Phage Vocabulary

 

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uL = microliter, which is 10^-6 L.  (1 million uL per L).

 

plate = a.)  to apply a specific volume of liquid to a media dish (i.e. a petri dish). 

            b.) the petri-dish containing media and perhaps microorganisms. 

 

high-titer phage preparation = a preparation of phage that contains more than 10^8 phage/mL.  It is desired to have at least 10^10 phage/mL for most work with mycobacteria. 

Student Entries: (Minor corrections made by Schwebach)

Electrophoresis

 in a nutshell is a technique used to identify relations in DNA (for our purposes, proteins (amino acids) can also be placed in electrophoresis). Prior to this the DNA used for this must be purified, cut (with a restriction enzyme into fragments[see restriction digestion]) and dyed (so it can be seen in the gel). Gel electrophoresis is based on two things mass and charge. DNA is an acid so there fore it has a negative charge. And when the gel is "run" the DNA is pulled to the positive charged end and repelled by the negatively charged end. This is why it is very important the load the DNA in the right side. While the DNA is being pulled through the gel its going through a sort of maze with different holes. Smaller fragments of DNA can get through the holes faster and that's why the end up farther  away from the well (where the DNA is loaded). Because restriction enzymes cut at a specific sequence that they  recognize on the DNA, the banding patterns will not be the same unless the DNA is the same. When comparing digested DNAs, the more similar the banding patterns the more similar the DNA. Also, the length of the fragments from the unknown DNA can be found by using a ladder. Which is composed of a DNA bands that have known bp equivalents.

Example:                ladder
___                           We know the ladder has 10,000 bps on the first band and 6000 on the second
             ___              band. therefore the unknown DNA band on the right must be about 8000 bp's.
 We used Electrophoresis as a tool to see if we have similarities between our phage's genomic DNA and other DNA's.

--Amanda.

Genome Map:
A genome map is the location of every piece of DNA in the organism (genes are located along the chromosome(s),
defined by its nucleotides (A's, T's, G's, and C's). A genome map of a 
phage lets us identify common points between it and other phages, in 
hopes that we can identify what each sequence within the DNA does.

Restriction digestion map:
A restriction digestion map is a map showing where a particular enzyme 
cut the DNA of a substance. With this information, you can identify a
phages genomic map by comparing it to other known genomes.


--Lazlo

Transmission Electron Miscroscope (TEM):

TEM:    A beam of electrons is passed through the specimen, which has
been stained with phosphotungstic acid in order to block some electrons and
form a “negative” image.  The electrons then strike a platform covered with
a substance that fluoresces when hit, creating a glowing image of the
specimen.  The image is further magnified by a simple light microscope
whose light source is the platform itself.
 

--Genevieve

Plaque Morphology 
 

A plaque is a (small) clearing in a lawn of bacteria grown on a plate. This plaque usually indicates the presence of a virus that infects the bacteria and uses it to reproduce (such viruses are called phages). Although some may look similar, each phage forms a unique plaque. The way a plaque looks is called its morphology. Plaque morphologies tell us a lot about the type of phages that made them. For example if the plaques the phage makes are very clear (one could see clearly through them) the phage is highly lytic1, whereas if the plaques are hazy or turbid (one could not see clearly when looking through them) the phage is probably lysogenic2. In some cases plaques have clear centers and hazy rings, or halos. No one is absolutely certain what causes these halos but one hypothesis is that the halos are rings of bacteria that are resistant to the phage. Larger plaques often mean more phage and smaller plaques, less phage. Looking at plaque morphologies is a preliminary way (before electron microscopy3) to tell if one has more than one phage on a plate. It is still unknown weather a phage’s plaque morphology is at all related to the phage’s morphology.

1 See definition for lytic in Chris’ description

2 See definition for lysogenic in Chris’ description

3 See definition for electron microscopy in Genevieve’s description

--Chiara

Lytic:  A method of phage reproduction where a phage injects its DNA
into a host bacteria.  The injected DNA leads to the creation of new phage
which eventually burst forth from or lyse the host bacteria.

Lysogenic:  The second known method of phage reproduction.  In
lysogeny, the phage injects its DNA into a host bacteria.  The DNA then blends with
the bacterial DNA or RNA which creates a new species immune to the phage
which created it.
--Chris

 

Icosahedral –  A many sided, three dimensional, hexagonal shape made up
of many small triangles.
 

Icosahedral Tailed – A bacteriophage with an icosahedral head attached
to a tail, which is often contractile. The tail often has fibers and is
used to inject the genetic material from it's head into the bacterium.
Icosahedral Tailless– A phage with an icosahedral head but no tail.
It’s head attaches to the cell and injects it's genetic material directly.
 

Filamentous- A phage with a rod-like structure in which the genetic
material is stored.

--Stephen