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Comment: sorry. butterfingers resulted in a premature post (Score 1) 183

Mind you, the chromosome is still damaged to some degree, but it doesn't get worse.

Cancer cells are observed to maintain viability this way - even though they are diseased and abnormal cells, they maintain just enough chromosomal health by activating the necessary telomere maintenance process to continue dividing without incurring even greater genomic damage.

Comment: Re:cancer (Score 5, Interesting) 183

Not offhand in any good laymen's literature I know of. But the process is described in a bunch of molecular biology textbooks I don't have access to at the moment. When chromosomes are not protected with telomere caps on the ends, the cellular machinery is likely to mistakenly treat them as DNA double strand breaks. What happens in such situations is that proteins involved in DNA repair will try to join the "naked" end to the nearest other piece of DNA, even if it belongs to another healthy chromosome. Fused chromosomes are always bad news for cellular health. The problem is amplified in what is called a breakage-fusion-bridge (b/f/b) cycle as cells try to continue dividing with abnormal chromosomes that now doesn't separate as they should.

The presence of healthy telomeres suppresses this process. Even if your chromosomes get messed up through the infrequent snags that still happens occasionally, a damaged chromosome that is able to restore the presence of telomeres at the end by one means or another (there are several) will stop undergoing b/f/b cycles. Mind you, the chromosome is still damaged to some degree, but it doesn't get worse.

Comment: Re:Wow .... (Score 1) 155

All jokes aside, maturation of this technique has huge ramifications for the treatment of diseases that are fundamentally due to misfolded proteins. Prion diseases, frightening as they are, might finally have a cure. I would dare say related disorders that involve plaque deposits such as Alzheimer's might also benefit from possible therapeutics.

Comment: Re:is this news? (Score 1) 221

I don't necessarily disagree with you completely. But I think your point is badly argued and perhaps unnecessarily harsh.

>As far as i know.

THAT is pretty much what it boils down to... WHAT do you know? HOW do you know it? Is it really fair of you to dismiss a position where one only seeks to know more than what you currently know?

>The very idea that some things outcompete others is one of our basic immunological defenses.

I don't know where you pulled this out of or where you're going with it. Perhaps a point can be made about host immunological tactics and responses to pathogens in the context of ecological adaptation and niches. But to draw some kind of connection via competition for resources is a pretty awkward and bizarre way of making that point. And what is purpose of bringing this up in the current context? Are you suggesting if our immune system doesn't need to handle something that can't compete in our ecological backyard, we shouldn't bother? I don't mean to put words in your mouth, but that is not a very scientific perspective.

>That we haven't seen something already.
>I doubt you'll find much outside of novel viruses because bacteria infest every corner of our world. around you, on you, inside you, above you and below you.

Are you sure you would know even if you were looking at it? Moreover, what are you looking with? If as it was postulated, a non-DNA based genetic code was used, our existing assays may not pick up anything at all. I'm not going to dive into a discussion about laboratory science just yet. But let's pull back for a minute and consider something even more conventional. There is a enigma in microbial ecology sometimes called "The Great Plate Count Anomaly" that simply stated is the fact many more microbial organisms exist than we can culture in the lab. Recent advances in metagenomic techniques has allowed us to sequence the DNA of these previously un-grow-able bugs and given microbiologists their first look at stuff they've never seen before. And this is only within the last couple of years.

New discoveries and advances are occurring much more recently than you believe. A few months ago, I came across a bit of relatively new research where modern techniques identified some symbiotic bacteria in the gut of an insect called the glassy winged sharpshooter which finally explained how it was able to feed on relatively un-nutritious xylem that lacked essential nutrients required for survival. It turned out there was a previously unknown microbial community in this hard to observe environment with different bacteria synthesizing different nutrients crucial for this insect's survival. Discoveries like this are possible because obstacles exist but researchers never stop asking how we can overcome the limits of existing methods and techniques. There are countless examples of such "things we haven't already seen" to paraphrase you. And I am confident that if we should dare to extend our search as was urged in the paper, we'll open up new door we can't even dream of at the moment.

