Thursday, January 31, 2008

Reminder: Lab Write Up Due Dates

Just a reminder that lab write ups are due in class when you return from break. If you would like me to look over your lab report, please email it to me NO LATER than 48 hours in advance of class.

Have a great midwinter break!

Tuesday, January 29, 2008

Working on Lab Write Ups

For the rest of the class periods before break (Tuesday and Thursday for B block and Wednesday for D block) students will be working on writing up the lab. For guidelines, click here.

D Block, come to class on Wednesday, if you have a computer bring it, all the computers are already reserved in the ARC. If you don't have a computer, there are some in the science computer lab we can use.

On Thursday B block will be working in the ARC.

Monday, January 28, 2008

PCR based VNTR Human DNA Typing

Below are the guidelines for writing up the experiment. This will be due when you return from midwinter break, IN CLASS. Late write ups will not be accepted. If you would like to email me a draft to read over the break, please do so no later than 48 hours before the write up is due. These guidelines have also been emailed to you as well.

Lab write up guidelines for VNTR on Human DNA

To help you answer these questions, see the lab guidelines, in a pdf, online at: You can also look at the blog for many helpful links in the sidebar on the top right of the page.

Title: should adhere to the guidelines (3 points)

Introduction (15 points total)

Background (12 points)

- What is polymorphic DNA? How is it used for identification purposes?

- What is CODIS? How is it used to solve crimes?

- What is an STR? What is VNTR? Which (STR or VNTR) is predominantly used

in law enforcement? Why?

Hypothesis (3 points)

Methods & Materials: (15 points)

Rather than write this section in the conventional way, answer the following questions in paragraph form that is well written. Do not answer the questions in a numbered format.

- Why is the lysis stage of DNA extraction important?

- What are the consequences if any chelex beads remain when PCR takes place?

- What is the purpose of Proteinase K?

- What is the importance of the changes in temperature in conducting PCR?

- What does it mean to “run to red” in gel electrophoresis. Why is this important?

Results (2 points)

Make a statement that summarizes your results. No table or graph is needed.

Discussion (15 points)

Use this space to talk about sources of error. You should have at least five sources of error AND an explanation for each one.

Conclusion: not needed.

Literature Cited (10 points)

You must cite at least five DISTINCT sources. To help you out, you can start with the three sources below. Please use MLA citations.

The Textbook

Remember that when you have a quote, it can not

Yes: The animation available from the Gene Almanac1 demonstrates the importance of temperatures in PCR, “[t]he temperature is lowered to 500-650C…this allows the primers to anneal.”

No: “The temperature is lowered to 500-650C…this allows the primers to anneal.”1

2 points will be deducted each time a quote is “standing alone.”

Gel Electrophoresis & Staining

In theory, this is what our results would have looked like for the lab we have been working on for the past 3 classes. The image of the gel shows the results of the amplification of the D1S80 loci through VNTR on human DNA. In the first lane is a ladder which can be used to compare the number of base pairs in a segment of DNA. Unfortunately, all you can see (barely) in our gels is the ladder. Despite this setback, I would certainly consider the lab in a success.

Thursday, January 24, 2008

Human DNA isolation

Today we started the first of three sections of the experiments using our own DNA. Step one is to isolate the DNA. Similar to the DNA extractions from common foods, we needed an enzyme and detergents; instead of meat tenderizer, we used proteinase K and we substituted a lysis solution for detergent. Tomorrow we will attempt PCR without using a thermocycler (we don't have one, so we will use three water baths). Stay tuned to see if we have any success!

Homework: rewrite the procedure for PCR, remember, you will only be using the procedure you have written, not the procedure in the handout.

Monday, January 21, 2008

Gel Electrophoresis Practice

Today students practiced making their own gels from scratch and pipetting food coloring in the gels.Patrick & Tak pour hot agarose into a gel form.

Using practice pipets to load the gel with food coloring.

Sunday, January 20, 2008

Never Say Prove Again!

I just finished grading your lab reports and for the most part they were impressive. However, the word "PROVE" has been officially banned from your scientific vocabulary (it never should have been there in the first place!).

In science you can never really PROVE anything; you can disprove a theory and you can find support for a hypothesis but you can't PROVE it. Hopefully this classy James Bond movie poster will help you remember.

Saturday, January 19, 2008

Gel Electrophoresis Lab Instructions

(NOTE: this post is for Friday and Saturday classes)

Objective: go over the procedure for making a gel and conducting gel electrophoresis by taking notes from a powerpoint, watching a short video and doing an online activity.

On Monday we will do a practice run using food coloring and see how it moves through various concentrations of agarose (o.7g, 1.0g and 1.5g)

Because of the special schedule D block will not need to leave lunch early to have enough time for the lab. There is even a video on youtube that shows the steps in gel electrophorsis.

Thursday, January 17, 2008

Working on Lab Reports

Today B block worked on writing their lab reports.

B Block's lab reports are due tomorrow (Friday)!

