Monday, November 30, 2015

Week 15. Human Impacts Lab.



Part 1 Ban Plastic Bags or Not (13 points)


What to submit on your blog:
Headings A, B, C, D, and E with questions answered.

A. Think about your opinion about the use of plastic bags for most purposes. Answer these questions.
1. Why do you think this way? For instance, have you ever read any scientific studies on the environmental impact of different types of “carry bags” or formed an opinion based on what a friend told you? (1 point)

I use plastic bags for many other reasons than putting groceries in them. I have not read any scientific studies about an impact of "carry bags" on the environment. I know that they are very handy when needed, and I also know that they don't simply disintegrate when left outside. They become brittle but are not absorbable by the soil. I also know that plastic material can cause harm to animals. 

 2. What type of bags do you prefer to use? (.5 point)

I mostly use the plastic bags, but I also have cloth baggies for when I need only a few items to put in them. We used to ask for the paper bags at a store, but I haven bot seeing this bags at any store for a long while now. 

B. Read the articles under the “Articles In Favor of Ban on Plastic Bags” heading. Do the further research, if you are interested. If you write using other sources, remember to cite them.

1. Summarize three arguments (three total) made in these sources in support of banning plastic bags in most circumstances. The summary is easy to find; you do not need to read the entire article! (1.5 points)

The majority of trash picked up are the plastic bags. 
Single items can be carried out without placing them in the bag.
Taxpayer's dollars can be saved by not expanding to the special sanitation department that in charge of cleaning out the plastic debris from our cities.  

2. How is the reasoning supported scientifically? Give two examples. (1 point)

I did not see any scientific support presented in any of the articles that I read. Only the logical explanations have been given, like how much money can be saved if the contract to pick up the litter around the solid waste site is terminated, and the other simply outlines the ordinance. 

3. List two exceptions to the plastic bag ban in Austin. (1 point)

In Austin, the thicker paper and plastic bags that have handles are acceptable, and of course, bags that made out of cloth and other durable materials are allowed. 

C. Read the articles under the “Articles Against Ban on Plastic Bags” heading. Do the further research, if you are interested. If you write using other sources, remember to cite them.
1. Summarize at three arguments (three total) made in these sources in support of “banning the ban” on plastic bags in most circumstances. (3 points)

The actual environmental impact of using the plastic bags is lower than of the limited-use of a cloth one. 
The CO2 emission by one plastic bag is minimal in comparison to other material's production. 
To reduce the trash, we would have to do much more than just ban the plastic bags, which only count for less than 1%. 

 2. How is the reasoning supported scientifically? Give two examples. (1 point)

 The study conducted by Dr. Chris Edwards and Jonna Meyhoff Fry is set to find out which seven types of bags have the lowest environmental impact by assessing pollution caused by extraction of raw materials, production, transportation, and disposal. Even though the study is still under the peer review, the findings being released by Environmental Agency. The HDPE plastic bag would have  a baseline global warming potential of 1.57 kg Co2 equivalent. If reused once, it will fall to 1.4kg Co2e. To have the similar outcome, the paper bag will have to be reused four times. 
The misconception of greater benefits from banning the use of the plastic bags raised the need of clarification of some terms. The benefit can be achieved if we would recycle all of the plastics. Also, use of the biodegradable materials for plastic production can reduce the overwhelming litter. 

D. Read or skim the Scientific Research Paper. Be sure to read the summary and study Figures 5.3 and 5.6
.Scientific Research Paper

United Kingdom Environmental Agency. Life cycle assessment of supermarket carrier bags: a review of the bags available in 2006. https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/291023/scho0711buan-e-e.pdf






1. Summarize two findings of the United Kingdom Environmental Agency publication. (2 points)
  • Whatever type of bag is used, the key to reducing the impacts is to reuse it as many times as possible and where reuse for shopping is not practicable, other reuse, e.g. to replace bin liners, is beneficial. 
  • Recycling or composting generally produce only a small reduction in global warming potential and abiotic depletion.
2. State two items in this article that surprised you. (1 point)

I did not know that the paper, LDPE, non-woven PP and cotton bags should be reused at least 3, 4, 11 and 131 times respectively to ensure that they have lower global warming potential than conventional HDPE carrier bags that are not reused. 


The finding of global warming potential between all of the researched materials showed that "much-hated" plastic baggie is the least harmful!

E. Revisit All About Bags, Bags Around the World (http://www.allaboutbags.ca/aroundtheworld.html).

1. In your own words, state two countries’ (besides the US) bag usage policies. (1 point)

In Belgium, the tax on plastic bags, aluminum and disposable cutlery (plastic forks and spoons) produce enough of the revenue to support the nationwide recycling program.  

 France figured out how to "kill two birds" with one stone! They banned all but biodegradable plastics. Shoppers get to have a convenient carry options and farmers have a new market opportunity; plant matter to use in bioplastics. Win-win for everyone.



Articles in Favor of Ban on Plastic Bags

Californians Against Waste: The Problem With Plastic Bags.
http://www.cawrecycles.org/issues/plastic_campaign/plastic_bags/problem

Muskegon County could be first in Michigan to ban stores' plastic bags http://www.mlive.com/news/muskegon/index.ssf/2015/04/muskegon_county_could_be_first.html

City of Assaquah Plastic Bag Ban. http://www.ci.issaquah.wa.us/index.aspx?NID=1170

Information on Bag Ban in Austin. http://www.austinbagban.com/


Articles Against Ban on Plastic Bags

All About Bags, Paper Plastic Studies. http://www.allaboutbags.ca/papervplasticstudies.html





Part 2 Greenwashing (7 points)

What to submit on your blog:
 Headings A, B, C, D, and E with questions answered. Four sentences each are required for C and E.

