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Find video protocols related to scientific articles indexed in Pubmed.
Rapid determination of major bioactive isoflavonoid compounds during the extraction process of kudzu (Pueraria lobata) by near-infrared transmission spectroscopy.
Spectrochim Acta A Mol Biomol Spectrosc
PUBLISHED: 07-27-2014
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Near-infrared (NIR) spectroscopy has been developed into an indispensable tool for both academic research and industrial quality control in a wide field of applications. The feasibility of NIR spectroscopy to monitor the concentration of puerarin, daidzin, daidzein and total isoflavonoid (TIF) during the extraction process of kudzu (Pueraria lobata) was verified in this work. NIR spectra were collected in transmission mode and pretreated with smoothing and derivative. Partial least square regression (PLSR) was used to establish calibration models. Three different variable selection methods, including correlation coefficient method, interval partial least squares (iPLS), and successive projections algorithm (SPA) were performed and compared with models based on all of the variables. The results showed that the approach was very efficient and environmentally friendly for rapid determination of the four quality indices (QIs) in the kudzu extraction process. This method established may have the potential to be used as a process analytical technological (PAT) tool in the future.
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Improved production, purification and bioactivity of a polysaccharide from submerged cultured Ganoderma lucidum.
Arch. Pharm. Res.
PUBLISHED: 04-02-2014
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Polysaccharides from Ganoderma lucidum showed multiple biological activities, such as immuno-modulating, antitumor, antioxidant, and hepatoprotective activity, etc. Adlay oil was added into the media to enhance polysaccharide production by submerged culture of G. lucidum in this work. The results revealed the optimal concentration of adlay oil was 1.5 % for polysaccharide production of G. lucidum. Analysis of the polysaccharide components confirmed that no novel components were biosynthesized by the addition of adlay oil. The main fraction of extracellular polysaccharide, GLEP-2, was isolated from the submerged culture broth of G. lucidum by ethanol precipitation, filtration, DEAE cellulose-52 and Sepharose CL-6B chromatography. GLEP-2, which was composed of glucose, galactose, mannose, arabinose, and rhamnose in a ratio of 332:55:32:13:3 respectively, had an average molecular weight of ~2.08 × 10(4) Da. The bioactivity tests demonstrated that GLEP-2 enhanced the T lymphocyte proliferation significantly at a concentration of 200 ?g/mL and B lymphocyte proliferation at lower concentrations of 50 ?g/mL. The results suggest polysaccharides from the submerged culture of G. lucidum are potential candidates for further development and possible commercial applications, especially in the pharmaceutical and functional foods industries.
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A convenient synthesis of novel aza-C-disaccharide analogues.
Carbohydr. Res.
PUBLISHED: 03-27-2014
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Novel aza-C-disaccharide analogues have been conveniently synthesized by using the isoxazoline-linked C-disaccharide derivatives as the intermediates. Firstly, the CN of isoxazoline was reduced to C-N by using DIBAL-H as reducing agent, then followed by the tandem multi-step reactions through catalytic hydrogenation with Pd(OH)2/C involving debenzylated, reductive cleavage of the N-O, condensation-cyclization of the aldehyde and the in situ generated amine group to form imine CN and then CN hydrogenation to form C-N, thus providing a practical and new access to the synthesis of novel aza-C-disaccharide analogues.
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Improved Polysaccharide Production in Submerged Culture of Ganoderma lucidum by the Addition of Coixenolide.
Appl. Biochem. Biotechnol.
PUBLISHED: 07-15-2013
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Polysaccharides from Ganoderma lucidum have various bioactivities and have been widely used as nutraceuticals and functional foods. Coixenolide was added into the media to enhance the production of mycelia biomass and polysaccharides in the submerged culture of G. lucidum in this work. The results showed that when a level of 0.2 % coixenolide was added at day 1, the biomass, exopolysaccharide, and intracellular polysaccharide reached 5.224, 0.222, and 0.399 g l(-1), respectively, which were 1.39-fold, 2.58-fold, and 2.24-fold compared to that of control. Analysis of the fermentation kinetics of G. lucidum suggested that glucose concentration in the coixenolide-added group decreased more quickly as compared to the control group from days 3 to 9 of the fermentation process, and the polysaccharides biosynthesis were promoted at the same culture period. However, the culture pH profile was not affected by the addition of coixenolide. Enzyme activities analysis indicated that coixenolide affected the synthesis level of phosphoglucose isomerase and ?-phosphoglucomutase.
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Identification and polymorphism discovery of the cathelicidins, Lf-CATHs in ranid amphibian (Limnonectes fragilis).
FEBS J.
