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Find video protocols related to scientific articles indexed in Pubmed.
Rhizobium straminoryzae sp. nov., isolated from the surface of rice straw.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 06-04-2014
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An aerobic, Gram-stain-negative, rod-shaped bacterium, designated strain CC-LY845(T), was isolated from the surface of rice straw in Taiwan. Cells were non-motile, and no flagellum was detected. Comparison of 16S rRNA gene sequences indicated that the strain was phylogenetically related to species of the genus Rhizobium, with closest similarity to Rhizobium pseudoryzae KCTC 23294(T) (97.6?%), R. rhizoryzae KCTC 23652(T) (97.0?%) and R. oryzae LMG 24253(T) (96.7?%); other species showed lower levels of similarity (<96.6?%). The DNA-DNA relatedness of strain CC-LY845(T) and R. pseudoryzae KCTC 23294(T) was 34.8±3.1?% (reciprocal value 39.2±2.2?%). Phylogenetic analysis based on the housekeeping atpD and recA genes showed that the novel strain could be distinguished from R. pseudoryzae KCTC 23294(T) (92.7 and 91.5?%, respectively) and other species of the genus Rhizobium. The temperature range for growth was 25-42 °C, the pH range was 5.0-9.0 and NaCl concentrations up to 4.0?% (w/v) were tolerated. Strain CC-LY845(T) did not form nodules on four different legumes, and the nodD and nifH genes were not detected by PCR. The major fatty acids were C16?:?0 and summed feature 8 (C18?:?1?7c/C18?:?1?6c). The polyamine pattern of strain CC-LY845(T) showed spermidine and putrescine as major polyamines. The predominant quinone system was ubiquinone 10 (Q-10). The DNA G+C content was 68.3±2.4 mol%. Base on its phylogenetic, phenotypic and chemotaxonomic features, strain CC-LY845(T) is proposed to represent a novel species within the genus Rhizobium, for which the name Rhizobium straminoryzae sp. nov. is proposed. The type strain is strain CC-LY845(T) (?=?BCRC 80698(T)?=?JCM 19536(T)).
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Combination of photoreactor and packed bed bioreactor for the removal of ethyl violet from wastewater.
Chemosphere
PUBLISHED: 04-26-2014
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An efficient treatment system that combines a photoreactor and packed bed bioreactor (PBR) was developed and evaluated for treating ethyl violet (EV)-containing wastewater. Initial experiments demonstrated that the optimal operating parameters for the photoreactor in treating EV-containing wastewater were 2h reaction time, pH of 7, and 2min liquid retention time. Under these conditions, the photocatalytic reaction achieved a 61% EV removal efficiency and resulted in a significant BOD/COD increase in the solution. The results displayed by the coupled photobiological system achieved a removal efficiency of 85% and EC50 of the solution increased by 19 times in a semi-continuous mode when the EV concentration was <150mgL(-)(1). The effect of shock loading on the EV removal was temporary but coexisting substrate (glucose and crystal violet) at specific levels would affect the EV removal efficiency of the PBR. Phylogenetic analysis in the PBR indicated that the major bacteria species were Bdellovibrio bacteriovorus, Ralstonia pickettii, Stenotrophomonas maltophilia, and Comamonas sp. Furthermore, the possible degrading mechanisms of this coupled system were demethylation, deethylation, aromatic ring opening, nitrification, and carbon oxidation. The intermediates were characterized using gas chromatography-mass spectrometry analysis. These results indicated that the coupled photobiological system provides an effective method of EV removal.
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Inhibition of cancer cell migration and invasion through suppressing the Wnt1-mediating signal pathway by G-quadruplex structure stabilizers.
