BIO 150 Lab Final JMU (example 2)

According to your reading, who is the POTENTIAL audience for a research article?

anyone with a computer

You must copy your photos to your lab notebook before the end of lab because they will be deleted from the computer at the end of the day.

True

Which of the following would you use to determine the length of a single read?

sequence viewer

According to your reading, a good abstract is like a:

mini version of your paper

Using AND between two search terms will narrow your search

narrow

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

T or F The photos in figure A are more properly formatted for size and alignment than figure B.

False

T or F: It's okay to add copyrighted images to iNaturalist. (These include images of boxes, labels, logos, and images downloaded from the internet).

False

What is the main purpose of PCR?

to amplify DNA

How many microliters of loading dye do we add to each sample?

2

What volume of PCR product goes into an individual sequencing tube?

8 ul

What goes in the green circle of this flow chart depicting the process of science?

Testing Ideas

Of the three choices below which image(s) are appropriately cropped?

Image B

Electrophoresis is used to:

-separate DNA fragments -determine the size of the DNA fragments -determine the presence of DNA fragments of a certain size

If there were two tables before this figure and no other figures in the paper, what would the proper figure # be?

1

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 original DNA molecule are made during that time?

1 billion

According to your reading, which of the following is NOT a typical part of an abstract?

1-2 sentences to cite the works referenced

1.23 mL (milliliters) = _______ µL (microliters)

1230 µL

How many groups will share a gel box?

2

Which of the following are examples of copyrighted photo(s) that you SHOULD NOT upload to iNaturalist (select all that apply).

A photo of the cover of bottle of aloe drink with logo and brand on it A photo of aloe plant that you download from google images

A) The energy needs of a resting sea otter are three times those of terrestrial animals of comparable size. To support such a high metabolic rate, the sea otter must eat about 25% of its body weight daily and often feed at night as well as during the day. B) —The energy needs of a resting sea otter are three times those of terrestrial animals of comparable size. The sea otter must eat about 25% of its body weight daily. Sea otters feed at night as well as during the day.

A) better flow B) worse flow

According to your reading, most people will decide whether or not to read your FULL paper based on your:

Abstract

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

To carry out Sanger sequencing, a mix is needed containing

All components listed are required (four deoxyribonucleotides (A, T, C, G), dideoxyribonucleotides (ddNTPs), DNA template, DNA polymerase, primer)

Which of the following best depicts the format for citations within the text of Ferrito et al.'s introduction?

Author(s), Year

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

Broad Background: larger issue at hand and most general background on this issue Specific background: specific organisms, systems, or techniques being studied and why they are worth being studied Very specific question/aim/goal: the precise issue that the study is going to tackle Hook: arguments or facts used to justify why anyone should care about the study. Used to appeal to the widest audience possible

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

COIbar-RFLP is a good method to ID fish

According to your lab manual, what are the 2 main things that citing your sources accomplishes? (check the two that apply)

Citing your sources provides readers with an "in-road" to the literature surrounding a particular topic Citing your sources establishes the source of facts that are stated in a paper and therefore the legitimacy (or illegitimacy) of these statements

After reading the following graph in an news article, Jerry concludes that Kanye West 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

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

DNA barcoding can ID fish

In sequential order, what are the three steps of PCR?

Denature DNA, Anneal Primers, Extend DNA

Match of each of the following to its meaning in a PHYLIP ML tree

Node: common ancestor Branch Length: evolutionary distance Red text: outgroup Branch tips: individual taxa (their DNA sequences)

According to your lab handout, which of the following is correct?

You should only upload samples that YOU collected and successfully barcoded

According to your lab manual: Each group member should create one single iNat observation for the individual sample they were in charge of during the semester. What should you do if you weren't able to barcode the organism/sample you were in charge of?

help out a group member that did barcode the organism they collected by helping them read/follow directions

μL stands for ________ , which is _____ liters:

microliter ; 10^-6 L

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

In general, scientists can identify a new species using only DNA barcoding

False

In many ways, Anna's gel is an example of an experimental study (as opposed to a descriptive or non-experimental study): it tests a hypothesis, it manipulates variables, it has treatments and controls. With this in mind, match each of the following parts of Anna's gel to the general part of experimental study that it represents:

Known DNA (gel lane p): control Water sample (gel lane -): control Sample 1 (gel lane 1): treatment Sample 2 (gel lane 2): treatment

Where should you record the serial numbers of your sequencing tubes? (check all that apply)

In the google spreadsheet linked to this week's Module in canvas In your printed lab manual In your lab notebook

What is the objective of a discussion section of a scientific research paper?

