School’s Out For Summer!

This year has been a fantastic year for Biology! This blog is the result of all of the hard work that was done throughout the year.
I am sad to say that this will be my final blog post for this Biology Blog. There were forty posts overall, this one included (for any that care). You never know- that may be a question on Jeopardy someday!  This blog also broke 1,500 views during the school year!  Whoo!
But anyway, I want to thank everyone who made the class enjoyable! It was a blast!  I’ll be back next year, hopefully, with two more advanced science blogs for you to read.
Until next year- have a great summer! Try and learn something you can’t learn in school!

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Evolution is No Small Concept!

We have been given many different assignments in our Biology class that compliment our learning of Evolution.  I have taken the liberty of creating a single presentation that combines the important concepts, terms, and answers to questions.  This presentation will provide a look into Darwin, other scientists who have been important to this field, Microevolution, Macroevolution, as well as examples of evolution at work.  Dig in whenever you’re ready!

Presentation is right here.

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An Exploration through Molecular Evolution

Our discussions in Biology class have been focused on the concept of evolution recently.  Basically, evolution is saying that species have evolved over time, through slight genetic changes, into the forms we know today.  Though this is only a theory, there is a wide evidence base to back it up.  One of the primary ways to support evolution is to compare the DNA sequences of similar species.  This is exactly what this assignment was about.  Throughout this webquest, we will use a computer program (Biology Workbench) to compare the genetic sequences of species, and see how similar or different they are.  We will be focusing specifically on a beta globin gene, as all of the animals in this lab produce beta globin (and therefore must have the gene).  From there, we can build “genetic trees” to represent the relationships between these species.

This presentation will be delivered in a manner similar to a Q & A column.  The concepts and ideas can be clearly found through the questions and answers provided down below.  For this post to be the most beneficial to you, I suggest you follow the same procedures I did.  They, as well as useful information into the world of this molecular evolution similarities, can be found here:
https://docs.google.com/a/lajunta.k12.co.us/presentation/d/1DwcEUEPQc-61Ft_8YsvHTdr3f0FPzFHTipCo34JKuiA/edit#slide=id.p5

1.)  Results of your pairwise alignment comparing the beta globin gene in humans and in chimps (the first two species to be compared):

-How many nucleotides are there in the beta globin gene for the chimp, and the human?  The chimp has 600 base pairs, while the human has 626 base pairs.

-Nucleotides that are the same in both sequences are said to be “conserved”.  The percentage of similar nucleotides are reported as a similarity score.  What percentage of the beta globin sequence is conserved in chimps and humans?  The chimp and human have genetic sequences that are 99% similar.

-Would you expect the protein structure to be highly similar or markedly different in the chimp and the human?  I would expect the protein structure to be highly similar between the chimp and the human.  This is because the DNA sequences are 99% equivalent.  As a result, the proteins made from this DNA will be very similar themselves.  In addition, chimps and humans are very closely related, and thus would most likely have many of the same attributes (such as protein structures).

2.)  Results of your pairwise alignment comparing the beta globin gene in humans and in chickens (the second two species to be compared):

-What is the percentage of sequence conservation between the beta globin gene in chickens and humans?  The percentage of sequence conservation is a mediocre 57%.

-Looking at the two pairwise alignments you have performed, would you expect the beta globin protein found in humans to be more similar to that found in chickens or chimps?  I would expect it to be more similar to that found in chimps, rather than chickens.  This is because the percentage of the DNA sequences are dramatically different (99% similarity to chimps, while only 57% to chickens).  As a result, the chimp is an overall closer relative to the human.  This implies that the DNA resembles each other also (and recall that DNA is instructions for making proteins).

-Do the results achieved by running these alignments support the results on evolutionary relationships determined by scientists using anatomical homology (similarities)?  Yes, these results are supported by the results on evolutionary relationships, based on the use of anatomical homology.  The anatomical homology shows that humans are very related to chimps (being that our body structures are extremely similar).  The results support this also, as it shows that our DNA sequences (and thus protein sequences) are very similar.  These both act as evidence to bridge the relationship gap between the chimp and the human.

