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Find video protocols related to scientific articles indexed in Pubmed.
Unveiling new biological relationships using shared hits of chemical screening assay pairs.
Bioinformatics
PUBLISHED: 08-28-2014
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Although the integration and analysis of the activity of small molecules across multiple chemical screens is a common approach to determine the specificity and toxicity of hits, the suitability of these approaches to reveal novel biological information is less explored. Here, we test the hypothesis that assays sharing selective hits are biologically related.
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Lycopene attenuates insulin signaling deficits, oxidative stress, neuroinflammation, and cognitive impairment in fructose-drinking insulin resistant rats.
Neuropharmacology
PUBLISHED: 08-08-2014
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Fructose intake is linked with the increasing prevalence of insulin resistance, and insulin resistance links Alzheimer's disease with impaired insulin signaling, oxidative damage, neuroinflammation, and cognitive impairment. As a member of the carotenoid family of phytochemicals, lycopene is used as a potent free scavenger, and has been demonstrated to be effective in anti-oxidative stress and anti-inflammatory reaction in the models of AD and other neurodegenerative diseases. Here, we investigated the effect of lycopene on learning and memory impairment and the possible underlying molecular events in fructose-drinking insulin resistant rats. We found that long-term fructose-drinking causes insulin resistance, impaired insulin signaling, oxidative stress, neuroinflammation, down-regulated activity of cholinergic system, and cognitive impairment, which could be significantly ameliorated by oral lycopene administration. The results from this study provide experimental evidence for using lycopene in the treatment of brain damage caused by fructose-drinking insulin resistance.
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The p65 subunit of NF-?B involves in RIP140-mediated inflammatory and metabolic dysregulation in cardiomyocytes.
Arch. Biochem. Biophys.
PUBLISHED: 04-13-2014
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The transcription factor NF-?B regulates expression of many genes that are involved in inflammation, fatty acid and glucose metabolism, and plays a crucial role in cardiac pathological processes. RIP140 is a corepressor that down-regulates expression of genes involved in the cellular substrate uptake and mitochondrial ?-oxidation. In addition to this, RIP140 also acts as a coactivator for p65-NF-?B, potentiating the secretion of proinflammatory cytokines in macrophages, but the effects in cardiomyocytes are still unknown. In this study, overexpression of RIP140 induced proinflammatory gene expression and cytokine release in neonatal rat cardiomyocytes, which could be reversed by p65-NF-?B inhibition. Furthermore, RIP140-mediated repression of metabolic-related genes, mitochondrial biogenesis and metabolic function were weakened after knocking down of p65-NF-?B. These findings suggest that p65-NF-?B plays an important role in RIP140-mediated proinflammatory response and energy metabolism in cardiomyocytes, and provide evidence for the crosstalk between proinflammatory processes and metabolic dysregulation in the heart.
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Arsenic pollution of agricultural soils by concentrated animal feeding operations (CAFOs).
Chemosphere
PUBLISHED: 03-09-2014
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Animal wastes from concentrated animal feeding operations (CAFOs) can cause soil arsenic pollution due to the widespread use of organoarsenic feed additives. This study investigated the arsenic pollution of surface soils in a typical CAFO zone, in comparison with that of agricultural soils in the Pearl River Delta, China. The mean soil arsenic contents in the CAFO zone were elevated compared to those in the local background and agricultural soils of the Pearl River Delta region. Chemical speciation analysis showed that the soils in the CAFO zone were clearly contaminated by the organoarsenic feed additive, p-arsanilic acid (ASA). Transformation of ASA to inorganic arsenic (arsenite and arsenate) in the surface soils was also observed. Although the potential ecological risk posed by the arsenic in the surface soils was relatively low in the CAFO zone, continuous discharge of organoarsenic feed additives could cause accumulation of arsenic and thus deserves significant attention.
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Splitting strategy for simulating genetic regulatory networks.
Comput Math Methods Med
PUBLISHED: 02-02-2014
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The splitting approach is developed for the numerical simulation of genetic regulatory networks with a stable steady-state structure. The numerical results of the simulation of a one-gene network, a two-gene network, and a p53-mdm2 network show that the new splitting methods constructed in this paper are remarkably more effective and more suitable for long-term computation with large steps than the traditional general-purpose Runge-Kutta methods. The new methods have no restriction on the choice of stepsize due to their infinitely large stability regions.
