BIO LAB FINAL

If you can't communicate a concept clearly through writing then you don't fully understand the concept. Furthermore, a teacher can only evaluate your understanding by what you write on your reports. Therefore, make sure sentences are communicating what you intend. Of the sentences below, which sentence is best edited for clarity?

-A new study investigating different approaches to embalming cadavers has shown that formaldehyde has a negative effects on human health. -New studies are investigating different approaches to embalming cadavers since formaldehyde has been shown to have negative effects on human health.

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

Dangers of "it" (Pronoun Clarity)

-We will collect and extract DNA from our tadpole samples. This DNA will then be further amplified and sequenced through polymerase chain reactions and sanger sequencing. -Tropical countries are home to both native and nonnative species. Nonnative species can be introduced to new regions by a variety of methods. -Harper and Case (2019) found that non-native fish were twice as likely to be mislabelled as native species.

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

According to your lab manual, which of the following is NOT one of the things you should be able to do by the end of this week's lab?

Correctly format citations in an introduction

CRAAP stands for?

Currency, Relevance, Authority, Accuracy, Purpose

Never tell the reader something is interesting, show it by explaining its significance. A way to help you avoid over selling an idea is to use fewer adjectives. Of the sentences below which is most correctly edited for over-selling and jargon?

DNA barcoding is one method that can be used to identify the mold species growing on cadavers. Since the fungi kingdom has an estimated 1.5 million different kinds of species, many of which with hard to distinguish morphological characteristics, DNA barcode sequences can be useful to aid in the identification of fungal species.

During this step in PCR, DNA is separated into two single strands.

Denaturation

DNA barcoding is useful to identify how much (%) of a product is made up of a particular ingredient.

FALSE

For the greatest accuracy in pipetting, one person should hold the pipettor while a second person holds the test tube the person is pipetting into or out of.

False

Low DNA purity can cause PCR reactions to fail

true

Low concentrations of DNA can cause a PCR reaction to fail

true

According to your readings from this week's lab, which of the following is/are question(s) that "science" can directly address. Note that not all answers must be about DNA barcoding to be correct. (check all that apply)

-Are sushi restaurants mislabelling the fish in their sushi? -What is the average number of burritos consumed by a JMU freshman? -How many species of insects are in cow dung?

Why are we learning how to write "scientific" introductions this week?

-Because learning how to write an introduction will improve our ability to communicate "scientifically" -Because an outline to the introduction to our project proposal is due next week

According to your lab manual, which of the following are the two major "types" of DNA barcoding projects that we can do in this class? (check all that apply)

-Biodiversity Assessments -Product Testing

According to your lab manual, 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

According to our exercise in class this week, what are the MAIN goals of an introduction to a scientific paper? (check the two answers that BEST apply)

-Enable the reader to understand the specific question/goal/aim of the study -Enable the reader to understand why the specific question/goal/aim of the study is important

Which of the following are advantages of scholarly literature? (Choose all that apply)

-It is transparent with sources of information -It is detailed -It is reliable

How can contamination be prevented in the laboratory?

-Keeping test tubes and pipette tip boxes closed as much as possible. -Using barrier pipette tips. -Changing pipette tips between solutions, or after tips have touched DNA.

Which of the following statements about gel electrophoresis is correct?

-Migration distance is inversely proportional to the fragment size

The rate at which DNA migrates through the gel is determined by (check all that apply)

-Molecular size of the DNA -Conformation of DNA

Electrophoresis is used to:

-Separate DNA fragments -Determine the size of DNA fragments -Help determine the success of a PCR reaction

citations:

-main purpose is to provide the exact information that a reader needs to locate the sources used by an author -are a standardized way of listing the sources used in a publication

Which of the following are advantages of a review article over a research article? (check all that apply)

-review articles can help you figure out findings from lots of different studies on your topic -review articles provide GOOD SUMMARIES: they summarize many separate studies on a similar topic that have been done by different researchers

μL stands for microliter, 10^-6 L

...

The three main stages of the PCR process are usually repeated around 30 times over several hours. Approximately how many copies of the target region of the original DNA molecule are made during that time (assuming perfect amplification)?

1 billion (= 2^30)

Which of the following BEST describes the general structure of an introduction:

An 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

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.

Pat wants to use DNA barcoding to determine what % of pork sausage is mislabelled at Walmart vs. Local Butchers, but he can only collect 20 total meat samples. Which of the following is the best experimental design to test this (based on the principals of sample independence and balanced design)?

Barcode 10 sausages each from 10 different packages at walmart and 10 from 10 different packages/batches from the butcher

Match each of the general parts of an introduction that we learned about in this week's lab to its DEFINITION.

Broad Background = Larger issue at hand and most general background Specific background = Specific organisms, system, or techniques Very specific question/aim/goal = The precise issue Hook = argument or facts to justify

Which of the following is the BEST short summary of paragraph 4?