3.) From here, the next step of the lab was to compare the beta globin gene within every animal from the lab, at once.  The complete species list is the human, chimp, mouse, wallaby, chicken, and goldfish.  By examining all of the sequences at the same time, it is easier to produce an Unrooted Tree diagram.  This can be seen below.

An Unrooted Tree diagram is used to compare the relationships of species that do not have common ancestry.  This is in comparison to a Rooted Tree diagram, where every species is traced back to one.  We will create one of these trees later.  In an Unrooted Tree, the distance between two animals/species is a representation of how closely related they are.  So, the closer the animals are together, the more related/similar they are.  Inversely, the farther apart the animals are, the less related they are.

-Which two species appear to be most closely related to each other, according to the Unrooted Tree?  The two species that are most closely related are the chimp and the human.  They both extend from the same branch.  The “leaves” of this branch are extremely close to each other, almost to the point of touching (and thus being most similar).

-Which two species seem to be the least closely related to each other?  It appears, through physical distance, that the farthest species from each other are either the human and the chicken, or the goldfish and the mouse.  Furthermore, I checked the percentage of similar DNA sequences between the species.  Human/chimp and chicken receive a 57%.  Goldfish and mouse receive a 55%.  These are the lowest percentages of similarities between the organisms listed in the tree.

The other similarity percentages, in the format provided by the online comparison site, can be seen below:

Sequence type explicitly set to DNA
Sequence format is Pearson
Sequence 1: Goldfish   441 bp
Sequence 2: Chicken    601 bp
Sequence 3: Chimp      600 bp
Sequence 4: Human      626 bp
Sequence 5: Mouse      630 bp
Sequence 6: Wallaby    444 bp
Start of Pairwise alignments
Aligning…
Sequences (1:2) Aligned. Score:  66
Sequences (1:3) Aligned. Score:  63
Sequences (1:4) Aligned. Score:  63
Sequences (1:5) Aligned. Score:  65
Sequences (1:6) Aligned. Score:  61
Sequences (2:3) Aligned. Score:  57
Sequences (2:4) Aligned. Score:  57
Sequences (2:5) Aligned. Score:  55
Sequences (2:6) Aligned. Score:  70
Sequences (3:4) Aligned. Score:  99
Sequences (3:5) Aligned. Score:  79
Sequences (3:6) Aligned. Score:  75
Sequences (4:5) Aligned. Score:  79
Sequences (4:6) Aligned. Score:  75
Sequences (5:6) Aligned. Score:  75

-Comparative evolutionary distance between species is indicated by the length of the branches they are on.  Give the comparative evolutionary distance (by percentage similarity score) between:
Mouse/Human?  Percent similar: 79%
Wallaby/Human?  Percent similar: 75%
Chimp/Human?  Percent similar: 99%

-Comment on the significance of these results given you knowledge of mammalian groups.   These results are significant because it demonstrates the relationship between mammals.  Clearly the chimp and human are the closest, being at 99%.  The other creatures, who are also mammals, are in the 75-80% range.  This is relatively close when you compare it to the goldfish and chicken, which comparatively only hit the 50-60% range.  This shows that mammals are closely related (the rodent types especially), and the more advanced mammals are closely related (humans and chimps).

4.)  Below is an example of a Rooted Tree.  While there is no common ancestor, it is clear to see how each species descended through the generations.  Please take note in the difference between a Rooted and Unrooted Tree, and what each one represents.

-Based on the diagram, which species is/are most closely related to:

The Goldfish?  The chicken.
The Mouse?  The Humans/Chimps.

-Homology is a term used to refer to a feature in two or more species that is similar because of descent; it evolved from the same feature in the last common ancestor of the species.  Hence, similarity in DNA or protein sequences between individuals of the same species or among different species is referred to as sequence homology.  Which two species in the tree above share the greatest homology with respect to the beta globin gene?  The Human and Chimp are most closely related.  This is shown by the short line lengths.  What this means is that the two species are not very distant from the similar ancestor that gave them certain components within their homology.  As a result, and as we have seen both characteristically and sequentially, humans and chimps are extremely similar.

