Microbiology:
The study of microorganisms such as fungi, bacteria, algae, archaea, and viruses.
JoVE General
Collection, Isolation and Enrichment of Naturally Occurring Magnetotactic Bacteria from the Environment
1School of Earth Sciences, The Ohio State University, 2School of Environment & Natural Resources, The Ohio State University, 3Institute of Geology and Geophysics, Chinese Academy of Sciences
We demonstrate a method to collect magnetotactic bacteria (MTB) that can be applied to natural waters. MTB can be isolated and enriched from sediment samples using a relatively simple setup that takes advantage of the bacteria's natural magnetism. Isolated MTB can then be examined in detail using both light and electron microscopy.
JoVE General
Aseptic Laboratory Techniques: Plating Methods
Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
When working with media and reagents used to culture microorganisms, aseptic technique must be practiced to ensure contamination is minimized. A variety of plating methods are routinely used to isolate, propagate, or enumerate bacteria and phage, all of which incorporate procedures that maintain the sterility of experimental materials.
JoVE Immunology and Infection
DNA Fingerprinting of Mycobacterium leprae Strains Using Variable Number Tandem Repeat (VNTR) - Fragment Length Analysis (FLA)
Department of Microbiology, Immunology and Pathology, Colorado State University
Leprosy, caused by Mycobacterium leprae, is still endemic in many places. In order to learn about the spread and mode of transmission of leprosy, it is important to determine which strain of M. leprae has infected a patient. Variable numbers of tandem repeats (VNTR) typing is one such method.
JoVE Application Notes
LookOut Mycoplasma Elimination Kit - ADVERTISEMENT
Product Management, Sigma-Aldrich
The LookOut Mycoplasma elimination kit combines biological agents that reliably and completely eliminate mycoplasma contamination with minimal cytotoxic effect on cells.
JoVE Immunology and Infection
Visualisation and Quantification of Intracellular Interactions of Neisseria meningitidis and Human α-actinin by Confocal Imaging
Department of Cellular and Molecular Medicine, University of Bristol, UK
Neisseria meningitidis (Nm), a gram negative human-specific respiratory pathogen, can bind to human α-actinin. Here we present a protocol for visualisation of colocalisation of the bacterium with intracellular α-actinin after bacterial entry into human brain microvascular endothelial cells (HBMECs).
JoVE Immunology and Infection
A 1.5 Hour Procedure for Identification of Enterococcus Species Directly from Blood Cultures
1Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Cente, 2Pasadena, CA, Southern California Permanente Medical Group, 3Detroit, Detroit Medical Center, 4Woburn, MA, AdvanDx
A rapid protocol for the direct identification of Enterococcus faecalis and other Enterococcus species from a positive blood culture using a Peptide Nucleic Acid fluorescent in situ hybridization assay (PNA FISH).
JoVE Immunology and Infection
The Citrobacter rodentium Mouse Model: Studying Pathogen and Host Contributions to Infectious Colitis
Division of Gastroenterology, BC Children's Hospital
Citrobacter rodentium infection provides a valuable model to study enteric bacterial infections as well as host immune responses and colitis in mice. This protocol outlines the measurement of barrier integrity, pathogen load and histological damage allowing for the thorough characterization of pathogen and host contributions to murine infectious colitis.
JoVE Immunology and Infection
Use of Fluorescent Immuno-Chemistry for the detection of Edwardsiella ictaluri in channel catfish (I. punctatus) samples
Department of Basic Sciences, Mississippi State University
Here we describe a procedure allowing the labeling of Edwardsiella ictaluri in situ in histological sections from channel catfish Ictalurus punctatus using indirect immunohistochemistry with monoclonal antibodies Ed9 as a primary, and fluorescent FitC labeled antibodies as a secondary. This allowed for the detection of the bacterium using fluorescent microscopy.
JoVE Immunology and Infection
In Vitro Assay of Bacterial Adhesion onto Mammalian Epithelial Cells
This protocol is a simple bacterial adhesion assay consisting in counting the numbers of bacterial colony forming units that are adhered onto cultured cells. The assay is robust, independent of the adhesin studied, and numerous variations are used in most laboratories working on bacterial pathogenesis.
