I can’t believe our Freshman year of college is almost over! It has been a whirlwind, a stressful, crazy, amazing mess that I am extremely grateful I got to spend with all of you. I couldn’t have asked for a better group to go through this program with. As finals come to a close, I wish you all the best of luck  with your summer ventures, whether that be research in Houston or simply relaxing at home. It has been a privilege to get to know each and every one of you.–And Dr. Addair and Dr. Gibbon, thank you both so much for all of the time and effort you have invested in us, I think I speak for all of us when I say that I’m eternally grateful for everything you have taught us.

I will see you all at the final!

–Chloë Sells

For the past month the Philosoraptors have been struggling with endless amounts of inconclusive data and confusing results from BLAST matches, but its finally starting to come together. We have actually discovered some pretty cool things regarding the connections between the genes  of Amigo and the other Arthrobacter phages. I’ll save the rest for our presentation. When we first started on this project I was worried we wouldn’t find anything interesting but nevertheless we did and now that our data finding is complete, all there is left to do is put together our presentation. Congrats to all the other teams and their successful research projects as well! I can’t wait to hear your results!

KATELYN GOD BLESS YOU. YOU ARE A BEAUTIFUL HUMAN BEING.

Haha I definitely needed something else to try for study tactics and this just might do the trick 🙂

According to research studies done recently, the Y chromosome is in a state of genetic decay. The Y chromosome apparently once had 600 genes in common with the X chromosome, but over the duration of its evolution throughout the years, lost all but 19 of them. There is a debate in the science world about this currently, but many scientists, called the “rotting Y” group, believe that since the chromosome has lost so many genes already, its extinction is likely if not inevitable. Another group of scientists has chosen to view this data in a completely different light and see it as the Y chromosome shedding all but the genes completely necessary for survival . Scientists Dr.Bellott and Dr. Page argue that XX cells are “subtly but fundamentally different” from the XY. And, “they are different throughout the body in tissues and organs that show no obvious anatomic differentiation.” They are using this knowledge to try and customize medicine to tailor to the differences between the cells, a concept that could possibly lead to major developments in the medical world.

As an additional note, I was reading an article a while ago that was similar to this, except it focused more on how survival is largely to do with the will of the mind. This is why people who are stranded in the desert or are seriously injured are able to survive longer than they were expected to. Even though their bodies may be giving out, their will power is what is keeping them going; they literally are keeping themselves alive when medically, they should be dead,  by sheer willpower. It is incredible what the mind can do. The article also pointed out that this lines up with the statistic you mentioned, Abby, about people who are depressed being 40% more likely to develop heart failure. Even though their bodies were relatively healthy to begin with, the lack of will to carry on, coupled with the lifestyle that results from that mindset often lead to the body giving out.

This past week scientists from Ireland discovered a new  way to make the “wonder material” graphene…. by using a kitchen blender. The team put powdered graphite, dish washing soap, and water into a kitchen blender and proceeded to blend it at high speeds; the result was the formation of the incredible material. Graphene is unique in that while it is only one atom thick it is very strong, flexible and electrically conductive. Because it has the potential to be used in such a wide array of fields including electronics, there have been many attempts to find a quick and cheap way to make it (In 2004 scientists were using Scotch tape to take the top layer of graphite off to make it). I’d say these scientists found just about the cheapest and easiest way to do it. Personally, what I find most puzzling about this entire thing is why top tier scientists decided a common kitchen blender would be the best way to try their experiment, but hey, it just goes to show that you don’t have to have the latest technological equipment in order to develop or discover something revolutionary.

If any of y’all want to read about it more in depth you can use this link to the article.

http://www.bbc.com/news/science-environment-27113732

1) That is really helpful and I wish I had found it before that last test! Bummer 🙁

2) It is now stuck in my head and I can’t stop humming it so thanks for that haha 🙂

Came across this while I was looking for my speciation article. I thought it was pretty interesting. Plus a pretty picture of a phage for your viewing pleasure. Have a great spring break everybody! http://www.sciencedirect.com/science/article/pii/S0022283697916107

After four straight lab periods of staring at “No known functions” and 1200 bp gaps with no coding potential, we are finally done! I don’t know about any of you guys but I know that I certainly did not expect there to be so many genes with no matches or known functions. It really helps show just how little is known about these little guys and how much new information can be derived from a single phage’s DNA. While it may have been frustrating for us to have so little definitive knowledge as to what the genes do, what we just did will help connect puzzle pieces so that in the future these gene’s functions can be determined and the database can be expanded. Yay us, go team!

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.

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!