PUBLISHED: 07-11-2013
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To protect themselves against the invasion of microorganisms, amphibians, especially the Rana frogs, are possibly equipped with complex combinations of antimicrobial peptides (AMPs). The two major AMP families, ranid skin secretion AMPs and cathelicidins might together constitute the host innate immune system of amphibians. Cathelicidins are a group of cationic peptides found in leukocytes and epithelial cells, and they play a central role in the early innate immune defense found in virtually all species of mammals. However, they have rarely been reported from amphibians. Here, we report the identification and discovery of polymorphism cathelicidins in Limnonectes fragilis. The expression profile indicated high cathelicidin transcript levels in frog spleen, liver and kidney, but lower levels in lung, skin and stomach. According to the amphibians unique proteolytic pattern, R125 and L121 of the prepropeptides are predicted to be the processing positions for protease to generate the mature peptides, Lf-CATH1 and -2, respectively. Both consist of 30 amino acid residues, of which two were cysteines positionally conserved among a few known amphibian cathelicidins. Homology modeling analysis revealed that Lf-CATH1 and -2 adopt a tertiary structure with a mostly ? helix that is representative of small cationic cathelicidin family peptides. Recombinant Lf-CATH1 (rLf-CATH1) was produced in Escherichia coli. Synthetic Lf-CATH1 and -2 displayed potent antimicrobial activities in vitro against a broad spectrum of microorganisms, including standard and clinically isolated drug-resistant strains, while showing neglectable hemolysis and cytotoxicities.
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A mycobacteriophage-derived trehalose-6,6-dimycolate-binding peptide containing both antimycobacterial and anti-inflammatory abilities.
FASEB J.
PUBLISHED: 04-19-2013
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Bacteriophages, the viruses of eubacteria, have developed unique mechanisms to interact with their host bacteria. They have been viewed as potential antibacterial therapeutics. Mycobacteriophage-derived compounds may interact with Mycobacterium tuberculosis (MTB) and/or its components, such as the cord factor, trehalose-6,6-dimycolate (TDM), which is the most abundant glycolipid produced on the surface of MTB. TDM emulsion injected intravenously into mice induces lung immunopathology that mimics many aspects of MTB infection. Thus, TDM is an important target for anti-MTB agent development. On the basis of genomics information of mycobacteriophages, 200 peptides were synthesized. Their effects on MTB, their interactions with TDM, and anti-inflammatory activities were tested. One of them (PK34) showed MTB-killing activity with a minimal inhibitory concentration of 50 ?g/ml and TDM-binding ability. In a mouse model, PK34 showed comparable ability to clear MTB as rifampin did in vivo. It also exerted strong activity to inhibit MTB or TDM-induced inflammation in vivo. PK34 significantly inhibited inflammatory cytokines secretions by inactivating MAPK and PKB signals while it maintained certain proinflammatory cytokine production. It is possible to prospect for TDM-binding and/or anti-MTB peptides by mining the mycobacteriophages genome. In addition to its direct MTB-killing ability, PK34 might be a useful adjunct in the treatment of granulomatous inflammation occurring during mycobacterial infection or a template for developing antituberculosis (TB) agents because of its immunoregulative effects. As a TDM-binding peptide, PK34 may be a promising tool to study TDMs interactions with corresponding receptors and signal pathways.
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Effect of hypobaric storage on quality, antioxidant enzyme and antioxidant capability of the Chinese bayberry fruits.
Chem Cent J
PUBLISHED: 01-10-2013
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The Chinese bayberry (Myrica rubra Sieb. and Zucc.) is a subtropical fruit native to China, with unique flavor, sweet and sour taste, and high nutrition and health values. The fruit is highly perishable and susceptible to mechanical injury, physiological deterioration and fungal decay once harvested. This study was to investigate the effect of hypobaric storage on the quality of Chinese bayberry fruit and then develop storage technology to prolong the supply of the fruit.
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Copper(I)-catalyzed synthesis of 1,3-enynes via coupling between vinyl halides and alkynes or domino coupling of vinyl halides.
Org. Biomol. Chem.
PUBLISHED: 09-14-2011
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1,3-Enynes were easily prepared from coupling between vinyl halides and alkynes or domino coupling of vinyl halides in the presence of copper iodide. It is noteworthy that the double-bond geometry of the vinyl halides was retained during the reaction. This ligand-free protocol is potentially useful and practical.
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Highly effective copper-catalyzed decarboxylative coupling of aryl halides with alkynyl carboxylic acids.
Org. Biomol. Chem.
PUBLISHED: 09-08-2011
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We have developed a highly effective copper-catalyzed decarboxylative coupling of alkynylcarboxylic acids with various aryl and alkyl halides at 2 mol% loading of copper. This method is simple, economical and practical for the synthesis of disubstituted alkyne compounds.