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Heavy metal pollution in surface soils of Pearl River Delta, China.
Environ Monit Assess
PUBLISHED: 01-21-2014
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Heavy metal pollution is an increasing environmental problem in Chinese regions undergoing rapid economic and industrial development, such as the Pearl River Delta (PRD), southern China. We determined heavy metal concentrations in surface soils from the PRD. The soils were polluted with heavy metals, as defined by the Chinese soil quality standard grade II criteria. The degree of pollution decreased in the order Cd?>?Cu?>?Ni?>?Zn?>?As?>?Cr?>?Hg?>?Pb. The degree of heavy metal pollution by land use decreased in the order waste treatment plants (WP)?>?urban land (UL)?>?manufacturing industries (MI)?>?agricultural land (AL)?>?woodland (WL)?>?water sources (WS). Pollution with some of the metals, including Cd, Cu, Ni, and Zn, was attributed to the recent rapid development of the electronics and electroplating industries. Cd, Hg, and Pb (especially Cd) pose high potential ecological risks in all of the zones studied. The soils posing significantly high and high potential ecological risks from Cd covered 73.3 % of UL, 50 % of MI and WP land, and 48.5 % of AL. The potential ecological risks from heavy metals by land use decreased in the order UL?>?MI?>?AL?>?WP?>?WL?>?WS. The control of Cd, Hg, and Pb should be prioritized in the PRD, and emissions in wastewater, residue, and gas discharges from the electronics and electroplating industry should be decreased urgently. The use of chemical fertilizers and pesticides should also be decreased.
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Inhibition of hypoxia-induced proliferation of pulmonary arterial smooth muscle cells by a mTOR siRNA-loaded cyclodextrin nanovector.
Biomaterials
PUBLISHED: 01-01-2014
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The proliferation of pulmonary arterial smooth muscle cells (PASMCs) is a key pathophysiological component of vascular remodeling in pulmonary arterial hypertension (PAH), an intractable disease, for which pharmacotherapy is limited and only slight improvement in survival outcomes have achieved over the past few decades. RNA interference provides a highly promising strategy to the treatment of this chronic lung disease, while efficient delivery of small interfering RNA (siRNA) remains a key challenge for the development of clinically acceptable siRNA therapeutics. With the aim to construct useful nanomedicines, the mammalian target of rapamycin (mTOR) siRNA was loaded into hybrid nanoparticles based on low molecular weight (Mw) polyethylenimine (PEI) and a pH-responsive cyclodextrin material (Ac-aCD) or poly(lactic-co-glycolic acid) (PLGA). This hybrid nanoplatform gave rise to desirable siRNA loading, and the payload release could be modulated by the hydrolysis characteristics of carrier materials. Fluorescence observation and flow cytometry quantification suggested that both Ac-aCD and PLGA nanovectors (NVs) may enter PASMCs under either normoxia or hypoxia conditions as well as in the presence of serum, with uptake and transfection efficiency significantly higher than those of cationic vectors such as PEI with Mw of 25 kDa (PEI25k) and Lipofectamine 2000 (Lipo 2k). Hybrid Ac-aCD or PLGA NV containing siRNA remarkably inhibited proliferation and activated apoptosis of hypoxic PASMCs, largely resulting from effective suppression of mTOR signaling as evidenced by significantly lowered expression of mTOR mRNA and phosphorylated protein. Moreover, these hybrid nanomedicines were more effective than commonly used cationic vectors like PEI25k and Lipo 2k, with respect to cell growth inhibition, apoptosis activation, and expression attenuation of mTOR mRNA and protein. Therefore, mTOR siRNA nanomedicines based on hybrid Ac-aCD or PLGA NV may be promising therapeutics for diseases related to hypoxic abnormal growth of PASMCs.
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HitPick: a web server for hit identification and target prediction of chemical screenings.
