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Newly Discovered Virus Widespread in Human Gut

timothy posted about 2 months ago | from the right-under-their-noses-and-stomachs dept.

Medicine 100

A newly discovered virus has been found by a San Diego State University team to live inside more than half of all human gut cells sampled. Exploring genetic material found in intestinal samples, the international team uncovered the CrAssphage virus. They say the virus could influence the behaviour of some of the most common bacteria in our gut. Researchers say the virus has the genetic fingerprint of a bacteriophage - a type of virus known to infect bacteria. Phages may work to control the behaviour of bacteria they infect - some make it easier for bacteria to inhabit in their environments while others allow bacteria to become more potent. [Study lead Dr. Robert] Edwards said: "In some way phages are like wolves in the wild, surrounded by hares and deer. "They are critical components of our gut ecosystems, helping control the growth of bacterial populations and allowing a diversity of species." According to the team, CrAssphage infects one of the most common types of bacteria in our guts. National Geographic gives some idea why a virus so common in our gut should have evaded discovery for so long, but at least CrAssphage finally has a Wikipedia page of its own.

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CrAssphage? (5, Funny)

Anonymous Coward | about 2 months ago | (#47546723)

come on...

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47546911)

Sure. I don't know what the "ass" part of the name signifies, but the second syllable is from the Greek phagein, to eat. That means this virus eats your butt. What a great name.

Re:CrAssphage? (1)

Anonymous Coward | about 2 months ago | (#47546927)

I know! This virus serves a great and useful purpose: its eats that nasty and redundant CR character that Windowz and friends like to insert as part of their line endings. In other words, this gut-living virus eats crap. Bring it on!

Re:CrAssphage? (-1)

Anonymous Coward | about 2 months ago | (#47547217)

i gave yo mama a bacteriophage in her gut when i fucked her up the ass

Cr(oss) Ass(embly) (4, Informative)

tepples (727027) | about 2 months ago | (#47546955)

I don't know what the "ass" part of the name signifies

The Nat Geo article states that crAss stands for the technique used to piece together fragments of the virus's genome: "They called it crAssphage after the cross-assembly method that revealed its existence."

Re:Cr(oss) Ass(embly) (1)

Anonymous Coward | about 2 months ago | (#47547135)

I'm sure there was no attempt at intentionally choosing an acronym with a double meaning. Nope, none at all.

Re:Cr(oss) Ass(embly) (4, Funny)

Cryacin (657549) | about 2 months ago | (#47547401)

Who would have thought that scientists would stoop to this CrAss attempt at humour.

Re:CrAssphage? (5, Funny)

sjames (1099) | about 2 months ago | (#47547155)

I believe the Cr is for chromium. Thus the correct translation is "bite my shiny metal ass".

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47547305)

This comment is funnier than all the others.

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47549957)

Epic!

Re:CrAssphage? (2)

tlambert (566799) | about 2 months ago | (#47547265)

Sure. I don't know what the "ass" part of the name signifies, but the second syllable is from the Greek phagein, to eat. That means this virus eats your butt. What a great name.

Chromium Chloride is purple, so clearly, this is a Purple People Eater... is it airborne?

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47547763)

The one time that the "fetid asshole copypasta" would actually be on topic!

It's still fucking gross though.

Re:CrAssphage? (1)

fj3k (993224) | about 2 months ago | (#47546999)

It's a little bit crass, I agree.

Re:CrAssphage? (1)

Anonymous Coward | about 2 months ago | (#47547137)

Well, the lead scientist was Dr. Seymore Butts.

.

Re:CrAssphage? (2)

nbauman (624611) | about 2 months ago | (#47547229)

Well, the lead scientist was Dr. Seymore Butts.

I was pretty sure you're joking but I did check.

One author is Noriko Cassman.

Another is Ramy K. Aziz.

You can laugh but they've got tenure.

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47550945)

You can laugh but they've got tenure.

Why would I laugh? I understand the joke being referenced, but I fail to see how either name is in any way fanny-related.

Unless it's as simple as "Cassman contains the word ass" and "Ramy, rhymes with fanny". But that's stretching it, don't you think?

Re:CrAssphage? (1)

nbauman (624611) | about 2 months ago | (#47547247)

I once read an article about how some Japanese graduate students discovered a bunch of new genes and gave them all names that were obscene in Japanese.

I can't cite a source. I was pretty sure I read it in Science News but an editor at Science News tried to find it and couldn't.

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47548119)

What a shitty name.

Re:CrAssphage? (0)

Anonymous Coward | about 2 months ago | (#47548625)

I couldn't resist the temptation, all I could do is post as AC.... .... crAssPhage: All your ass are belong to us.