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Proteomic analysis of skin defensive factors of tree frog Hyla simplex.
J. Proteome Res.
PUBLISHED: 08-09-2011
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Tree frogs produce a variety of skin defensive chemicals against many biotic and abiotic risk factors for their everyday survival. By proteomics or peptidomics and coupling transcriptome analysis with pharmacological testings, 27 peptides or proteins belonging to 9 families, which act mainly as defensive functions, were identified and characterized from skin secretions of the tree frog, Hyla simplex. They are: (1) a novel family of peptides with EGF- and VEGF-releasing activities; (2) a novel family of analgesic peptides; (3) a family of neurotoxins acting on sodium channel; (4) a snake venom-like presynaptically active neurotoxin; (5) a snake venom-like neurotoxin targeting cyclic nucleotide-gated ion channels; (6) a tachykinin-like peptide, which is the first report from tree frogs; (7) two antimicrobial peptides; (8) a alpha-1-antitrypsin-like serpin; and (9) a wasp venom-like toxin with serine protease inhibitors activity. Families of 1, 2, 4, 5, and 8 proteins or peptides are first reported in amphibians. The chemical array in the tree frog skin shares some similarities with snake venoms. Most of these components in this tree frog help defend against predators, heal wounds, or attenuate suffering.
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Amphibian cathelicidin fills the evolutionary gap of cathelicidin in vertebrate.
Amino Acids
PUBLISHED: 07-09-2011
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Cathelicidins comprise a family of antimicrobial peptides (AMPs) sharing a highly conserved cathelin domain, and play a central role in the innate defense against infection in most of vertebrates. But so far it has not yet been found in amphibians although a large number of other groups of AMPs have been identified. In the current work, the first amphibian cathelicidin (cathelicidin-AL) has been characterized from the frog skin of Amolops loloensis. Cathelicidin-AL (RRSRRGRGGGRRGGSGGRGGRGGGGRSGAGSSIAGVGSRGGGGGRHYA) is a cationic peptide containing 48 amino acid residues (aa) with 12 basic aa and no acidic aa. The chemical synthesized peptide efficiently killed bacteria and some fungal species including clinically isolated drug-resistance microorganisms. The cDNA encoding cathelicidin-AL precursor was cloned from the skin cDNA library of A. loloensis. As other cathelicidins, the precursor of cathelicidin-AL also contains highly conserved anionic cathelin domain of cysteine proteinase inhibitor followed by the AMP fragment at C-terminus. Phylogenetic analysis revealed that as connecting link, the amphibian cathelicidin predates reptilia but postdates fish cathelicidin. The peptide purification combined with gene cloning results confirms the presence of cathelicidin in amphibians and filled the evolutionary gap of cathelicidin in vertebrate, considering amphibians special niche as the animals bridging the evolutionary land-water gap.
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Bi-functional peptides with both trypsin-inhibitory and antimicrobial activities are frequent defensive molecules in Ranidae amphibian skins.
Amino Acids
PUBLISHED: 06-15-2011
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Amphibian skins act as the first line against noxious aggression by microorganisms, parasites, and predators. Anti-microorganism activity is an important task of amphibian skins. A large amount of gene-encoded antimicrobial peptides (AMPs) has been identified from amphibian skins. Only a few of small protease inhibitors have been found in amphibian skins. From skin secretions of 5 species (Odorrana livida, Hylarana nigrovittata, Limnonectes kuhlii, Odorrana grahami, and Amolops loloensis) of Ranidae frogs, 16 small serine protease inhibitor peptides have been purified and characterized. They have lengths of 17-20 amino acid residues (aa). All of them are encoded by precursors with length of 65-70 aa. These small peptides show strong trypsin-inhibitory abilities. Some of them can exert antimicrobial activities. They share the conserved GCWTKSXXPKPC fragment in their primary structures, suggesting they belong to the same families of peptide. Signal peptides of precursors encoding these serine protease inhibitors share obvious sequence similarity with those of precursors encoding AMPs from Ranidae frogs. The current results suggest that these small serine protease inhibitors are the common defensive compounds in frog skin of Ranidae as amphibian skin AMPs.
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Ligand-free highly effective iron/copper co-catalyzed formation of dimeric aryl ethers or sulfides.
Org. Biomol. Chem.
PUBLISHED: 06-07-2011
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Highly selective coupling of diiodoarenes with phenols or phenthiols can be performed by using a low-cost, benign character and readily available Fe/Cu catalytic system in the absence of ligands. It is noteworthy that the desired dimeric aryl ethers or sulfides could be obtained in high yields by coupling between diiodoarenes and phenols, or diphenols with aryl iodides.
