Since we are studying ecosystems and populations, I thought it would be interesting to learn about the effect of ecosystems on organisms.  I was reading through Science Daily and there is some research being done on the effect of environments on individual’s health.  Duke University performed a study on the poor health results of people living in poor Chicago neighborhoods.  I found this very interesting.  It is incredible just the amount of evidence they have found in the correlation between one’s living situation and one’s health.  This applies directly to what we are learning in class pertaining to the spread and dispersion of populations throughout areas (with much dependence upon environment).  This research makes me wonder about public health systems that can be implemented in poorer communities to help the health issues of communities.

I was reading a little about research done in the medical field on Science Daily.  It was very interesting.  The more and more I read, I realize just how related our physical and emotional states are.  It is incredible just how great of an effect emotional instability (as seen in depression) can play on one’s life.  For example, people with depression have a 40% higher chance of developing heart failure (according to research done by Ms. Gustad – see article on Science Daily).  At first glance this seems like a shocking statistic.  However, upon closer examination, it is quite self-explanatory.  If one is depressed, their lifestyle completely changes.  They are less active and tend to eat unhealthy foods.  It just continues to amaze me how much affect one’s mental state can have on their physical state.

I found an interesting article on the Science Daily website concerning the method plants use to silence genes.  In Biology class we are just beginning to discuss plants and their methods of growth and formation.  I just read a section in our book over the differentiation of cells in plants.  This differentiation is the result of many things including gene silencing.  Each plant cell contains the same genome, but the cells perform different functions.  Therefore, this must be a result of gene silencing, where certain genes are expressed and others are not expressed.  A team from Indiana University was researching how plants cells know which genes to silence.  They observed that unlike some thought, this ability to know which genes to silence is not “hardwired” into their DNA.  In other words, it is not an inherited trait, built into their DNA.  Instead, the ability to silence genes seems to be a learned characteristic, through “molecular memory.”  The genes recognize heritable chemical marks on the genes, and remember to silence or express these based on past experience.  The chemical marks/tags serve as “molecular memory” to help the gene remember to silence these specific genes in future generations.  This was a very interesting article published on March 20, considering we are currently learning about the basics of plant differentiation in class!

Today we found a much more efficient method of merging our annotation work.  We got in our groups and discussed our reasoning for extending, inserting, deleting the genes.  This process actually worked wonderfully!  We almost finished and came to a consensus on the entire genome.  However, one thing I learned was just the uncertainty of science.  The importance of educated guessing and asking stupid questions became so much clearer to me in this lab. There were many points in lab today where no of us had any idea of what we were doing.  There was no evidence either way, and we simply had to make an educated guess in one direction.  Because this genome has never been annotated, we are exploring totally unchartered territory.  We are researchers asking stupid questions and making educated guesses, hoping it will lead to further understanding!

Yesterday, an article was posted on a biology news site concerning research done on lentiviruses.  Lentiviruses are retroviruses that are used as vectors.  They are used as vectors to exchange/replace certain genetic material in cells.  One issue they were confronted with concerned the target cells with these lentiviruses.  How do they minimize the amount of virus cells used, while making sure the viruses attach to target cells alone?  Research was done at an institution in Germany concerning these questions, and major developments were made.  The scientists at the research institution covered the surface of the viruses with specific glycoproteins fused with an antibody.  When facilitated by the glycoproteins, the viruses  attached only to the target cells.  This, in turn, resolved the second question raised.  Because the viruses only attached to the target cells now, the rate of “infection” was much quicker, therefore less lentiviruses were needed.  This research has great medical significance.  This more efficient procedure can be used in gene therapy now to treat specific genetic disorders!

This is just a brief/quick post about the research being done all around us everyday!

As many of you know, our class has finally begun to annotate Amigo’s genome!  I learned two things really fast.  Firstly, Dr. Gibbon and Dr. Adair were right – you eventually get the hang of what you are doing.  A few posts ago I was complaining about how confused I was in lab.  However, I am pretty sure that I finally got the hang of what I was doing today!  It is an exciting feeling not being totally confused in lab:)  Secondly, I am learning that a lot of scientific research is educated guessing.  For example, Yasmene and I are annotating part of the genome together.  There was one section where we thought a potential tiny gene could be inserted.  A few classmates said no.  A few classmates said yes.  One teacher said no.  One teacher said yes.  In the end we decided to insert the gene because of the high coding potential.  However, all of that goes to say that a lot of what we are doing is opinion based.  It is totally up to our decision making if we insert, delete, or extend a gene – that is a lot of pressure it feels like!