Introduction
Greenwashing is a term that describes the concept of businesses or organizations spending more time and money claiming to act in environmentally conscious ways through advertising and marketing than actually implementing business practices that minimize environmental impact. It’s whitewashing, but with a green brush. This is also referred to as “green sheen.”
A classic example might be an energy company that runs an advertising campaign touting “green” technology they’re working on, but that “green” technology represents only a sliver of the company’s otherwise not-so-green business, or may be marketed on the heels of an oil spill or plant explosion.
Or a hotel chain that calls itself “green” because it allows guests to choose to sleep on the same sheets and reuse towels, but does very little to save water and energy where it counts, on its grounds, with its appliances and lighting, in its kitchens, and with its vehicle fleet. (http://www.greenwashingindex.com/about-greenwashing/)
Greenwashing. Each characterization is valued at 1 point. Read each carefully, decide if the ad qualifies for that particular designation, and then add up the points for a final score.
  • The ad misleads with words. 
Do you believe the ad misleads the viewer/reader about the company’s/product’s environmental impact through the things it says? Does it seem the words are trying to make you believe there is a green practice when there isn’t? Focus on the words only — what do you think the ad is saying?
  • The ad misleads with visuals and/or graphics.
Do you think the advertiser has used green or natural images in a way designed to make you think the product/company is more environmentally friendly than it really is?
  • The ad makes a green claim that is vague or seemingly not provable.
Does the ad claim environmental benefits without sufficiently identifying for you what they are? Has the advertiser provided a source for claims or for more information? Are the claims related to the company/product?
  • The ad overstates or exaggerates how green the product/company/service actually is.
Do you believe the advertiser is overstating how green the product/company actually is? Are the green claims made by the ad believable? Do you think it's possible for the product/company to do the things depicted/stated?
  • The ad leaves out or masks important information, making the green claim sound better than it is.
Do you think the ad exists to divert attention from something else the company does? Do you believe the relevant collateral consequences of the product/service are considered in the ad? Does it seem to you something is missing from the ad?

Activity

Find an advertisement that you believe engages in greenwashing. The ad can be in print, online, or multimedia. After you view the ad, summarize it, and research the background of the organization, business, or product and its environmental impacts. Provide the ad with a score of one to five based on the above scoring criteria.

See http://www.greenwashingindex.com/ads/ for examples.

A. Company/Organization, product name, and image of ad, if visual (1 point)





Hummer.


The add:

B. Summary of the ad in at least four sentences (2 points)

The add is showing a vegetarian buying, well, vegetarian foods. The guy behind him stocking up for some serious BBQ party with plenty of meat. So, our planet-loving, tofu guy is rushing to the GM dealer and buys a Hummer! So much for the GREEN. What I see here, is that GM wants to show us that their gas-guzzlers are also accepted by the "nature-preserving" population. What I actually see, is that being vegetarian doesn't mean you are all for the health of the planet. You are just another Joe who wants to show off at whatever cost but cry "clean" in the same day. The GM tried to say that their vehicles are good for all of us, but they forgot to mention about negative effects their product emits.


Unabashed attempt to hype its green cred while also selling Hummers speaks for itself. GM’s ‘Gas-Friendly to Gas-Free’ ad campaign sought to reframe GM as eco-friendly, but the company is still the leading producer of gas-guzzling vehicles and has fought to undermine attempts to improve CAFE fuel economy standards.

C. Greenwashing score and justification for each characterization of the score in at least four sentences. (2 points)

I would give this add 3 points.

 One - for misleading with visuals.
Showing a "clean" eater, and trying to illustrate the connection of being vegetarian to a Hummer.
Like this supposed to make us think that this SUV is environmentally friendly. Or, seeing the "power" of the animal protein next to his radishes, and a glimpse on the magazine add, makes one desire the power of the true machine and makes you forget the responsibilities to which you previously committed. (I can also add, that maybe, just maybe by not having proper nutrition makes you do crazy things? [ please don't attack me for this opinion, I know that tofu contains adequate amount of protein for healthy body support])

 Two - for overstating how "green" the vehicle is.
"Restore the balance" it claims.
It doesn't make me believe that this car is providing a benefit to our climate regulation. A tofu-eater buying this car has no relation to the cleanness of the product advertised.

 Three - GM is trying to make the green claim in hopes that more people would buy this car. It seems that mentioning 20 MPG HWY should lure the buyers in, But, even the price of the vehicle understated. Starting at 29,500. The actual price of shown SUV is 32,880 excluding any additional fees. The "H-3 is like nothing else" is appears at the end. To what exactly are we supposed to compare it?


D. MLA citation of source(s). (2 points)

"Find the GM Vehicle." General Motors. Web. 3 Dec. 2015.
       <http://www.gm.com/>.

"Tofu (Hummer Ad)." YouTube. YouTube. Web. 2 Dec. 2015.
       <https://www.youtube.com/watch?v=lL4ZkYPLN38>.

"HUMMER H3." . Price, Modifications, Pictures. MoiBibiki. Web. 2 Dec. 2015.  
         <http://www.moibbk.com/HUMMER H3.html>.

The moral of the story: don't believe everything that is shown on TV or stated on the internet.

Be responsible and do your part in protecting our home, the Earth. 