Interpret your results in the context of the specific question you set out to address

Why do we run our H2O control (aka negative control) from our PCR reactions on the gel?

It enables you to tell if your PCR was contaminated by DNA that was not from your sample

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

Is this article a research article or a review article? An emergent science on the brink of irrelevance: a review of the past 8 years of DNA barcoding

Review article

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

True

T or F: it's okay to add captive/cultivated organisms to iNaturalist

True

Of the images below which has been overly adjusted, and is altering key features?

A

Of the three choices below which image(s) has/have an appropriate scale?

A

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

Since dideoxy (Sanger) sequencing is based on chain termination, why are normal dNTPs (deoxyribonucleotides like A, T, G, and C) also included in the reaction?

to produce a range of sizes of DNA synthesis products that terminate at variety of lengths

How can contamination be prevented in the laboratory?

Any of these methods will help prevent contamination in the laboratory. (Using barrier pipette tips, Keeping test tubes and pipette tip boxes closed as much as possible, Changing pipette tips between solutions, or after tips have touched DNA)

Which of the following BEST describes how Ferrito et al. use citations in their introduction:

Citations are being used to legitimize statements that Ferrito et al. are stating as facts by providing the source(s) those statements came from.

CRAAP stands for?

Currency, Relevance, Authority, Accuracy, Purpose

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

Descriptive

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

European Hake are often mislabeled

Which of the following is the typical "entryway" into the process of science?

Exploration and Discovery

Where would the following item best fit in this flowchart of the "process of science"? You conduct a web search to learn more about DNA barcoding and what kinds of questions it is being used to answer

Exploration and discovery

Nucleotides are added to the growing DNA strand during the _________ phase

Extension

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

According to the formatting used in the Ferrito et al. paper, which of the following is a properly formatted citation?

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.

Which is a disadvantage of scholarly literature?

Less accessible to non-experts

Assuming any citation 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

Of the sentences below, which is best edited for clarity?

Pill bugs belong to a subgroup of crustaceans called isopods, and most isopods live in marine environments.

Match the following (answers are in the searching a database pdf)

Primary article: research article Secondary article: review article Original research: research article Summary of previously conducted research: review article Provides good background on a topic: review article Includes LOTS of references: review article Overview of particular field/topic: review article

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

Scholarly literature is typically short in length

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

Seafood mislabeling is big problem

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).

The advantages of outbreeding include reduced exposure of deleterious recessive alleles and increased heterosis, the increased fitness commonly associated with increased heterozygosity.

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 FALSE regarding this citation?

The title of this paper is "Molecular characterization of icefish, (Salangidae family), using direct sequencing of mitochondrial cytochrome b gene"

If no DNA polymerase (or Taq polymerase) were included in your PCR, the reaction would not work because:

There is no enzyme to make new complementary strands of DNA

According to the formatting used in the Ferrito et al. paper, which of the following is a properly formatted in text citation?

Though difficult, there is mounting evidence that Santa is accessing North American homes via chimneys (Kringle, Claus, & St. Nick, 2003).

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. 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

T or F: In addition to a legend it is good practice to include a title above your figure(s)

True

According to your lab manual, citations: (check all that apply)

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

Which of the following is not a "SEQUENCE ASSEMBLY' substop in the DNA subway blue line?

BLASTN

Check each answer that is TRUE. (select all that apply).

Each group needs to run a negative PCR control You should label the tops AND sides of your PCR reaction tubes

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

Hook: beginning Broad background: beginning but immediately follows hook Specific background: middle Very specific question/goal/aim: end

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

Molecular size of the DNA Conformation of DNA

What would be the most likely outcome of a Sanger dideoxy DNA synthesis reaction if ddNTPs were present in large numbers relative to the number of dNTPs (normal A's, T's, G's, and C's)?

