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Find video protocols related to scientific articles indexed in Pubmed.
Past and future of a century old Citrus tristeza virus collection: a California citrus germplasm tale.
Front Microbiol
PUBLISHED: 01-01-2013
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Citrus tristeza virus (CTV) isolates collected from citrus germplasm, dooryard and field trees in California from 1914 have been maintained in planta under quarantine in the Citrus Clonal Protection Program (CCPP), Riverside, California. This collection, therefore, represents populations of CTV isolates obtained over time and space in California. To determine CTV genetic diversity in this context, genotypes of CTV isolates from the CCPP collection were characterized using multiple molecular markers (MMM). Genotypes T30, VT, and T36 were found at high frequencies with T30 and T30+VT genotypes being the most abundant. The MMM analysis did not identify T3 and B165/T68 genotypes; however, biological and phylogenetic analysis suggested some relationships of CCPP CTV isolates with these two genotypes. Phylogenetic analysis of the CTV coat protein (CP) gene sequences classified the tested isolates into seven distinct clades. Five clades were in association with the standard CTV genotypes T30, T36, T3, VT, and B165/T68. The remaining two identified clades were not related to any standard CTV genotypes. Spatiotemporal analysis indicated a trend of reduced genotype and phylogenetic diversity as well as virulence from southern California (SC) at early (1907-1957) in comparison to that of central California (CC) isolates collected from later (1957-2009) time periods. CTV biological characterization also indicated a reduced number and less virulent stem pitting (SP) CTV isolates compared to seedling yellows isolates introduced to California. This data provides a historical insight of the introduction, movement, and genetic diversity of CTV in California and provides genetic and biological information useful for CTV quarantine, eradication, and disease management strategies such as CTV-SP cross protection.
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Thermal percolation in stable graphite suspensions.
Nano Lett.
PUBLISHED: 12-19-2011
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Different from the electrical conductivity of conductive composites, the thermal conductivity usually does not have distinctive percolation characteristics. Here we report that graphite suspensions show distinct behavior in the thermal conductivity at the electrical percolation threshold, including a sharp kink at the percolation threshold, below which thermal conductivity increases rapidly while above which the rate of increase is smaller, contrary to the electrical percolation behavior. Based on microstructural and alternating current impedance spectroscopy studies, we interpret this behavior as a result of the change of interaction forces between graphite flakes when isolated clusters of graphite flakes form percolated structures. Our results shed light on the thermal conductivity enhancement mechanisms in nanofluids and have potential applications in energy systems.
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Occurrence of grapevine leafroll-associated virus complex in Napa Valley.
PLoS ONE
PUBLISHED: 08-01-2011
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Grapevine leafroll disease (GLD) is caused by a complex of several virus species (grapevine leafroll-associated viruses, GLRaV) in the family Closteroviridae. Because of its increasing importance, it is critical to determine which species of GLRaV is predominant in each region where this disease is occurring. A structured sampling design, utilizing a combination of RT-PCR based testing and sequencing methods, was used to survey GLRaVs in Napa Valley (California, USA) vineyards (n?=?36). Of the 216 samples tested for GLRaV-1, -2, -3, -4, -5, and -9, 62% (n?=?134) were GLRaV positive. Of the positives, 81% (n?=?109) were single infections with GLRaV-3, followed by GLRaV-2 (4%, n?=?5), while the remaining samples (15%, n?=?20) were mixed infections of GLRaV-3 with GLRaV-1, 2, 4, or 9. Additionally, 468 samples were tested for genetic variants of GLRaV-3, and of the 65% (n?=?306) of samples positive for GLRaV-3, 22% were infected with multiple GLRaV-3 variants. Phylogenetic analysis utilizing sequence data from the single infection GLRaV-3 samples produced seven well-supported GLRaV-3 variants, of which three represented 71% of all GLRaV-3 positive samples in Napa Valley. Furthermore, two novel variants, which grouped with a divergent isolate from New Zealand (NZ-1), were identified, and these variants comprised 6% of all positive GLRaV-3 samples. Spatial analyses showed that GLRaV-3a, 3b, and 3c were not homogeneously distributed across Napa Valley. Overall, 86% of all blocks (n?=?31) were positive for GLRaVs and 90% of positive blocks (n?=?28) had two or more GLRaV-3 variants, suggesting complex disease dynamics that might include multiple insect-mediated introduction events.
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Clostridium butyricum activates TLR2-mediated MyD88-independent signaling pathway in HT-29 cells.
