Bacterial ID lab questions

Bacterial ID Lab

Completing this virtual lab and answering the following questions helps meet Standard 3: Lab Skills.

First, go to:

http://www.hhmi.org/biointeractive/vlabs/bacterial_id/index.html or the iPad app

In this virtual lab you will assume the role of a lab technician in a modern molecular biology laboratory.  As such, you are responsible for providing lab results to medical doctors for use in diagnosing their patients.  Be sure to follow the steps of the procedure in order and to make use of the notes on the right side of the computer screen.  As you work through the lab, answer the following questions:

1. As the medical technician in charge of this investigation, what are you trying to determine about the tissue sample provided to you?

I am trying to determine whether or not the sequence contains a significant level of similarity to another known sequence.

2. How did you prepare the DNA to be used in this investigation?

I prepared the DNA to be used here with positive and negative reactions. The positive was the controlled reaction.

3. Describe how PCR is used to make copies of DNA sequences. Use the animation and notebook entries in the PCR Amplification step to guide your answer. Note that you may replay the animation as needed.

The PCR separates strands of DNA. The double stranded DNAs are undone by enzymes and pretty much have new functions. They serve as different templates.

4. Summarize the technique used to purify the PCR product.

When the PCR product is put into the gel, it can be cut out by using a centrifuge and microfiltering it all out!

5. What is produced during the sequencing prep PCR run? Use the animation and notebook as needed in thinking through your answer.

Copies are made, and that's how you are identified.

6. Describe how the automatic sequencer determines the sequences of the PCR products.

It is done several times (thousands) so that an accurate answer comes out.

7. What does BLAST stand for?

Basic Local Alignment Search Tool

8. What conclusions did you make using the results of the BLAST search?  Did these conclusions support a clinical diagnosis for the patient (what disease did they have)?
It's very easy to figure out what disease each of them had and the conclusions did support a clinical diagnosis. The diagnosis was bartonella henselae.

DNA Extraction from Wheat Germ

Instructions:

1. Place 1 gram of raw wheat germ in 50 ml test tub.

2. Add 20 ml of hot (50-60 C) tap water and mix constantly for 3 minutes.

3. Add 1 ml or a scant 1/4 teaspoon of detergent and mix gently every minut for 5 minutes. Try not to create foam.

4. Use an eyedropper, pipette, or piece of paper towel to remove any foam from the top of the solution.

5. Tilt the test tube at an angle. SLOWLY pour 14 ml of alcohol down the side so that it forms a layer on top of the water/wheat germ/detergent solution. Do not mix the two layers together. DNA precipitates at the water-alcohol interface (the boundary between the water and the alcohol). Therefore, it is crucial to pour the alcohol very slowly so that it forms a layer on top of the water solution. If the alcohol mixes with the water, it will become too dilute and the DNA will no precipitate.

6. Let the test tube sit for a few minutes. White, stringly, filmy DNA will begin to appear where the water and alcohol meet. You will usually see DNA precipitating from the solution at the water-alcohol interface as soon as you pour in the alcohol. If you let the preparation sit for 15 minutes or so, the DNA will float to the top of the acohol.
     You can usually get more DNA to precipitate from the solution by using one of the DNA-collecting tools (such as glass or paper clip hook) to gently lift the water solution up into the alcohol. This allows more DNA to come in contact with the alcohol and precipitate. You may find it helpful to pour the water/detergent solution into a clean test tube, leaving behind the wheat germ, before adding the alcohol.

7. Use a glass or paper clip hook or wooden stick to collect the DNA.

OBSERVATIONS

1. What does the "wheat germ soup" look like?
     The "wheat germ soup" looks much like watery snot...interesting....different.

2. How does its appearance change as you add the detergent and swirl it in?
     The "snot look" begins to form. The DNA, or "stringy parts" start to develop.

3. What do you think is happening at this step?
     The DNA is beginning to form.

4. Describe the appearance of the mixture just after you add the alcohol.
     The two solutions are separate, but in the same tube. It looks layered.

5. What do you think is happening at this step?
     The two solutions are separating so that DNA can form in between them. They're working as glues.

