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Find video protocols related to scientific articles indexed in Pubmed.
Combination of 4-1BB Agonist and PD-1 Antagonist Promotes Anti-tumor Effector / Memory CD8 T cells in a Poorly Immunogenic Tumor Model.
Cancer Immunol Res
PUBLISHED: 11-13-2014
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Immunotherapies targeting Programmed death 1 (PD-1) co-inhibitory receptor have shown great promise for a subset of cancer patients. However, robust and safe combination therapies are still needed to bring the benefit of cancer immunotherapy to broader patient populations. In our effort to search for an optimal strategy of combinatorial immunotherapy, we have compared the anti-tumor activity of anti-4-1BB/anti-PD-1 combination with that of anti-PD-1/anti-LAG-3 combination in the poorly immunogenic B16F10 melanoma model. Pronounced tumor inhibition occurred only in animals receiving anti-PD-1 and anti-4-1BB concomitantly, while combining anti-PD-1 with anti-LAG-3 led to a modest degree of tumor suppression. The activity of anti-4-1BB/anti-PD-1 combination was dependent on IFN-? and CD8+ T cells. Both 4-1BB and PD-1 proteins were elevated on the surface of CD8+ T cells by anti-4-1BB/anti-PD-1 co-treatment. In the tumor microenvironment, an effective anti-tumor immune response was induced as indicated by increased CD8+/Treg ratio and the enrichment of genes such as CD3?, CD8?, IFN-? and Eomesodermin. In the spleen, the combination treatment shaped the immune system to an effector/memory phenotype and increased the overall activity of tumor-specific CD8+ CTLs, reflecting a long-lasting systemic anti-tumor response. Furthermore, combination treatment in C57BL/6 animals showed no additional safety signals, and only minimally increased severity of the known toxicity relative to 4-1BB agonist alone. Therefore, in the absence of any cancer vaccine, anti-4-1BB/anti-PD-1 combination therapy is sufficient to elicit a robust anti-tumor effector/memory T cell response in an aggressive tumor model and is therefore a candidate for combination trials in patients.
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Performances of a diode end-pumped GYSGG/Er,Pr:GYSGG composite laser crystal operated at 2.79 ?m.
Opt Express
PUBLISHED: 10-17-2014
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We demonstrate a comparative investigation on Er,Pr:GYSGG and GYSGG/Er,Pr:GYSGG composite crystals at 2.79 ?m. Simulating results show the highest temperatures are 369 K and 318 K, respectively. A maximum output power of 825 mW with slope efficiency of 19.2% and maximum laser energy of 3.65 mJ with slope efficiency of 22.7% are obtained in the GYSGG/Er,Pr:GYSGG composite crystal, which have an obvious improvement than those of Er,Pr:GYSGG crystal. The thermal focal lengths are respectively 41 and 62 mm when the pump power is 2.5 W. All these results indicate that the GYSGG/Er,Pr:GYSGG composite crystal has great advantages in reducing the influence of thermal effects and improving laser performances.
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Transcriptome-wide Landscape of Pre-mRNA Alternative Splicing Associated with Metastatic Colonization.
Mol. Cancer Res.
PUBLISHED: 10-03-2014
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Metastatic colonization is an ominous feature of cancer progression. Recent studies have established the importance of pre-mRNA alternative splicing (AS) in cancer biology. However, little is known about the transcriptome-wide landscape of AS associated with metastatic colonization. Both in vitro and in vivo models of metastatic colonization were utilized to study AS regulation associated with cancer metastasis. Transcriptome profiling of prostate cancer cells and derivatives crossing in vitro or in vivo barriers of metastasis revealed splicing factors with significant gene expression changes associated with metastatic colonization. These include splicing factors known to be differentially regulated in epithelial-mesenchymal transition (ESRP1, ESRP2, RBFOX2), a cellular process critical for cancer metastasis, as well as novel findings (NOVA1, MBNL3). Finally, RNA-seq indicated a large network of AS events regulated by multiple splicing factors with altered gene expression or protein activity. These AS events are enriched for pathways important for cell motility and signaling, and affect key regulators of the invasive phenotype such as CD44 and GRHL1. Implications: Transcriptome-wide remodeling of AS is an integral regulatory process underlying metastatic colonization and AS events impact the metastatic behavior of cancer cells.
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[Current quality management situation and administration countermeasure study of enterprises marketing corneal contact lens].
Zhongguo Yi Liao Qi Xie Za Zhi
PUBLISHED: 09-23-2014
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Study the current quality management situation of enterprises marketing corneal contact lens via systemic investigations and explore effective administration countermeasures in the future.
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Production and characterization of a monoclonal antibody against GRAM domain-containing protein 1A.
Monoclon Antib Immunodiagn Immunother
PUBLISHED: 08-30-2014
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From the proteomic analysis, we identified hundreds of novel proteins that have never been characterized for their expression profile and function on human embryonic stem (hES) cells. In this study, we produced a group of monoclonal antibodies against the GRAM domain-containing protein 1A, which was found on hES cells. Using these antibodies, we analyzed the expression of GRAMD1A in various tissues and tumor cell lines. The results showed that GRAMD1A is expressed in the nucleus and cytoplasm of hES cells, cancer cell lines and ectoderm, mesoderm, and endoderm tissues. The development of the monoclonal antibody to GRAMD1A and the characterization of the expression pattern of this protein could have significant implications in the functional characterization of this novel protein.
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Mitochondrial KATP Channels Control Glioma Radioresistance by Regulating ROS-Induced ERK Activation.
Mol. Neurobiol.
PUBLISHED: 07-08-2014
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Malignant glioma is the most prevalent form of malignant brain tumor. Although radiotherapy is widely used in glioma treatment, the radioresistance of glioma cells limits the success of the glioma treatment. The lack of effective targets and signaling pathways to reverse glioma radioresistance is the critical obstacle in successful treatment. In this study, we demonstrate that mitochondrial ATP-sensitive potassium channels (mtKATP channels) are overexpressed in glioma cells and are closely related to the malignancy grade and the overall survival of the patients. Importantly, we showed that mtKATP channels could control glioma radioresistance by regulating reactive oxygen species (ROS)-induced ERK activation. The inhibition of mtKATP channels suppresses glioma radioresistance by inhibiting ERK activation both in vitro and in vivo. These findings reveal the important roles of the mitochondria and mtKATP channels as key regulators in the radioresistance of glioma cells, and suggest that mtKATP channel blockers and MAPK/ERK kinase (MEK) inhibitors are potential targets for drug development of glioma treatments.
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Multi-image position detection.
Opt Express
PUBLISHED: 07-01-2014
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The exact measurement of positions is of fundamental importance in a multitude of image-sensor based optical measurement systems. We propose a new method for enhancing the accuracy of image-sensor based optical measurement systems by using a computer-generated hologram in front of the imaging system. Thereby, the measurement spot is replicated to a predefined pattern. Given enough light to correctly expose the sensor, the position detection accuracy can be considerably improved compared to the conventional one-spot approach. For the evaluation of the spot position we used center-of-gravity based averaging. We present simulated as well as experimental results showing an improvement by a factor of 3.6 to a positioning accuracy of better than three thousandths of a pixel for a standard industrial CCD sensor.
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A complex mechanism for HDGF-mediated cell growth, migration, invasion, and TMZ chemosensitivity in glioma.
J. Neurooncol.
PUBLISHED: 06-17-2014
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HDGF is overexpressed in gliomas as compared to normal brain. We therefore analyzed the molecular mechanisms of HDGF action in gliomas. HDGF was downregulated in normal brain tissue as compared to glioma specimens at both the mRNA and the protein levels. In glioma samples, increased HDGF expression was associated with disease progression. Knocking down HDGF expression not only significantly decreased cellular proliferation, migration, invasion, and tumorigenesis, but also markedly enhanced TMZ-induced cytotoxicity and apoptosis in glioma cells. Mechanistic analyses revealed that CCND1, c-myc, and TGF-? were downregulated after stable HDGF knockdown in the U251 and U87 glioma cells. HDGF knockdown restored E-cadherin expression and suppressed mesenchymal cell markers such as vimentin, ?-catenin, and N-cadherin. The expression of cleaved caspase-3 increased, while Bcl-2 decreased in each cell line following treatment with shHDGF and TMZ, as compared to TMZ alone. Furthermore, RNAi-based knockdown study revealed that HDGF is probably involved in the activation of both the PI3K/Akt and the TGF-? signaling pathways. Together, our data suggested that HDGF regulates glioma cell growth, apoptosis and epithelial-mesenchymal transition (EMT) probably through the Akt and the TGF-? signaling pathways. These results provide evidence that targeting HDGF or its downstream targets may lead to novel therapies for gliomas.
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Alzheimer's disease and methanol toxicity (part 2): lessons from four rhesus macaques (Macaca mulatta) chronically fed methanol.
J. Alzheimers Dis.
PUBLISHED: 05-03-2014
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A recently established link between formaldehyde, a methanol metabolite, and Alzheimer's disease (AD) pathology has provided a new impetus to investigate the chronic effects of methanol exposure. This paper expands this investigation to the non-human primate, rhesus macaque, through the chronic feeding of young male monkeys with 3% methanol ad libitum. Variable Spatial Delay Response Tasks of the monkeys found that the methanol feeding led to persistent memory decline in the monkeys that lasted 6 months beyond the feeding regimen. This change coincided with increases in tau protein phosphorylation at residues T181 and S396 in cerebrospinal fluid during feeding as well as with increases in tau phosphorylated aggregates and amyloid plaques in four brain regions postmortem: the frontal lobe, parietal lobe, temporal lobe, and the hippocampus. Tau phosphorylation in cerebrospinal fluid was found to be dependent on methanol feeding status, but phosphorylation changes in the brain were found to be persistent 6 months after the methanol feeding stopped. This suggested the methanol feeding caused long-lasting and persistent pathological changes that were related to AD development in the monkey. Most notably, the presence of amyloid plaque formations in the monkeys highlighted a marked difference in animal systems used in AD investigations, suggesting that the innate defenses in mice against methanol toxicity may have limited previous investigations into AD pathology. Nonetheless, these findings support a growing body of evidence that links methanol and its metabolite formaldehyde to AD pathology.