Re:CrAssphage? (1)

sabbede (2678435) | about 2 months ago | (#47548775)

Bit too "on the nose" right?

Re:CrAssphage? (1)

DoctorBonzo (2646833) | about 2 months ago | (#47548783)

If I remember correctly, there is a fruit fly gene discovered in Japan that was named fushi tarazu, abbreviated ShiTz.

A temperature sensitive variant was subsequently named HotShiTz.

Just goes to show that biologists can be as sophomoric as us geeky guys 'n gals.

Someday, maybe, they'll get past 3-letter names for genes & proteins...

Why is it called "CrAssphace?" (0)

Anonymous Coward | about 2 months ago | (#47546731)

Why did the scientists call it "CrAssphace"? Don't they realize that it sounds a lot like "see our ass face" in English? Or are they just playing a joke on us?

Re: Why is it called "CrAssphace?" (0)

Anonymous Coward | about 2 months ago | (#47547159)

CrAssphage, not CrAssphace.

Re: Why is it called "CrAssphace?" (-1)

Anonymous Coward | about 2 months ago | (#47547221)

It's pronounced like a question - "See our ass, faggy?"

CrAssphage (0)

Anonymous Coward | about 2 months ago | (#47546749)

That sounds like the name of a type of a virus that infects operating systems instead of humans.

The description doesn't help: (0)

Anonymous Coward | about 2 months ago | (#47546761)

'The circular viral genome is around 97 kbp in size and contains 80 predicted open reading frames.' from http://en.wikipedia.org/wiki/CrAssphage: So it's a 97 kilobyte circular virus with 80 frames of code?

Well hopefully someone will add it to the virus dbs fast :)

The description doesn't help: (0)

Anonymous Coward | about 2 months ago | (#47546935)

I don't care how big it is, so long as it's in Source Control

Re:The description doesn't help: (1)

Nutria (679911) | about 2 months ago | (#47547015)

kb == kilobits

Thus, it's 12416 kilobyte-pairs.

Re:The description doesn't help: (2)

Megane (129182) | about 2 months ago | (#47547079)

A base pair is 2 bits of information. So it's actually around 24KB of information. And a reading frame is just a valid start point in the DNA. Codons are 3 base pairs, but only a couple of combinations start a reading frame.

Re:CrAssphage (1)

thieh (3654731) | about 2 months ago | (#47546763)

That sounds like the name of a type of a virus that infects operating systems instead of humans.

Maybe one is already in development...

Re:CrAssphage (1)

Megane (129182) | about 2 months ago | (#47547037)

"Phage" means it eats something. So it sounds more like a virus that eats your ass.

I heard it comes from McDonalds food. (0)

dicobalt (1536225) | about 2 months ago | (#47546755)

That's all, did you expect a joke?

Re:I heard it comes from McDonalds food. (0)

Anonymous Coward | about 2 months ago | (#47547499)

A dose of wood meat pulp from concentrate! : ---]]

The Phage (5, Funny)

Chad Smith (3448823) | about 2 months ago | (#47546757)

Vidiians are going to be pissed.

Re:The Phage (2)

Kultiras (2589819) | about 2 months ago | (#47546765)

Well played, sir. Never any mod points when you need them...

Re:The Phage (-1, Troll)

Anonymous Coward | about 2 months ago | (#47546849)

I don't get it. Why are you commending him for merely dropping a rather mainstream sci-fi reference?

I always think it's quite stupid when somebody drops a reference to some Family Guy or The Simpsons scene in totally unrelated discussion. Half the time the other people in the conversation don't even get it, since they've got better things to do than watch season 27 of The Simpsons, or season 18 of Family Guy. And those who do get it often just think that the reference-dropper is a bit of a dickface.

If dropping pop culture references is stupid, then so is dropping sci-fi references. Please don't encourage anyone who is dumb enough to engage in such stupid behavior.

Re:The Phage (0)

Anonymous Coward | about 2 months ago | (#47546949)

If dropping pop culture references is stupid, then so is dropping sci-fi references. Please don't encourage anyone who is dumb enough to engage in such stupid behavior.

Unless they link a video clip of less than one minute duration...

Re:The Phage (0)

Anonymous Coward | about 2 months ago | (#47546979)

If dropping pop culture references is stupid, then so is dropping sci-fi references.

Since when is referencing popular culture considered a stupid thing to do? Not that I got it either, I don't follow... Star Trek I guess... Thanks Google... But your claim is still pretty CrAss.</bad pun>

Re:The Phage (0)

Anonymous Coward | about 2 months ago | (#47547053)

Half the time the other people in the conversation don't even get it, since they've got better things to do than watch season 27 of The Simpsons, or season 18 of Family Guy.

