Bio Lab Take 2! Action!

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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!

Answering the Question: What Will Stem Cells Become?

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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!

Starting fresh

I’m pumped, I feel like this is where the actual ‘research’ begins, where we get into the real genetics and the true uncovering of something new. I was looking around to find some cool new thing about viruses and I actually found some stuff that really freaks me out

http://diabetes.diabetesjournals.org/content/early/2013/07/31/db13-0619

Who knew that the effects of a virus could be related to the onset of type 1 diabetes!? That’s crazy to me; between that and the possible effects that this phage stuff could have on treatment for tuberculosis, I’m really hoping we can find something new or actually discover something really important this semester. We’re going to do some cool stuff, guys!

I also found a pretty cool one about bacteriophages!

http://www.medicalnewstoday.com/releases/271113.php

Unfortunately, this one is a bit defaming to phages, as it tells of how a specific phage targets and kills, “preys upon,” a bacteria that is neceessary for fixing atmospheric nitrogen into the soil.

Mimivirus

Hey y’all!

I hope everyone had a great Christmas break! It’s good to be blogging again! I did not have the chance to share the virus I researched in class, but I thought I would share it now. It is hands-down the coolest virus I have ever read about. It’s called the mimivirus and it infects amoeba. What is really interesting about this virus is the sheer size. It has a diameter of about 400 nm, which is the third largest capsid size ever discovered. It has an icosahedral shaped capsid, which contains lots of enzymes and the virus’ double stranded DNA genome.  The genome is large, at over a million base pairs! Its genes do not only code for the typical virus things, but also code for aminoacyl tRNA synthase, and other proteins involved in protein synthesis and metabolism.

What makes this virus even more incredible is how it replicates. After it is engulfed by the amoeba by receptor-mediated endocytosis, it uses its own enzymes to replicate its DNA and transcribe it to mRNA. Most dsDNA viruses send their DNA to the nucleus to be replicated and transcribed using the host’s mechanism, but the mimivirus uses its own. It has a viral core, which does not degrade in the host’s cytoplasm, that acts as the new nucleus of the cell. It has both RNA and DNA polymerases, which it uses in replication and transcription. After transcription, the virus uses the host’s ribosomes to make the necessary proteins for the capsid and enzymes inside the viral core. When more viral cores are made, those cores begin replication and transcription. This continues until the cell is lysed, releasing all of the new mimiviruses.

Crazy, right? This is one of the only known viruses that replicate in this manner!

If you want to know more about how the mimvirus works and how scientists discovered it, you should read this article:

http://www.pnas.org/content/107/13/5978.full

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!

Borna Disease Virus

Last week I decided to research the Borna Disease Virus (BDV), partially because I love neuroscience and partially because it isn’t a commonly known virus! BDV a neurotropic virus that is most common in horses and other animals that usually causes abnormal behavior and fatality. It is still controversial if BDV plays any role in human mental disorders, although there has been recorded linkage between BDV and bipolar and schizophrenia (present BDV antibodies detected). It is thought that it is transmitted through saliva or nasal secretions. Through experiments with rats, it appears that the virus causes learning impairments and altered social behavior (in some cases meningitis). Its been demonstrated that the virus infects the limbic system (emotion). As the disease develops, seizures, ataxia, paraplegia, and other neurodegenerative symptoms persist; the immune response usually results in immune-mediated death of infected and neighboring cells, thus degradation of mental processes.

BDV is non-segmented, negative-sense ssRNA virus with at least six identified orfs producing proteins N, P, M, G, L, and p10 (uses enzymes to create a + strand). It is known to replicate in the nucleus of neural cells. The method of transmission is still unclear.

Bridges Across the Periplasmic Moat

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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

 

 

Good semester guys

Even though none of this went quite like I expected, I’ve got to say this has been one of the funnest things. It’s been a fantastic semester, everybody. I’m pumped to dive in deeper this spring.

Final Post!

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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!

This is the End

Although my phage ended up dying at the last minute, this has been one interesting semester of lab. I have never learned so much about research and biology than I have in this class. The different methods that we would do every day and be able to interact with each other whenever we needed assistance or an opinion made me want to come to lab everyday. I made a lot of new friends in this class and we still have one more semester together. I can’t wait to come back next semester and finish what we have started!

Chimalakonda out.

Th-th-th-that’s all folks! (Well for this semester)

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So our last lab for this semester has come and gone. And making smores is an awesome tradition for the last day! And now that Bonesquad is shipped of and in the data banks, all that is left to do is to analyze the bands on the electrophoresis!
So I said in my last blog that I found a study in a Smithsonian magazine that was super cool so I thought I would summarize it for y’all. This was a study published in 2007 by Yale’s Infant Cognition Center. This study was attempt to tackle the question of wether or not humans are wired to know the difference between good and evil (or lesser good), or if the concept of good is like anything else, just a skill we pick up along the way.
The test was performed on 6 and 10 month old infants. A group of these kids were shown a puppet show which had this story line:
There was a bunny that was struggling to open a box. Then along came a bunny in a purple shirt. The bunny in the purple shirt held the box down and prevented the original bunny from opening the box. The next scene was similar. The same bunny was trying to open the box and another bunny came along in a green shirt and aided the original bunny and together they opened the box!
This scenario was played over several times for the kids to ensure that they understood what had happened. Then following the last showing of the play, they had a chance to meet the bunnies of the story! When they met the bunnies, both the bunny in the purple and green shirt offered each infant a cracker, but could only take one. While the magazine didn’t give exact percentages, they did say the kids “overwhelmingly” choose the cracker from the bunny in the green shirt.
While of course this offers no concrete evidence, (because what if the good bunny offered a cracker while the “bad” offered a cookie?) it does kind of point towards the idea that the knowledge of goods is something humans might be born with.

Wow, Look What We’ve Done!

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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!

Last day of lab

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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.