Bioinformatics
PUBLISHED: 05-28-2013
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High-throughput phenotypic assays reveal information about the molecules that modulate biological processes, such as a disease phenotype and a signaling pathway. In these assays, the identification of hits along with their molecular targets is critical to understand the chemical activities modulating the biological system. Here, we present HitPick, a web server for identification of hits in high-throughput chemical screenings and prediction of their molecular targets. HitPick applies the B-score method for hit identification and a newly developed approach combining 1-nearest-neighbor (1NN) similarity searching and Laplacian-modified naïve Bayesian target models to predict targets of identified hits. The performance of the HitPick web server is presented and discussed.
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Assessing heavy metal pollution in the surface soils of a region that had undergone three decades of intense industrialization and urbanization.
Environ Sci Pollut Res Int
PUBLISHED: 03-20-2013
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Heavy metals in the surface soils from lands of six different use types in one of the worlds most densely populated regions, which is also a major global manufacturing base, were analyzed to assess the impact of urbanization and industrialization on soil pollution. A total of 227 surface soil samples were collected and analyzed for major heavy metals (As, Cd, Co, Cr, Cu, Fe, Hg, Mn, Ni, Pb, and Zn) by using microwave-assisted acid digestion and inductively coupled plasma-mass spectrometry (ICP-MS). Multivariate analysis combined with enrichment factors showed that surface soils from the region (>7.2?×?10(4) km(2)) had mean Cd, Cu, Zn, and As concentrations that were over two times higher than the background values, with Cd, Cu, and Zn clearly contributed by anthropogenic sources. Soil pollution by Pb was more widespread than the other heavy metals, which was contributed mostly by anthropogenic sources. The results also indicate that Mn, Co, Fe, Cr, and Ni in the surface soils were primarily derived from lithogenic sources, while Hg and As contents in the surface soils were controlled by both natural and anthropogenic sources. The pollution level and potential ecological risk of the surface soils both decreased in the order of: urban areas?>?waste disposal/treatment sites???industrial areas?>?agricultural lands???forest lands?>?water source protection areas. These results indicate the significant need for the development of pollution prevention and reduction strategies to reduce heavy metal pollution for regions undergoing fast industrialization and urbanization.
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A pH-responsive cyclodextrin-based hybrid nanosystem as a nonviral vector for gene delivery.
Biomaterials
PUBLISHED: 01-26-2013
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The absence of safe, efficient, cost-effective, and easily scalable delivery platforms is one of the most significant hurdles and critical issues that limit the bench to bedside translation of oligonucleotides-based therapeutics. Acid-labile materials are of special interest in developing nonviral vectors due to their capability of intracellularly delivering therapeutic payload. In this study, a nanovector was designed by integrating a pH-responsive cyclodextrin material and low molecular weight polyethylenimine (PEI). Antisense oligonucleotide (ASON) Bcl-xl could be encapsulated into this hybrid nanosystem with extremely high loading efficiency by a nanoemulsion technique. The developed pH-responsive ASON nanotherapeutics could be efficiently transfected into human lung adenocarcinoma cells in a time- and dose-dependent manner, resulting in effective cell growth inhibition, significant suppression on the expression of Bcl-xl mRNA/protein, and efficient cell apoptosis. Importantly, the new nanovector showed drastically higher efficacy and lower cytotoxicity when compared with PLGA-based counterpart and commonly used cationic vectors like branched PEI (25,000 Da) and Lipofectamine 2000. This pH-responsive hybrid nanosystem may serve as a safe and efficient nonviral vector that may find wide applications in gene therapy.
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Rutile TiO2 nanowires on anatase TiO2 nanofibers: a branched heterostructured photocatalysts via interface-assisted fabrication approach.
J Colloid Interface Sci
PUBLISHED: 05-13-2011
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A water-dichloromethane interface-assisted hydrothermal method was employed to grow rutile TiO(2) nanowires (NWs) on electrospun anatase TiO(2) nanofibers (NFs), using highly reactive TiCl(4) as precursor. The water-dichloromethane interface inhibited the formation of rutile NWs in water phase, but promoted the selective radial growth of densely packed rutile NWs on anatase NFs to form a branched heterojunction. The density and length of rutile NWs could be readily controlled by varying reaction parameters. A formation mechanism for the branched heterojunction was proposed which involved (1) the entrapment of rutile precursor nanoparticles at water-dichloromethane interface, (2) the growth of rutile NWs on anatase NFs via Ostwald ripening through the scavengering of interface-entrapped rutile nanoparticles. The heterojunction formed at anatase NF and rutile NW enhanced the charge separation of both under ultraviolet excitation, as evidenced by photoluminescence and surface photovoltage spectra. The branched TiO(2) heterostructures showed higher photocatalytic activity in degradation of rodamine B dye solution than anatase NFs, and the mixture of anatase NFs, and P25 powders, which was discussed in terms of the synergistic effect of enhanced charge separation by anatase-rutile heterojunction, high activity of rutile NWs, and increased specific area of branched heterostructures.