-A node is a branch point representing a divergence event from a common ancestor.  Which two species have the most ancestral nodes (divergence events) in the tree above?  The Human and Chimp, once again, have the largest number of ancestral nodes.  They have, from the unknown root of this tree, three nodes of ancestry.  For comparison, the wallaby has one, and the chicken and goldfish have two.  This helps defend the theory of evolution, as it shows how humans have changed from their common ancestors (thus suggesting progressive adaptation). 

-Which two organisms diverged from their common ancestor most recently?  Least recently?
Most recently- Human/chimp (due to the most ancestral nodes.  This means that the current species we know took the longest to develop/emerge).
Least recently- Wallaby/mouse (due to how they developed into their current forms rather quickly, and remained that way over long periods of time.  There are longer periods of no adaptations, as signified by longer, nodeless lines).

-How would the tree above change if the beta globin gene for a kangaroo was added?  The kangaroo would be rooted right next to the wallaby, potentially as a recent ancestor.  This is because they are both very similar (they are marsupials with pouches).

5.) It is important to understand that the trees you generated using bioinformatic tools are based on sequence data alone.  While sequence relatedness can be a very powerful predictor of relations between species, other methods can be used in sequence homology as well.  Describe three other methods that could be used to determine evolutionary relationships:

  • Geographic location.  Where the animals are located on a map, in relation to each other, can help determine evolutionary relationships.  This would be based on the type of environments that the species live in, how they relate around the world, etc.
  • Physical Features.  If the species have similar features that look alike, then this could be used to determine evolutionary relationships.  It would be easy to watch physical features change over time, and see how some species are related based on how those features are used/developed.  This would include things such as coloration changes, fur, etc. and could be seen through fossil records.
  • Behavior.  How the animal species interact in their environment may be clues to their evolutionary relationships.  If certain animals act in similar ways, for similar reasons, then an argument may be made that they are related (to an extent).  This would be based on studying animals for a long period of time to learn their behaviors and actions.  If nothing else, this evidence could lead to predictions of how species may have acted.

I’m sure as we continue to explore the world of Molecular Evolution, we will continue to find many groundbreaking things.  As for now, take a moment to think:  the animals you learn about on TV may be more closely related to you than you think!

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Transformation Lab

Out of all of the labs that we have done in Biology this year, this one is definitely one of the coolest!  So, being the incredibly lucky person that I am, this is the one lab that I am absent for in class!  You can stop laughing now.  Anyway, regardless of my misfortune, I was lucky enough to be able to see the results of this lab, and learn about what happened.  After all, the blog posts must go on!

The concept, and title, of this lab are very simple: transformation.  This lab is all about taking a piece of DNA, which contains a certain characterstic, and inserting it into a cell of bacteria.  The bacteria will then, hopefully, read the DNA as one of its own, and produce the proper proteins for it.  Then, assuming all goes to plan, the bacteria will display the characteristic that was inserted into the bacteria cells.  Sounds pretty cool, right?  Wait until you hear that the characteristic we inserted will make the bacteria glow!

Before we go any further, we need to discuss the key component of this lab: the DNA.  What is inserted into the bacteria cell is what is known as a plasmid (see diagram below).  Plasmids are loops of DNA material.  The DNA is still in its double helix form, of course.  The only difference is that its overall shape is a circle.  There are a few components that are attached to this DNA loop.  For one, there is an Amp Gene.  This gene resists the antibiotic ampicillian (which, as you know, antibiotics kill bacteria).  The Amp Gene allows the cell to survive off of ampicillian, to some extent anyway.  The other important feature is the Green Gene (GFP).  Attached to the top of the GFP is a Promoter.  The Green Gene is what causes the bacteria to display a fluorescent effect and glow.  But, the only way for this gene to work is if the Promoter is working.  The Promoter detects arabinose sugar from inside the structure, and uses it to start producing genes.  If there is no sugar, than the Promoter won’t start making GFP genes, and the bacteria won’t glow!

