Looking back on a great year

After a full year in the Biology 1406 class, I’m so glad I got this opportunity. Allow me to list Three Things That I Think I Thought about This year…

1. What a great group!

I absolutely loved getting to know everyone in the class – there’s only been a few times in my life that I’ve been part of a class where everyone (literally, everyone) was excited about the subject matter, extremely quick to pick up the material, and always willing to go the extra mile. This was by far my favorite class peer group of my freshman year.

2. Doing real science

While my friends complained about dissecting rats and memorizing the names of fungi, I had the chance to participate in truly novel research that has significance to science. Furthermore, I actually had the opportunity to work on an independent research project!

3. A true challenge

More than any other class, this class made me really work for my grades and I appreciate that very much. Dr. Adair and Dr. Gibbon made this class interesting and challenging, difficult but also engaging.

The seeming lack of attP sites in Amigo

In the past week, our group investigated looking for attP sites in our genome but we started to run into complications. First, the attP sites for Arthrobacter are not known so we resorted to running the entire genome through BLAST to find similar conserved sequences compared against the entire Arthrobacter taxa. Surprisingly, even after changing search parameters, few similar sequences were found and none had good e-values. We were looking for short, highly conserved (near 100% identity) sequences but they were not found.

We even considered the possibility that Amigo is not actually an Arthobacter phage and ran it against all kinds of categories – micrococcinae (the family Arthrobacter belongs to), etc., and yet, we still couldn’t find anything with significant similarity. This made it near impossible for us to continue with this particular project so we ended up switching last Wednesday to a new and more doable project. Although it was a little frustrating to hit a dead-end twice, we are confident that we learned a lot from it and that our new project shows a lot of potential.

New Method for Making Stem Cells

I was inspired by the presentation made in class about stem cells to do a little research on the topic. I found out that on January 29th, a new method for making stem cells was announced in the journal Nature.

Apparently, scientists can take cells from a mouse spleen and expose to them to an acidic environment. Upon doing so, these cells become pluripotent. This is very spectacular because scientists neither have to manipulate the nucleus or tinker with the translation process. This is a phenomenal discovery.

Read about it here: http://www.livescience.com/42926-new-method-for-making-stem-cells.html

The Awakening

A man explores the deep recesses of Africa and inadvertently awakens a sleeping monster. He begins feeling feverish, vomiting blood. When he stumbles to the nearest hospital, the doctors witness a gruesome and horrifying death – his organs and brain slowly liquefies, with massive internal bleeding, till finally everything just spills out on the hospital floor, each drop of liquid carrying thousands of toxic poisonous particles.

Sound like the plot of a horror film? Truth is stranger than fiction. In 1980, a man in Africa contracted the deadly Marburg virus after exploring a mountain cave. The symptoms are even more scary than what I’ve described. Check out the book “The Hot Zone” by Richard Preston, a book described as a “thriller” but is actually a dramatized nonfiction. Here are some excerpts from the case I’ve described:

“Then, on the third day after his headache started, he became nauseated, spiked a fever, and began to vomit. His vomiting grew intense and turned into dry heaves. At the same time, he became strangely passive. His face lost all appearance of life and set itself into an expressionless mask, with the eyeballs fixed, paralytic, and staring. The eyelids were slightly droopy, which gave him a peculiar appearance, as if his eyes were popping out of his head and half-closed at the same time. The eyeballs themselves seemed almost frozen in their sockets, and they turned bright red. The skin of his face turned yellowish, with brilliant starlike red speckles. He began to look like a zombie. His appearance frightened the temporary housekeeper. She didn’t understand the transformation in this man. His personality changed. He became sullen, resentful, angry, and his memory seemed to be blown away.”

