virology
sa smith | December 4, 2008Gene therapy is easy, in theory.
Born with a bad gene? No prob!! Just replace it with one that works! We have lots of ways of doing that! I mean, retroviruses plop new genes into our cells all the time! Half of your genome is made of leftover retroviruses! So why dont we just put a functional version of your 'bad' gene in a retrovirus, and let it do all the work? Yay!
Wait... no yay.
Retroviruses are still wild broncos. We cant tame them yet. Force them to insert here, but not here... so our previous efforts to use retroviruses as gene therapy vectors ended in disaster (cancer).…
sa smith | December 3, 2008Lets say Im holding in my hand, a syringe.
In this syringe is an experimental vaccine for HSV-2. The dreaded genital herpes.
The vaccine is a live HSV virus with one gene deleted, ICP0 (free paper about this virus). When ICP0 is gone, the virus can still establish life long infection (if you get this vaccine, you will be infected with HSV), but the viruses produced from this infection will be extraordinarily susceptible to interferon. This means that rather than getting a freak-out-inflammatory response where your immune system goes nuts when the vaccine virus reactivates (causing painful…
sa smith | October 17, 2008I love the intrawebz!
I was bopping around on Google last night, looking for neat info about Cauliflower Mosaic Virus (post on that later!), and I stumbled upon a really awesome article from 1994:
The use of Cauliflower Mosaic Virus (CaMV) in genetic engineering: 35S Promoter (CaMV) in Calgene's Flavr Savr Tomato Creates Hazard
Now I have no idea who "Joseph E. Cummins" is. He might be as embarrassed by that article today as I am amused by it. But the website that is hosting that article is concerned about two things: FRANKENSTEIN GMOs, and cell phones mutating your DNA.
hehe.
Anyway,…
sa smith | October 14, 2008After generations of humans whined and moaned about how awful viruses are, turns out those 'wads of nucleic acid and protein' might just save our sorry asses when we ruin Earth and are forced to establish colonies on other planets/moons.
A key to establishing permanent residence on another planet is our ability to terraform. A key to terraforming is getting plants to grow to transform the land and atmosphere.
Well, there is a grass that grows in Yellow Stone National Park (among other places). Nothing much special about it-- just a regular switchgrass/panicgrass sorta thing, Dichanthelium…
grrlscientist | September 24, 2008tags: x-ray crystallography, foot and mouth disease, research, viral research, streaming video
Below the fold is an utterly fascinating video that documents the current state of the research in one lab that is developing a drug that stops foot and mouth disease virus from replicating in the host cells. Even better, this beautfully executed video was created by the lab members themselves! I can hardly wait for more scientists and labs to document their research in real-people accessible videos such as these [6:03]
This lab has its own blog, so go there!
sa smith | September 17, 2008Though HIV-1 is the retrovirus that gets all the press these days, it was not the first human retrovirus discovered. The 'first' human retrovirus was discovered in 1980-- Human T-lymphotropic virus, HTLV.
HTLV has a couple of things in common with HIV-1-- Though it is not a lentivirus, it is still 'complex', meaning it has gag, pol, env and a couple accessory genes. And it likes to infect activated CD4+ T-cells like HIV-1.
But there is an interesting difference-- You cant take a bunch of HTLV viruses, throw them on CD4+ T cells, and infect the cells. That is, 'free' virus is relatively non…
sa smith | August 27, 2008Being a young scientist, I take a lot of 'science' for granted. Weve 'always' had PCR. Weve 'always' had restriction enzymes. We 'always' knew HIV-1 is a retrovirus, and uses CD4 and CCR5/CXCR4 to infect cells. Weve 'always' known that retroviruses are important for the evolution of life on this planet. We 'always' knew about micro-RNA and the RNA silencing machinery.
So its wonderful fun to read papers written before we knew X, Y, Z-- watching the discoveries take place. Considering my last entry was about how much you totally dont want ERVs to be functional, I thought Id write about a…
sa smith | August 27, 2008This is a repost from the old ERV. A retrotransposed ERV :P I dont trust them staying up at Blogger, and the SEED overlords are letting me have 4 reposts a week, so Im gonna take advantage of that!
I am going to try to add more comments to these posts for the old readers-- Think of these as 'directors cut' posts ;)
Retroviruses: They like causing cancer. Therefore, you really, really dont want endogenous retroviruses to be functional. But you dont have to take my word for it *rainbow shoots across the screen*
Chickens so rarely get honorable places in history. Yet they do have at least…
sa smith | August 13, 2008I found out through Google News yesterday that the FDA approved a new drug for the treatment of Hepatitis B.
Now, normally, I would have ignored a story like that. Im not really all that interested in antivirals-- pharm research is on the opposite end of the research-spectrum of me. And theyre coming out with new drugs all the time (and pulling drugs off the market all the time...). Drugs arent my thing. Plus, Hepatitis B is a DNA virus, not a retrovirus... so, I mean "YAY! New therapy!" but this news story just isnt my cup of tea.
... Or is it? hehehehehe!!
The drug the FDA approved isnt…
sa smith | August 11, 2008Like any curious pup, the second Arnie encounters hedging/bushes/shrubbery, his first instinct is to dive right in in the hopes of flushing out some yummy yummy bunnies/kittens/boars.
Like any over-protective owner, I run after him screaming "GET OUTTA THERE YER GUNNA GET BITTEN BY A SNAKE!!!"
Cause when you start poking your nose in places you arent supposed to be-- you dont always find yummy squirrels. Sometimes you flush out bad things... like rabies infected vampire bats. Thats exactly what logging/mining expeditions in Venezuela have done. Theyve displaced colonies of vampire bats...…
sa smith | August 8, 2008Quote:
"I think ultimately we will find a huge number of novel viruses in the ocean and other places," Suttle says -- 70% of viral genes identified in ocean surveys have never been seen before. "It emphasizes how little is known about these organisms -- and I use that term deliberately."