I guess I can't really fault you for your perspective as it appears biology isn't your field of expertise. But for those of us bio-hackers here on slashdot, compelling questions of what we should be looking for and where/how to look for it, is most definitely "News for Nerds, Stuff that Matters". For the good of the community, I would ask that you and others not try to knock something simply because you don't understand it. Please try not to ask questions on the premise of unfounded assumptions.

Comment: Re:is this news? (Score 1) 221

That's a pretty narcissistic and arrogant world view which does little to advance the current state of knowledge. When we stop daring to think ambitiously and asking improbable questions about the world around us, we settle into a valley of complacency from which we loose the momentum of curiosity that has driven science and technological innovation. Imagine Einstein never bothered to write that letter which lead to the Manhattan project. Or if DARPA thought the packet switching ARPANET was a waste of time and money. Or if the DOE thought sequencing the human genome was someone elses responsibility.

Believe me, as a lab rat who's been doing bench work in molecular and cell biology for the last 3 years I am more qualified than anyone to sing the praises of our current power to probe the depth, diversity, and extent of life. It is easy for me to sympathize with those who are jaded by these routine "miracles" where we can send out a DNA sample and have it sequenced overnight. If we wanna know something, the answer is literally a bunch of mouse clicks and a few pipette pumps away. Not much to get excited about at all.

But any self respecting biologist who works with modern molecular tools and technique has seen the frightening pace of progress that has allowed us to do the previously unimaginable. For example, the 2007 Nobel prize was awarded for the development of the "knock-out" mouse. This has lead to all sorts of experiments that has elucidated protein (mal)functions that have lead to a revolutionary understanding of countless diseases and illnesses. In more recent years, we are poised for another such quantum leap with bacteria-derived "genomic editing" techniques such as TALEN and CRISPR that allows us to make precise changes in the DNA of model organisms.

If biologists have the mindset you espouse, that everything worth discovering has been found, none of these type of breakthroughs would be possible. I've talked to colleagues who often muse wishfully, "If only we can do ****** more easily, our experiment would be so much better." There isn't one among us who don't hope some newly discovered microbe from the deep ocean or where ever will lead to some new technique or method that will allow us to do different kinds of experiments to generate data we didn't think was possible to collect.

And that is not as far-fetched as it sounds. It has been pointed out before that more people have walked on the moon than been to the deepest part of Earth's oceans. Of the little bit we have seen down there, entire ecosystems run on biochemistry that might as well be from another planet. You think it is *easy* to go down there and do science on those critters? There is a reason why astronauts outnumber aquanauts and ease/simplicity isn't one of them. You can't just bring them to you either because, those organisms don't live in the kind of environment we operate most lab equipment.

And it isn't necessarily about who can out-compete who on this planet. Everyone gets to shine in the spot light because everyone potentially has a role to play on the stage of life. How unimpressed will you be if it is discovered that some newly identified ocean trench bottom dweller can help us clean up the "Deep Horizon" oil spill in the gulf of Mexico? Or what if some rare sparsely growing thing-in-a-rock synthesizes a potent life-saving anti-cancer compound? We are not out to make discoveries for something that can necessarily colonize and take over the planet. The motivation for such quests are as varied as life itself, but for me personally, it is about finding something that can be of use to humanity. New biology may mean our current tools/techniques don't work. But therein also lies opportunities for new technologies and new discoveries. And you can bet there will be spin-offs to spare!

Sure, it may be not much more than viruses we find out there. There may NOT be some exotic thing out there that confounds established biology of life. But who are YOU to say? Plenty of reputable scientists have expressed the sentiment, "That's impossible! Don't be so ridiculous!" only to eat crow as their more open minded colleagues scope them. All things being equal, I'd rather bet on the long shot with anticipation, open eyes, and an open mind.