Then the man gets on a plane…

“Perhaps he glances around, and then you see that his lips are smeared with something slippery and red, mixed with black specks, as if he has been chewing coffee grounds. His eyes are the color of rubies, and his face is an expressionless mass of bruises. The red spots, which a few days before had started out as starlike speckles, expanded and merged into huge, spontaneous purple shadows; his whole head is turning black-and-blue. The muscles of his face droop. The connective tissue in his face is dissolving, and his face appears to hang from underlying bone, as if the face is detaching itself from the skull. He opens his mouth and gasps into the bag, and the vomiting goes on endlessly. It will not stop, and he keeps bringing up liquid, long after his stomach should have been empty. The airsickness bag fills up to the brim with a substance known as vomit negro, or the black vomit. The black vomit is not really black; it is a speckled liquid of two colors, black and red, a stew of tarry granules mixed with fresh red arterial blood. It is hemorrhage, and it smells like a slaughterhouse. The black vomit is loaded with virus. It is highly infective, lethally hot, a liquid that smell of the vomit negro fills the passenger cabin. The airsickness bag is brimming with black vomit, so Monet closes the bag and rolls up the top. The bag bulging and softening, threatening to leak, and he hands it to a flight attendant.”

Let’s fast forward to the autopsy…

“They opened him up for an autopsy and found that his kidneys were destroyed and that his liver was dead. His liver had ceased functioning several days before he died. It was yellow, and parts of it had liquefied-it looked like the liver of a three-day-old cadaver. It was as if Monet had become a corpse before his death. Sloughing of the gut, in which the intestinal ling comes off, is another effect that is ordinarily seen in a corpse that is days old. What, exactly, was the cause of death? It was impossible to say because there were too many possible causes. Everything had gone wrong inside this man, absolutely everything, any one of which could have been fatal: the clotting, the massive hemorrhages, the liver turned into pudding, the intestines full of blood. Lacking words, categories, or language to describe what had happened, they called it, finally, a case of “fulminating liver failure”. His remain were placed in a waterproof bag and, according to one account, buried locally. ”

If that doesn’t scare you, I don’t know what will. Preston ends his book by concluding that eventually these super viruses will resurface. It is also notable that the USSR and the United States experimented with weaponized Marburg at one point.

Marburg is a form of Ebola virus, part of a class of hemorrhaging fever viruses. It has around a 25% mortality rate but its effects during the sickness are scary. It is extremely contagious and thus is handled in labs using biohazard suits.

It is an ssRNA virus, attaching to the NPC1 receptor on cells, and transcribing negative strand RNA to positive mRNA which then can produce the proteins required for replication. This is interesting because scientists are currently trying to develop an inhibitor for the NPC1 receptor, thus hopefully creating a cure for Ebola and its ilk, one of the deadliest killers on earth.

Anyway, I hope you enjoyed this post and I would encourage you to read the book – its a fascinating read!

Cool update on bacteriophage research…

Hey guys,

Here is an article about a scientist who is actively trying to get bacteriophage treatment approved as a weapon against e. coli and other pathogenic bacteria.


Waiting for Supername

If you’re like me, you have spent serious time thinking about what to name your phage. Some of you are probably just waiting for that perfect name to come to mind. I waited till I got to see the microscope image. So on a lighter note, I went through the phage database online to see how other people named their phages. In general, there are four categories…

Names: This is a lame category like Donovan, Selene, etc. I mean, I understand you want to name it after yourself, but it’s not super exciting.

Books and Movies: I noticed a lot of Harry Potter names, but it ranged from TV series’ like Spartacus and Game of Thrones to Jane Austen books. I think there are some solid choices in this category.

History: People picked things like DaVinci and Napoleon. Again, there are some solid choices to be had here.

Random Names for Personal Reasons: This encompasses almost everything else. One person named their phage for their cat. Another combined their middle and last names together. Someone else named theirs FruitLoop for the cereal.

Having said that, here are my top 10 favorite/cool/bizarre names from the database.

Aragog – Just because its a perfect Harry Potter world name for a phage.

Broseidon – Poseidon+Bro = awesomeness? I don’t even know.

Velveteen – I’ll allow the finder, Jonathan Lapin, to say it in his words: “Considering that “Lapin” in French means rabbit, and that the children’s book, “The Velveteen Rabbit,” is one of the greatest children’s stories, I decided to name this phage, Mycobacteriophage Velveteen.”

