BIO LAB 150 FINAL (QUIZZES)

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

1-2 sentences to cite the works referenced

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

DNA possesses: A net negative charge A net positive charge No net charge

A net negative charge

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

Abstract

Which of the following should you typically include in a discussion section?

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

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

Answer 1: Correct! First stop Answer 2: Correct! the air Answer 3: Correct! slowly Answer 4: Correct! quickly Answer 5: Correct! second

How can contamination be prevented in the laboratory? Changing pipette tips between solutions, or after tips have touched DNA. 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.

Any of these methods will help prevent contamination in the laboratory.

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) Examination of the effects of elevation on pollen diversity Are GM's up to code?: DNA barcodes of genetically modified corn are different from barcodes of non-GM corn Using DNA barcoding to explore earthworm diversity in NW Virginia DNA barcoding reveals frequent mislabeling of sushi on JMU campus A comparison of DNA barcodes from genetically modified versus non-GM corn DNA barcoding of sushi in Harrisonburg, VA restaurants

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

which of the following is/are question(s) that "science" can address. (check all that apply) Should DNA barcoding be used to regulate the nutritional supplement industry? Correct! Are sushi restaurants selling cheap species of fish for more $$? How did scientists come about the decision of using DNA barcoding for testing for artificial/mislabeled seafood across the globe? Correct! How many species of insects are in cow dung? How can DNA barcoding help to improve human life/health (ex: Food consumed) or can it not help? Will DNA barcoding eventually effect what we eat and buy in the grocery store? How does DNA barcoding make people more concerned with how they treat the environment? Correct! What is the average number of burritos consumed by a JMU freshman?

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

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

BLASTN

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

ccording 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

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 you can see the DNA moving in the gel

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

Which of the following is the BEST short summary of paragraph 4? We don't have any good ways to genetically ID fish COIbar-RFLP is a good method to ID fish RFLP means restriction fragment length polymorphism

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 Citing your sources demonstrates that you know how to follow directions and properly format citations Citing your sources satisfies the requirements of your instructor or the journal you are writing for

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

results technique

Consider beginning the first or second sentence in each paragraph with the word "To..." This technique will force you to begin each aspect of the results section with a justification of why you performed the experiments.

CRAAP stands for? Currency, Relevance, Authority, Accuracy, Purpose Another word for poop Clout, Recentness, Authors, Awareness, Prose Columnist, Readers, Advertisements, Articles, Publisher

Currency, Relevance, Authority, Accuracy, Purpose

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? Figure 5 is a MUSCLE alignment that shows that our sample has seven polymorphisms compared to humans and 25 polymorphisms compared to chimpanzees. The sequence differences of DNA barcodes between genetically modified (GM) tomatoes versus non-GM tomatoes is presented in Figure 3. DNA barcodes of genetically modified (GM) tomatoes were identical to those of non-GM tomatoes (Fig. 3). The top ten BLAST matches to our samples were all the same species, the common cow, Bos taurus (Fig. 7). Our sample sequence was more similar to humans than chimpanzees (Fig. 5). In Figure 7 we show the top 10 BLAST matches to our sample along with bit scores and alignment lengths.

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

Which of the following is the BEST short summary of paragraph 2? There are large databases of Barcodes DNA barcoding can ID fish The International Barcoding Conference was important

DNA barcoding can ID fish

dependent variable

DOES depend on variation of the independent variable. or example, if you were studying the effects of location (say forest vs. field) on the range of plants that bees pollinate, location would be the independent variable and plant species would be the dependent variable: the plant species that a bee visits "depends" on the location of that bee.

Which of the following is the BEST short summary of paragraph 3? European Hake are often mislabeled Hake are easy to DNA barcode Overfishing Hake is not a problem

European Hake are often mislabeled

You find an article on the web that explains how DNA barcoding is being used to identify cockroaches in Arizona and this gives you the idea to test what kinds of cockroaches are in Virginia (note: you have not yet actually tested anything)

Exploration and Discovery

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

T or F: DNA barcodes are typically useful to determine the genetic variation between individuals of the same species.