Other sources cited:

"California Bans Use of Plastic Bags Statewide [Video]." Guardian Liberty Voice. 1 Sept. 2014.
       Web. 3 Dec. 2015. <http://guardianlv.com/2014/09/california-bans-use-of-plastic-bags-statewide-        video/>.

Web.2Dec.2015<https://www.gov.uk/government/uploads/system/uploads/attachment_data/file/
      /scho0711buan-e-e.pdf>.

"Plastic Bags - Google Search." Plastic Bags - Google Search. Web. 3 Dec. 2015.
   <https://www.google.com/search?q=plastic         bags&rlz=1C1GGGE_enUS594US614&espv=2&biw=1492&bih=745&source=lnms&tbm=isch&sa=X&ved=0ahUKEwiVz6S-mMDJAhXDGR4KHaC7BaIQ_AUICCgD#tbm=isch&tbs=simg:CAQSCQnDwmlWMiVrDw&q=plastic bags>.

"Paper and Plastic Bag Bans Continue. And Recyclers Ain't Happy About It." Core77. Web. 3 Dec.        . <http://www.core77.com/posts/25320/paper-and-plastic-bag-bans-continue-and-recyclers-aint-
       happy-about-it-25320>.



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Thursday, November 19, 2015

Week 13. Genetics and Inheritance Lab.




Part 1.

Flip-a-coin (or let's make a baby)


Allele(s) from
Mother		 Allele(s) from
Father		 Genotype Phenotype
Sex of child:  b XY Boy
Face shape r R Rr round
Chin Shape (I) V v Vv very preminent
Chin Shape (II) R r Rr round
Cleft chin A A AA absent
Skin color abcd AbcD AabbccDd very light brown
Hair type c c cc straight
Widow’s Peak w W Ww present
Eyebrows (I) b b bb fine
Eyebrows (II) N n Nn not connected
Eyebrow color H h Hh same color as hair
Eyes distance apart e E Ee average
Eyes size E e Ee medium
Eyes shape A a Aa almond
Eyes slant H H HH horizontal
Eyelashes L L LL long
Eye color abcD aBCD aaBbCcDD light brown
Mouth size m M Mm average
Lips l L Ll thick
Protruding lower lip h h hh absent
Dimples d d dd absent
Nose size N N NN big
Nose shape r r rr pointed
Nostril shape r r rr pointed
Earlobe Attachment f F Ff free
Freckles on checks F F FF present
Hair color aBcD abcd aaBbccDd blond








Now let's see what this child will look like! As you all know, by now, I am not an artist, but I will try to do my best on drawing this child as he grows and reaches age 16.
And here you go. I hope he doesn't scare you too much; but because he is my "creation" I love him just the way he is.



Part 2.

Genetics problem calculator.

1.       For each of the diploid genotypes presented below, determine the genetic make up for all of the possible gametes that would result through the process of meiosis. Remember, each egg or sperm must have one of each letter. That letter can be upper or lower case.

a.       Rr            Rr

b.       RrYy       Rr, RY, Ry, Yr, Yy, ry.

c.       rrYy        rr, Yr, Yy, ry.


d.       RrYY      RY, Rr, YY, Yr

2.       For each of the following, state whether the genotype of a diploid or haploid cell is represented.

a.       D     - Haploid

b.       GG   - Diploid

c.       P      - Haploid

d.       ee     - Diploid

3.       Yellow guinea pigs crossed with white ones always produce cream-colored offspring. 
      Two cream colored guinea pigs when crossed produced yellow, cream and white offspring in the ratio of 
      l yellow: 2 cream: l white. 

     Explain how are these colors inherited?  No calculations needed! Name the type of inheritance this represents.

Because the cream guinea pigs carrying both white and yellow alleles, their offsprings are inheriting these traits and becoming the color of the dominance. 
Thatis is an incomplete inheritance

4.       In sheep, white is due to a dominant gene (B), black to its recessive allele (b). A white ewe mated to a white ram produces a black lamb. What are the genotypes of the parents? You might need to construct Punnet squares experimenting with different crosses to come up with this answer. Name the type of inheritance this represents.

Even though both parents ar white, they carry the recessive black allele that will show
itself, eventually, by producing a black lamb.
This is a recessive inheritance.




5.       In peas, yellow color (G) is dominant to green color (g). A heterozygous yellow is crossed with a green. What is the expected phenotype ratio of the offspring? Name the type of inheritance this represents.

The dominant yellow peas possess the green alleles that become noticeable by the green
color of its offsprings. There is a 50/50 chance for this type of phenotype. 
That is a dominant inheritance



6.       White color (Y) is dominant to yellow color (y) in squash. A heterozygous white fruit plant is crossed with a yellow fruit plant. What is the expected phenotype ratio of the offspring? What is this type of inheritance called?

As with the yellow and green peas, the squash will illustrate the dominant inheritance and
there will be a 50/50 chance to see them white or green.



7.       In certain flowers, a cross between homozygous red and a homozygous white will always result in a pink flower. A cross is made between two pink flowers. What is the predicted phenotype ratio of the colors red, pink and white appearing in the offspring? What is this type of inheritance called.

Because all of the pink flowers carry one of each of the alleles from white and red, their
offsprings will have a 1/4, 1/2, 1/4 ratio for the white, pink and red colors. (or 1:2:1)
This is an exemple of incomplete inferitance. 




8.       In humans, the condition for normal blood clotting dominates the condition for non-clotting or hemophilia. Both alleles are linked to the X chromosome. A male hemophiliac marries a woman who is a carrier for this condition. In this respect, a carrier is a woman who has an allele for normal blood clotting and an allele for hemophilia. What are the chances that if they have a male child he will be normal for blood clotting? What is this type of inheritance called?