Gingko Maracino – They thought it looked like a Gingko leaf and they liked the Maraschino cherries.

MisterCuddles – 🙂

MadamMonkFish – Because.

Phaedrus – the name of a dialogue by Plato between Socrates and Phaedrus, another Greek thinker. That’s a pretty cool reference.

Waterdiva – because it was from a stream apparently.

TygerBlood – Yay for dated pop-culture references!

HanShotFirst – #starwars

Close Encounters of the Phage Kind

For months, we’ve worked to find and observe phages. After some initial bad luck, I found a phage and was able to steadily work to progress through a series of tests and purifications. Recently, I finally came face to face with the beast itself.

I chose the title of this post because to me, phage hunting is like alien hunting. In the movie, many people become obsessed with tracking an elusive and unknown object. As the movie draws to a climax, they are able to come face to face with it – the spaceship – a sight that satisfies all their wildest dreams about it. I’ve been completely obsessed with finding and hunting this phage. Like a hunter tracking a bear, I saw the claw marks on the trees, the lysed plates, but never encountered it…until now:

Due to its ridged long tail (which reminds me of a screw) and the ability of a phage to “possess” a bacterium and use it to propagate, I named it Screwtape. 🙂

Into the Wild (World of Conjecture)

In our last unit, we have studied cell signaling, including the way bacteria use it to control colony growth. Many times, bacteria work together to form what is called a “biofilm”, a thin layer of bacteria that attaches itself to a surface. These films are responsible for most cavities as well.

Every week, I plate bacteria and spot soil samples, looking for the clear spots that indicate a phage. I suddenly had a weird thought – what if there are phages specific to bacteria responsible for cavities? After all, there are probably billions of unique phages. Would it be possible to find specific bacteriophages that could destroy biofilms? If so, is there a way to apply this knowledge practically?

Just a random thought. I have no idea if this is a really dumb idea or if it actually is plausible.

Cloudy with a Chance of Lysis

It’s been three weeks, I’ve tested three soil samples, and I’ve received three negatives. Three cloudy plates containing no phage whatsoever. Today, I spent half of lab time collecting four new samples from around the Baylor campus. By next week, I’ll get to know if I have any phage.

Needless to say, many of my friends have asked me what I do in this “research biology” course. As I describe the process of isolating soil samples, testing them on arthrobacter cultures, and waiting to see if the tell-tale clear spots have appeared, most people quickly move to the next question: “Have you found one yet?” And for the past few weeks, the answer has been a reluctant no. Now, most people react with condolences, like I’ve just got a C on a big test. “Don’t worry, I’m sure you’ll get it soon.” “Even though you wasted a couple of weeks, I’m sure it will work out for you.”

But have I wasted a couple weeks? What exactly have I accomplished? We live in a results-oriented world. People measure others by their awards, accomplishments, proof, etc. For three weeks of work, I have very little to show. I swabbed some soil onto some plates and didn’t find anything. But as Dr. Gibbon explained to us in the first week, one can’t measure success in science simply by results. The scientific process is as important as the scientific result. I’ve resolved to avoid being disappointed about my experience so far – instead, I view it as time spent well. I was able to understand the process of phage-hunting, I learned the techniques involved, I gained hands-on lab experience. In comparison with my results-oriented traditional chemistry lab (follow pre-ordered steps to obtain a known result), I’m truly embarking into an unknown frontier of science.

And yet, are there any specific lessons I can learn? What can I take away that can then inform my future lab adventures? Is it that my growing conditions are not right? Dr. Adair has been suggesting various modifications to these. Is it that I’m not picking the right soil areas? I tried some really strange places this second time around. What more can I do to improve my forecast? Can I learn from these “failures” and apply my new understanding to my next set of attempts? My goal is to find clues, landmarks if you will, for the next set of explorers of this frontier. If my negative plates can result in greater understanding of even how to find phages, I would consider my results a smashing success.