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There are abundant antimicrobial peptides in brains of two kinds of Bombina toads.
J. Proteome Res.
PUBLISHED: 03-10-2011
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It is well-known that there is a large amount of antimicrobial peptides in amphibian skins but few antimicrobial peptides are found in amphibian brains. Twenty-two and four antimicrobial peptides were purified and characterized from the brain homogenate of Bombina maxima and B. microdeladigitora, respectively. One hundred fifty-eight cDNA clones encoding 79 antimicrobial peptides were isolated from brain cDNA libraries of B. maxima and B. microdeladigitora. These antimicrobial peptides belong to two peptide groups (maximin and maximin-H). Twenty of them are identical to previously reported antimicrobial peptides (maximin 1-8, 10, 11, maximin H1, 3-5, 7, 9, 10, 12, 15, 16) from B. maxima skin secretions. Fifty-nine of them are novel antimicrobial peptides. Some of these antimicrobial peptides showed strong antimicrobial activities against tested microorganism strains including Gram-positive and -negative bacteria and fungi. The current diversity in peptide coding cDNA sequences is, to our knowledge, the most extreme yet described for any animal brains. The extreme diversity may give rise to interest to prospect the actual functions of antimicrobial peptides in amphibian brains.
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Cathelicidin-BF, a snake cathelicidin-derived antimicrobial peptide, could be an excellent therapeutic agent for acne vulgaris.
PLoS ONE
PUBLISHED: 02-19-2011
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Cathelicidins are a family of antimicrobial peptides acting as multifunctional effector molecules in innate immunity. Cathelicidin-BF has been purified from the snake venoms of Bungarus fasciatus and it is the first identified cathelicidin antimicrobial peptide in reptiles. In this study, cathelicidin-BF was found exerting strong antibacterial activities against Propionibacterium acnes. Its minimal inhibitory concentration against two strains of P. acnes was 4.7 µg/ml. Cathelicidin-BF also effectively killed other microorganisms including Staphylococcus epidermidis, which was possible pathogen for acne vulgaris. Cathelicidin-BF significantly inhibited pro-inflammatory factors secretion in human monocytic cells and P. acnes-induced O2.- production of human HaCaT keratinocyte cells. Observed by scanning electron microscopy, the surfaces of the treated pathogens underwent obvious morphological changes compared with the untreated controls, suggesting that this antimicrobial peptide exerts its action by disrupting membranes of microorganisms. The efficacy of cathelicidin-BF gel topical administering was evaluated in experimental mice skin colonization model. In vivo anti-inflammatory effects of cathelicidin-BF were confirmed by relieving P. acnes-induced mice ear swelling and granulomatous inflammation. The anti-inflammatory effects combined with potent antimicrobial activities and O2.- production inhibition activities of cathelicidin-BF indicate its potential as a novel therapeutic option for acne vulgaris.
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Analgesic and anti-inflammatory effects of the amphibian neurotoxin, anntoxin.
Biochimie
PUBLISHED: 02-17-2011
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Anntoxin is the first gene-encoded neurotoxin identified from amphibians, which is a 60-residue neurotoxin peptide, acting as an inhibitor of tetrodotoxin-sensitive (TTX-S) voltage-gated sodium channel (VGSC). Sodium channels have been considered as therapeutic targets for pain. Several animal models of persistent inflammatory and neuropathic pain (tail-flick test, hot plate test, acetic acid-induced writhing test, formalin-induced paw licking, carrageenan-induced paw edema) were used to test analgesic functions of recombinant anntoxin (r-anntoxin). In all these animal models, r-anntoxin showed strong analgesic functions. R-anntoxin obviously inhibited secretions of both tumor necrosis factor alpha (TNF-?) and cyclooxygenase-2 (COX-2). Histopathological study indicated that r-anntoxin reduced the edematous epidermis induced by carrageenan. All these results indicate that r-anntoxin has strong analgesic and anti-inflammatory activities.
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A bi-functional anti-thrombosis protein containing both direct-acting fibrin(ogen)olytic and plasminogen-activating activities.
PLoS ONE
PUBLISHED: 02-03-2011
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Direct-acting fibrin(ogen)olytic agents such as plasmin have been proved to contain effective and safety thrombolytic potential. Unfortunately, plasmin is ineffective when administered by the intravenous route because it was neutralized by plasma antiplasmin. Direct-acting fibrin(ogen)olytic agents with resistance against antiplasmin will brighten the prospect of anti-thrombosis. As reported in Compendium of Materia Medica, the insect of Eupolyphaga sinensis Walker has been used as traditional anti-thrombosis medicine without bleeding risk for several hundreds years. Currently, we have identified a fibrin(ogen)olytic protein (Eupolytin1) containing both fibrin(ogen)olytic and plasminogen-activating (PA) activities from the beetle, E. sinensis.