Now that we have this understanding of what we are working with, it was time to perform the lab itself.  As I mentioned earlier, I was unable to physically do the lab myself.  However, we were given a very elaborate instruction sheet that contained each step to executing this lab.  As I won’t explain every detail, I will give you a quick summary.  The steps of this lab are as followed:

  • Insert transformation solution into two test tubes, labeled +pGlo and -pGlo.
  • Let sit on ice.  Then, using a sterile loop, insert a single colony of bacteria into both test tubes.
  • Retrieve a piece of “film” from the plasmid DNA container, and insert into the +pGlo test tube.  Let sit on ice.
  • From the ice, move to a 42 degrees C hot water bath, for approximately a minute.  Then back to the ice.  This is known as heat shock.
  • Insert LB nutrient into both test tubes.
  • Spread each test tube evenly across two agar plates (two each).
  • Leave in incubator over night, set at temperature of 37 degrees C.  Return the next day to view results.

The four plates were labeled “-LB”, “-LB/Amp”, “+LB/Amp”, and “+LB/Amp/Ara”.  The LB stands for the nutrient given in the second to last step.  Amp refers to the presence of ampicillian, and Ara refers to the presence of arabinose sugar.  The – or + signs refer to whether a plasmid was introduced or not.  The + means yes, and the – means no.

The plate labeled “-LB” showed evidence of an increased bacteria colony size.  This was expected, as these were normal conditions (nothing was influencing it).  The plate labeled “-LB/Amp” (with the ampicillian) had no bacteria on the plate.  This is because the bacteria, with no plasmid, stood no chance against the antibiotic.  The next plate, labeled “+LB/Amp” (with ampicillian and plasmid), also showed a growing colony.  However, they did not show any signs of glowing properties.  The cause is due to the fact that there was no sugar to excite the Promoter.  Finally, we have plate “+LB/Amp/Ara”.  As you might expect, the bacteria here did grow, and they also were fluorescent under UV light.  The pictures of the results can be seen below.

Note: Be sure to compare the two + plates that contain the plasmid.  You can see how one glows more than the other under UV light.  That is what the experiment is all about!

This lab was exciting as it shows that it is possible to transform, and alter, the DNA of bacteria!  Right now, scientists are working with these same methods on larger creatures, such as cats and mice.  These experiments will open many new doors in the world of genetics.  Who knows what unusual sights we will be seeing once scientists unlock the secret to inserting DNA into creatures!  For now, however, we must be happy with our glowing bacteria!  Of course, every major achievement must start somewhere!

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Genetic Testing: Would You Want to Know?

Article:  http://www.usatoday.com/news/health/story/2012-04-09/genetic-testing-huntingtons-disease/54475708/1

Huntington’s Disease, in my humble opinion, is one of the most difficult diseases to tolerate.  The individual diagnosed with such a disease is forced down a road of pain and horrible symptoms.  The family of the diagnosed must stand by, and suffer as their family member slowly dies.  For those of you who don’t know, Huntington’s Disease is a fatal, neurodegenerative disease.  Symptoms include loss of coordination, increased jerky muscle movements, dementia, changed behavior (psychotic and depressed), and inability to be independent.  As if that isn’t enough, this disease can start surfacing around age 30.

The link above is to the inspirational story of Kristen Powers.  She is an 18 year old girl whose family has had a history of Huntington’s Disease.  Due to the fact that her mother had the disease, Kristen has a 50/50 shot of having it also.  What separates Kristen from any other patient is her active attitude and willingness to make a difference.  She is working on a documentary, about her own life, and the impacts Huntington’s Disease has on her and her family.  As she strides toward this goal, she poses one question:  Would you like the opportunity to know about your future, and the potential diseases you will develop in your lifetime?

This question has been made possible by DNA testing.  The Human Genome Project, having mapped out the diseases and traits associated with the entire set of chromosomes in the human body, has made this knowledge a reality.  On one hand, there are positives to knowing your fate.  You can ensure you live the life you want to live.  You can ensure your children won’t be affected, or take preventative steps to helping yourself.  After all, knowledge is power.  On the other hand, knowing can be a bad thing.  You will have the information looming over your head.  There is a chance to make unsafe or bad decisions.  Insurance agencies or companies may not accept you, or you may not achieve what you originally planned.  After all, you cannot unlearn something once you know it.

Kristen has decided that it would be best to know whether she has Huntington’s Disease.  She goes to be tested on May 18th, 2012.  Personally, I wish her the best of luck!  The important message that she stresses is to be sure to live life to its fullest.  Enjoy every moment, and always embrace the “inner kid” inside of you (whether you are diseased or not)!

