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Find video protocols related to scientific articles indexed in Pubmed.
PAIDB v2.0: exploration and analysis of pathogenicity and resistance islands.
Nucleic Acids Res.
PUBLISHED: 10-23-2014
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Pathogenicity is a complex multifactorial process confounded by the concerted activity of genetic regions associated with virulence and/or resistance determinants. Pathogenicity islands (PAIs) and resistance islands (REIs) are key to the evolution of pathogens and appear to play complimentary roles in the process of bacterial infection. While PAIs promote disease development, REIs give a fitness advantage to the host against multiple antimicrobial agents. The Pathogenicity Island Database (PAIDB, http://www.paidb.re.kr) has been the only database dedicated to providing comprehensive information on all reported PAIs and candidate PAIs in prokaryotic genomes. In this study, we present PAIDB v2.0, whose functionality is extended to incorporate REIs. PAIDB v2.0 contains 223 types of PAIs with 1331 accessions, and 88 types of REIs with 108 accessions. With an improved detection scheme, 2673 prokaryotic genomes were analyzed to locate candidate PAIs and REIs. With additional quantitative and qualitative advancements in database content and detection accuracy, PAIDB will continue to facilitate pathogenomic studies of both pathogenic and non-pathogenic organisms.
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Single CdTe microwire photodetectors grown by close-spaced sublimation method.
Opt Express
PUBLISHED: 10-17-2014
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We demonstrate single CdTe microwire field-effect transistors (FETs) that are highly sensitive to ultraviolet (UV) light. Dense CdTe microwires were catalytically grown using a close-spaced sublimation system. Structural, morphological and transport properties in conjunction with the optoelectronic properties were systemically investigated. CdTe microwire FETs exhibited p-type behaviors with field-effect mobilities up to 1.1 × 10-3 cm2 V-1 s-1. Optoelectronic properties of our CdTe microwire FETs were studied under dark and UV-illumination conditions, where photoresponse was highly dependent on the back-gate bias conditions. Our CdTe microwire FET-based photodetectors are promising for high-performance micro-optoelectronic applications.
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Sulfitobacter geojensis sp. nov., Sulfitobacter noctilucae sp. nov., and Sulfitobacter noctilucicola sp. nov., isolated from coastal seawater.
Int. J. Syst. Evol. Microbiol.
PUBLISHED: 08-13-2014
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Four Gram-stain-negative, aerobic, rod-shaped bacterial strains, MM-124, MM-126, NB-68 and NB-77, were isolated from the coastal seawater or a region with a bloom of sea sparkle around Geoje island in Korea. The sequence similarity values of the 16S rRNA gene between the isolates and Sulfitobacter mediterraneus DSM 12244(T) ranged from 97.7 to 98.2?%, and phylogenetic relationships suggested that they belong to a phylogenetic branch that includes the genera Sulfitobacter and Roseobacter. The isoprenoid quinone of all three novel strains was ubiquinone-10 and the major fatty acid was cis-vaccenic acid, as in other species of the genus Sulfitobacter. However, there were several differences in the morphological, physiological and biochemical characteristics among the four strains and the reference species of the genus Sulfitobacter. Moreover, the average nucleotide identity values between the three sequenced isolates and the reference strains were below 76.33, indicating that genomic variation exists between the isolates and reference strains. Chemotaxonomic characteristics together with phylogenetic affiliations and genomic distances illustrate that strains MM-124, NB-68 and NB-77 represent novel species of the genus Sulfitobacter, for which the names Sulfitobacter geojensis sp. nov. (type strain MM-124(T)?=?KCTC 32124(T)?=?JCM 18835(T)), Sulfitobacter noctilucae sp. nov. (type strain NB-68(T)?=?KCTC 32122(T)?=?JCM 18833(T)) and Sulfitobacter noctilucicola sp. nov. (type strain NB-77(T)?=?KCTC 32123(T)?=?JCM 18834(T)) are proposed.
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Anti-Helicobacter pylori activities of FEMY-R7 composed of fucoidan and evening primrose extract in mice and humans.
Lab Anim Res
PUBLISHED: 08-07-2014
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Helicobacter pylori-eliminating effects of FEMY-R7, composed of fucoidan and evening primrose extract, were investigated in mice and humans. Male C57BL/6 mice were infected with the bacteria by intragastric inoculation (1×10(9) CFU/mouse) 3 times at 2-day intervals, and simultaneously, orally treated twice a day with 10 or 100 mg/kg FEMY-R7 for 2 weeks. In Campylobcter-like organism-detection test, FEMY-R7 markedly reduced the urease-positive reactivity. In a clinical sudy, human subjects, confirmed to be infected with Helicobacter pylori, were orally administered twice a day with a capsule containing 150 mg FEMY-R7 for 8 weeks. FEMY-R7 significantly decreased both the Delta over baseline-value in urea breath test and the serum pepsinogens I and II levels. The results indicate that FEMY-R7 not only eliminates H. pylori from gastric mucosa of animals and humans, but also improves gastric function.
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Simultaneous determination of five naphthoylindole-based synthetic cannabinoids and metabolites and their deposition in human and rat hair.
J Pharm Biomed Anal
PUBLISHED: 07-29-2014
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The continuing appearance of new synthetic cannabinoids has been a major issue in the field of forensic and clinical toxicology. In response to that, analytical methods for synthetic cannabinoids have been increasingly established in a variety of biological matrices. Since most of synthetic cannabinoids with structure similarity share some enzymatic metabolites, making the interpretation of analytical results and the discovery of the parent drug actually ingested very complicated, the investigation on metabolites of the first generation of synthetic cannabinoids with their relatively short side chains in chemical structure could be more important. Therefore, in the present study, we developed the analytical method for AM-2201, JWH-122 and MAM-2201 with JWH-018 as a precursor and their monohydroxylated metabolites in hair matrix. Also, using a rat model, AM-2201 and its monohydroxylated metabolites were identified and then the ratios of metabolite-to-parent drug were estimated to be used as criteria on external contamination. All analytes were extracted with methanol from washed and cut hair samples and the extracts were injected into LC-MS/MS with electrospray ion source in the positive ionization mode. Matrix effect and recovery were evaluated in hair matrices and no significant variations were observed. The validation results for precision and accuracy were satisfactory in both human and rat hair. The LOD and LOQ were 0.5pg/10mg and 1.0pg/10mg in human hair and 0.5pg/20mg and 1.0pg/20mg in pigmented and non-pigmented rat hair, respectively. Additionally, as a result of the animal study, there were not significant differences in the effect of pigmentation on the distribution of AM-2201 and its monohydroxylated metabolites in hair. Wide variations were observed for the concentrations of the naphthoylindole-based synthetic cannabinoids and metabolites in authentic hair samples from nine cases; those were 0.4-59.2pg/mg for JWH-018, 0.1-0.8pg/mg for JWH-073, 1.7-739.0pg/mg for AM-2201, 0.1-402.0pg/mg for JWH-122, 0.2-276.0pg/mg for MAM-2201, 0.2-1.1pg/mg for JWH-018 N-COOH, 0.3-37.2pg/mg for JWH-018 N-5-OH, 0.3pg/mg for JWH-073 N-COOH, 0.4pg/mg for AM-2201 N-4-OH, 0.2-3.1pg/mg for AM-2201 N-6-OHindole and 0.1-3.5pg/mg for JWH-122 N-5-OH. This quantitative LC-MS/MS analytical method for five naphthoylindole-based synthetic cannabinoids and their metabolites was very useful to be applied to authentic hair samples, of which their analytical results suggested the incorporation of synthetic cannabinoids in the hair matrix and provided the information on ingested parent drugs.
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Differences in gastric mucosal microbiota profiling in patients with chronic gastritis, intestinal metaplasia, and gastric cancer using pyrosequencing methods.
Helicobacter
PUBLISHED: 07-23-2014
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Helicobacter pylori (H. pylori) infection plays an important role in the early stage of cancer development. However, various bacteria that promote the synthesis of reactive oxygen and nitrogen species may be involved in the later stages. We aimed to determine the microbial composition of gastric mucosa from the patients with chronic gastritis, intestinal metaplasia, and gastric cancer using 454 GS FLX Titanium.
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Proteome-wide remodeling of protein location and function by stress.
Proc. Natl. Acad. Sci. U.S.A.
PUBLISHED: 07-15-2014
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Protein location and function can change dynamically depending on many factors, including environmental stress, disease state, age, developmental stage, and cell type. Here, we describe an integrative computational framework, called the conditional function predictor (CoFP; http://nbm.ajou.ac.kr/cofp/), for predicting changes in subcellular location and function on a proteome-wide scale. The essence of the CoFP approach is to cross-reference general knowledge about a protein and its known network of physical interactions, which typically pool measurements from diverse environments, against gene expression profiles that have been measured under specific conditions of interest. Using CoFP, we predict condition-specific subcellular locations, biological processes, and molecular functions of the yeast proteome under 18 specified conditions. In addition to highly accurate retrieval of previously known gold standard protein locations and functions, CoFP predicts previously unidentified condition-dependent locations and functions for nearly all yeast proteins. Many of these predictions can be confirmed using high-resolution cellular imaging. We show that, under DNA-damaging conditions, Tsr1, Caf120, Dip5, Skg6, Lte1, and Nnf2 change subcellular location and RNA polymerase I subunit A43, Ino2, and Ids2 show changes in DNA binding. Beyond specific predictions, this work reveals a global landscape of changing protein location and function, highlighting a surprising number of proteins that translocate from the mitochondria to the nucleus or from endoplasmic reticulum to Golgi apparatus under stress.