False

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

False

The primer used in Sanger sequencing

Has a nucleotide sequence complementary to the area that flanks the region you want to sequence

Which of the following is NOT a tip for successful pipetting? Set the pipettor within its range Change the tip when pipetting a new solution Hold the pipettor horizontally after pulling a sample Apply a tip before using a pipettor Pipet slowly and evenly to prevent bubbles

Hold the pipettor horizontally after pulling a sample

Which of the following would typically be included in the results section of a scientific research paper

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

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 It enables you to tell whether or not you included primers in your PCR It enables you to tell whether or not the polymerase was functioning properly in your PCR

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

Which of the following are advantages of scholarly literature? (Choose all that apply) It is reliable It is detailed It uses common vocabulary It is transparent with sources of information

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

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 To fill in all the slots on the gel so you can run it To practice loading the DNA before you get to the important DNA. So you know how long the gel needs to run

It makes it easier to determine sizes of unknowns using comparison techniques

Which is a disadvantage of scholarly literature? Can be less reliable or not factual Can be less transparent about sources of information Can be opinionated, biased, or sensationalized Less accessible to non-experts

Less accessible to non-experts

Which of the following statements about gel electrophoresis is correct? Longer DNA fragments migrate farther than shorter fragments Migration distance is inversely proportional to the fragment size Positively charged DNA migrates more rapidly than negatively charged DNA None of these statements are true

Migration distance is inversely proportional to the fragment size

Dideoxy (aka Sanger) DNA sequencing makes use of monomers called ddNTPs that stop DNA synthesis in predictable ways. This allows researchers to determine the sequence of bases present in a strand of DNA. The master mix of ingredients used in the DNA synthesis reactions of Sanger dideoxy sequencing include few ddNTPs relative to normal dNTPs (A's, T's, G's, and C's). 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)? (NOTE: a daughter strand is a strand of DNA that is replicated from the original DNA template that is being sequenced)

Most daughter strands would be very short. why? 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.

hypothesis

Observations of the natural world can reveal something entirely new or result in a new way of looking at a phenomenon. One way to explain a phenomenon about the natural world is to formulate a hypothesis to explain a set of observations. A hypothesis must be testable to be useful—this is typically expressed in terms of being "falsifiable." A falsifiable hypothesis is one that has the potential to be shown false if it is indeed false. If a hypothesis cannot be tested (i.e., cannot be falsified), it cannot contribute to scientific progress. Example of Observations: The sushi I've been eating from store X has been tasting strange compared to other sushi restaurants. The sushi at store X is cheaper than other sushi restaurants. The sushi at store X looks and smells different from the same sushi at other restaurants. Example of a falsifiable hypothesis: Store X is mislabeling their sushi

Predictions

Once we have generated a hypothesis, we of course want to know whether that hypothesis is correct. Though we can never definitively prove a hypothesis is correct, we can test a hypothesis to see if it is supported. To test a hypothesis we first generate one or more predictions that follow from the hypothesis. When testing hypotheses, we actually test the predictions of the hypothesis and then infer whether the hypothesis is supported from whether our predictions were correct. Predictions are logical outcomes of hypotheses that describe what we expect to see under a given set of circumstances if the hypothesis is supported. In other words, predictions help determine the type of study or experiment that needs to be done to test the hypothesis. Example of a prediction: Hypothesis: Store X is mislabeling their sushi Prediction: DNA barcode sequences of sushi from store X will reveal that their sushi is mislabelled

What does peer-reviewed mean? The author's friend verified the information The author and coauthors have checked each other's work Other experts in the field have verified the integrity of the information The literature was written on a boat dock

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

Which of the following is FALSE regarding a scientific research proposal? (see section on "proposals" in lab manual print out for answers) Professors at JMU that do research typically write proposals to pay for the costs of their research You will be writing a scientific research proposal this semester in BIO150 Research proposals are typically one to two paragraphs in length The typical goal of a research proposal is to convince funding agencies that the research being proposed is valuable, well researched, and capable of accomplishing its goals Scientific research proposals are written to get $$$ from funding agencies to help pay for the costs of conducting research

Research proposals are typically one to two paragraphs in length

Which of the following statements is FALSE with regards to scholarly literature? Scholarly literature typically has lots of jargon Scholarly literature is typically structured like a lab report Scholarly literature is typically published in a journal Scholarly literature is typically short in length

Scholarly literature is typically short in length

Which of the following is the BEST short summary of paragraph 1? Globalization is killing fish None of these Seafood mislabeling is big problem Literature on seafood is growing

Seafood mislabeling is big problem

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

process of science CENTER

TESTING ideas

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? They think barcoding is best way to analyze fish Their goal is to regulate hake mislabeling Their goal was to use COIbar-RFLP to examine mislabelling in 3 types of fish

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

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

Title

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

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

True

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 following questions could DNA barcoding successfully address? Are are hotdogs made up of mostly pork or chicken? What species of mosquitos live in the pond behind my house What % of a garlic pill is actually made of garlic? What is the genetic variability of the mosquitos behind my house?

What species of mosquitos live in the pond behind my house

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?

