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?

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?

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

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!

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.

I’m finally about to catch up with most of you guys in lab! Yesterday, I went into lab and prepped/purified my DNA pellet for DNA digestion. Thankfully, I had help from Dr. Adair and was able to conduct the procedures without much trouble.  Otherwise, I probably would have been stressing out.

Something funny that did happen though–when we placed the microcentrituge tubes into the mini-centrifuge to spin/dry the filter for the final time, we heard a loud click as it began spinning.  We didn’t think much of it, and assumed that it must’ve been something snapping into place as the tubes were spun.  We were wrong.  When we looked inside the machine after the two minutes was up, we found that the plastic microcentrifuge tubes had cracked and shattered.  It’s never happened before, but luckily, my columns with the were undamaged, meaning my phage DNA is still safe! Yay!

I’m not even sure what I would’ve done if my phage DNA just splattered everywhere in the centrifuge.. I probably would’ve had a mini melt down. No joke.

I’m really excited to start the digestion today! I can’t wait to finally see the infamous DNA that we’ve been studying for so long.

Today I finished my restriction digest. It was kind of stressful in the since that sometimes when pipetting .69 micro litters, its hard to tell if anything is actually being pipetted! (And not to mention the entertaining frenzy of everyone on that same step fighting for each of the enzymes and their perspective buffers!) But now that thats all done, i’m moving onto the final steps including the electrophoresis. This part of the lab has been so cool because i’ve gotten to work first hand with some unbelievable equipment for any undergraduate, especially for a freshman! (Heck, I even got to troubleshoot the photo spectrometer!) So I really am sad to see this experience go, but next semester is where we get to actually dive into our results and that too is exciting.

I remember when I first applied to this program. I was expecting to see some pretty cool stuff under a microscope and actually get some biology lab experience. But it really has turned out to be so much more. It still blows my mind with all the stuff that we’ve been able to do this semester! I want to believe Dr. Gibbon when he says that next semester is super cool, but I feel like comparing it to this semester is going to be pretty tough!

Oh, and I found a really really interesting study for my last blog post! So be on the lookout.

Hey everyone!

Our first semester is coming to an end and unfortunately, I won’t be with you guys next semester! I switched my major to biomedical engineering a couple weeks ago and turns out that biology isn’t a part of the degree plan for BIOmedical engineering. Hmm…Weird. But, it is what it is!

But on a more exciting note–I am SO pumped about our EM phage photos! I literally squealed when I saw mine.  I was just a litttttle too excited. All the more reason I switched into biomedical engineering! The technology is just so fascinating.

On Monday, I plated a spot test for my ten 10-fold dilutions of my newly purified lysate. When I was spotting the 10 microliter drops of lysate dilutions, the drops didn’t form a circle/drop. The top agar seemed to be solidified (I waited about 7 minutes and doubled checked to make sure it wasn’t runny or moving). Either way, the drops spread out and made odd shapes, only to be absorbed by the TA within seconds.

My concern is that the drops ran together and will affect the titer calculation.. Hopefully this won’t be a huge problem since we only really look at the lower concentrations for calculations. Fingers crossed!

Well not every day in research is worth bragging about.. yesterday was one of those days where not much got done and there wasn’t too much anyone could do about it. Yesterday I learned how to operate the spectrophotometer. While this is an amazing piece of equipment that at the end of the day did its job, it goes to show that sometimes things just don’t go as you planned. But! I did get my concentration for the DNA sample. I’m not sure if mine was really that concentrated, or if there is some contaminant DNA hiding somewhere in there.. but! I’ll be ready to calculate and perform my restriction digest on Wednesday!

http://www.colbertnation.com/the-colbert-report-videos/430096/october-30-2013/jack-andraka?xrs=share_copy

I know not all of us are pre-med students, but this is really interesting. Stephen Colbert interviews this high school student who found a way to screen for cancer! I Wish I was a genius like this kid, it is crazy that there are these people out there!

This has been rather confusing. my last two experiments have been a bit interesting, trying to figure out why my phage won’t show up (at all, even at a 10^0 concentration), and whatever my mistake was, it has left me phageless. I went in to do my Electron Microscopy and I broke Dr. Rushing’s perfect record, as she was unable to find any phages, and she had to give up after about 15 minutes of looking.