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Adjustment of Suboptimally Placed Lumbar Pedicle Screws Decreases Pullout Strength and Alters Biomechanics of the Construct: A Pilot Cadaveric Study.
World Neurosurg
PUBLISHED: 04-23-2014
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Lumbar pedicle screws are placed for internal fixation and help to enhance bony fusion. Optimal screws are medially directed, should be parallel or pointing to the superior endplate, and penetrate 50%-80% of the vertebral body. "Nonparallel" pedicle screws can be inadvertently placed within the confines of the pedicle and vertebral body but are sometimes replaced to obtain a more acceptable postoperative image. A nonparallel (suboptimal) screw is one that is located within the pedicle and body and does not violate bone; however, it is not parallel to the superior endplate. These "cored-out" grooves left in the bone from the initial tap and screw placement may compromise the integrity of the bone and the construct.
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Potential risk of mitomycin C at high concentrations on peripheral nerve structure.
Neural Regen Res
PUBLISHED: 03-21-2014
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Although the local application of mitomycin C may prevent epidural adhesion after laminectomy, mitomycin C can induce neurotoxicity in optic and acoustic nerves at high concentrations. To determine the safe concentration range for mitomycin C, cotton pads soaked with mitomycin C at different concentrations (0.1, 0.3, 0.5, and 0.7 mg/mL) were immediately applied for 5 minutes to the operation area of rats that had undergone laminectomy at L1. Rat sciatic nerves, instead of dorsal nerves, were used in this study. The results showed that mitomycin C at 0.1-0.5 mg/mL did not damage the structure and function of the sciatic nerve, while at 0.7 mg/mL, mitomycin C significantly reduced the thickness of the sciatic nerve myelin sheath compared with lower concentrations, though no functional change was found. These experimental findings indicate that the local application of mitomycin C at low concentrations is safe to prevent scar adhesion following laminectomy, but that mitomycin C at high concentrations (> 0.7 mg/mL) has potential safety risks to peripheral nerve structures.
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Characterization and function analysis of an anti-lipopolysaccharide factor (ALF) from the Chinese shrimp Fenneropenaeus chinensis.
Dev. Comp. Immunol.
PUBLISHED: 03-19-2014
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Anti-lipopolysaccharide factor (ALF) is one of the widely-studied antimicrobial peptides (AMPs) with broad-spectrum antibacterial activity and antiviral property. Previous studies show the existence of multiform of ALFs in crustacean which are important for immunity of the animals. In the present study, we characterized one isoform of ALF from the Chinese shrimp Fenneropenaeus chinensis (FcALF2). Tissue distribution analysis revealed that FcALF2 showed the highest expression level in the lymphoid organ (Oka) of the shrimp. The expression level of FcALF2 in shrimp was significantly up-regulated when they were injected with Micrococcus lysodeikticus and Vibrio anguillarum. A peptide corresponding to the LPS-binding domain of FcALF2 (FcALF2-LBD) was synthesized to analyze its antimicrobial activities. Data demonstrated that FcALF2-LBD possessed strong antibacterial activity against Gram-positive bacteria Micrococcus luteus and M.lysodeikticus with MIC ranges of 2-4 ?M and 1-2 ?M respectively and significant inhibition activity against white spot syndrome virus (WSSV). The antibacterial activities of the sequence modified peptides (FcALF2-LBDb, FcALF2-LBDv) were apparently enhanced and broadened after the amount of basic amino acids was increased in the synthetic LPS-binding domain. These data provide more insights into understanding the function of LPS-binding domain of ALF and the role of ALF in shrimp immunity.
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Function of shrimp STAT during WSSV infection.
Fish Shellfish Immunol.
PUBLISHED: 03-11-2014
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JAK/STAT signaling pathway plays key roles in the antiviral immunity of mammals, fish and insect. However, limited knowledge is known about the function of JAK/STAT signaling pathway in the antiviral immunity of shrimp although virus disease has caused severe mortality in shrimp aquaculture. In order to understand the function of JAK/STAT signaling pathway in the antiviral immunity of shrimp, dsRNA interfering technique was used to silence the expression of STAT gene in Litopenaeus vannamei, and the mortality of shrimp was detected after WSSV infection. Furthermore, the expressions of some potential target genes regulated by STAT or genes related to RNA interfering pathway were detected in STAT silenced shrimp during WSSV infection. The WSSV copy number in STAT silenced shrimp was 10(2)-10(3) copies/ng DNA which was much lower than that in the control. The mortality in STAT silenced shrimp caused by WSSV infection decreased very significantly compared to their controls. The function of STAT was verified in vitro cultured cells of hematopoietic tissue of crayfish Cherax quadricarinatus by adding specific inhibitor of STAT3(S3I-201), and the cultured cells treated with S3I-201 showed much less WSSV copy number than their controls, which further suggested that STAT might be helpful for the replication of WSSV. Expression analysis on the potential STAT target genes and genes in RNA interfering pathway provide important information for understanding the functional mechanism of STAT in antiviral immunity of shrimp.
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Effects of low-intensity pulsed ultrasound on integrin-FAK-PI3K/Akt mechanochemical transduction in rabbit osteoarthritis chondrocytes.
Ultrasound Med Biol
PUBLISHED: 02-22-2014
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The effect of low-intensity pulsed ultrasound (LIPUS) on extracellular matrix (ECM) production via modulation of the integrin/focal adhesion kinase (FAK)/phosphatidylinositol 3-kinase (PI3K)/Akt pathway has been investigated in previous studies in normal chondrocytes, but not in osteoarthritis (OA). Therefore, we investigated the LIPUS-induced integrin ?1/FAK/PI3K/Akt mechanochemical transduction pathway in a single study in rabbit OA chondrocytes. Normal and OA chondrocytes were exposed to LIPUS, and mRNA and protein expression of cartilage, metalloproteinases and integrin-FAK-PI3K/Akt signal pathway-related genes was determined by quantitative reverse transcription polymerase chain reaction and Western blotting, respectively. Compared with levels in normal chondrocytes, expression levels of ECM-related genes were significantly lower in OA chondrocytes and those of metalloproteinase-related genes were significantly higher. In addition, integrin ?1 gene expression and the phosphorylation of FAK, PI3K and Akt were significantly higher in OA chondrocytes. The expression of all tested genes was significantly increased except for that of metalloproteinase, which was significantly decreased in the LIPUS-treated OA group compared to the untreated OA group. LIPUS may affect the integrin-FAK-PI3K/Akt mechanochemical transduction pathway and alter ECM production by OA chondrocytes. Our findings will aid the future development of a treatment or even cure for OA.
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A pilot investigation of a Pediatric Surgery Journal Club.
J. Pediatr. Surg.
PUBLISHED: 02-11-2014
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The CanMEDS competency "scholar" encompasses the creation, dissemination, application, and translation of medical knowledge. We hypothesize that a structured journal club (JC) for pediatric surgical trainees would meet these objectives in an enjoyable and long-lasting manner.
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Bioinformatic prediction of WSSV-host protein-protein interaction.
Biomed Res Int
PUBLISHED: 02-05-2014
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WSSV is one of the most dangerous pathogens in shrimp aquaculture. However, the molecular mechanism of how WSSV interacts with shrimp is still not very clear. In the present study, bioinformatic approaches were used to predict interactions between proteins from WSSV and shrimp. The genome data of WSSV (NC_003225.1) and the constructed transcriptome data of F. chinensis were used to screen potentially interacting proteins by searching in protein interaction databases, including STRING, Reactome, and DIP. Forty-four pairs of proteins were suggested to have interactions between WSSV and the shrimp. Gene ontology analysis revealed that 6 pairs of these interacting proteins were classified into "extracellular region" or "receptor complex" GO-terms. KEGG pathway analysis showed that they were involved in the "ECM-receptor interaction pathway." In the 6 pairs of interacting proteins, an envelope protein called "collagen-like protein" (WSSV-CLP) encoded by an early virus gene "wsv001" in WSSV interacted with 6 deduced proteins from the shrimp, including three integrin alpha (ITGA), two integrin beta (ITGB), and one syndecan (SDC). Sequence analysis on WSSV-CLP, ITGA, ITGB, and SDC revealed that they possessed the sequence features for protein-protein interactions. This study might provide new insights into the interaction mechanisms between WSSV and shrimp.
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Modification of a synthetic LPS-binding domain of anti-lipopolysaccharide factor from shrimp reveals strong structure-activity relationship in their antimicrobial characteristics.
Dev. Comp. Immunol.
PUBLISHED: 01-29-2014
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Anti-lipopolysaccharide factor (ALF) is a small protein with broad-spectrum antimicrobial activities and certain antiviral property. Its putative lipopolysaccharide (LPS) binding domain was deduced to be important for its activities. However, there is still no report revealing how the structure of the LPS-binding domain affects its biological function until now. In the present study, we designed and synthesized a peptide corresponding to the LPS-binding domain of ALF from the Chinese shrimp (designated as FcALF-LBDc) and its structure-modified isoforms in order to analyze the relationship between its structure and antimicrobial activities. Results showed that FcALF-LBDc exhibited apparent antibacterial activities against both Gram-negative bacteria Escherichia coli and Vibrio anguillarum and Gram-positive bacteria Micrococcus luteus and Micrococcus lysodeikticus with MIC ranges of 32-64, 2-4, 1-2, and 32-64?M, respectively. The disulfide loop and the basic amino acids in the LPS-binding domain (LBD) of ALF played key roles in its antibacterial activities. In addition, FcALF-LBDc could reduce the propagation of white spot syndrome virus (WSSV) in vivo, and its lysine residue is indispensable for its antiviral property. This is the first attempt to testify the effects of the sequence features of the LPS-binding domain on its antimicrobial activities.
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Cell surface proteomics analysis indicates a neural lineage bias of rat bone marrow mesenchymal stromal cells.
