Stories
Slash Boxes
Comments

SoylentNews is people

posted by janrinok on Saturday October 24 2015, @10:28PM   Printer-friendly

Scientists at the Max Planck Institute of Biochemistry in Martinsried near Munich and at the MPI of Molecular Cell Biology and Genetics in Dresden have now drawn a detailed map of human protein interactions. Using a novel mass spectrometric quantification method, the researchers determined the strength of each interaction. "Our data revealed that most interactions are weak, but critical for the structure of the entire network," explains Marco Hein, first author of the study. The paper has now been published in the journal Cell.

Proteins are the building blocks and central protagonists of the cell and contribute to all processes of life at the molecular level. They carry out their tasks by binding to each other and building interaction networks. With the help of quantitative mass spectrometry, scientists can determine precisely which proteins interact with each other. The technology can be described as molecular fishing: One protein is selected as bait. Fishing it out of a complex mixture retrieves all its interaction partners as well, which are then identified by a mass spectrometer. Scientists from Martinsried and Dresden have now analyzed 1,100 such bait proteins in a large-scale project. They mapped a network of over 5,400 proteins, which are connected by 28,000 interactions.

The different interactions have very distinct properties. Some connections are strong and serve a structural role, others are weak and transient, for instance in signal transduction pathways. Measuring the strength of an interaction is very laborious and hence complicated in high throughput studies. Using a novel strategy, the German scientists established a method of estimating the strength of each interaction indirectly. They measure the copy numbers of all proteins in the cell, and quantify the ratio at which each interactor is retrieved along with its corresponding bait protein. The stronger an interaction, the more of an interactor is recovered.


Original Submission

 
This discussion has been archived. No new comments can be posted.
Display Options Threshold/Breakthrough Mark All as Read Mark All as Unread
The Fine Print: The following comments are owned by whoever posted them. We are not responsible for them in any way.
  • (Score: 2) by Phoenix666 on Sunday October 25 2015, @04:21AM

    by Phoenix666 (552) on Sunday October 25 2015, @04:21AM (#254231) Journal

    graphene hype stories

    Ah, you're that AC. Graphene is an amazing material [graphenea.com] that is stronger than steel, more conductive than copper, and lighter than both. It has many other amazing properties as well. You aren't, perchance, descended from that one guy in the Stone Age who was always complaining about the hype around metal, are you?

    "PC is dead" disruptive drivel

    Oh that was one article the editors published today. I thought it was silly myself but thought I'd allow for the possibility that young'uns might find it "not silly." We'll mark you down in the "silly" column. Good to have you aboard.

    constant proselytizing about the coalescence of science and social networks

    That's not something I have ever done. I don't really care about social networks (if by "social network" you mean Facebook or Twitter). I do, however, find network theory interesting because it obtains in so many areas in nature. As for science, I am quite interested in that. Guilty as charged. But then, maybe the fact that this is "News for Nerds, Things that Matter" might have given that away...? I'll go a step further and say I am also quite interested in the social implications of science and technology, ie. how people will use new discoveries and how it might transform the human experience the way the automobile did, the airplane has, or information technology continues to do.

    Since you have established that you are that AC, the one with particular contempt for social sciences, I'll address that as well. I don't share that contempt. Social sciences study human beings, how they behave, the structures they create. It seems legitimate to me, in that human beings are part of nature and what is science but the drive to understand nature in all its aspects? Contrary to the physical sciences, however, social science is much more difficult to achieve the same level of reproducibility because its subjects have consciousness. It is devilishly difficult when in mose cases it is impractical or unethical to subject human test subjects to conditions necessary to isolate causal variables.

    And in fact medical science is just this side of the same set of complications, and it's not a coincidence that it owes large portions of its knowledge to special circumstances when those restrictions were lifted, such as how the knowledge of how extreme heat or cold or various traumas affect human beings stems from the experimentation the Nazis performed on those in concentration camps. Even today there is a great deal of variability in effects surrounding drugs prescribed to people all over the planet and tidily swept up in the catch-all, "side effect," which indeterminacy you accept in medical science but are particularly intolerant of when social scientists work to isolate the effects they study. I'll warrant you do not sputter in contempt at the mention of "doctor" or "medicine," eh?

    all of Phoenix666's submissions are going into my virtual "Soylent bozo bin"

    Fair enough. I agree that what you find in the phys.org, BBC Science, Der Spiegel Netzwelt, and arstechnica's of the world are not scientific papers like you'd find in a scientific journal. They're not going to have the depth of field that a piece on CRISPR written by geneticists for geneticists will. As such they're not going to be serious, rigorous. They will be "bozo" pieces written by "bozo" journalists who may or may not get it right. If you were a real geneticist reading such an article posted on Soylent, you'd spot errors right away and be able to speak to them. But should you post a serious, rigorous piece on CRISPR you'd probably mostly hear crickets because most of us aren't geneticists and wouldn't share your jargon and wouldn't be able to understand the context of your submission without a lot more summary than you'd be willing to write. But let's say you were a geneticist and did post such a serious article (somehow finding a way around the paywall everybody else here would not have a subscription to), and did take the time to provide enough context for the layman to understand the significance of the story. Then you got all of 4 comments, half of which are goofy. How likely would you be to repeat that experience again?