At this point, my options are very limited. Based on the current trends, my current lysates are all either faulty, contaminated, or simply containing a phage that refuses to grow (even my lysates that are from my purification rounds) and I have actually been forced to start a plaque assay from my original lysate: the one we all made together at the end of september.

It doesn’t matter very much, since we already have the phage we need, but it is just kinda discouraging to have failed like this. Oh well, I’m definitely looking forward to next semester’s lab more, now.

Hope everybody has a great break.

I finally got to see my baby on Wednesday! After going through so much to have one, my phage’s pretty little face presented itself to me through the use of the electron microscope. The titer I used was extremely high, so we had plenty to choose from when we went to take the picture. We were able to find one that was in amazing condition for the image. It has an excellent angular head with a tail approximately twice the length of its head. I am in love.

So today was the coolest day of lab by far. I filtered my lycate from my 10 plate and then did both steps of the microscopy! Its absolutely insane that I’ve been able to be a part of this as a freshman. As soon as I got to band I told several people (upperclassmen) about it and some of them didn’t even know that Baylor even had an electron microscope! And ironically enough, the day I was super excited about my fancy bio lab it was “nerd day” for the band. (The last rehearsal of the week is always a spirit day and people dress up according to the theme) So while others wore suspenders and thick glasses, I just showed up and got to act like it! Even though it was far from acting.

But now that I think about it, I was in a rush to get to band and forgot to write all this in the lab notebook… looks like i’ll be stopping by tomorrow to do that!

So I feel like I’ve past that checkpoint. Now I’m done with my 10 plate web that I flooded on Monday and will collect the lycate. Wednesday I will start on the graphing for the microscope, and ill get to start working with the DNA of the phage.

So it makes sense why we all have to switch next semester to arthro for the sequencing of the phage, but it defiantly makes me wish I had tried just one more time to get that phage! But I still would be doing the same thing, so in the end theres no difference.

Its kind of funny when I talk to my parents from time to time, they will ask about the lab and earlier in the year I would be able to simplify it enough where they had the general idea of what I was working on. But now and especially the rest of the semester, its gotten pretty complicated for just a casual phone conversation! But I really feel like I have a firm grip on what i’m doing and what i’m going to do next!

Today in lab I found out that all ten plates of my ten plate test and my spot test were all contaminated! I think that it is the Top Agar because my negative was also contaminated. It looked like I had a webbed plate but I didn’t want to flood a plate that was contaminated so I decided to redo both tests. I made new Top Agar and made sure to be extra careful about using the aseptic technique. I am doing two tests at once (the 10 plate test and the spot test of my new lysate to find the titer) to make sure that I don’t have to back track. Hopefully on Wednesday I will get good results and be able to move forward!!

Well maybe not.. but regardless that was the story of today’s lab: Math. I carefully took my titer count and made my table for my webbing dilutions.

So I feel like in this lab, finding the phage is the obvious first checkpoint, and I feel like the next is getting your calculations and product of 10 webbed plates. So now that I’m getting closer to that second checkpoint, i’m getting excited!

On Wednesday in lab I spent the entire class coming up with the calculations for what concentration of phages I would need to make my webbed plate. After many attempts and crossed out numbers, I came up with 14 as my ideal number! According to my calculations I need 14 micro-liters of the 10(6) dilution to make my webbed plate. I am also plating 28 and 56 micro-liters of 10(6) and 7 and 3.5 micro-liters of 10(7) incase my math was slightly off. I am hoping, praying, and crossing my fingers that I calculated correctly and I will have a perfectly webbed plate on Wednesday! Wish me luck! 🙂

So I was taking a break from studying and surfing the internet when I came across a really interesting article! A national geographic research team went to the top of Cape Melville, a mountain range in norther Australia that has been cut off from the rest of the world for centuries. While on this cliff they found 3 new species of animals, like obvious ones too! The picture below shows where in Australia they were searching and the 3 species they found. Nat Geo said that they will be sending another expedition there within the next several months to look for smaller species.