The Sequencing of DNA, Old School

I really like DNA sequencing. There's something about it that just interest me. Maybe it's that you can "read" people, or the thought that you're seeing something that different people don't ever get to see. And it's all possible today because Frederick Sanger saw what other people hadn't seen before. We did a worksheet earlier this week and you can see the data I collected from it above.
The worksheet had us reading DNA and protein sequences from 3 different patients and comparing them to a normal sequence of DNA/protein. A normal sequence would be seen as:

                   "ATG GTG CAC CTG ACT CCT GAG GAG AAG TCT GCC"

At least according to the worksheet, ;). The proteins were shown as this:

                   "Met Val His Leu Thr Pro Glu Glu Lys Ser Ala"

Don't worry, it starts getting interesting from here. As you can tell from the graph above, none of the patients have a DNA sequence that perfectly matches the norm. Abby and Bob have the most "normal" of the sequences, and it may lead you to believe that they are completely ok, just a little different. But when you look at Carol, you think,"Oh wowza, she's a mutant!"

But in reality, all of these patients have a problem. With Abby, she is only has one base change, right at the first GAG/Glu. Her's is instead GTG/Val. This is called a "point mutation". It doesn't seem like a single mutation could mess anything up, but it does. It all comes down the protein sequence. The Glu is positively charged and goes along with the sequence well, but the Val is hydrophobic. That means it will probably mutate the sequence. This is seen in people with cystic fibrosis. But she could not have! :D

With Bob, he has a Truncation mutation. He only has one changed base, like Abby. But his AAG/Lys base is a TAG/stop instead. That means that his sequence stops early, 3 early in his case. This makes the protein too short.

Carol probably has skin cancer. Her type of mutation is called a Frameshift Mutation. She has a normal sequence but is missing, it's completely gone, her T from the ACT/Thr base, so instead it is a ACC/Thr. This can be caused by radiation from the sun, or other things that could kill off one of her letters.

It makes me pretty happy that I can read all that in a single sequence. It's amazing all that can happen in a human body.
Ok, now you can take a step back, stretch, and wipe that yawn off your face. You learned something!

Human Chromosome Webquest blog

These questions have been taken from a webquest I've been doing in Biology. I researched Narcolepsy and I think it's pretty interesting. I also looked at insomnia, but that isn't very important but it was neat to finally know what went on with it. Watch the Prezi!!!

Insomnia on Prezi

 *What disease did you choose and what gene is/genes are associated with this disease? I chose Narcolepsy to research. The prepro-orexin gene is associated with Narcolepsy.

*On what chromosome are these genes/is this gene located? The prepro-orexin gene is located on the chromosome 17q21-22.

·      When was the disease first reported in the scientific literature? In the 1990’s.

·      What are some of the clinical symptoms of this disease? Daytime drowsiness, cataplexy (sudden weakness of muscles), and occurrences of REM during wakefulness are the clinical symptoms of Narcolepsy.

·      What lab findings (gene function or biochemical data) are associated with the disease? Narcolepsy appears at random instead of being inherited. It was thought that the cause of narcolepsy was because the body’s immune cells were attacking neurons that secrete hypocretin.

·      What type of inheritance governs this disease? There is no specific inheritance that deals with this disease. Instead it is appears randomly.

In Sickness and Health!

In Biology we've been working on the sickness and health activity where we work at being genetic counselors. The following questions are each of the stages that i passed to finish the activity. Check out the website here.

Questions

1. Do autosomal dominant disorders skip generations? No because they need to have a female carrier. 
2. Could Greg or his mother be carriers of the gene that causes myotonic dystrophy? His mother could be a carrier but Greg could not because he is male.
3. Is there a possibility that Greg’s aunt or uncle is homozygous for the myotonic dystrophy (MD) gene? Yes.
4. Symptoms of myotonic dystrophy sometimes don’t show up until after age fifty. What is the possibility that Greg’s cousin has inherited the MD gene? There is a 50/50 chance that Greg's cousin inherited MD. 
5. What is the possibility that Greg and Olga’s children could inherit the MD gene? There isn't a chance because Greg can not be a carrier without having symptoms of the disease. 

Questions

1. What are the hallmarks of an autosomal recessive trait? There are five hallmarks of autosomal recessive inheritance:
   1. Males and females are equally likely to be affected.
      
   2. On average, the recurrence risk to the unborn sibling of an affected individual is 1/4.
      
   3. The trait is characteristically found in siblings, not parents of affected or the offspring of affected.
      
   4. Parents of affected children may be related. The rarer the trait in the general population, the more likely a consanguineous mating is involved.
      
   5. The trait may appear as an isolated (sporadic) event in small sibships
2. What does consanguineous mean? Why is this concept especially important when discussing recessive genetic disorders? It means people coming from the same ancestor, this is important because if two people are related then it is more likely they will receive the disease.
3. What is it about the inheritance pattern of factor VIII deficiency seen in Greg and Olga’s pedigree that point toward it not being an autosomal recessive trait? The pattern seems to stay mostly in boys, making women carriers. 