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Effect of pioglitazone on altered expression of A? metabolism-associated molecules in the brain of fructose-drinking rats, a rodent model of insulin resistance.
Eur. J. Pharmacol.
PUBLISHED: 01-27-2011
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Accumulation of ?-amyloid (A?) peptide in the brain is a major hallmark of Alzheimers disease. An optimal brain insulin level promotes A? clearance, which may play protective roles against Alzheimers disease. In this study we examined the role of dietary conditions leading to insulin resistance on amyloidosis in fructose-drinking rats. Further investigations tested pioglitazone, an insulin sensitizer, intervention on the altered amyloidosis in this rodent model of insulin resistance. Six-week-old male Wistar rats were fed a standard commercial diet and water without (control) or with 10% fructose for 16 weeks. The animals were randomly divided into 4 groups (n=10): non-treated and water-drinking rats (control group); pioglitazone treated and water-drinking (control treatment group); non-treated and fructose-drinking rats (fructose group) and pioglitazone-treated and fructose-drinking rats (fructose treatment group). Pioglitazone was given at the dose of 10mg/kgd by gavage for the last 12 weeks of the 16-week period. We found that diet-induced insulin resistance induced A? overproduction with altered expression of A? metabolism-associated molecules, which corresponded with increased ?-secretase-1 (BACE1), ?-secretase (PS-1) activities and decreased insulin degrading enzyme (IDE) activities, but not neprilysin in the cortex and hippocampus. Additionally, pioglitazone treatment prevented all these observed abnormalities. This study indicates that insulin resistance induced by fructose-drinking affects the expression of A? metabolism-associated molecules that are responsible for A? deposition and pioglitazone treatment negatively modulate amyloidogenesis.
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HIT: linking herbal active ingredients to targets.
Nucleic Acids Res.
PUBLISHED: 11-21-2010
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The information of protein targets and small molecule has been highly valued by biomedical and pharmaceutical research. Several protein target databases are available online for FDA-approved drugs as well as the promising precursors that have largely facilitated the mechanistic study and subsequent research for drug discovery. However, those related resources regarding to herbal active ingredients, although being unusually valued as a precious resource for new drug development, is rarely found. In this article, a comprehensive and fully curated database for Herb Ingredients Targets (HIT, http://lifecenter.sgst.cn/hit/) has been constructed to complement above resources. Those herbal ingredients with protein target information were carefully curated. The molecular target information involves those proteins being directly/indirectly activated/inhibited, protein binders and enzymes whose substrates or products are those compounds. Those up/down regulated genes are also included under the treatment of individual ingredients. In addition, the experimental condition, observed bioactivity and various references are provided as well for users reference. Derived from more than 3250 literatures, it currently contains 5208 entries about 1301 known protein targets (221 of them are described as direct targets) affected by 586 herbal compounds from more than 1300 reputable Chinese herbs, overlapping with 280 therapeutic targets from Therapeutic Targets Database (TTD), and 445 protein targets from DrugBank corresponding to 1488 drug agents. The database can be queried via keyword search or similarity search. Crosslinks have been made to TTD, DrugBank, KEGG, PDB, Uniprot, Pfam, NCBI, TCM-ID and other databases.
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Inhibitory effect of target binding on hairpin aptamer sticky-end pairing-induced gold nanoparticle assembly for light-up colorimetric protein assay.
Anal. Chem.
