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27 Cards in this Set
- Front
- Back
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Acridine orange |
- nonspecific fluorescent dye used to stain DNA in microbial cells in a natural sample - Stain cells orange of greenish-orange - Cannot differentiate between live and dead cells |
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DAPI |
- Nonspecific fluorescent dye that stains DNA in microbial cells - Used to obtain total cell numbers in natural samples - Cells fluoresce bright blue - Cannot differentiate between live and dead cells |
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Denaturing gradient gel electrophoresis (DGGE) |
An electrophoretic technique capable of separating genes of the same size based on differences in base sequence |
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Enrichment bias |
- A problem with enrichment cultures in which "weed" species tend to dominate in the enrichment |
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Enrichment culture |
Highly selective lab culture methods for obtaining microbes from natural samples |
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Metagenomics (Environmental genomics) |
Use of genomic methods (sequencing and analyzing genomes) to characterize natural microbial communities |
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Flow cytometry |
Technique for counting and examining microscopic particles by suspending them in a stream of fluid and passing them by an electronic detection device |
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Fluorescence in situ hybridization (FISH) |
Method employing a fluorescent dye covalently bonded to a specific nucleic acid probe for IDing or tracking organisms in the environment |
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Fluorescent protein |
Any of a lg group of proteins that fluoresce different colors for tracking GMO and determining conditions that induce the expression of specific genes |
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Fundamental niche |
Range of environments in which a species will be sustained when it is not resource limited |
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Laser tweezers |
Device for obtaining pure cultures by optically trapping a single cell with a laser beam and moving it away from surrounding cells into sterile growth medium |
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MAR-FISH |
technique the combines ID of microbes with measurement of metabolic activities |
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Metatranscriptomics |
Measurement of whole-community gene expression using RNA sequencing |
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Metaproteomics |
Measurement of whole community protein expression using mass spectrometry to assign peptides to the amino acid sequences coded by unique genes |
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Microautoradiography (MAR) |
Measurement of the uptake of radioactive substrates by visually observing the cells in an exposed photographic emulsion |
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Microbial ecology |
Study of the interaction of microbes with each other and their environment |
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Winogradsky column |
Glass column packed with mud and overlaid with water to mimic an aquatic environment, in which various bacteria develop over a period of months |
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Viability stains |
- Differentiate dead and lives cells - Green = live; Red = dead - Can have issues with nonspecific staining in environmental samples |
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Fluorescent antibodies |
- Making antibodies is time consuming and expensive - Highly specific |
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Nucleic acid probe |
An oligonucleotide complementary in base sequence to a nucleic acid sequence in a target gene or RNA |
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CARD-FISH |
A FISH method that enhances the signal called Catalyzed reporter deposition FISH |
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What can FISh be used for? |
To measure gene expression in organisms in a natural sample |
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T-RFLP |
- Terminal restriction fragment length polymorphism - Target gene is amplified by PCR, restriction enzymes are used to cut the PCR products |
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What is a phylochip and what does it help |
- A microarray that focuses on phylogenetic members of microbial communities - Circumvents the time-consuming steps of DGGE and TRFLP |
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What are stable isotopes |
- Nonradioactive isotopes of an element - Used to study microbial transformation in nature |
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Isotope Fractionation |
Discrimination by enzymes against the heavier isotope of the various isotopes of carbon and sulfur, leading to enrichment of the lighter isotopes |
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What is Killed cell control |
- Some isotopic transformations might be due to abiotic processes - Shows that the transformation being measured stops when chemical agents or heat treatments that kill microbes are applied to the sample |