Biomed Res Int
PUBLISHED: 01-16-2014
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Mesenchymal stromal cells (MSCs) are one of the most intensively studied stem cell types with application aims. However, the molecular characterisation and the relationship between the molecular characterisation and functional properties of MSCs are largely unknown. In this study, we purified the surface proteins from rat bone marrow MSCs (rBMMSCs) and characterised their surface proteome by LC-MS/MS. Moreover, we comparatively analysed the data from this study with the surface proteomics data of mouse and human embryonic stem (ES) cells and human mesenchymal stromal cells (hMSCs). The data showed that, in contrast to ES cells and human mesenchymal stromal cells, rBMMSCs possessed a surface proteomics pattern biased to neural and neural-endocrine lineages, indicating a neural/neural crest bias, and suggested a neural differentiation tendency of these cells. The different surface proteomics pattern between rBMMSCs and hMSCs also suggested that MSCs of different origin might possess a different lineage bias.
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Phantom alternatives influence food preferences in the eastern honeybee Apis cerana.
J Anim Ecol
PUBLISHED: 01-06-2014
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Most models of animal choice behaviour assume that desirable but unavailable options, such as a high quality, but inhabited nest sites, do not influence an individual's preferences for the remaining options. However, experiments suggest that in mammals, the mere presence of such 'phantom' alternatives can alter, and even reverse, an individual's preferences for other items in a choice set. Phantom alternatives may be widespread in nature, as they occur whenever a resource is visible, but unavailable at the time of choice. They are particularly relevant for nectar-foraging animals, where previously rewarding flowers may sometimes be empty. Here, we investigate the effect of phantom alternatives on feeder preferences in the eastern honeybee, Apis cerana. First, we tested the effects of unattractive and attractive phantom alternatives by presenting individual bees with either a binary choice set containing two feeders that differed strongly in two qualities, but were equally preferred overall ('option 1' and 'option 2'), or a ternary choice set containing option 1, option 2 and one of two phantom types (unattractive and attractive). Secondly, we determined whether phantoms increase (similarity effect) or decrease (dissimilarity effect) preference for phantom-similar choices. In binary trials, bees had no significant preference for option 1 or option 2. However, after encountering an attractive phantom alternative, individual bees preferred option 2. The unattractive phantom did not influence bee preferences. Phantoms consistently changed individual bee preferences in favour of the phantom-similar choice. This means that the presence of an attractive food source, even if it is unavailable, can influence preference relationships between remaining items in the choice set. Our findings highlight the importance of considering the potential for phantom effects when studying the foraging behaviour of animals. Our results are particularly relevant for nectarivores, where empty but previously rewarding flowers are a common occurrence. Since an increase in pollinator visits can result in higher seed set, our results open up the possibility that by shifting pollinator preferences, empty flowers could have otherwise-unpredicted influences on community composition, plant-pollinator interactions and pollinator behaviour.
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Measurement of the efficacy of 2% lipid in reversing bupivacaine- induced asystole in isolated rat hearts.
BMC Anesthesiol
PUBLISHED: 01-01-2014
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The reversal efficacy of 2% lipid emulsion in cardiac asystole induced by different concentrations of bupivacaine is poorly defined and needs to be determined.
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Imidacloprid alters foraging and decreases bee avoidance of predators.
PLoS ONE
PUBLISHED: 01-01-2014
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Concern is growing over the effects of neonicotinoid pesticides, which can impair honey bee cognition. We provide the first demonstration that sublethal concentrations of imidacloprid can harm honey bee decision-making about danger by significantly increasing the probability of a bee visiting a dangerous food source. Apis cerana is a native bee that is an important pollinator of agricultural crops and native plants in Asia. When foraging on nectar containing 40 µg/L (34 ppb) imidacloprid, honey bees (Apis cerana) showed no aversion to a feeder with a hornet predator, and 1.8 fold more bees chose the dangerous feeder as compared to control bees. Control bees exhibited significant predator avoidance. We also give the first evidence that foraging by A. cerana workers can be inhibited by sublethal concentrations of the pesticide, imidacloprid, which is widely used in Asia. Compared to bees collecting uncontaminated nectar, 23% fewer foragers returned to collect the nectar with 40 µg/L imidacloprid. Bees that did return respectively collected 46% and 63% less nectar containing 20 µg/L and 40 µg/L imidacloprid. These results suggest that the effects of neonicotinoids on honey bee decision-making and other advanced cognitive functions should be explored. Moreover, research should extend beyond the classic model, the European honey bee (A. mellifera), to other important bee species.
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Transcriptome analysis of the initial stage of acute WSSV infection caused by temperature change.
PLoS ONE
PUBLISHED: 01-01-2014
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White spot syndrome virus (WSSV) is the most devastating virosis threatening the shrimp culture industry worldwide. Variations of environmental factors in shrimp culture ponds usually lead to the outbreak of white spot syndrome (WSS). In order to know the molecular mechanisms of WSS outbreak induced by temperature variation and the biological changes of the host at the initial stage of WSSV acute infection, RNA-Seq technology was used to analyze the differentially expressed genes (DEGs) in shrimp with a certain amount of WSSV cultured at 18°C and shrimp whose culture temperature were raised to 25°C. To analyze whether the expression changes of the DEGs were due to temperature rising or WSSV proliferation, the expression of selected DEGs was analyzed by real-time PCR with another shrimp group, namely Group T, as control. Group T didn't suffer WSSV infection but was subjected to temperature rising in parallel. At the initial stage of WSSV acute infection, DEGs related to energy production were up-regulated, whereas most DEGs related to cell cycle and positive regulation of cell death and were down-regulated. Triose phosphate isomerase, enolase and alcohol dehydrogenase involved in glycosis were up-regulated, while pyruvate dehydrogenase, citrate synthase and isocitrate dehydrogenase with NAD as the coenzyme involved in TCA pathway were down-regulated. Also genes involved in host DNA replication, including DNA primase, DNA topoisomerase and DNA polymerase showed down-regulated expression. Several interesting genes including crustin genes, acting binding or inhibiting protein genes, a disintegrin and metalloproteinase domain-containing protein 9 (ADAM9) gene and a GRP 78 gene were also analyzed. Understanding the interactions between hosts and WSSV at the initial stage of acute infection will not only help to get a deep insight into the pathogenesis of WSSV but also provide clues for therapies.
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Different Hydration Patterns in the Pores of AmtB and RhCG Could Determine Their Transport Mechanisms.
Biochemistry
PUBLISHED: 09-24-2013
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The ammonium transporters of the Amt/Rh family facilitate the diffusion of ammonium across cellular membranes. Functional data suggest that Amt proteins, notably found in plants, transport the ammonium ion (NH4(+)), whereas human Rhesus (Rh) proteins transport ammonia (NH3). Comparison between the X-ray structures of the prokaryotic AmtB, assumed to be representative of Amt proteins, and the human RhCG reveals important differences at the level of their pore. Despite these important functional and structural differences between Amt and Rh proteins, studies of the AmtB transporter have led to the suggestion that proteins of both subfamilies work according to the same mechanism and transport ammonia. We performed molecular dynamics simulations of the AmtB and RhCG proteins under different water and ammonia occupancy states of their pore. Free energy calculations suggest that the probability of finding NH3 molecules in the pore of AmtB is negligible in comparison to finding water. The presence of water in the pore of AmtB could support the transport of proton. The pore lumen of RhCG is found to be more hydrophobic due to the presence of a phenylalanine conserved among Rh proteins. Simulations of RhCG also reveal that the signature histidine dyad is occasionally exposed to the extracellular bulk, which is never observed in AmtB. These different hydration patterns are consistent with the idea that Amt and Rh proteins are not functionally equivalent and that permeation takes place according to two distinct mechanisms.
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Angle-stable RGBW top-emitting organic light-emitting devices with Ag/Ge/Ag cathode.
Opt Lett
PUBLISHED: 08-14-2013
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Ag/Ge/Ag (AGA) is investigated as a transparent cathode for top-emitting organic light-emitting devices (TEOLEDs). TEOLEDs of different colors with excellent performances can be gained by simply adopting a corresponding emitting layer, without changing the thickness of the device and cathode. Especially, the blue and white TEOLEDs exhibit high efficiency as well as the bottom OLEDs and show an excellently angle-stable characteristic. The white TEOLED exhibits a maximum current efficiency of 12.4 cd/A, and the CIE coordinates at 6 V only shift by (0.048, 0.046) from 0° to 60°. It can be attributed to the less angle-dependent cavity emission of the TEOLED with AGA cathode.
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Identifying differential alternative splicing events from RNA sequencing data using RNASeq-MATS.
Methods Mol. Biol.
PUBLISHED: 07-23-2013
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RNA sequencing (RNA-Seq) has emerged as a powerful and increasingly cost-effective technology for analysis of transcriptomes. RNA-Seq has several significant advantages over gene expression microarrays, including its high sensitivity and accuracy, broad dynamic range, nucleotide-level resolution, ability to detect novel mRNA transcripts, and ability to analyze pre-mRNA alternative splicing. A major application of RNA-Seq is to detect differential alternative splicing, i.e., differences in exon splicing patterns among different biological conditions. We recently developed a statistical method multivariate analysis of transcript splicing (MATS) for detecting differential alternative splicing events from RNA-Seq data. Here, we describe a computational pipeline RNASeq-MATS based on the MATS algorithm. This pipeline automatically detects and analyzes differential alternative splicing events corresponding to all major types of alternative splicing patterns from RNA-Seq data.
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Similarity of markers identified from cancer gene expression studies: observations from GEO.
Brief. Bioinformatics
PUBLISHED: 06-19-2013
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Gene expression profiling has been extensively conducted in cancer research. The analysis of multiple independent cancer gene expression datasets may provide additional information and complement single-dataset analysis. In this study, we conduct multi-dataset analysis and are interested in evaluating the similarity of cancer-associated genes identified from different datasets. The first objective of this study is to briefly review some statistical methods that can be used for such evaluation. Both marginal analysis and joint analysis methods are reviewed. The second objective is to apply those methods to 26 Gene Expression Omnibus (GEO) datasets on five types of cancers. Our analysis suggests that for the same cancer, the marker identification results may vary significantly across datasets, and different datasets share few common genes. In addition, datasets on different cancers share few common genes. The shared genetic basis of datasets on the same or different cancers, which has been suggested in the literature, is not observed in the analysis of GEO data.