Most daughter strands would be very short. (Incorporation of chain-terminating ddNTPs (as opposed to normal dNTPs) would be very likely during the early stages of synthesis of new strands of DNA. As a result, synthesis of daughter strands would terminate very early, resulting in many short daughter strands)

According to your reading, which of the following is one of the most important factors in determining whether ANY part of your research article will be read?

Title

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

Using OR between two search terms will broaden your search

broaden

What are you supposed to do with a captive/cultivated organism when you upload it to iNaturalist?

make sure to check the box that marks it as Captive/Cultivated

What does 99% sequence similarity in a MUSCLE alignment mean?

only 1% of the base pairs are different between the two sequences being compared

Which of the following sentences is correct?

None of these answers are correct

T or F: the purple tubes in this image are balanced

True

Assuming the legend is correct, would this example figure appear as the first figure or second figure in a paper?

neither

Match each of the following parts of research article to its meaning

A presentation of all your experiments and data, represented both as text and in tables, charts, diagrams, and photographs. (RESULTS) A complete summary of the paper designed for experts and non-experts (ABSTRACT) An opportunity to interpret your results and explore your findings within the context of the larger scientific record. (DISCUSSION) A brief but detailed description about the tools and methods you used to perform experiments and analyze results. (MATERIALS AND METHODS) A specific statement that conveys the topic and conclusion of the paper. (TITLE) Your citations (REFERENCES) The beginning of a paper that transitions from a general background to a specific research question or goal. (INTRODUCTION)

According to your reading, which of the following are reasons to publish a research article? (check all that apply)

Add your results to the permanent domain of scientific knowledge Establish your reputation among your peers Help you advance in your career as a scientist Demonstrate to funding agencies that you can deliver results

Match each of the following BLASTN measures to its meaning

Aln. length: length of sequence used to make the match mismatches: # of non-common bases between query and hit e: likelihood that the match BLAST made between our query sequence and your match could happen only by chance bit score: summary statistic based on the length of the alignment and number of mismatches

Which of the following should you typically include in a discussion section? (check all that apply).

Any follow up questions you might logically ask based on your results How your results compare to what you expected to see. An explanation of unexpected results

According to your reading, titles are better when they are "conclusion-based". Which of the following titles are conclusion-based (and therefore better)? (check all that apply)

Are GM's up to code?: DNA barcodes of genetically modified corn are different from barcodes of non-GM corn DNA barcoding reveals frequent mislabeling of sushi on JMU campus

According to your lab handout, which project should you add your iNat observations to?

Barcoding JMU - Captive and Cultivated Species

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

Because an outline to the introduction to our project proposal is due next week (Wk. 3) Because learning how to write an introduction will improve our ability to communicate "scientifically"

Which of the following provides clues that your gel electrophoresis is running properly (check all that apply)

Bubbles rise from the electrodes You can see the loading dye move from the well into the gel

According to your reading, it is best to avoid describing figures in text. Instead you should describe the "results" and use the figures to illustrate these points. This is called "marrying the figures" with text. Which of the following are the best examples of this? (check all that apply)

DNA barcodes of genetically modified (GM) tomatoes were identical to those of non-GM tomatoes (Fig. 3). Our sample sequence was more similar to humans than chimpanzees (Fig. 5). The top ten BLAST matches to our samples were all the same species, the common cow, Bos taurus (Fig. 7).

Match each of the following statements as a DO or DON'T for photographs

DO use photographs to show data or as a deliberate visual tool to enhance your scientific story DONT misrepresent data by unethically manipulating images DONT allow labels in data figures to distract from the data themselves DO be picky about the images you use, selecting the best for your needs DO consider cropping or adjusting the image settings of your photos to better suit your needs DO follow image adjustment guidelines to ensure that you enhance images only for quality and not to alter conclusions DO assume that critical scientists will scrutinize your data images and look for obvious, indisputable results DONT use photographs as decoration

According to your reading: Mark each of the following as a DO or DON'T for a research article

DONT write your results section as a long stretch of continuous findings DO emphasize your results, citing your figures rather than describing them DO use a title that emphasizes what is most important about your study—usually the conclusion DONT use your discussion to simply recapitulate all of your results DO use your discussion to highlight the significance of your results and compare your findings with those of previous studies

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)

You should be sure to include marker in each well of your gel

False

You should be sure to put BOTH a forward AND reverse primer in EACH sequencing tube.