JoVE Immunology and Infection
Pseudomonas aeruginosa and Saccharomyces cerevisiae Biofilm in Flow Cells
1Department of Systems Biology, Danish Technical University, 2Department of Biology, University of Copenhagen
Protocol describing the application of a flow cell system for growing and analyzing microbial biofilms for Confocal Laser Scanning Microscopy (CLSM).
JoVE Immunology and Infection
Customization of Aspergillus niger Morphology Through Addition of Talc Micro Particles
Institute of Biochemical Engineering, Technische Universität Braunschweig
A method to precisely generate and to comprehensively characterize morphology of filamentous fungus Aspergillus niger is described, which allows the mathematical correlation of morphological appearance and productivity.
JoVE Editorial
February 2012: This Month in JoVE
Here are some highlights from the February 2012 Issue of Journal of Visualized Experiments (JoVE).
JoVE Editorial
April 2012: This Month in JoVE
Here are some highlights from the April 2012 Issue of Journal of Visualized Experiments (JoVE).
JoVE General
Window on a Microworld: Simple Microfluidic Systems for Studying Microbial Transport in Porous Media
1Vanderbilt Institute for Integrative Biosystems Research and Education, Vanderbilt University, 2Department of Biomedical Engineering, Vanderbilt University, 3Department of Molecular Physiology and Biophysics, Vanderbilt University, 4Department of Physics and Astronomy, Vanderbilt University, 5Department of Chemical, Materials and Biomolecular Engineering, University of Connecticut, 6Center for Environmental Sciences and Engineering, University of Connecticut
Microfluidic devices can be used to visualize complex natural processes in real time and at the appropriate physical scales. We have developed a simple microfluidic device that mimics key features of natural porous media for studying growth and transport of bacteria in the subsurface.
JoVE Immunology and Infection
In vitro Biofilm Formation in an 8-well Chamber Slide
Center for Microbial Pathogenesis, The Research Institute at Nationwide Children's Hospital
This article describes the procedure for the formation and visualization of a bacterial biofilm grown within an 8-well chamber slide
JoVE General
Genome-wide Analysis of Aminoacylation (Charging) Levels of tRNA Using Microarrays
Department of Biochemistry and Molecular Biology, University of Chicago
We describe a method for microarray analysis to determine relative aminoacylation levels of all tRNAs from S. cerivisiae.
JoVE Immunology and Infection
ampliPHOX Colorimetric Detection on a DNA Microarray for Influenza
InDevR, Inc.
ampliPHOX colorimetric detection technology is presented as an inexpensive alternative to fluorescence detection for microarrays. Based on photopolymerization, ampliPHOX produces solid polymer spots visible to the naked eye in just a few minutes. Results are then imaged and automatically interpreted with a simple yet powerful software package.
JoVE Immunology and Infection
Separation of Single-stranded DNA, Double-stranded DNA and RNA from an Environmental Viral Community Using Hydroxyapatite Chromatography
1Department of Microbial and Environmental Genomics, The J. Craig Venter Institute, 2Department of Synthetic Biology and Bioenergy, The J. Craig Venter Institute
We describe an efficient method to separate single-stranded DNA, double-stranded DNA and RNA molecules from environmental viral communities. Nucleic acids are fractionated using hydroxyapatite chromatography with increasing concentrations of phosphate-containing buffers. This method permits the isolation of all viral nucleic acid types from environmental samples.
JoVE General
A High Throughput Screen for Biomining Cellulase Activity from Metagenomic Libraries
Microbiology and Immunology, University of British Columbia - UBC
This protocol describes a high throughput screen for cellulolytic activity from a metagenomic library expressed in Escherichia coli. The screen is solution based and highly automated, and uses one-pot chemistry in 384 well microplates with the final readout as an absorbance measurement.
JoVE Immunology and Infection
'Bioluminescent' Reporter Phage for the Detection of Category A Bacterial Pathogens
1BioSciences Division, Guild Associates, Inc., 2Department of Molecular Genetics and Microbiology, University of Texas at Austin, 3Department of Craniofacial Biology, Medical University of South Carolina
A simple method for the identification of priority bacterial pathogens is to use genetically engineered reporter phage. These reporter phage, which are specific to their particular host species, are capable of rapidly transducing a bioluminescent signal response to host cells. Herein, we describe the use of reporter phage for the detection of Yersinia pestis.