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GPU acceleration of Dock6s Amber scoring computation.
Adv. Exp. Med. Biol.
PUBLISHED: 09-25-2010
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Dressing the problem of virtual screening is a long-term goal in the drug discovery field, which if properly solved, can significantly shorten new drugs R&D cycle. The scoring functionality that evaluates the fitness of the docking result is one of the major challenges in virtual screening. In general, scoring functionality in docking requires a large amount of floating-point calculations, which usually takes several weeks or even months to be finished. This time-consuming procedure is unacceptable, especially when highly fatal and infectious virus arises such as SARS and H1N1, which forces the scoring task to be done in a limited time. This paper presents how to leverage the computational power of GPU to accelerate Dock6s (http://dock.compbio.ucsf.edu/DOCK_6/) Amber (J. Comput. Chem. 25: 1157-1174, 2004) scoring with NVIDIA CUDA (NVIDIA Corporation Technical Staff, Compute Unified Device Architecture - Programming Guide, NVIDIA Corporation, 2008) (Compute Unified Device Architecture) platform. We also discuss many factors that will greatly influence the performance after porting the Amber scoring to GPU, including thread management, data transfer, and divergence hidden. Our experiments show that the GPU-accelerated Amber scoring achieves a 6.5× speedup with respect to the original version running on AMD dual-core CPU for the same problem size. This acceleration makes the Amber scoring more competitive and efficient for large-scale virtual screening problems.
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Two novel antimicrobial peptides from skin secretions of the frog, Rana nigrovittata.
J. Pept. Sci.
PUBLISHED: 07-13-2010
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Two novel antimicrobial peptides with similarity to brevinin-2 family are purified and characterized from the skin secretions of the frog, Rana nigrovittata. Their amino acid sequences were determined as GAFGNFLKGVAKKAGLKILSIAQCKLSGTC (brevinin-2-RN1) and GAFGNFLKGVAKKAGLKILSIAQCKLFGTC (brevinin-2-RN2), respectively, by Edman degradation. Different from brevinin-2, which is composed of 33 amino acid residues (aa), both brevinin-2-RN1 and -RN2 contain 30 aa. Five cDNA sequences (Genbank accession numbers, EU136465-9) encoding precursors of brevinin-2-RN1 and -RN2 were screened from the skin cDNA library of R. nigrovittata. These precursors are composed of 72 aa including a predicted signal peptide, an acidic spacer peptide, and a mature brevinin-2-RN. Both brevinin-2-RN1 and -RN2 showed strong antimicrobial activities against gram-positive and gram-negative bacteria and fungi. The current work identified and characterized two novel antimicrobial peptides with unique primary structure.
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Two immunoregulatory peptides with antioxidant activity from tick salivary glands.
J. Biol. Chem.
PUBLISHED: 02-23-2010
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Ticks are blood-feeding arthropods that may secrete immunosuppressant molecules, which inhibit host inflammatory and immune responses and provide survival advantages to pathogens at tick bleeding sites in hosts. In the current work, two families of immunoregulatory peptides, hyalomin-A and -B, were first identified from salivary glands of hard tick Hyalomma asiaticum asiaticum. Three copies of hyalomin-A are encoded by an identical gene and released from the same protein precursor. Both hyalomin-A and -B can exert significant anti-inflammatory functions, either by directly inhibiting host secretion of inflammatory factors such as tumor necrosis factor-alpha, monocyte chemotectic protein-1, and interferon-gamma or by indirectly increasing the secretion of immunosuppressant cytokine of interleukin-10. Hyalomin-A and -B were both found to potently scavenge free radical in vitro in a rapid manner and inhibited adjuvant-induced inflammation in mouse models in vivo. The JNK/SAPK subgroup of the MAPK signaling pathway was involved in such immunoregulatory functions of hyalomin-A and -B. These results showed that immunoregulatory peptides of tick salivary glands suppress host inflammatory response by modulating cytokine secretion and detoxifying reactive oxygen species.
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Frog skins keep redox homeostasis by antioxidant peptides with rapid radical scavenging ability.
Free Radic. Biol. Med.
