquatica RIB1-6(T). Strain QH(T) contained iso-C15?:?0, summed feature 3 (comprising one or more of C16?:?1?7c, C16?:?1?6c and iso-C15?:?0 2-OH) and iso-C15?:?1 G as the predominant fatty acids. The predominant polar lipid of strain QH(T) and members of the genus Terrimonas was phosphatidylethanolamine. The major isoprenoid quinone of strain QH(T) was MK-7 and the DNA G+C content was 41.0 mol%. DNA-DNA relatedness between strain QH(T) and T. lutea BCRC 17944(T), T. ferruginea BCRC 17943(T) and T. aquatica BCRC 17941(T) was 32, 23 and 22?%, respectively. On the basis of phylogenetic inference, differential phenotypic data and low DNA-DNA relatedness with members of the genus Terrimonas, strain QH(T) represents a novel species, for which the name Terrimonas pekingensis sp. nov. is proposed. The type strain is QH(T) (?=?CICC 10452(T) ?=?NCCB 100397(T)). The descriptions of the genus Terrimonas and T. ferruginea, T. lutea and T. aquatica are also emended.
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Recombination, transcription, and diversity of a partially germline-joined VH in a mammal.
Immunogenetics
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Full or partially germline-joined V genes have been described in a number of different vertebrate lineages where they can contribute to the expressed antibody repertoire through different mechanisms. Here we demonstrate that VH3.1, a partially germline-joined VH gene in the opossum Monodelphis domestica, can undergo V(D)J recombination to generate productive IgH transcripts. VH3.1 is fused to a DH gene segment in the germline DNA and is the only known example of a germline-joined VH in a mammal. B cells that have recombined VH3.1 were not detected until nearly 2 months of age, around the time of weaning, and much later than B cells using the conventional VH. Compared to opossum IgH transcripts using the conventional VH genes, those with VH3.1 have unusually long CDR3 due to the length of the germline-joined DH.
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A VpreB3 homologue in a marsupial, the gray short-tailed opossum, Monodelphis domestica.
Immunogenetics
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A VpreB surrogate light (SL) chain was identified for the first time in a marsupial, the opossum Monodelphis domestica. Comparing the opossum VpreB to homologues from eutherian (placental mammals) and avian species supported the marsupial gene being VpreB3. VpreB3 is a protein that is not known to traffic to the cell surface as part of the pre-B cell receptor. Rather, VpreB3 associates with nascent immunoglobulin chains in the endoplasmic reticulum. Homologues of other known SL chains VpreB1, VpreB2, and ?5, which are found in eutherian mammals, were not found in the opossum genome, nor have they been identified in the genomes of nonmammals. VpreB3 likely evolved from earlier gene duplication, independent of that which generated VpreB1 and VpreB2 in eutherians. The apparent absence of VpreB1, VpreB2, and ?5 in marsupials suggests that an extracellular pre-B cell receptor containing SL chains, as it has been defined in humans and mice, may be unique to eutherian mammals. In contrast, the conservation of VpreB3 in marsupials and its presence in nonmammals is consistent with previous hypotheses that it is playing a more primordial role in B cell development.
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