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Spine and spinal cord trauma: diagnosis and management.
Neurol Clin
PUBLISHED: 06-01-2013
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Spine trauma is a devastating clinical condition that affects many people annually on a worldwide basis. Management of spinal trauma has become much more surgically oriented with advances in stabilization techniques over the past two decades. The degree of injury to the spinal cord dictates the prognosis of the patient in cervical and thoracolumbar trauma. Traumatic spinal cord injury is a major area of socioeconomic burden and, as such, is a burgeoning area of ongoing research interest.
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Role of inflammation and its mediators in acute ischemic stroke.
J Cardiovasc Transl Res
PUBLISHED: 05-21-2013
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Inflammation plays an important role in the pathogenesis of ischemic stroke and other forms of ischemic brain injury. Increasing evidence suggests that inflammatory response is a double-edged sword, as it not only exacerbates secondary brain injury in the acute stage of stroke but also beneficially contributes to brain recovery after stroke. In this article, we provide an overview on the role of inflammation and its mediators in acute ischemic stroke. We discuss various pro-inflammatory and anti-inflammatory responses in different phases after ischemic stroke and the possible reasons for their failures in clinical trials. Undoubtedly, there is still much to be done in order to translate promising pre-clinical findings into clinical practice. A better understanding of the dynamic balance between pro- and anti-inflammatory responses and identifying the discrepancies between pre-clinical studies and clinical trials may serve as a basis for designing effective therapies.
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AAPL: Assessing Association between P-value Lists.
Stat Anal Data Min
PUBLISHED: 04-30-2013
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Joint analyses of high-throughput datasets generate the need to assess the association between two long lists of p-values. In such p-value lists, the vast majority of the features are insignificant. Ideally contributions of features that are null in both tests should be minimized. However, by random chance their p-values are uniformly distributed between zero and one, and weak correlations of the p-values may exist due to inherent biases in the high-throughput technology used to generate the multiple datasets. Rank-based agreement test may capture such unwanted effects. Testing contingency tables generated using hard cutoffs may be sensitive to arbitrary threshold choice. We develop a novel method based on feature-level concordance using local false discovery rate. The association score enjoys straight-forward interpretation. The method shows higher statistical power to detect association between p-value lists in simulation. We demonstrate its utility using real data analysis. The R implementation of the method is available at http://userwww.service.emory.edu/~tyu8/AAPL/.
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Synthesis and biological evaluation of novel benzyl-substituted (S)-phenylalanine derivatives as potent dipeptidyl peptidase 4 inhibitors.
Bioorg. Med. Chem.
PUBLISHED: 04-23-2013
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A series of novel benzyl-substituted (S)-phenylalanine derivatives were synthesized and evaluated for their dipeptidyl peptidase 4 (DPP-4) inhibitory activity and selectivity. It was found that most synthesized target compounds were potent DPP-4 inhibitors with IC50 values in 3.79-25.52 nM, which were significantly superior to that of the marketed drug sitagliptin. Furthermore, the 4-fluorobenzyl substituted phenylalanine derivative 6g not only displayed the potent DPP-4 inhibition with an IC50 value of 3.79 nM, but also showed better selectivity against DPP-4 over other related enzymes including DPP-7, DPP-8, and DPP-9. In an oral glucose tolerance test (OGTT) in normal Sprague Dawley rats, compound 6g reduced blood glucose excursion in a dose-dependent manner.
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Screening of genes regulated by Relish in Chinese shrimp Fenneropenaeus chinensis.
Dev. Comp. Immunol.
PUBLISHED: 04-17-2013
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Relish is a key NF-?B transcription factor in the innate immunity. Learning the function of Relish in regulating the related genes of shrimp will be helpful to understand the shrimp immunity. In the present study, RNA interference (RNAi) and suppression subtractive hybridization (SSH) techniques were combined together to identify the genes regulated by Relish. A forward SSH library represents the genes whose transcription was regulated by Relish, and the reverse SSH library represents the genes whose transcription was up-regulated after Relish was silenced in shrimp responsive to Vibrio anguillarium (VA) stimulation. In the forward library, 43 unique genes were identified, and in the reverse library, 57 genes were identified. The expression of ten differentially expressed genes, including early cuticle protein5 (ECP5), Toll-like receptor protein (TLRP), antiviral factor (AV), C-type lectin receptor (CLR), thrombospondin (TSP), S-adenosylmethionine synthetase (SAMS), carcinolectin 5b-5 (CL5b-5), QM protein (QMP), heat shock protein 67B2 (HSP67B2), and Thioredoxin-related protein 14 (TRP14) were further confirmed by real-time PCR. The present data provides us a wide view to understand the function of Relish gene in the innate immunity of shrimp.
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In vitro and in vivo mechanical properties of human ulnar and median nerves.
J Biomed Mater Res A
PUBLISHED: 04-09-2013
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Peripheral nerves are often subjected to mechanical stretching, which in excess results in various degrees of impairment of their function. An understanding of the biomechanical behavior of peripheral nerves is important to the prevention of nerve injury during surgical manipulation. Here, in vitro mechanical properties and viscoelastic behavior of human ulnar/median nerves were measured with a tensile tester. In vivo stress and deformation of an ulnar nerve was also examined in continuity during a surgical procedure. Finite element models were developed to determine in vitro and in vivo viscoelastic parameters of the nerves. The results show that in vitro mechanical properties of fresh ulnar nerve are different from those measured in vivo. Several factors that are possibly attributed to the difference were analyzed. The in situ strain of the nerves is one of the major factors that must be considered to obtain accurate strain-stress relationship in the in vivo measurement.
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Expression and function analysis of Rac1 homolog in Chinese shrimp Fenneropenaeus chinensis.
Fish Shellfish Immunol.
PUBLISHED: 04-07-2013
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Rac1 is a ubiquitous GTP-binding protein that plays a crucial role in multiple cellular processes. In the present study, a Rac1 homolog (FcRac1) was cloned from the Chinese shrimp Fenneropenaeus chinensis. The open reading frame (ORF) of FcRac1 consists of 579 bp encoding 192 aa. The predicted molecular weight (MW) of the deduced amino acid sequence of FcRac1 was 21.46 kDa, and its theoretical pI was 8.62. Homology analysis showed that the amino acid sequence of Rac1 had high conservation among those from different species. Phylogenetic analysis showed that FcRac1 closely related to Rac1 proteins from other arthropods. FcRac1 showed the highest expression level in the hemocytes. In situ hybridization detection showed that it distributed in all types of hemocytes. Recombinant protein of FcRac1 showed apparent activity of GTPase. The transcription of FcRac1 in juvenile shrimp changed after bacteria or WSSV challenge. The present data suggests that FcRac1 might play important roles in the innate immunity of shrimp.
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Design, synthesis and biological evaluation of novel 3,4,5-trisubstituted aminothiophenes as inhibitors of p53-MDM2 interaction. Part 1.
Bioorg. Med. Chem.
PUBLISHED: 02-25-2013
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A series of 3,4,5-trisubstituted aminothiophenes were designed, synthesized, and evaluated for their p53-MDM2 binding inhibitory potency and anti-proliferation activities against A549 and PC3 tumor cell lines. Fourteen compounds had appreciably improved MDM2 binding affinities than lead compound MCL0527 (3) and a few compounds showed comparable activities to that of Nutlin-3. Meanwhile, most of the 3,4,5-trisubstituted aminothiophenes displayed better or equivalent anti-proliferation activities against wild-type p53 cell line A549 compared to that of Nutlin-3. Over ten compounds exhibited desirable selective profiles of p53 status. Particularly, compounds 9, 16 and 18 displayed 22-, 6- and 22-fold selectivity of p53 status, respectively, much better than that of Nutlin-3 (fourfold).
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Design, synthesis and evaluation of 3-(2-aminoheterocycle)-4-benzyloxyphenylbenzamide derivatives as BACE-1 inhibitors.
Molecules
PUBLISHED: 02-17-2013
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Three series of 3-(2-aminoheterocycle)-4-benzyloxyphenylbenzamide derivatives, 2-aminooxazoles, 2-aminothiazoles, and 2-amino-6H-1,3,4-thiadizines were designed, synthesized and evaluated as ?-secretase (BACE-1) inhibitors. Preliminary structure-activity relationships revealed that the existence of a 2-amino-6H-1,3,4-thiadizine moiety and ?-naphthyl group were favorable for BACE-1 inhibition. Among the synthesized compounds, 5e exhibited the most potent BACE-1 inhibitory activity, with an IC50 value of 9.9 ?? and it exhibited high brain uptake potential in Madin-Darby anine kidney cell lines (MDCK) and a Madin-Darby canine kidney-multidrug resistance 1 (MDCK-MDR1) model.
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The Ets transcription factor GABP is a component of the hippo pathway essential for growth and antioxidant defense.
Cell Rep
PUBLISHED: 02-15-2013
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The transcriptional coactivator Yes-associated protein (YAP) plays an important role in organ-size control and tumorigenesis. However, how Yap gene expression is regulated remains unknown. This study shows that the Ets family member GABP binds to the Yap promoter and activates YAP transcription. The depletion of GABP downregulates YAP, resulting in a G1/S cell-cycle block and increased cell death, both of which are substantially rescued by reconstituting YAP. GABP can be inactivated by oxidative mechanisms, and acetaminophen-induced glutathione depletion inhibits GABP transcriptional activity and depletes YAP. In contrast, activating YAP by deleting Mst1/Mst2 strongly protects against acetaminophen-induced liver injury. Similar to its effects on YAP, Hippo signaling inhibits GABP transcriptional activity through several mechanisms. In human liver cancers, enhanced YAP expression is correlated with increased nuclear expression of GABP. Therefore, we conclude that GABP is an activator of Yap gene expression and a potential therapeutic target for cancers driven by YAP.
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A CMOS-compatible approach to fabricate an ultra-thin germanium-on-insulator with large tensile strain for Si-based light emission.
