Archive for January, 2014

Jan 31 2014

DNA from caveman reveals interesting physical traits

Published by under Uncategorized

Recently, DNA from the wisdom tooth of a hunter-gatherer in a cave in Spain was analyzed and the data revealed some interesting new finds. The man exhibited a darker toned skin, although the exact shade is unpredictable due to many environmental factors. This is surprising, because it was thought that the Europeans of this time has already developed lighter skin. Furthermore, the man has blue eyes. The blue eye gene wasn’t thought to have developed for some time after this man lived. In many respects the analysis of this caveman’s DNA has changed the way we view people from the Neolithic time period. For more information about the DNA analysis you should definitely check out the article below.

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature12960.html

Comments Off on DNA from caveman reveals interesting physical traits

Jan 30 2014

Phreaks and Geeks

Published by under Uncategorized

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.

IMG_2979

No responses yet

Jan 29 2014

Neurology

Published by under Uncategorized

Ok, I don’t know what it is, but something about neurology is just absolutely captivating to me. The idea of a nerve working with a charge and being SO precise about it is just dumbfounding to me. I mean, how can nerves be that precise and consistent when they are working with a charge as tiny as -50 milliVolts? I mean in my high school robotics competition, we had voltage gradation for different parts of the robots that made it so they would only work within a 3 or 4 volt range. If the stuff that us humans make can only work within a precision of 3000-4000 mV and that seems stringent, how much more amazing is it that God can make something (and trillions of that something) that works very precisely at changes as small as this. I don’t know, but it’s amazing to me. Take a second to think about how wonderful this all is. I mean, how ridiculous it all is! Just saying, we’ve got amazing stuff we get to learn about and we are some of the only few in the world that will ever get the chance to look into stuff like this as their JOB. Don’t waste any opportunities, guys.

Comments Off on Neurology

Jan 28 2014

Fish are friends… not food!

Published by under Uncategorized

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!

2 responses so far

Jan 28 2014

Cloning Advance: Caffeine

Published by under Uncategorized

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.

No responses yet

Jan 27 2014

Hello world!

Published by under Uncategorized

Comments Off on Hello world!

Jan 27 2014

Vaccine for Staph?

Published by under Uncategorized

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?

 

 

One response so far

Jan 26 2014

Polio Virus

Published by under Uncategorized

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!

No responses yet

Jan 26 2014

Monkeypox Virus

Published by under Uncategorized

When we shared viruses the other day in class, we ran out of time before I had the chance to tell you all about the monkeypox virus. Made of double-stranded DNA, it is of the poxviridae family, putting it in the same family as cowpox and smallpox. This virus can affect animals, such as monkeys and prairie dogs, as well as humans. It can be transmitted through a bite or fluid contact, and its incubation period is ten to fourteen days long. It undergoes a lytic cycle for replication. While there have been very few cases of monkeypox in the US, it is something to watch out for while traveling in Africa.

Comments Off on Monkeypox Virus

Jan 25 2014

Mental Disability Test for Infants

Published by under Uncategorized

Comments Off on Mental Disability Test for Infants

Jan 24 2014

The Viral World

Published by under Uncategorized

I researched the polio virus last week. The polio virus is also called Poliomyelitis and it is in the genus Enterovirus. Being in the Enterovirus genus means that the polio virus is a relatively small virus, has a single stranded RNA genome, and thrives in the gastrointestinal tract. It occasionally attacks the nerves of the individual. The polio virus has been eradicated from the western hemisphere.

Here is a good website about the poliovirus:

http://wwwnc.cdc.gov/travel/yellowbook/2014/chapter-3-infectious-diseases-related-to-travel/poliomyelitis

I can’t wait for our genome to come back guys! So excited to start analyzing the genome.

Comments Off on The Viral World

Jan 23 2014

Royals

Published by under Uncategorized

(to the tune of Royals by Lorde)

I’ve never been an infection in the flesh

I put my DNA in amoebas of the Acanthamoeba genus

And I’m not proud of my assets,

With no ribosomes, only replication envy

 

But every virus is like sneezing, coughing, trippin’ in flu season

Weight loss, fever, look its AIDS,

We don’t care, we’ve got 1100 genes.

But virus is like fever, soreness, causing humans panic.

Headache, skin rash, infecting bacteria.

We don’t care, we aren’t caught up in their infection affair.

 

And we’ll never be royals.

It don’t run in our genes,

That kind of luxe just ain’t for us.

We crave a different kind of buzz.

Let me be your ruler,

You can call me queen Pandoravirus

And baby I’ll rule, I’ll rule, I’ll rule, I’ll rule.

Let me live that fantasy.

 

My friend and I—we’ve cracked the code.

We count our micrometers on the way to the amoeba.

And everyone who knows us knows that we’re huge like this,

We didn’t come from era.

 

But every virus is like sneezing, coughing, trippin’ in flu season

Weight loss, fever, look its AIDS,

We don’t care, we’ve got 1100 genes.

But virus is like fever, soreness, causing humans panic.

Headache, skin rash, infecting bacteria.

We don’t care, we aren’t caught up in their infection affair.

 

And we’ll never be royals.

It don’t run in our genes,

That kind of luxe just ain’t for us.

We crave a different kind of buzz.

Let me be your ruler,

You can call me queen Pandoravirus

And baby I’ll rule, I’ll rule, I’ll rule, I’ll rule.

Let me live that fantasy.

 

Ooh ooh oh

We’re bigger than they’ve ever dreamed,

And I’m in love with being queen.

Ooh ooh oh

Life is great without a care

We aren’t caught up in their infection affair.

 

And we’ll never be royals.

It don’t run in our genes,

That kind of luxe just ain’t for us.

We crave a different kind of buzz.

Let me be your ruler,

You can call me queen Pandoravirus

And baby I’ll rule, I’ll rule, I’ll rule, I’ll rule.

Let me live that fantasy.

 

Comments Off on Royals

Jan 23 2014

Bio Lab Take 2! Action!

Published by under Uncategorized

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!

No responses yet

Jan 22 2014

Answering the Question: What Will Stem Cells Become?

Published by under Uncategorized

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!

No responses yet

Jan 22 2014

Starting fresh

Published by under Uncategorized

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.

Comments Off on Starting fresh

Jan 22 2014

Abelson Murine Leukemia Virus

Published by under Uncategorized

Comments Off on Abelson Murine Leukemia Virus

Jan 22 2014

Mimivirus

Published by under Uncategorized

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

Comments Off on Mimivirus

Jan 22 2014

The Awakening

Published by under Uncategorized

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!

Comments Off on The Awakening

Jan 21 2014

Borna Disease Virus

Published by under Uncategorized

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.

Comments Off on Borna Disease Virus

Jan 21 2014

Bridges Across the Periplasmic Moat

Published by under Uncategorized

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

 

 

No responses yet

Jan 19 2014

Take 2!

Published by under Uncategorized

Comments Off on Take 2!

Jan 17 2014

New Semester, New Lab, New Opportunities… Let’s Get This Party Started!

Published by under Uncategorized

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. 🙂

No responses yet