Lab: CSI Wildlife, Case 1

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Complete all the activities in this lab instruction packet: CSI Wildlife, Case 1. Work through the instruction packet step by step. Record your results directly in the worksheet as you progress through the questions.

For any sections that request that you “take notes”, the notes should be in your own words summarizing information learned. You should not copy and paste information from the Internet including media and resources accessed in this lab. Directly copying and pasting information is considered plagiarism in this course.

See attached worksheet

Lab: CSI Wildlife, Case 1

 

General Instructions

 

Be sure to read the general instructions from the Lessons portion of the class prior to completing this packet.

 

Background

 

The scenarios investigated are based on the recently published literature: Wasser, S. K., Brown, L., Mailand, C., Mondol, S., Clark, W., Laurie, C., & Weir, B. S. (2015). Genetic assignment of large seizures of elephant ivory reveals Africa’s major poaching hotspots. Science, 349(6243), 84–87. The underlying data are available on the Dryad Digital Repository: http://dx.doi.org/10.5061/dryad.435p4.

 

Remember, DNA is made up of nucleotides and an allele is an alternative form of a gene which may be from mutation, but is found on the same place in a chromosome in individuals and functions similarly. If you are unfamiliar with these terms, make sure to review them in your book prior to completing the lab.

 

 

Specific Lab Instructions

 

Name:

Date:

 

Go to: CSI Wildlife on HHMI Biointeractive

 

Link: https://media.hhmi.org/biointeractive/click/elephants/dna/index.html

 

Part 1: The Introduction

1. Read the instructions on the home page. Then, watch the opening video from the CSI Wildlife Introduction.

2. What is a keystone species?

Lab: CSI Wildlife, Case 1

 

Page 1 of 9

 

3. Dr. Wasser states that approximately 50,000 African elephants are killed each year. According to the video, it is estimated that there are around 470,000 African elephants. If these numbers are correct, approximately what percentage of African elephants are killed each year? (Show your work.)

 

4. In one or two sentences, summarize Dr. Wasser’s research and how it is being used to conserve elephants.

 

 

 

Part 2: Case One

1. Watch the crime scene video on the first slide of Case One. Explain the goal of the case.

 

2. Look at the map provided; in what type of location are the majority of African elephants located?

3. Proceed to the How DNA Profiling Works section.

a.

b. What does “STR” stand for and how are they important for identification?

 

c. Look at the gel on the screen. What do the bands on the agarose gel represent?

d. What is the purpose of the DNA ladder on the agarose gel?

 

e. DNA profiling is also called DNA fingerprinting. A common misconception about DNA fingerprinting is that the analysis has to do with actual fingerprints. Explain one similarity and one difference between a human being’s pattern of bands on an electrophoresis gel and a human fingerprint.

 

4.

5. Click on Technique.

a. List three sources to obtain elephant DNA for analysis.

 

b. Watch the animation on the polymerase chain reaction under Technique. What is the purpose of heating the DNA strand? What is the purpose of cooling the DNA strand?

 

c. What is the relationship between the size of a DNA fragment and the distance it migrates in the gel?

 

d. Why does DNA migrate to the positive electrode?

 

e. Run the gel in the Technique section by pressing the Start button. Which elephant (left or right) has both the largest and smallest fragments?       Approximately what size is the largest fragment (bp)?       Smallest?      .

6. Proceed to the Application section and look at the gel.

a. For Marker C, are the two elephants in the gel on the left homozygous or heterozygous? How do you know?

 

7. Read the Review section, and make sure you can answer the questions.

8.

9. Go to Finding a Match

a. Click on the “+” next to each marker. Compare the bands in the agarose gel from the unidentified elephant and the known elephants. Which elephant (there are two pages of them) matches the unidentified elephant?

10. Watch the video on the “Case Solved” slide.

a.

b. Name two properties of a good marker and explain why good markers are important.

 

Adapted from: Click and Learn “CSI Wildlife” (2016). CSI Wildlife Explorer Worksheet. HHMI Biointeractive Teaching Materials.

 
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Case Study a Infections of the Skin, Eyes, and Underlying Tissues

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MICROBIOLOGY

Case Study a

  1. Infections of the Skin, Eyes, and Underlying Tissues

It was so exciting! Caitlyn was the only freshman girl selected for Varsity Singers, her high school’s touring show choir. Their summer “retreat” was a six-day mega-rehearsal to learn all of the choreography for their upcoming show season. Monday through Saturday the week before school resumed, the 28 performers danced from 8 A M to 8 P M in their un-air-conditioned gymnasium. Caitlyn didn’t particularly mind the hot, humid rehearsal conditions, but sweating profusely in dance leotards every day was really starting to aggravate the acne on her shoulders and back. After a special preliminary performance for their families on Saturday night, Caitlyn showered and dressed to go home. It was then she discovered a very large, angry “pimple” that rubbed uncomfortably on the back waistband of her jeans. By morning, it was raised and the size of a dime. Caitlyn’s mother washed the

affected area, cleansed it with hydrogen peroxide, and applied an antibiotic ointment, telling her they would call the doctor tomorrow if it didn’t improve.