Opt Express
PUBLISHED: 02-08-2013
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We present a method to introduce a large biaxial tensile strain in an ultra-thin germanium-on-insulator (GOI) using selective oxidation of SiGe epilayer on silicon-on-insulator (SOI) substrate. A circular patterned Si0.81Ge0.19 mesa on SOI substrate with the sidewall protected by Si3N4 or SiO2 is selectively oxidized to generate local 12 nm GOI with high crystal quality, which shows enhanced photoluminescence due to large tensile strain. Direct band photoluminescence peak significantly shifts to longer wavelength as compared to that from bulk Ge due to a combination of strain-induced band gap reduction and quantum confinement effect.
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Transcriptome analysis on Chinese shrimp Fenneropenaeus chinensis during WSSV acute infection.
PLoS ONE
PUBLISHED: 02-05-2013
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Previous studies have discovered a lot of immune-related genes responding to white spot syndrome virus (WSSV) infection in crustacean. However, little information is available in relation to underlying mechanisms of host responses during the WSSV acute infection stage in naturally infected shrimp. In this study, we employed next-generation sequencing and bioinformatic techniques to observe the transcriptome differences of the shrimp between latent infection stage and acute infection stage. A total of 64,188,426 Illumina reads, including 31,685,758 reads from the latent infection group and 32,502,668 reads from the acute infection group, were generated and assembled into 46,676 unigenes (mean length: 676 bp; range: 200-15,094 bp). Approximately 24,000 peptides were predicted and classified based on homology searches, gene ontology, clusters of orthologous groups of proteins, and biological pathway mapping. Among which, 805 differentially expressed genes were identified and categorized into 11 groups based on their possible function. Genes in the Toll and IMD pathways, the Ras-activated endocytosis process, the RNA interference pathway, anti-lipopolysaccharide factors and many other genes, were found to be activated in shrimp from latent infection stage to acute infection stage. The anti-bacterially proPO-activating cascade was firstly uncovered to be probably participated in antiviral process. These genes contain not only members playing function in host defense against WSSV, but also genes utilized by WSSV for its rapid proliferation. In addition, the transcriptome data provides detail information for identifying novel genes in absence of the genome database of shrimp.
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The association of tea consumption with bladder cancer risk: a meta-analysis.
Asia Pac J Clin Nutr
PUBLISHED: 01-29-2013
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The association between tea consumption and bladder cancer has been confirmed in several animal studies, but one epidemiological study in 2001 showed no association between them. In order to provide an accurate assessment of this, we conducted a meta-analysis on tea consumption and bladder cancer risk. Studies were identified by a literature search in PubMed from January 1980 to March 2012 and the reference lists of relevant studies. Random effect models were used to calculate summary relative risk estimates (RR) and their corresponding 95% confidence intervals (CI) based on high contrast to low intake values. Twenty-four publications (6 cohort studies and 18 case-control studies) based on consumption of overall tea, black tea, and green tea to bladder cancer risk were included in this analysis. For overall tea, the summary RR indicated no association between tea consumption and bladder cancer (RR= 1.09, 95%CI: 0.85-1.40). In subgroup analyses, we found a moderate increase of bladder cancer risk in smoking group (RR= 1.77, 95%CI: 1.04-3.01). In the black tea group, no statistically significant association was observed (RR= 0.84, 95%CI: 0.70-1.01). Interestingly, in the subgroup of sex, a protective effect was observed between tea consumption and bladder cancer risk in female (RR= 0.61, 95%CI: 0.38- 0.98). For green tea group, there was no relationship associated with bladder cancer risk (RR= 1.03, 95%CI: 0.82- 1.31). In conclusion, our data suggest that high overall tea intake in smokers increased the risk of bladder cancer, and high black tea intake in female may reduce the risk of bladder cancer.
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The RNA binding protein RBM38 (RNPC1) regulates splicing during late erythroid differentiation.
PLoS ONE
PUBLISHED: 01-01-2013
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Alternative pre-mRNA splicing is a prevalent mechanism in mammals that promotes proteomic diversity, including expression of cell-type specific protein isoforms. We characterized a role for RBM38 (RNPC1) in regulation of alternative splicing during late erythroid differentiation. We used an Affymetrix human exon junction (HJAY) splicing microarray to identify a panel of RBM38-regulated alternatively spliced transcripts. Using microarray databases, we noted high RBM38 expression levels in CD71(+) erythroid cells and thus chose to examine RBM38 expression during erythroid differentiation of human hematopoietic stem cells, detecting enhanced RBM38 expression during late erythroid differentiation. In differentiated erythroid cells, we validated a subset of RBM38-regulated splicing events and determined that RBM38 regulates activation of Protein 4.1R (EPB41) exon 16 during late erythroid differentiation. Using Epb41 minigenes, Rbm38 was found to be a robust activator of exon 16 splicing. To further address the mechanism of RBM38-regulated alternative splicing, a novel mammalian protein expression system, followed by SELEX-Seq, was used to identify a GU-rich RBM38 binding motif. Lastly, using a tethering assay, we determined that RBM38 can directly activate splicing when recruited to a downstream intron. Together, our data support the role of RBM38 in regulating alternative splicing during erythroid differentiation.
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Static mechanical stress induces apoptosis in rat endplate chondrocytes through MAPK and mitochondria-dependent caspase activation signaling pathways.
PLoS ONE
PUBLISHED: 01-01-2013
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Mechanical stress has detrimental effects on cartilaginous endplate chondrocytes due to apoptosis in vivo and in vitro. In this study, we investigated the possible apoptosis signaling pathways induced by mechanical stress in cultured rat cervical endplate chondrocytes. Static mechanical load significantly reduced cell viability in a time- and load-dependent manner, as demonstrated by the Cell Counting Kit-8 (CCK-8) assay. Chondrocyte apoptosis induced by mechanical stress was confirmed by annexin V/propidium iodide (PI) staining and terminal deoxynucleotidyl transferase dUTP nick-end labeling (TUNEL). Western blot analysis revealed that static load-induced chondrocyte apoptosis was accompanied by increased phosphorylation of c-Jun N-terminal kinase (JNK), extracellular signal-regulated kinase 1/2 (ERK1/2), and p38 mitogen-activated protein kinase (MAPK). The loss of mitochondrial membrane potential (??m), increased Cytochrome c release, and activated Caspase-9 and Caspase-3, indicating that the mitochondrial pathway is involved in mechanical stress-induced chondrocyte apoptosis. Treatment with inhibitors of JNK (SP600125), p38 MAPK (SB203580), and ERK (PD98059) prior to mechanical stimulation reversed both the static load-induced chondrocyte apoptosis and the activation of JNK, p38 MAPK, and ERK. Taken together, the data presented in this study demonstrate that mechanical stress induces apoptosis in rat cervical endplate chondrocytes through the MAPK-mediated mitochondrial apoptotic pathway.
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One-step transepithelial topography-guided ablation in the treatment of myopic astigmatism.
PLoS ONE
PUBLISHED: 01-01-2013
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To evaluate one-step topography-guided transepithelial ablation in the treatment of low to moderate myopic astigmatism using a 1KHz excimer laser.
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A new potassium tetrabromoaurate (III)-luminol chemiluminescence system for the determination of folic acid in milk powder.
J. Food Sci.
PUBLISHED: 11-10-2011
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A new chemiluminescence (CL) system based on the CL-emitting reaction between potassium tetrabromoaurate (III) [Au(III)] and luminol in alkaline medium is described in this paper. On the basis of this study, folic acid (FA) could dramatically enhance CL intensities, and incorporated with flow injection (FI) and solid-phase extraction (SPE), the novel CL system has been applied for the determination of FA in infant formula milk powder. Under optimum conditions, the CL intensities were linearly related to the concentration of FA in the range of 8.0 × 10?? to 4.0 × 10?? g/L with a correlation coefficient of 0.999, and the detection limit was 2.0 × 10?? g/L. The relative standard deviation was 3.5% for 1.0 × 10?? g/L FA. The optimal conditions for the detection of FA were evaluated, and the interferences from some common inorganic ions and a couple of relevant organic compounds were also investigated.
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Global and grain-specific accumulation of glycoside hydrolase family 10 xylanases in transgenic maize (Zea mays).
Plant Biotechnol. J.
PUBLISHED: 06-20-2011
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In planta expression of cell wall degrading enzymes is a promising approach for developing optimized biomass feedstocks that enable low-cost cellulosic biofuels production. Transgenic plants could serve as either an enzyme source for the hydrolysis of pretreated biomass or as the primary biomass feedstock in an autohydrolysis process. In this study, two xylanase genes, Bacillus sp. NG-27 bsx and Clostridium stercorarium xynB, were expressed in maize (Zea mays) under the control of two different promoters. Severe phenotypic effects were associated with xylanase accumulation in maize, including stunted plants and sterile grains. Global expression of these xylanases from the rice ubiquitin 3 promoter (rubi3) resulted in enzyme accumulation of approximately 0.01 mg enzyme per gram dry weight, or approximately 0.1% of total soluble protein (TSP). Grain-specific expression of these enzymes from the rice glutelin 4 promoter (GluB-4) resulted in higher-level accumulation of active enzyme, with BSX and XynB accumulating up to 4.0% TSP and 16.4% TSP, respectively, in shriveled grains from selected T0 plants. These results demonstrate the potential utility of the GluB-4 promoter for biotechnological applications. The phenotypic effects of xylanase expression in maize presented here demonstrate the difficulties of hemicellulase expression in an important crop for cellulosic biofuels production. Potential alternate approaches to achieve xylanase accumulation in planta without the accompanying negative phenotypes are discussed.
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Amyloid-beta42 interacts mainly with insoluble prion protein in the Alzheimer brain.