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Indoor environmental factors associated with wheezing illness and asthma in South Korean children: phase III of the International Study of Asthma and Allergies in Childhood.
J Asthma
PUBLISHED: 07-11-2014
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Abstract Background: The relationship between exposure to indoor environmental pollutants and incidence of asthma and wheezing illness in children is unclear. This study aimed to clarify this relationship by identifying the risk factors associated with these conditions in South Korean children aged 6-7 years.
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Chemical etching behaviors of semipolar (11?22) and nonpolar (11?20) gallium nitride films.
Phys Chem Chem Phys
PUBLISHED: 06-28-2014
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Wet chemical etching using hot KOH and H3PO4 solutions was performed on semipolar (11?22) and nonpolar (11?20) GaN films grown on sapphire substrates. An alternating KOH/H3PO4/KOH etch process was developed to control the orientation of the facets on the thin-film surface. The initial etch step in KOH produced c- and m-plane facets on the surface of both semipolar (11?22) and nonpolar (11?20) GaN thin-films. A second etch step in H3PO4 solution additionally exposed a (?1?12?2) plane, which is chemically stable in H3PO4 solution. By repeating the chemical etch with KOH solution, the m-plane facets as seen in the original KOH etch step were recovered. The etching methods developed in our work can be used to control the surface morphologies of nonpolar and semipolar GaN-based optoelectronic devices such as light-emitting diodes and solar cells.
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Post-growth CdCl? treatment on CdTe thin films grown on graphene layers using a close-spaced sublimation method.
Opt Express
PUBLISHED: 06-13-2014
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We investigated the morphological, structural and optical properties of CdCl?-treated cadmium telluride (CdTe) thin films deposited on defective graphene using a close-spaced sublimation (CSS) system. Heat treatment in the presence of CdCl? caused recrystallization of CSS-grown CdTe over the as-deposited structures. The preferential (111) orientation of as-deposited CdTe films was randomized after post-growth CdCl? treatment. New small grains (bumps) on the surface of CdCl?-treated CdTe films were ascribed to nucleation of the CdTe grains during the CdCl? treatment. The properties of as-deposited and CdCl?-treated CdTe films were characterized by room temperature micro-photoluminescence, micro-Raman spectroscopy, scanning electron microscopy, and X-ray diffraction analysis. Our results are useful to demonstrate a substrate configuration CdTe thin film solar cells.
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GaN-based light-emitting diodes on graphene-coated flexible substrates.
Opt Express
PUBLISHED: 06-13-2014
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We demonstrate GaN-based thin light-emitting diodes (LEDs) on flexible polymer and paper substrates covered with chemical vapor deposited graphene as a transparent-conductive layer. Thin LEDs were fabricated by lifting the sapphire substrate off by Excimer laser heating, followed by transfer of the LEDs to the flexible substrates. These substrates were coated with tri-layer graphene by a wet transfer method. Optical and electrical properties of thin laser lift-offed LEDs on the flexible substrates were characterized under both relaxed and strained conditions. The graphene on paper substrates remained conducting when the graphene/paper structure was folded. The high transmittance, low sheet resistance and high failure strain of the graphene make it an ideal candidate as the transparent and conductive layer in flexible optoelectronics.
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Prognostic Value of Metabolic Tumor Volume Estimated by (18)?F-FDG Positron Emission Tomography/Computed Tomography in Patients with Diffuse Large B-Cell Lymphoma of Stage II or III Disease.
Nucl Med Mol Imaging
PUBLISHED: 05-29-2014
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The purpose of this study was to evaluate the prognostic value of metabolic tumor volume (MTV) measured by (18)F-fluorodeoxyglucose positron emission tomography-computed tomography (FDG-PET/CT) in patients with diffuse large B-cell lymphoma (DLBCL) treated with rituximab-containing immunochemotherapy.
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Comparative effects of plant oils on the cerebral hemorrhage in stroke-prone spontaneously hypertensive rats.
Nutr Neurosci
PUBLISHED: 05-27-2014
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Objectives Since oils and fats can induce metabolic syndrome, leading to cardiovascular and cerebrovascular diseases, the present study was performed to find out whether the plant oils affect the cerebral hemorrhage in stroke-prone spontaneously hypertensive (SHR-SP) rats. Methods From 47 days of age, male SHR-SP rats were given drinking water containing 1% NaCl to induce hypertension, and simultaneously fed semi-purified diets containing 10% perilla oil, canola oil, or shortening. The onset time of convulsion following cerebral hemorrhage was recorded, and the areas of hemorrhage and infarction were analyzed in the stroke brains. Results In comparison with 58-day survival of SHR-SP rats during feeding NaCl alone, perilla oil extended the survival time to 68.5 days, whereas canola oil shortened it to 45.7 days. Feeding perilla oil greatly reduced the total volume of cerebral hemorrhage from 17.27% in the control group to 4.53%, while shortening increased the lesions to 21.23%. In a microscopic analysis, perilla oil also markedly decreased the hemorrhagic and infarction lesions to 1/10 of those in control rats, in contrast to an exacerbating effect of shortening. In blood analyses, perilla oil reduced blood total cholesterol and low-density lipoproteins which were increased in SHR-SP, but canola oil further increased them and markedly lowered platelet counts. Discussion Perilla oil delayed and attenuated cerebral hemorrhage by improving hyperlipidemia in hypertensive stroke animals, in contrast to the aggravating potential of canola oil and shortening. It is suggested that perilla oil should be the first choice oil for improving metabolic syndrome in hypertensive persons at risk of hemorrhagic stroke.
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An ethanolic extract of Angelica gigas improves atherosclerosis by inhibiting vascular smooth muscle cell proliferation.
Lab Anim Res
PUBLISHED: 05-26-2014
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The effects of an ethanolic extract of Angelica gigas (EAG) on the vascular smooth muscle cell (VSMC) proliferation and high-cholesterol diet-induced hypercholesterolemia and atherosclerosis were investigated. Rat aortic VSMCs were stimulated with platelet-derived growth factor-BB (25 ng/mL) for the induction of DNA synthesis and cell proliferation. EAG (1-10 µg/mL) significantly inhibited both the thymidine incorporation and cell proliferation in a concentration-dependent manner. Hypercholesterolemia was induced by feeding male New Zealand white rabbits with 0.5% cholesterol in diet for 10 weeks, during which EAG (1% in diet) was given for the final 8 weeks after 2-week induction of hypercholesterolemia. Hypercholesterolemic rabbits exhibited great increases in serum total cholesterol and low-density lipoproteins (LDL) levels, and finally severe atheromatous plaque formation covering 28.4% of the arterial walls. EAG significantly increased high-density lipoproteins (HDL), slightly decreased LDL, and potentially reduced the atheroma area to 16.6%. The results indicate that EAG attenuates atherosclerosis not only by inhibiting VASC proliferation, but also by increasing blood HDL levels. Therefore, it is suggested that EAG could be an alternative or an adjunct therapy for the improvement of hypercholesterolemia and atherosclerosis.
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Relationship between indoor air pollutant levels and residential environment in children with atopic dermatitis.
Allergy Asthma Immunol Res
PUBLISHED: 04-26-2014
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This study was aimed to investigate the relationship between indoor air pollutant levels and residential environment in children with atopic dermatitis (AD) living in Seoul.
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Application of damage control resuscitation strategies to patients with severe traumatic hemorrhage: review of plasma to packed red blood cell ratios at a single institution.
J. Korean Med. Sci.
PUBLISHED: 04-24-2014
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When treating trauma patients with severe hemorrhage, massive transfusions are often needed. Damage control resuscitation strategies can be used for such patients, but an adequate fresh frozen plasma: packed red blood cell (FFP:PRBC) administration ratio must be established. We retrospectively reviewed the medical records of 100 trauma patients treated with massive transfusions from March 2010 to October 2012. We divided the patients into 2 groups according to the FFP:PRBC ratio: a high-ratio (?0.5) and a low-ratio group (<0.5). The patient demographics, fluid and transfusion quantities, laboratory values, complications, and outcomes were analyzed and compared. There were 68 patients in the high-ratio and 32 in the low-ratio group. There were statistically significant differences between groups in the quantities of FFP, FFP:PRBC, platelets, and crystalloids administered, as well as the initial diastolic blood pressure. Bloodstream infections were noted only in the high-ratio group, and the difference was statistically significant (P=0.028). Kaplan-Meier plots revealed that the 24-hr survival rate was significantly higher in the high-ratio group (71.9% vs. 97.1%, P<0.001). In severe hemorrhagic trauma, raising the FFP:PRBC ratio to 0.5 or higher may increase the chances of survival. Efforts to minimize bloodstream infections during the resuscitation must be increased.