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 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

One last thought for today…… Most articles that can be found regarding phages discuss their medicinal implications such as their ability to combat certain types of human conditions such as MRSA or TB, however I found this article interesting because it shows the wide range of implications that phages and the research we are working on can have on our world. In this article the author discusses how even diseases that affect plants can be targeted by phages to save entire ecosystems, in this case the Australian Great Barrier Reef.

http://www.bbc.co.uk/news/science-environment-23773672

Today, everything came to an end. It was the final day of lab and we finished up and made final modifications on everything that we have spent the last semester working so diligently on.  Not all of us received the results we anticipated at the beginning but I don’t think any of us regret going through this process. We have learned so much over the course of the past sixteen weeks and have been able to do bona fide research, something that the vast majority of college freshman will never get the opportunity to participate in. This past lab I archived my phage, the final step in this long process, and while I am glad that I have achieved my goal of making it to the end of the phage-finding and isolating process, I can’t help but feel a bit sad that it is over. This has been an incredible opportunity and I am so grateful to have been able to spend it with each and every one of you. I have learned an immense number of things that will help me to become a better student and scientist over the course of this semester including but not limited to, keeping a lab book, creating an EM grid, running restriction digests,  creating serial dilutions,  and yes, even working with disgusting smelling Arthrobacter plates. All these skills have changed me for the better, but I would never have developed them were it not for this experience.

Looking back over my lab book, it is amazing how much progress was made.  The beginning weeks of the semester, nothing was working, and by nothing I mean NOTHING. My pipetting skills, or more accurately my lack thereof, kept giving me inaccurate measurements, everything was getting contaminated due to poor aseptic technique, my first six samples all came back negative for lysogenic spots and overall, my spirits were in the dumps. It is astounding to see how practically all of this has changed in the matter of a few months. I can now use a pipette easily, aseptic technique has practically become instinctive, and I have a fully purified and isolated phage who is being sent of for sequencing. So much progress was made this semester, and I cannot wait to see what new developments the next semester has in store for me. It’s been fun everybody! See you at the final exam!

This was something I have had to tell myself countless times throughout the semester, especially when I realized I had been working on someone else’s phage haha. While your gel did come back negative for DNA, you have been successful in dozens of other aspects throughout this semester’s lab- for instance you have experienced something most college students wont have the opportunity to do, freshman research, and you have also learned numerous valuble skills that will help you in the lab in the years to come. So no, you definitely did not fail, and although results can sometimes vary from what we desire, they teach us something new which is a success in itself. 🙂

This past week I have been able to finally get a close up look at just what it is that we have been working towards this entire semester. As strange as it sounds, I feel so incredibly proud of those tiny little black spots with tails because they are representative of every hour we have spent working and researching in the lab. It is such a great feeling to be able to look at the finished product of your work and be able to say “all of that time and effort has paid off”. Those itty-bitty little clear spots we were working with at the beginning of the semester have matured  (not really, but it feels like it) into a fully grown phage with DNA we can look at and analyze. I’m looking forward to completing the next steps in the process, whatever they may be.

Firstly, my apologies for having not blogged in a very, very long time, but life got hectic and I tend to get forgetful when that happens. So here begins the first post of a sequence of several to follow within the following week and half.

Since my last blogging adventure, a lot has happened. After selecting a plaque from a serial dilution of my ninth sample, I proceeded to run my three rounds of purification, which included unfathomable numbers of arthrobacter plates and serial dilutions. These steps ran very smoothly, so smoothly in fact that I had a nagging feeling that something must have gone wrong (let’s be honest here, when has anything in this research project run smoothly without one single kink?). I guess you could say I was right. Somehow, between rounds 2 and 3 of my purifications, the phage I had been purifying became contaminated by Yazmine’s hulk-strong phage; and thus, the phage I had been purifying was no more :(.
Unfortunately, I did not realize this at the time and continued to perform the next few steps as if everything was normal. There were a few passing suspicions that we were both working with the same phage based on plaque size and the distinctive halo which formed around each lysogenic spot; however our titers were so drastically different that those suspicions were, for the most part, ignored. Even if we had caught the mistake at this point in the process, there wasn’t much that could have been done about it since all of the old plates containing my phage had been disposed of and it was already too far into the semester to begin again from the soil sample.
Needless to say this has been an interesting experience, but informative nevertheless as I am now aware of just how little it takes for contamination to occur and have become much more aware of my aseptic technique. This has also allowed me to see the variation that can exist between experiments even when they are done using the same methodology. While this may not have turned out like it was intended to, if everything always went as it was supposed to in a scientific experiment, the scientific community would miss out on the numerous numbers of innovations that have stemmed from mishaps. While it is still disappointing that I wasn’t able to analyze my own unique phage, I am still glad that I was able to contribute some assistance to the isolation and purification of Yazmine’s ultra-phage, Amigo, who now going to be sent off for sequencing. Adios Amigo! See you next semester.

         The best things in life are often the unexpected ones. I was on my final round of testing before I called it quits on trying for an anthrobacter phage and switched over to mSMEG, when these little beauties finally appeared. I almost didn’t run this spot test since all four of these samples had been tested before, but when I saw that the enrichments had developed mold anaerobically after I accidentally tightened the lids on them, I figured I might as well give it shot. To be honest I was not expecting much, but needless to say I was pleasantly surprised. None of these samples produced a phage after being enriched and incubated aerobically, yet being allowed to sit in anaerobic conditions for a week or so seems to have had a strengthening effect on the phages in the samples since they produced lysogenic spots when tested for a second time. My only guess is that perhaps the kind of phage that cleared the anthrobacter thrives in those conditions and becomes stronger when subjected to them. That would explain why all four of these previously negative samples have now produced positive results. Either way, I am excited to start the next stage of the process- purification rounds here I come…