JoVE Visualize What is visualize?
Stop Reading. Start Watching.
Advanced Search
Stop Reading. Start Watching.
Regular Search
Find video protocols related to scientific articles indexed in Pubmed.
Evaluation of the Bruker Biotyper matrix-assisted laser desorption ionization-time of flight mass spectrometry system for identification of blood isolates of Acinetobacter species.
J. Clin. Microbiol.
PUBLISHED: 06-04-2014
Show Abstract
Hide Abstract
Matrix-assisted laser desorption ionization-time of flight mass spectrometry (MALDI-TOF MS) (Bruker Biotyper) was able to accurately identify 98.6% (142/144) of Acinetobacter baumannii isolates, 72.4% (63/87) of A. nosocomialis isolates, and 97.6% (41/42) of A. pittii isolates. All Acinetobacter junii, A. ursingii, A. johnsonii, and A. radioresistens isolates (n = 28) could also be identified correctly by Bruker Biotyper.
Related JoVE Video
A cluster of endophthalmitis caused by Mycobacterium abscessus after cataract surgery.
J Microbiol Immunol Infect
PUBLISHED: 01-29-2014
Show Abstract
Hide Abstract
We report two cases of postoperative endophthalmitis after cataract surgery caused by the same strain of Mycobacterium abscessus confirmed by arbitrarily primed polymerase chain reaction, sequencing of the erythromycin ribosome methyltransferase gene and pulsed-field gel electrophoresis. The outcomes were poor despite aggressive treatments. This is the first report of nontuberculous mycobacteria as a causative pathogen for a cluster of endophthalmitis.
Related JoVE Video
Acute Meningitis Caused by Cladosporium sphaerospermum.
Am. J. Med. Sci.
PUBLISHED: 11-23-2013
Show Abstract
Hide Abstract
: Phaeohyphomycosis of the central nervous system is rare but typically associated with high mortality. Treatment has not been standardized, but the combination of antifungal chemotherapy with surgical debridement is recommended. We report a 73-year-old, retired, male timber merchant with acute meningitis caused by Cladosporium sphaerospermum. The patient, who had well-controlled type 2 diabetes mellitus, presented with fever and weakness of the lower limbs. No brain abscess was apparent by cranial computed tomography. C. sphaerospermum was isolated from the cerebral spinal fluid and identified based on both morphology and DNA sequencing. He was treated with combination antifungal chemotherapy with amphotericin B and voriconazole for 28 days, followed by voriconazole monotherapy for 46 days. To date, the patient has recovered without significant sequelae. This patient represents the first reported case of cerebral phaeohyphomycosis caused by C. sphaerospermum. Moreover, the therapy was successful for totally less than 3 months of treatment duration.
Related JoVE Video
Acrophialophora fusispora brain abscess in a patient with acquired immunodeficiency syndrome: a case report and review of the literature.
Diagn. Microbiol. Infect. Dis.
PUBLISHED: 02-16-2013
Show Abstract
Hide Abstract
We reported a fatal case of brain abscess caused by Acrophialophora fusispora in a patient with acquired immunodeficiency syndrome. Identification of the fungus was based on microscopic morphology and sequence analyses of the internal transcribed spacer 1 (ITS1) and 2 (ITS2) of ribosomal RNA gene from the isolate recovered from brain abscess. Four published cases were reviewed as well.
Related JoVE Video
Evaluation of a membrane array for detection of Mycobacterium tuberculosis complex and nontuberculous mycobacteria in positive liquid cultures.
Diagn. Microbiol. Infect. Dis.
PUBLISHED: 01-02-2013
Show Abstract
Hide Abstract
Molecular identification of mycobacteria in positive Mycobacteria Growth Indicator Tube (MGIT) cultures can accelerate mycobacterial diagnosis. A membrane hybridization array (Blue Point) was evaluated for this purpose in 284 positive MGIT cultures. Discrepant results were resolved by testing with the GenoType Mycobacterium kit, TBc ID test, sequencing of the 16S rRNA gene and internal transcribed spacer. Total recovery from culture and the array (if confirmed) was considered 100%. The sensitivity, specificity, positive, and negative predictive values of the array for detection of Mycobacterium tuberculosis complex were 99.4%, 100%, 100%, and 99.2%, respectively, while the corresponding values of culture were 95.1%, 100%, 100%, and 93.8%, respectively, with significant differences in sensitivity and negative predictive value being found between the 2 methods. The recoveries of nontuberculous mycobacteria and mixed cultures of the array were also significantly higher than those of culture. The array can be adopted in routine mycobacteriology laboratory.
