Hey Y’all!

I am so excited that Amigo is finished! I feel like it came and went so quickly! We just got Amigo and now his annotations are almost complete. Our group, Olaf’s Fan Club, divided our section of the annotations into two groups, and Sierra and I annotated the last 18 genes of Amigo’s sequence. Most of the genes we had were fairly easy to annotate. Glimmer and GeneMark called the longest ORF, all the coding potential was covered, but there were no BLAST matches. This, though somewhat disappointing that we do not know what any of those genes do, made annotating a pretty quick process. The bulk of our time was spent on the large gaps in between genes. Between a lot of genes, there were 60-100 bp gaps, which is larger than expected for a bacteriophage but too small to have a gene in between. Sierra and I decided that Amigo had a less dense genome, so it will be interesting to see if other schools had the same type of problem with their genomes. Some of the gaps were over 200 bp and had little blips of coding potential, and in those we added genes. We are not entirely sure if some of the added genes are actually valid, but we used the guidelines and tried to do what looked the best. I cannot wait to see what the other groups came up with and if we are consistent in our annotations throughout the class!

I hope everyone has a wonderful and safe spring break!

Good luck on the test tomorrow!

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!

So this week and last week, my group had so much fun annotating Amigo’s genes. Our group finally finished on Monday. On Monday, we found the major tail protein for Amigo. It is so cool to find genes that code for proteins that are structurally important to our phage. We did find a gene between gene 20 and 21. It coded for a hypothetical protein, and it had good coding potential. I can’t wait to see what you guys found when we collaborate together

Since we are currently studying evolution, I thought I would post about some recent discovers in our own lineage. Recently, some scientists from the University of Washington put the mystery of the Neanderthal extinction to rest. By sequencing modern human genomes, the scientists discovered that more than 20% of the Neanderthal genome survives today through contemporary humans. This proves that humans and Neanderthals interbred somewhere along the line. What I find most interesting is the selection from these genes. It appears that the Neanderthal genes for skin pigmentation were more fit for local conditions at the time (due to the high amount of Neanderthal DNA present in the genes known to contribute to skin pigmentation). Moreover, the genomes appeared to have been mismatched at certain points, due to the low concentration of Neanderthal DNA in other parts of the contemporary human genome. For example, a strong depletion of Neanderthal DNA was found in a gene that is thought to play an important role in human speech and language. If you wish to read the article, it is linked below.

Neanderthal lineages excavated from modern human genomes

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!

Hey Guys,

I can not wait to start on our genome tomorrow. I have been anticipating this day all semester. To celebrate this milestone, I found an article on the history of phages, and how phages are used in phage therapy. We have read some of this stuff before, but there is some new information dealing with how we found phages. I would look specifically at the “Discovery of Bacteriophages and Early Phage Therapy Research” part of the article. This part has some neat history.

http://aac.asm.org/content/45/3/649.short

As we speak on the topic of human evolution, a recent study has shown that nearly 20% of the Neanderthal DNA is matched in the human genome, including numerous skin genes that may have contributed to our adaptation to the ancient environment. Benjamin Vernot, a population geneticist at the University of Washington, speaks on the importance of technology in making such discoveries: “I think it’s really interesting how careful application of the correct statistical and computational tools can uncover important aspects of health, biology and human history.” This is applicable to both our topics in class and in lab – the very techniques we are utilizing in lab are very much alike to those that other genetic scientists are using! From studying molecular trends we can attribute those findings to larger forms of life, and how they are all interconnected. He also stated that in the future, scientists may be able to examine and determine hominid ancestors just by studying human DNA: “…the “fossil free” method of sequencing archaic genomes… holds promise in revealing aspects of the evolution of now-extinct archaic humans and their characteristic population genetics…scientists will be able to identify DNA from other extinct hominid, just by analyzing modern human genomes.” This is both very exciting for in shedding new light on human evolution, but also emphasizes that the research we are performing on bacteriophages can relate to the data analyzation that scientists are using in their own labs, and that it is indeed the future of science. Pretty cool!

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:)

As you all write your papers, maybe think about these ideas

Did God Create Earth with an Appearance of Age?

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!

Hey guys!

I haven’t blogged in a couple of weeks, but with the last class’ discussion on the seemingly indisputable conflict between science and religion, I thought it might be a good topic to blog about. I am a Christian, and I believe that the conflict between science and religion stems from confusion and misconception. Science aims to investigate the “how” of life, by explaining principles that govern the natural world and can be observed. Religion, on the other hand, seeks to find the “why” of life by providing a belief system based on God and the supernatural. These two things are fundamentally different, but people often compare them like they concern the same things. Take the Ham-Nye debate that happened a few weeks ago. I think that debates between creationists and evolutionary scientists are unnecessary and unproductive. Creationists argue the “why,” and scientists argue the “how.” The arguments used in these debates presupposes the false dilemma, an either-or argument, but the two parties are comparing apples and oranges. Each side asserts that because this is an apple, that cannot be an orange, and vise-versa. I think such arguments just leave the majority of people offended or confused, and each side leaves without anything being resolved. I found an article that I thought was interesting about the subject. The link is below:

http://www.abpnews.com/ministry/congregations/item/8417-can-christianity-and-evolution-co-exist#.UwQeefldWSo

Hope you enjoy!

This is an interesting article on virus research. Scientist are trying to find out how a virus could become airborne. Once they find out how a virus can become airborne, they will be able to provide a remedy for this pandemic. It was funded by the U.S. government and researched by a Dutch scientist. This is extremely controversial because some scientists think that this research can be used in the wrong way. Many scientists still think it is worth it, though, because we can be ready when an airborne virus does arise.

http://www.cnn.com/2012/05/12/us/journal-avian-flu/index.html?iref=allsearch

I recently read an article that was mentioned in bioremediation presentation last week, building off of the clean up of the 2010 Deepwater Horizon disaster in the Gulf of Mexico; this article discusses its affect on marine life in the area. Researchers have found from samples of the area that the crude oil prolonged the action potential (up to 90%) of isolated cardiomyocytes in juvenile tuna neurons, thus blocking potassium reabsorption during the repolarization period following synapse. This was also found to decrease the calcium current that in turn disrupted excitation-contraction coupling in cardiomyocytes.

During early fish development, embryos are significantly vulnerable to high PAH (hydrocarbon constitute in crude oil) toxicity levels resulting from such disasters, and ultimately lead to long term acute and chronic side effects. Although the exact mechanisms leading to such cardiac functions are unknown, there is plenty of evidence validating the toxicity effects on marine life; following the Exxon Valdez spill, exposed fish embryos characterized significant heart failure, bradycardia, arrhythmias, reduction of contractibility, and edema surrounding the heart.

To explore these mechanisms, researchers assessed juvenile bluefin and yellowfin tuna captured in the area and held at the Tuna Research Conservation Center for observation. The cardiotoxic effects of four crude oil samples were assessed. The cardiac depolarization disorder is suggested to lead to cardiac arrhythmias, as the human homolog for the disorder causes such conditions and can lead to death. With PAHs interfering with EC coupling, lowered Ca2+ output levels during shortened depolarization (blockage of K+ pores in ion channels) periods result in the deficiency in producing contractile movements in cardiomyocytes.

With these findings, it is critical to understand the devastating effects of such disasters, and the need to control and properly clean up such events.

Since we had a short discussion about origins this morning, I thought I would post a book review that I read in Science.  It also has a short Bibliography of other books written on the subject.

http://www.sciencemag.org/content/342/6154/39.full