COIbar-RFLP is a good method to ID fish

Which is a disadvantage of scholarly literature?

Can be less accessible to non-experts

The following are examples of questions/studies that students designed in previous semesters. Which of the following is NOT a good question for DNA barcoding to address?

Can we find evidence to support the claim that orange colored fruits and vegetables have an association with the risk of colorectal cancer by using DNA barcoding?

After reading the following graph in an news article, Jerry concludes that Taylor Swift is causing global warming. What is the FUNDAMENTAL problem with Jerry's conclusion? (Hint: answer is under the "Types of Studies" paragraphs).

Correlation in a non-experimental study does NOT determine causation

Scientists follow 100 people for a year and record the following information: 1) How much vitamin C they consumed and 2) How many colds they had. They publish the following result:

Correlation is not causation: There could be other underlying factors associated with vitamin C intake that are responsible for this trend

Match each substance to the peak wavelength of light it absorbs

DNA = 260nm Proteins = 280nm Salts = 230 nm Carb = 230nm

You are testing the hypothesis that generic brands of herbal tea are more likely to mislabel the types of herbs they use in their tea than brand name herbal teas. Your friends come up with some ideas for studies to test this hypothesis, but some of their ideas seem a bit off. Which study does the BEST job of testing this hypothesis?

DNA barcode 10 brand name teas and 10 generic teas and compare the % that are mislabelled

Which of the following is the BEST short summary of paragraph 2?

DNA barcoding can ID fish

Danielle wants to use DNA barcoding to determine the identity of the plants in her backyard. What kind of study is she conducting?

Descriptive

After running your DNA extract through a nanodrop spectrophotometer you find that your extract has a DNA concentration of 1000 ng/uL and your A260:280 is 0.50, which of the following should you do to increase the likelihood of your DNA extract PCR amplifying correctly? (If you're torn between two answers, choose the one that requires the least time/effort).

Dilute your DNA extract to a more ideal concentration for PCR

Why is 70% ethanol used in the plant DNA extraction protocol?

Ethanol helps wash away impurities from your DNA

Which of the following is the BEST short summary of paragraph 3?

European Hake are often mislabeled

Which of the following is NOT a term that can be used for the DNA that you want to make copies of in a PCR?

Expansion DNA (or DNA expansion)

Which area(s) of the process of science were we working in today?

Exploration and Discovery

You cannot balance a centrifuge with an odd number of tubes.

False

Which of the following is NOT a tip for successful pipetting?

Hold the pipettor horizontally after pulling a sample

Match each of the general parts of an introduction that we learned about in this week's lab to the general LOCATION where it is typically found in an introduction

Hook Broad Specific Very specific

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

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

Which of the following is the BEST short summary of paragraph 1?

Seafood mislabeling is big problem

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

"third-hand" information that is typically written by non-experts, often lacks citations, often prone to generalizations and simplifications, and not typically peer reviewed

Tertiary literature

If no primers were included in your PCR the reaction would not work because:

The DNA polymerase would not amplify the specific region of DNA you want to be amplified

You want to see if a new chemical you have will help improve the success of PCR amplification of DNA from your samples. To test this you extract DNA from 10 samples that you know have worked in the past with the normal PCR chemicals you always use. Then you use two different PCR MASTER MIXES on the DNA extracts. In one PCR mix you use the NEW chemical. In the other PCR mix you use the old chemicals. Everything else is exactly the same. Then you run ALL the PCR products out on a gel to see which ones successfully amplified DNA. What is the control treatment in this study?

The original PCR mix with the old chemicals

Jaime wants to determine what % of sushi are mislabelled at the grocery store, so he buys a single box of sushi and barcodes 4 different pieces of sushi that were cut from a single sushi roll (Fig. 1). What is the FUNDAMENTAL problem with the design of Jaime's study?

The samples are not independent from one another

Which of the following is the BEST short summary of paragraph 5?

Their goal was to use COIbar-RFLP to examine mislabelling in 3 types of fish

Colds are negatively correlated with vitamin C consumption. The more vitamin C a person takes the fewer colds they have:

There is a significant relationship between vitamin C intake and cold frequency, but it cannot be determined whether the relationship represents cause and effect

What would the resulting gel look like if your primers matched more than one region in the genome of your organism or sample?

There would be more than 1 band

In the first sentence of the first paragraph of the Ferrito et al. paper, the authors cite (Armani et al., 2015). Which of the following is correct regarding this citation?

This article can be found in the journal "Food Control"

Your initial DNA extract has a DNA concentration of 10 ng/uL. What volume of this extract would you add to water to get 50 uL of 100 ng/uL DNA solution.

This is not possible

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).

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.

Your question/aim/hypo.

