150 L final Flashcards
List the major sections of a formal scientific manuscript
methods, results, discussion, and introduction
main parts of the flow chart
exploration
testing ideas
community analysis and feedback
benefits and outcomes
what is the entryway into the process of science?
exploration and discovery
t/f DNA barcoding is useful to identify how much (%) of a product is made up of a particular ingredient.
false
What are the MAIN goals of an introduction to a scientific paper?
enable the reader to understand why the specific question/goal/aim of the study is important
scholarly literature
disseminate information, peer-reviewed, reliable but not always accessible
non scholarly literature
want to make money, not as reliable, not peer reviews, more accessible
primary literature (def)
original research that is communicated “first-hand” by the people who collected and analyzed the data
primary literature (example)
journal articles
secondary literature (def)
second hand summary, sometimes peer reviewed, lacks method section, ok for citing`
an expert summary or synthesis of someone else’s original research that is communicated “second-hand” by people who did NOT collect or analyze the original data
secondary literature (example)
scientific books
tertiary literature (def)
‘third hand’ general background information, not written by experts and rarely peer reviewed, should be avoided
tertiary literature (example)
encyclopedia and textbooks
where and how to find scientific papers
scopus and jmu library
Broad Background (Beginning but immediately follows hook)
larger issue at hand and most general background on this issue
advantages of SCOPUS
free access to scholarly articles, content is curated for accuracy and authority, information is stable, specialized subject specific databases for the topic
specific background (middle)
specific organisms, system or technique being studied and why they are worth studying
very specific question/goal/aim (end)
the precise issue that the study is going to tackle
Hook (beginning)
argument or facts used to justify why anyone should care about the study. Used to appeal to the widest audience possible.
your question/aim/hypothesis
The proposed research would address this problem by making the first detailed examination of links between groundwater and concentrations of trace metals in avocados. We will test the hypothesis that heavy metal concentrations in groundwater affect their concentrations in avocados.
Which of the following BEST describes the general structure of an introduction
A upside down pyramid that starts with a hook to get the audience interested and all of the following information helps the reader to understand the specific aim of the study and its importance
CRAAP stands for?
Currency, Relevance, Authority, Accuracy, Purpose
currency in CRAAP
how up to date something is
What does peer-reviewed mean?
Other experts in the field have verified the integrity of the information
what are scientific testable questions
addressed the issues/ questions using data
what are non scientific testable questions
addresses issues/ questions using values, beliefs or judgements
what is independent variable
variation does not depend on another variable
dependent variable
does depend on variation of independent variable
control
designed to show change ( is not manipulated)
descriptive study
scientist is not testing a hypothesis; they are simply making observations
non experimental study
variable is not manipulated and just gathering data to test a hypothesis, examine if there is a relationship between the two variables but not a casual relationship, hypothesis is tested
Which of the following is a major advantage of a subject specific database (like Scopus) over Google Scholar?
Scopus has better filters than Google Scholar to help narrow down your results
This is a short summary of a scholarly article that will help you identify whether the article is relevant. This short summary will save you a lot of time, because you won’t have to read an entire article before discovering it is not relevant to your topic or interests.
abstract
Which of the following best depicts the format of citations in the references section of the Ferrito et al. paper? Note: references are found at the end of the paper.
Author(s). (Year). Title. Journal, Vol. Pgs.
Which of the following best depicts the format for citations within the text of Ferrito et al.’s introduction?
Author(s) last name(s), Year
What are the 2 main things that citing your sources accomplishes?
Citing your sources establishes the source of facts that are stated in a paper and therefore the legitimacy (or illegitimacy) of these statements
Citing your sources provides readers with an “in-road” to the literature surrounding a particular topic
Which of the following statements is correct regarding in text citations in the Ferrito et al. paper?
In text citations are most often at the end of sentences
According to the formatting used in the Ferrito et al. paper, which of the following is a properly formatted reference?
Kringle, K., Claus, S., & St. Nick, O. (2003). Evidence for the presence of Santa Claus in North American Chimneys. J North Pole Research, 270, 421-431.
According to the formatting used in the Ferrito et al. paper, which of the following is a properly formatted citation?
Though difficult, there is mounting evidence that Santa is accessing North American homes via chimneys (Kringle, Claus, & St. Nick, 2003).
experimental study
hypothesis tested, variable is manipulated to measure response of dependent variable, good at establishing casual relationships
what studies require independent and dependent variables?
experimental and non experimental studies
a non experimental study that does not determine causation
correlation
pipettor parts
plunger, tip ejector, shaft, pipette tip
how to use a pipette
vertical position
correct volume is middle to top volume range
units used for pipetting
microliters
why are there so many protocols for pipetting?
to avoid contamination
Currency
when was the information published?
Relevance
Is the information appropriately related to the topic you are interested in?
Authority
is there an author? What are their credentials and affiliations? Could they bebiased or have an agenda
Accuracy
are sources of the information cited? Is this fact or opinion?
Purpose
Is this article clearly biased or trying to sell your something? What are theaffiliations of the source?
empirical
it relies on measurements of the real world
This is an enzyme whose function is to synthesize new DNA by attaching nucleotides that are complementary to a single strand of DNA.
DNA polymerase
The building blocks of DNA are:
nucleotides
Nucleotides are added to the growing DNA strand during the _________ phase
extension
During the annealing step…
Primers bind to the newly separated DNA strand
the following that is a necessary “ingredient” for a PCR to proceed.