Comment: Re:Yeah but ... (Score 5, Insightful) 128

Mod parent up. The article as written is dumbed down and misleading in many ways. Against my usual temperament I'm going to make a sociological/anthropological argument that someone reading the article will draw very wrong conclusions about the nature of prehistoric Neanderthal-modern human interaction. Genetic inheritance or progeny happens to be the only evidence we have right now about early Neanderthal-modern human interaction. But it does not say anything useful about when we "first had sex with" them as the article claims. Consider the following: Archaeological evidence suggests that large scale violence we would consider warfare was a part of human life as far as 7,500 or possibly 14,000 years ago. Does that mean ancient society was all about peace and love before that time? No. There is too little information to make such sweeping conclusions. To return to the subject at hand, not all sexual encounters with Neanderthals are going to leave evidence for us to conveniently find. What we *DO* know at this point is that at least one such encounter resulted in a pregnancy that was carried to term and the resulting offspring lived long enough to have children of his/her own who continued to survive. That's ALL we know. Put another way, imagine the young men and women of ancient communities playing a game of "fuck, marry, or kill" that included their funny looking neighbors. The visual may not be pleasant, but any earlier incidents of war-rape and deliberate infanticide due to parental rejection will leave little to no evidence behind for us. And barring extreme luck, there is almost NO WAY we can know if/when such incidents occurred. Who really knows when Neanderthals and us *FIRST* had sex?

Comment: Re:so...... (Score 2) 352

Why is this comment modded off topic? Anyone who has bothered to read the linked webpages would know they are not talking about photovoltaics. What perhaps *IS* off topic is that examiner.com is usually a really poor source of good science. The feed they provide to YAHOO is almost always filled with sensationalist nonsense.

Comment: Re:the next logical step (Score 1) 85

I don't have very deep background in this area, but a bit of trivia from a neuroscience class two years ago is relevant here. Decades ago, before research ethics developed to its current state, there was an experiment using a de-brained but still living cat that showed the neural circuitry in the spinal cord was sophisticated enough to coordinate walking/running with no input/output to the brain. The following youtube clip shows film footage of the cat suspended over a treadmill where the motion of the tread stimulated anatomically correct gaits of normal healthy animals. https://www.youtube.com/watch?... In other words, the artificial stimulation doesn't really control *how* they walk or perform other tasks that are "instinctual". Most of that is an innate ability of the central nervous system. Voluntary control of muscles and movement, especially fine control, like dodging obstacles, for example, are still a bit tricky to hack at the current state of understanding.

Comment: the next logical step (Score 3, Insightful) 85

After they optimize this for human physiology and gain commercial approval, this technology will obviously be a boon for accident victims. However, the engineer in me can't help but think of how far they can take the cyborg theme. ALS is a disease where motor neurons selectively waste away. Do we dare hope that we can eventually bypass the whole path of neuro connections to directly stimulate individual muscle groups?

Comment: Re:You completely missed the point of the article (Score 1) 27

by Doubting Sapien (#47821211) Attached to: CPU's Heat Output to Amplify DNA Could Make Drastically Cheaper Tests
Mod parent up. I've read only the abstract of the article, but even still, the proposed system as described is a terribly expensive way to do PCR for another reason. Typical PCR reaction runs usually thermocycle around 20-30 times. That is 20 to 30 times you will need to change the temperature of your heat sink from a high denaturing temp to a low annealing temp to facilitate DNA replication. One of the first things I was taught in heat transfer as an electrical engineer is that the overwhelming factor involved in electronics failure is material fatigue due to thermo expansion/contraction. If you try to turn the CPU of a commodity PC into a thermocycling heat sink, you are going kill that machine really fast. Better to put in the investment for a proper thermocycler and related equipment designed to do the job correctly and reliably. Molecular biology is cheap enough these days that you don't need to do these crazy ostentatious hacks.