  1. What possible infections might Caitlyn have?
  2. What microbes would normally cause these infections? Are these microorganisms normal skin flora, pathogens, or both? Explain.

Monday morning, the first day of school, Caitlyn’s back was sore. “A great way to start high school,” she thought. Caitlyn’s mother took her to the pediatrician’s office right after school. The PA examined her back and was alarmed to see a lesion almost two inches in diameter. It was tender to the touch with poorly demarcated margins. The region was raised, warm, and Erythematous (reddened) with several smaller red lines radiating outward.

  1. What is your diagnosis? Describe the nature of this condition.

After consulting with the pediatrician, Keflex was prescribed for Caitlyn. She was sent home with instructions to monitor the infection. If it was not obviously improved by the next day, she was to return for reevaluation.

  1. To what class of antibiotics does Keflex belong? How does this drug work? What group of microbes is especially susceptible to it?

On Tuesday morning, Caitlyn went immediately to see her pediatrician. The lesion was the size of an egg and quite sore. Caitlyn also presented with a temperature of 38.4°C (101.2°F). Motrin and compresses were advised as comfort measures. The Keflex was continued and the lesion cultured for laboratory

analysis. Again, she was told to return if she didn’t notice improvement.

  1. How would you collect a specimen from Caitlyn’s lesion? Name several types of transport media commonly used. Why is it so important to appropriately transport a specimen to the microbiology laboratory?
  2. What media will likely be inoculated when this sample arrives in the laboratory? State your reason(s) for choosing the media you’ve indicated.
  3. In addition to media inoculation, what other procedure will be performed immediately using the specimen?

The preliminary Gram stain of the specimen showed many Gram-positive cocci in clusters. After 24 hours, the TSA with 5% sheep blood plate demonstrated pure growth of small, round, smooth, white, gamma-hemolytic colonies.  The same colony morphology was observed on the PEA (or CNA) plate with zero growth on the EMB (or MacConkey) plate. Colonies were also observed on the MSA plate, which was completely pink in color.

  1. What is meant by the term “pure growth”? What does it say regarding the quality of your specimen collection?
  2. Based upon these laboratory results, what microbe do you predict is causing Caitlyn’s infection? Explain. What two chemical tests would you perform next to verify your answer?

Colonies from the TSA plate were suspended in sterile saline and introduced into the Vitek II analyzer. It confirmed Staphylococcus epidermidis was the pathogen involved and indicated Keflex sensitivity.

HATS Off to MRSA b

They had toyed with the idea for years, and now, Jacob, Tony, and Tom had finally made their dream of a family business a reality. With Jacob’s computer expertise, Tom’s experience from his marketing internship, and Tony’s apprenticeship with a master painter, the three brothers were confident that “Color Your World Painters, Inc.” would be a successful business venture. After only six months, their Internet and local TV advertising had made them a household name in their community. Tony had to hire additional painters to handle their burgeoning workload. The brothers moved to a larger office, purchased improved equipment, and issued all employees uniforms and painter’s caps with their flashy new logo.

Business that summer was booming. The hot, sweaty paint crew worked from sun up to sun down every day. Upon returning to headquarters, they hung their caps on the wall, changed out their uniforms for street clothes, and collected nice fat paychecks. Jacob boasted smugly that things couldn’t be better…until one morning Tony didn’t show up for work. Annoyed, Jacob grabbed a uniform and Tony’s hat, got the painters organized, and took his brother’s place on the work crew while Tom tried to track down Tony. Tom’s second phone call reached his five-year-old niece, who was answering her mother’s cell phone. In a small and tearful voice, she told her uncle that they were at the hospital and daddy was

very sick because he had slime leaking out of his head. Confident that his niece’s imagination had run away with her, Tom reassured the little girl and told her he would be right there. Tom left a voicemail message on Jacob’s cell phone and headed to the hospital. When he met his sister-in-law, Julia, Tom was shocked to find his brother was in surgery. Stunned, Tom listened to Julia describe the events of the last few days. Out of embarrassment, Tony never mentioned to his brothers that he periodically suffered from boils around his hairline when working under hot, humid conditions. Two days ago, when Tony noticed the first few boils appear, he assumed it was just a recurrence of his seasonal problem. But, after 24 hours, Tony was becoming concerned. This was the worst case he had ever experienced. He had at least a dozen boils on the back of his neck and into his hairline. Despite his discomfort, Tony continued work without complaint, although he secretly blamed his problem on wearing the new company cap that made him sweat more around his hairline.