6. What do you observe at the water-alcohol interface?
     The wheat germ met the alcohol, so that's where the filmy DNA film started forming.

7. What does DNA look like?
     The DNA looks like snot. Creation of life is beautiful...but really not too pretty!

Investigating Independent Assortment

INVESTIGATING INDEPENDENT ASSORTMENT

Mendel observed the effects of independent assortment when he carried out his dihybrid crosses. When he crossed two plants that bred true for different versions of two traits, the first-generation offspring all displayed the same phenotype (the dominant phenotype for both traits). However, when these plants were crossed, the second-generation offspring included four different phenotypes.

Mendel carefully recorded the numbers of phenotypes among the offspring of many dihybrid crosses. He found that certain combinations of phenotypes among the second-generation offspring occur in a 9:3:3:1 ratio, on the average. We now know that this pattern occurs because genes on pairs of homologous chromosomes are sorted out for distribution into one gamete or another independently of gene pairs of other chromosomes.

Activity

In this activity, you will first access the meiosis tutorial provided by the University of California, Santa Barbara. The tutorial demonstrates the random assortment of chromosomes into gametes. Next you will complete a tutorial quiz about independent assortment. This is part of The Biology Project from the University of Arizona.

Part 1.

Use your browser to go to the meiosis tutorial at

http://www.sumanasinc.com/webcontent/animations/content/independentassortment.html

Use the tutorial to learn how to determine which allele combinations are possible in two or even three trait crosses.

Part 2.

Use your browser to go to the independent assortment tutorial at
http://www.biology.arizona.edu/mendelian_genetics/problem_sets/dihybrid_cross/dihybrid_cross.html
Go through questions 1-9 of the tutorial. If you answer any question incorrectly, review the tutorial material and try again.
When you have completed this much of the tutorial, answer the questions below:
1. What type of gametes will be produced by a plant of genotype AaBb?
cross, the phenotypic ratio is 9:3:4. There are only three different phenotypes 
for hair color, agouti, black and albino. The individual with genotype recessive 
for both traits, i.e. aabb, has the same albino phenotype as the aaBB and aaBb 
individuals due to epistasis.
2. What type of gametes will be produced by a plant of genotype aabb?
might be caused by the recessive homozygous, recessive bb genotype.

Rather than the 9:3:3:1 seqregation of phenotypes normally seen with an AaBb x AaBb dihybrid 

Same as stated above, only the albino phenotype masks any phenotype that 

3. List all the genotypes you would find among the offspring of an AaBb x aabb test cross.Half of the gametes get a dominant S and a dominant Y allele; the other half of the gametes get a recessive s and a recessive y allele.Both parents produce 25% each of SY, Sy, sY, and sy.

4. What is the expected phenotypic ratio of the offspring of an AaBb x aabb test cross?
These phenotypes will appear in a predicted 1:1s:1:1 ratio.

5. List all possible gametes from a trihybrid individual whose genotype is RrSsTt.
If only recessive traits were scored, we would only consider offspring with one
phenotype: dented, green seeds. A 9:3:3:1 ratio phenotypes would be impossible.

Let's Make A Baby!

     For this experiment, my classmates and I were to partner up and make a baby! Not literally-but on paper with the cool, fun techniques of biology! As my class evened out to an ODD number of students that day, we decided that it would only be fair to make my partner the great and glorious Enrique Iglecias!

(Two pretty attractive people, we know!)

So for this project, my partner and I were to look at each others' faces and match up listed features on the page in order to decide upon which features our child will likely have. This helped us determine exactly how our child will look.

A long and tough process, but we were able to define each others' beautiful traits our child would probably be getting.














Following are the final results...

(Adorable!!)

Onion Root Tips Mitosis WebQuest

ONION ROOT TIPS AND THE CELL CYCLE


In this activity, you will calculate the lengths of the various phases of the cell cycle in an onion root tip. First you will view some slides and graphics of onion root tips provided by the Molecular Expressions Photo Gallery. Then you will complete the online activity provided by the Biology Project at the University of Arizona.

Part 1.