Related JoVE Video
Profiling of influenza viruses by high-throughput carbohydrate membrane array.
Future Med Chem
PUBLISHED: 03-31-2011
Show Abstract
Hide Abstract
Carbohydrate-protein interactions participate in many biological functions. To characterize the binding interactions represents a longstanding challenge.
Related JoVE Video
Evaluation of the Bactec MGIT 960 system in combination with the MGIT TBc identification test for detection of Mycobacterium tuberculosis complex in respiratory specimens.
J. Clin. Microbiol.
PUBLISHED: 03-30-2011
Show Abstract
Hide Abstract
The sensitivity and specificity of the MGIT TBc identification (TBc ID) test for Mycobacterium tuberculosis complex (MTC) detection in positive Bactec MGIT cultures were 95.2% and 99.2%, respectively. When MTC-positive results obtained from two additional molecular methods were included, the sensitivity of the MGIT TBc ID test was 85.4%, while that of culture was 95.7%.
Related JoVE Video
Identification of lethal Aspergillus at early growth stages based on matrix-assisted laser desorption/ionization time-of-flight mass spectrometry.
Diagn. Microbiol. Infect. Dis.
PUBLISHED: 03-09-2011
Show Abstract
Hide Abstract
Delayed and incorrect diagnoses are potential risk factors leading to high mortality of invasive aspergillosis (IA). Matrix-assisted laser desorption/ionization time-of-flight mass spectrometry was used to acquire a wide mass spectral range and characterize the early process of asexual sporulation of lethal IA pathogens recovered on agar plates. Proteins were extracted using trifluoroacetic acid and soft ionized using an ultraviolet laser with the assistance of ferulic acid. At the second stage of sporulation with various differentiated structures, there are more specific peaks that can be used to discriminate different Aspergillus species than at the first stage, which features vegetative hyphae. Certain specific peaks are found in different strains of the same species, Aspergillus fumigatus. In addition, the relative standard deviations of the m/z ratios are much smaller than those of the relative intensities in these peaks. Therefore, common lethal Aspergillus species can be identified after short-term cultivation by matching species-specific m/z values.
Related JoVE Video
Evaluation of the Cobas TaqMan MTB test for direct detection of Mycobacterium tuberculosis complex in respiratory specimens.
J. Clin. Microbiol.
PUBLISHED: 12-22-2010
Show Abstract
Hide Abstract
The Cobas TaqMan MTB test, based on real-time PCR technology, was evaluated for direct detection of Mycobacterium tuberculosis complex (MTBC) in respiratory specimens. A total of 1,093 samples from 446 patients, including 118 acid-fast smear-positive and 975 acid-fast smear-negative specimens, were investigated. Diagnostic cultures performed with 7H11 agar, Löwenstein-Jensen medium, and the Bactec MGIT 960 system were considered the reference methods. When discrepant results between the Cobas TaqMan MTB test and culture occurred, additional results from the BD MGIT TBc identification test and the GenoType Mycobacterium CM test performed on growth-positive and acid-fast-stain-positive MGIT tubes and review of the patients medical history were used for discrepancy analysis. The overall sensitivity, specificity, positive predictive value, and negative predictive value for the Cobas TaqMan MTB test were 91.5%, 98.7%, 91.5%, and 98.7%, respectively. In general, the performance of the new Cobas TaqMan MTB test was comparable to that of the replaced Cobas Amplicor MTB system. The most prominent feature of the new system was its extraordinarily high sensitivity (79.5%) for detecting MTBC in smear-negative specimens; out of 44 smear-negative but culture-positive specimens, 35 were positive by the new system. The Cobas TaqMan MTB assay, including DNA extraction, can be completed within 3 h.
Related JoVE Video
Electro-microchip DNA-biosensor for bacteria detection.
