Posts in: MB231

Week 3: HIV Tomatoes?

Okay, so this title clearly requires a bit of context but don’t worry it all comes together in the end. Let’s start by talking about GMOs. Yikes. But what exactly is a GMO? Dubbed as “Frankenfood” it undoubtedly has a negative reputation among most today. But what is it that incites so much fear in us about the idea of “genetic modification”?

Let’s face it: Colorado tomatoes are nothing to ride home about. That’s probably because they’re from Florida, or California and have been picked while they’re still green so they don’t over ripen on the truck ride to Colorado Springs. But being picked so early has its downfalls; theses premature tomatoes have failed to receive nutrients and proteins that make them flavorful.

At one point, scientists had proposed a clever way to resolve this problem. Let’s examine some background information first. DNA is transcribed into mRNA, which is translated into proteins, which perform a myriad of functions in cells. A long time ago it was discovered that plants had a pretty nifty defense mechanism against viruses: they are able to recognize double stranded RNA viruses and target them for destruction. Back to our tomato situation: fruit ripens due to a gene coding for the expression of ethylene. When you put a pre-ripe fruit next to a banana to ripen, it’s because the ethylene secreted by the banana will stimulate ripening. Scientists figured that if they could somehow slow down the expression of the ethylene gene in a tomato, it would slow ripening. This would allow tomatoes to be picked when they were riper and not over ripen before reaching the store. After the tomato transcribes the ethylene DNA into mRNA scientists engineered the tomato to make another mRNA from the same gene that would bind to the first mRNA. What do we get? Double stranded RNA, which will be seen as a virus and degraded. Bottom line? Less mRNA means less ethylene protein translated: slower ripening.

This idea seems pretty clever, plausible, and benign. Yet it was not taken quite as well. Double stranded RNA? They’ve put a virus in a tomato. HIV is an RNA virus right? Does this tomato have HIV?

Now I’m not saying all GMOs are completely harmless but I think it’s important to understand what something actual is before forming a definitive opinion. I guess my point is that GMOs and non-GMOs aren’t necessarily antitheses…maybe more like tom-A-to tom-AH-to.

Week 2: Genes are Accommodating

While it seems logical to think that gene expression is a fixed, unchanging thing, like the Rosetta Stone of human biology this isn’t necessarily the case. Genes are often viewed as sequences written into our DNA that remain unaltered through our lives, yet today we spent the majority of class time disproving this idea.

As it turns out gene expression can be influenced by many factors, one of the main being one’s environment. Different stimulus in our surroundings can have a great impact on our genes such as causing one section of the genome with specific genes to be replicated multiple times, a phenomenon known as gene amplification. Think of it as a supply and demand type situation. Genes code for proteins, which perform specialized functions; as the need for a protein goes up, our bodies respond by supplying more copies of the corresponding gene. For example, when small mammals are exposed to heavy metal (not just the headbanging kind) there is a significant increase in replication of a gene coding for a particular protein that will remove metal from the bloodstream. Conversely, sometimes it may be desirable to prevent gene amplification. Take chemotherapy as an example. Chemotherapy is generally given in large doses. This helps to prevent cancer cells from undergoing gene amplification and subsequently being able to protect themselves from treatments aimed to destroy them.

So at this point in class we’ve firmly established that gene expression is malleable. But how does this idea apply to things that are more relevant to the general population (i.e. something other than disease treatment or metal exposure)? Well there’s another mechanism in the cell that can result in the generation of genetic material, a process called gene duplication. When there are multiple copies of the same gene this means that one copy could theoretically develop a mutation and the cell would still have one functional copy. As it turns out this is one way in which new genes come onto the playing field. It’s kind of like if you have your best player bat cleanup so top of the line you have more room to experiment.

Needless to say, by now I’ve become more than convinced of the incredibly adaptable nature of gene expression. Maybe if the human genome is anything like the Rosetta Stone it at least has some extra carving space and an eraser.