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

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

You should only upload samples that YOU collected and successfully barcoded

What will happen if you misplace or incorrectly record the serial # on your DNA sequencing tube?

You will have no data to sequence this semester

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

a photo of a cow that you downloaded from a google image search a photo of hamburger meat that you download from the internet a photo of a hamburger in its wrapper with the macdonalds logo

A complete summary of the paper designed for experts and non-experts

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

According to your reading, which of the following are reasons to publish a research article?

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

Electrophoresis is used to: Separate DNA fragments Determine the size of DNA fragments Determine the presence of DNA fragments of certain size All of these

all of these

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

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

anyone with a computer

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

aloe in lotion

captive/ cultivated

foods

captive/ cultivated

plants in vitamins

captive/ cultivated

plants that were raised and planted by humans

captive/ cultivated

tuna in sushi

captive/cultivated

plant samples

crude DNA extraction with DNA precipitation

animal samples

crude alkaline lysis

dog/cat food

crude alkaline lysis

fish samples

crude alkaline lysis

fungi samples

crude alkaline lysis

insect samples

crude alkaline lysis

invertebrate samples

crude alkaline lysis

types of studies

desciptive experiemntal nonexperiemental

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

descriptive

An opportunity to interpret your results and explore your findings within the context of the larger scientific record.

discussion

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

do

use your discussion to highlight the significance of your results and compare your findings with those of previous studies

do

use your discussion to simply recapitulate all of your results

dont

write your results section as a long stretch of continuous findings

dont

Studies that test hypotheses

experimental and nonexperimental Both of these types of studies include independent and dependent variables.

typical entry way into the process of science

exploration and discovery

WK. 1 process ofd science

exploration and discovery testing hypothesis benefits and outcomes community analysis and feedback

Once you've loaded your gel you can throw away the remaining PCR product.

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

Test tubes should always be placed into a centrifuge with the hinges facing inward.

false

examples of exploration and discovery

finding inspiration asking questions exploring the literature making observations sharing data and ideas

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

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

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

The beginning of a paper that transitions from a general background to a specific research question or goal.

intro

independent variable

is a variable whose variation does NOT depend on that of another.

What are the benefits of building a consensus sequence?

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

According to your lab manual, citations: (check all that apply) main purpose is to provide the exact information that a reader needs to locate the sources used by an author a warning or fine from a police officer or other official are mostly often included because teachers say you need at least 3 to get an A on your paper 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 are a standardized way of listing the sources used in a publication

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

A brief but detailed description about the tools and methods you used to perform experiments and analyze results.

materials and methods

μL stands for microliter , which is 10^-6 L liters:

microliter 10^-6 L

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

mini-version of your paper

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

Non-Experimental Studies

non-experimental (or observational) study the researcher does not manipulate any variable, but merely gathers data needed to test a hypothesis.

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?

nonexperimental

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

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

research article

primary source

Your citations

references

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

remove bad ends from your sequence to improve accuracy

original research

research article

A presentation of all your experiments and data, represented both as text and in tables, charts, diagrams, and photographs.

results

includes lots of references

review article

overview of a particle field/ topic

review article

provides food background on topic

review article

secondary source

review article

summary of previously conducted research

review article

In the last steps of Sanger sequencing, the DNAs produced in a DNA sequencing reaction are analyzed on the basis of their ______.

size or length

The dideoxyribonucleotides (ddNTPs) used in DNA sequencing work to ______

stop the growth of a DNA strand at a particular base (A, T, G, or C)

For the purposes of this course, what does it mean for a sequence to be "high quality

the base calls are correct it is greater than 500 bp long

descriptive studies

the scientist is not testing a hypothesis, but simply making observations. For example, you might barcode the types of flowers that a bee visits, simply to figure out what they are, how frequently the bee visits the different flower species, and how many species of plants are pollinated by bees. You would then look for relationships among the observations and generate hypotheses that would explain the observations and relationships. Descriptive studies are common in new fields or when new systems are studied in established fields.

A specific statement that conveys the topic and conclusion of the paper.

title

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

title abstract intro materials and methods results discussion references

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/ attempts to summarize entire source

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

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 quotes

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 quotes

a plant you found in a forest

wild

insect captured in arboretum

wild

Sharing a more recent common ancestor on a PHYLIP NJ tree means:

you are more closely related

Which of the following is/are true regarding the procedure to select BLAST hits for later analysis? (see pg. 9 in your manual, check all that apply)

you should select the top 7 taxonomically unique hits In general you should avoid selecting hits that are NOT ID'd to the species level (Ex. Uncultured Basidiomycota or Gomphidae or Tristus spp.)

According to your reading, your title has failed if

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