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Stem cell research funding policies and dynamic innovation: a survey of open access and commercialization requirements.
Stem Cell Rev
PUBLISHED: 03-29-2014
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This article compares and contrasts the pressures of both open access data sharing and commercialization policies in the context of publicly funded embryonic stem cell research (SCR). First, normative guidelines of international SCR organizations were examined. We then examined SCR funding guidelines and the project evaluation criteria of major funding organizations in the EU, the United Kingdom (UK), Spain, Canada and the United States. Our survey of policies revealed subtle pressures to commercialize research that include: increased funding availability for commercialization opportunities, assistance for obtaining intellectual property rights (IPRs) and legislation mandating commercialization. In lieu of open access models, funders are increasingly opting for limited sharing models or "protected commons" models that make the research available to researchers within the same region or those receiving the same funding. Meanwhile, there still is need for funding agencies to clarify and standardize terms such as "non-profit organizations" and "for-profit research," as more universities are pursuing for-profit or commercial opportunities.
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Infrared camera-proven water-damaged homes are associated with the severity of atopic dermatitis in children.
Ann. Allergy Asthma Immunol.
PUBLISHED: 03-21-2014
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Moisture problems in dwellings have been linked to respiratory symptoms, but little is known about their association with symptoms of atopic dermatitis (AD). Moreover, the questionnaire-based survey or visual inspection for water damage does not use a standardized approach for assessing dampness.
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Characterization of age signatures of DNA methylation in normal and cancer tissues from multiple studies.
BMC Genomics
PUBLISHED: 03-07-2014
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DNA methylation (DNAm) levels can be used to predict the chronological age of tissues; however, the characteristics of DNAm age signatures in normal and cancer tissues are not well studied using multiple studies.
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Prevalence of immediate-type food allergy in early childhood in seoul.
Allergy Asthma Immunol Res
PUBLISHED: 03-04-2014
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There are scanty epidemiologic data on the prevalence of food allergy (FA) among preschool children in Asia. We performed this study to determine the prevalence and causative foods of immediate-type FA in early childhood in Korea.
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In vitro and in vivo anti-Helicobacter pylori activities of FEMY-R7 composed of fucoidan and evening primrose extract.
Lab Anim Res
PUBLISHED: 02-13-2014
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Effects of FEMY-R7, composed of fucoidan and evening primrose extract, on the bacterial growth and intragastric infection of Helicobacter pylori as well as gastric secretion were investigated in comparison with a proton-pump inhibitor pantoprazole. For in vitro anti-bacterial activity test, H. pylori (1×10(8) CFU/mL) was incubated with a serially-diluted FEMY-R7 for 3 days. As a result, FEMY-R7 fully inhibited the bacterial growth at 100 µg/mL, which was determined to be a minimal inhibitory concentration. In addition, 6-hour incubation with H. pylori, FEMY-R7 inhibited urease activity in a concentration-dependent manner, showing a median inhibitory concentration of 1,500 µg/mL. In vivo elimination study, male C57BL/6 mice were infected with the bacteria by intragastric inoculation (5×10(9) CFU/mouse) 3 times at 2-day intervals, and simultaneously, orally treated twice a day with 10, 30 or 100 mg/kg FEMY-R7 for 7 days. In Campylobcter-like organism-detection test and bacterial identification, FEMY-R7 exerted a high bacteria-eliminating capacity at 30-100 mg/kg, comparably to 30 mg/kg pantoprazole. In contrast to a strong antacid activity of pantoprazole in a pylorus-ligation study, FEMY-R7 did not significantly affect gastric pH, free HCl, and total acidity, although it significantly decreased fluid volume at a low dose (10 mg/kg). The results indicate that FEMY-R7 eliminate H. pylori from gastric mucosa by directly killing the bacteria and preventing their adhesion and invasion, rather than by inhibiting gastric secretion or mucosal damage.
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Shell-crosslinked hyaluronic acid nanogels for live monitoring of hyaluronidase activity in vivo.
Macromol Biosci
PUBLISHED: 02-06-2014
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A hyaluronidase (HAdase) has been noticed as a potential drug target as well as prognostic marker because of its close associations with tumor invasion, metastasis, and angiogenesis. Accordingly, precise monitoring of HAdase activity in vivo seems to be crucial not only for the evaluation of HAdase activity but also for non-invasive molecular imaging. In our study, we propose a new organic, near-infrared fluorescence imaging probe, indocyanine green (ICG)-based stimuli-responsive fluorescence probe for selective imaging of HAdases with appreciable signal-to-noise (S/N) ratios in serum and in vivo. Shell-crosslinked hyaluronic acid (HA) nanogels (sc-nanogels) are generated via a reducible covalent linkage which incorporate ICG derivatives. The ICG-embeded HA nanogels via shell-crosslinking have preferable properties for ideal selective imaging and detection of HAdase activity in vivo. The sc-nanogels exhibit prominent chemical stability against external light, greatly control background signals in serum, and small size compared to use of self-assembled ICG-based carriers. Collapsed ICG in the hydrogel core is selectively disentangled by HAdase treatment for selective near-infrared imaging without unwanted background signal. The newly designed sc-nanogels may have great potential to serve as probes for improved selective imaging of HAdase-associated diseases in clinics as well as HAdase-activity screening in vivo.
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Perilla oil improves blood flow through inhibition of platelet aggregation and thrombus formation.
Lab Anim Res
PUBLISHED: 01-31-2014
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The inhibitory effects of perilla oil on the platelet aggregation in vitro and thrombosis in vivo were investigated in comparison with aspirin, a well-known blood flow enhancer. Rabbit platelet-rich plasma was incubated with perilla oil and aggregation inducers collagen or thrombin, and the platelet aggregation rate was analyzed. Perilla oil significantly inhibited both the collagen- and thrombin-induced platelet aggregations, in which the thromboxane B2 formation from collagen-activated platelets were reduced in a concentration-dependent manner. Rats were administered once daily by gavage with perilla oil for 1 week, carotid arterial thrombosis was induced by applying 35% FeCl3-soaked filter paper for 10 min, and the blood flow was monitored with a laser Doppler probe. Perilla oil delayed the FeCl3-induced arterial occlusion in a dose-dependent manner, doubling the occlusion time at 0.5 mL/kg. In addition, a high dose (2 mL/kg) of perilla oil greatly prevented the occlusion, comparable to the effect of aspirin (30 mg/kg). The results indicate that perilla oil inhibit platelet aggregation by blocking thromboxane formation, and thereby delay thrombosis following oxidative arterial wall injury. Therefore, it is proposed that perilla oil could be a good candidate without adverse effects for the improvement of blood flow.
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Identification of a novel mutation in the CHD7 gene in a patient with CHARGE syndrome.
Korean J Pediatr
PUBLISHED: 01-31-2014
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CHARGE syndrome has been estimated to occur in 1:10,000 births worldwide and shows various clinical manifestations. It is a genetic disorder characterized by a specific and a recognizable pattern of anomalies. The major clinical features are ocular coloboma, heart malformations, atresia of the choanae, growth retardation, genital hypoplasia, and ear abnormalities. The chromodomain helicase DNA-binding protein 7 (CHD7) gene, located on chromosome 8q12.1, causes CHARGE syndrome. The CHD7 protein is an adenosine triphosphate (ATP)-dependent chromatin remodeling protein. A total of 67% of patients clinically diagnosed with CHARGE syndrome have CHD7 mutations. Five hundred twenty-eight pathogenic and unique CHD7 alterations have been identified so far. We describe a patient with a CHARGE syndrome diagnosis who carried a novel de novo mutation, a c.3896T>C (p. leu1299Pro) missense mutation, in the CHD7 gene. This finding will provide more information for genetic counseling and expand our understanding of the pathogenesis and development of CHARGE syndrome.
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Identification of a Novel Mutation in the CYBB Gene, p.Asp378Gly, in a Patient With X-linked Chronic Granulomatous Disease.
Allergy Asthma Immunol Res
PUBLISHED: 01-20-2014
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Chronic granulomatous disease (CGD) is a rare immunodeficiency disease, which is characterized by the lack of a functional nicotinamide adenine dinucleotide phosphate (NADPH) oxidase in phagocytes. The disease presents leukocytosis, anemia, hypergammaglobulinemia, and granuloma formation of the skin, lung, or lymph nodes. The mutation of the CYBB gene encoding gp91phox, located on chromosome Xp21.1 is one of the causes of CGD. We report a patient with X-linked CGD who carried a novel mutation, a c.1133A>G (paAsp378Gly) missense mutation, in the CYBB gene.
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Regulation of diastereoselectivity in the carbocyclization of allenyl (S)-N-tert-butylsulfinimines through a three-component assembly.
J. Org. Chem.
PUBLISHED: 01-17-2014
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Allenyl sulfinimines can be stereoselectively cyclized with hexamethylditin under palladium catalysis conditions followed by a selection of additives for an activated transmetalation. Reactivity and diastereoselectivity for the cyclization strongly depend on the characteristics of additives. A highly diastereoselective synthesis of five-membered rings is achieved from the reaction of the corresponding allenyl (S)-N-tert-butylsulfinimies through the following sequence. After the distannylation of the allenyl group with hexamethylditin catalyzed by the Pd complex, stereochemical routes are additive dependent: addition of SnCl4 affords a cis ring exclusively, whereas a trans ring is formed predominantly by the introduction of B-bromocatecholborane. Extension of the methodology to the synthesis of six-membered cis rings is achieved by using B-bromocatecholborane. Stereochemical relationships of products were unambiguously deduced by X-ray crystallography.