PUBLISHED: 01-14-2010
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The question of how amphibians can protect themselves from reactive oxygen species when exposed to the sun in an oxygen-rich atmosphere is important and interesting, not only from an evolutionary viewpoint, but also as a primer for researchers interested in mammalian skin biology, in which such peptide systems for antioxidant defense are not well studied. The identification of an antioxidant peptide named antioxidin-RL from frog (Odorrana livida) skin in this report supports the idea that a peptide antioxidant system may be a widespread antioxidant strategy among amphibian skins. Its ability to eliminate most of the 2,2-azino-bis(3-ethylbenzthiazoline-6-sulfonic acid) radical tested within 2 s, which is much faster than the commercial antioxidant factor butylated hydroxytoluene, suggests that it has a potentially large impact on redox homeostasis in amphibian skins. Cys10 is proven to be responsible for its rapid radical scavenging function and tyrosines take part in the binding of antioxidin-RL to radicals according to our nuclear magnetic resonance assay.
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Cloning and characterization of the first amphibian bradykinin gene.
Biochimie
PUBLISHED: 11-09-2009
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More than ten bradykinin-related peptides and their cDNAs have been identified from amphibians, but their genes are unknown. In present study, four cDNAs encoding one, two, four and six copies of bradykinin-related peptides were cloned from the frog (Odorrana grahami) skin cDNA library, respectively. Three bradykinin-related peptides (bradykinin, Thr6-bradykinin, Leu5Thr6-bradykinin) were deduced from these four cDNA sequences. Based on the cDNA sequence, the gene sequence encoding an amphibian bradykinin-related peptide from O. grahami was determined. It is composed of 7481 base pairs including two exons and two introns. The first exon codes signal peptide and the second exon codes acidic spacer peptide and Thr6-bradykinin. The promoter region of the bradykinin gene contains several putative recognition sites for nuclear factors, such as SRY, GATA-1, LYF-1, DeltaE, CDXA, NKX-2.5, MIF1 and S8. The current work may facilitate to understand the regulation and possible functions of amphibian skin bradykinin-related peptides.
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Five novel antimicrobial peptides from skin secretions of the frog, Amolops loloensis.
Comp. Biochem. Physiol. B, Biochem. Mol. Biol.
PUBLISHED: 07-25-2009
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While investigating antimicrobial peptide diversity of Amolops loloensis, five novel antimicrobial peptides belonging to two families were identified from skin secretions of this frog. The first family including two members is esculentin-2-AL (esculentin-2-ALa and -ALb); the second family including three members is temporin-AL (temporin-ALd to -ALf). The family of esculentin-2-AL is composed of 37 amino acid residues (aa); the family of temporin-AL is composed of 16, 13 and 10 aa, respectively. All of these antimicrobial peptides showed antimicrobial activities against tested microorganisms. cDNAs encoding precursors of esculentin-2-ALs and temporin-ALs were cloned from the skin cDNA library of A. loloensis. All the precursors share similar overall structures. There is a typical prohormone processing signal (Lys-Arg) located between the acidic propiece and the mature peptide. The antimicrobial peptide family of esculentin-2 is firstly reported in the genus of Amolops. Combined with previous reports, a total of four antimicrobial peptide families have been identified from the genus of Amolops; three of them are also found in the genus of Rana. These results suggest the possible evolutionary connection between the genera Amolops and Rana.
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The first gene-encoded amphibian neurotoxin.
J. Biol. Chem.
PUBLISHED: 06-17-2009
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Many gene-encoded neurotoxins with various functions have been discovered in fish, reptiles, and mammals. A novel 60-residue neurotoxin peptide (anntoxin) that inhibited tetrodotoxin-sensitive (TTX-S) voltage-gated sodium channel (VGSC) was purified and characterized from the skin secretions of the tree frog Hyla annectans (Jerdon). This is the first gene-encoded neurotoxin found in amphibians. The IC50 of anntoxin for the TTX-S channel was about 3.4 microM. Anntoxin shares sequence homology with Kunitz-type toxins but contains only two of three highly conserved cysteine bridges, which are typically found in these small, basic neurotoxin modules, i.e. snake dendrotoxins. Anntoxin showed an inhibitory ability against trypsin with an inhibitory constant (Ki) of 0.025 microM. Anntoxin was distributed in skin, brain, stomach, and liver with a concentration of 25, 7, 3, and 2 microg/g wet tissue, respectively. H. annectans lives on trees or other plants for its entire life cycle, and its skin contains the largest amount of anntoxin, which possibly helps defend against various aggressors or predators. A low dose of anntoxin was found to induce lethal toxicity for several potential predators, including the insect, snake, bird, and mouse. The tissue distribution and functional properties of the current toxin may provide insights into the ecological adaptation of tree-living amphibians.
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Anti-thrombosis repertoire of blood-feeding horsefly salivary glands.