False

Which of the following are true regarding BLASTN? (check all that apply)

If your aln. length is less than 400 bp, your data are often not reliable to ID organisms at the species level If the # of mismatches/Aln. Length > 1%, this often means the match is a different species

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

What are the benefits of building a consensus sequence? (check all that apply)

It is longer than a single read (therefore more information) It is more accurate than a single read

Click each of the following that is a necessary "ingredient" for a PCR to proceed.

Nucleotides Template DNA Forward Primer Reverse Primer DNA polymerase (or Taq polymerase)

What does peer-reviewed mean?

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

Match each sample type to the primer set that should be used to amplify the barcoding region of that organism's genome:

Plant: RbcL Spider: MT-CO1 Octopus (invertebrate): MT-CO1 Mushroom: ITS Fish: MT-CO1 VF2/R2 Mouse: MT-CO1 VF1/VR1 Cow: MT-CO1 VF1/VR1

During PCR, DNA polymerase (or Taq polymerase) starts copying at

Primers attached to the end of the desired DNA sequence

Which of the following is NOT an item that belongs in the process of science flow chart?

Research

Is this article a research article or a review article? The Use of DNA Barcoding in Identification and Conservation of Rosewood

Research article

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 set of photos is formatted for all the above criteria?

Series 3

Typically it is appropriate to BEGIN a discussion section by:

Stating your main hypothesis/question, followed by whether or not your results supported your main hypothesis/addressed your question

What should you do once you've finished uploading your iNat observation to the course project and double checked that 1) the information is all correct 2) there are no copyrighted images and 3) no one in your group or in other classes has duplicated your observation?

Submit the link to your iNaturalist observation to the canvas assignment, "iNaturalist Observation Submission" for grading

What is the objective of a results section of a scientific research paper?

Summarize your findings using tables, graphs, and words

Which of the following DNA sequences would be derived from the sequencing gel below? (Note: top of image represents top of gel. Top = end with with wells)

TTGATCAGGT

Which of the following would typically be included in the results section of a scientific research paper? (check all that apply)

Text that "marries" written descriptions of your data to the the figures or tables they describe Images or tables that summarize your data In text citations of your figures/tables (Ex. (Fig.1))

Anna ran marker (M), PCR products from 2 DNA extracts (1&2), and a H2O (negative) control (-) through a gel. She got the following result: Which of the following does she know for sure? (Check all that apply)

The Gel worked successfully

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

When two bands match up between two different samples on a gel electrophoresis plate this means

The samples share a fragment of DNA that is the same length

Check each of the following that is/are items that you are required to record in your lab notebook this week. (check all that apply)

The serial # of your sequencing tubes (assuming you have samples to sequence) Your DNA subway log in and password hint The ID of the sample associated with each sequencing tube serial #

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 is/are reasons why the ITS, Rbcl, and MT-CO1 regions of the genome were selected for use in DNA barcoding? (check all that apply)

These regions typically have high enough inter-specific variation to distinguish barcode sequences of one species from another DNA sequences flanking these regions are highly conserved (aka they are NOT very variable) These regions typically have low intra-specific divergence There are typically many copies of these regions w/in a cell

What is the main goal of the "BLASTN" substop?

This compares your sequence to other sequences in the GENBANK database

According to your reading, a good results section should write each paragraph as something like a "mini-paper", with its own rationale, method, result, and conclusion. Which of the following demonstrates this point? (check all that apply)

Three of our four samples were sequenced (Table 1). DNA subway analyses revealed that all of our sequences were high quality consensus reads over 500 bp in length (Table 1). This ensured the reliability of our sequences for further bioinformatic analyses.

According to your reading, put the following sections of a research article in their typical order from first to last:

Title Abstract Introduction Materials and Methods Results Discussion References

The alkaline lysis DNA extraction procedure uses high pH and heat to break open cells and release the DNA.

True

Which of the following would you label as captive/cultivated organisms vs. wild in iNaturalist?