PUBLISHED: 04-17-2010
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Gold nanoparticles (GNPs) possessing strong distance-dependent optical properties and high extinction coefficients have emerged as important colorimetric materials. Almost all colorimetric studies are based on two working mechanisms: sandwich cross-linking and non-cross-linking systems. In the present study, a new working mechanism, hairpin sticky-end pairing-induced GNP assembly, is introduced based on the discovery of unique aggregation behavior of aptamer-functionalized GNPs. The salt-induced aggregation of oligonucleotide probe-modified GNPs can readily occur due to the sticky-end pairing effect while addition of target molecules favors the formation of the hairpin structure of probe sequences and substantially inhibits the nanoparticle assembly. Along this line, we developed a proof-of-concept colorimetric homogeneous assay using immunoglobulin E (IgE) as an analyte model via transforming a commonly designed "light-down" colorimetric biosensor into a "light-up" one. From the point of view of both conformational transition of aptamer and steric bulk, oligonucleotide-GNPs display an additional stability upon binding to target molecules. The assay showed an extremely high sensitivity from both naked eye observations and absorbance measurements. Compared with almost all existing IgE sensing strategies, the proposed colorimetric system possesses a substantially improved analytical performance. Investigating the assembly behavior of hairpin aptamer-modified GNPs could offer new insight into the dependence of the GNP properties on the structure switching and open a new way to design signaling probes and develop colorimetric assay schemes.
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An aptazyme-based electrochemical biosensor for the detection of adenosine.
Anal. Chim. Acta
PUBLISHED: 02-01-2010
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In this work, an aptazyme-based electrochemical biosensor for the detection of adenosine is reported. Aptazyme activity was modulated by appending an "inhibitor" oligonucleotide strand containing a 32-base adenosine aptamer to the 8-17 DNAzyme. In the absence of adenosine, the DNAzyme could not form appropriate catalytic structure due to the binding with the inhibitor strand. Upon adenosine binding to the aptamer, the inhibitor strand was dissociated from the DNAzyme sequence. This allowed the DNAzyme to open and bind with the hairpin substrate, and DNAzyme activity was thereby induced, cleaving the substrate at its ribonucleotide site in the presence of Pb(2+). Cleavage of the substrate yields two single-stranded products, one of which was ferrocene-tagged and acted as the signal probe. The thiolated probe modified on the gold electrode could capture the signal probe. As a result, the ferrocene (Fc) moiety was brought in close proximity to the electrode surface and the Faradaic current was observed. This electrochemical biosensor was proved to have a wide dynamic range from 5 nM to 2000 nM with a detection limit of 5 nM. The fabricated sensor is shown to exhibit high sensitivity and desirable selectivity, which might be promising for the rational construction of aptazyme-based biosensors and the determination of adenosine in clinical examination.
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An electrochemical molecular switch for one-step, reusable detection of a single-base mutation of DNA.
Analyst
PUBLISHED: 11-10-2009
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A new strategy for one-step, reusable and sensitive detection of a single-base mutation based on an electrochemical molecular switch is developed in the present work. When the hybridization reaction takes place in the presence of target DNA, the Fc-labeled terminal of the open switch molecule can be captured by the probe through the predesigned complementary bases of both sequences. By this method, a signal-on sensor featuring both generalizability and simplicity towards reagentless detection of DNA with sensitivity and selectivity electrochemical system is built on. The approach had been demonstrated with the identification of a single-base mutation of alpha-thalassemia point mutation in Hb Constant Spring codon 142 (TAA --> CAA). The wild-type and mutant-type of the synthetic 16 mer DNA sequences as the model targets were successfully discriminated. The results showed that the response signal was linear to the logarithm of the target concentration in the range from 0.01 to 100 pM with a detection limit of 0.01 pM. The regeneration experiment demonstrated that the sensor interface can be easily and successfully regenerated. All these revealed that the present system is a promising candidate for single-base mutation discrimination.
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Effect of pioglitazone on insulin resistance in fructose-drinking rats correlates with AGEs/RAGE inhibition and block of NADPH oxidase and NF kappa B activation.
Eur. J. Pharmacol.