It finally hit me this morning: we are actually doing research.  This sounds like a horrible fact to just realize.  Firstly, it sounds stupid.  And secondly, you would think that I would have figured this out by then.  However, it finally hit me just today that the research we are doing has not been done before.  All throughout high school I just repeated experiments given to me by my teachers.  However, we are now entering the area of science/research, where we actually have freedom.  We can research what we want convening phages, and we will have to present on it!  Our class has the potential of noticing something that has never been noticed before.  We are not just repeating experiments that other scientists already have the answers to.  Our research is actually being used for research by scientists!  This just finally hit me today – so I figured I should post about it:)

Maybe I am the only one who gets like this, but many times as I am studying something, I lose sight of its importance.  After investing hours of time into something I get fed up with it and ask myself, “Why should I even care about this?”  Therefore, today as I was thinking about biology lab, I stepped back and asked myself, “What is so important about phages anyway?  Why do we care so much about them?”  In my opinion, if there is no real purpose to studying something, why study it?  Now I could probably convince myself that the study of phages is important solely for the fact that it enhances my research and learning abilities, and knowledge learned in this field can apply in other fields.  However, those reasons are not very satisfying to me.  So I, as any student in the modern era would, googled why phages were so important.  What resettled actually surprised me.  Therefore, if you are in the place that I was and felt a little discouraged with the study of phages, read on!  Maybe we already knew this, and I forgot about it, but either way I am going to restate it.  Phages have much importance to humans!  In fact, there is a method called phage therapy that can help humans fight against bacterial infections.  Yes, we do have antibiotics to help fight these infections.  However, scientists are encountering numerous problems with antibiotics.  Bacterial cells are “evolving” and becoming resistant to these antibiotics.  One may say that the cells may soon become resistant to the phages as well.  However, there is a much lower likelihood of this happening, and based on the development of phages, the phages should be able to combat against any resistance.  This is only one of the many applications of phages!  Therefore, do not lose hope!  Our study of phages is not for nothing.  There are many advantages and possible applications with the study of phages!

I stumbled across this article on the NY Times website today, and it caught my eye.  It was written yesterday and is titled, “The Path to Reading a Newborn’s DNA Map.”  Here is the link: http://www.nytimes.com/2014/02/09/business/the-path-to-reading-a-newborns-dna-map.html?ref=science.  As of now, doctors perform basic testing of infants for sickle-cell anemia, and other treatable diseases.  But they are trying to develop certain procedures to sequence the DNA of infants so that parents can be aware of certain diseases at birth.  As of now, the National Institutes of Health have given $5 million to four pilot grants in this research program.  However, as always, there are strong ethical considerations to be considered.  Is the doctor trying to play the role of God by doing this?  Is too much information dangerous?  What if the information is wrong, and decisions are made solely based on this inaccurate predications, which can harm the child?  It is a very interesting article, and I encourage y’all to read it!

Where has the time gone? It feels like yesterday that I was awkwardly digging through the soil, trying to find a phage. But literally just yesterday I basically completed the lab – I finally got my picture of the gel! (I essentially know what the DNA of my phage looks like!) I had the opportunity to tell a few of my friends what I have been doing in this lab, and they were amazed. They thought it was incredible that I had the opportunity to do all of these advanced laboratory procedures. And looking back, it has been crazy! In the beginning I did not even know what a microcentrifuge tube was. And I cannot wait for next semester when we spend time in the library researching and further understanding everything we learned in the lab.

When I was about 4 years old, my grandfather died of ALS. My mom told me that after he died, I said that I wanted to research this disease so no other grandfather had to die of it. I hate to admit it, but the older I got, I forgot about this dream of mine. But just today, something reminded me of my dreams of research in ALS. So I researched a little about any discoveries they have made in the treatment/cause of ALS. The first page it brought me to said that they have made a landmark discovery that a genetic abnormality is the likely cause of ALS. They found a short DNA sequence that is repeated many more times in patients than it is on healthy people. The intrigued me because we are studying DNA right now! I read a little further and it appears that the repeated DNA sequence is located on the non-coding region of a gene (the telomere). This however does not make sense to me. Because if it is located on the telomere it shouldn’t really affect the DNA, because it is on the non-coding section. But obviously it still has some affect. It will be interesting to see what comes of this research!