Analyst
PUBLISHED: 08-12-2010
Show Abstract
Hide Abstract
This paper presents a bacteria biosensor based on DNA hybridization detection with an electro-microchip transducer. Acinetobacter baumannii was chosen as DNA sample source, because the occurrence of bacteremia caused by Acinetobacter baumannii is high in hospitals worldwide. Our strategy is based on DNA hybridization of PCR amplified bacteria DNA with biotin labelled primers and detection enhancement using gold-streptavidin nanoparticles and Ag(+)-hydroquinone solution. Gold nanoparticles catalyze silver ions reduction by hydroquinone. The gradually precipitated silver metal between the two electrodes of the electro-microchip allows electrons to pass. The detection limit for Acinetobacter baumannii genomic DNA sample is 0.825 ng mL(-1) (1.2 fM). Probe specificity was investigated by screening various species of bacteria, various strains of a single species and various species of a single genus. The proposed DNA hybridization method is easy, convenient, and rapid. Moreover, it has potential applications in detection of bacteria causing infections and clinical diagnosis.
Related JoVE Video
A newly developed immunoassay method based on optical measurement for Protein A detection.
Talanta
PUBLISHED: 06-22-2010
Show Abstract
Hide Abstract
We describe the development of an immunoassay using an antibody-silver nanoparticle (Ab-AgNP) conjugate as a catalyst for the silver enhancement reaction. The immuno-reaction signals that were magnified by silver metal precipitation were quantified using a commercial flatbed scanner. Protein A from Staphylococcus aureus (S. aureus), a common clinical pathogenic bacterium, was used in this research. The ease of infection of S. aureus necessitates the development of a fast detection method. The framework of the method described in this paper is based on the sandwich immunoassay and contains a 1st antibody (immunoglobulin G, IgG), an antigen (Protein A), and a 2nd antibody-colloidal silver conjugate (IgG-AgNPs). The silver enhancement reaction, a signal amplification method in which silver ions are reduced to metallic silver, is used to magnify the immuno-reaction signal. The change in signal, as visualized in grayscale, can be easily observed and analyzed by our optical scanning detection system. The relationship between antigen concentration and grayscale value is discussed. The detectable concentration limit for the antigen was found to be 1 ng/mL with 10 ?g/mL of IgG and 300 ?M of the IgG-AgNP conjugate. This immunoassay method provides the advantages of low cost, easy operation, and short detection time. Moreover, it has potential applications in clinical diagnoses.
Related JoVE Video
Grape seed extract inhibits the growth and pathogenicity of Staphylococcus aureus by interfering with dihydrofolate reductase activity and folate-mediated one-carbon metabolism.
Int. J. Food Microbiol.
PUBLISHED: 04-16-2010
Show Abstract
Hide Abstract
Staphylococcus aureus (S. aureus) is one of the most common pathogens that causes infectious and foodborne diseases worldwide. Searching for drug and chemical compounds against this bacterium is still in demand. We found that grape seed extract (GSE), a natural food product rich in polyphenols, inhibited the dihydrofolate reductase activity and growth of S. aureus. In addition, the intracellular content of tetrahydrofolate (THF), the major folate species identified in S. aureus, was significantly decreased when GSE was present in medium. The GSE-induced growth inhibition was reversed by adding, THF, 5,10-methylenetetrahydrofolate or methionine to the medium. The differential rescuing effects elicited by thymidine and methionine indicated that GSE-induced perturbation in folate-mediated one-carbon metabolism has more profound impact on methionine cycle than on thymidine monophosphate (TMP) synthesis. Significantly reduced inflammatory responses and mortality were observed in zebrafish infected with S. aureus pre-incubated with GSE. We conclude that GSE might serve as an effective natural alternative for the control of food poisoning caused by S. aureus with proper safety measure.
Related JoVE Video
Clinical manifestations, antimicrobial therapy, and prognostic factors of monomicrobial Acinetobacter baumannii complex bacteremia.
J. Infect.
PUBLISHED: 03-17-2010
Show Abstract
Hide Abstract
Bacteremia due to Acinetobacter baumannii complex (ABC), which composed of four genomic species (gen. sp.), is a serious and potentially fatal condition. The epidemiology and outcome of such infections due to individual gen. sp. remain undefined.
Related JoVE Video
Identification of clinically important anaerobic bacteria by an oligonucleotide array.