Remember to print off the rubric and complete a self evaluation in the points awarded section. Check out the links at the top of the sidebar on this page for more info on how to write your lab report.

Tuesday, January 15, 2008

Writing a scientific paper

Today students took a quiz on the guide to writing scientific papers. After completing the quiz, we read a sample paper and answered questions about the information that was (and in some cases was not) presented.

Lab report due dates & nit-picky details.

* B block your lab write up is due Friday in class.
* D block your lab is due Saturday in class.
* Each person will need to write his or her own lab report.
* Please print out the rubric and complete the self evaluation before turning in you lab report.
* 5 points will be deducted if you have not printed out the rubric and completed the self evaluation.

Monday, January 14, 2008

Lab Report Rubric

In addition to being posted here, the lab report rubric has been emailed to students in a chart which includes as self evaluation section, so that they can check and make sure they have all the necessary components.

Title 3 points

Includes the environmental factors that were manipulated (1 pt).

The parameter that was measured (1pt)

The specific organism that was studied (1pt).

Introduction 12 points

Includes the observation (2 pts)

Question that led to the hypothesis (2 pts)

Relevant background information (5 pts)

hypothesis (3pts)

Materials and Methods 15 points

Describes (not lists) how the experiment was conducted. The equipment used in the experiment is NOT listed, instead is part of the narrative. If well-known methods were used without changes, simply name the methods (e.g., standard microscopic techniques).

Results 10 points

Here the researcher presents summarized data for inspection using narrative text (4 pts)

Tables and/or figures to display summarized data (6pts)

***If Raw data is present 4 points will be subtracted ****

Formatting of tables/graphs 7 points

All tables and/or graphs have…

Title (1pt)

A description explaining what is presented (4 pts)

X and Y axis are labeled (2 pts)

Discussion 13 points

Here, the researcher interprets the data in terms of any patterns that were observed (5 pts)

An explanation of how the results differed from those hypothesized (5 pts)

Include at least 3 sources of error (3 pts)

Conclusion 7 points

This section simply states what the researcher thinks the data mean, and, as such, should relate directly back to the problem/question stated in the introduction.

Acknowledgements 3 points

In this section you should give credit to people who have helped you with the research or with writing the paper. If your work has been supported by a grant, you would also give credit for that in this section.

Literature Cited (Will vary..max 5 points)

This section lists, in alphabetical order by author, all published information that was referred to anywhere in the text of the paper. It provides the readers with the information needed should they want to refer to the original literature on the general problem.

Spelling, Grammar & Formatting 5 points

Report is free from spelling and grammatical errors. All section headings are in bold and centered.

Sample Lab Report

Below is a sample lab I wrote for the Eggsperiment. You may use this as a guide for writing your papers. Pay close attention to formatting & use of the past tense.

Ms. Saxe

A Block

Month Day, Year

The Effect of Various Concentrations of Sugar Solutions

on the Percent Change in Mass of a Chicken Egg.


Osmosis and diffusion are essential to maintaining equilibrium of solutes and water in cells. Osmosis is the movement of water across a semi-permeable membrane, where as diffusion is the movement of solutes from an area of high concentration to an area of low concentration1. Various transport proteins located in the cell membrane assist in moving large solute molecules across the cell membrane. Solutions where the concentration of solutes outside of the cell is less than in the cell are said to be hypotonic. Cells in hypotonic solutions tend to swell as water enters the cell to maintain equilibrium. Solutions where the concentration of solutes outside the cell is greater than inside the cell are hypertonic. In hypertonic solutions, water leaves the cell to try to maintain equilibrium. Lastly, when the concentration of solutes outside and inside the cell is equal the solution is isotonic. Using a chicken egg (without a shell) as a model of the cell membrane, is it possible to observe the effects of osmosis with the naked eye? If an egg without a shell is placed in a sugar solution, then there will be some change in the mass of the egg due to osmosis.


One dozen large white chicken eggs from the Jackson Star supermarket were submerged in Best’s white vinegar for 72 hours in a three liter bowl. During this period, every 24 hours the vinegar was changed to increase the rate at which the shell decomposed. Eggs were moved around in the vinegar once every 24 hours to ensure all sides of the shells were equally submerged. Any time eggs were handled rubber gloves were used to protect the individual from any bacteria that may have been present. After 72 hours, the eggs were ready to be used for the experiment.

The control egg was removed from the vinegar and weighed on an electronic balance to obtain the initial mass. This egg was placed in a 400mL beaker containing 350mL of tap water and labeled as the control. The experimental egg was weighed using an electronic balance and placed aside in a weigh boat while the sugar solution was created. The sugar solution contained 15g of table sugar and 35g of sucrose added to 250mL of tap water, in a 400mL beaker. The sugar solution was stirred thoroughly until all of the grains of sugar were dissolved. The sugar concentrations were recorded in a data table on a lab handout. The beaker was labeled with the last names of group members, class block and placed in a cabinet to sit undisturbed for 48 hours over the weekend. After 48 hours, the secondary observations of the egg were completed including obtaining the final mass of the egg using an electronic balance. Final mass was recorded in the lab handout. Eggs were disposed of by the instructor.