Tuna in Sushi: captive/cultivated Plants in Vitamins: captive/cultivated An insect you captured in the arboretum: wild Plants that were raised and planted by humans: captive/cultivated Foods: captive/cultivated Aloe in Lotion: captive/cultivated Caviar you bought from the store: captive/cultivated A mushroom you found in the forest: wild A mushroom you found in the grocery store: captive/cultivated Fruit in Yogurt: captive/cultivated An apple you picked from an orchard: captive/cultivated A plant you found in the forest: captive/cultivated

According to your lab manual: Each group member should create one single iNat observation for the individual sample they were in charge of during the semester. What should you do if your group wasn't able to barcode any of the organisms/samples they were in charge of? (aka you got all your barcodes from a different group).

You should not upload anything to iNat, but you can help other groups out by reading them directions

What is our working definition of a captive/cultivated organism for this lab?

any organism/sample that is store bought and/or planted/grown/raised/made by a human

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 (Although she is testing a hypothesis, she is not manipulating any variables in this study. She is just collecting data from the "natural" environment to test her hypothesis)

What is the main goal of the "sequence viewer" substop?

visualize your sequence and determine if you have an accurate or inaccurate read

According to your reading, your title has failed if:

your audience needs to look at your abstract to determine what you studied

Which of following questions could DNA barcoding successfully address?

What species of mushrooms are being sold at the local market?

Today we will set up reactions with a total volume of 30 µL. A typical reaction would consist of: 15 µL PCR reactants 1 µL Primer Mix 12 µL H2O + 2 µL DNA extract

According to you lab manual 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? - NA (THIS DOESN'T 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

A) Pill bugs are terrestrial organisms. Pill bugs have gills. Respiration cannot occur unless the environment is moist. Pill bugs cannot survive if submerged under water. B) Pill bugs are terrestrial organisms yet they have gills. Thus, respiration cannot occur unless the environment is moist. However, pill bugs cannot survive if submerged under water.

A) worse flow B) better flow

When filling a pipette you should begin by depressing the plunger to the BLANK 1 in BLANK 2. Next you should insert the tip into the liquid and let the plunger out BLANK 3 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.

BLANK 1: first stop BLANK 2: the air BLANK 3: slowly

Match each of the following excerpts from student papers to the citation-related mistake they are making (one choice will be used twice).

Algae have been connected with the "development of contact dermatitis, asthma like symptoms,and symptoms resembling hay fever during bathing in cyanobacterial blooms have been also described" (Torokne et al., 2001). USING DIRECT QUOTE On top of health issues, algal blooms have recreational downsides as well, "blooms degrade the ecosystem and interfere with quality targets and lake restoration" (Ibelings, 2007). USING DIRECT QUOTE Elevated CO2 levels and a rise in global temperatures have caused a massive increase in the production of both beneficial and harmful algal blooms (HABs) in freshwater and marine ecosystems (Li et al., 2016, pg. 241). BAD FORMATTING Li and fellow scientists strictly examined the impact of CO2 and temperature increases on freshwater ecosystems. The types of worldwide freshwater algae species observed were green algae, diatom, and cyanobacteria. All three species showed an increased production in cells under conditions with higher levels of CO2 and higher temperatures. The rise in CO2 levels in aquatic ecosystems is dangerous to aquatic life. The overproduction of cyanobacteria can change the whole freshwater carbon cycle, which therefore creates a collapse in ecosystem function (Li et al., 2016). TOO MUCH INFO In the Shenandoah Valley, many freshwater areas are highly impacted by human activity, which range from farming to hiking and fishing. Nutrient runoff from farms causes a huge influx of nutrients enabling algae to feed and grow much faster than times when these excess nutrients are not present, impacting marshes, ditches, and many other wetlands. MISSING CITATION WHERE NEEDED Algal neurotoxins can negatively affect humans who drink contaminated water or swim in water that has algal blooms (Wehr et al., 2015). NO MISTAKE

Peer reviewed literature is typically printed in scientific journals with names like: The journal of XXX, Proceedings of the XXXX society, Nature, Science, Food Science, etc. Typically if you see a journal name listed in a citation, it means that source is peer reviewed and therefore reliable. If you aren't sure of the reliability of a source, you can google the name of the journal the source is from to determine its reliability. Which of the following citations from Ferrito et al's paper is NOT from a peer reviewed journal (and therefore may not be reliable).