    Not likely. Not likely at all.

    or actual nerdy topics that aren't slathered with marketing smarm and pseudoscience

    Wow, so biochemistry doesn't make the cut as an "actual nerdy topic?" How about cosmology ("In Unexpected Discovery, Comet Contains Alcohol, Sugar" or "Hubble Spies Big Bang Frontiers")? No? Physics ("Physicists Learn How to Control the Movement of Electrons in a Molecule")? You're a tough, tough crowd. What does make your cut as an "actual nerdy topic?" Should we post lines of Perl? How about stanzas of machine code? Encrypted passages you have to decrypt before reading, and that will only accept comments submitted in gramatically correct Akkadian? Perhaps something you need an 8th dimensional jeweler's loupe to view?

    好, 同志, 你可以来工作一点, 我想去休息一会.

    --
    Washington DC delenda est.
    Starting Score:    1  point
    Karma-Bonus Modifier   +1  

    Total Score:   2  
  • (Score: 0) by Anonymous Coward on Sunday October 25 2015, @05:31AM

    by Anonymous Coward on Sunday October 25 2015, @05:31AM (#254249)

    Graphene is an amazing material that is stronger than steel...

    I know on a basic level what graphene is, and yes, it's interesting, but we're still not anywhere near a level of practical productization with it. It's useless misguided fanboyism, much like fanaticizing over Elon Musk's "Hyperloop", or like people 10 years ago fanaticized over OLED (ten years later, we now know that despite their excellent contrast, traditionally manufactured OLED screens succumb to burn-in, as well as having a brightness half-life of about 3 years; also, that fantasy of spraying OLED "paint" on a wall to make a giant display still hasn't become a reality, and probably never will). More to the point, do you realize how many graphene stories have been spammed to SoylentNews by someone who can't get a handle on how obsessed they are with the subject? Don't [soylentnews.org] you [soylentnews.org] realize [soylentnews.org] how [soylentnews.org] annoying [soylentnews.org] it [soylentnews.org] is [soylentnews.org] to [soylentnews.org] see [soylentnews.org] THIS? [soylentnews.org] (Here's a hint: that obsessed submitter is you. Please find another outlet to spam, at least until a company developing actual real-world products prints the first graphene board interoperable with other electronics without risking shorting out into a mysteriously noxious cloud, 30 years after which we find out that graphene is carcinogenic, and humanity shouldn't have been obsessed with it, much like asbestos. I don't know if this will actually happen, but stranger things have happened in human history.)

    I thought it was silly myself but thought I'd allow for the possibility that young'uns might find it "not silly."

    Go post that trash over on The Verge. I consider the SoylentNews editors as an accessory to this headline equivalent of clickbaiting.

    You're a tough, tough crowd. What does make your cut as an "actual nerdy topic?"

    How about some actionable news that isn't so far in its esotericism as to be obscure, irrelevant, and barely provable? (Remember the "stuff that matters" clause from the green site?) You joke about "lines of Perl", but I've always been surprised about what new things people are constructing with the veritable duct tape of interpreted languages. How about Linux kernel development breakthroughs? Once upon a time, that was a key topic of the green site. (Let's not talk about systemd, until a sane group finally rewrites most of what is ultimately a good dependency-based framework surrounded by hundreds of misguided and overreaching concepts force-fed by freedesktop and Red Hat. I'm already seeing people compare systemd to Windows 10 in terms of OS related disasters.)

    One developing area is flash storage, especially NVMe. This past week, the Samsung 950 was released, and it didn't review so well [techreport.com] when put under some decent scrutiny; it also seems to throttle down under heat, which is probably why performance SSDs won't be in the M.2 2280 form factor; Samsung should instead be thinking of making a 2.5" SSD package connecting via U.2 connector. All of these new interconnects, NAND technologies, and driver concerns are a new frontier in personal computing as well as server-side computing.

    • (Score: 2) by Phoenix666 on Sunday October 25 2015, @02:34PM

      by Phoenix666 (552) on Sunday October 25 2015, @02:34PM (#254339) Journal

      I know on a basic level what graphene is, and yes, it's interesting, but we're still not anywhere near a level of practical productization with it.

      Then you're clearly going to have to turn in your geek credentials if you don't appreciate how revolutionary the material is, and if you fail to understand that bringing those properties to bear in the many applications graphene will have is a process with many steps along the way. These stories are about those steps, about that process, and are entirely legitimate as fare for SN. But do filter them out. Retreat fast and far because you will come to see graphene talked about nearly everywhere in science and tech. It's that big.

      It's not spam if you're not trying to sell anything. It's not fanboyism if you're not trying to make a fashion or lifestyle statement. Do you similarly despise all the stories about "damn computers" and "faddish programming languages?" Do you tire of endless articles about systemd? Because those things are all spam and fanboyism, too, by your measure. How about gravity? Are you just sick to death of people talking about gravity, with all their snooty particle accelerators trying to figure out why matter has mass? Goddamn scientists, spammers, and fanboys. They're just out trying to grasp more research dollars and sell you crap, right?