So now, I ask you: what would you do, if you were in this situation?  The results would change your life completely, one way or another.  This is a tough question that many of us don’t want to have to face.  Take some time to think about it, though.  Right now, your future is unknown.  Would you want to change that?  If given the choice, would you want to know which genetic diseases you will encounter during your lifetime?

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Now Hiring: DNA Detectives! (DNA Fingerprint Webquest)

Everyone at some point in their lives dreamed of being a detective.  There was something thrilling and exciting about using clues to solve mysteries, and bringing those responsible to justice.  As technology exploded onto society, the mysteries and crimes became more advanced.  Luckily, so did the methods of collecting clues.  For those who are achieving their life goal of being a detective, collecting evidence at a crime scene has never been easier!  Detectives today can take the smallest piece of organic material (such as hair or blood), and find the person it belongs to.  How is this possible?  DNA.

When detectives find organic evidence at the scene of a crime, they send it in for DNA testing.  This process requires taking the sample, and separating it into sections of different lengths through enzymes.  Next, the lengths are organized through a process known as gel electrophoresis.  The end result is a series of bars that show a sequence of DNA.  Using this sequence, scientists and detectives can compare it to the DNA of their suspects, to see if they match.  Criminals never expect that they would be leaving a DNA fingerprint at a crime scene!  Many are caught by this unrefutable evidence.  Many of the wrongfully accused are exonerated, as the evidence proves their innocence.

This blog post begins with Dr. Sam Sheppard, a man accused of murdering his wife.  He was sentenced to jail for life over his crime.  Years later, Dr. Sheppard’s son, also named Sam, has come back to argue his father’s innocence.  The questions you see are designed to bring forth the key aspects of this historic trial.  (See for yourself! Article can be found at: http://www.pbs.org/wgbh/nova/sheppard/).  This time, DNA testing will be used to find out the truth behind the Sheppard murder trial!

1.) In your opinion, what role (if any) did newspaper stories and editorials have in the outcome of the original trial of Dr. Sam Sheppard?

The press had a major role in this trial.  Throughout this entire ordeal, the press was there to get the scoop.  Sadly, they seem to have caused more complications than they were worth.  For one, many of the headlines of news reports were very biased.  They would read “Doctor Balks at Lie Test”, or “Why Isn’t Sheppard in Jail?”.  Most of the time, these articles were chalk full of false, or misinterpreted information.  This would influence not only the officials (for example, Dr. Sheppard was arrested shortly after the second headline I mentioned was released), but also the public.  Countless editorials, rumors, cartoons, inuendos, and articles were written about the case.  As if this wasn’t bad enough, all of his court trials were fully publicised.  His son, Sam, was unable to attend his mother’s funeral, as the press was so overwhelming.
As a whole, the press effected the situation in a negative fashion.  They were causing Dr. Sheppard to lose his sense of privacy, as well as turning him into a public “bad guy”.  As a whole, this really impacted him and his remaining family.  Inversely, when his trial was revisited, public releases such as the movie ‘The Fugitive” and Paul Holmes’ book “The Sheppard Murder Case” started to support him, rather than cause him trouble.

2.)  What is the function of the restriction enzymes in DNA fingerprinting?

The function of the restrictive enzymes used in DNA fingerprinting is to cut the sample of DNA into segments of different lengths.  For example, say there is the pattern “GATTCTA” within a segment of genetic material.  There is a certain enzyme that, whenever it finds that pattern, will attach and seperate the material at that point.  There are many different types of enzymes that break the sample at different points.  As the patterns occur differently in each person, the end result (their DNA sequence) will be unique.

3.)  What is the function of  the agarose gel electrophoresis step?

The function of the agarose gel electrophoresis step is to separate and organize the segments of genetic material according to lengths.  An electric current runs through the gel. Genetic material has a slightly negative charge. As a result, the material will be attracted through the gel to the positive side of the current.  The gel acts as a filter of sorts, allowing smaller molecules (shorter strands) to travel farther.  The end result will be the strands being lined up, according to size.

4.)  Why is a nylon membrane used to blot the DNA?

