http://www.the-scientist.com//?articles.view/articleNo/39332/title/Convergent-Fish-Fins/

Some researchers are looking at another morphological structure of modern day fish to investigate fish evolution.

“Adipose fins are small, fleshy and usually not as elaborately structured as other fins. Although some 6,000 species of fish—including trout, catfish, and salmon—have them, relatively few researchers have studied these structures in the last half-century.”

They plan to explore early changes that may be linked to the transition to tetrapods.  The beauty of cience is there is always another question!

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

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?

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?

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. 

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

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!

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!

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!

So I watched to Bill Nye debate earlier this week. The topic was “Is creationism a viable model of creation in today’s modern Science?” The debate was really well moderated I thought and the questions selected from the audience were equally fair. But I watched this because I had never really taken the time to watch anything like this before so I was curious on how it worked.

I don’t really like the question or the aspect of “winning” a debate…. I like to see debates as formal, moderated discussions during which both sides gain an understanding of each others stance. Because I’m sure both of them will admit they learned form each other. Also along that note, very few people that take stances on this sort of topic are looking to possibly be persuaded. People tend to stick to their guns when it comes to religious controversy. So also that kind of takes away the “debating” i guess? Possibly in a sense.. So it really is just a heated discussion on which some people take score. Regardless, here’s one of the main things I took from it.

One of Nye’s high points was when he was asked “What came before the big-band?” Obviously he knew that would be brought up so he had an answer well rehearsed, but none the less a good answer. The answer reminded me of one of the first articles that Dr. Gibbon gave us during the wet lab, about constructive stupidity in science. Nye enthusiastically answered: (paraphrase) I don’t know! But  questions like that are what get me out of bed and to work every day. Its questions like that, that excite me and make me dig in and try to understand the question at hand! We have ideas! But nothing more, no proof.. Yet! Hopefully someone from Kentucky (Where the debate was being held) can some day answer that question for you!

So I thought that was a really good answer, he demonstrated he knew a lot of stuff earlier in his presentation (kinda sounded like a lecture at times, but I mean hey, its a scientific debate what do you expect??) but at the same time he showed that there’s just as much we don’t know as what we do know!

I would suggest if you have some free time to nerd out, to watch it! I enjoyed it and gave me several things to think about.

The SEA Phage members that isolated cluster J Phages all got together and published a paper in PLoS.

http://www.plosone.org/article/info%3Adoi%2F10.1371%2Fjournal.pone.0069273

This is a great paper to read slowly over this semester as you learn more about phage genomes.

I think it is so interesting how they discovered 2 introns using the alignment tools and then confirmed their hypothesis by isolating and analyzing the predicted proteins.

They described a “luxuriant mobilome”….Maybe we will see something similar?

First off, if you get that reference I’d be seriously impressed… But anyways…I feel like I did at the beginning of last semester, with no clue how to do anything but still eager to get started nonetheless. The annotating we did today with Phreak made me beyond confused but it’s funny knowing how in a few months what we did today will be second nature to us and take us next to no time at all. Last semester we finished as pipetting masters and champions of the serial dilution and I expect this semester to be the same. We may feel clueless now but once we get started and start to pick things up, we’ll be working through that genome at top speed in no time. I just hope the program doesn’t prove to be as problematic as finding a phage was. So thats all for this post my fellow phage-finding friends. See you friday!

Oh, and just because I can… here’s a picture of a phage riding a goldfish. Enjoy.

http://theweek.com/article/index/255527/inside-the-world-of-bioflourescent-fish

The Week is one of my all-time favorite news sources, and this is a good example of why! I think it’s absolutely amazing that so many species of fish have this trait… Especially since many of them aren’t closely related at all! This reminded me of the jellyfish gene for biofluorescence that we learned about being inserted into a plasmid… but now they come in many colors! It will be exciting to learn what evolutionary advantages this brings to the fish and how they utilize it in their interactions with those around them!

I don’t know if y’all have read through the entire chapter 20 yet, but the next section covers cloning. I remembered reading a recent article about new stem cell research they have been investigating, so I thought i would share. As you know, stem cell research has been an ethical concern due to the harvesting of embryos. Adult stem cells aren’t as versatile, but they have found a new twist that may cease the use of ES cells.

Scientists at the Oregon National Primate Research Center have found that dunking adult stem cells in caffeine provides the desirable environment for reprogramming of the cell. Somatic cell nuclear transfer replaces the nucleus of a cell with a nucleus from an adult cell. Caffeine presence provides the suitable condition for human cells to transform to embryonic stem cells; research is still being preformed to uncover the suitable conditions for other organisms. This could transform the way stem cells are produced and utilized.

I think most of you know that I am interested in Staphylococcus aureus, particularly alternatives to treating this disease with antibiotics.  This week I read a news report that describes a hopeful vaccine.  http://www.sciencedaily.com/releases/2013/12/131220143124.htm

The research was published in the Journal of Infectious Disease.  I wonder what type of biotech is required to make this vaccine?