I believe that the male child will have a 50/50 chnce of having a normal blood clotting. 
This is a sex-linked inheritance.



9.       A person with an allele for type A blood and type O blood marries someone with an allele for type B blood and type O blood. List the types of offspring they could have and the probability for each blood type in the offspring. (A allele = IA, B allele = IB, O allele = i) What is the expected phenotype ratio of the offspring? What is this type of inheritance called?

Because A and B blood types are dominant, when both A and O present, A will dominate.
According to the Punnet square, The chance of having one of four possible combinations is 1:4.
This is an example of codominant inheritance. 



10.      Skin color in humans becomes darker by the number of dominant alleles; AABBCC have the darkest skin and aabbcc have the lightest skin. Place these genotypes in sequence according to the color of skin expected for each. Place the darkest skin first. What is this type of inheritance called?
Genotypes: AaBbCc, AAbbcc, aabbCc, AaBBCc, AaBBCC.

Because there are many possibilities and variations, this iheritance is called polygenic.






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Wednesday, November 11, 2015

Week 12. DNA Technology



Part 1
Here we will be performing a DNA Extraction. 

Let's begin this technology assignment with visiting the virtual lab site:



As with any laboratory experiment, we must begin with an acquisition of materials and equipment for it. As I collect the supply, I will be explaining how we will be using it and for what. 

1) Buccal swab
Collection of the specimen

2) Eppendorf tubes, three count
Mixing, viewing, and storing the specimen

3) Scissors
Cutting off the top of the swab

4) Micropipettor
Extracting, transporting, and expelling droplets of the liquid with the specimen
5) Lysis solution
This is a unique mix of kind of a detergent and enzyme K. (The DNA wrapped around special proteins called histones, and the K enzyme releases them and unwraps the DNA)

6) Warm water bath

         Not this one.                                                     

  







                                      This one!



7) Concentrated salt solution
Causing the proteins and other debris clumps together

8) Micro-Centrifuge
Spinning apparatus. Separation of clumped waste from the rest of liquid in the Eppendorf's tube, here we need an extra tube with just water in it to balance the centrifuge

9) Isopropyl alcohol
We can see the undissolved, clumped DNA 


Q: What is the specific type of tissue inside the mouth?

A: Oral mucosa. The oral mucosa is the mucous membrane lining the inside of the mouth and consists of stratified squamous epithelium termed oral epithelium, and an underlying connective tissue termed lamina propria.



Part 2

Electrophoresis

Electrophoresis is a technique used in laboratories to separate macromolecules based on size. The method applies a negative charge, so proteins move towards a positive charge. This is used for both DNA and RNA analysis.

And now we can go to another site and perform this lab:



EQUIPMENT AND MATERIALS NEEDED 
AGAR GEL (Background - Agar is a gelatinous substance found in the cell walls of certain red marine algae, particularly those in the genus Gelidium. It is used to make vitamin and drug capsules, as a dental impression material, as a base for cosmetics, and as a culture medium for bacteria and other microorganisms. In foods, it is used as a moisture retention (anti-drying) agent in bakery products, in the preparation of rapid settling jellies and desserts, and as a temporary preservative for meat and fish in tropical regions. While a very expensive, highly purified form of sugar, called agarose, is needed for separating DNA or proteins in gels, several kinds of agar can be used for separating scientific stains in gels. These less expensive agars include agars used for microbiological culture media and agar available from health food stores and Asian markets. (Note: Unflavored gelatin, such as Knox“, does not work. The gelatin has a greater affinity to surfaces than to itself, causing the wells to tear out of the gel when the comb is removed. Also, gelatin melts at a much lower temperature and a gel prepared from gelatin is likely to melt while running.)

Gel form and comb 

Electrophoresis chamber, 

Electrophoresis power supply 

Salt solution 

Scientific stains to use as samples 

Sample-loading device 

Masking tape, if needed to seal gel form 



GEL ELECTROPHORESIS BRIEF PROCEDURE  



1. Dissolve the agar, cool the solution, and pour the gel. 
Combine agar and water. Bring the mixture to a boil and heat until the agar is dissolved. 
Cool the agar until you can comfortably touch the flask. 
Place tape across the ends of the gel form (if needed) and place the comb in the form. 
Pour cooled agar into the form; the bottom 1/3-1/2 of the comb should be immersed. 
When the agar has solidified, carefully remove the comb. Remove the tape (if used) from the ends of the gel form. 

When the gel is being prepared a chemical is added to it, this chemical will bind to the DNA and is visible under UV light. The DNA molecules will then appear as series of bands on the gel.

2. Load samples in the wells in the gel. 
Make a written record of which sample you will load in each well of the gel. 
Place the gel form on a black or dark surface to help you see the wells in the agar. 
DNA is added into wells at the top of a pre-made gel. The gel is submerged in a tank of liquid. A power pack can be attached to the tank.

3. Place the gel in the electrophoresis chamber with the wells closest to the negative (black) electrode. 

Gel electrophoresis works by using an electric current to pass DNA samples through a gel. The gel acts like a sieve allowing smaller DNA molecules to migrate through the gel quicker than larger molecules. 

4. Prepare the salt solution and add it to the chamber. 
Add salt to tap water and swirl it to dissolve. 
Fill each half of the chamber, adding solution until it is close to the top of the gel. 
Then gently flood the gel from the end opposite the wells to minimize sample diffusion. 