A nylon membrane is used to blot the DNA because it is a successful absorbent material.  The gel with the DNA segments is too thin and too fragile to handle.  So the membrane, being more durable, is placed over the gel.  DNA is then sucked up onto, and impresses upon, the membrane.  Then, radioactively labeled probes are added to the membrane, as they attach to certain sequences.  This will help in identifying the components of the sample.

5.)  What does a dark spot on the X-ray film indicate?

A dark spot represents where the probes have attached themselves on the DNA fragments, which is on the nylon membrane.  This represents the DNA “fingerprint”.  The information gathered from the X-ray film is then compared to the DNA gathered from various suspects, to help solve the mystery/crime.

Thanks to the case of Dr. Sam Sheppard, we now have a better understanding of how the whole DNA fingerprinting process works.  Now we know how a sample of organic material can be used to solve a crime.  This blog post is now going to switch gears, and focus on another case.  The new case is about a man named Ronald Cotton, who was wrongfully accused of rape.  Among the people listed in this discussion are DNA expert Peter Neufeld and Cotton’s lawyer Barry Scheck.  We will apply what we learned from Sheppard’s case to Cotton’s case, and see how DNA testing can be used to exonerate (free) an innocent man!

6.)  What evidence was initially used to convict Cotton?

The evidence that convicted Cotton was not very definitive (sadly, it was enough to send him to prison).  This evidence includes a victim making identifications in both photos and a police line up, a flashlight used in the case was similar to one Cotton owned in his house, and the rubber consistancy of Cotton’s shoe matched that found at the scene.  Needless to say, this evidence is not very worthy or substantial.

7.)  What did the DNA evidence show?

When DNA testing was applied, the evidence, found on both underwear and private region of a victim (from semen), concluded that Cotton was innocent.  The DNA of Cotton did not match the specimen found at the scene.  Ironically, it matched a man from prison who openly admitted to the crime (the jury was not able to hear his confession, however, to validate his claim).

8.)  How could DNA fingerprinting be used to prevent a false conviction if a case like this was being tried today?

DNA fingerprinting can be used to provide a definitive and conclusive answer as to who is responsible for the crime committed.  By going straight to DNA testing, many false convictions can be prevented.  Had this occured with the Cotton case, Cotton would have been able to avoid 10 and a half years of prison time (he was sentenced to life, but only served the given amount before being proven innocent).  By properly using these tests, conviction rates can be more accurate!

9.)  What percentage of convicts are unjustly convicted of sexual assault cases, according to Neufeld and Scheck?

DNA expert Neufeld, and Cotton lawyer Scheck, both agree upon the number of unjustly convicted convicts in sexual assault cases.  They say 25% of the convicts are being exonerated, having been proven innocent.  This number is extremely high!  Plus, it shows just how frequently the wrong people are punished, while the guilty are free (which is disturbing to think about, in my opinion).

10.)  The O.J. Simpson trial was one of the most visible trials that attempted to use DNA evidence.  In the end, the DNA evidence was not satisfying to the jury, who acquitted Simpson.  What do Neufeld and Scheck believe about the impact of the O.J. Simpson trial on the use of DNA evidence?

When looking back at the O.J. Simpson trial, a case that made DNA testing famous, Neufeld and Scheck have very similar things to say.  They say that this case shows the tremendous potential within the technology we have today.  This technology is very important, as it holds the power to decide the fate of some people.  Also, Neufeld made a point ins aying that this “is not a law of science, but more of an applied science”.  This means people have to be involved to apply the technology to the case.  In turn, since people are involved, mistakes can happen.  It is very important to be cautious, and apply this science wisely.  Scheck said that many innocent people, using only a fraction of the resources O.J. Simpson used in his case, could be exonerated.  This represents the responsibility involved in using this effective method during investigations.

As you can see, DNA testing is a very crucial component in criminal investigations.  We have looked into Dr. Sam Sheppard, and discovered through his case how DNA testing works.  Then we applied this knowledge to Ronald Cotton’s case, and saw how this process can be used to save an innocent man.  Clearly, the outcomes of many cases will be drastically changed by this advanced region of science.  All that is needed is for a detective to find a single, DNA fingerprint!

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Bacterial I.D. Lab

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