J. Clin. Microbiol.
PUBLISHED: 02-03-2010
Show Abstract
Hide Abstract
Anaerobic bacteria can cause a wide variety of infections, and some of these infections can be serious. Conventional identification methods based on biochemical tests are often lengthy and can produce inconclusive results. An oligonucleotide array based on the 16S-23S rRNA intergenic spacer (ITS) sequences was developed to identify 28 species of anaerobic bacteria and Veillonella. The method consisted of PCR amplification of the ITS regions with universal primers, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 35 oligonucleotide probes (17- to 30-mers) immobilized on a nylon membrane. The performance of the array was determined by testing 310 target strains (strains which we aimed to identify), including 122 reference strains and 188 clinical isolates. In addition, 98 nontarget strains were used for specificity testing. The sensitivity and the specificity of the array for the identification of pure cultures were 99.7 and 97.1%, respectively. The array was further assessed for its ability to detect anaerobic bacteria in 49 clinical specimens. Two species (Finegoldia magna and Bacteroides vulgatus) were detected in two specimens by the array, and the results were in accordance with those obtained by culture. The whole procedure of array hybridization took about 8 h, starting with the isolated colonies. The array can be used as an accurate alternative to conventional methods for the identification of clinically important anaerobes.
Related JoVE Video
Using an electro-microchip, a nanogold probe, and silver enhancement in an immunoassay.
Biosens Bioelectron
PUBLISHED: 05-27-2009
Show Abstract
Hide Abstract
This paper presents a novel immunoassay that uses an electro-microchip to detect the immuno-reaction signal, gold nanoparticles (ANPs) as a label of antigen or antibody and as a catalyst for silver precipitation, and the silver enhancement reaction to magnify the detection signal. This study is based on the direct immunoassay (two-layer format) and the sandwich immunoassay (three-layer format). The ANPs were introduced into the electro-microchip by the specific binding of the antibodies-ANPs conjugates and then were coupled with silver enhancement to produce black spots of silver metal. The silver precipitation constructs a "bridge" between two electrodes of the electro-microchip allowing electrons to pass. The variation of impedance can be easily measured with a commercial LCR meter. Various gap sizes (20, 50, 100, and 200 microm) of the electrodes of electro-microchips were designed for the sensitivity study. The experimental data show that a chip with a 20microm gap has the highest sensitivity. There was a significant difference in impedance between the experiment sample and the negative control after 10 min of reaction time. The proposed method requires less time and fewer steps than the conventional enzyme-linked immunosorbent assay (ELISA). In addition, it shows a high detection sensitivity (10 microg/mL of 1st antibody (IgG) immobilized on slides and 1 ng/mL of antigen (protein A)). There is a clear distinction between the signal intensity and the logarithm of the sample concentration. The proposed new immunoassay method has potential applications in proteomics research and clinical diagnosis.
Related JoVE Video
Identification of non-fermenting Gram-negative bacteria of clinical importance by an oligonucleotide array.
J. Med. Microbiol.
PUBLISHED: 04-17-2009
Show Abstract
Hide Abstract
Many species of non-fermenting Gram-negative bacilli (non-fermenters) are important opportunistic and nosocomial pathogens. Identification of most species of non-fermenters by phenotypic characteristics can be difficult. In this study, an oligonucleotide array was developed to identify 38 species of clinically relevant non-fermenters. The method consisted of PCR-based amplification of 16S-23S rRNA gene intergenic spacer (ITS) regions using bacterial universal primers, followed by hybridization of the digoxigenin-labelled PCR products with oligonucleotide probes immobilized on a nylon membrane. A total of 398 strains, comprising 276 target strains (i.e. strains belonging to the 38 species to be identified) and 122 non-target strains (i.e. strains not included in the array), were analysed by the array. Four target strains (three reference strains and one clinical isolate) produced discrepant identification by array hybridization. Three of the four discordant strains were found to be correctly identified by the array, as confirmed by sequencing of the ITS and 16S rRNA genes, with the remaining one being an unidentified species. The sensitivity and specificity of the array for identification of non-fermenters were 100 and 96.7%, respectively. In summary, the oligonucleotide array described here offers a very reliable method for identification of clinically relevant non-fermenters, with results being available within one working day.
Related JoVE Video
Pulmonary nodules caused by Schizophyllum commune after cardiac transplantation.
J. Infect.
PUBLISHED: 03-25-2009
Show Abstract
Hide Abstract
The incidence of pulmonary nodules after cardiac transplantation is not uncommon, and prompt diagnostic procedures are necessary to minimize disease-related morbidity and mortality. We report a 56-year-old woman who was found to have bilateral pulmonary nodules four months after cardiac transplantation. The microorganism was identified with a molecular diagnostic method as Schizophyllum commune, which had not been reported in English literature as a pathogen inducing pulmonary nodules after transplantation. She remained asymptomatic during the therapeutic period and the pulmonary nodules resolved six months later.
Related JoVE Video
Identification of legionella species by use of an oligonucleotide array.
