Showing posts with label Genetics. Show all posts
Showing posts with label Genetics. Show all posts
Saturday, January 26, 2013
"Quadruple helix" DNA discovered in Humans Also, "Quadruple Helix" DNA is a Thing, Sort of
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| Digital rendering of the "crystal structure of parallel quadruplexes from human telomeric DNA." (Image credit: Wikipedia Commons) |
As I have attempted to make clear many times in the past, I know nothing. Meaning, I have no scientific education or expertise beyond the trivial bits of knowledge I learned in school, and the things I have managed to shove into my own brain over the years. But, obviously, I have a thing for science. And my interest in biology and genetics ranks just behind my fascination with all of the various forms of physics in the world. So usually I could at least say; Oh ya. That's a thing I heard about before, but wound up loosing somewhere in the background noise of my brain. But other than some vague recollections of futurist postulations about potentially engineering such a thing, or speculations about the genetics of as of yet unknown alien species, this time around- I got nothin. So my first thought upon reading the headlines "Quadruple helix DNA found in humans" was- well, that can't possibly be right. And, as is often the case, if you took the headline to mean the same thing I did anyway, it isn't what you think.
As you (hopefully) already know, DNA is the molecule which carries the genetic instructions that make you what you are. Fish, sheep, person, plant, virus, we all become what we become, because our DNA tells us too. DNA itself, is built from the pairing of four base chemicals, adenine (A), guanine (G), cytosine (C), and thymine (T). Once bonded together, these base pairs in turn attach themselves to a sugar molecule and a phosphate molecule, to form a nucleotide. Those nucleotides are in turn strung together along a sugar-phosphate backbone, forming the typical double stranded sequence of genetic information that is our DNA. Because these chemical bases always form specific parings -A to t and C to G- that
means, that as long as either side of the helix is copied during cell
division etc, the other half can always be replicated.It's all admittedly more complicated than that, obviously. But for our purposes here, I think that description pretty well illustrates why one might find the notion of 4 stranded DNA sequences... Surprising. Because, it's this redundancy of the double helix structure of our genetic code, that gives DNA superiority over it's likely predecessor RNA, as a means of successfully replicating complex biological sequences. So, taking all of the above into consideration. What the hell then is a quadruple helix? And what does IT do?
Previously seen only under laboratory conditions, a paper just published in the journal Nature Chemistry, based on a study conducted by scientists at the University of Cambridge, describes the first identification of these structures within human cancer cells. Unlike the double helix which controls our genetic development, G-quadruplexes appear to be non-coding genetic structures built from four guanine bases, which join together to form a square planar structure called a guanine tetrad.
Obviously, little is yet known for certain about the absolute purpose and function of these genetic structures. But The findings of the study seem to indicate a correlation between high concentrations of G-quadruplexes, and the process of cell division and replication; a theory which is supported by the finding that these structures appear more likely to occur in the genes of rapidly dividing cells, such as cancer. If their apparent genetic function proves true, researchers hope that removing the structures could potentially turn off the ceaseless replication that occurs within cancer cells, and experiments have already begun using specific molecules to isolate and capture the structures, so that they can do exactly that.
So, if like me, your initial reaction upon reading a headline containing the phrase "quadruple helix DNA" was to immediately start wondering about chromosome counts, evolutionary origins, and what not. First- we both REALLY need to get out more. Second, try not to be too disappointed. Because, while the actual nature of G-quadruplets is, admittedly, not as exciting as discovering an entirely new structure of DNA, potentially curing cancer is pretty good too, I think. And it' still undeniably cool, either way.
-CAINE-
Sources: Nature Chemistry, Phys.org
Monday, September 5, 2011
How to Make "Bullet Proof" Skin From Spider Silk
Image credit:Luc ViatourNamed 2.6g 329m/s, after the maximum weight and velocity of a .22 calibre Long Rifle bullet from which a Type 1 bulletproof vest is meant to protect you; the skin was created by first acquiring the protein which makes the spider silk itself -which is several times stronger than steel- from the milk of goats genetically modified to produce the protein in their milk. Once extracted, the protein was then woven into a lattice work of fibers, which was in turn sandwiched between two layers of otherwise normal human skin cells grown on top of the silk matrix.
As for the goats themselves -since I'm sure you're curious- they were created using a method developed by researcher Randy Lewis and his team from Utah State University, in which the gene responsible for producing the silk is extracted from the spiders which would naturally create the substance, and ultimately inserted into a goat's egg.
While Essaidi's final product was ultimately unable to reach the minimum standard for modern bullet proof vests by stopping a .22 cal riffle bullet shot at normal speed, and the notion that we might someday replace the keratin in our skin with this silk using the same methods as those used to create the modified goats, though entirely plausible, is at best, a distant dream. In the short term, Lewis asserts that the most exciting part about Jalila's experiment is that they were able to grow the skin cells on top of the fibers in the first place, and the potential applications for the skin today in skin grafts and other treatments.
-CAINE-
Source: techcocktail.com
Saturday, August 13, 2011
Some of The Building Blocks of DNA May Have Come From Space
Artist concept credit: NASA's Goddard Space Flight Center/Chris Smith
By grinding up and analyzing samples of twelve carbon-rich meteorites, nine of which were recovered from Antarctica, a research group from NASA's Goddard Space Flight Center, in Greenbelt, Md, found both adenine and guanine; two of the primary nucleobases contained within our DNA, as well as hypoxanthine and xanthine; neither of which are used in the construction of DNA, but are utilized by other biological processes.