JoVE Immunology and Infection
Antimicrobial Susceptibility Testing of Mycobacterium Tuberculosis Complex for First and Second Line Drugs by Broth Dilution in a Microtiter Plate Format
Department of Laboratory Medicine and Pathology, Mayo Clinic
Antimicrobial susceptibility testing of Mycobacterium tuberculosis is challenging but critical for patient care. This microtiter plate format offers testing of 12 antimycobacterial drugs and provides minimum inhibitory concentration (MIC) values, which will aid in appropriate treatment.
JoVE General
Optimized PCR-based Detection of Mycoplasma
Product Management, Sigma-Aldrich
The LookOut Mycoplasma PCR Detection Kit utilizes the polymerase chain reaction (PCR), which is established as the method of choice for highest sensitivity in the detection of Mycoplasma, Acholeplasma, and Ureaplasma contamination in cell cultures and other cell culture derived biologicals.
JoVE General
Isolation of Native Soil Microorganisms with Potential for Breaking Down Biodegradable Plastic Mulch Films Used in Agriculture
1Biology Department, Western Washington University, 2Washington State University Northwestern Research and Extension Center, 3Department of Plant and Soil Science, Texas Tech University
Plastic films labeled "biodegradable" are commercially available for agricultural use as mulches. Tillage represents an attractive disposal method, but degradation under field conditions is poorly understood. The purpose of this study was to develop methods for isolating native soil fungi and bacteria that colonize plastic mulch films after field burial.
JoVE Immunology and Infection
Estimating Virus Production Rates in Aquatic Systems
Department of Microbiology, University of Tennessee
The turnover rate of viruses in marine and freshwater systems can be estimated by a reduction and reoccurrence technique. The data allow researchers to infer rates of virus-mediated microbial mortality in aquatic systems.
JoVE Bioengineering
Bacterial Detection & Identification Using Electrochemical Sensors
1Research Service, Veterans Affairs Greater Los Angeles Healthcare System, 2Department of Urology, The David Geffen School of Medicine, University of California, Los Angeles, 3GeneFluidics, 4Division of Infectious Diseases, Veterans Affairs Greater Los Angeles Healthcare System, 5Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles
We describe an electrochemical sensor assay method for rapid bacterial detection and identification. The assay involves a sensor array functionalized with DNA oligonucleotide capture probes for ribosomal RNA (rRNA) species-specific sequences. Sandwich hybridization of target rRNA with the capture probe and a horseradish peroxidase-linked DNA oligonucleotide detector probe produces a measurable amperometric current.
JoVE Clinical and Translational Medicine
Intraductal Injection of LPS as a Mouse Model of Mastitis: Signaling Visualized via an NF-κB Reporter Transgenic
1Cancer Biology Department, Vanderbilt University Medical Center, 2Department of Medicine, Vanderbilt University Medical Center, 3Department of Pharmaceutical Sciences, University of Hawaii at Hilo College of Pharmacy
Described here is a technique in which lipopolysaccharide is injected into the lactating mouse mammary gland via the nipple to simulate mastitis, a condition commonly caused by bacterial infection. Lipopolysaccharide injection results in increased nuclear factor kappa B (NF-κB) signaling, visualized through bioluminescent imaging of an NF-κB luciferase reporter mouse.
JoVE General
Depletion of Ribosomal RNA for Mosquito Gut Metagenomic RNA-seq
Department of Biology, New Mexico State University
A ribosomal RNA (rRNA) depletion protocol was developed to enrich messenger RNA (mRNA) for RNA-seq of the mosquito gut metatranscriptome. Sample specific rRNA probes, which were used to remove rRNA via subtraction, were created from the mosquito and its gut microbes. Performance of the protocol can result in the removal of approximately 90-99% of rRNA.
JoVE General
Bioelectric Analyses of an Osseointegrated Intelligent Implant Design System for Amputees
1Department of Veteran Affairs, 2Department of Bioengineering, University of Utah, 3Scientific Computing and Imaging Institute , University of Utah, 4Department of Physical Medicine and Rehabilitation, University of Utah, 5Department of Orthopaedics, University of Utah
There is a need to develop alternative prosthesis attachment due to limb loss attributed to vascular occlusive diseases and trauma. The goal of the work is to introduce an osseointegrated intelligent implant design system to increase skeletal fixation and reduce periprosthetic infection rates for patients needing osseointegrated technology.