All of these references appear to be from reliable, peer reviewed journals.

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

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

Are sushi restaurants selling cheap species of fish for more $$? What is the average number of burritos consumed by a JMU freshman? How many species of insects are in cow dung?

Which of the following identify items that are wrong with this figure? (check all that apply)

Aspect ratio is compressed on sample T3B Samples T1A and T1B do not have photographs associated with them Numbering and labeling system is unnecessarily complicated (why use T4B vs just 4B?) Why does only one sample show the brand name in the right column? Shouldn't we see the same info for each sample? Caption is ABOVE the image (it should be below it) No explanation of what sample labels (ex. T1 and A and B) represent Can't know for sure which sample is A vs B in each row

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.

Of the three choices below which image has be the best detail in terms of aiding in the ability to identify the organism? (ignore lack of scale).

B

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

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: (graph) After seeing this graph in an news article, Jesse concludes that vitamin C is causing people to have fewer colds. What is the FUNDAMENTAL problem with Jesse's conclusion? (Hint: answer is under the "Types of Studies" paragraphs).

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

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

Use the drop downs to fill in the following table based on the reading above:

Descriptive study: tests a hypothesis (FALSE), can establish causation (FALSE) Non-experimental study: tests a hypothesis (TRUE), can establish causation (FALSE) Experimental study: tests a hypothesis (TRUE), can establish causation (TRUE)

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 BEST describes how Ferrito et al. describe the papers they cite in the text of their introduction:

Ferrito et al. rarely summarize the entire paper they cite

Which of the following are examples of "Exploration and Discovery" (check all that apply)

Finding inspiration Sharing data and ideas Asking questions Making observations Exploring the literature

Of the sentences below, which sentence is best edited for clarity?

None of the sentences are edited for clarity.

Match each sentence from the example proposal summary paragraph in your lab manual to the typical part of a research proposal that BEST represents this sentence. (Some choices will NOT be used).

Roughly 70% of the American population eats avocados at least once each year, so that potential exposure of the populace to contaminants in avocados is widespread (Why the area of study is important) Nonetheless, little research has been done with regard to the uptake of trace metals by avocados during their growth (why previous work is inadequate) The proposed research would address this problem by making the first detailed examination of the controls on concentrations of trace metals in avocados (Research you plan to do, and how it will advance knowledge) Specifically, groundwater in 15 groves of avocados will be sampled and concentrations of trace metals determined by atomic absorption (How your research will specifically address or test this question/hypothesis (methods)) We will test the hypothesis that concentrations of Hg and Cd in avocados are correlated with the levels of these trace metals in the surrounding groundwater (Specific question/aim/hypothesis)

Examine the figure below for formatting errors and answer True or False for each statement below.

The images are all cropped properly. FALSE The images are all the same size. FALSE The images have an appropriate scale. FALSE The images labels have the same font, color, and consistent labeling. FALSE

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

You need to make sure the lid to the centrifuge rotor is on tight. You can confirm this by hearing a "click" sound when you push it down.

True

Of the sentences below which is most correctly edited for over-selling and jargon?

UV irradiation (wavelengths 280-400 nm) from sunlight is important because it severely damages DNA and other biological molecules in a variety of marine plant and animal species (Gleason. M., Wellington. J., 1995).

Select the item from the drop down that matches the letter in the 150 lab timeline below:

Wk 1-3: Develop questions Wk 2-5: Write project proposal wk 3-5: Collect Samples for DNA barcoding project Wk 5-10: Extract DNA, PCR, and Barcode samples Wk 10-11: Write up results Wk 12-14: Write Discussion and Abstract

Match the type of sample with the extraction protocol you should use:

animal samples: crude alkaline lysis plant samples: crude DNA extraction w/ DNA precipitation fungi samples: crude alkaline lysis fish samples: crude alkaline lysis insect samples: crude alkaline lysis invertebrate samples: crude alkaline lysis dog/cat food: crude alkaline lysis