Mol. Cell Proteomics
PUBLISHED: 06-16-2009
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Blood-feeding arthropods rely heavily on the pharmacological properties of their saliva to get a blood meal and suppress immune reactions of hosts. Little information is available on antihemostatic substances in horsefly salivary glands although their saliva has been thought to contain wide range of physiologically active molecules. In traditional Eastern medicine, horseflies are used as anti-thrombosis material for hundreds of years. By proteomics coupling transcriptome analysis with pharmacological testing, several families of proteins or peptides, which exert mainly on anti-thrombosis functions, were identified and characterized from 60,000 pairs of salivary glands of the horsefly Tabanus yao Macquart (Diptera, Tabanidae). They are: (I) ten fibrin(ogen)olytic enzymes, which hydrolyze specially alpha chain of fibrin(ogen) and are the first family of fibrin(ogen)olytic enzymes purified and characterized from arthropods; (II) another fibrin(ogen)olytic enzyme, which hydrolyzes both alpha and beta chain of fibrin(ogen); (III) ten Arg-Gly-Asp-motif containing proteins acting as platelet aggregation inhibitors; (IV) five thrombin inhibitor peptides; (V) three vasodilator peptides; (VI) one apyrase acting as platelet aggregation inhibitor; (VII) one peroxidase with both platelet aggregation inhibitory and vasodilator activities. The first three families are belonging to antigen five proteins, which show obvious similarity with insect allergens. They are the first members of the antigen 5 family found in salivary glands of blood sucking arthropods to have anti-thromobosis function. The current results imply a possible evolution from allergens of blood-sucking insects to anti-thrombosis agents. The extreme diversity of horsefly anti-thrombosis components also reveals the anti-thrombosis molecular mechanisms of the traditional Eastern medicine insect material.
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Peptidomics and genomics analysis of novel antimicrobial peptides from the frog, Rana nigrovittata.
Genomics
PUBLISHED: 05-20-2009
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Much attention has been paid on amphibian peptides for their wide-ranging pharmacological properties, clinical potential, and gene-encoded origin. More than 300 antimicrobial peptides (AMPs) from amphibians have been studied. Peptidomics and genomics analysis combined with functional test including microorganism killing, histamine-releasing, and mast cell degranulation was used to investigate antimicrobial peptide diversity. Thirty-four novel AMPs from skin secretions of Rana nigrovittata were identified in current work, and they belong to 9 families, including 6 novel families. Other three families are classified into rugosin, gaegurin, and temporin family of amphibian AMP, respectively. These AMPs share highly conserved preproregions including signal peptides and spacer acidic peptides, while greatly diversified on mature peptides structures. In this work, peptidomics combined with genomics analysis was confirmed to be an effective way to identify amphibian AMPs, especially novel families. Some AMPs reported here will provide leading molecules for designing novel antimicrobial agents.
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The genome of the cucumber, Cucumis sativus L.
Nat. Genet.
PUBLISHED: 05-06-2009
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Cucumber is an economically important crop as well as a model system for sex determination studies and plant vascular biology. Here we report the draft genome sequence of Cucumis sativus var. sativus L., assembled using a novel combination of traditional Sanger and next-generation Illumina GA sequencing technologies to obtain 72.2-fold genome coverage. The absence of recent whole-genome duplication, along with the presence of few tandem duplications, explains the small number of genes in the cucumber. Our study establishes that five of the cucumbers seven chromosomes arose from fusions of ten ancestral chromosomes after divergence from Cucumis melo. The sequenced cucumber genome affords insight into traits such as its sex expression, disease resistance, biosynthesis of cucurbitacin and fresh green odor. We also identify 686 gene clusters related to phloem function. The cucumber genome provides a valuable resource for developing elite cultivars and for studying the evolution and function of the plant vascular system.
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Antioxidant peptidomics reveals novel skin antioxidant system.
Mol. Cell Proteomics
PUBLISHED: 04-30-2009
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It is generally agreed that reactive oxygen species (ROS) contribute to skin aging, skin disorders, and skin diseases. Skin possesses an extremely efficient antioxidant system. This antioxidant activity is conferred by two systems: antioxidant enzymes and small molecules that can scavenge ROS by donating electrons. No gene-encoded secreted ROS scavengers have been reported. Amphibian skin is a multifunctional organ acting in defense, respiration, and water regulation, although it seems susceptible. Amphibian skins are easily harmed by biological or non-biological attacks such as microorganism infection or radiation injury. Among vertebrates, skins of amphibian are exposed to more dangers of radiation injury than others. Radiation toxicity occurs by directly attacking the genetic material and/or by generating ROS. In addition, amphibian skin respiration and inflammatory response also induce ROS generation. It is rational to hypothesize that amphibian skins should have potent free radical scavenging and radioprotective ability for their survival. Rana pleuraden is distributed in Southwest of China; it lives in the subtropical plateau (altitude around 2300 m) where there is strong ultraviolet radiation and long duration of sunshine. By peptidomics and genomics approaches, a large amount of antioxidant peptides belonging to 11 different groups with variable structures were isolated from the skin secretions of R. pleuraden. Their free radical scavenging and anti-inflammatory abilities were studied. All of these peptide share highly homologous preproregions, although mature antioxidant peptides have very divergent primary structures, suggesting the possibility of a common ancestor. Some peptides were also found to have multifunctional properties, such as combined antioxidant, anti-inflammatory, and antimicrobial activities. According to our knowledge, no gene-encoded specific antioxidant peptides have been reported except metallothionein. Our work possibly reveals a new skin antioxidant system. The current work also provides a large amount of peptide candidates with medical-pharmaceutical significance.