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Long-Term Outcomes and Dynamics of Mutants Associated with Lamivudine- Adefovir Rescue Therapy in Patients with Lamivudine-Resistant Chronic Hepatitis B.
Gut Liver
PUBLISHED: 01-15-2014
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To investigate the association between the baseline profiles and dynamics of hepatitis B virus (HBV) DNA polymerase gene mutations and the long-term virological response of lamivudine (LAM)-adefovir (ADV) combination therapy in patients with LAM-resistant chronic hepatitis B.
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Small private key MQPKS on an embedded microprocessor.
Sensors (Basel)
PUBLISHED: 01-15-2014
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Multivariate quadratic (MQ) cryptography requires the use of long public and private keys to ensure a sufficient security level, but this is not favorable to embedded systems, which have limited system resources. Recently, various approaches to MQ cryptography using reduced public keys have been studied. As a result of this, at CHES2011 (Cryptographic Hardware and Embedded Systems, 2011), a small public key MQ scheme, was proposed, and its feasible implementation on an embedded microprocessor was reported at CHES2012. However, the implementation of a small private key MQ scheme was not reported. For efficient implementation, random number generators can contribute to reduce the key size, but the cost of using a random number generator is much more complex than computing MQ on modern microprocessors. Therefore, no feasible results have been reported on embedded microprocessors. In this paper, we propose a feasible implementation on embedded microprocessors for a small private key MQ scheme using a pseudo-random number generator and hash function based on a block-cipher exploiting a hardware Advanced Encryption Standard (AES) accelerator. To speed up the performance, we apply various implementation methods, including parallel computation, on-the-fly computation, optimized logarithm representation, vinegar monomials and assembly programming. The proposed method reduces the private key size by about 99.9% and boosts signature generation and verification by 5.78% and 12.19% than previous results in CHES2012.
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Phylogenetic comparison of oskar mRNA localization signals.
Biochem. Biophys. Res. Commun.
PUBLISHED: 01-11-2014
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As a way to spatially control the expression of genes within cells, RNA localization is being recognized as an important process by which proteins are restricted to specific subcellular domains, which occurs in more diverse types of tissue than previously considered. Although many localized RNAs have been identified, information on cis-acting elements of localization is still limited. As transcripts of oskar (osk) are known to localize to the posterior pole of oocytes, we computationally analyzed a conserved sequence among eight Drosophila species and tested its role as a localization element. Dimerization of osk mRNA did not occur when the motif was deleted, but this did not affect assembly of osk mRNA-containing ribonucleoprotein (RNP) complexes. Without the motif, however, large RNP complex particles accumulated in nurse cells, and only a small fraction of these RNP complexes was transported into oocytes and properly localized to the posterior pole. Therefore, this motif may be required for the early transport of osk mRNA into oocytes. Also, as dimerization of osk mRNA does not seem to be a prerequisite for the assembly of RNP complexes, a dimerization-independent mechanism may also serve to localize osk mRNA to the posterior pole.
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Quantitative determination of 11-nor-9-carboxy-tetrahydrocannabinol in hair by column switching LC-ESI-MS(3).
J. Chromatogr. B Analyt. Technol. Biomed. Life Sci.
PUBLISHED: 01-02-2014
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Hair analysis has been regarded as an alternative method to urine analysis in forensic and criminal cases. Cannabis (marijuana) is one of the most widely used drugs in the world and it has been controlled in South Korea since 1976. Identification of 11-nor-9-carboxy-tetrahydrocannabinol (THCCOOH) in hair can be an important proof of cannabis use because it can exclude the possibility of passive cannabis smoke exposure. In this study, we described a quantitative method of THCCOOH in hair using simple liquid-liquid extraction (LLE), selective column switching liquid chromatography with electrospray ionization (ESI)-MS(3). For the column switching system three columns (precolumn, trap column and analytical column) were used. Valve switch from the precolumn to the trap column was set from 3.0 to 4.0 min because THCCOOH appeared around 3.5 min with this precolumn. After 4.0 min the valve was switched to the original position and the analytes in the trap column were eluted onto the analytical column. Resolution occurred in this column and eluted into the ESI-MS(3) system. The internal standard was THCCOOH-d3. We used ESI-negative-MS(3) transition of ions at m/z 343 to 299 to 245 (343/299/245) and m/z 346 to 302 to 248 (346/302/248) for quantification of THCCOOH and THCCOOH-d3, respectively. The validation results of selectivity, matrix effect, recovery, linearity, precision and accuracy, and processed sample stability were satisfactory. The limit of detection (LOD) was 0.05 pg/mg and the limit of quantification (LOQ) was 0.10 pg/mg. The range of concentration of THCCOOH from 98 authentic human hair was 0.13-15.75 pg/mg. This method was successfully applied in the analysis of authentic human hair samples.
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Genome information of Methylobacterium oryzae, a plant-probiotic methylotroph in the phyllosphere.
PLoS ONE
PUBLISHED: 01-01-2014
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Pink-pigmented facultative methylotrophs in the Rhizobiales are widespread in the environment, and many Methylobacterium species associated with plants produce plant growth-promoting substances. To gain insights into the life style at the phyllosphere and the genetic bases of plant growth promotion, we determined and analyzed the complete genome sequence of Methylobacterium oryzae CBMB20T, a strain isolated from rice stem. The genome consists of a 6.29-Mb chromosome and four plasmids, designated as pMOC1 to pMOC4. Among the 6,274 coding sequences in the chromosome, the bacterium has, besides most of the genes for the central metabolism, all of the essential genes for the assimilation and dissimilation of methanol that are either located in methylotrophy islands or dispersed. M. oryzae is equipped with several kinds of genes for adaptation to plant surfaces such as defense against UV radiation, oxidative stress, desiccation, or nutrient deficiency, as well as high proportion of genes related to motility and signaling. Moreover, it has an array of genes involved in metabolic pathways that may contribute to promotion of plant growth; they include auxin biosynthesis, cytokine biosynthesis, vitamin B12 biosynthesis, urea metabolism, biosorption of heavy metals or decrease of metal toxicity, pyrroloquinoline quinone biosynthesis, 1-aminocyclopropane-1-carboxylate deamination, phosphate solubilization, and thiosulfate oxidation. Through the genome analysis of M. oryzae, we provide information on the full gene complement of M. oryzae that resides in the aerial parts of plants and enhances plant growth. The plant-associated lifestyle of M. oryzae pertaining to methylotrophy and plant growth promotion, and its potential as a candidate for a bioinoculant targeted to the phyllosphere and focused on phytostimulation are illuminated.
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Renal manifestations in 2007 Korean patients with Behçets disease.
Yonsei Med. J.
PUBLISHED: 10-30-2013
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Behçets disease (BD) theoretically affects all sizes and types of blood vessels and results in multi-organ involvement. However, renal BD has not been fully characterized, though the kidneys are histologically rich in blood vessels.
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In situ atomic imaging of coalescence of Au nanoparticles on graphene: rotation and grain boundary migration.
Chem. Commun. (Camb.)
PUBLISHED: 10-15-2013
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Using in situ transmission electron microscopy, we demonstrated that gold nanoparticles are unified via "oriented attachment" assisted either by nanoparticle rotation or grain boundary migration at the attachment interface. We also observed that the combined nanoparticle changes shape with stable facet planes via surface diffusion, along with recrystallization.
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Characterizing the secondary protein structure of black widow dragline silk using solid-state NMR and X-ray diffraction.
Biomacromolecules
PUBLISHED: 09-26-2013
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This study provides a detailed secondary structural characterization of major ampullate dragline silk from Latrodectus hesperus (black widow) spiders. X-ray diffraction results show that the structure of black widow major ampullate silk fibers is comprised of stacked ?-sheet nanocrystallites oriented parallel to the fiber axis and an amorphous region with oriented (anisotropic) and isotropic components. The combination of two-dimensional (2D) (13)C-(13)C through-space and through-bond solid-state NMR experiments provide chemical shifts that are used to determine detailed information about the amino acid motif secondary structure in black widow spider dragline silk. Individual amino acids are incorporated into different repetitive motifs that make up the majority of this protein-based biopolymer. From the solid-state NMR measurements, we assign distinct secondary conformations to each repetitive amino acid motif and, hence, to the amino acids that make up the motifs. Specifically, alanine is incorporated in ?-sheet (poly(Alan) and poly(Gly-Ala)), 3(1)-helix (poly(Gly-Gly-Xaa), and ?-helix (poly(Gln-Gln-Ala-Tyr)) components. Glycine is determined to be in ?-sheet (poly(Gly-Ala)) and 3(1)-helical (poly(Gly-Gly-X(aa))) regions, while serine is present in ?-sheet (poly(Gly-Ala-Ser)), 3(1)-helix (poly(Gly-Gly-Ser)), and ?-turn (poly(Gly-Pro-Ser)) structures. These various motif-specific secondary structural elements are quantitatively correlated to the primary amino acid sequence of major ampullate spidroin 1 and 2 (MaSp1 and MaSp2) and are shown to form a self-consistent model for black widow dragline silk.