Your initial DNA extract has a DNA concentration of 900 ng/uL. What volume of this extract would you add to water to get 50 uL of 100 ng/uL DNA solution.

add 5.56 uL of extract to 44.44 uL of water

In the context of our labs, what does "bp" stand for?

base pairs

Using OR between two search terms will broaden your search

broaden

The plant DNA extraction protocol includes several extra steps that use isopropanol, ethanol, and TE buffer. What is the overall goal of these "extra" steps?

concentrate and clean your DNA

tertiary literature

encyclopedia entry

Why is it important to grind your samples well during DNA extraction?

grinding helps to break open cells and cell membranes to release DNA

Match each nanodrop read out to its ideal number for PCR amplification (according to your lab manual):

ideal DNA concentration (ng/uL) = 100 ideal A260:280 = 1.8 ideal A260:230 = 2.2 A260:230 ratio, below which indicates potentially significant contamination 1.4 A260:280 ratio, below which indicates potentially significant contamination 1.4

Using AND between two search terms will narrow your search

narrow

Sheila has noticed that the wasabi (a spicy paste for sushi) she buys from one restaurant is way cheaper than the wasabi she purchases from her favorite restaurant, but the cheaper stuff just doesn't taste as good. After doing some research, she learns that oftentimes horseradish will be dyed green and substituted for real wasabi. She decides to use DNA barcoding to test whether or not the cheap wasabi is horseradish or real wasabi. What kind of study is Sheila doing?

non-experimental

Primary literature

research article in peer-reviewed

Secondary Literature

review article or scientific book

Which of the following is a fundamental difference between a review article vs. a research article?

review articles typically explain work done by other scientists and use this to summarize what's going on in that field or identify larger trends

Why are the primers we use to DNA barcode often referred to as "universal" primers?

they work across a wide variety of taxa

What does peer-reviewed mean?

Other experts in the field have verified the integrity of the information

Pipettors are most accurate in the middle to top end of their volume range.

True

What is NCBI Genbank?

One of the world's largest DNA sequence Databases

You have 50 uL of DNA extract with a DNA concentration of 200 ng per uL. What is your Total Yield of DNA?

10,000 ng

0.753 mL (milliliters) = _______ µL (microliters)

753 µL

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

This number can indicate a the amount of protein contaminants in your DNA extract

A260:280

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

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.

Assuming any reference that lists authors, year, title, journal name, volume and page numbers can be considered a reliable source from a scholarly journal, how do you know whether you can trust the sources Ferrito et al. use in their paper?

Most of their sources are likely to be reliable because they come from peer reviewed journals

Which of the following citations from Ferrito et al. would probably help you learn the most about the history and dynamics of Hake fish populations?

Murua, Lucio, Santurtun, & Motos, 2006

Of the sentences below which is most correctly edited for jargon? (Note, typically you don't have to define every word. For example, in the following sentences you can assume the reader knows the definitions of outbreeding and deleterious recessive alleles).

One effective method to identify the species growing on the cadavers is DNA barcoding. DNA barcoding is defined as.....(assume correct definition is written here).

original research that is communicated "first-hand" by the people who collected and analyzed the data

Primary Literature

During the annealing step...

Primers bind to the newly separated DNA strand

Which of the following is FALSE regarding a scientific research proposal? (see section on "proposals" in lab manual print out for answers)

Research proposals are typically one to two paragraphs in length

Which of the following (if anything) is a FUNDAMENTAL problem with this conclusion?

Sample size is too small (need to test more hamburgers to make this conclusion)

Which of the following statements is FALSE with regards to scholarly literature?

Scholarly literature is typically short in length

During the crude alkaline lysis DNA extraction procedure for animal samples, many proteins are precipitated and the DNA remains in solution.

True

If you are photographing products you need to take photos both with AND without product labels before you come to lab this week. That way you can have all the relevant information in one photo, but also have photos that you can publish that don't share brand names.

True

You must have sample photos entered in your lab notebook BEFORE the start of lab this week because the samples themselves will be used/destroyed when you do the DNA extractions.

True

Which of following questions could DNA barcoding successfully address?

What species of mosquitos live in the pond behind my house

...

When filling a pipette you should begin by depressing the plunger to the first stop in the air. Next you should insert the tip into the liquid and let the plunger out slowly to prevent air bubbles and splash back. Once you remove the tip from the liquid, you should expel it by quickly depressing the plunger to the second stop.

Which of the following statements is FALSE regarding the in-text citations in the Ferrito et al. paper?

When multiple citations are used at the end of a single sentence, each citation is placed in chronological order from oldest to newest

Roughly 70% of the American population eats avocados at least once each year, so the potential exposure of the populace to contaminants in avocados is widespread (WHO, 2012).

Why area of study is important (hook)

Nonetheless, little research has been done with regard to the uptake of trace metals by avocados during their growth (Haas et al. 2019).

Why previous work it is inadequate