Let me catch you up:
https://www.youtube.com/watch?v=gomXiPa0nc8 [youtube.com]

Re:The Phage (0)

Anonymous Coward | about 2 months ago | (#47547879)

dropping pop culture references is stupid

unless it is funny, Sheldon.

Agreed (0)

Anonymous Coward | about 2 months ago | (#47548621)

I totally agree with you. Childish stuff. Then, even worse, you get 5 people jumping on you. Sadly, this referencing stuff has been a mainstay of Slashdot for so long that, like other oft-repeated lies, it starts to make sense to the majority. "Beef sounds good", "fluoridation is safe and effective in preventing tooth decay", "violent video games don't make you violent", etc. = lies our forefathers told our fathers who told us. The majority really don't Think Of The Children.

crAss (5, Informative)

GrahamCox (741991) | about 2 months ago | (#47546759)

OK, I wondered. I'm sure you did. It is short for 'cross Assembler' - the software used to sequence the genome (I skimmed the paper). Not what you thought. No.

No shit.

Re:crAss (4, Funny)

Nemyst (1383049) | about 2 months ago | (#47546805)

It's still a pretty shitty name though. I wonder if the scientists are bummed about the realization.

Re:crAss (1)

gargleblast (683147) | about 2 months ago | (#47547087)

This is bottom-grade science. Too much Farquharson around at SDSU. Even the Wikipedia page is bog standard.

Re:crAss (2)

roman_mir (125474) | about 2 months ago | (#47547313)

FRY: This is a great, as long as you don't make me smell Uranus. ... I'm sorry, Fry, but astronomers renamed Uranus in 2620 to end that stupid joke once and for all. FRY: Oh. What's it called now? PROFESSOR FARNSWORTH: Urectum.

Re:crAss (0)

Anonymous Coward | about 2 months ago | (#47548037)

Scientists love that kind of thing. Especially medics (and non-medics in related fields). Loads of new techniques are given highly implausible names, just so they can shoehorn them into some "clever" acronym. Or copronym, in this case. Apparently it improves the chances of getting future funding.

Re:crAss (1)

sillybilly (668960) | about 2 months ago | (#47549761)

Sometimes somebody else gives you a crass name, as a way of mocking you, such as Anal as an abbreviation for Analytical. And then you're stuck with it, love it or not. You yourself would have probably chosen a more respectable name, so with a name like this there may be a reason to look for tension, Abel-Kain or racism related social and psychological issues with the people that came up with the name. What a fun task for all these humanities college graduates analyzing the anthropological/psycho-sexual-freudian ramifications surrouding biotech muscle-minds. Now I don't envy the scientists involved in this research, but they can send all these humanities grads away for a while by keeping them busy analyzing some really heavy duty pscyho issue loaded topics like weird porn, and then they can get some breathing space for themselves in the meantime. As in here, analyze this, you psycho freaks. And leave me alone for a while.

And by the way, in biotech we should take on a more voyeuristic approach, as in watching all the life that's already there, and learning it, without creating too much new biotech variation in a dish, that's so cheap to do, but it can dangerously get out of hand. And hold off on it while with outer space, instead of having a voyeuristic Hubble telescope and the like attitude, we should take on a more practical and pragmatic invade nobody's territory and claim it as our own approach, and live there, safely, securely, isolated from the atmosphere and biosphere down here, which is very expensive to do, but safety first. Then you an go more wild tinkering with biotech in a dish and carrying it on your skin outside and infecting the whole atmosphere with it.

Re:crAss (1)

bistromath007 (1253428) | about 2 months ago | (#47546877)

I read that. I think it's full of shit. They can claim it's an accident all they want, but they're obviously blowing smoke up our ass.

Re:crAss (1)

Sooner Boomer (96864) | about 2 months ago | (#47546899)

Is this the cause of (cr)Assburger's?

Re:crAss (0)

tepples (727027) | about 2 months ago | (#47546969)

Just because vaccines don't cause autism doesn't mean that a wild virus (the opposite of a vaccine) necessarily causes it.

Re:crAss (2)

alzoron (210577) | about 2 months ago | (#47547409)

Actually regular viruses can act as vaccines as well, for instance contracting cowpox can result in an immunity to smallpox.

Re:crAss (2)

LordLucless (582312) | about 2 months ago | (#47547061)

Yeah, in the same way GIMP stands for Gnu Image Manipulation Program

Re:crAss (1)

John.Banister (1291556) | about 2 months ago | (#47547979)

And their reason not to choose xasm was...