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Isolation and Characterization of a Novel Agar-Degrading Marine Bacterium, Gayadomonas joobiniege gen, nov, sp. nov., from the Southern Sea, Korea.
J. Microbiol. Biotechnol.
PUBLISHED: 08-23-2013
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An agar-degrading bacterium, designated as strain G7(T), was isolated from a coastal seawater sample from Gaya Island (Gayado in Korean), Republic of Korea. The isolated strain G7(T) is gram-negative, rod shaped, aerobic, non-motile, and non-pigmented. A similarity search based on its 16S rRNA gene sequence revealed that it shares 95.5%, 90.6%, and 90.0% similarity with the 16S rRNA gene sequences of Catenovulum agarivorans YM01(T), Algicola sagamiensis, and Bowmanella pacifica W3-3A(T), respectively. Phylogenetic analyses demonstrated that strain G7(T) formed a distinct monophyletic clade closely related to species of the family Alteromonadaceae in the Alteromonas-like Gammaproteobacteria. The G+C content of strain G7(T) was 41.12 mol%. The DNA-DNA hybridization value between strain G7(T) and the phylogenetically closest strain YM01(T) was 19.63%. The genomes of G7(T) and YM01(T) had an average ANIb value of 70.00%. The predominant isoprenoid quinone of this particular strain was ubiquinone-8, whereas that of C. agarivorans YM01(T) was menaquinone-7. The major fatty acids of strain G7(T) were Iso-C15:0(41.47%), Anteiso-C15:0(22.99%), and C16:1?7c/iso-C15:02-OH (8.85%), which were quite different from those of YM01(T). Comparison of the phenotypic characteristics related to carbon utilization, enzyme production, and susceptibility to antibiotics also demonstrated that strain G7(T) is distinct from C. agarivorans YM01T. Based on its phenotypic, chemotaxonomic, and phylogenetic distinctiveness, strain G7(T) was considered a novel genus and species in the Gammaproteobacteria, for which the name Gayadomonas joobiniege gen. nov. sp. nov. (ATCC BAA-2321 = DSM25250(T) = KCTC23721(T)) is proposed.
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Inhibitory effects of a ?-dunnione compound MB12662 on gastric secretion and ulcers.
Lab Anim Res
PUBLISHED: 08-06-2013
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The effects of a ?-dunnione compound MB12662 on the gastric secretion and ulcers were investigated in rats. In order to assess the effects of MB12662 on the gastric secretion and acidity, rats were subjected to pylorus ligation operation, and 6 hours later, gastric fluid was collected. Treatment with MB12662 reduced the gastric fluid volume to 47.3% of control level and increased pH. In an alcohol-induced ulcer model, rats were orally administered 3 mL/kg of ethanol, and 1 hour later, the ulcer lesions ware measured under a stereomicroscope. MB12662 reduced ulcer index in a dose-dependent manner which was much stronger than a proton-pump inhibitor pantoprazole. In a stress-induced ulcer model, rats were subjected to water-immersion restraint stress, and 5 hours later, the ulcer lesions ware examined. MB12662 also attenuated the stress-induced gastric lesions, although the efficacy of MB12662 was lower than that of pantoprazole. Therefore, it is suggested that MB12662 could be a candidate compound for the prevention or treatment of gastric ulcers induced by gastric over-secretion and alcoholic hangover.
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Simultaneous determination of 18 abused opioids and metabolites in human hair using LC-MS/MS and illegal opioids abuse proven by hair analysis.
J Pharm Biomed Anal
PUBLISHED: 08-05-2013
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Natural and synthetic opioids have efficient analgesic activity but can also be addictive. Thus, the determination of opioids and their metabolites in biological specimens is of interest in clinical and forensic toxicology laboratories. The analysis of drugs in hair provides valuable information on previous chronic drug use and has been successfully applied to the diagnosis of drug abuse, tolerance, compliance and gestational drug exposure. Despite the abuse of prescription opioids along with heroin and other illegal opiates, few studies have been conducted on the simultaneous determination of the broad range of opioids covering those drugs in hair. In the present study, an analytical method for the simultaneous detection in hair of 18 opioids and metabolites considered to have a high abuse risk based on the results of urine drug screening was established and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS) for the purpose of clinical and forensic applications. The drugs and metabolites were extracted from hair using methanol and analyzed using LC-MS/MS. The validation results proved that the method was selective, accurate and precise with acceptable linearity within calibration ranges. No significant variation was observed by different sources of matrices. The limits of detection and the limits of quantification ranged from 0.05 to 0.25ng/10mg hair and from 0.05 to 0.5ng/10mg hair, respectively. The developed method was successfully applied to 15 hair samples from opioids users. This method will be very useful for monitoring the inappropriate use of opioid drugs.
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An expansin from the marine bacterium Hahella chejuensis acts synergistically with xylanase and enhances xylan hydrolysis.
Bioresour. Technol.
PUBLISHED: 07-06-2013
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HcEXLX2 is a bacterial expansin found in a marine bacterium, Hahella chejuensis. Previously, HcEXLX2 was reported to act synergistically with a commercial cellulase preparation on the cellulose hydrolysis. The aim of the present study was to investigate the possible synergistic activity of HcEXLX2 with an endo-type xylanase from Saccharophagus degradans 2-40(T) (Xyn10C) in the hydrolysis of xylan. When 160 ?g of HcEXLX2 was incubated with 12 ?g of Xyn10C, the yield of reducing sugar increased 3.1 times when compared to that without HcEXLX2. The optimal temperature and pH for the synergism of HcEXLX2 with Xyn10C were 30°C and pH 7, respectively. In addition, binding experiments revealed that HcEXLX2 binds to xylan more preferentially than to Avicel. These results imply that HcEXLX2 could be used as an accessory protein to boost the activity of xylanase if its synergistic effect is strengthened at lower dosages.
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Deposition of JWH-018, JWH-073 and their metabolites in hair and effect of hair pigmentation.
Anal Bioanal Chem
PUBLISHED: 06-11-2013
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Analysis of drugs in hair is often used as a routine method to obtain detailed information about drug ingestion. However, few studies have been conducted on deposition of synthetic cannabinoids and metabolites in hair. The first purpose of this study was to establish and validate an analytical method for detection of JWH-018, JWH-073, and their metabolites in hair, by use of UHPLC-MS-MS, for forensic application. The second purpose was to investigate the distribution of synthetic cannabinoids metabolites in hair and the effect of hair pigmentation, by use of an animal model. For this, JWH-073 was chosen as a representative synthetic cannabinoid. Finally, the developed method was applied to hair samples from 18 individuals suspected of synthetic cannabinoids use. JWH-018, JWH-073, and their metabolites were extracted from hair with methanol. The extract was then filtered and analyzed by UHPLC-MS-MS with an electrospray ion source in positive-ionization mode. Validation proved the method was selective, sensitive, accurate, and precise, with acceptable linearity within the calibration ranges. No significant variations were observed when different sources of both human and rat hair were used. The animal study demonstrated that JWH-073 N-COOH M was the major metabolite of JWH-073 in rat hair, and hair pigmentation did not have a significant effect on incorporation of JWH-073 and its metabolites into hair. In the analysis of 18 authentic hair samples, only JWH-018, JWH-018 N-5-OH M, and JWH-073 were detected, with wide variation in concentrations.
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A facile method for highly uniform GaN-based nanorod light-emitting diodes with InGaN/GaN multi-quantum-wells.
Opt Express
PUBLISHED: 06-06-2013
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We report on a simple and reproducible method for fabricating InGaN/GaN multi-quantum-well (MQW) nanorod light-emitting diodes (LEDs), prepared by combining a SiO2 nanosphere lithography and dry-etch process. Focused-ion-beam (FIB)-deposited Pt was contacted to both ends of the nanorod LEDs, producing bright electroluminescence from the LEDs under forward bias conditions. The turn-on voltage in these nanorod LEDs was higher (13 V) than in companion thin film devices (3 V) and this can be attributed to the high contact resistance between the FIB-deposited Pt and nanorod LEDs and the damage induced by inductively-coupled plasma and Ga + -ions. Our method to obtain uniform MQW nanorod LEDs shows promise for improving the reproducibility of nano-optoelectronics.
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Charting microbial phenotypes in multiplex nanoliter batch bioreactors.
Anal. Chem.
PUBLISHED: 05-24-2013
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High-throughput growth phenotyping is receiving great attention for establishing the genotype-phenotype map of sequenced organisms owing to the ready availability of complete genome sequences. To date, microbial growth phenotypes have been investigated mostly by the conventional method of batch cultivation using test tubes, Erlenmeyer flasks, or the recently available microwell plates. However, the current batch cultivation methods are time- and labor-intensive and often fail to consider sophisticated environmental changes. The implementation of batch cultures at the nanoliter scale has been difficult because of the quick evaporation of the culture medium inside the reactors. Here, we report a microfluidic system that allows independent cell cultures in evaporation-free multiplex nanoliter reactors under different culture conditions to assess the behavior of cells. The design allows three experimental replicates for each of eight culture environments in a single run. We demonstrate the versatility of the device by performing growth curve experiments with Escherichia coli and microbiological assays of antibiotics against the opportunistic pathogen Pseudomonas aeruginosa. Our study highlights that the microfluidic system can effectively replace the traditional batch culture methods with nanoliter volumes of bacterial cultivations, and it may be therefore promising for high-throughput growth phenotyping as well as for single-cell analyses.