The overall results in E and F block varied greatly: in E block all of the eggs had a negative percent change meaning that they gained mass, where as in F block, all of the eggs had a positive percent change meaning they lost mass.

Figure 1: This graph shows the percent change in mass for all of the eggs tested. Egg number 1 is the control. Eggs 2-5 were from E block and eggs 6-8 were from F block.


Perhaps what is most interesting to note about this experiment is that each block experienced the same overall result: E block eggs were all placed in hypotonic solutions and F block eggs were all placed in hypertonic solutions. The results do support the hypothesis that, if an egg is placed in a sugar solution a change in mass will occur. No possible explanation can be found at this current time to explain why the eggs in the various classes reacted so differently to the solutions. Possible sources of error for this experiment include: incorrect labeling of sugar in the large plastic bag; incorrect notation for what and how much was placed in solution and allow the eggs to sit for too long in solution. The table sugar that was used for this lab came from the chem. storage room and had been sitting for an unknown amount of time in a plastic baggy that was loosely secured with a knot. Exposure to fumes and potentially other chemicals may have left residue in the sugar which changed how it reacted in the experiment. If the solutes added to water were incorrectly written down this could certainly have impacted how the eggs reacted. Lastly, since the eggs sat over the weekend, nobody observed them at 24 hours, perhaps the greatest change in mass was visible then, but nobody was able to observe it. Further study would be needed to determine the possible causes of the anomalies in the results.


While the data in this experiment is inconsistent between E and F blocks, it does support the hypothesis that if an egg is placed in a sugar solution there will be a change in mass. Further tests using a larger sample size would be needed to establish more consistent events.


Thanks to Mr. Brummer for supplying the vinegar and Ms. Saxe for soaking the eggs in advance so they could be used in the experiment.


1. Memorial University of Newfoundland. Principles of Osmosis and Diffusion. [Online]. October 22, 2007 URL:

Independent DNA extraction

Today students conducted the experiments they wrote over the weekend to extract DNA from various substances. Most students tested the effectiveness of various enzymes on the yield of DNA.

Tonight for homework, please go to the guide for writing scientific papers.
1. Read it, seriously actually read it.
2. You will have a mini quiz on how science papers should be written. If you take notes, you will be able to use them.

Tomorrow in class we will talk about how you will write your papers as well as give out a rubric from paper writing.

Saturday, January 12, 2008

Pictures from the DNA extraction

Step 1: Combine spinach, water and salt. Blend for 15 seconds on high and the strain the solution.
Add detergent and then let sit for at least 10 minutes. Pour into test tubes, so the tube is about 1/3 full. Add a pinch of enzymes (in this case meat tenderizer).
Gently stir the enzymes and then at isopropyl alcohol so the test tube is now 2/3 full. Let the magic of chemical reactions and density go to work....and voila! DNA.

If you look closely, you will see a white stringy matter floating the in the tube. That's DNA!

Homework (see the post below). D block class, we will be starting early at 12:15/12:20 so you will have time to complete your experiment.

Thursday, January 10, 2008

DNA extraction!

Today (and Saturday) we will be extracting DNA from spinach. You can extract DNA from just about anything. To see how we did this check out the instructions from Utah Genetics.

Homework: Read the 20 Most Frequently Asked Questions about this experiment. You and your partner will be conducting your own version of this lab in class on Monday.

You and your partner should have a procedure written and bring any materials you will need (if they vary from what we used in class).

Article discussions & cloning

Today we finished watching the animation of how a gene is cloned and students presented their biotechnology articles. Below are some of the summaries.

Liver cancer really fatal in China, hard to diagnose, because therapies are limited.

Gel electrophoresis was used to look for proteins whose copies are increased or decreased in patients with the liver cancer. In looking through the variation in proteins, they discovered two proteins that could serve as screening markers for liver cancer.

Towards a faster prenatal test for Down Syndrome

Normal test the results take two weeks, scientists are using a variation of PCR to find out if the child has down syndrome in two hours. The new process is called digital PCR so they are able to see the extra chromosome present. Put on a microfluid chip.

Judges concerns over the smallest of clues

Using PCR tests on crime scene, benefit will require only one nanogram (only 150 cells). Disadvantage, because you only need a little bit of evidence that the sample could become contaminated. Ex: touch an object, pick up some cells, these cells can find their way into the crime scene.

Homework: none

Tuesday, January 8, 2008

Again, nothing says welcome back like...

a quiz!

Here's our plan for B block today:
1. reading quiz with notes
2. discuss answers
3. hand back papers
4. hand out progress reports
5. discuss homework.

Chapter 20 is all about DNA technology and how techniques such as PCR, gel electrohoresis and southern blot are used. Your homework for tonight is to choose one of those techniques and find a news article from 2007 (or 2008) where your technique of choice is used.
* read the article
* print it out
* come to class prepared to explain why this technique was used.

A good place to look for articles is Science Daily