I hear (0)

Anonymous Coward | about 2 months ago | (#47546777)

I hear if you take "aciphex" (ass effects) .. you be good to go!!!

uh, (1)

mark_reh (2015546) | about 2 months ago | (#47546797)

it smell like ASS up in here!

Is this the virus that killed Eric Garner? (-1, Offtopic)

NemoinSpace (1118137) | about 2 months ago | (#47546811)

The police say they didn't do it, so what else could it be?

Did they sampled it? (0)

Anonymous Coward | about 2 months ago | (#47546833)

A newly discovered virus has been found by a San Diego State University team to live inside more than half of all sampled human gut cells sampled.

Sample at twice the bandwidth (2)

tepples (727027) | about 2 months ago | (#47546977)

Nyquist's theorem [wikipedia.org] states that you have to sample twice to make sure you get both the high and the low points.

Re:Did they sampled it? (1)

RDW (41497) | about 2 months ago | (#47548297)

There's a bigger problem with the summary than that - timothy has misread the BBC article, which refers to 'half of all samples from the gut'. These aren't human cell samples, they're faecal samples. The phage presumably infects gut bacteria, not human cells. From the proteins that the phage encodes, the researchers predict the genus of bacteria the host belongs to (Bacteroides).

My pandemic (3, Funny)

cablepokerface (718716) | about 2 months ago | (#47546835)

Lol, so you guys finally discovered it! Well you're too late, haha. I am now going to invest my points in heart failure and liver failure and your doctors will never have a cure in time!

Re:My pandemic (1)

Anonymous Coward | about 2 months ago | (#47547379)

Did you infect Madagascar yet?

Re:My pandemic (1)

Flounder (42112) | about 2 months ago | (#47550639)

Frigging Greenland!

Chromium Assphage (1)

Anonymous Coward | about 2 months ago | (#47546921)

My new heavy metal band, come check us out on tuesday nights, $2 PBRs

Oh my god! We're not humans (0)

Anonymous Coward | about 2 months ago | (#47546925)

We're just ecosystems of microbes fighting and fucking, and eww,peeing inside us!

Good grief! MORE symbiotes? (1)

BoogieChile (517082) | about 2 months ago | (#47547117)

So does this mean that as well as the bacteria that we have living in a symbiotic relationship with us, there's viruses in our internal ecosystems that we need to keep us alive as well now?

Re:Good grief! MORE symbiotes? (0)

Anonymous Coward | about 2 months ago | (#47547601)

Drawing a line saying "this is strictly a human" and "this is strictly a bacteria|virus|other" is ridiculous. We are complex jumbles of whole bunches of shit tossed together and the lines get really blurry at the lower levels. It's just a line in the middle of the Sahara.

Their next focus for research should (0)

Anonymous Coward | about 2 months ago | (#47547323)

be the human gunt. What's in there?

Re:Their next focus for research should (1)

mark_reh (2015546) | about 2 months ago | (#47547367)

What's a gunt?

Re:Their next focus for research should (0)

Anonymous Coward | about 2 months ago | (#47547403)

What's a search engine?

Re:Their next focus for research should (0)

Anonymous Coward | about 2 months ago | (#47547407)

ask your wife...

Re:Their next focus for research should (1)

sillybilly (668960) | about 2 months ago | (#47551307)

haha, that was very funny.. should have been: ask your baby momma, but this is Slashdot, for Pete's sake..

Obama Is The Virus (-1)

Anonymous Coward | about 2 months ago | (#47547355)

And amongst Obama's brood are the employees of the Environmental Protection Agency. Talk about vermin, they are and need to be eradicated. Burn baby burn.

Re:Obama Is The Virus (1, Funny)

bigfinger76 (2923613) | about 2 months ago | (#47547963)

I specifically came here to joke about no one shoehorning Obama into this discussion yet. No shit.

You people are amazing.

Re:Obama Is The Virus (1)

geekoid (135745) | about 2 months ago | (#47549871)

The media of AC on slashdot was created becasue people should be able to say what they want without repercussions.
I now think they where wrong and should remove AC.

People will scream about whistle blowers et. al, but that doesn't really happen on slashdot It's mostly an excuse to be an ass, and/or not think. Or troll.