5. Place the lid on the chamber and connect the electrode leads to the power supply. 
Connect the black lead to the negative terminal and the red lead to the positive terminal. 

6. Turn on the power supply and adjust the voltage to 50-100 volts. 

7. Run the gel for 5-10 minutes. 
You will be able to observe the samples separating into different colors. 


An electric current is applied across the gel. As DNA is negatively charged it will move from the well towards the bottom of the gel. The gel acts like a sieve, separating different DNA molecules according to their size, as smaller DNA molecules will be able to move through the gel quicker than larger molecules.

8. Turn off the power supply, disconnect the electrode leads, and remove the chamber lid. 

9. Remove the gel from the electrophoresis chamber. 
Record and evaluate the results of the electrophoresis. 



The gel is then visualised under UV light where DNA samples appear as bands. Bands which have migrated further down the gel are smaller than those which have not moved as far.

The image seen under UV light is photographed so it can be analysed. A series of DNA bands will be visible on the gel, and how far they have migrated through the gel will depend on their size.

The PCR will have been set up so scientists can detect the presence or absence of certain sections of DNA which may indicate an alteration to the DNA sequence; for example one band may only be present if there is an alteration in this section of the gene.

10. Clean up. Discard the gel in the trash and pour the salt solution down the drain. Rinse the electrophoresis chamber and gel form with tap water; turn them upside down to dry.


And now we know!

The vast applications of electrophoresis are most evident in the health or medical industry, including antibiotic and vaccine analysis. Protein and DNA analysis are also important electrophoresis applications. Aside from allowing researchers to map and see the differences in the genetic code of species on earth, electrophoretic DNA analysis also provides a reliable tool for forensic investigations.

The movement of charged molecules is called mobility. The movement of molecules is towards the opposite charge, for instance, a protein molecule with negative charge moves toward the positive pole of the support medium. The medium may be a paper, gel or a capillary tube.

Vaccine Analysis
Vaccine analysis is one of the many important applications of electrophoresis. There are several vaccines that have been purified, processed and analyzed through electrophoreses, such as the influenza vaccine, hepatitis vaccine, and polio vaccine. The exact steps are done in the vaccine analysis, however, cannot be determined due to confidentiality reasons of the pharmaceutical companies. Nevertheless, data reports from vaccine manufacturers such as Wyeth, Merck and Sanofi-Aventis presents electrophoresis as an effective vaccine analysis method.




Works cited:

"Sterile Round Foam Buccal Swab - Arrowhead Forensics." Sterile Round Foam Buccal Swab - Arrowhead Forensics. Web. 11 Nov. 2015. <http://www.crime-scene.com/store/A-701.shtml>.

"Eppendorf Tube 5.0 ML and Tube Rack 5.0 ML." Red Dot 21. Web. 11 Nov. 2015. <http://www.red-dot-21.com/design/eppendorf-tube-5-0-ml-and-tube-rack-5-0-ml/>.

"Robot Check." Robot Check. Web. 11 Nov. 2015. <http://www.amazon.com/Scilogex-MicroPette-Single-Channel-Adjustable-Pipettor/dp/B0079MASIQ>.

"Eppendorf 022620700 | 5427 R Refrigerated Microcentrifuge with 48 X 1.5/2mL Aerosol-Tight QuickLock Rotor & Lid, Temperature Range: -11 to 40°C, 120V." Eppendorf 022620700. Web. 11 Nov. 2015. <http://www.capitolscientific.com/Eppendorf-022620700-5427-R-Refrigerated-Microcentrifuge-with-48-x-1-5-2mL-Aerosol-Tight-QuickLock>.

"Lysis Buffer #1662002EDU." Lysis Buffer #1662002EDU. Web. 11 Nov. 2015. <http://www.bio-rad.com/en-cn/sku/1662002edu-lysis-buffer>.

"Google." Google. Web. 11 Nov. 2015. <https://www.google.com/search?noj=1&tbm=isch&sa=1&q=warm water bath chemistry&oq=warm water bath&gs_l=img.1.1.0l2j0i24l8.7935.13433.0.15455.15.12.0.3.3.0.153.1418.3j9.12.0....0...1c.1.64.img..0.15.1434.J1bLLmHMGIM#imgrc=ajYdK8Tyj4Y9aM:>.

"MG Chemicals 824 99.9% Isopropyl Alcohol Liquid Cleaner, 125 Ml Bottle, Clear." Amazon.com: : Industrial & Scientific. Web. 11 Nov. 2015. <http://www.amazon.com/MG-Chemicals-Isopropyl-Alcohol-Cleaner/dp/B008UH4AI8>.

"Mouth Tissue - Google Search." Mouth Tissue - Google Search. Web. 11 Nov. 2015. <https://www.google.com/search?q=mouth tissue&rlz=1C1GGGE_enUS594US614&es_sm=122&biw=1444&bih=775&source=lnms&sa=X&ved=0CAUQ_AUoAGoVChMI8veE2YKJyQIVQsFjCh3HuwWO&dpr=1>.

"Google." Google. Web. 11 Nov. 2015. <https://www.google.com/webhp?sourceid=chrome-instant&ion=1&espv=2&ie=UTF-8#q=electrophoresis>.

