Difference between revisions of "Vpachec3 Week 11"
From LMU BioDB 2015
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==10 Biological Terms and Definitions== | ==10 Biological Terms and Definitions== | ||
| − | #Aminoglycoside antibiotic | + | #'''Aminoglycoside antibiotic'''- group of antibiotics active against many acrobic Gram-negative and some Gram-positive bacteria. Composed of two or more amino sugars attached by a glycosidic linkage to a hexose nucleus; polycationic and highly polar compounds. Inhibit bacterial protein synthesis by binding to a site on the 30S ribosomal subunit thereby altering codon-anticodon recognition. |
| − | #Fluoroquinolone | + | #'''Fluoroquinolone'''- bactericidal and inhibit the activity of DNA gyrase. Newer fluoroquinolones (e.g. ciprofloxacin) had a broader spectrum of activity |
#Sessile cells | #Sessile cells | ||
| − | #cDNA | + | #'''cDNA'''-Complementary DNA Viral reverse transcriptase can be used to synthesize DNA that is complementary to RNA. The cDNA can be used, for example, as a probe to locate the gene or can be cloned in the double-stranded form. |
| − | #Flow cytometry | + | #'''Flow cytometry'''-Slightly imprecise but common term for the use of the fluorescence activated cell sorter (FACS). Cells are labelled with fluorescent dye and then passed, in suspending medium, through a narrow dropping nozzle so that each cell is in a small droplet. A laser-based detector system is used to excite fluorescence and droplets with positively fluorescent cells are given an electric charge. Charged and uncharged droplets are separated as they fall between changed plates and so collect in different tubes. the machine can be used either as an analytical tool, counting the number of labelled cells in a population, or to separate the cells for subsequent growth of the selected population. further sophistication can be built into the system by using a second laser system at right angles to the first look at a sec on fluorescent label or to gauge cell size on the basis of light scatter. The great strength of the system is that it looks at larger numbers of individual cells and makes possible the separation of populations with, for example, particular surface properties. |
| − | #Isocitrate | + | #'''Isocitrate'''- an intermediate in the tricarboxylic acid cycle (citric acid cycle) |
#Persister | #Persister | ||
#Exconjugants | #Exconjugants | ||
#Mutagenesis | #Mutagenesis | ||
| − | #Glyoxylate shunt | + | #'''Glyoxylate shunt'''- (See glyoxalate cycle) Glyoxylate cycle: metabolic pathway present in bacteria and in the glyoxisome of plants, in which two acetyl-CoA molecules are converted to a 4-carbon dicarboxylic acid, initially succinate. Includes two enzymes not found elsewhere, isocitrate lyase and malate synthase. Permits nest synthesis of carbohydrates from lipid, and hence is prominent in those seeds in which lipid is the principle food reserve. |
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| + | Definitions for numbers 1, 2, 4, 5,6 and 10 were found in ''Dictionary of Cell and Molecular Biology'' (Citation below). | ||
| + | Lackie, J. M. (2007). Dictionary of Cell and Molecular Biology. Kidlington, GBR: Academic Press. Retrieved from http://www.ebrary.com | ||
==Article Outline== | ==Article Outline== | ||
Revision as of 09:53, 16 November 2015
10 Biological Terms and Definitions
- Aminoglycoside antibiotic- group of antibiotics active against many acrobic Gram-negative and some Gram-positive bacteria. Composed of two or more amino sugars attached by a glycosidic linkage to a hexose nucleus; polycationic and highly polar compounds. Inhibit bacterial protein synthesis by binding to a site on the 30S ribosomal subunit thereby altering codon-anticodon recognition.
- Fluoroquinolone- bactericidal and inhibit the activity of DNA gyrase. Newer fluoroquinolones (e.g. ciprofloxacin) had a broader spectrum of activity
- Sessile cells
- cDNA-Complementary DNA Viral reverse transcriptase can be used to synthesize DNA that is complementary to RNA. The cDNA can be used, for example, as a probe to locate the gene or can be cloned in the double-stranded form.
- Flow cytometry-Slightly imprecise but common term for the use of the fluorescence activated cell sorter (FACS). Cells are labelled with fluorescent dye and then passed, in suspending medium, through a narrow dropping nozzle so that each cell is in a small droplet. A laser-based detector system is used to excite fluorescence and droplets with positively fluorescent cells are given an electric charge. Charged and uncharged droplets are separated as they fall between changed plates and so collect in different tubes. the machine can be used either as an analytical tool, counting the number of labelled cells in a population, or to separate the cells for subsequent growth of the selected population. further sophistication can be built into the system by using a second laser system at right angles to the first look at a sec on fluorescent label or to gauge cell size on the basis of light scatter. The great strength of the system is that it looks at larger numbers of individual cells and makes possible the separation of populations with, for example, particular surface properties.
- Isocitrate- an intermediate in the tricarboxylic acid cycle (citric acid cycle)
- Persister
- Exconjugants
- Mutagenesis
- Glyoxylate shunt- (See glyoxalate cycle) Glyoxylate cycle: metabolic pathway present in bacteria and in the glyoxisome of plants, in which two acetyl-CoA molecules are converted to a 4-carbon dicarboxylic acid, initially succinate. Includes two enzymes not found elsewhere, isocitrate lyase and malate synthase. Permits nest synthesis of carbohydrates from lipid, and hence is prominent in those seeds in which lipid is the principle food reserve.
Definitions for numbers 1, 2, 4, 5,6 and 10 were found in Dictionary of Cell and Molecular Biology (Citation below). Lackie, J. M. (2007). Dictionary of Cell and Molecular Biology. Kidlington, GBR: Academic Press. Retrieved from http://www.ebrary.com
Article Outline
- Introduction
- Materials and Methods
- Strains and Culture Conditions
- 18 strains in the Burkholderia cepacia group
- Plated on agar plates at 37 degrees Celsius over night
- Cultures diluted in broth and incubated at 37 degrees Celsius
- Minimal Inhibitory Concentration (MIC)
- Used EUCAST broth microdiluation protocol to find MICs
- Quantification of Persister Cells in Biofilms and Planktonic Cultures
- Aim: to see how many surviving persister cells there are
- Day old biofilms and planktonic cultures were treated with tobramycin and ciprofloxacin
- Used 96 well micro titer plate for growth
- After 24 hrs, the supernatant was removed and put into antibiotic solution mixed in physiological saline
- Cells were harvested and plated onto agar plates
- Planktonic cultures needed extra preparation to reach optical density of 1
- RNA Extraction and Microarray Analysis
- Biofilms exposed to either antibiotic or 0.9% salt solution
- After 24hr, the sessile cells were prepped to take out the RNA
- Right before microarray analysis, the samples were concentrated and amplified
- Gene expression analysis was executed
- Data used 2 color Agilent microarrays
- T-test analysis was used
- Quantitative RT-PCR
- Chose 11 selected genes to use RT-qPCR on
- RNA was extracted from biofilms
- Flow Cytometry
- Aim: to see induction of reactive oxygen species by tobramycin
- Stained biofilms with ROS-specific dyes
- Dye sits for 30 mins in the dark
- Rinsed off and physiological saline was added in well
- Cells harvested and resuspended in diluted physiological saline
- Cells were measured using flow cytometer
- 50,000 cells per sample
- Strains and Culture Conditions