Re:Obama Is The Virus (1)

sillybilly (668960) | about 2 months ago | (#47550255)

Yeah, not everything is Obama's fault. Lots of things are, but the EPA is a good thing. So is OSHA. Without them we have things like shown on http://www.filtersfast.com/art... [filtersfast.com] to which should be added Fukushima and West, TX fertilizer disasters (which is why urea is a safer nitrogen fertilizer than ammonium nitrate, but requires a carbon source, such as coal or oil or natural gas, to make. On the other hand ammonium nitrate makes a great explosive for makeshift bombs and makeshift ammo for self defense if social security fails and the welfare checks stop coming and an economic apocalypse or an Asian invasion hits, and people start eating each other, but it's also a bad explosive in the hands of terrorists with a cause, such as the Oklahoma bomber bitchin about the Waco TX FBI tank invasion, citing "my head is bloody but unbowed" Invictus poem at his execution. So that West, TX, explosion is a bad thing, but it has a yin yang good side to it, that less ammonium nitrate and more urea will be made and supplied bulk to the public. Liquid ammonia, if handled properly, is cheaper in massive bulk per unit cost, but urea is cheaper to handle in smaller quantities, and can be sold in bags at Walmart, and is safer than both ammonia or ammonium nitrate.) The EPA and OSHA only become a bad thing if they don't properly exercise balance, or common sense, i.e. they are too overbearing, or not overbearing enough. It's difficult to balance economics and jobs with environmental protection, and heavy swings in either direction may happen due to simple incompetence. Rule #1 of any job: we are all incompetent at what we do, some are just more incompetent than others. And the opposite is true too, we are all experts at what we do, some are just better than others. Usually practice makes the masters, and that's why employers look for experience above anything else when trying to get a job done, but experience alone is not a guarantee of great competence.

catalyst CrAssphage (1)

nottynavi (3766359) | about 2 months ago | (#47548493)

Looks like the virus acts as a catalyst; Helping other viruses in reacting fast and become more potent !!!

Re:catalyst CrAssphage (1)

sillybilly (668960) | about 2 months ago | (#47551135)

Any virus is a form of life, in that it is negative entropy, in an entropy tending universe. Life seeks to create order, and maintain order, oftentimes in a fight, at an expense of another life form. A virus, because it cannot sustain itself on its own, has no functioning cell or nucleus, it is a parasite, a predator of other life. A predators function in an ecology is extremely complex, but there is one rule to any long term successful predator or parasite, is that you don't exterminate your food supply, you don't overgraze, if you want to live long. But most unintelligent life is blind, because a lot of predatory lifeforms don't follow this principle, such as humans driving mammoths extinct, and almost the American bison, or buffalo, extinct, also lots of invasive species such as cats on small islands, they don't right away live in harmony and equilibrium with their ecosystem, but instead drive lots of things extinct while promoting their own self interest to the point of driving themselves extinct or to a collapse when their food supply collapses. Amongst blind parasites or predators you can count the folks of Wall Street, who made a shit load of money betting against the housing bubble(and that's not a crime, because that is serious risk taking by those involved, but not that serious once the signs of idiotic bubble vs. high paying jobs gone is obvious). Blind parasites are the folks of Wall Street who killed off or made completely dysfunctional union jobs that Archie bunker used to make a living on, when you didn't need no welfare state, everybody pulled his weight, guys like us we had it made, those were the days. And he was a responsible fucker, because as soon as he lost his job and food supply, his dick went limp, to the sorrow of his woman, who always wants it, more babies, more babies, more life, always want to fuck, that's how women are. With some exceptions though. But he reproduced in balance with his available resources, and it is on the shoulders of the male that the duty of limiting population growth out of control falls, because the woman, even if she doesn't want it, she can be made pregnant, but he cannot get raped if he has a limp dick, the mechanics make it very difficult, if not impossible to get a child out of him under dire economic circumstances. And even if he produced a stiffy, he could consciously not make a baby. Unions provided the middle class jobs to the bulk of the nation through the nations heydays, and there was an environment where a company breaking even, but paying all its bills plus the humongous union wages was acceptable, without turning much quarterly profit or dividends, or just minimal. Unions owned the companies they worked for, because they made so much money in them, they made sure their money supply was alive and healthy. They fixed problems where rubber meets the road, on the shop floors, and sustained an array of remote-from-where the rubber meets the road executives charting pretty graphs, doing overhead slide presentations, etc, as a luxury item, because the money was good, because in a stable job experience was high, competence was high, efficiency was high, and there was money to blow on such office people. Drawing a pretty chart or a statistical cause and effect analysis has nothing to do with the real world problems of hey this part is out of spec, and that thing there is stuck, and I can't get it unstuck, and maintenance is busy for 2 hrs, and I can run the machine at a high setting that lowers its lifetime, but still profitably because I can make the product, and if not, shut the machine down and wait two hours. These life and death decisions about profit can only happen by the competent worker. The office charting and presentation bullshit has almost nothing to do with making a quality product that the customer wants to buy, and make it cheaply for him, while you collect $25/hr and get to sleep 4 hrs out of 8 hrs on the job. I mean literally sleep. If the guy on the floor can't make the product, I don't care how expert and good the office people are, it's hopeless. Everything rides on their backs, and the more they get paid, the more devoted they get. I'm talking a pay where Archie bunker can sustain a stay at home wife, so he can sit in his stinky old armchair to recuperate for an hour when he gets home dead tired, and dinner's ready, and she interrogates him how work was. Behind every great man there is a woman pushing his buttons correctly, and pulling his puppet strings correctly. Her life was kinda hell always at home, living very sheltered, alone at home, but women loved to stay home if there were babies. And there were always neighbors, and tv, and radio, and paper, and Sunday church. And the kids get raised well, so tomorrow you have a good crop of competent workers again. Without a job she was OK, because being a mom educating kids is a full time job, and he, when he could sustain such a home, pretty much devoted his life to his job in ways that minimum wage temp agency workers can't comprehend. A dynamic job market is good for the economy. Yeah, observe with your own two the miracle of the dynamic job market, and unstable families around you. Baby momma. Baby daddy. What happened to wife, and husband? We can't afford such a luxury anymore. All because of the parasites on Wall Street demanding higher quarterly profits for their shareholders. Everybody can be a shareholder. There is this ad on line, with Warren Buffet saying anybody with $40 can make a lot of money on the stock market, maybe even a living. They should ban such ads. There are enough parasites already, and not enough prey to feed on or graze on. It all got off shored.