Web. 11 Nov. 2015. <http://www.colorado.edu/Outreach/BSI/pdfs/electrophoresis_teacher.pdf>

"Gel Electrophoresis." Gel Electrophoresis. Web. 11 Nov. 2015. <http://www.geneticseducation.nhs.uk/laboratory-process-and-testing-techniques/gel-electrophoresis>.
"Gel Electrophoresis Procedure - Google Search." Gel Electrophoresis Procedure - Google Search. Web. 11 Nov. 2015. <https://www.google.com/search?q=gel electrophoresis procedure&rlz=1C1GGGE_enUS594US614&espv=2&biw=1445&bih=775&source=lnms&tbm=isch&sa=X&ved=0CAcQ_AUoAmoVChMI1Ofd3Z6JyQIVVC-ICh35cAgU#imgrc=8aqQ1svoc67YOM:>.

"Electrophoresis." - Biology Encyclopedia. Web. 11 Nov. 2015. <http://www.biologyreference.com/Dn-Ep/Electrophoresis.html>.

Dephoff, Jacklyn. "List of the Applications of Electrophoresis." EHow. Demand Media. Web. 12 Nov. 2015. <http://www.ehow.com/about_5606215_list-applications-electrophoresis.html>.




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Thursday, November 5, 2015

Week 11 DNA Lab.


Part 1.
 My Personal Chromosome 

I was designated chromosome number 13. 

By going to the website HTTP://www.dnai.org/., I can find my chromosome by going through a few steps
  • First, I choose Genome on the top menu. 
  • Then, I choose Tour on the top menu. 
  • Next, I choose Genome Fishing on the top menu. 
  • And now I can find my chromosome # 13 from the drop-down menu at the bottom.


Now I can view the individual Genomes and find out what role do they play and what genetic information do they carry. 

http://www.ncbi.nlm.nih.gov/mapview/maps.cgi?ORG=hum&MAPS=ideogr,ugHs,loc&CHR=13

1) HMGB1 high mobility group box 1 [ Homo sapiens (human) ]

Gene ID: 3146, updated on 4-Nov-2015

Summary

Official Symbol
HMGB1provided by HGNC
Official Full Name
high mobility group box 1provided by HGNC
Primary source
HGNC:HGNC:4983
See related
Ensembl:ENSG00000189403; HPRD:01228; MIM:163905; Vega:OTTHUMG00000016670
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HMG1; HMG3; HMG-1; SBP-1
Summary
This gene encodes a protein that belongs to the High Mobility Group-box superfamily. The encoded non-histone, nuclear DNA-binding protein regulates transcription and is involved in the organization of DNA. This protein plays a role in several cellular processes, including inflammation, cell differentiation, and tumor cell migration. Multiple pseudogenes of this gene have been identified. Alternative splicing results in multiple transcript variants that encode the same protein. [provided by RefSeq, Sep 2015]

In other words: This gene regulates the transcription and organizes the DNA. It plays the role in cellular processes, including inflammation, cell differentiation, and tumor cell migration.

2) RB1 retinoblastoma 1 [ Homo sapiens (human) ]

Gene ID: 5925, updated on 25-Oct-2015

Summary

Official Symbol
RB1provided by HGNC
Official Full Name
retinoblastoma 1provided by HGNC
Primary source
HGNC:HGNC:9884
See related
Ensembl:ENSG00000139687; HPRD:01574; MIM:614041; Vega:OTTHUMG00000016900
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
RB; pRb; OSRC; pp110; p105-Rb; PPP1R130
Summary
The protein encoded by this gene is a negative regulator of the cell cycle and was the first tumor suppressor gene found. The encoded protein also stabilizes constitutive heterochromatin to maintain the overall chromatin structure. The active, hypophosphorylated form of the protein binds transcription factor E2F1. Defects in this gene are a cause of childhood cancer retinoblastoma (RB), bladder cancer, and osteogenic sarcoma. [provided by RefSeq, Jul 2008]

In other words: First tumor suppressor gene found. The chromatin in regions of the chromosomes that are invariably heterochromatic; it contains highly repetitive sequences of DNA that are genetically inactive and serves as a structural element of the chromosome. The active, hypophosphorylated form of the protein binds transcription factor.

3) BRCA2 breast cancer 2, early onset [ Homo sapiens (human) ]

Gene ID: 675, updated on 1-Nov-2015

Summary

Official Symbol
BRCA2provided by HGNC
Official Full Name
breast cancer 2, early onsetprovided by HGNC
Primary source
HGNC:HGNC:1101
See related
Ensembl:ENSG00000139618; HPRD:02554; MIM:600185; Vega:OTTHUMG00000017411
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FAD; FACD; FAD1; GLM3; BRCC2; FANCD; PNCA2; FANCD1; XRCC11; BROVCA2
Summary
Inherited mutations in BRCA1 and this gene, BRCA2, confer increased lifetime risk of developing breast or ovarian cancer. Both BRCA1 and BRCA2 are involved in maintenance of genome stability, specifically the homologous recombination pathway for double-strand DNA repair. The BRCA2 protein contains several copies of a 70 aa motif called the BRC motif, and these motifs mediate binding to the RAD51 recombinase which functions in DNA repair. BRCA2 is considered a tumor suppressor gene, as tumors with BRCA2 mutations generally exhibit loss of heterozygosity (LOH) of the wild-type allele. [provided by RefSeq, Dec 2008]

In other words: Inherited mutations in this gene increase the risk of developing a breast cancer or ovarian cancer. It involved in a maintenance of genome stability and considered to be a tumor suppressor gene. 