That evening, Tony showed Julia his neck and asked her to help him disinfect and bandage the area. His frightened wife pleaded with him to go to the emergency room, but Tony flatly refused. Number one, they didn’t have health insurance and he certainly did want to run up a bill. But number two, Tony was not about to be humiliated by going to the hospital for something so simple. In his mind, boils could hardly be considered life-threatening. Julia gently cleansed the area for her husband, counting 13 boils the size of a dime or larger. Tony winced in pain.

  1. What microbes commonly cause boils?
  2. What is another name for a boil?
  3. What is the incubation time for boil development?
  4. What factors are facilitating Tony’s problem?
  5. What at-home cleansing and treatment options would you have recommended Julia try?

line. Tony found it humorous that his “gooey zits” got quick attention at an ED known for its long wait times. Dr. Bergmann, an infectious disease physician, examined Tony, noting heat, extreme erythema, folliculitis, 15 boils ~1–2 cm in diameter, some draining copious amounts of pus, and numerous seeping  ulcerations. Dr. Bergmann applied a topical anesthetic before lancing several boils for culture. He ordered four sets of blood cultures drawn, started broad spectrum IV antibiotics, and immediately scheduled Tony for surgical debridement of his infection.

  1. Why did the doctor lance boil to collect a specimen for culture when many others were already draining pus?
  2. Why did Dr. Bergmann start Tony on antibiotics even though he didn’t know the microbe involved or its drug sensitivity?
  3. Why were blood cultures ordered?
  4. Why was Tony a candidate for immediate surgery?

Tom and Julia sat for about an hour in the waiting room before Dr. Bergmann arrived with an update on Tony’s condition. Preliminary Gram stain results from the lab confirmed Gram-positive clusters of cocci in Tony’s boils. Due to the extensive tissue damage, Dr. Bergmann confided to the family that he suspected community acquired-MRSA. Although Tony was “resting uncomfortably,” the surgical debridement of a 3.5 cm  10 cm area was a success. Tony would receive a three-week course of IV vancomycin before being permitted to return to work.

  1. What common skin microbes demonstrate this Gram morphology and staining?
  2. What does MRSA stand for?
  3. What is the difference between community acquired-MRSA and hospital acquired-MRSA?
  4. How does the resistance demonstrated by this organism differ from the resistance it typically shows to penicillin?
  5. Why is vancomycin a good treatment choice when penicillin and methicillin are ineffective?
  6. What complications are associated with IV vancomycin treatment?
  7. Tony’s infection progressed rapidly and resulted in substantial soft tissue damage. Why is MRSA able to cause this problem?
 
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Determining Population Growth Assignment

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In one year, biologists tracking a bear population counted 33 new baby bear cubs in a population of 546 bears.

  1. Calculate the birth rate (b) of this population.
  2. In the same year, the biologists counted 28 black bear deaths. Calculate the death rate for this population.
  3. What is the per capita rate of increase for this black bear population?
  4. What would you estimate the change in black bear population size would be for the following year? Be sure to adjust the N to reflect the new births and deaths. When you get your answer, round to the “nearest bear” and answer the question – is this population increasing or decreasing in size?
  5. Determine the number of births and deaths you would expect the following year. Round to the “nearest bear
 
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Pre-lab 1- Myths in Science

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Name:______________________ Date: _______

Lab Section:___________

Pre-lab 1- Myths in Science (10 pts)

Read the introduction and “myths” 1, 2, 3, 5, 6, 8, & 9 in the article, The Principle Elements of the Nature of Science: Dispelling the Myths, by W.F. McComas (Posted on Blackboard in the lab folder). Complete the questions below and turn this page in at the beginning of lab.

PLEASE ALWAYS WEAR CLOSED TOED SHOES AND PANTS TO LAB!

1) Explain what the author means when he says that there is no well-accepted theory of gravity.

 

Answer

 

A scientific law or scientific principle is a concise verbal or mathematical statement of a relation that expresses a fundamental principle of science, like Newton’s law of universal gravitation. A scientific law must always apply under the same conditions, and implies a causal relationship between its elements. A law differs from a scientific theory in that it does not posit a mechanism or explanation of phenomena: it is merely a distillation of the results of repeated observation. As such, a law limited in applicability to circumstances resembling those already observed, and is often found to be false when extrapolated.