Unions were only provided to the bulk of the population while there was the communist threat from Russia, once that threat is gone, it's time to disenfranchise the population again, turning everyone back into serfs. The Great War, aka as WWI, is not over yet, the nobility is coming back, and coming back with a vengeance. The war of Independence of 1776, and war of 1812, the first invasion of the USA, the war about the land of the Free and the home of the brave, is not over. The nobility is coming back. And this time they have tools of never before - cameras on every intersection, GPS tracked cell phones with surveillance audio and video secretly always on in every pocket - the tools of mass control are tremendous now. And I look at it half sad, half happy, there is a good side to the nobility coming back, such as having government coffers that contain some wealth again. Hey dear politicians, the government coffers are empty, empty squared, empty plus plus. Quit pork barreling your way through the bottomless negative worth of the coffers, and try to have a treasury again, full of wealth. In a sense what the country is missing is an owner, who cares about his property. Aka a king, or monarch. And hey, there was this text somewhere that "the rain may enter, the wind may enter, but the King of England and his mighty army may not enter the ruined tenement" somewhere, even if that's naive wishful thinking. But I for one would welcome such an overlord, who leaves my ruined rain may enter tenement alone and allows me to prosper.

Re: catalyst CrAssphage (0)

Anonymous Coward | about 2 months ago | (#47553255)

What is up with you and your 100 page dissertation rants? They make no fucking sense.

Re: catalyst CrAssphage (1)

sillybilly (668960) | about 2 months ago | (#47595899)

I'm fuckin insane, dood. I'm the illest nigga on this block. Hold me back, hold me back, or I'll tell it like it is, in yo face, mutha fuckas. They are trying to turn me into some kind of terrorist, through some psychological warfare. Terrorist in the making. Fuck that. The only kind of terrorist I'll ever be is a verbal one, plug ya eeyas if u don't like it. I'll make y'all feel uncomfortable, and nobody is safe, I'll pick equally on everybody. And if you don't like it, you don't have to read my post, just skip it, move on to the next one please. I'm all anti violence. I'm half ass vegetarian. I stick up for bugs, against Da Man, represented by Monsanto, and y'all who mow your lawns, y'all are Da Man fucking up nature. All I ask is that you leave half of your lot unmowed. 50/50. Or at least a patch. And by the way the 50/50 guiding principle could go for things like stock market profits vs. jobs, share the income or revenue or whatever you can come up with, halfway. If the company makes 20 million, 10 million goes to the owners and stockholders, 10 million goes to the union. If stockholders elect a president who seeks improved quarterly bottom lines by screwing the workers out of their 50%, regulators could get involved. Families around the country depend on jobs. And the concentration of wealth in the hands of a very few, way about 10 million, what good does that do for the world? Don't get me wrong, I'm all for people having 20 million dollar yachts, but they should get it by also providing 20 million to their workers if their company has over 20 people. Not screwing them out of their creative value. Then everybody wins. Not 99/1, either which way, and if it has to be 99/1, it should be the union getting 99, and the owners 1, not the other way around like it is in this fully abusive property world. Like book publishers and science article publishers, and music labels, etc. They should split the bounty halfway, don't abuse contracts and property rights just because you got the upper hand. The Romans with Pontius Pilate had some kind of don't abuse your power mentality, but by Caligula it degraded into absolute porn and deviance and dogfights and gladiators vs. lions cutting each other down alive for entertainment, and abuse, like trying to introduce the statue of the Caesar as a God to be worshipped, into the Temple of Jerusalem. It's like it was better for the Temple to be destroyed, then suffer such a thing. I don't understand, what's so complicated about all this do not abuse your upper hand thing? It's called finding a middle ground, a golden middle way, between an abusive property exploitative world, where the high class bourgeoisie exploits the proletariat working class, and an unrealistic communist world, where the proletariat guillotined or at least chased away the bourgeoisie, but without property, but liberty, fraternity, and equality, nobody gives a damn, nor cares, nor feels any incentive to do anything about overgrazing in the tragedy of the commons. Why can't we all figure out a way for everyone to live well.