J. Biol. Chem.
PUBLISHED: 03-10-2011
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The prion protein (PrP) is best known for its association with prion diseases. However, a controversial new role for PrP in Alzheimer disease (AD) has recently emerged. In vitro studies and mouse models of AD suggest that PrP may be involved in AD pathogenesis through a highly specific interaction with amyloid-? (A?42) oligomers. Immobilized recombinant human PrP (huPrP) also exhibited high affinity and specificity for A?42 oligomers. Here we report the novel finding that aggregated forms of huPrP and A?42 are co-purified from AD brain extracts. Moreover, an anti-PrP antibody and an agent that specifically binds to insoluble PrP (iPrP) co-precipitate insoluble A? from human AD brain. Finally, using peptide membrane arrays of 99 13-mer peptides that span the entire sequence of mature huPrP, two distinct types of A? binding sites on huPrP are identified in vitro. One specifically binds to A?42 and the other binds to both A?42 and A?40. Notably, A?42-specific binding sites are localized predominantly in the octapeptide repeat region, whereas sites that bind both A?40 and A?42 are mainly in the extreme N-terminal or C-terminal domains of PrP. Our study suggests that iPrP is the major PrP species that interacts with insoluble A?42 in vivo. Although this work indicated the interaction of A?42 with huPrP in the AD brain, the pathophysiological relevance of the iPrP/A?42 interaction remains to be established.
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How bullet trajectory affects outcomes of civilian gunshot injury to the spine.
J Clin Neurosci
PUBLISHED: 02-08-2011
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We analysed retrospectively the effect of missile trajectory on outcomes from civilian gunshot injury to the spine (GSIS) between 1994 and 2008. Most of the 98 patients were male (88.8%). A minority (8%) of patients had multiple column injuries and a bone or bullet fragment in the spinal canal (14%). Neurologic injury was seen in 33%; and external bracing was applied to 30% of patients. The odds of bracing among patients with multiple levels of damage were 3.4 times than for patients with a single vertebral level of damage. The odds of paralysis among black patients were 6.33 times the odds among non-black patients. The odds of paralysis among patients with a fragment in the spinal canal were 12.99 times those without. We conclude that the supero-inferior trajectory affects the number of vertebral levels involved and consequently the need for bracing. The lateral trajectory affects neurological outcomes.
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Widespread establishment and regulatory impact of Alu exons in human genes.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 01-31-2011
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The Alu element has been a major source of new exons during primate evolution. Thousands of human genes contain spliced exons derived from Alu elements. However, identifying Alu exons that have acquired genuine biological functions remains a major challenge. We investigated the creation and establishment of Alu exons in human genes, using transcriptome profiles of human tissues generated by high-throughput RNA sequencing (RNA-Seq) combined with extensive RT-PCR analysis. More than 25% of Alu exons analyzed by RNA-Seq have estimated transcript inclusion levels of at least 50% in the human cerebellum, indicating widespread establishment of Alu exons in human genes. Genes encoding zinc finger transcription factors have significantly higher levels of Alu exonization. Importantly, Alu exons with high splicing activities are strongly enriched in the 5-UTR, and two-thirds (10/15) of 5-UTR Alu exons tested by luciferase reporter assays significantly alter mRNA translational efficiency. Mutational analysis reveals the specific molecular mechanisms by which newly created 5-UTR Alu exons modulate translational efficiency, such as the creation or elongation of upstream ORFs that repress the translation of the primary ORFs. This study presents genomic evidence that a major functional consequence of Alu exonization is the lineage-specific evolution of translational regulation. Moreover, the preferential creation and establishment of Alu exons in zinc finger genes suggest that Alu exonization may have globally affected the evolution of primate and human transcriptomes by regulating the protein production of master transcriptional regulators in specific lineages.
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Comparison of anterior segment measurements with rotating Scheimpflug photography and partial coherence reflectometry.
J Cataract Refract Surg
PUBLISHED: 01-19-2011
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To compare central corneal thickness (CCT), anterior chamber depth (ACD), and keratometry (K) readings measured using optical low-coherence reflectometry (OLCR) biometry and high-resolution rotating Scheimpflug photography.
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Subependymoma at the foramen of Monro presenting with intermittent hydrocephalus: case report and review of the literature.
J La State Med Soc
PUBLISHED: 10-02-2010
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Subependymomas are benign neoplasms, accounting for 0.5 % of all central nervous system tumors. These tumors are frequently asymptomatic, often discovered incidentally at autopsy. However, patients may be symptomatic with the symptoms depending on location of the tumor. Since subependymomas typically arise from the ventricular wall, obstruction of cerebrospinal fluid is a major cause of onset symptoms. We present a rare case report of a subependymoma at the foramen of Monro presenting with intermittent hydrocephalus. The patients tumor was asymptomatic for many years. Imaging findings included asymmetry of the lateral ventricles. The patient developed sudden onset of headache and altered mental status followed by complete resolution, likely due to intermittent hydrocephalus. She developed two more such episodes necessitating an emergent external ventricular drain placement followed by surgical resection. Our report illustrates a case of intermittent hydrocephalus due to a sessile subependymoma. Even though our patient presented with a histologically benign ventricular tumor, she demonstrated rapidly worsening symptoms that culminated in herniation. By presenting our case report, we hope to draw attention to this rare but potentially life-threatening presentation of subependymoma. Once diagnosed, we recommend early tumor removal and restoration of normal cerebrospinal fluid (CSF) pathways for these intraventricular tumors.
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Friction and adhesion of hierarchical carbon nanotube structures for biomimetic dry adhesives: multiscale modeling.
ACS Appl Mater Interfaces
PUBLISHED: 08-17-2010
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With unique hierarchical fibrillar structures on their feet, gecko lizards can walk on vertical walls or even ceilings. Recent experiments have shown that strong binding along the shear direction and easy lifting in the normal direction can be achieved by forming unidirectional carbon nanotube array with laterally distributed tips similar to geckos feet. In this study, a multiscale modeling approach was developed to analyze friction and adhesion behaviors of this hierarchical fibrillar system. Vertically aligned carbon nanotube array with laterally distributed segments at the end was simulated by coarse grained molecular dynamics. The effects of the laterally distributed segments on friction and adhesion strengths were analyzed, and further adopted as cohesive laws used in finite element analysis at device scale. The results show that the laterally distributed segments play an essential role in achieving high force anisotropy between normal and shear directions in the adhesives. Finite element analysis reveals a new friction-enhanced adhesion mechanism of the carbon nanotube array, which also exists in gecko adhesive system. The multiscale modeling provides an approach to bridge the microlevel structures of the carbon nanotube array with its macrolevel adhesive behaviors, and the predictions from this modeling give an insight into the mechanisms of gecko-mimicking dry adhesives.
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Measurement of central corneal thickness by high-resolution Scheimpflug imaging, Fourier-domain optical coherence tomography and ultrasound pachymetry.
Acta Ophthalmol
PUBLISHED: 06-18-2010
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To compare the repeatability and reproducibility of central corneal thickness (CCT) measurements by high-resolution (HR) rotating Scheimpflug imaging and Fourier-domain optical coherence tomography (FD-OCT). CCT measurements were compared to those determined by ultrasound pachymetry (UP).
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An ESRP-regulated splicing programme is abrogated during the epithelial-mesenchymal transition.
EMBO J.
PUBLISHED: 05-23-2010
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Alternative splicing achieves coordinated changes in post-transcriptional gene expression programmes through the activities of diverse RNA-binding proteins. Epithelial splicing regulatory proteins 1 and 2 (ESRP1 and ESRP2) are cell-type-specific regulators of transcripts that switch splicing during the epithelial-mesenchymal transition (EMT). To define a comprehensive programme of alternative splicing that is regulated during the EMT, we identified an extensive ESRP-regulated splicing network of hundreds of alternative splicing events within numerous genes with functions in cell-cell adhesion, polarity, and migration. Loss of this global ESRP-regulated epithelial splicing programme induces the phenotypic changes in cell morphology that are observed during the EMT. Components of this splicing signature provide novel molecular markers that can be used to characterize the EMT. Bioinformatics and experimental approaches revealed a high-affinity ESRP-binding motif and a predictive RNA map that governs their activity. This work establishes the ESRPs as coordinators of a complex alternative splicing network that adds an important post-transcriptional layer to the changes in gene expression that underlie epithelial-mesenchymal transitions during development and disease.
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Evolution of alternative splicing in primate brain transcriptomes.
Hum. Mol. Genet.
PUBLISHED: 05-11-2010
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Alternative splicing is a predominant form of gene regulation in higher eukaryotes. The evolution of alternative splicing provides an important mechanism for the acquisition of novel gene functions. In this work, we carried out a genome-wide phylogenetic survey of lineage-specific splicing patterns in the primate brain, via high-density exon junction array profiling of brain transcriptomes of humans, chimpanzees and rhesus macaques. We identified 509 genes showing splicing differences among these species. RT-PCR analysis of 40 exons confirmed the predicted splicing evolution of 33 exons. Of these 33 exons, outgroup analysis using rhesus macaques confirmed 13 exons with human-specific increase or decrease in transcript inclusion levels after humans diverged from chimpanzees. Some of the human-specific brain splicing patterns disrupt domains critical for protein-protein interactions, and some modulate translational efficiency of their host genes. Strikingly, for exons showing splicing differences across species, we observed a significant increase in the rate of silent substitutions within exons, coupled with accelerated sequence divergence in flanking introns. This indicates that evolution of cis-regulatory signals is a major contributor to the emergence of human-specific splicing patterns. In one gene (MAGOH), using minigene reporter assays, we demonstrated that the combination of two human-specific cis-sequence changes created its human-specific splicing pattern. Together, our data reveal widespread human-specific changes of alternative splicing in the brain and suggest an important role of splicing in the evolution of neuronal gene regulation and functions.
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Changes in ocular response analyzer parameters after LASIK.
J Refract Surg
PUBLISHED: 04-07-2010
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To investigate changes in Ocular Response Analyzer parameters after myopic LASIK.
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Cloning and expression profiles of two isoforms of a CHH-like gene specifically expressed in male Chinese shrimp, Fenneropenaeus chinensis.
Gen. Comp. Endocrinol.