 

2) Compare the difference between the application of laws in biology versus the physical sciences.

Answer

 

The main difference is that Biology deals with living organisms, but the ramifications of this fact go beyond just the subject matter, because it also affects the nature of the scientific methods employed by biologists.

Understanding Organisms: One approach to understanding a phenomenon is to reduce it to its fundamental aspects, and, by understanding each component, you can gain some appreciation of the overall process. This approach, often referred to as reductionism, is useful, especially in the physical sciences, where, for example, a knowledge of the behavior of individual atoms allows you to predict the dynamics of a reaction system. However, the hierarchical organization of biological systems makes it impossible to understand all aspects of even a single organism by studying each of its components. Furthermore, there are certain biological processes, like Natural Selection, which cannot be predicted based on only a knowledge of Physics and Chemistry. In other words, the entire range of material phenomena are to be found in biological systems, whereas Physics and Chemistry only deal with a subset of these phenomena.

 

3) Explain what is meant by “generalizing” versus “explanatory” when applied to hypotheses.

 

Answer

 

Hypothesis simply means an educated guess. The reality of hypothesis can be complex. Explanatory hypothesis often referred as Trial Theory, is where hypothesis relates to an idea that may become a theory with more evidence and agreement from scientists. In other words, the trial hypothesis or idea is not yet validated, but if it is it becomes a scientific theory. While

Generalizing hypothesis or trial law is where hypothesis relates to an idea that may become a law with more evidence and agreement from scientists. In other words, the trial hypothesis or idea is not yet validated, but if it is it becomes a scientific law.

 

 

4) Explain the problem of induction in your own words and provide an example to illustrate this problem.

Answer

 

The problem of induction is the philosophical question of whether inductive reasoning leads to knowledge understood in the classic philosophical sense, since it focuses on the alleged lack of justification for either:

Generalizing about the properties of a class of objects based on some number of observations of particular instances of that class (for example, the inference that “all swans we have seen are white, and therefore all swans are white”, before the discovery of black swans) or

Presupposing that a sequence of events in the future will occur as it always has in the past (for example, the laws of physics will hold as they have always been observed to hold).

 

 

 

5) In your own words, explain why a scientist should never say that their hypothesis is “proven true”?

Answer

 

Well since a hypothesis is an educated guess it only come from what you think. It’s almost like an opinion. Example. If someone doesn’t like a movie but you say it’s the best, you can’t prove it to somebody else because it all depends on their opinion. Or another way to explain it is if you were talking to the person who didn’t like the movie you can’t prove it to them that it was good because that person has another opinion and thinks the opposite.

 

6) What does it mean for something to be falsifiable? Provide an example of a falsifiable hypothesis and a non-falsifiable hypothesis.

Answer

 

A statement is called falsifiable if it is possible to conceive an observation or an argument which proves the statement in question to be false. In this sense, falsify is synonymous with nullify, meaning not “to commit fraud” but “show to be false”.

 

For example, Newton’s Theory of Gravity was accepted as truth for centuries, because objects do not randomly float away from the earth. It appeared to fit the figures obtained by experimentation and research, but was always subject to testing.

 

However, Einstein’s theory makes falsifiable predictions that are different from predictions made by Newton’s theory, for example concerning the precession of the orbit of Mercury, and gravitational lensing of light. In non-extreme situations Einstein’s and Newton’s theories make the same predictions, so they are both correct. But Einstein’s theory holds true in a superset of the conditions in which Newton’s theory holds, so according to the principle of Occam’s Razor, Einstein’s theory is preferred. On the other hand, Newtonian calculations are simpler, so Newton’s theory is useful for almost any engineering project, including some space projects. But for GPS we need Einstein’s theory.

 

 

7) Consider the first chapter reading from the text book, give an example of a scientist(s) failure to be objective when drawing conclusions from their data in that reading.

 

Answer

 

Steven Jay Gould pointed out in science textbook “The Case of the Creeping Fox Terrier Clone (1988)”

The “fox terrier” refers to the classic comparison used to express the size of the dawn horse, tiny precursor to the modern horse. This comparison was unfortunate because of two reasons. Not only was this horse ancestor much bigger than a fox terrier, but the fox terrier breed of dog is virtually unknown to American students.

The major criticism leveled by Gould is that once this comparison took hold, no one bothered checking its validity or utility. Through time, one author after another simply repeated the inept comparison and continued a tradition making many science texts virtual clones of each other on this and countless other points.

 

 

 

 

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Edited 8/26/15 Biology 111 Lab Page

 
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