Use your browser to go to Molecular Expressions Photo Gallery: Mitosis

http://www.microscopy.fsu.edu/micro/gallery/mitosis/mitosis.html

Notice in the micrograph at the top of the page that there are cells in a variety of stages. View the onion slides in this section, then click on "mitosis" in the sentence "Learn the steps in mitosis ... " This will take you to a Java tutorial.  Keep in mind what you have learned here as you proceed to the second part of the activity.

Part 2.

Use your browser to go to Online Onion Root Tips at

http://www.biology.arizona.edu/cell_bio/activities/cell_cycle/assignment.html
Begin by reading the description of the five major cell phases. You will need to keep this information in mind during the activity.

Make a copy of the data sheet that appears on the second page. You will need it to answer the questions.

Proceed through the activity, identifying the phase for each cell you are shown. Pay attention to the hints if you misidentify a cell at first.

When you have completed the activity, answer the following questions:

1. What percent of cells were in interphase?
20%2. What percent were in mitosis?
100% All of the cells are in different stages of mitosis.3. Which phase of mitosis takes the longest?
Interphase
4. During which stage is the nucleolus visible as a dark spot?
Prophase5. How can you recognize a cell in metaphase?
It doesn't seem as dark as prophase; It's much lighter and looks like it's beginning to separate.6. How might you figure out how long (in minutes and/or seconds) each phase of the cell cycle takes based on the data from these onion root cells? Explain your logic and show your calculations and results below.

7. Produce a pie chart in Create-a-Graph that shows the relative lengths of each stage of the cell cycle in these cells including interphase and each stage of mitosis. You can embed the graph here.

	Interphase	Prophase	Metaphase	Anaphase	Telophase
Number of Cells	20	10	3	2	1	36
Percentage	55.55%	28%	8.33%	5.56%	2.78%	100%

Cancer Cells

Cells go through a cycle which includes many processes. These are:
1. Interphase
2. Prophase
3. Metaphase
4. Anaphase
5. Telophase

How do cancers...happen??
When cancers develop, it is because proteins don't work the same way because cells don't go from one stage to the next properly in their cycle. The cancer cells reproduce at a far faster rate than normal cells do. But those cells all seem to have a loss of function. This happens because the cell division does not happen properly. In most cases, cancer takes many years to develop.

So...give an example of a cancer and how it happens...
Let's use breast cancer as an example!
So breast cancer is a type of cancer that will form in any part of the breast. It's more commonly seen in women, but men are also at risk of getting this cancer, too. When cancer begins to occur, cells begin to go through a change which rapidly spreads through the body (as previously stated). Women release a hormone, estrogen, which stimulates cell division, but may effect cells and DNA to be damaged or permanently effected. Women who have not been through a first term of pregnancy still have immature cells and can be more easily effected by this because their cells contain carcinogens that are not as strong or able to repair damaged cells as easily.

How can one treat this?
Through cell technology and radiation techniques, scientists have found new ways to practically zap away the bad! Treatment programs can be created to help the side effects of the cancer be reduces and can even eliminate the cancer altogether!

Sources:
Scitable by Nature Education

The Biology of Breast Cancer

Breast Cancer

As it is the new year, I would like to present to you this month's end-of blog-picture topic! The snake! Happy 2013, the year of the snake!

What You'll Wish You'd Known Response

What You'll Wish You'd Known

     In the article, What You'll Wish You'd Known, I read about how the average graduation speech about "never giving up" and "following your dreams"...is all misleading and wrong. I definitely agree with this speech because things are always different in high school than they are in the real world. When we are in high school, we are still fairly new to the world, and learning exactly where our place is. If we follow the dreams that we have while we don't really know ourselves, we're bound to end up somewhere later on that we don't want to be. However, if we do what the article tells us to do and just keep pushing on, believing that we're gonna make it, then we're more fit to get somewhere good. I can see how this speech was denied for graduation, however. At this time in our lives, we've all figured out that the tooth fairy, Santa Claus, and even the Easter bunny are all- yes- fake. But we still believe in some kind of magic. A magic of hope, dreams, and never giving up. We're still children, in this sense. But if we hold on to something forever, we're bound to have so many corpses of dreams that it could potentially lead down a path to self destruction. So basically, we must go with the flow and keep fighting!