PUBLISHED: 03-19-2010
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Two full-length cDNA sequences (Fc-CHH1, Fc-CHH2) encoding a crustacean hyperglycemic hormone (CHH) precursor homolog and their DNA sequences were cloned from Chinese shrimp Fenneropenaeus chinensis. The deduced amino acid sequences of them are predicted to contain a signal peptide and a mature peptide. The mature peptides of Fc-CHH1 and Fc-CHH2 shared 78% identity, but they showed low identities (less than 40%) to CHH peptides from other species. Both Fc-CHH1 and Fc-CHH2 proteins contain six highly conserved cysteine residues which are characteristic of the CHH family peptides. The transcripts of Fc-CHH1 and Fc-CHH2 were shown to be specifically present in the spermatophore sac of mature male Chinese shrimp through reverse transcription-polymerase chain reaction (RT-PCR) detection. The transcripts of Fc-CHH1 and Fc-CHH2 begin to appear at the immature stage (115 days after the first post-larvae stage) when the spermatophore sac was first observed to be appeared. In situ hybridization analyses showed that Fc-CHH1 and Fc-CHH2 transcripts located at the epithelial cells in the internal wall of the spermatophore sac. In the cloned DNA sequences of Fc-CHH1 and Fc-CHH2, the predicted transcription factor binding sites in the 5 flanking sequences are different from those previously reported for CHH family genes of crustacean. To our knowledge, these are novel CHH-like genes expressed specifically in male shrimp. Their function needs to be further investigated.
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Proteomic analysis of differentially expressed proteins in lymphoid organ of Fenneropenaeus chinensis response to Vibrio anguillarum stimulation.
Fish Shellfish Immunol.
PUBLISHED: 03-12-2010
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To gain an insight into the function of shrimp lymphoid organ at protein level, we analyzed the proteome of lymphoid organ in healthy Chinese shrimp Fenneropenaeus chinensis (F. chinensis) through two-dimensional gel electrophoresis (2-DE) based proteomic approach. A total of 95 spots representing 75 protein entries were identified by liquid chromatography tandem mass spectrometry (LC-MS/MS) with both online and in-house database. According to Gene Ontology (GO) annotation of biological process, the identified proteins were classified into 13 categories. Among them, approximately 36% of proteins related to cytoskeleton are noticeable. Then, a comparative proteomic approach was employed to investigate the differentially expressed proteins in lymphoid organ of Vibrio anguillarum-challenged F. chinensis. At 24 h post-injection (hpi), 17 differentially expressed protein spots were successfully identified, including 4 up-regulated protein spots (represent 4 proteins: cathepsin L, protein similar to squid CG16901-PC, protein kinase C and protein similar to T-complex Chaperonin 5 CG8439-PA), and 13 down-regulated protein spots (represent 9 proteins: actin, beta-actin, cytoplasmic actin CyII, alpha tubulin, beta tubulin, protein similar to proteasome delta, vacuolar ATP synthase subunit B, elongation factor 2, carboxypeptidase B). These data may help us to understand the function of lymphoid organ and the molecular immune mechanism of shrimp responsive to pathogen infection.
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A Dorsal homolog (FcDorsal) in the Chinese shrimp Fenneropenaeus chinensis is responsive to both bacteria and WSSV challenge.
Dev. Comp. Immunol.
PUBLISHED: 02-16-2010
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Rel/NFkappaB is a family of transcription factors. In the present study, a Rel/NFkappaB family member, Dorsal homolog (FcDorsal) was cloned from the Chinese shrimp Fenneropenaeus chinensis. The full length cDNA of FcDorsal consists of 1627bp, revealed a 1071bp open reading frame encoding 357 aa. The predicted molecular weight (MW) of the deduced amino acid sequence of FcDorsal was 39.78kDa, and its theoretical pI was 8.85. Amino acid sequence analysis showed that FcDorsal contains a Rel homolog domain (RHD) and an IPT/TIG (Ig-like, plexins and transcriptions factors) domain. The signature sequence of dorsal protein existed in the deduced amino acid sequence. Spatial expression profiles showed that FcDorsal had the highest expression level in the hemocytes and lymphoid organ (Oka). The expression profiles in the hemocytes and lymphoid organ were apparently modulated when shrimp were stimulated by bacteria or WSSV. Both Gram-positive (G(+)) bacteria (Micrococcus lysodeikticus) and Gram-negative (G(-)) bacteria (Vibrio anguillarium) injection to shrimp caused the up-regulation of FcDorsal at the transcription level. DsRNA approach was used to study the function of FcDorsal and the data showed that FcDorsal was related to the transcription of Penaeidin 5 in shrimp. The present data provide clues that FcDorsal might play potential important roles in the innate immunity of shrimp. Through comparison of the expression profiles between FcDorsal and another identified Rel/NFkappaB member (FcRelish) in shrimp responsive to WSSV challenge, we speculate that FcDorsal and FcRelish might play different roles in shrimp immunity.
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Topography-guided transepithelial surface ablation followed by corneal collagen cross-linking performed in a single combined procedure for the treatment of keratoconus and pellucid marginal degeneration.
J Refract Surg
PUBLISHED: 02-12-2010
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To evaluate a combination of topography-guided custom ablation and corneal collagen cross-linking (CXL) in a single procedure for the treatment of keratectasia.
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Screening of genes related to ovary development in Chinese shrimp Fenneropenaeus chinensis by suppression subtractive hybridization.
Comp. Biochem. Physiol. Part D Genomics Proteomics
PUBLISHED: 02-01-2010
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The ovary of triploid shrimp Fenneropenaeus chinensis was apparently impaired compared to that of the diploid shrimp at the same age. Therefore triploid shrimp ovary is possible to be taken as a model to understand the mechanism of ovary development of shrimp compared to that of the ovary of diploid shrimp at the same age. In the present study, a suppression subtractive hybridization (SSH) technique was applied to identify differentially expressed genes in the ovary between diploid and triploid shrimp. For the forward library (RNA from the ovary of triploid shrimp as the tester), 54 genes were identified. For the reverse library (RNA from the ovary of diploid shrimp as the tester), 16 genes were identified. The identified genes encoded proteins with multiple functions, including extracellular matrix components, cytoskeleton, cell growth and death, metabolism, genetic information processing, signal transduction/transport or immunity related proteins. Eleven differentially expressed genes were selected to be confirmed in the ovaries of triploid and diploid shrimp by semi-quantitative RT-PCR. Genes encoding spermatogonial stem-cell renewal factor, cytochrome c oxidase subunits I and II, clottable protein, antimicrobial peptide and transposase showed up-regulated expressions in the ovary of triploid shrimp. Genes encoding tubulin, cellular apoptosis susceptibility protein, farnesoic acid O-methyltransferase, thrombospondin and heat shock protein 90 genes showed higher expressions in the ovary of diploid shrimp. The differential expressions of the above genes are suggested to be related to the ovary development of shrimp. It will provide a new clue to uncover the molecular mechanisms underlying the ovarian development in penaeid shrimp.
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The nuclear experience of CPEB: implications for RNA processing and translational control.
RNA
PUBLISHED: 12-29-2009
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CPEB is a sequence-specific RNA binding protein that promotes polyadenylation-induced translation in early development, during cell cycle progression and cellular senescence, and following neuronal synapse stimulation. It controls polyadenylation and translation through other interacting molecules, most notably the poly(A) polymerase Gld2, the deadenylating enzyme PARN, and the eIF4E-binding protein Maskin. Here, we report that CPEB shuttles between the nucleus and cytoplasm and that its export occurs via the CRM1-dependent pathway. In the nucleus of Xenopus oocytes, CPEB associates with lampbrush chromosomes and several proteins involved in nuclear RNA processing. CPEB also interacts with Maskin in the nucleus as well as with CPE-containing mRNAs. Although the CPE does not regulate mRNA export, it influences the degree to which mRNAs are translationally repressed in the cytoplasm. Moreover, CPEB directly or indirectly mediates the alternative splicing of at least one pre-mRNA in mouse embryo fibroblasts as well as certain mouse tissues. We propose that CPEB, together with Maskin, binds mRNA in the nucleus to ensure tight translational repression upon export to the cytoplasm. In addition, we propose that nuclear CPEB regulates specific pre-mRNA alternative splicing.
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The epithelial splicing factors ESRP1 and ESRP2 positively and negatively regulate diverse types of alternative splicing events.
RNA Biol
PUBLISHED: 11-22-2009
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Cell-type and tissue-specific alternative splicing events are regulated by combinatorial control involving both abundant RNA binding proteins as well as those with more discrete expression and specialized functions. Epithelial Splicing Regulatory Proteins 1 and 2 (ESRP1 and ESRP2) are recently discovered epithelial-specific RNA binding proteins that promote splicing of the epithelial variant of the FGFR2, ENAH, CD44 and CTNND1 transcripts. To catalogue a larger set of splicing events under the regulation of the ESRPs we profiled splicing changes induced by RNA interference-mediated knockdown of ES RP1 and ES RP2 expression in a human epithelial cell line using the splicing sensitive Affymetrix Exon ST1.0 Arrays. Analysis of the microarray data resulted in the identification of over a hundred candidate ESRP regulated splicing events. We were able to independently validate 38 of these targets by RT-PCR. The ESRP regulated events encompass all known types of alternative splicing events, most prominent being alternative cassette exons and splicing events leading to alternative 3 terminal exons. Importantly, a number of these regulated splicing events occur in gene transcripts that encode proteins with well-described roles in the regulation of actin cytoskeleton organization, cell-cell adhesion, cell polarity and cell migration. In sum, this work reveals a novel list of transcripts differentially spliced in epithelial and mesenchymal cells, implying that coordinated alternative splicing plays a critical role in determination of cell type identity. These results further establish ESRP1 and ESRP2 as global regulators of an epithelial splicing regulatory network.
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MADS+: discovery of differential splicing events from Affymetrix exon junction array data.
Bioinformatics
PUBLISHED: 11-17-2009
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The Affymetrix Human Exon Junction Array is a newly designed high-density exon-sensitive microarray for global analysis of alternative splicing. Contrary to the Affymetrix exon 1.0 array, which only contains four probes per exon and no probes for exon-exon junctions, this new junction array averages eight probes per probeset targeting all exons and exon-exon junctions observed in the human mRNA/EST transcripts, representing a significant increase in the probe density for alternative splicing events. Here, we present MADS+, a computational pipeline to detect differential splicing events from the Affymetrix exon junction array data. For each alternative splicing event, MADS+ evaluates the signals of probes targeting competing transcript isoforms to identify exons or splice sites with different levels of transcript inclusion between two sample groups. MADS+ is used routinely in our analysis of Affymetrix exon junction arrays and has a high accuracy in detecting differential splicing events. For example, in a study of the novel epithelial-specific splicing regulator ESRP1, MADS+ detects hundreds of exons whose inclusion levels are dependent on ESRP1, with a RT-PCR validation rate of 88.5% (153 validated out of 173 tested).