JoVE Editorial
November 2012: This Month in JoVE
1Department of Ophthalmology, Massachusetts Eye and Ear, 2JoVE Content Production
In this issue, Oestreicher et al. show us how to isolate magnetotactic bacteria from freshwater samples, and concentrate the bacteria at one end of a glass capillary. The magnetotactic bacteria can then be visualized by light and transmission electron microscopy, and used for various other assays.
JoVE General
Preparation and Using Phantom Lesions to Practice Fine Needle Aspiration Biopsies
1Department of Pathology, University of Wisconsin - Milwaukee, 2BioInnovation LLC
Practicing of fine needle aspiration biopsies (FNAB) by trainees is relatively challenging, due to the lack of an easily available, appropriate lesion. Preparation of an AV phantom lesion for practicing the FNAB procedure and mastering proficiency is relatively easy.
JoVE General
Live Cell Response to Mechanical Stimulation Studied by Integrated Optical and Atomic Force Microscopy
1Department of Systems Biology and Translational Medicine, College of Medicine, Cardiovascular Research Institute, Texas A&M Health Science Center, 2Department of Biomedical Engineering, Texas A&M University
This paper aims to instruct the reader in the operation of an integrated atomic force-optical imaging microscope for mechanical stimulation of live cells in culture. A step-by-step protocol is presented. A representative data set that shows live cell response to mechanical stimulation is presented.
JoVE Immunology and Infection
Co-culture Models of Pseudomonas aeruginosa Biofilms Grown on Live Human Airway Cells
1Department of Physiology, Dartmouth College, 2Department of Biology, Indiana University Purdue University Indianapolis
This paper describes different methods of growing Pseudomonas aeruginosa biofilms on cultured human airway epithelial cells. These protocols can be adapted to study different aspects of biofilm formation, including visualization of the biofilm, staining of the biofilm, measuring the colony forming units (CFU) of the biofilm, and studying biofilm cytotoxicity.
JoVE General
Sexual Development and Ascospore Discharge in Fusarium graminearum
1Genetics Program, Michigan State University, 2Department of Plant Biology, Michigan State University, 3Human Biology Program, Michigan State University, 4Department of Plant Pathology, Michigan State University
Sexual crosses and isolation of recombinant progeny are important research tools for the filamentous fungus, Fusarium graminearum, The techniques necessary successfully carry out these processes are presented.
JoVE Bioengineering
Microfluidic Chip Fabrication and Method to Detect Influenza
1Department of Mechanical Engineering, Boston University, 2Department of Biomedical Engineering, Boston University
An integrated microfluidic thermoplastic chip has been developed for use as a molecular diagnostic. The chip performs nucleic acid extraction, reverse transcriptase, and PCR. Methods for fabricating and running the chip are described.
JoVE Editorial
August 2011: This Month in JoVE
Here are some highlights from the August 2011 Issue of Journal of Visualized Experiments (JoVE).
JoVE Editorial
October 2011: This Month in JoVE
Here are some highlights from the October 2011 Issue of Journal of Visualized Experiments (JoVE).
JoVE Editorial
May 2012: This Month in JoVE
Here are some highlights from the May 2012 Issue of Journal of Visualized Experiments (JoVE).
JoVE Editorial
June 2012: This Month in JoVE
1Department of Ophthalmology, Massachusetts Eye and Ear, 2JoVE Content Production
Back in 1905, in what is now the Czech Republic, Eduard Zirm performed the first corneal transplantation surgery (keratoplasty), which restored vision to a patient blinded by corneal injury. Today, eye banks all over the world prepare, store, and distribute donated corneas to hospitals so that thousands of sight-saving keratoplasties can be performed every year. In June 2012, JoVE has its eye on two research groups, one from Italy and the other from Michigan, who demonstrate two distinct methods for corneal graft preparation prior to transplantation.
JoVE General
Chemotactic Response of Marine Micro-Organisms to Micro-Scale Nutrient Layers
Environmental Microfluidics Group, MIT - Massachusetts Institute of Technology
The fabrication of microfluidic channels and their implementation in experiments for studying the chemotactic foraging behaviour of marine microbes within a patchy nutrient seascape and the swimming behaviour of bacteria within shear flow are described.
JoVE General
Aseptic Laboratory Techniques: Volume Transfers with Serological Pipettes and Micropipettors
Microbiology, Immunology, and Molecular Genetics, University of California, Los Angeles
When working in a laboratory, it is imperative to minimize sources of contamination. Aseptic technique refers to procedures that permit transfer of cultures and reagents while avoiding contact with non-sterile surfaces. Serological pipettes and micropipettors are used to measure precise volumes without compromising sterility of solutions used in experiments.
