Archive for February, 2014

Feb 27 2014

Update

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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!

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Feb 26 2014

Finally Moving

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Can I just say how nice it feels to be working on genomic annotation? I’ve been relatively un-surprised at the number of genes with unknown functions, but also at the number of genes with oddly-specific fuctions: or portions of a gene that code for things like immunoglobins that have no business being in a phage genome. I’m excited to see where this takes everybody in terms of the independent projects

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Feb 25 2014

Amigo Annotation! Day 1

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Finally beginning to annote our novel phage Amigo is such a neat proposition. As a class, we are marking new territory with each gene with annotate. On our first day, Jackie, Sydney, and I encounted a lot of hypothetical protein matches in our Protein BLASTS. From our practice annotations, we usually got at least a real protein match each time, so encountering these hypothetical proteins was definitely something new! Our phage, after just one day of annotating, is clearly very unique.

Overall, the feeling of treading into the unknown with this whole process is very exciting. As we begin to annotate more parts of our phage, I wonder how our questions and discoveries will unfold.

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Feb 24 2014

Genome Analysis

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http://www.genengnews.com/gen-news-highlights/supercomputer-analyzes-240-full-genomes-in-two-days/81249533/

 

I saw this headline today-
February 20, 2014, 10:30 AM EST.
Supercomputer Analyzes 240 Full Genomes in Two Days

 

It will probably take us several weeks with all of your brains put together to analyze 1 very small genome. The technology is changing fast.  Sequencing is getting faster and cheaper, but what about the time and expense of analyzing?  Data doesn’t mean much if it is just sitting on the desktop.

Your generation will be analyzing and utilizing genome sequences more and more for diagnostics.  Computers will be doing the analysis.  Who will decide what to do with the results? What do you think?

 

 

 

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Feb 24 2014

Phage History

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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

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Feb 24 2014

The fun begins!

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Can’t wait to start analyzing the sequence for amigo’s  genome tomorrow! It will be a challenge but I am looking forward to it!

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Feb 23 2014

Evolution and Interconnection

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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!

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Feb 22 2014

Whoa…this is real.

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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:)

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Feb 21 2014

What do you guys think about this?

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

Did God Create Earth with an Appearance of Age?

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Feb 19 2014

What is the big deal about phages?

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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!

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Feb 19 2014

Science and Religion

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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!

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Feb 17 2014

Darwin’s Frog

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Did you know that Darwin discovered a frog in South America that is only about 2 cm in size? The male frogs carry the baby frogs in their mouth while they mature.  Watch this!  http://video.nationalgeographic.com/video/animals/amphibians-animals/frogs-and-toads/weirdest-darwins-frog/

 

Read more about it here.

It may be extinct?

 

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Feb 17 2014

Virus Research

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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

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Feb 14 2014

Heartbreak

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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.

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Feb 14 2014

Phages in Nature

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Saw this little guy on the ground in the parking lot today and I totally thought it looked like a phage. They’re out there guys. photo

 

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Feb 14 2014

From Matter to Self-Organizing Life

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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

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Feb 14 2014

Pre-human one-year old child’s Genome Sequenced

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Clovis is a group of what became native americans. Here is a cool short article on the genome they sequenced and some information they were to able to extrapolate from the data.

http://www.sci-news.com/genetics/science-genome-clovis-boy-01760.html

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Feb 12 2014

GMOs in the News!

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Last week, my group presented a project on genetically modified foods… We focused mainly on the current events and history within the United States (for somewhat obvious reasons), but as I was reading the New York Times this afternoon, I noticed this interesting article about genetically modified corn in Europe! I think it’s pretty cool that they might let this new crop through after such a long time … Also, did I mention it’s about corn? Yes, C-O-R-N, the spirit animal of our Biology class 🙂

http://www.nytimes.com/2014/02/12/business/international/modified-corn-a-step-closer-to-approval-in-europe.html?ref=science&_r=0

Take a look-see and tell me what you think!