      Go post that trash over on The Verge. I consider the SoylentNews editors as an accessory to this headline equivalent of clickbaiting.

      You know what? There was actually some decent discussion about that story. I thought it was silly. It struck me as a thinly disguised Kickstarter pitch, which it was. I half-expected Soylentils to tear it apart. But there was a grain of doubt that I might be wrong, that maybe I'm just older and more jaded and that can lead you to undervalue new tech that will come to be important. So I submitted it. It was a slow news day, and where is it written that everything a person submits MUST. BE. SERIOUS. VERY, VERY SERIOUS?

      How about some actionable news that isn't so far in its esotericism as to be obscure, irrelevant, and barely provable?

      Sounds great. Such as? Submit it.

      How about Linux kernel development breakthroughs?

      Sounds great. Such as? Submit it.

      (Let's not talk about systemd, until a sane group finally rewrites most of what is ultimately a good dependency-based framework surrounded by hundreds of misguided and overreaching concepts force-fed by freedesktop and Red Hat. I'm already seeing people compare systemd to Windows 10 in terms of OS related disasters.)

      Oh, no? Because that's the one big topic in linux kernel development these days that I'm aware of, so you've just blasted away that as a zone interdit for SN discussion topics. Oh well, guess we can't talk about linux kernel development at all until that whole thing sorts itself out. A narrow escape for you, I'm sure, because then you might have had to get off your ass and contribute article submissions to the SN story queue instead of endlessly whining about how others aren't spoon-feeding you the tech interests you have.

      One developing area is flash storage, especially NVMe. This past week, the Samsung 950 was released, and it didn't review so well when put under some decent scrutiny; it also seems to throttle down under heat, which is probably why performance SSDs won't be in the M.2 2280 form factor; Samsung should instead be thinking of making a 2.5" SSD package connecting via U.2 connector. All of these new interconnects, NAND technologies, and driver concerns are a new frontier in personal computing as well as server-side computing.

      That sounds awesome? See? That wasn't so hard, was it? You could have put that into the submit form in SN's "submit a story" page and voila! You would have become a productive contributor to the Soylent community instead of a useless, vituperative termagant.

      But try to change it up a bit, OK, pal? Because all you ever talk about is flash storage; somebody could well wonder if you didn't own stock in flash storage companies and you're just trying to spam the Soylent community. Seriously it's tedious. Flash, flash, flash from you all the time. We should dub you the "flasher."

      (No, not really. But sometimes it can impart a lesson to reflect a shrew's drivel back at a shrew, replacing one set of keywords with the shrew's. Chew, and digest.)

      • (Score: 0) by Anonymous Coward on Sunday October 25 2015, @06:34PM

        by Anonymous Coward on Sunday October 25 2015, @06:34PM (#254399)

        Oh, no? Because [systemd is] the one big topic in linux kernel development

        Systemd is NOT kernel development. It may submit things to the kernel now and then, but if it was more deeply tied to the kernel, the entire project would have been kicked out and told to go rewrite itself (a stance I agree with, considering how mismatched the mentalities of the freedesktop developers are from the rest of the Linux kernel base). It's also been a topic that has been churned up into bitter bitching that hasn't resulted in much of a positive outcome Even though systemd may be "here to stay" after being force-fed to an unwilling audience, it will not look the same as its current form three years from now.

        It's not spam if you're not trying to sell anything.

        A quick Google search for the definition of the word "spam" turns up this: "irrelevant or inappropriate messages sent on the Internet to a large number of recipients." Nowhere in that definition does it say anything about sales, therefore by that definition, you are spamming esoteric, if not completely irrelevant, articles about graphene. Please hold off until we see the first graphene-printed circuit boards that can be commercially interoperable with copper-and-gold PCBs, or are the first 100% graphene-printed board products. Until then, I will tell all my friends, colleagues, family, and strangers I meet that SoylentNews is a site about graphene, ripping off articles from El Reg and The Grauniad, and pumping up the next tech buzzword bubble.

        I already tried to submit an article, about when Mike Snitzer attempted to disable slab merging for all of device-mapper, which then resulted in Linus Torvalds going into a "what the hell are you doing?!" tantrum, as is his trademark, for better or worse. Everyone got their steam out, and realized that yes, disabling slab merging was a bad idea. Here's a quick reprint from the email that touched it off [redhat.com]:

        You are basically making this one-sided decision based on your notion of convenience, and just forcing that thing unconditionally on people. Your rationale seems _totally_ bogus: you say that it's to be able to observe the sizes of the dm slabs without using slab debugging. First off, you don't have to enable slab debugging. You can just disable slab merging. It's called "slab_nomerge". It does exactly what you would think it does. And what is it that makes dm slabs such a special little princess? What makes you think that the fact that _you_ want to look at slab statistics means that everybody else suddenly must have separate slabs for dm, and dm only? Or xfs?

        The submission was left off in the dust, probably in preference for approving articles about graphene and articles from The Register.