Everyone has been emailing me about a sweet new virus my Virus Boyfriend and his posse discovered: Sputnik.
A long time ago, in a galaxy far far away, people thought that viruses were 'degenerate' forms of life. Scientists saw viruses assimilating genes from their hosts and plopping them into new hosts (ie…
grrlscientist | August 6, 2008tags: virology, mimivirus, sputnik, virophage, microbiology, molecular biology
Now here's an astonishing discovery that's hot off the presses: a virus that infects other viruses! This amazing finding is being published tomorrow in the top-tier peer-reviewed journal, Nature.
I don't know about you, but when I was in school, I was taught that viruses could only infect other living cells, and further, I was taught that viruses are not living cells. So, logically, one could conclude that viruses cannot infect other viruses. But a new discovery by a group of scientists in France reveals otherwise…
sa smith | July 24, 2008EMAIL!
Dear ERV--
I have a question about virus transportation inside, say, blood. I did a rough estimate of the average virus Reynolds Number and it turned out to be around .0051. So aside from some good old Brownian Motion, those viruses aren't really going anywhere without some sort of flagella or what-have-you. Do any viruses have a propulsion mechanism or do they all just loaf around wait for stuff to bump into them?
Cool question!
Short answer- No, viruses dont have their own propulsion systems :) That would require ATP and a means to generate ATP, ie metabolism. Viruses dont have…
sa smith | July 22, 2008STEP 1: Profess your undying love for a revolutionary person in your field of study, on your blog.
STEP 2: ???
STEP 3: PROFIT!
Dear ERV
As I notice that you are interested in the origin of virus and role in evolution. I send you a recent chapters that I wrote on the subject
Best regardsYour virus boyfriend
Patrick
*blink*
ROFL!!!
Oh well, my embarrassment is your alls gain! Forterre sent me a chapter he recently wrote for the Encyclopedia of Virology on the origin of viruses, and Im gonna review it for you all! Omg, its so dreamy you guys :D He expands upon how he would connect viruses…
sa smith | July 22, 2008This is a repost from the old ERV. A retrotransposed ERV :P I dont trust them staying up at Blogger, and the SEED overlords are letting me have 4 reposts a week, so Im gonna take advantage of that!
I am going to try to add more comments to these posts for the old readers-- Think of these as 'directors cut' posts ;)
Gimme a sec. Youll see why Im reposting this. *melts with embarrassment*
Me: "OMG! My boyfriend published another paper!!"
Bossman: "Ugh. Do you have any idea how old he is?"
Me: "Our love, it is forbidden."
My virus boyfriend Patrick Forterre is still fighting the good…
sa smith | July 10, 2008Darwin isnt the only one celebrating a very special birthday soon!
This year is the 30th anniversary of 'quasispecies'!!!
To celebrate, there is going to be a drool-inducing conference in Barcelona Spain later this year!!
QUASISPECIES: PAST, PRESENT AND FUTURE, 30TH ANNIVERSARY (they dont have a website up, but they have a doc file with a list of speakers!)
While I will be working my ass off in the lab to enter a hail-mary abstract in the hopes of attending myself, Im trying to convince the conference organizers to record the main speakers and put them up on the web for everyone to watch!
'…
sa smith | July 9, 2008Use #1-- Identifying the exact source of HIV-1 and HIV-2.
Use #2-- Determining the ecological/zoonotic/epidemiological implications of Simian Foamy Virus infection in chimpanzees!
Simian Foamy Virus (SFV) is another complex retrovirus, like HIV-1, but on a different branch of the retroviral family tree. So it still has the same basic proteins (gag, pol, and env-- Im getting to env), just different bells and whistles.
It also performs its own unique twists on the retroviral life-cycle, like going through the process of reverse transcription as the baby viruses bud off! Yeah not in the new…
sa smith | June 24, 2008You know when professors say something thats really obvious, but they say it in such a way that suddenly the universe makes sense, and your head explodes?
I had one of those moments yesterday while listening to a professors presentation on a nifty herpes virus, cytomegalovirus (CMV is like EBV-- pretty much everyone has been infected, but it doesnt hurt you unless youre immunocompromised).
Now in contrast to my elegant, streamlined retroviruses, herpes viruses are friggen monsterous. HIV-1 is about 10,000 base-pairs long (single stranded RNA), with nine genes, while CMV is 235,000 base-pairs…
sa smith | June 11, 2008Last Saturday evening I went to a friends house to let Arnie play in their backyard, and today Im scratching a dozen mosquito bites.
Arg.
But what does a virologist think when they get mosquito bites?
West Nile! WHOOOO!!!
And what does a girl who studies HIV-1 env think of when she thinks of West Nile?
Convergent evolution! WHOOOWHOOO!!!
WN was all over the news a few years ago because it can kill people. But there is no reason to be a spaz about it. Im under the impression that lots of us have been infected with WN, got a minor fever, and recovered without even noticing anything was…
sa smith | June 4, 2008This is a repost from the old ERV. A retrotransposed ERV :P I dont trust them staying up at Blogger, and the SEED overlords are letting me have 4 reposts a week, so Im gonna take advantage of that!
I am going to try to add more comments to these posts for the old readers-- Think of these as 'directors cut' posts ;)
So like, you know when people go all Monty-Burns-as-Howard-Hughes and start seeing germs everywhere?
I dont have that. But I kind of have that. Somehow, I work viruses into every aspect of my life... Including poop.
So I gotta say to PalMD:
Its not the bacteria! Its bacteria…