J. Clin. Microbiol.
PUBLISHED: 03-04-2009
Show Abstract
Hide Abstract
The genus Legionella contains a diverse group of motile, asaccharolytic, nutritionally fastidious gram-negative rods. Legionella pneumophila is the most important human pathogen, followed by L. micdadei, L. longbeachae, L. dumoffii, and other rare species. Accurate identification of Legionella spp. other than L. pneumophila is difficult because of biochemical inertness and phenotypic identity of different species. The feasibility of using an oligonucleotide array for identification of 18 species of Legionella was evaluated in this study. The method consisted of PCR amplification of the macrophage infectivity potentiator mip gene, followed by hybridization of the digoxigenin-labeled PCR products to a panel of 30 oligonucleotide probes (16- to 24-mers) immobilized on a nylon membrane. A collection of 144 target strains (strains we aimed to identify) and 50 nontarget strains (44 species) were analyzed by the array. Both test sensitivity (144/144 strains) and specificity (50/50 strains) of the array were 100%. The whole procedure for identification of Legionella species by the array can be finished within a working day, starting from isolated colonies. It was concluded that species identification of clinically relevant Legionella spp. by the array method is very reliable and can be used as an accurate alternative to conventional or other molecular methods for identification of Legionella spp.
Related JoVE Video
Development of an oligonucleotide array for direct detection of fungi in sputum samples from patients with cystic fibrosis.
J. Clin. Microbiol.
PUBLISHED: 02-03-2009
Show Abstract
Hide Abstract
Cystic fibrosis (CF) is the most common inherited genetic disease in Caucasian populations. Besides bacteria, many species of fungi may colonize the respiratory tract of these patients, sometimes leading to true respiratory infections. In this study, an oligonucleotide array capable of identifying 20 fungal species was developed to directly detect fungi in the sputum samples of CF patients. Species-specific oligonucleotide probes were designed from the internal transcribed spacer (ITS) regions of the rRNA operon and immobilized on a nylon membrane. The fungal ITS regions were amplified by PCR and hybridized to the array for species identification. The array was validated by testing 182 target strains (strains which we aimed to identify) and 141 nontarget strains (135 species), and a sensitivity of 100% and a specificity of 99.2% were obtained. The validated array was then used for direct detection of fungi in 57 sputum samples from 39 CF patients, and the results were compared to those obtained by culture. For 16 sputum samples, the results obtained by the array corresponded with those obtained by culture. For 33 samples, the array detected more fungal species than culture did, while the reverse was found for eight samples. The accuracy of the array for fungal detection in sputum samples was confirmed (or partially confirmed) in some samples by cloning and resequencing the amplified ITS fragments. The present array is a useful tool for both the simultaneous detection of multiple fungal species present in the sputa of CF patients and the identification of fungi isolated from these patients.
Related JoVE Video
Catheter-related fungemia caused by Candida dubliniensis.
J Microbiol Immunol Infect
Show Abstract
Hide Abstract
Infections caused by Candida dubliniensis in humans are rare and have never been reported in Taiwan. We report two cancer patients with catheter-related fungemia due to C. dubliniensis infection in Taiwan. The two isolates were confirmed to the species level using an oligonucleotide array system and sequence analysis, and both showed high in vitro susceptibilities to nine antifungal agents. The catheters were removed, and both patients responded well to antifungal treatment. Although this type of infection is rare, physicians should consider C. dubliniensis as one of the possible pathogens causing catheter-related infections in Taiwan.
Related JoVE Video
Impact of molecular diagnosis on treating Mendelian susceptibility to mycobacterial diseases.
J Microbiol Immunol Infect
Show Abstract
Hide Abstract
The IL-12-IFN-? axis is critical for immune defense against mycobacterial infections. Inherited mutations that affect normal activation of this self-amplifying cytokine reaction lead to increased chances of mycobacterial infections, known as Mendelian susceptibility to mycobacterial diseases (MSMD). Delayed diagnosis and difficulty in identifying pathogenic mycobacteria hinder proper treatment of patients, so the aim of this study was to facilitate the diagnosis of mycobacterial infections in MSMD patients using an oligonucleotide array method.
Related JoVE Video

What is Visualize?

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

How does it work?

We use abstracts found on PubMed and match them to JoVE videos to create a list of 10 to 30 related methods videos.

Video X seems to be unrelated to Abstract Y...

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.