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Feb 11 2014

Stem Cell Research

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Last week my group presented on the present and future implications of stem cell research. One things we talked about was induced pluripotent stem cells. Recently researchers in Japan developed a technique that allows adult blood cells to return to their embryonic state. This process only takes about thirty minutes, a significant decrease in time compared to past methods, and the results are even better than expected. This research brings humankind one step closer to the main goal of limb regeneration, even anti-aging. Linked I have a brief video that talks about the process of and hope from this research.

http://www.euronews.com/2014/02/06/organ-regeneration-moves-closer-with-stem-cell-breakthrough/

 

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Feb 10 2014

The Future of Gene Sequencing is Here

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I was reading an article today about the progress of gene expression analysis over the years which is very relevant to the topics we are discussing in class! As we know, sequencing has increased from 10,000 bases per day to around a billion base pairs a day and the price has been cut significantly, almost reaching the $1000 mark. With prices and time cut, this allows whole genome sequencing (WGS) to be utilized in diagnoses and treatments like cancer. Currently, WGS is helping in the study of the genetics of acral melanoma (20% lower survival rate than non-acral melanoma) in order to create an effective treatment. With WGS, researchers can now measure tumor-specific alterations in chromosome structure, point-mutations and gene expression via a combination of whole genome, whole exome and RNA sequencing. With these approaches, it is hopeful that treatments will be personalized in the future. The “improvement” of genome sequencing over the years is very exciting, and there will undoubtably be more applications and technologies in the years to come!

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Feb 10 2014

More Bioengineering in the News

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I really enjoyed your presentations last week.  All of the topics demonstrated to me that we have only just begun to understand how cells work and communicate, but knowing what we know allows so many good things to occur.

Imagine being the scientists that spend their life designing and testing a prosthetic hand and then learning that the individual trying it out can actually feel with it!  This is the latest of several breakthroughs in this area.

https://www.sciencenews.org/article/prosthetic-provides-sense-touch-man-who-lost-hand

The future looks bright to me!

 

 

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Feb 10 2014

Sequencing your genome is now (sort of) cost effective.

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That is if you have ~$1000 to spare. San Diego DNA sequencing company Illumina announced last month that they are now opening the door for a complete human genome sequence to the public by offering a whole-genome sequencing for under $1000.  This is done by the new HiSeq X Ten Sequencing System.  The announcement was a surprise to many in the field of genetics.  Link to the full article here.

 

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Feb 09 2014

Reading a Newborn’s DNA Map

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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!

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Feb 09 2014

Earth from Mars

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Sea Phagers!

I don’t know about you guys, but I am ready for our phage genome to come back. We have been separated from our phage way too long. I think that this gene sequencing and bioinformatics work is so interesting and I hope to start on our genome soon.

On another note, this is a cool picture from Mars of Earth. We are always looking at the sky from our planet, but this time we get to see our planet from another. It is kinda cool how the earth has a blueish color because of the dominant polar molecule on our surface.

http://www.foxnews.com/science/2014/02/06/pale-blue-dot-amazing-nasa-photo-sees-earth-from-mars/

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Feb 08 2014

Biotech and Viruses

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I found this article on ScienceDaily and thought it was really cool since we have been talking about biotechnology. These scientists have been studying the mechanisms that allow hantavirus, a virus contracted from rodent feces, into human cells in the respiratory system. Cases of hantavirus are very rare and localized here in the United States, but this virus has a 30-40% death rate among individuals that contract it. The main pathway this virus follows is linked with cholesterol transport in and out of cells. The studies done suggest that drugs created to lower cholesterol greatly reduce the susceptibility of respiratory cells to this virus. Lowering cellular cholesterol content seems to be an easily attainable preventative measure against this virus.

Here’s the link if you’re interested!

http://www.sciencedaily.com/releases/2014/02/140207083927.htm

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