JMU Bio 140 Lab checkpoint quiz 7-12
What clues tell you that your electrophoresis is running properly?
- Bubbles rise from the electrodes - You can see the loading dye move from the well into the gel
To carry out Sanger sequencing, a mix is needed containing what?
- DNA polymerase - ddNTPs - Primer - A, T, C, G - DNA template
What is the function of gel loading dye?
- Increase density of DNA sample - Allows you to visually monitor progress of gel electrophoresis
What are the "do's" for a diagram?
- consider which elements are of primary importance, which are of secondary importance, and how elements relate over time and space - test the communication power of your diagrams by soliciting feedback from others - use diagrams to introduce and summarize concepts, as well as to visualize experimental design and methodology - remember the goal of your diagram, discarding elements that don't help convey your specific message - only include elements that help transmit a message to your audience
A good scientific poster should what?
- contain enough information to stand alone without the presenter - serve as a backdrop for the presenter - be as concise as possible
What are the "don'ts" of a scientific poster?
- place your abstract on your poster itself - think of a scientific poster as a text-based document that reads like a large version of a research article - include information on a poster that doesn't address your poster's central concept or goal - overwhelm your poster with text - begin designing a poster by focusing on layout
What is required on a scientific poster?
- title - results - summary/conclusion - background/introduction - hypothesis/question/goal
When should you use a diagram?
- when conveying background information to an audience - when proposing a model - when showing experimental strategies and techniques
What is the conversion of base pairs (bp) to kilobases (kb)?
1000 base pairs = 1 kilobase
What are transects?
Area being sampled
If you paste a figure onto a blue background, what color should you make the figure's background?
Blue
Why do we run our H20 (negative control) from our PCR reactions on the gel?
Enables us to tell if our PCR was contaminated by DNA not from our sample
To perform DNA barcoding what do you need to do?
Extract DNA from the rest of the cellular component
How should your title be written on a poster?
First word uppercased, everything else lowercases EX. Dissecting bacteriophage genomes for useful molecular tools
What is agarose?
Gelatinous medium that restricts DNA movement
What is biodiversity?
Increase as more tips and branches are added to the tree of life
What type of correlation is there between the amount of text on a poster and the likelihood that someone will read it?
Inverse, more text = less likely to be read
Why do scientists load DNA of known sizes (also called "marker" or "ladder") into the agarose gel?
It makes it easier to determine sizes of unknowns using comparison techniques
The final step in a Sanger DNA sequencing reaction is to run the DNA fragments on a gel. What purpose does this serve?
It separates DNA fragments generated during the sequencing reaction based on one-nucleotide differences in their size
What is the best flow of a diagram?
Left to Right, zig zag
What is detergent and salt?
Method used to extract DNA from the rest of cellular component in plants and fungi
What is alkaline lysis?
Method used to extract DNA from the rest of cellular components in animals and fish
What is optional on a scientific poster?
Methods
DNA possesses what type of net charge?
Negative net charge
What is species richness?
Number of unique species found in an area
What is PCR Amplicon?
Short region of the DNA, after successful PCR, amplified with primers
The rate at which DNA migrates through the gel during electrophoresis is determined by what?
Size of DNA
What is base pairs?
Size of your PCR amplicon can be measured in the number of base pairs
In the last steps of Sanger sequencing, the DNAs produced in a DNA sequencing reaction are analyzed on the basis of their what?
Size or length
ddNTPs (dideoxyribonucleotides) does what in DNA sequencing?
Stop growth of a DNA strand at a particular base (A, T, C, or G)
What is agarose gel electrophoresis?
Technique used to separate and view fragments of DNA based on size, demonstrating whether or not DNA is present, and can allow us to determine the size of the DNA fragments
What does it mean when 2 bands match up between 2 different samples on a gel after electrophoresis?
The samples share a fragment of DNA that is the same length
Why do we dye our gels with Ethidium bromide or Gel Red dyes?
They stain the double stranded DNA in our gel
What is The most important consideration for designing a good diagram?
To clearly define the purpose of the diagram
What is Sanger sequencing?
Widely and most common method of sequencing DNA 1. Incubate reaction mixture 2. DNA synthesis 3. Collect DNA strands that are produced 4. Separate fragments 5. Read output
Should a good poster have borders around each section?
Yes, it helps to separate discrete sections and different categories
What are ecosystem services?
direct and indirect benefits that humans derive from other organisms
What is a DNA barcode?
he "sequence," or the specific order, of the 500+ base pairs (A's, T's, G's, and C's) that make up the region of DNA we amplified in our PCRs
What is Shannon diversity?
measure of biodiversity that account for species richness and evenness
What is habitat destruction?
reduction in the quality of any remaining habitat
A laboratory might use ddNTPs (dideoxyribonucleotides) to what?
sequence DNA fragment
What is habitat fragmentation?
the splitting of contiguousareas of natural habitats into small, isolated fragments
How does an audience intuitively read a poster?
top to bottom