Questions

1. What are the characteristics of X-linked recessive inheritance? The characteristics are that they are only passed on to boys and the disease does not affect women.
2. Why does a son never inherit his father’s defective X chromosome? The mother has to pass on the gene to her son.
3. What is required for a woman to display a sex-linked recessive trait? She would have had to inherit it from her mother.
4. Return to the pedigree drawn earlier for Greg and Olga; mark those persons who are carriers of the factor VIII deficiency gene. Link to Picture
5. What is the chance that Olga carries the gene for factor VIII deficiency? Calculate the probability that she will pass it to her offspring. Will male children be affected in a different way than female children? There is a 50% chance that she will pass the VII deficiency to her children.
6. What is the chance that Greg carries the factor VIII gene? Can he pass the gene on to his sons? His daughters? How will each be affected? There is a 25% chance that he will the gene onto his children. He wouldn't be able to pass the genes onto his children.

Questions

1. What is the second equation? 1 of 3,000
2. The incidence of cystic fibrosis in Hispanic Americans is 1/4500 while in African Americans cystic fibrosis is seen in 1 of every 15,000 births. What is the carrier frequency for each of these populations? 1 in every 3 women.
3. What is the probability of two Hispanic Americans having a child with cystic fibrosis, given that there is no history of the disease in either’s family? Zero percent.
4. Carol is an African American woman who does not suffer from CF. Both of her parents are healthy but her brother has cystic fibrosis. Carol is planning a family with her husband Marcus, who is also African American but who has no history of CF in his family. What is the probability of their having a child with CF? 50%

Questions

1. What are some of the risks and benefits of genetic testing as it relates to legal (not medical) issues? Risks of genetic testing are that the child could miss out on job opportunities or be prejudiced. Benefits are that they can catch the disease early on and help. 
2. Do you think an unintended consequence of genetic testing could be that people would be less liable to seek medical care out of fear that they could later be denied life or health insurance? What laws should be used to govern the use of genetic data of this type? Yes, that is a viable consequence. A law should be made to provide everyone with equal insurance rights. 

Eugenics!

The definition of eugenics is the following. (Taken from dictionary.com.)

–noun ( used with a singular verb )
the study of or belief in the possibility of improving the qualities of the human species or a human population, especially by such means as discouraging reproduction by persons having genetic defects or presumed to have inheritable undesirable traits(negative eugenics)  or encouraging reproduction by persons presumed to have inheritable desirable traits (positive eugenics).

For the past week or so we’ve been working on eugenics. It’s interesting to think that people used to be sterilized (neutered) because of a defect that had a possibility of being passed on in a mother or father’s chromosome. I think this is a little bit unnecessary because sometimes certain genes aren’t passed on. There is always a chance that the child won’t receive a gene for brown eyes if the mother’s eyes are dominantly blue and the father’s eyes are brown with a recessive gene for blue eyes.

A little history on eugenics now, yes? Eugenics originates in America after the Civil War. During reconstruction many immigrants were moving in. There was a decline of births in elite families and an incline in poor families. Social Darwinism was on the incline also. It basically says “survival of the fittest” and it was taken from there that the elite were the fittest. It was decided that because much money was spent on the “degenerate” poor, sterilization would be the best option for the survival and betterment of our race. They based a lot of their work on IQ tests and behavior, such as criminal activity, prostitution, and social standing. Richard Dugdale did research on a family of 700 of these degenerates. He thought that the degeneration may have been based on poor environment, but when the degenerate family was mixed with an elite family, the “degenerate” genes were passed on. From there, increased marriage restrictions occurred, and the 8th of the 18 suggestions of dealing with these types of genes was euthanasia. People were sterilized unfairly, people like Carrie Buck, who was put in a home for the “feeble-minded” with her mother, both were accused of being promiscuous and imbeciles. Carrie’s seven month daughter was also labeled feeble-minded, although later grades showed the opposite. Hitler’s eugenics seem much crueler, as he sterilized thousands of Jews and Gypsies, preferring a blond and blue eyed race. But the United States also preformed involuntary sterilizations on criminals in prisons. I can’t determine which could be worse, as they’re both involuntary. But I believe Hitler took his too far. Way too far.

I really don’t agree with eugenics, like Punnett said at the first meeting of international eugenics in 1911, “Except in very few cases, our knowledge of heredity in man at present is far to slight and far too uncertain to base legislation upon.”