4) POSTN periostin, osteoblast specific factor [ Homo sapiens (human) ]

Gene ID: 10631, updated on 1-Nov-2015

Summary

Official Symbol
POSTNprovided by HGNC
Official Full Name
periostin, osteoblast specific factorprovided by HGNC
Primary source
HGNC:HGNC:16953
See related
Ensembl:ENSG00000133110; HPRD:12295; MIM:608777; Vega:OTTHUMG00000016751
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PN; OSF2; OSF-2; PDLPOSTN
Summary
This gene encodes a secreted extracellular matrix protein that functions in tissue development and regeneration, including wound healing, and ventricular remodeling following myocardial infarction. The encoded protein binds to integrins to support adhesion and migration of epithelial cells. This protein plays a role in cancer stem cell maintenance and metastasis. Mice lacking this gene exhibit cardiac valve disease, and skeletal and dental defects. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Sep 2015]

In other words: This gene encodes the extracellular protein that functions in the tissue development and regeneration. It supports the cardiac and skeletal muscles, and dental development and maintenance. 

5) TNFSF11 tumor necrosis factor (ligand) superfamily, member 11 [ Homo sapiens (human) ]

Gene ID: 8600, updated on 1-Nov-2015

Summary

Official Symbol
TNFSF11provided by HGNC
Official Full Name
tumor necrosis factor (ligand) superfamily, member 11provided by HGNC
Primary source
HGNC:HGNC:11926
See related
Ensembl:ENSG00000120659; HPRD:04031; MIM:602642; Vega:OTTHUMG00000016807
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
ODF; OPGL; sOdf; CD254; OPTB2; RANKL; TRANCE; hRANKL2
Summary
This gene encodes a member of the tumor necrosis factor (TNF) cytokine family which is a ligand for osteoprotegerin and functions as a key factor for osteoclast differentiation and activation. This protein was shown to be a dentritic cell survival factor and is involved in the regulation of T cell-dependent immune response. T cell activation was reported to induce expression of this gene and lead to an increase of osteoclastogenesis and bone loss. This protein was shown to activate antiapoptotic kinase AKT/PKB through a signaling complex involving SRC kinase and tumor necrosis factor receptor-associated factor (TRAF) 6, which indicated this protein may have a role in the regulation of cell apoptosis. Targeted disruption of the related gene in mice led to severe osteopetrosis and a lack of osteoclasts. The deficient mice exhibited defects in early differentiation of T and B lymphocytes, and failed to form lobulo-alveolar mammary structures during pregnancy. Two alternatively spliced transcript variants have been found. [provided by RefSeq, Jul 2008]

In other words: Encoded by this gene, the protein have a role in the regulation of cell apoptosis ( apoptosis is a highly regulated and controlled process that confers advantages during an organism's lifecycle. For example, the separation of fingers and toes in a developing human embryo occurs because cells between the digits undergo apoptosis. Apoptosis produces cell fragments called apoptotic bodies that phagocytic cells can engulf and quickly remove before the contents of the cell can spill out onto surrounding cells and cause damage.) It also was shown to be a dendritic (branched) cell survival factor and is involved in the regulation of T cell-dependent immune response.

6) CPB2 carboxypeptidase B2 (plasma) [ Homo sapiens (human) ]

Gene ID: 1361, updated on 25-Oct-2015

Summary

Official Symbol
CPB2provided by HGNC
Official Full Name
carboxypeptidase B2 (plasma)provided by HGNC
Primary source
HGNC:HGNC:2300
See related
Ensembl:ENSG00000080618; HPRD:04374; MIM:603101; Vega:OTTHUMG00000016867
Gene type
protein-coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CPU; PCPB; TAFI
Summary
Carboxypeptidases are enzymes that hydrolyze C-terminal peptide bonds. The carboxypeptidase family includes metallo-, serine, and cysteine carboxypeptidases. According to their substrate specificity, these enzymes are referred to as carboxypeptidase A (cleaving aliphatic residues) or carboxypeptidase B (cleaving basic amino residues). The protein encoded by this gene is activated by trypsin and acts on carboxypeptidase B substrates. After thrombin activation, the mature protein downregulates fibrinolysis. Polymorphisms have been described for this gene and its promoter region. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Jun 2013]

In other words: Plasma carboxypeptidase B2, also known as carboxypeptidase U (CPU) and thrombin-activatable fibrinolysis inhibitor (TAFI), is synthesized by the liver and circulates in plasma as a plasminogen-bound zymogen. When it is activated by the thrombin/thrombomodulin complex, CPB2 exhibits carboxypeptidase B-like activity. CPB2 potently attenuates fibrinolysis by removing the C-terminal fibrin residues that are important for the binding and activation of plasminogenThe CPB2 genotype accounted for approximately 3% of the total variation in diastolic blood pressure, consistent with the expected magnitude of a modest genetic effect in a complex trait such as blood pressure.

7) HTR2A 5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupled [ Homo sapiens (human) ]

Gene ID: 3356, updated on 15-Oct-2015

Summary

Official Symbol
HTR2Aprovided by HGNC
Official Full Name
5-hydroxytryptamine (serotonin) receptor 2A, G protein-coupledprovided by HGNC
Primary source
HGNC:HGNC:5293
See related
Ensembl:ENSG00000102468; HPRD:01638; MIM:182135; Vega:OTTHUMG00000016881
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HTR2; 5-HT2A
Summary
This gene encodes one of the receptors for serotonin, a neurotransmitter with many roles. Mutations in this gene are associated with susceptibility to schizophrenia and obsessive-compulsive disorder, and are also associated with response to the antidepressant citalopram in patients with major depressive disorder (MDD). MDD patients who also have a mutation in intron 2 of this gene show a significantly reduced response to citalopram as this antidepressant downregulates expression of this gene. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2009]

In other words: This gene encodes one of the receptors for serotonin, a neurotransmitter with many roles. Mutations in this gene are associated with susceptibility to schizophrenia and obsessive-compulsive disorder and are also associated with response to the antidepressant citalopram in patients with major depressive disorder (MDD).