Mol. Cell. Biochem.
PUBLISHED: 07-26-2011
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Oral administration of Clostridium butyricum as probiotic is increasingly gaining importance in the treatment of diarrhea and the improvement of animal performance. However, the mechanisms of host cell receptor recognition of C. butyricum and the downstream immune signaling pathways leading to these benefits remain unclear. The objective of this study was to analyze the mechanisms involved in C. butyricum induction of the toll-like receptor (TLR) signaling. Knockdown of myeloid differentiation primary response protein 88 (MyD88) expression using small interfering RNA in this manner did not affect C. butyricum-induced elevated levels of nuclear factor ?B (NF-?B), interleukin-8 (IL-8), IL-6, and tumor necrosis factor alpha (TNF-?), suggesting a MyD88-independent route to TLR signaling transduction. However, a significant reduction in the levels of NF-?B, IL-8, IL-6, and TNF-? was evident in the absence of TLR2 expression, implying the need for TLR2 in C. butyricum recognition. Hence, C. butyricum activates TLR2-mediated MyD88-independent signaling pathway in human epithelial cells, which adds to our understanding of the molecular mechanisms of this probiotic action on gut epithelium.
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Genetic diversity in the 3 terminal 4.7-kb region of grapevine leafroll-associated virus 3.
Phytopathology
PUBLISHED: 03-12-2011
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Grapevine leafroll-associated virus 3 (GLRaV-3; Ampelovirus, Closteroviridae), associated with grapevine leafroll disease, is an important pathogen found across all major grape-growing regions of the world. The genetic diversity of GLRaV-3 in Napa Valley, CA, was studied by sequencing 4.7 kb in the 3 terminal region of 50 isolates obtained from Vitis vinifera Merlot. GLRaV-3 isolates were subdivided into four distinct phylogenetic clades. No evidence of positive selection was observed in the data set, although neutral selection (ratio of nonsynonymous to synonymous substitution rates = 1.1) was observed in one open reading frame (ORF 11, p4). Additionally, the four clades had variable degrees of overall nucleotide diversity. Moreover, no geographical structure among isolates was observed, and isolates belonging to different phylogenetic clades were found in distinct vineyards, with one exception. Considered with the evidence of purifying selection (i.e., against deleterious mutations), these data indicate that the population of GLRaV-3 in Napa Valley is not expanding and its effective population size is not increasing. Furthermore, research on the biological characterization of GLRaV-3 strains might provide valuable insights on the biology of this species that may have epidemiological relevance.
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TRIM-9 functions in the UNC-6/UNC-40 pathway to regulate ventral guidance.
J Genet Genomics
PUBLISHED: 02-23-2011
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TRIpartite Motif (TRIM) family proteins are ring finger domain-containing, multi-domain proteins implicated in many biological processes. Members of the TRIM-9/C-I subfamily of TRIM proteins, including TRIM-9, MID1 and MID2, have neuronal functions and are associated with neurological diseases. To explore whether the functions of C-I TRIM proteins are conserved in invertebrates, we analyzed Caenorhabditis elegans and Drosophila trim-9 mutants. C. elegans trim-9 mutants exhibit defects in the ventral guidance of hermaphrodite specific neuron (HSN) and the touch neuron AVM. Further genetic analyses indicate that TRIM-9 participates in the UNC-6-UNC-40 attraction pathway. Asymmetric distribution of UNC-40 during HSN development is normal in trim-9 mutants. However, the asymmetric localization of MIG-10, a downstream effector of UNC-40, is abolished in trim-9 mutants. These results suggest that TRIM-9 functions upstream of MIG-10 in the UNC-40 pathway. Moreover, we showed that TRIM-9 exhibits E3 ubiquitin ligase activity in vitro and this activity is important for TRIM-9 function in vivo. Additionally, we found that Drosophila trim-9 is required for the midline attraction of a group of sensory neuron axons. Over-expression of the Netrin/UNC-6 receptor Frazzled suppresses the guidance defects in trim-9 mutants. Our study reveals an evolutionarily conserved function of TRIM-9 in the UNC-40/Frazzled-mediated UNC-6/Netrin attraction pathway.
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Metered-dose inhaler efficiency enhancement: a case study and novel design.