Comment: Beyond human efforts. (Score 4, Interesting) 190

Laboratory samples are not necessarily the only sources of still viable small pox virus. With climate change now a global reality, thawing of the arctic permafrost means that the remains of victims who died of smallpox before eradication, even if buried (but especially if not), can potentially still release the disease into the current population. There was some news a while ago when the the Spanish Flu of 1918 was recovered in this way, albeit intentionally in the interest of science. But who knows if/when nature should take it's course this way with small pox, without our help?

Comment: Re:How long before... (Score 1) 105

by Doubting Sapien (#47338159) Attached to: Fixing Faulty Genes On the Cheap
It is hard to predict the progress of technology, so - NO: I won't tell you "how long before...." But I'll try to explain why CRISPR is special enough to be exciting in my experience and what technological/engineering hurdles need to be overcome in order to reach your objective.
At the moment, variations of the CRISPR-CAS system can only edit the genome of individual cells in vitro with varying efficiency. This is assuming you can culture the cells to begin with. For example, I work with human embryonic stem cells, which are particularly finicky. They won't tolerate much roughness and will even up and die on you if the growth conditions are just a bit off. This is very hard to achieve reliably as some culturing reagents (coating matrix, for example) are "undefined" products with variations in composition from batch to batch.
To go to a chop shop and treat your issue at the genetic level requires an in vivo way to introduce a CRISPR-enabled vector into your cells. This is not easy to do with today's technology, but it may not necessarily be a deal breaker. In the example you gave, a food allergy can probably be addressed by treating only the GI tract and the immune system that comes into contact with the offending allergen. As such, there is no need to target every living cell in your body in this case. However, if you are treating an illness involving a more fundamental life process, that is not the case. For example, a mitochondrial disease where basic cellular metabolism is defective would probably be best tackled when an individual is still a developing embryo or at least very, very young. Otherwise, tissues and organs that are not convenient to access will still retain the genetic defect and present problems for the host organism.
Another question is where in the genome you want to edit. So far, one of our experiments involving the targeted insertion (non-CRISPR method) of a construct into our hESCs have been a bust. Our best guess is that the intended site of transfection (sub-telemeric regions of chromosomes) is critical for cell survival and too much fiddling in the area is fatal. CRISPR-CAS was a compelling solution for us because of how ideally targeted it is supposed to be. We are not aware of anyone else who've used CRISPR with hESCs in the way that we are doing, but what has been reported so far with other experiments using notoriously difficult subjects has been encouraging. So far, the experiment shows clear evidence of true integration into the genome as opposed to a transient transfection. In about a week, a Southern blot verification will tell us if the integration was random or indeed targeted.
As rosy as I can paint a picture about what is possible, however, strong caution follows the introduction of any new technology. Anonymous Coward may be an asshole, but (s)he isn't wrong for being a cynic about the commercial deployment of this as a consumer product. Considering how complex human biology is, the chance of an unintended edit with unanticipated consequences is more than likely. Many genes are linked in very convoluted ways. Even with the human genome project having ostensibly mapped everything, we are still looking at just the tip of the iceberg. Having a complete manuscript, is very different from understanding all the nuances of the story. To get back to the spirit of your question, I would imagine that the scenario probably is more similar to dental service, where you go back periodically to check on the integrity of any major service, with tweaks along the way as necessary.

+ - Y Chromosome Is More Than a Sex Switch->

Submitted by sciencehabit
sciencehabit writes: The small, stumpy Y chromosome—possessed by male mammals but not females, and often shrugged off as doing little more than determining the sex of a developing fetus—may impact human biology in a big way. Two independent studies have concluded that the sex chromosome, which shrank millions of years ago, retains the handful of genes that it does not by chance, but because they are key to our survival. The findings may also explain differences in disease susceptibility between men and women.
Link to Original Source

1 Mole = 007 Secret Agents