On Monday a few of us were able to head down to the Microbiology Lab and do some really cool stuff! We essentially wanted to get a picture of our phage, so did a few procedure steps on on the phage lysate, and then Dr. Gibbon was going to stick in in the electron microscope! After treating the lysate, we went in the back room to look at the electron microscope – who knew we even had one! It was so incredibly cool! I felt like a legitimate researcher! I was then telling my friends about what we did in lab, and they all said, “Wow…I have only been able to read about stuff like that!” It finally hit me how cool of experimentation we are doing, because not many people get to use the equipment and procedures that we are doing.

When most people think about scientific research, they envision a mad scientist working for days without seeing another human being. At least that is how I saw scientific research! However, through this lab I have discovered just the opposite. Now, one could attempt to do everything alone…and it would probably work. However, it would be ten times harder. Jade and I are on the same step in this purification process, and it makes the whole process more enjoyable. In fact, I am learning even more about what I am doing, because I can always compare my results with her results, and see how our phages differ. It is truly exciting to be able to work through an experiment like this with someone else.

Today’s lab work took only 20 minutes…WOW. I have purified my phage four times; therefore, today I simply flooded my plate with phage buffer! I would say today was a successful and rewarding day in the lab…:)

Many times when I am lab, I always think that we are doing a very complicated process. In other words, I always just assume that I just need to follow every instruction because I am too stupid to know what else to do. However, I thought that the directions told me to pick multiple plaques as I was purifying the sample. I did not even think twice about it. I just figured, “Well, if the directions told me to do it…then I might as well do it.” Finally after my third purification I thought about what I was doing. I thought to myself, “Why am I just following the directions without understanding fully what I am doing? Why would I pick multiple plaques if my goal is to purify ONE phage?” I only then realized that I needed to purify all over again, picking just one plaque…following what is logical. This was a crucial lesson for me to learn, that especially in a lab, I should not do anything until I understand what and why I am doing it.

I felt quite stupid during Wednesday’s lab…but that is normal in a first year bio lab I am told! Well, I pulled out my 5 plates, which I had plated by possible plaque on. I knew that my -1 and -2 samples should have the highest concentration of phage on them. But when I looked at the plates, there was nothing! It was essentially just my lawn of M-Smeg. But then I pulled out my -3 and -4 plates, and noticed there were spots of clearing on them. I figured it was contamination and started preparing to get soil. However, I quickly wanted to check with Dr. Gibbon to make sure I was doing everything correctly. He quickly looked at my samples and said, “Wow, you have a lot of phage!” Thinking I knew better than him, I quickly proceeded to explain that my -1 and -2 samples should have a higher concentration, but they have nothing on them. Therefore, it didn’t work. He just laughed and quickly explained that I had so much phage on my -1 and -2 plates, that all of the clearings ran together and covered the entire plate! That is how my lab on Wednesday quickly turned from disappointment to excitement!

Today was an interesting lab. As I entered lab, I just assumed I would have a phage. I set my soil samples in M. Smeg instead of Arthrobacter, so I just assumed that it would work. However, as I grabbed my plate, I noticed something peculiar. My bacteria lawn had not completely grown. It was very splotchy; there was not a smooth bacteria lawn. I immediately assumed that there was not phage. I thought that there could not have been because the bacteria did not even fully grow. However, one of my classmates asked me to hold it up to the light. When I did this, it became evident that though the lawn was splotchy, there was a slight clearing in section 6.0! It appears that there is a phage in my sample! However, one cannot be certain…it is only very tiny (see attached picture). In light of this, I picked this plaque, and by Wednesday I will know if it is actually a phage!! Keeping my fingers crossed!

Well, last class was a bit of a disappointment. Still no phages. This means that I am “giving up” and using SMEG instead of Arthrobacter. SMEG is easier to use. I feel like a slacker, but it seems like the only option at this point….which is truly disappointing. But in 30 minutes, I will get to see if my SMEG soil sample actually worked! I will keep you updated if anything grew!