J. Biol. Chem.
PUBLISHED: 04-08-2014
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WNT1 encodes a multifunctional signaling glycoprotein that is highly expressed in several malignant tumors. Patients with Wnt1-positive cancer are usually related to advanced metastasis. Here, we found that a stretch of G-rich sequences located at the WNT1 promoter region is capable of forming G-quadruplex structures. The addition of G-quadruplex structure stabilizers, BMVC and BMVC4, raises the melting temperature of the oligonucleotide formed by the WNT1 promoter G-rich sequences. Significantly, the expression of WNT1 was repressed by BMVC or BMVC4 in a G-quadruplex-dependent manner, suggesting that they can be used to modulate WNT1 expression. The role of G-quadruplex stabilizers on Wnt1-mediated cancer migration and invasion was further analyzed. The protein levels of ?-catenin, a mediator of the Wnt-mediated signaling pathway, and the downstream targets MMP7 and survivin were down-regulated upon BMVC or BMVC4 treatments. Moreover, the migration and invasion activities of cancer cells were inhibited by BMVC and BMVC4, and the inhibitory effects can be reversed by WNT1-overexpression. Thus the Wnt1 expression and its downstream signaling pathways can be regulated through the G-quadruplex sequences located at its promoter region. These findings provide a novel approach for future drug development to inhibit migration and invasion of cancer cells.
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Co-expression of a heat shock transcription factor to improve conformational quality of recombinant protein in Escherichia coli.
J. Biosci. Bioeng.
PUBLISHED: 02-05-2014
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A co-expression system was established in Escherichia coli for enhancing the cellular expression of heat shock transcription factor, sigma 32 (?(32)). A Shine-Dalgarno sequence and the rpoH gene of E. coli, which encodes ?(32), were cloned into a bacterial plasmid containing a gene fusion encoding a doubly tagged N-acetyl-d-neuraminic acid aldolase (GST-Neu5Ac aldolase-5R). After the IPTG induction, a substantially higher level of sigma 32 was observed up to 3 h in the co-expression cells, but an enhancement in the solubility of target protein was manifest only in the first hour. Nevertheless, the co-expression of sigma 32 led to higher level of Neu5Ac aldolase enzymatic activity in both the soluble and insoluble (inclusion body) fractions. The Neu5Ac aldolase activity of the supernatant from the lysate of cells co-expressing GST-Neu5Ac aldolase-5R and recombinant ?(32) was 3.4-fold higher at 3 h postinduction than that in cells overexpressing GST-Neu5Ac aldolase-5R in the absence of recombinantly expressed ?(32). The results of acrylamide quenching indicated that the conformational quality of the fusion protein was improved by the co-expression of recombinant ?(32). Thus, the increased level of intracellular ?(32) might have created favorable conditions for the proper folding of recombinant proteins through the cooperative effects of chaperones/heat shock proteins expressed by the E. coli host, which resulted in smaller inclusion bodies, improved conformational quality and a higher specific activity of the overexpressed GST-Neu5Ac aldolase-5R protein.
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Acid-induced hyperalgesia and anxio-depressive comorbidity in rats.
Physiol. Behav.
PUBLISHED: 01-23-2014
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Fibromyalgia is a prevalent disorder characterized by chronic widespread pain (CWP) and complex comorbid symptoms. A CWP model is developed through repeated unilateral intramuscular injections of acid saline resulting in bilateral mechanical hyperalgesia in rats. The present study aims to evaluate whether both anxious and depressive comorbidities exist in this acid-induced pain model, similarly to patients with CWP syndromes. The anxiety-like behaviors were evaluated using the open field and elevated plus maze tests, and depression-like behaviors were measured by the forced swimming, sucrose consumption, and sucrose preference tests. The pain group receiving acidic saline displayed significantly lower paw withdrawal thresholds for 4weeks than animals in the vehicle group after repetitive intramuscular injections. The pain group showed a significantly shorter duration of exploring the central zone of the open field and the open arms of the elevated plus maze compared to the vehicle group. The pain group had a significantly lower preference for and consumption of the hedonic sucrose. Moreover, rats with chronic pain showed significantly longer immobility than the vehicle group in the forced swimming test. The results indicate that psychiatric behaviors are exacerbated in the CWP model. This study provides evidence for the validity of the acid-induced pain model analogous to patients with CWP syndromes.
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Adenosine A(2A) receptor up-regulates retinal wave frequency via starburst amacrine cells in the developing rat retina.