Week 1: A Peek into the Genome

Imagine a stack of textbooks, packed like sardines with words, and standing four stories high. Now think about being given the task to find not one page, not one paragraph, but one word. Seems like an impossible task. To some extent, this is comparable to the task scientists were charged with in the late 1980s while attempting to pinpoint the location of a mutant gene responsible for causing cystic fibrosis. When I initially heard this daunting analogy I could scarcely imagine any way in which one could accomplish this job. And yet in three hours, minus time for water and snacks, our professor was able to give us a pretty good idea.

Our DNA is made up of different bases abbreviated with letters, which are wound around proteins that make up structures called chromosomes. And incredibly, some three billion letters are all able to fit into 23 pairs of chromosomes, which reside happily in the cell of each nucleus in each cell. I find sometimes in class as we work through problems, attack complex scenarios, and delve deep into peculiar topics it’s easy to get caught up in minute details that demand your attention and forget the sheer vastness and breadth of genetics. But when I take a step back it’s pretty astonishing to me, even as a science major, that genetics can weave its way into nearly any subject imaginable. And I guess that’s obvious, I mean biology is the study of life after all, but its scope and relevance is pretty impressive.

It’s T-minus 5 minutes to the start of class and I’m anxiously filtering through yesterday’s information trying to make room for today’s. Class typically begins at 9:00 am and lasts until lunchtime. Rather than watching slides on a PowerPoint or reading from a textbook our professor engages us in often seemingly different topics which somehow always manage to come down to one thing: the gene, a pair of genes, or some combination of genes. From hypercholesterolemia to baldness to chocolate and yellow labs I usually manage to leave class with more questions that I came in with. But one week in and I’m trying to accept that maybe that’s the whole idea of genetics: to realize how much there is and how much is still widely unknown.

Ethics of Genetics

Trisomy – Possession of 3 copies of a chromosome instead of the normal 2.

Trisomies occur in non disjunction events: when chromosomes do not properly separate during the production of gametes (egg or sperm). In that scenario, an embryo conceived from gametes with improper number of chromosomes may be missing or have more than the normal number of chromosomes. In these cases – spontaneous abortions usually occur because the embryo is not viable due the lack of or the abundance of the chromosome in question. A very common disorder that results from a trisomy is trisomy 21 – Down Syndrome.  In autosomes, a trisomy usually produces a non viable embryo. However, if a trisomy occurs in the sex chromosomes, the embryo is viable will most likely develop. There are a bunch of different variations of the trisomies.

In a normal biological female and male, the sex chromosome are XX and XY respectively. However, a trisomy can cause XXX, XXY, or XYY to occur. In these cases, the people that possess these combinations can live a relatively normal life.

People with XYY have a disorder called “Jacob’s Syndrome”. Jacob’s Syndome has also been dubbed “XYY Supermale”. The reason why is that the extra Y chromosome causes a dosage problem. Even though females may have two copies of the XX chromosome – one is inactivated to compensate for the dosage issue  that might occur. However, the extra Y in this case, can not be inactivated. The dosage issue caused by the extra Y can have dramatic effects.

The following signs may be an indication that a young boy or teenager has XYY Syndrome:

  • an autism diagnosis
  • an inability to grow facial or body hair
  • attention difficulties
  • delayed motor skill development, such as writing
  • delayed or difficult speech
  • delayed or absent puberty
  • emotional or behavioral issues
  • gynecomastia, or enlarged breast tissue
  • hand trembling or involuntary muscle movements
  • hypogonadism, or low testosterone levels
  • hypotonia, or weak muscle tone
  • learning disabilities
  • low energy levels
  • small penis
  • small, undersized testicles
  • taller than average height
  • weak bone

taken from: http://www.healthline.com/health/xyy-syndrome#Symptoms4

The reason why we spent quite a bit of time on this particular syndrome was that, in the past there was a huge issue about association of genetics and behavior. There was study done in the early 20th century with looking at the karyotypes of prisoners. They found that in the prison population compared to the general population, the prevalence of Jacob’s Syndrome was slightly higher. This was later debunked with further research. However, it brought about the debate on whether or not genetics predetermines behavior. Professor Ralph Bertrand presented the question of whether or not it was right to test for Jacob’s Syndrome at birth just like one would be tested for Cystic Fibrosis or Phenylketonuria. He asked about the rightness or wrongness of such testing because the results may then change the way the parents and society treats children who have been labeled at birth to be “future criminals”. Some students said it was wrong to do such testing because genetics is not destiny. Some students said the test should take place in order to give children with this disorder the proper care and education. Such subject exist in the realms of ethical purgatory. In the end, behavior is so complicated – that the explanation of having an extra Y predetermines criminal activity is simply inadequate.