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Quantitative analysis of propofol-glucuronide in hair as a marker for propofol abuse.
Anal Bioanal Chem
PUBLISHED: 04-01-2013
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The inappropriate or illegal use of propofol has recently come to the fore as a serious social issue in South Korea. Thus, in spite of its superior potency as a therapeutic drug, propofol was classified as a controlled drug under the purview of Narcotics Control Law in South Korea in February of 2011. Accordingly, the determination of propofol and/or its metabolites in biological specimens is required to prove ingestion. Therefore, to demonstrate chronic ingestion, a quantitative analytical method for propofol-glucuronide in hair was developed and validated using liquid chromatography-tandem mass spectrometry (LC-MS/MS). This method was applied to measure propofol-glucuronide in hair samples from 23 propofol abuse suspects and in both pigmented and nonpigmented hair from rats which had ingested propofol. Propofol-glucuronide in hair was extracted in methanol and then filtered and analyzed by LC-MS/MS with electrospray ionization in negative mode. The validation results of selectivity, matrix effect, recovery, linearity, precision and accuracy, and processed sample stability were satisfactory. The limit of detection was 20 pg/10 mg hair and the limit of quantification was 50 pg/10 mg hair. The concentration range of propofol-glucuronide in hair segments from 23 propofol abuse suspects was shown up to 1,410 pg/mg. The animal study demonstrated that the presence of melanin did not affect the deposition of propofol-glucuronide in hair. Thus, we propose propofol-glucuronide in hair as a marker for propofol abuse. This method will be very useful for monitoring the inappropriate use of propofol for both legal and public health aspects.
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Probing lipid-cholesterol interactions in DOPC/eSM/Chol and DOPC/DPPC/Chol model lipid rafts with DSC and (13)C solid-state NMR.
Biochim. Biophys. Acta
PUBLISHED: 03-25-2013
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The interaction between cholesterol (Chol) and phospholipids in bilayers was investigated for the ternary model lipid rafts, DOPC/eSM/Chol and DOPC/DPPC/Chol, with differential scanning calorimetry (DSC) and (13)C cross polarization magic angle spinning (CP-MAS) solid-state NMR. The enthalpy and transition temperature (Tm) of the L? liquid crystalline phase transition from DSC was used to probe the thermodynamics of the different lipids in the two systems as a function of Chol content. The main chain (13)C (CH2)n resonance is resolved in the (13)C CP-MAS NMR spectra for the unsaturated (DOPC) and saturated (eSM or DPPC) chain lipid in the ternary lipid raft mixtures. The (13)C chemical shift of this resonance can be used to detect differences in chain ordering and overall interactions with Chol for the different lipid constituents in the ternary systems. The combination of DSC and (13)C CP-MAS NMR results indicate that there is a preferential interaction between SM and Chol below Tm for the DOPC/eSM/Chol system when the Chol content is ?20mol%. In contrast, no preferential interaction between Chol and DPPC is observed in the DOPC/DPPC/Chol system above or below Tm. Finally, (13)C CP-MAS NMR resolves two Chol environments in the DOPC/eSM/Chol system below Tm at Chol contents >20mol% while, a single Chol environment is observed for DOPC/DPPC/Chol at all compositions.
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Special consideration is required for the component-resolved diagnosis of egg allergy in infants.
Ann. Allergy Asthma Immunol.
PUBLISHED: 03-09-2013
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There are few reports regarding differences in reactivity to the major egg allergens according to childrens age, although component-resolved diagnosis is gradually being used.
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Dendritic cell expression of the signaling molecule TRAF6 is critical for gut microbiota-dependent immune tolerance.
Immunity
PUBLISHED: 02-21-2013
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The intracellular signaling molecule TRAF6 is critical for Toll-like receptor (TLR)-mediated activation of dendritic cells (DCs). We now report that DC-specific deletion of TRAF6 (TRAF6?DC) resulted, unexpectedly, in loss of mucosal tolerance, characterized by spontaneous development of T helper 2 (Th2) cells in the lamina propria and eosinophilic enteritis and fibrosis in the small intestine. Loss of tolerance required the presence of gut commensal microbiota but was independent of DC-expressed MyD88. Further, TRAF6?DC mice exhibited decreased regulatory T (Treg) cell numbers in the small intestine and diminished induction of iTreg cells in response to model antigen. Evidence suggested that this defect was associated with diminished DC expression of interleukin-2 (IL-2). Finally, we demonstrate that aberrant Th2 cell-associated responses in TRAF6?DC mice could be mitigated via restoration of Treg cell activity. Collectively, our findings reveal a role for TRAF6 in directing DC maintenance of intestinal immune tolerance through balanced induction of Treg versus Th2 cell immunity.
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Specific nephrotoxicity and cardiotoxicity of BT-CAL®, Sigma Anti-bonding Molecule Calcium Carbonate, in mice.
Lab Anim Res
PUBLISHED: 02-06-2013
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According to a high anti-osteoporotic efficacy of Sigma Anti-bonding Molecule Calcium Carbonate (SAC), repeated-dose toxicities of SAC were investigated to assess its feasibility as drug or functional food ingredient. Male ICR mice were given drinking water containing 0.006, 0.02 or 0.06% SAC for 4 weeks. SAC feeding decreased the body weights and feed and water consumptions of mice in a dose-dependent manner, especially, leading to severe emaciation and 70% death in 3 weeks in the high-dose (0.06%) group. Not only kidney and heart weights, but also the levels of blood urea nitrogen, creatinine, aspartate transaminase, and creatine phospokinase significantly increased after SAC administration, indicative of nephrotoxicity and cardiotoxicity. Such renal and cardiac toxicities were also confirmed by microscopic findings, exhibiting renal crystals and cardiac fibrosis, which may be due to the insoluble crystal formation and calcium overload, respectively. In conclusion, it is suggested that no observed adverse effect level of SAC is lower than 0.006% in mice, and that a long-term intake may cause serious adverse effects on renal and cardiac functions.
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Nutrient intake and food restriction in children with atopic dermatitis.
Clin Nutr Res
PUBLISHED: 01-29-2013
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This study was performed to investigate the status of food restriction and the list of restricted foods in children with moderate to severe atopic dermatitis (AD), and to find out the effect of food restriction on the changes in nutrient intake and the severity of the disease. Sixty two patient children aged 12 months to 13 years presenting AD with a SCORing of Atopic Dermatitis (SCORAD) index between 20 and 50 were enrolled. The presence of food limitation, and list of restricted foods were surveyed through the caretakers and the patients were divided into 3 groups by the number of restricted food: non-restricted group, one to three restricted group, and more than three restricted group. Dietary intake was assessed for 3 months using a food frequency questionnaire (FFQ). Half of the subjects restricted foods. The restriction was higher in the order of soda, food additives, walnut, peanut, and other nuts as a single food item; and shellfish and crustacean group, processed foods, nuts, milk & dairy products, and meats as a food group. More than three restricted group ingested more fruits and less fish and meats, resulting in high consumption of vitamin C (p = 0.027). No significant difference in the ratio of nutrient intake by the number of restricted foods was observed in other nutrients. Significant improvement of AD symptom was observed in non-restricted group (p = 0.036) and one to three restricted group (p = 0.003). It is necessary to provide proper nutrition information and systematic and continuous nutrition management for balanced nutrient intake and disease improvement in children with AD.
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Reprogramming of mouse fibroblasts into induced pluripotent stem cells with Nanog.
Biochem. Biophys. Res. Commun.
PUBLISHED: 01-16-2013
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Oct4-Sox2-Nanog transcriptional networks are critical for the maintenance of embryonic stem (ES) cell self-renewal and induction of pluripotency. However, in transcription factor-induced reprogramming of somatic cells into induced pluripotent stem cells (iPSCs), Nanog is initially dispensable and Oct4 remains the sole factor that could not be substituted/omitted. Here, we show that mouse fibroblasts could be reprogrammed into iPSCs by Nanog and Bmi1, which replaces Sox2, Klf4, and c-Myc, in the absence of Oct4. Furthermore, we show that in the presence of shh agonists (oxysterol and purmophamine), which replaces the function of Bmi1, a single transcription factor, Nanog is sufficient to reprogram mouse fibroblasts into iPSCs. Nanog-induced iPSCs resemble mESCs in terms of morphology, global gene expression profiles, epigenetic status and pluripotency both in vitro and in vivo. These findings support that Nanog can replace the Oct4 for the somatic cell reprogramming and underlie the mechanisms of Nanog in reprogramming process.
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Musicians show general enhancement of complex sound encoding and better inhibition of irrelevant auditory change in music: an ERP study.