Inhal Toxicol
PUBLISHED: 04-15-2010
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The efficiency of the metered-dose inhaler (MDI) is a critical issue in aerosol medicine because it deals with delivering a life-saving medication to patients with various lung diseases. Mouthpiece diameter, air flow rate, and entrance angle are among many parameters that influence the MDI penetration efficiency. It is well known that inertial impaction accounts for the massive aerosol deposition in the oral airway. In this study, the authors present a novel simple modification of the inhaler mouthpiece using a wire-based jet depressor to reduce the inertial impaction of aerosols. A 0.5 mm diameter wire is placed inside the MDI mouthpiece at a distance of 2 mm in front of the MDI nozzle. Two mouthpieces were modified and employed in the experiments (16 and 20 mm). The penetration efficiencies are measured and the results of the modified mouthpiece are compared with the conventional mouthpiece. The experiments are conducted at three different air flow rates (30, 60, and 90 L/min) and five entrance/spray angles (0 degrees, 10 degrees, 20 degrees, 30 degrees, and 40 degrees). The results show that the new modified mouthpiece has higher aerosol penetration efficiency than the ones with the conventional mouthpiece. A second type of experiment is conducted to evaluate the relative strength of the aerosol impaction.
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Lettuce infectious yellows virus (LIYV) RNA 1-encoded P34 is an RNA-binding protein and exhibits perinuclear localization.
Virology
PUBLISHED: 04-07-2010
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The Crinivirus, Lettuce infectious yellows virus (LIYV) has a bipartite, positive-sense ssRNA genome. LIYV RNA 1 encodes replication-associated proteins while RNA 2 encodes proteins needed for other aspects of the LIYV life cycle. LIYV RNA 1 ORF 2 encodes P34, a trans enhancer for RNA 2 accumulation. Here we show that P34 is a sequence non-specific ssRNA-binding protein in vitro. P34 binds ssRNA in a cooperative manner, and the C-terminal region contains the RNA-binding domain. Topology predictions suggest that P34 is a membrane-associated protein and the C-terminal region is exposed outside of the membrane. Furthermore, fusions of P34 to GFP localized to the perinuclear region of transfected protoplasts, and colocalized with an ER-specific dye. This localization was of interest since LIYV RNA 1 replication (with or without P34 protein) induced strong ER rearrangement to the perinuclear region. Together, these data provide insight into LIYV replication and possible functions of P34.
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Agroinoculation of the Crinivirus, Lettuce infectious yellows virus, for systemic plant infection.
Virology
PUBLISHED: 05-11-2009
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Lettuce infectious yellows virus (LIYV) is phloem-limited, non-mechanically transmissible, and is transmitted to plants only by Bemisia tabaci. Here, we developed agroinoculation to deliver LIYV to plants thereby obviating the need for B. tabaci. Agroinfiltration of RNA 1 containing a green fluorescent protein gene into Nicotiana benthamiana leaves resulted in subliminal infections, as judged by green fluorescence. Agroinfiltration of LIYV wild-type RNA 1 and 2 constructs resulted in systemic infections in N. benthamiana plants and typical LIYV symptoms. In addition, partially purified LIYV virions from agroinoculated N. benthamiana plants were successfully acquired via membrane-feeding and transmitted to lettuce plants by B. tabaci. Agroinoculation coupled with targeted mutagenesis technologies will greatly enhance LIYV reverse genetics studies to characterize LIYV gene functions in planta for processes such as virus replication, recombination, trafficking, symptom elicitation and virus-vector interactions.
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Synergistic interaction between the Potyvirus, Turnip mosaic virus and the Crinivirus, Lettuce infectious yellows virus in plants and protoplasts.
Virus Res.
PUBLISHED: 01-17-2009
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Lettuce infectious yellows virus (LIYV), the type member of the genus Crinivirus in the family Closteroviridae, is specifically transmitted by the sweet potato whitefly (Bemisia tabaci) in a semipersistent manner. LIYV infections result in a low virus titer in plants and protoplasts, impeding reverse genetic efforts to analyze LIYV gene/protein functions. We found that synergistic interactions occurred in mixed infections of LIYV and Turnip mosaic virus (TuMV) in Nicotiana benthamiana plants, and these resulted in enhanced accumulation of LIYV. Furthermore, we examined the ability of transgenic plants and protoplasts expressing only the TuMV P1/HC-Pro sequence to enhance the accumulation of LIYV. LIYV RNA and protein titers increased by as much as 8-fold in these plants and protoplasts relative to control plants. LIYV infections remained phloem-limited in P1/HC-Pro transgenic plants, suggesting that enhanced accumulation of LIYV in these plants was due primarily to increased replication efficiency, not to greater spread.