Most of you have it... (5, Informative)

robedwards (134136) | about 2 months ago | (#47548611)

I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department [sdsu.edu] at SDSU [sdsu.edu] ...

It was named after our analysis software, crAss (cross assembly) for comparing DNA sequences from different samples (called metagenomics [wikipedia.org] ). Here is the crAss article [nih.gov] that was published in 2012. Everyone else had missed this virus that was in their DNA samples, most of which have been published (many in high profile journals like Science and Nature). However, it wasn't until we used crAss that we recognized the virus was abundant and everywhere. When we looked at the NCBI [nih.gov] database of nucleotide sequences the virus is there and scientists had seen it before in fragments but not been able to piece it together to a whole genome.

We only find the phage in poo samples (they usually call them fecal samples...) from people (oh, and very occasionally on the skin of people, but we suspect they don't have great hygiene). We haven't been able to find it anywhere else that we have looked, and so we don't know what its range is beyond the intestine.

This is one of those situations where the computational biology is really driving the question and the biologists. You often head that bioinformatics is just a support science for "real biology" - that's not true. In this case, based on the questions the bioinformatics group came up with, the biology was supporting the bioinformatics analysis. The biologists were able to determine that the assembly of DNA fragments was correct, and confirm, using PCR [wikipedia.org] , that it is indeed a whole genome.

We (and others) are working on isolating the phage and designing experiments to test exactly what it does in our guts. That doesn't mean we can't speculate!

A couple of answers to comments:
1. Everyone (including the scientists that write grants and papers) confuses gut and fecal samples (sometimes deliberately). To be clear, almost all the samples we have are feces because it is everyone has it, it is easy to get, and everyone seems to want to share it. To get samples other than feces you need surgery, and so the non-fecal samples tend to be associated with other issues that require surgical intervention (and thus are complicated).
2. Noriko (Nori) Cassman is a graduate student (and so doesn't have tenure yet)
3. We were not responsible for the wikipedia page (or the twitter account)
4. phages are viruses that attack bacteria only. There is no evidence or suggestion that this virus does anything to human cells.

Re:Most of you have it... (3, Funny)

ArsenneLupin (766289) | about 2 months ago | (#47548793)

everyone seems to want to share it.

... and I just thought only monkeys behaved like this...

Re:Most of you have it... (1)

DoctorBonzo (2646833) | about 2 months ago | (#47548819)

I'm really curious as to what kind of comments about the name that you got in pre-publication reviews...

Re:Most of you have it... (5, Informative)

robedwards (134136) | about 2 months ago | (#47548939)

In one of the early versions of the paper we didn't have a name for it and just called it "the new virus". A (anonymous) reviewer said "The new virus would seem to need a name ("the new virus" is clumsy).", so we came up with crAssphage. It turns out there was an unexpected side benefit - there were essentially no Google results for crassphage until last week!

Re:Most of you have it... (0)

Anonymous Coward | about 2 months ago | (#47549365)

honestly, i think it's a mnemonic thing. All these scientists understand what a pain d-bio is, and so they help the next crop by naming their genes the stupidest, most moronically memorable names they can think of. :)

would you want to remember crAssphage or some odd combination of numbers and letters?

Re:Most of you have it... (1)

steelfood (895457) | about 2 months ago | (#47552861)

But did you really have to capitalize the 'A'?

Physical structure of the phage? (2)

Guppy (12314) | about 2 months ago | (#47549427)

I'm the last author on the paper and it was discovered in my bioinformatics lab in the CS department at SDSU ...