PUBLISHED: 08-06-2009
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Insulin resistance, which may influence Alzheimers disease, is associated with an increase in circulating advanced glycosylation end products (AGEs) and the increased expression of the receptor for AGEs (RAGE). Inhibition of AGE/RAGE system has been shown to attenuate neuronal damage. Specific ligands for peroxisome proliferator-activated receptor gamma (PPARgamma), which have proven effective in the animal models of Alzheimers disease and other neuroinflammatory diseases, have been shown to decrease RAGE expression. Here we investigated the effect of PPARgamma agonist, pioglitazone, on cognition function and AGE/RAGE system in a rodent model of insulin resistance, the fructose-drinking rats. Six-week-old male Wistar rats were fed a standard commercial diet and water without (control) or with 10% fructose for 16weeks. The animals were randomly divided into 4 groups (n=10): non-treated and water-drinking rats (control group); pioglitazone-treated and water-drinking (control treatment group); non-treated and fructose-drinking rats (fructose group) and pioglitazone-treated and fructose-drinking rats (fructose treatment group). Pioglitazone was given at the dose of 10mg/kgd by gavage for the last 12weeks of the 16-week period. The results showed that pioglitazone treatment reduced the escape latency in Morris water maze test, decreased AGE/RAGE expression in the cerebral cortex of fructose-drinking rats. Furthermore, we found that the expression of p47phox component of NAPDH oxidase, phosphorylated nuclear factor NF-kappaB p65, tumor necrosis factor alpha and interleukin-1 beta was significantly increased in the cerebral cortex of fructose-drinking rats (P<0.001). These effects were reversed by pioglitazone treatment (P<0.01 or 0.001). Taken together, these findings suggest that the activation of AGEs-RAGE system contribute to the brain damage of insulin resistance. Pioglitazone administration can improve cognition function probably related to its effect of decreasing the activation of AGEs-RAGE system, which correlates with block of NAPDH oxidase and NF-kappaB activation in this rodent model of insulin resistance.
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Biocatalyzed deposition amplification for detection of aflatoxin B1 based on quartz crystal microbalance.
Anal. Chim. Acta
PUBLISHED: 02-24-2009
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An ultrasensitive piezoelectric method for the detection of the aflatoxin B1 (AFB1) based on the indirect competitive immunoassay and the biocatalyzed deposition amplification has been developed. In this method, the quartz crystal surface was coated with a self-assembled monolayer of 3-mercaptopropionic acid (MPA) for covalently immobilization of the BSA-AFB1 conjugate, which could compete with the free AFB1 for binding to the anti-AFB1 antibody (MsIgG). After the competitive immunoreaction, the horseradish peroxidase (HRP) labeled goat anti-mouse IgG (G-Anti-MsIgG) was introduced into the detection cell to combine with the anti-AFB1 antibody on the crystal surface. The enzyme labeled G-Anti-MsIgG as a biocatalyst could accelerate the oxidation of 4-chloro-1-naphthol by H2O2 to yield the insoluble product benzo-4-chlorohexadienone on the surface of quartz crystal microbalance (QCM), resulting in a mass increase that was reflected by a decrease in the resonance frequency of the QCM. The proposed approach could allow for the determination of AFB(1) in the concentration range of 0.01-10.0 ng mL(-1). Furthermore, several artificially contaminated milk samples were analyzed with good recoveries obtained, which demonstrated the suitability of the proposed method for detecting AFB1.
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Heavy metal pollution in sediments of a typical mariculture zone in South China.
Mar. Pollut. Bull.
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The heavy metal inventory and the ecological risk of the estuarine sediments in Hailing Bay, an important maricultural zone along the southern coast of China, were investigated. Results show that the surface sediments were mainly polluted by As (2.17-20.34 mg/kg), Ni (1.37-42.50mg/kg), Cu (1.21-58.84 mg/kg) and Zn (11.69-219.22 mg/kg). Furthermore, the aquafarming zone was significantly more polluted than the non-aquafarming zone, and cluster analysis suggested additional sources of heavy metal input in the aquafarming zone. As, Cr, Cu, Ni, Pb and Zn were mainly present in the non-bioavailable residual form in the surface sediments, whereas Cd was predominantly in the highly mobile acid soluble and reducible fractions. The ecological risk of the polluted sediments stemmed mainly from Cd, and from As, Cu and Pb to less degrees. The highest potential risks occurred near the aquaculture base, indicating the need to control heavy metal inputs from aquafarming activities.
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What is Visualize?

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

How does it work?

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

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

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