They really didn’t know enough about a person’s genetic structure to be allowed to kill or neuter said person. I don’t believe that in any way should it be justified by a few defects that may not even be passed on. A few days ago, I tested my mother and sister with the little strips Mr. Ludwig handed out. They could (much to my glee) taste them. My mom said that it was a decent taste, but I think that may have been the result of her previous gum chewing. I didn’t warn my sister about what I was giving her and got a wonderful reaction from her. I had the same reaction. What does it mean? Would it have meant back in the day that we needed to be sterilized? (Just so you know what I’m talking about, it means “neutered”.) People were sterilized for the silliest reasons. At one point, it was believed that you could have a predisposition to be a criminal if you father was due to a gene that could be passed on. I heard once that you have a predisposition to like broccoli. I guess that makes sense seeing as how half the population hates vegetables. What if we sterilized people who didn’t like broccoli? I suppose it would cut down on the amount of picky children but what if all those people had  gene that made the body more susceptible to cancer cures? What if they could stop radiation? Then it’d be horrible to make sure they didn’t have any children.


Take a look at the eugenics archive to see what I'm talking about :).

Cloning!! And More Meiosis

I have to say, I love this Biology Unit. I love learning about the mechanics of the machine that is our body. It's interesting (to me at least) to know that meiosis is what starts the baby making process! Learning about the 18 Ways to Make a Baby was really neat, and one of the ways was cloning.

Introducing, the amazing Cloning Charlie! He uses his super hero skills to divide and conquer evil. Unlike the process that goes on in cloning animals, Charlie's super powers could be compared to the production of sperm or plant mitosis.

 So, what goes into the animal cloning process? I'm not quite sure myself, but let's look at how a mouse is cloned and try and determine what in the heck is going on.

1. Meiosis here. That is how the regular splitting of cells occurs. After a woman's egg becomes fertilized it moves onto meiosis 2, the fetic and embryonic stages. But with cloning, you are going to have to exact same DNA as the creature you took the DNA from.  From here on is the recipe for cloning.

Ingredients

1 Mouse Somatic Cell
1 Mouse Egg
1 Surrogate Mouse
1 Dividing Agent (mouse sperm)

1. Extract a somatic cell from the 1st mouse. Harvest the egg from the 2nd.
2. Remove the nucleus from the egg cell. Replace with the nucleus from the somatic cell.
3. Fertilize the new egg cell.
4. Implant the egg into the surrogate mouse.
5. Hurray for babies!

A Blog About Meiosis

I think new borns are extremely weird looking. Like little aliens. At an embryonic 12 weeks, they are even more frightening. I once told my friend that I thought at that point in the gestation period they looked like predators. Like Alien Vs. Predator. They frighten me. It's hard to believe that at one point that weird little red thing was once just an even littler gamete. Beginning as gametes, then they're a zygote with a diploid, then it turns to a haploid cell. It's like mitosis, but this creates what become little kids who become adults who make more little kids. So I was curious and decided to research how to make a baby!

Step 1 (AKA Prophase 1): A diploid cell splits, making four haploid daughter cells (this is what creates genetic diversity). The paired chromosomes are called chiasmata, which are caused by genetic recombination.

Step 2 (Prometaphase 1): One kinetochore (the protein structure where chromosomes attach) forms for each chromosome and the chromosomes begin to move.

Step 3 (Metaphase 1): The two chromosomes, now bivalents, line up at the metaphase plate. At this point there is a 50/50 chance that  the daughter cells will get either the mother or father's feature.

Step 4 (Anaphase 1): The daughter cells become haploid cells after chiasmata separate (chiasmata is where the cells exchange DNA).

Step 5 (Telophase 1): The cell either reforms or starts meiosis 2.

Step 6 (Cytokinesis): This is where the two daughter cells form.


There we have it, meiosis! This process keeps happening in men, but in women it doesn't continue until an egg is fertilized. Which will be continued in a separate blog on.... meiosis II.... DUN DUN DUN!

Stem Cell Research

Important Terms:

Cell-based therapies: stems cells are induced to differentiate into a specific cell type.

Differentiation: where a unspecialized cell acquires the specialized features of a specific cell.

Embryonic stem cell line: embryonic stem cells that allow proliferation without differentiation for months to years.

Proliferation: the expansion of the number of cells from two identical daughter cells.

Plasticity: ability to be different.

Pluripotent: Having the ability to give rise to all the various cells types of the body.

Answer the following questions:

1. What are the unique properties of all stem cells?  Explain in your own words what each property means.

Stem cells are able to proliferate; splitting and reuniting, can become any cell, and can differentiate; can become a specific type of cell.

2. What are the two main kinds of stem cells used by researchers?  What are the major differences between the two types in terms of their sources and usefulness to researchers?  Give examples for each type of stem cell.

The two main kinds of stem cells used by researchers are embryonic cells and adult stem cells.

3. List some of the diseases that scientists think may be treated using stem cell research and suggest how stem cells might be used to treat each disease.

Scientists think that stem cells may be used to cure diseases such as cancer and birth defects.

4. What are the necessary characteristics that laboratory-manipulated stem cells will need to have in order to be successfully used in cell-based therapies?
The stem cells need to be unspecialized.