 

Studying Genetics with Context

End of Week 1

Often times, I feel as if we forget that science is often closely flanked by social issues. So far in the course, the ethics of science and in particular, genetics has come up again and again. Professor Ralph Bertrand constantly reminds us to think of the bigger picture and that science should not be studied in a vacuum. He often asks “Why is this important? Why are we teaching this material in the first place?”  The answer to these why questions are quite selfish. After all, we live in an anthropocentric society. Studying genetics allow us to better understand how living organisms thrive and propagate, how to mitigate or solve genetic disorders, and how to better the human condition.

On the second day, we had a discussion on genetic mutations and genetic modification. As you all know, the discourse on genetically modified organisms(GMOs) in popular media is not particularly informative nor helpful. A classmate had brought up the question of where you would draw the line in calling something a GMO, afterall nothing is inherently “natural” about the food we eat. Is artificial selection or selective breeding consider part of creating a GMO? Because for a lot of the foods that we eat – corn, almonds, tomatoes and etc, were inedible before selective breeding. Almonds contained a level of cyanide that would have killed us. The precursor to modern corn is a tiny grain called Teosinte, but after years of selective breeding, had finally become domesticated around 6,000 years ago. Is the line drawn at DNA splicing, DNA insertion, or DNA deletion? Is the backlash on GMOs due to the “unnatural” way humans have intervene with “nature”?

In addition to discussing genetics and its role in society, we’ve review the basic tools necessary to study genetics. Things like Western Blots, Northern Blots, Southern Blots, DNA microarrays, and DNA hybridization are all techniques to studying molecular genetics.

A little side note: Whoever said scientists don’t have senses of humor is very wrong. The name of Northern, Southern, and Western blots started because a man name Edwin Southern developed the Southern Blot.  The Northern and Western Blots came afterwards as a joke created by other scientists about the cardinal directions and Edwin Southern’s name.

These techniques help study changes in DNA sequences. Single nucleotide polymorphisms (SNPs), short tandem repeats (STRs), and copy number variants (CNVs) can all be detected by these techniques.  These different types of differences are helped to differentiate individuals from one another as well differentiate populations. They’re also used to detect defects such as genetic diseases that may be associated with the changes in nucleotide sequences.

Examples brought up in class were about how STRs are used for identification of suspects as well as paternity testing.

There are about 13 core loci looked at by the FBI to check for identity. The way STRs are used for the identification of suspects is to compare unique combinations of STR found in the recovered DNA and the suspect’s DNA. An STR – standing for “short tandem repeat” is a 2 – 6 nucleotide sequence that repeats at least twice in tandem. For example, if the short sequence is “atg” then STR of “atgatgatgatg” has 4 repeats. The number of repeats are unique and are pass down from parent to child. We all have a copy from our dad and from our mom. In this identification, the suspect may have a 4 and 6 copy at STR # 1 and the recovered DNA may have a 4 and 6 copy at STR # 1. This information can not correctly match the suspect to the DNA because many people may have that combination of 4 and 6 at STR # 1. Thus many STRs must be used. The chances of a mistaken identification decreases as the number of STRs increase.

Another usage of STRs is in day time television shows. The Maury Show has been running for over 20 years. One of the big motifs of the show is paternity testing. So if you have ever turned on the TV in the early afternoons, you might have heard the line“YOU are NOT the FATHER” or  “YOU ARE the father!” Well paternity testing works very much the same way  as the suspect identification mentioned in the above paragraph. However, with paternity testing you need DNA from both parents. The child’s STRs combination is some sort of amalgation of the parent’s STRs combinations.

It’ be a fascinating week thus far. Please continue to follow the progress of our class!