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cis preferential replication of Lettuce infectious yellows virus (LIYV) RNA 1: the initial step in the asynchronous replication of the LIYV genomic RNAs.
Virology
PUBLISHED: 01-06-2009
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A series of Lettuce infectious yellows virus (LIYV) RNA 1 mutants was created to evaluate their ability to replicate in tobacco protoplasts. Mutants DeltaEcoRI, DeltaE-LINK, and Delta1B, having deletions in open reading frames (ORFs) 1A and 1B, did not replicate when individually inoculated to protoplasts or when co-inoculated with wild-type RNA1 as a helper virus. A fragment of the green fluorescent protein (GFP) gene was inserted into the RNA 1 ORF 2 (P34) in order to provide a unique sequence tag. This mutant, P34-GFP TAG, was capable of independent replication in protoplasts. Mutants derived from P34-GFP TAG having frameshift mutations in the ORF 1A or 1B were unable to replicate in protoplasts alone or in trans when co-inoculated with wild-type RNA1 as a helper virus. Taken together, these data strongly suggest that LIYV RNA 1 replication is cis-preferential.
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Ability of Clostridium butyricum to inhibit Escherichia coli-induced apoptosis in chicken embryo intestinal cells.
Vet. Microbiol.
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The beneficial effects of Clostridium butyricum in the treatment of intestinal inflammatory disorders are well known. However, it is not fully understood how such bacteria inhibit pathogen-induced intestinal diseases. For this purpose, we investigated the effects of C. butyricum and its spent culture supernatants (SCS) on Escherichia coli (EHEC) growth and adherence to chicken embryo intestinal cells (CEICs). We also evaluated the potential of C. butyricum to inhibit EHEC-induced apoptosis in CEICs. C. butyricum and its SCS exhibited significant inhibitory activity on EHEC growth and adherence to CEICs. C. butyricum also showed a significant inhibitory effect on EHEC-induced apoptosis by modulating the expression of XIAP (X-linked inhibitor of apoptosis protein), BclXL (B-cell lymphoma-extra large), FAS, Bcl2 (B-cell leukemia/lymphoma-2), BAX (Bcl-2-associated X protein), P53 (Tumor protein 53) and via inhibition of caspase-9 and caspase-3 activation. These results together indicate that C. butyricum possesses the ability to prevent EHEC-induced intestinal disorders both directly, through inhibiting EHEC viability, and indirectly, via medicating EHEC-induced apoptosis. These observations may help explain the beneficial properties of C. butyricum. Furthermore, our data is novel in the case of poultry and the manner in which C. butyricum prevents the EHEC-induced apoptosis provides supportive information for the treatment of colibacillosis in poultry.
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An important role of interleukin-10 in counteracting excessive immune response in HT-29 cells exposed to Clostridium butyricum.
BMC Microbiol.
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Clostridium butyricum has become increasingly important in preventing and treating intestinal inflammation. In the intestine it may increase the resistance of the gut to pathogen invasion via inducing the secretion of anti-inflammatory cytokines. Interleukin 10 (IL-10) plays a central role in preventing certain inflammatory diseases by down-regulating inflammatory cascades. In a previous study, we observed that the level of IL-10 mRNA was modulated by C. butyricum. The aim of this study was to investigate whether C. butyricum achieves its beneficial effects through IL-10.
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Midlife gene expressions identify modulators of aging through dietary interventions.
Proc. Natl. Acad. Sci. U.S.A.
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Dietary interventions are effective ways to extend or shorten lifespan. By examining midlife hepatic gene expressions in mice under different dietary conditions, which resulted in different lifespans and aging-related phenotypes, we were able to identify genes and pathways that modulate the aging process. We found that pathways transcriptionally correlated with diet-modulated lifespan and physiological changes were enriched for lifespan-modifying genes. Intriguingly, mitochondrial gene expression correlated with lifespan and anticorrelated with aging-related pathological changes, whereas peroxisomal gene expression showed an opposite trend. Both organelles produce reactive oxygen species, a proposed causative factor of aging. This finding implicates a contribution of peroxisome to aging. Consistent with this hypothesis, lowering the expression levels of peroxisome proliferation genes decreased the cellular peroxide levels and extended the lifespan of Drosophila melanogaster and Caenorhabditis elegans. These findings show that transcriptional changes resulting from dietary interventions can effectively reflect causal factors in aging and identify previously unknown or under-appreciated longevity pathways, such as the peroxisome pathway.
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What is Visualize?

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

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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.