Eur. J. Neurosci.
PUBLISHED: 01-10-2013
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Using electrophysiology, we have examined two questions in relation to musical training - namely, whether it enhances sensory encoding of the human voice and whether it improves the ability to ignore irrelevant auditory change. Participants performed an auditory distraction task, in which they identified each sound as either short (350 ms) or long (550 ms) and ignored a change in timbre of the sounds. Sounds consisted of a male and a female voice saying a neutral sound [a], and of a cello and a French Horn playing an F3 note. In some blocks, musical sounds occurred on 80% of trials, while voice sounds on 20% of trials. In other blocks, the reverse was true. Participants heard naturally recorded sounds in half of experimental blocks and their spectrally-rotated versions in the other half. Regarding voice perception, we found that musicians had a larger N1 event-related potential component not only to vocal sounds but also to their never before heard spectrally-rotated versions. We therefore conclude that musical training is associated with a general improvement in the early neural encoding of complex sounds. Regarding the ability to ignore irrelevant auditory change, musicians accuracy tended to suffer less from the change in timbre of the sounds, especially when deviants were musical notes. This behavioral finding was accompanied by a marginally larger re-orienting negativity in musicians, suggesting that their advantage may lie in a more efficient disengagement of attention from the distracting auditory dimension.
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The indoor level of house dust mite allergen is associated with severity of atopic dermatitis in children.
J. Korean Med. Sci.
PUBLISHED: 01-08-2013
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We attempted to investigate the correlation between the severity of atopic dermatitis (AD) in children and the indoor level of house dust mite (HDM) allergens. Ninety-five patients (31.1 ± 19.5 months of age) with AD were enrolled in this study, and serum specific IgE against Dermatophagoides pteronyssinus and D. farinae was measured. The severity of AD was assessed using the visual analogue scale on the same day of house dust collection. Living rooms and mattresses where the child usually slept were vacuumed for 2 minutes and concentrations of Der f 1 were measured by enzyme-linked immunosorbent assay. The skin symptoms were more severe in patients with Der f 1 concentrations in living room > 2 µg/g dust than ? 2 µg/g dust (P = 0.018). This difference was noted in AD patients without sensitization to HDM (P = 0.004), but not in patients with sensitization. There was no difference in symptom severity according to Der f 1 concentrations in mattresses (P = 0.062). The severity of skin symptoms is associated with indoor concentrations of HDM in children with AD, and it is likely to act as nonspecific irritants as well as allergens in AD skin lesions.
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Genomic makeup of the marine flavobacterium Nonlabens (Donghaeana) dokdonensis and identification of a novel class of rhodopsins.
Genome Biol Evol
PUBLISHED: 01-08-2013
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Rhodopsin-containing marine microbes such as those in the class Flavobacteriia play a pivotal role in the biogeochemical cycle of the euphotic zone (Fuhrman JA, Schwalbach MS, Stingl U. 2008. Proteorhodopsins: an array of physiological roles? Nat Rev Microbiol. 6:488-494). Deciphering the genome information of flavobacteria and accessing the diversity and ecological impact of microbial rhodopsins are important in understanding and preserving the global ecosystems. The genome sequence of the orange-pigmented marine flavobacterium Nonlabens dokdonensis (basonym: Donghaeana dokdonensis) DSW-6 was determined. As a marine photoheterotroph, DSW-6 has written in its genome physiological features that allow survival in the oligotrophic environments. The sequence analysis also uncovered a gene encoding an unexpected type of microbial rhodopsin containing a unique motif in addition to a proteorhodopsin gene and a number of photolyase or cryptochrome genes. Homologs of the novel rhodopsin gene were found in other flavobacteria, alphaproteobacteria, a species of Cytophagia, a deinococcus, and even a eukaryote diatom. They all contain the characteristic NQ motif and form a phylogenetically distinct group. Expression analysis of this rhodopsin gene in DSW-6 indicated that it is induced at high NaCl concentrations, as well as in the presence of light and the absence of nutrients. Genomic and metagenomic surveys demonstrate the diversity of the NQ rhodopsins in nature and the prevalent occurrence of the encoding genes among microbial communities inhabiting hypersaline niches, suggesting its involvement in sodium metabolism and the sodium-adapted lifestyle.
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Single n-GaN microwire/p-Silicon thin film heterojunction light-emitting diode.
Opt Express
PUBLISHED: 11-24-2011
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The emission and waveguiding properties of individual GaN microwires as well as devices based on an n-GaN microwire/p-Si (100) junction were studied for relevance in optoelectronics and optical circuits. Pulsed photoluminescence of the GaN microwire excited in the transverse or longitudinal direction demonstrated gain. These n-type GaN microwires were positioned mechanically or by dielectrophoretic force onto pre-patterned electrodes on a p-type Si (100) substrate. Electroluminescence from this p-n point junction was characteristic of a heterostructure light-emitting diode. Additionally, waveguiding was observed along the length of the microwire for light originating from photoluminescence as well as from electroluminescence generated at the p-n junction.
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The standard range of peak expiratory flow rates of Korean children.
Asian Pac. J. Allergy Immunol.
PUBLISHED: 10-11-2011
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The importance in asthma management of monitoring of peak expiratory flow rate (PEFR) has been emphasized.
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Genome sequence of an ammonia-oxidizing soil archaeon, "Candidatus Nitrosoarchaeum koreensis" MY1.
J. Bacteriol.
PUBLISHED: 09-15-2011
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Ammonia-oxidizing archaea are ubiquitous microorganisms which play important roles in global nitrogen and carbon cycle on earth. Here we present the high-quality draft genome sequence of an ammonia-oxidizing archaeon, "Candidatus Nitrosopumilus koreensis" MY1, that dominated an enrichment culture of a soil sample from the rhizosphere. Its genome contains genes for survival in the rhizosphere environment as well as those for carbon fixation and ammonium oxidation to nitrite.
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Nanostructured n-ZnO / thin film p-silicon heterojunction light-emitting diodes.
Opt Express
PUBLISHED: 09-02-2011
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Electroluminescence (EL) was obtained from a p-Si (100) thin film/nanostructured n-ZnO heterojunction diode fabricated by a simple dielectrophoresis (DEP) method. The Si substrate was pre-patterned with electrodes and an insulating separation layer by a standard photolithographic process. ZnO nanostructures were formed by a simple solution chemistry and subsequently transferred to the pre-patterned substrate. Application of the DEP force at a frequency of 100 kHz and 6 V peak-to-peak voltage allowed precise positioning of the ZnO nanostructures at the edge of the metal electrodes. The physically formed p-Si (100) thin film/nanostructured n-ZnO heterojunction displayed multi-color emission from the ZnO near band edge as well as emission from defective states within the ZnO band gap.
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Changes in Major Peanut Allergens Under Different pH Conditions.
Allergy Asthma Immunol Res
PUBLISHED: 08-09-2011
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Regional dietary habits and cooking methods affect the prevalence of specific food allergies; therefore, we determined the effects of various pH conditions on major peanut allergens. Peanut kernels were soaked overnight in commercial vinegar (pH 2.3) or acetic acid solutions at pH 1.0, 3.0, or 5.0. Protein extracts from the sera of seven patients with peanut-specific IgE levels >15 kU(A)/L were analyzed by SDS-PAGE and immunolabeling. A densitometer was used to quantify and compare the allergenicity of each protein. The density of Ara h 1 was reduced by treatment with pH 1.0, 3.0, or 5.0 acetic acid, or commercial vinegar. Ara h 2 remained largely unchanged after treatment with pH 5.0 acetic acid, and was decreased following treatment with pH 1.0, 2.3, or 3.0 acetic acid. Ara h 3 and Ara h 6 appeared as a thick band after treatment with pH 1.0 acetic acid and commercial vinegar. IgE-binding intensities to Ara h 1, Ara h 2, and Ara h 3 were significantly reduced after treatment with pH 1.0 acetic acid or commercial vinegar. These data suggest that treatment with acetic acid at various pH values affects peanut allergenicity and may explain the low prevalence of peanut allergy in Korea.
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Three-dimensional multilayered nanostructures with controlled orientation of microdomains from cross-linkable block copolymers.
ACS Nano
PUBLISHED: 07-20-2011
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Three-dimensional (3D) nanostructures were obtained by the directed formation of multilayer block copolymer (BCP) thin films. The initial step in this strategy involves the assembly and cross-linking of cylinder-forming polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) BCP, in which 1.5 mol % of reactive azido (-N(3)) groups were randomly incorporated along the styrene backbone. Significantly, assembly of thin films of lamellar-forming BCPs on top of the underlying cross-linked cylindrical layer exhibited perpendicular orientations of microdomains between lamellae and cylinder layers. From the theoretical calculation of free energy in the multilayers, it was found that the nematic interactions between polymer chains at the interface play a critical role in the perpendicular orientation of lamellae on the cross-linked cylinder layers. Removal of the PMMA domains then affords nonsymmetrical nanostructures which illustrate the promise of this strategy for the design of well-defined 3D nanotemplates. It was also demonstrated that this structure can be effectively used to enhance the light extraction efficiency of GaN light-emitting diodes. Furthermore, we anticipate that such 3D nanotemplates can be applied to various areas, including advanced BCP nanolithography and responsive surface coating.