8) F10 coagulation factor X [ Homo sapiens (human) ]

Gene ID: 2159, updated on 4-Nov-2015

Summary

Official Symbol
F10provided by HGNC
Official Full Name
coagulation factor Xprovided by HGNC
Primary source
HGNC:HGNC:3528
See related
Ensembl:ENSG00000126218; HPRD:01966; MIM:613872; Vega:OTTHUMG00000017374
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FX; FXA
Summary
This gene encodes the vitamin K-dependent coagulation factor X of the blood coagulation cascade. This factor undergoes multiple processing steps before its pre-proprotein is converted to a mature two-chain form by the excision of the tripeptide RKR. Two chains of the factor are held together by 1 or more disulfide bonds; the light chain contains 2 EGF-like domains while the heavy chain contains the catalytic domain which is structurally homologous to those of the other hemostatic serine proteases. The mature factor is activated by the cleavage of the activation peptide by factor IXa (in the intrinsic pathway), or by factor VIIa (in the extrinsic pathway). The activated factor then converts prothrombin to thrombin in the presence of factor Va, Ca+2, and phospholipid during blood clotting. Mutations of this gene result in factor X deficiency, a hemorrhagic condition of variable severity. Alternative splicing results in multiple transcript variants encoding different isoforms that may undergo similar proteolytic processing to generate mature polypeptides. [provided by RefSeq, Aug 2015]

In other words: This gene encodes the vitamin K-dependent coagulation factor X of the blood. Mutations in this gene result in factor X deficiency, a hemorrhagic condition of variable severity.

9) CDX2 caudal type homeobox 2 [ Homo sapiens (human) ]

Gene ID: 1045, updated on 15-Oct-2015

Summary

Official Symbol
CDX2provided by HGNC
Official Full Name
caudal type homeobox 2provided by HGNC
Primary source
HGNC:HGNC:1806
See related
HPRD:02622; MIM:600297
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
CDX3; CDX-3; CDX2/AS
Summary
This gene is a member of the caudal-related homeobox transcription factor gene family. The encoded protein is a major regulator of intestine-specific genes involved in cell growth an differentiation. This protein also plays a role in early embryonic development of the intestinal tract. Aberrant expression of this gene is associated with intestinal inflammation and tumorigenesis. [provided by RefSeq, Jan 2012]

In other words: This encoded protein is a major regulator of intestine-specific genes involved in cell growth and differentiation it also plays a role in an early embryonic development of the intestinal tract.

10) FLT1 fms-related tyrosine kinase 1 [ Homo sapiens (human) ]

Gene ID: 2321, updated on 25-Oct-2015

Summary

Official Symbol
FLT1provided by HGNC
Official Full Name
fms-related tyrosine kinase 1provided by HGNC
Primary source
HGNC:HGNC:3763
See related
Ensembl:ENSG00000102755; HPRD:01297; MIM:165070; Vega:OTTHUMG00000016648
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
FLT; FLT-1; VEGFR1; VEGFR-1
Summary
This gene encodes a member of the vascular endothelial growth factor receptor (VEGFR) family. VEGFR family members are receptor tyrosine kinases (RTKs) which contain an extracellular ligand-binding region with seven immunoglobulin (Ig)-like domains, a transmembrane segment, and a tyrosine kinase (TK) domain within the cytoplasmic domain. This protein binds to VEGFR-A, VEGFR-B and placental growth factor and plays an important role in angiogenesis and vasculogenesis. Expression of this receptor is found in vascular endothelial cells, placental trophoblast cells and peripheral blood monocytes. Multiple transcript variants encoding different isoforms have been found for this gene. Isoforms include a full-length transmembrane receptor isoform and shortened, soluble isoforms. The soluble isoforms are associated with the onset of pre-eclampsia.[provided by RefSeq, May 2009]

In other words: This gene encodes a member of the vascular endothelial growth factor receptor. It is found in vascular endothelial cells, placental trophoblast cells, and peripheral blood monocytes. This protein binds to VEGFR-A, VEGFR-B, and placental growth factor and plays an important role in angiogenesis (the development of the new blood cells) and vasculogenesis (is the term used for the formation of new blood vessels when there are no pre-existing ones.)
.
Part 2. 

Genetic Blueprints. 


 I will begin this part by logging into the website:


I have completed the lesson up to the level 17, (from where I shall continue when the glitch is resolved and corrected.)
Update: The glitch has been fixed, and the lab proceeded to explain the formation and structure of the DNA molecule.  
Following the lesson through the visual graphics, like an illustration of the dead and alive mice made the learning fun and comprehencible. The introduction to the discovery of the double helix form of the DNA and example of the bonding of the bases makes this lab a useful learning tool. 
Aside of the glitch that was discovered by one of the classmates; the lesson seems to be structured and preceded on smoothley.  I would like to have these kind of lessons in the future.
The only dislike I have about this lesson, I don't get to see my score at the end.



Works cited:

Wikipedia. Wikimedia Foundation. Web. 5 Nov. 2015.

 Web. 5 Nov. 2015. 

"DNA Interactive: Discovering the DNA Structure and beyond." DNA Interactive: Discovering the DNA Structure and beyond. Web. 5 Nov. 2015.


Https://aelp.smartsparrow.com/v/open/adcudyn4. Web. 5 Nov. 2015
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