PLoS ONE
PUBLISHED: 01-01-2014
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Developing retinas display retinal waves, the patterned spontaneous activity essential for circuit refinement. During the first postnatal week in rodents, retinal waves are mediated by synaptic transmission between starburst amacrine cells (SACs) and retinal ganglion cells (RGCs). The neuromodulator adenosine is essential for the generation of retinal waves. However, the cellular basis underlying adenosine's regulation of retinal waves remains elusive. Here, we investigated whether and how the adenosine A(2A) receptor (A(2A)R) regulates retinal waves and whether A(2A)R regulation of retinal waves acts via presynaptic SACs.
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Neoadjuvant chemotherapy can improve outcome of colorectal cancer patients with unresectable metastasis.
Int J Colorectal Dis
PUBLISHED: 05-08-2013
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The prognosis for colorectal cancer (CRC) patients with unresectable metastases is dismal. This study compared outcomes of different metastatic treatments.
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Orchidstra: an integrated orchid functional genomics database.
Plant Cell Physiol.
PUBLISHED: 01-16-2013
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A specialized orchid database, named Orchidstra (URL: http://orchidstra.abrc.sinica.edu.tw), has been constructed to collect, annotate and share genomic information for orchid functional genomics studies. The Orchidaceae is a large family of Angiosperms that exhibits extraordinary biodiversity in terms of both the number of species and their distribution worldwide. Orchids exhibit many unique biological features; however, investigation of these traits is currently constrained due to the limited availability of genomic information. Transcriptome information for five orchid species and one commercial hybrid has been included in the Orchidstra database. Altogether, these comprise >380,000 non-redundant orchid transcript sequences, of which >110,000 are protein-coding genes. Sequences from the transcriptome shotgun assembly (TSA) were obtained either from output reads from next-generation sequencing technologies assembled into contigs, or from conventional cDNA library approaches. An annotation pipeline using Gene Ontology, KEGG and Pfam was built to assign gene descriptions and functional annotation to protein-coding genes. Deep sequencing of small RNA was also performed for Phalaenopsis aphrodite to search for microRNAs (miRNAs), extending the information archived for this species to miRNA annotation, precursors and putative target genes. The P. aphrodite transcriptome information was further used to design probes for an oligonucleotide microarray, and expression profiling analysis was carried out. The intensities of hybridized probes derived from microarray assays of various tissues were incorporated into the database as part of the functional evidence. In the future, the content of the Orchidstra database will be expanded with transcriptome data and genomic information from more orchid species.
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Serum immunoglobulin E can predict minimal change disease before renal biopsy.
Am. J. Med. Sci.
PUBLISHED: 08-27-2009
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Minimal change disease (MCD) is a major cause of nephrotic syndrome in both children and adults. The diagnosis of MCD in adults relies on findings of renal biopsy. Complications, although rare, may occur. This invasive procedure is also a suffering experience for some patients. Although Shu et al described the increase of serum immunoglobulin E (IgE) level in patients with MCD, whether IgE could be a predicting factor of MCD has not been determined.
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Demonstration of expression of a neuropeptide-encoding gene in crustacean hemocytes.
Comp. Biochem. Physiol., Part A Mol. Integr. Physiol.
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Crustacean hyperglycemic hormone (CHH) was originally identified in a neuroendocrine system-the X-organ/sinus gland complex. In this study, a cDNA (Prc-CHH) encoding CHH precursor was cloned from the hemocyte of the crayfish Procambarus clarkii. Analysis of tissues by a CHH-specific enzyme-linked immunosorbent assay (ELISA) confirmed the presence of CHH in hemocytes, the levels of which were much lower than those in the sinus gland, but 2 to 10 times higher than those in the thoracic and cerebral ganglia. Total hemocytes were separated by density gradient centrifugation into layers of hyaline cell (HC), semi-granular cell (SGC), and granular cell (GC). Analysis of extracts of each layer using ELISA revealed that CHH is present in GCs (202.8±86.7 fmol/mg protein) and SGCs (497.8±49.4 fmol/mg protein), but not in HCs. Finally, CHH stimulated the membrane-bound guanylyl cyclase (GC) activity of hemocytes in a dose-dependent manner. These data for the first time confirm that a crustacean neuropeptide-encoding gene is expressed in cells essential for immunity and its expression in hemocytes is cell type-specific. Effect of CHH on the membrane-bound GC activity of hemocyte suggests that hemocyte is a target site of CHH. Possible functions of the hemocyte-derived CHH are discussed.
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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.