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Draft genome sequence of the Paenibacillus polymyxa type strain (ATCC 842T), a plant growth-promoting bacterium.
J. Bacteriol.
PUBLISHED: 07-08-2011
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Paenibacillus polymyxa is an endospore-forming Gram-positive soil bacterium that is well-known for its ability to promote plant growth. Here we report the draft genome sequence of P. polymyxa ATCC 842(T), the type strain of the species P. polymyxa, and the family Paenibacillaceae. The P. polymyxa genome contains a repertoire of biosynthetic genes for antibiotics and hydrolytic enzymes that account for its beneficial effects in the rhizosphere to the host plants it associates with.
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A proposal: Atopic Dermatitis Organizer (ADO) guideline for children.
Asia Pac Allergy
PUBLISHED: 07-01-2011
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Atopic dermatitis (AD) is the most common chronic inflammatory skin disorder in children, with a worldwide cumulative prevalence in children of 8-20%. The number of AD patients is beyond the level that can be dealt with at clinics and it is time to make an effort to reduce the number of AD patients in the community. Thus, caregivers and all persons involved with AD management, including health care providers, educators, technologists and medical policy makers, should understand the development and the management of AD. Although a number of guidelines such as Practical Allergy (PRACTALL) report have been developed and used, community understanding of these is low. This is probably because there are still remarkable differences in management practices between specialists and between countries and most of the reported guidelines have been prepared for physicians. From the viewpoint of providing a basis for a multidisciplinary team approach, easily comprehensible guidelines for organizing treatment of AD, i.e. an Atopic Dermatitis Organizer (ADO), are required. guidelines should be simple and well organized. We suggest an easy approach with a new classification of AD symptoms into early and/or progressive lesions in acute and/or chronic symptoms. The contents of this ADO guideline basically consist of 3 steps approaches: conservative management, topical anti-inflammatory therapy, and systemic anti-inflammatory therapy.
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Complete genome sequence of the polycyclic aromatic hydrocarbon-degrading bacterium Alteromonas sp. strain SN2.
J. Bacteriol.
PUBLISHED: 06-24-2011
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Alteromonas sp. strain SN2, able to metabolize polycyclic aromatic hydrocarbons, was isolated from a crude oil-contaminated sea-tidal flat. Here we report the complete 4.97-Mb genome sequence and annotation of strain SN2. These will advance the understanding of strain SN2s adaptation to the sea-tidal flat ecosystem and its pollutant metabolic versatility.
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Fabrication of GaAs subwavelength structure (SWS) for solar cell applications.
Opt Express
PUBLISHED: 06-07-2011
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We developed a novel GaAs subwavelength structure (SWS) as an antireflective layer for solar cell applications. The GaAs SWS patterns were fabricated by a combination of nanosphere lithography (NSL) and reactive ion etching (RIE). The shape and height of the GaAs SWS were controlled by the diameter of the SiO2 nanospheres and the etching time. Various GaAs SWS were characterized by the reflectance spectra. The average reflectance of the polished GaAs substrate from 200nm to 800nm was 35.1%. However, the average reflectance of the tapered GaAs SWS was reduced to 0.6% due to scattering and moth-eye effects.
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Sensitization to aeroallergens in Korean children: a population-based study in 2010.
J. Korean Med. Sci.
PUBLISHED: 06-02-2011
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We performed this study to assess the prevalence of sensitization to aeroallergens and to analyze the difference between prevalence rates according to childrens ages and residential areas. In this nationwide cross-sectional study, first grade students of 45 elementary schools and 40 middle schools were randomly selected, and skin prick tests were performed for 18 inhalant allergens between October and November 2010. Of 7,829 analyzed subjects, 3,753 (47.9%) were sensitized to at least one aeroallergen. Sensitization to Dermatophagoides farinae was found to be the most prevalent in elementary schoolchildren (32.4%), followed by Dermatophagoides pteronyssinus, Tyrophagus putrescentiae, Japanese hop, and oak. In middle schoolchildren, D. pteronyssinus yielded the highest prevalence (42.7%), followed by D. farinae, T. putrescentiae, Japanese hop, and cat. In middle schoolchildren, the sensitization rate to aeroallergens in metropolitan, urban, and rural areas was 57.2%, 54.3%, and 49.8%, respectively (P = 0.019). In this age group, the sensitization rate in low, middle, high, and very high income groups was 53.8%, 51.8%, 59.0%, and 59.6%, respectively (P = 0.002). In conclusion, the sensitization rate is 47.9% and house dust mite is the most prevalent allergen in the pediatric population in Korea. The rate is higher in metropolitan areas and the highest income group than in rural areas and low income groups.
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LEOPARD Syndrome with PTPN11 Gene Mutation Showing Six Cardinal Symptoms of LEOPARD.
Ann Dermatol
PUBLISHED: 05-27-2011
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LEOPARD multiple congenital anomaly syndrome inherited in an autosomal dominant manner. LEOPARD is an acronym for Lentigines, Eletrocardiographic conduction defects, Ocular hypertelorism, Pulmonary valve stenosis, Abnormalities of the genitalia, Retardation of growth, and Deafness. Clinical diagnosis is primarily based on multiple lentigines, typical facial features, and the presence of hypertrophic cardiomyopathy and/or café-au-lait macules. We report a typical case of LEOPARD syndrome with PTPN11 gene mutation associated with lentigines, electrocardiograph abnormality, ocular hypertelorism, pulmonary valve stenosis, growth retardation, and sensorineural hearing loss.
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Feasibility of rat hair as a quality control material for the determination of methamphetamine and amphetamine in human hair.
Arch. Pharm. Res.
PUBLISHED: 05-05-2011
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A quality control material (QCM) is a necessity in hair drug analysis, but it is not always easy to have an authentic hair sample containing various target drugs and metabolites. In the present study, the feasibility of rat hair as a QCM was examined for its application in the determination of methamphetamine (MA) and amphetamine (AP) in human hair. MA was administered to lean Zucker rats, from which only pigmented hair was collected for the preparation of a QCM. The rat hair was then washed, homogenized and finally bottled. Both homogeneity and stability were examined in order to demonstrate the suitability of rat hair as a QCM in hair drug analysis. The concentrations of MA and AP in each bottle were determined using extraction with 1% HCl in methanol at 38°C followed by gas chromatography/mass spectrometry after derivatization with trifluoroacetic anhydride. Furthermore, the prepared QCM was used in an inter-laboratory quality assurance program. In the homogeneity test, no significant difference was observed between bottles of the QCM. The statistical results also showed no significant trends in stability for three months at room temperature. An inter-laboratory quality assurance program was also performed successfully using this material. Thus, rat hair will be useful as an alternative QCM sample for the determination of a variety of drugs and their metabolites in human hair.
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The incidence and risk factors of immediate type food allergy during the first year of life in Korean infants: a birth cohort study.
Pediatr Allergy Immunol
PUBLISHED: 05-04-2011
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We conducted this study to determine the incidence of food allergy (FA) in Korean infants and identify the risk factors of FAs during the first year of life in a birth cohort study.
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Prolonged bedtime bottle feeding and respiratory symptoms in infants.
Asia Pac Allergy
PUBLISHED: 04-05-2011
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Infants with chronic respiratory symptoms should be evaluated thoroughly because there are various causes which are different from those of children and adolescents.
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Natural course of cows milk allergy in children with atopic dermatitis.
J. Korean Med. Sci.
PUBLISHED: 03-14-2011
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Cows milk is one of the most common food allergens in children with atopic dermatitis (AD). This study was conducted to describe the natural course of cows milk allergy in children with AD, and to identify factors predictive of outcome. To accomplish this, we reviewed the medical records of 115 children who were diagnosed with AD and cows milk allergy before 24 months of age to evaluate their clinical characteristics and prognostic factors. During a follow-up period of 24 to 114 months, the median age for tolerance to cows milk was found to be 67 months. Multivariate analysis using the Cox proportional hazard model revealed that the peak cows milk-specific IgE level within 24 months after birth was the most important factor for prediction of the outcome of cows milk allergy. In conclusion, half of the children younger than 24 months of age with AD and cows milk allergy could tolerate cows milk at 67 months of age. The peak cows milk-specific IgE level within the first 24 months of birth is useful to predict the prognosis of cows milk allergy in children with AD.
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Association of infant feeding practices in the general population with infant growth and stool characteristics.
Nutr Res Pract
PUBLISHED: 03-10-2011
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This was a prospective cohort study of 976 infants from birth to 12 months of age. Infants were fed breast milk, goat infant formula, cow infant formula, or a combination of formula and breast milk during the first 4 months of age. Data on type of milk feeding and infant growth (weight and height) were collected at birth and at 4, 8, and 12 months during routine clinical assessment. The number and consistency of bowel motions per day were recorded based on observational data supplied by the mothers. Infants fed breast milk or goat or cow infant formula during the first 4 months displayed similar growth outcomes. More of the infants fed cow infant formula had fewer and more well-formed bowel motions compared with breast-fed infants. The stool characteristics of infants fed goat formula resembled those of infants fed breast milk.
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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.