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Identification of cancer-associated gene clusters and genes via clustering penalization.
Stat Interface
PUBLISHED: 07-21-2009
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Identification of genes associated with cancer development and progression using microarray data is challenging because of the high dimensionality and cluster structure of gene expressions. Here the clusters are composed of multiple genes with coordinated biological functions and/or correlated expressions. In this article, we first propose a hybrid approach for clustering gene expressions. The hybrid approach uses both pathological pathway information and correlations of gene expressions. We propose using the group bridge, a novel clustering penalization approach, for analysis of cancer microarray data. The group bridge approach explicitly accounts for the cluster structure of gene expressions, and is capable of selecting gene clusters and genes within those selected clusters that are associated with cancer. We also develop an iterative algorithm for computing the group bridge estimator. Analysis of three cancer microarray datasets shows that the proposed approach can identify biologically meaningful gene clusters and genes within those identified clusters.
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Comparative proteomic profiles of the hepatopancreas in Fenneropenaeus chinensis response to hypoxic stress.
Proteomics
PUBLISHED: 07-07-2009
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Hypoxia, as one suboptimal environmental condition, can affect the physiological state of shrimp during pond aquaculture. To better understand the mechanism of response to hypoxic stress in Chinese shrimp Fenneropenaeus chinensis, proteome research approach was utilized. Differentially expressed proteins of hepatopancreas in adult Chinese shrimp between the control and hypoxia-stressed groups were screened. By 2-DE analysis, 67 spots showed obvious changes after hypoxia. Using LC-ESI-MS/MS, 51 spots representing 33 proteins were identified including preamylase, arginine kinase, phosphopyruvate hydratase, citrate synthase, ATP synthase alpha subunit, chymotrypsin BI, chitinase, ferritin, C-type lectin receptors, transketolase, formylglutathione hydrolase, formyltetrahydrofolate dehydrogenase, aldehyde dehydrogenase, glutathione peroxidase, cytosolic manganese superoxide dismutase, protein disulfide isomerase, beta-actin, oncoprotein nm23, crustacyanin-C1 and so on. These proteins could be functionally classified into several groups such as proteins related to energy production, metabolism-related proteins, immune-related proteins, antioxidant proteins, chaperones, cytoskeleton proteins and ungrouped proteins. The transcription levels of ten selected genes encode the identified proteins were analyzed by real-time PCR at different sampling times of hypoxia. This study is the first analysis of differentially expressed proteins in the hepatopancreas of shrimp after hypoxia and provides a new insight for further study in hypoxic stress response of shrimp at the protein level.
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A molecular dynamics study of chirality transfer from chiral surfaces to nearby solvent.
J Chem Phys
PUBLISHED: 07-02-2009
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The presence of a chiral surface can alter the characteristics of nearby solvent molecules such that, on average, these molecules become chiral. The extent of this induced chirality and its dependence on the surface and solvent characteristics are explored in this article. Three surfaces employed in chiral chromatography are examined: The Whelk-O1 interface, a phenylglycine-derived chiral stationary phase (CSP), and a leucine-derived CSP. All three interfaces are "brush type" in that the chiral molecules are attached to the underlying substrate via an achiral tether. The solvents consist of ethanol, a binary n-hexane/ethanol solvent, 2-propanol, and a binary n-hexane/2-propanol solvent. Molecular dynamics simulations of the solvated chiral interfaces form the basis of the analysis. The chirality induced in the solvent is assessed based on a chirality index originally proposed by Osipov et al. [Mol. Phys. 84, 1193 (1995)]. Solvent chirality will depend on the solvent position relative to the surface. For this reason, a position-dependent chirality index is analyzed in detail.
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Ultrasound enhanced electrochemical oxidation of phenol and phthalic acid on boron-doped diamond electrode.
J. Hazard. Mater.
PUBLISHED: 05-26-2009
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The enhancement on degradation of two typical organic pollutants, phenol (Ph) and phthalic acid (PA) on boron-doped diamond (BDD) electrode is particularly investigated in this study. Results show that ultrasound (US) has remarkable influence on electrochemical (EC) oxidation of the two pollutants including degradation efficiency, EC oxidation energy consumption, mass transport and electrochemical reaction. With US, the enhancement on degradation efficiency and decreasing of EC oxidation energy consumption of Ph are more obvious. US can also efficiently reduce the average electrochemical oxidation energy consumption (AE), decreasing by 74 and 69% for Ph and PA, respectively. Mass transport process can be greatly accelerated by US. The mass transport coefficients of Ph and PA both reach 2.0 x 10(-5)ms(-1) in ultrasound-assisted electrochemical (US-EC) process, from 5.4 x 10(-6) and 6.7 x 10(-6) ms(-1) in EC, increasing by 270 and 199%, respectively. The reaction amount of Ph decreases by 79% with US, from 6.49 x 10(-10) to 1.39 x 10(-10) mol cm(-2). For PA, the reaction amount decreases from 1.25x10(-11) to 3.11 x 10(-12) mol cm(-2) with US. The oxidation peak current increases by 32% for Ph. While for PA, there is no direct oxidation happened in US-EC process.
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Identification of a novel relish homolog in Chinese shrimp Fenneropenaeus chinensis and its function in regulating the transcription of antimicrobial peptides.
Dev. Comp. Immunol.
PUBLISHED: 05-01-2009
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Penaeid shrimp, as an invertebrate, relies on the innate immunity to oppose the microbial invaders. Antimicrobial peptides (AMP) are an integral component of the innate immune system in most organisms and function as an early first line of defense against pathogens, but the knowledge about the pathways to regulate the shrimp AMP gene expression is still absent up to date. In the current study, a Relish homolog (FcRelish) was cloned from Chinese shrimp Fenneropenaeus chinensis. The full length cDNA of FcRelish consists of 2157 bp, including 1512 bp open reading frame, encoding 504 amino acids. The predicted molecular weight of FcRelish is 57 kDa, and the theoretical PI is 7.00. Spatial expression profiles showed that FcRelish had the highest expression levels in the hemocytes and lymphoid organ. Both Vibrio anguillarium and Micrococcus lysodeikticus stimulation to shrimp can affect the transcription profile of FcRelish. Silencing of FcRelish through DsRNA interference can greatly change the transcription profile of AMP. Therefore, we suggest that FcRelish identified in the present study is closely related to the transcription of AMP, and then we inferred that Imd pathway might exist in shrimp.
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A general integrative genomic feature transcription factor binding site prediction method applied to analysis of USF1 binding in cardiovascular disease.
Hum. Genomics
PUBLISHED: 05-01-2009
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Transcription factors are key mediators of human complex disease processes. Identifying the target genes of transcription factors will increase our understanding of the biological network leading to disease risk. The prediction of transcription factor binding sites (TFBSs) is one method to identify these target genes; however, current prediction methods need improvement. We chose the transcription factor upstream stimulatory factor 1 ( USF1 ) to evaluate the performance of our novel TFBS prediction method because of its known genetic association with coronary artery disease (CAD) and the recent availability of USF1 chromatin immunoprecipitation microarray (ChIP-chip) results. The specific goals of our study were to develop a novel and accurate genome-scale method for predicting USF1 binding sites and associated target genes to aid in the study of CAD. Previously published USF1 ChIP-chip data for 1 per cent of the genome were used to develop and evaluate several kernel logistic regression prediction models. A combination of genomic features (phylogenetic conservation, regulatory potential, presence of a CpG island and DNaseI hypersensitivity), as well as position weight matrix (PWM) scores, were used as variables for these models. Our most accurate predictor achieved an area under the receiver operator characteristic curve of 0.827 during cross-validation experiments, significantly outperforming standard PWM-based prediction methods. When applied to the whole human genome, we predicted 24,010 USF1 binding sites within 5 kilobases upstream of the transcription start site of 9,721 genes. These predictions included 16 of 20 genes with strong evidence of USF1 regulation. Finally, in the spirit of genomic convergence, we integrated independent experimental CAD data with these USF1 binding site prediction results to develop a prioritised set of candidate genes for future CAD studies. We have shown that our novel prediction method, which employs genomic features related to the presence of regulatory elements, enables more accurate and efficient prediction of USF1 binding sites. This method can be extended to other transcription factors identified in human disease studies to help further our understanding of the biology of complex disease.
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Cloning of cytoplasmic heat shock protein 90 (FcHSP90) from Fenneropenaeus chinensis and its expression response to heat shock and hypoxia.
Cell Stress Chaperones
PUBLISHED: 04-11-2009
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Heat shock protein 90 (HSP90) works as a multi-functional chaperone and is involved in the regulation of many essential cellular pathways. In this study, we have identified a full-length complementary DNA (cDNA) of HSP90 (FcHSP90) from Chinese shrimp Fenneropenaeus chinensis. FcHSP90 full-length cDNA comprised 2,552 bp, including a 2,181-bp open reading frame encoding 726 amino acids. Both homology analyses using alignment with previously identified HSP90 and a phylogeny tree indicated that FcHSP90 was a cytoplasmic HSP90. Real-time reverse transcription polymerase chain reaction analysis revealed that FcHSP90 was ubiquitously expressed in all the examined tissues but with highest levels in ovary of F. chinensis. FcHSP90 mRNA levels were sensitively induced by heat shock (from 25 degrees C to 35 degrees C) and reached the maximum at 6 h during heat shock treatment. Under hypoxia conditions, FcHSP90 mRNA levels, in both hemocytes and gill, were induced at 2 h and depressed at 8 h during hypoxia stress. The assessment of FcHSP90 mRNA levels under heat shock and hypoxia stresses indicated that the transcription of FcHSP90 was very sensitive to heat shock and hypoxia, so we deduced that FcHSP90 might play very important roles for shrimp to cope with environmental stress.
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JoVE Visualize is a tool created to match the last 5 years of PubMed publications to methods in JoVE's video library.

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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.