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Purification, characterization and cloning of two novel tigerinin-like peptides from skin secretions of Fejervarya cancrivora.
Peptides
PUBLISHED: 03-02-2009
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While investigating the innate defense of brackish water-living amphibian and its comparison with freshwater-living amphibians, two novel 12-residue antimicrobial peptides were purified from the skin secretions of the crab-eating frog, Fejervarya cancrivora which typically inhabits brackish water of mangrove forests of Southeast Asia. These two antimicrobial peptides, tigerinin-RC1 and -RC2 share significant structural similarity with tigerinins found in the skin of Indian frog, Hoplobatrachus tigerinus. cDNAs encoding tigerinin-RC1 and -RC2 were also cloned from the skin cDNA library of F. cancrivora. Tigerinin-RC precursors are composed of 71 amino acid residues including a signal peptide, acidic spacer peptide, which are very similar to other amphibian antimicrobial peptide precursors and mature tigerinin-RC. The current results confirmed that both amphibians inhabiting freshwater and brackish water share the same antimicrobial peptide family to exert innate defense. Furthermore, the current work was also the first report of precursor and cDNA cloning of the tigerinin antimicrobial peptide family.
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The oyster genome reveals stress adaptation and complexity of shell formation.
Nature
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The Pacific oyster Crassostrea gigas belongs to one of the most species-rich but genomically poorly explored phyla, the Mollusca. Here we report the sequencing and assembly of the oyster genome using short reads and a fosmid-pooling strategy, along with transcriptomes of development and stress response and the proteome of the shell. The oyster genome is highly polymorphic and rich in repetitive sequences, with some transposable elements still actively shaping variation. Transcriptome studies reveal an extensive set of genes responding to environmental stress. The expansion of genes coding for heat shock protein 70 and inhibitors of apoptosis is probably central to the oysters adaptation to sessile life in the highly stressful intertidal zone. Our analyses also show that shell formation in molluscs is more complex than currently understood and involves extensive participation of cells and their exosomes. The oyster genome sequence fills a void in our understanding of the Lophotrochozoa.
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Copper-catalyzed decarboxylative C(sp2)-C(sp3) coupling reactions via radical mechanism.
Chem. Commun. (Camb.)
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We have successfully developed an example of copper-catalyzed decarboxylative C(sp(2))-C(sp(3)) coupling reactions via C-H functionalization for the first time. It is noteworthy that our catalytic system is very stable, low-cost, palladium-free, ligand-free, and easily accessible.
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Proteomics and transcriptome analysis coupled with pharmacological test reveals the diversity of anti-thrombosis proteins from the medicinal insect, Eupolyphaga sinensis.
Insect Biochem. Mol. Biol.
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The insect of Eupolyphaga sinensis Walker has been used as traditional anti-thrombosis medicine without bleeding risk for several hundreds years in eastern countries. Our previous work has identified a bi-functional anti-thrombosis protein containing both direct-acting fibrin(ogen)olytic and plasminogen-activating activities from the insect. By proteomics and transcriptome analysis, 105 serine proteases belonging to four families were identified from the ground beetle, E. sinensis and the classification is for serine proteases of this organism. Pharmacological test indicated that 5 (eupolytin 1-5) of them have the abilities to hydrolyze fibrin(ogen) and/or activate plasminogen. The current work revealed the extreme diversity of anti-thrombosis components in E. sinensis and anti-thrombosis molecular mechanisms of the traditional medicinal insect, and provided many templates for the development of new thrombolytic agents. Especially, these proteins, which contain both plasmin- and PA (plasminogen-activating)-like activities, are excellent candidates for anti-thrombosis medicines.
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The ligand and base-free Pd-catalyzed oxidative Heck reaction of arylboronic acids and olefins.
Org. Biomol. Chem.
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Highly effective Pd-catalyzed Heck-type oxidative couplings between arylboronic acids and terminal olefins were reported. It is noteworthy that such reactions could be carried out in the absence of the base and the ligand.
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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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