A few classes ago we were asked to select a virus and research it; I chose polio and the following is what I learned.

Polio also known as poliomyelitis is an extremely contagious virus that is most prominent in 3rd world countries and regions without easy access to medicine. It is a ssRNA virus that replicates through the lysogenic cycle . The virus attaches primarily to motor neurons where it is taken up into the nerve cell through endocytosis. It uses the cell’s ribosomes to produce more viral DNA until the cell lyses and the viral particles are released back into the blood stream to find other cells to infect. Polio was an extremely prominent problem up through the 1900’s but recently the numbers of cases have fallen dramatically and even India, which used to have one of the largest Polio problems, has declared itself polio-free.

So that’s all I have on Polio. If anybody knows anything else let me know, I’d love to know more about it!

Well its only the 3rd day of lab and its safe to say that the overwhelming feeling is scary familiar to the beginning of last semester! But even that in itself is comforting, after a few weeks in the wet lab I was very confident in what I was doing and that I was doing it right. But I am really excited to learn about this side of science. Its one thing to put a couple things in a test tube or a petri dish, but another to actually be performing this research and figuring out this mystery puzzle that i’m sure amigo is going to be. The element of uncertainty died down last semester after I switched to M-smeg, but now that we’re all back on arthrobacter I feel like i’m back in the real deal! So even after the crazy awesome concepts that we went over today, I’m ready to get into the groove of putting this puzzle together!

Hey Guys! So Dr. Adair showed this awesome link today in class which discusses some recent uses of biotechnology. I read this article on stem cell techniques, and I thought it’d be worth sharing on our blog. Here’s the link- http://www.genengnews.com/gen-news-highlights/answering-the-question-what-will-stem-cells-become/81249012/.

This article talks about a technique that was developed by the scientists at the University of Toronto. This new technique has the potential to rapidly screen stem cells to control what they will turn into in the future. The technology can be used in regenerative medicine and drug development; it can also give a better understanding of how to turn stem cells into clinically useful cell types. Science is amazing!

Have you ever read Small Things Considered?  It is the Microbe Blog put out by American Society for Microbiology.  A recent blog describes how phages infect bacteria.  It seems that some icosahedral phages “grow” a tail after absorption.  These describe Gram negative bacteriophage, but Gram positive bacteria have a thicker peptidoglycan cell wall.  I wonder if any cryo EM has been taken on Mycobacteriophage adsorbing and infecting?

http://schaechter.asmblog.org/schaechter/2014/01/bridges-across-the-periplasmic-moat.html?utm_source=feedburner&utm_medium=feed&utm_campaign=Feed%3A+schaechter+%28Small+Things+Considered%29

Here we go, round 2 of the phage research! Hopefully the sequenced genome arrives soon so we can begin the next step in this process.  It was amazing getting the opportunity to work with you all last semester and I can’t wait to see everything this semester has to offer for our class. 🙂

Hey everyone,

Happy (almost end of ) Finals Week! Hope the odds were EVER in your favor… (Hunger Games, anyone? Yeah?)

This goes without saying, but I’m so thankful that I had the opportunity to work in this lab with all you guys! Thanks for making this semester truly amazing. From all the corny bio jokes to the sporadic worry sessions about whether we’re doing the lab right, this lab has been an unforgettable experience.

I wish I could continue this lab with you all next semester..

Best of luck to everyone next semester, and Merry Christmas everyone!

Hey everybody, the following are a few articles I came across when I was researching for my lab report. I wasn’t able to include them since they aren’t original research articles, but I thought some of you might enjoy them too! Have a great Christmas break!

http://www.bbc.co.uk/news/health-21799534

http://www.futuremedicine.com/doi/full/10.2217/fmb.13.47

Wow! I can’t believe we did it! After a whole semester we finally have our DNA, I almost stopped believing this would ever happen. There were so many times during the semester when I just wanted to quit. Maybe I would come in to lab and find that my whole plate was contaminated or spend an hour figuring out why the TA would not settle. However, now I know all those mess-ups were completely necessary for my learning. I have learned so much more by messing up all those times than if everything had gone by the book. Looking back on this lab course I would not change a single day of lab. All of the things we have learned throughout the course, the perseverance, the teamwork, everything has been such a valuable experience that I would not change. And now I have Ranger and he is the best little phage there has ever been.

Peace Out SEA-Phages 2013!

This was it! It is a crazy, good, and bad feeling knowing that the lab portion of Phages has come to an end. Just think, guys, next semester we will have a whole new set of #phageworldproblems ! Today, this last day of lab, I came to find out that I accidentally left my restriction enzymes in the incubator for three days (36 times the optimal amount of time) so my restriction digests were VERY digested (except one, which didn’t digest at all…who knows?). But that gel was really cool! I had no idea what it was supposed to be showing but when Hao starting explaining it, it all started making a weird sort of sense.

The conclusions I have reached regarding many things in this class.

Science is crazy.

Mind = Blown.

Logic is No.