Forward Primer
DNA polymerase
Reverse Primer
Template DNA
Nucleotides
What primer set would be used to amplify each organism’s genome (Fungi,
Plant, Vertebrate)
fungi- ITS
plant- RncL
animal- MT-CO1
A typical reaction would consist of:
15 µL PCR reactants
1 µL Primer Mix
12 µL H2O
+ 2 µL DNA extract
what volume of PCR reactants would you add to your master mix if you wanted to amplify 6 samples?
105 microliters
What volume of DNA extract would you add to your master mix before you distribute it to individual PCR tubes if you wanted to amplify 6 samples?
this doesnt go in the master mix
This is the volume of master mix that will go into an individual PCR reaction tube (before any DNA is added)
28 microliters
Which of the following would be a GOOD region of the genome to use for DNA barcoding?
a region that has lots of copies in the genome
Why are the primers we use to DNA barcode often referred to as “universal” primers?
they work across a wide variety of taxa
in the context of our labs, what does “bp” stand for?
base pairs
What is NCBI Genbank?
One of the world’s largest DNA sequence Databases
You want to develop primers for the blue and red regions of the following DNA template sequence:
5’-ATGCAATTGCAGTCGATTGCTCGATCGATCTTCGAAATTTCCCGAGCTTCGATCGC-3’
Which of the following is the appropriate Reverse Primer sequence?
5’-GCGATCGAAGCTCG-3’
What would the resulting gel look like if your primers did not match a DNA sequence found in your organism or sample?
Correct!
there would be no bands
Electrophoresis is used to:
-Separate DNA fragments
-Determine the size of DNA fragments
-Help determine the success of a PCR reaction
The rate of migration of DNA within an agarose gel in the gel electrophoresis technique is primarily based on what factor?
the size of the DNA fragments
Which of the following provides evidence that electric current is running through your gel (check all that apply)
-bubbles rise from the electrodes
-you can see the loading dye move from the well into the gel
When two bands from two different samples line up on a gel this means
The samples share a fragment of DNA that is the same length
Why do we run our H2O control (aka negative control) from our PCR reactions on the gel?
t enables you to tell if your PCR was contaminated by DNA that was not from your sample
t/f You should be sure to include marker/ladder in each well of your gel
false
Why do we dye our gels with intercalating agents like Gel Red dye or Ethydium bromide?
This dye stains the double stranded DNA in our gel
To carry out Sanger sequencing, a mix is needed containing:
dideoxyribonucleotide (ddNTPs)
DNA polymerase
Primer
DNA template
four deoxyribonucleotides (A, T, C, G)
The primer used in Sanger sequencing
has a nucleotide sequence complementary to the area that flanks the region you want to sequence
What volume of PCR product goes into an individual sequencing tube?
8 ul
t/f You should remove the rubber cap of the sequencing tube before injecting your sample DNA or primer.
false
t/f You should use 2 sequential sequencing tubes for each sample that successfully amplified. One tube for a reverse read and one tube for a forward read.
true
t/f You should be sure to put BOTH a forward AND reverse primer in EACH sequencing tube.
False
You only put a forward OR reverse primer in each tube
What is the main goal of the “sequence viewer” substop?
visualize your sequence and determine if you have an accurate or inaccurate read
What is the main goal of the “PHYLIP NJ” substop?
Creates a phylogenetic tree based on your DNA sequence(s)
trace file
this depicts the raw results of automated sanger sequencing. typically include lots of colored humps that represent each nucleotide
base call
the nucleotide at a given position in your DNA sequence according to the results of automated sanger sequencing
phred score
a measure of the quality of the identification of the nucleobases generated by automated DNA sequencing
consensus sequence
combination of trimmed forward and reverse DNA sequences that is typically more accurate than each sequence alone.
accession number
unique identifier # given to each sequence in the blast database
muscle
an alignment of multiple DNA sequences that allows you to visualize similarities and differences between the DNA sequences
blast
basic local alignment search tool- used to find matching DNA sequences from a database
Which of the following would you use to remove “bad calls” from your original sequence?
trim sequence
A260:A280 ratio
1.8
A260:A230 ratio
2-2.2
ideal concentration for PCR
50-250 ng/ul
wavelength dna is absorbed at
260
3 basic steps of pcr
denature, anneal, extend
anneal
temperature reduced to 55 and the PCR primer anneal/ base pair with the DNA template
denature
heat is increase to 94 and the hydrogen bonds break so the two strands separate
extend
heated up to 72. TAQ polymerase binds to the primers and new DNA begins to be synthesized
PCR primers role in PCR reaction
PCRs will anneal to the template DNA and that will be the starting point for DNA replication. They also select the region of DNA that will be amplified
DNA polymerase role in PCR reaction
A
an enzyme that can synthesize new DNA. TAQ polymerase is used because it can withstand the heat and allows us to perform repeated rounds of DNA replication
what primers are needed for PCR reaction
A
forward and reverse
dNTPs
A
monomers/ building blocks of DNA. DNA polymerase links dNTPs together into a new DNA strand
A short branch length on a PHYLIP ML tree means:
species are closely related
What numbers are associated with the concentration of DNA, salt contaminents, and protein contaminents
DNA: A260
SALT: A230
PROTEIN: A280
list the 8 major levels of the Linnean taxonomic hierarchy
domain, kingdom,phylum,class,order, family,genus,species
the typical size (bp) of a DNA barcode sequence
400–800 bp