JoVE Clinical and Translational Medicine
Detection and Genogrouping of Noroviruses from Children's Stools By Taqman One-step RT-PCR
1Laboratorio de Investigación y Desarrollo (LID), Universidad Peruana Cayetano Heredia, 2Bloomberg School of Public Health, Johns Hopkins University, 3Laboratorio de Diagnostico Molecular, Facultad de Medicina, University of Concepcion,Chile, 4University of California San Diego School of Medicine
A One-Step RT-PCR assay for detection and genogroup identification of Norovirus isolates from children’s stools, that utilizes primers and TaqMan probes specific to the open reading frame 1 (ORF1)-ORF2 junction region, the most conserved region of the Norovirus genome is described. A non-commercial, cost-effective RNA extraction method is detailed.
JoVE General
Cryosectioning Yeast Communities for Examining Fluorescence Patterns
Division of Basic Sciences, Fred Hutchinson Cancer Research Center
We present a protocol for freezing and cryosectioning yeast communities to observe internal patterns of fluorescent cells. The method relies on methanol-fixing and OCT-embedding to preserve the spatial distribution of cells without inactivating fluorescent proteins within a community.
JoVE Immunology and Infection
Staphylococcus aureus Growth using Human Hemoglobin as an Iron Source
Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical School
Here we describe a growth assay for Staphylococcus aureus using hemoglobin as the sole source of available nutrient iron. This assay establishes the role of bacterial factors involved in hemoglobin-derived iron acquisition.
JoVE General
DNA Stable-Isotope Probing (DNA-SIP)
Department of Biology, University of Waterloo
DNA stable-isotope probing is a cultivation-independent method to identify and characterize active communities of microorganisms that are capable of utilizing specific substrates. Assimilation of substrate enriched in heavy isotope leads to incorporation of labelled atoms into microbial biomass. Density gradient ultracentrifugation retrieves labelled DNA for downstream molecular analyses.
JoVE General
Metabolic Pathway Confirmation and Discovery Through 13C-labeling of Proteinogenic Amino Acids
1Department of Energy, Environmental and Chemical Engineering, Washington University, 2Department of Biology, Washington University, 3Department of Energy, Environmental and Chemical Engineering and Department of Biology, Washington University
13C-isotope labeling is a useful technique for determining the cell central metabolism for various types of microorganisms. After cells have been cultured with a specific labeled substrate, GC-MS measurement can reveal functional metabolic pathways based on unique labeling patterns in proteinogenic amino acids.
JoVE General
The Logic, Experimental Steps, and Potential of Heterologous Natural Product Biosynthesis Featuring the Complex Antibiotic Erythromycin A Produced Through E. coli
1Chemical and Biological Engineering Department, State University of New York at Buffalo, 2Chemical Engineering Department, Massachusetts Institute of Technology
The heterologous biosynthesis of erythromycin A through E. coli includes the following experimental steps: 1) genetic transfer; 2) heterologous reconstitution; and 3) product analysis. Each step will be explained in the context of the motivation, potential, and challenges in producing therapeutic natural products using E. coli as a surrogate host.
JoVE General
Denaturing Gradient Gel Electrophoresis (DGGE)
Department of Microbiology and Molecular Genetics, Harvard Medical School
JoVE General
Biology of Microbial Communities - Interview
Department of Microbiology and Molecular Genetics, Harvard Medical School
JoVE General
Transplantation of GFP-expressing Blastomeres for Live Imaging of Retinal and Brain Development in Chimeric Zebrafish Embryos
1Department of Ophthalmology, University of Pittsburgh, 2Department of Microbiology and Molecular Genetics, University of Pittsburgh
We demonstrate a protocol to generate chimeric zebrafish embryos for live imaging cellular behavior during embryogenesis.
JoVE Immunology and Infection
Microtiter Dish Biofilm Formation Assay
Microbiology and Immunology, Dartmouth Medical School
The assay describes a rapid means to measure early biofilm formation in bacteria and fungi. This method uses a microtiter plate as the substratum for microbial biofilm formation, and the biofilm is visualized using crystal violet strain. The assay provides either a qualitative or quantitative assay for early biofilm formation.
More Results...