Quick question -- I see from your paper, do you have an idea what it looks structurally? A bunch of media sites have pictures but are using what is obviously stock art (mostly of T-even phages), but from your paper I see that it has no close phylogenetic relationship to known phages (and if your group had e-microscopy or crystallographic data, it would have been in the paper already).

Still, I figured someone skilled in virology might be able to identify some capsid sequences or something, and be able to make a decent guess.

Re:Physical structure of the phage? (1)

robedwards (134136) | about 2 months ago | (#47557003)

We don't have that capability yet. We have not isolated the virus, yet, (we're trying hard...) and so we don't have EMs of the particle which would tell us the T-number and other information, and our computational tools are not yet able to take a raw protein sequence, like that we can predict from the DNA sequence, and predict what the structure would look like. There are lots of groups working on that prediction step, and an annual competition (Critical Assessment of protein Structure Prediction) to see who is the best at predicting structure from sequence.

We also have a new modeler starting at San Diego State University in 2015 who focuses on phage capsid models, and hopefully we'll get something from that!

Re:Most of you have it... (1)

geekoid (135745) | about 2 months ago | (#47549893)

AMA ?

Re:Most of you have it... (-1)

Anonymous Coward | about 2 months ago | (#47549971)

Noriko (Nori) Cassman is a graduate student (and so doesn't have tenure yet)

Ah, thank you. So now we know who did all the work, because it is well known that the tenured are overpaid bums on an eternal vacation that just sign the work of their grad students and pretend its their own work. Amiright or amiright?

Re:Most of you have it... (1)

robedwards (134136) | about 2 months ago | (#47557065)

Well, we try not to pretend they did all the work ....

Re:Most of you have it... (1)

proto (98893) | about 2 months ago | (#47552211)

Google has just recently started a "Google X" project to create a complete picture of what a healthy human being should be. [slashdot.org] Google should be all over this if they really want a complete picture. Their commitment to studying the human genome could give afflicted people legitimate hope that their condition can be properly diagnosed. They may not find a cure for anything in X amount of years but at least they are on the right track.

Re:Most of you have it... (1)

robedwards (134136) | about 2 months ago | (#47557055)

The human genome is only a small part of what you are, the microbiome and virome (the microbial and viral components, respectively) have profound impacts on our health in ways that we really don't tet understand. However, this is an area where big data approaches that Google are good at will succeed. The only reason we found crAssphage is by comparing a lot of samples from different people. Imagine if we have genomes, microbiomes, and viromes from thousands of volunteers, together with health data about them, we can make a lot of intricate predictions about our health based on that data.

Re:Most of you have it... (1)

Reziac (43301) | about 2 months ago | (#47558473)

Have you looked at animal samples too? Seems to me it would be easier to get those upper gut samples...

Is it human-host only, or opportunistic wherever its favored bacteria thrive?

Has any of this virus been incorporated in our DNA?

Completely OT, having been preconditioned by the crAss cracks, my brain decided to parse your username as "robed wards" which made no sense. :)

Re:Most of you have it... (1)

robedwards (134136) | about 2 months ago | (#47562767)

We have looked at quite a few animal samples, and it is not that common. There are a few mouse studies, but many of those now have "humanized" gut bacteria! They actually make the mouse look like the human!

We think it is mostly human associated, but it would sure be good to sequence some poo from chimps and apes to see if we can figure out where it is in our evolutionary tree. But that is not something we're going to do ... hopefully others will.

Re:Most of you have it... (1)

Reziac (43301) | about 2 months ago | (#47563527)

Considering that wild mice who live in proximity to humans markedly prefer to eat stuff humans have touched ... I imagine you'd have to find wilderness mice to study!

Zoo primates could be 'contaminated' as well.

Looks like some future researcher is in for a long tramp through the back of beyond. :)

OH MY GOD! (0)

Anonymous Coward | about 2 months ago | (#47550333)

Am I going to die?

I've played enough Plague Inc... (1)

Flounder (42112) | about 2 months ago | (#47550627)

Hit over 50% worldwide infection rate, then start buying the symptoms that kill and spread. Just make sure you've infected the islands before they cut off water and air travel (Greenland, Iceland, Madagascar, New Guinea and New Zealand have defeated me often enough). Oh, and target the countries that are contributing the most to finding a cure.

Error in this article description (0)

Anonymous Coward | about 2 months ago | (#47550841)

" live inside more than half of all human gut cells sampled"

should be "live inside more than half of all humans sampled"

If it is a phage, it wouldn't infect human cells, only bacteria.

Good or Bad? (0)

Anonymous Coward | about 2 months ago | (#47558471)

Fine, a great discovery, my question is whether the new bug is good for us or bad for us...
should we try and get some for ourselves?

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