In two of the meteorites, the team also discovered for the first time, trace amounts of three molecules related to nucleobases (nucleobase analogues), purine, 2,6-diaminopurine, and 6,8-diaminopurine; two of which rarely appear in biology. According to Dr. Michael Callahan, lead author of a paper on the discovery appearing in Proceedings of the National Academy of Sciences of the United States of America;
"You would not expect to see these nucleobase analogs if contamination from terrestrial life was the source, because they're not used in biology, aside from one report of 2,6-diaminopurinecyanophage S-2L,"
While the presence of molecules not known to commonly appear in biology was a strong indication that the findings were not the result of contamination. Callahan's group further confirmed this fact by analyzing a sample of ice taken from Antarctica, where most of the meteorites in the study were found. The result showed much smaller concentrations of the nucleobases, as well as xanthine and hypoxanthine, all of which appeared in parts per trillion in the ice sample, as oppose to the parts per billion generally found within the samples taken from the meteorites. None of the Nucleobase analogues were discovered in the sample. Analysis of the soil taken from the surrounding area where one of the meteorites used in study fell in Austraila, also failed to detect those analogs.
In one final experiment designed to rule out terrestrial contamination and confirm the extraterrestrial origin of the molecules. Callahan's team was able to successfully generate all of the nucleobases and analogues found within the meteorite samples in a completely non-biological chemical reaction in the lab, using hydrogen cyanide, ammonia, and water. Showing not only that the find was almost certainly not the result of contamination, but more importantly, that chemical processes taking place within certain types of asteroids could potentially produce all of the molecules detected in the study.
If confirmed by further research, the findings of Callahan and his team could be a major step towards understanding the true origins of life on Earth. Particularly when considered along with previous research conducted by the team which detected amino acids, the molecules responsible for building proteins, within similar samples; as well samples taken from the Comet Wild 2 during NASA's stardust mission. All of which, adds to the growing body of evidence supporting the theory that the chemistry taking place within comets and asteroids is capable of generating the basic building blocks of essential biological molecules, and that life may owe it's existence, at least in part, to materials delivered from space via meteorite and comet impacts.
-CAINE-
Source: NASA
Image credit: NASA's Goddard Space Flight Center/Chris Smith
For a deeper explanation of the Nucleobases and nucleobase analogues, as well as the findings of his research, check out the following video from NASA, featuring Dr. Callahan.
Sunday, May 29, 2011
Cephalopods In Space!
Which is why, amongst the various cargo carried into space by Endeavor on it's final flight, is a sample of juvenile Bobtail squid. These baby cephalopods were sent up by microbiologist Jamie foster, to determine what effect, if any, the environment has on helpful bacteria, like those which give the squid the ability to generate bioluminescence.
Bobtail squid are a tiny variety of cepholopods which have evolved their ability to generate bioluminescence by forming a symbiotic relationship with a particular species of bacteria called Vibiro Fischeri, the juvenile squid are exposed to this bacteria shortly after hatching, which take up residence in the animals light organs. Fed on a solution of sugar and amino acids by the squid, the bacteria in turn helps the animal to avoid predators by matching the amount of light hitting the top of it's mantle, thus helping to hide it's silhouette from predators below. Because the animal is not born with the bacteria in it's system, and because the process only involves a single species, unlike the symbiotic relationships human beings form with the thousands of species of bacteria which inhabit our digestive and immune systems, The Bobtail squid seems an ideal candidate for this sort of test.
Preliminary experiments conducted in simulated microgravity on Earth appear to have shown problems with the uptake of bacteria by the squid. And if the shuttle study shows the same result, it would suggest that astronauts' relationships with their own microbes might also be affected.
-CAINE-
Source: New Scientist.com VIA: GGB on tumblr
Image credit: Jenny Huang
For more about the Bobtail squid, check out this video from Science Nation:
Posted by Youtube user: VideosatNSF
Posted by Youtube user: VideosatNSF
Saturday, December 4, 2010
Matt Ridley and Richard Dawkins on DNA, Extraterrestrial Life and More...
Posted by YouTube user:AtheistMediaBlog
Since we've been discussing astrobiology and genetics over the past few days, now seemed like a good time to share this video of evolutionary biologist Richard Dawkins ( that's right kids, he's more than JUST an atheist) and journalist Matt Ridley discussing Alternative biochemistry, extraterrestrials, DNA, synthetic life, artificial life, and all sorts of other interesting things relating to biology, evolution, and life in general. It's very, very, cool and I think you will enjoy it, so check it out!
-CAINE-
-CAINE-
Friday, December 3, 2010
NASA Press Conference Disappoints Many, But it Really Shouldn't Have
[*UPDATE*]Turns out, not only have NASA's observations NOT been confirmed by any other researchers, but there's also been no shortage of scientists coming forward to criticize the conclusions as well as the methods of NASA scientists. Some have even gone so far as labeling the entire thing one big publicity stunt and given this new information, I largely agree. So maybe we should have been disappointed after all. [*UPDATE*]In case you missed it, yesterday NASA held a press conference to announce the discovery of a bacteria (GFAJ-1 of Halomonadaceae) living in the highly alkaline waters as well as in the mud surrounding Mono Lake in California. Lab tests showed that this bacteria is capable of not only surviving in an environment saturated with arsenic, but that it can actually incorporate the normally highly toxic chemical into it's DNA and use it in place of phosphorous.
One would be hard pressed to exaggerate the "wow-factor" of this discovery from a biological stand point as it is a real life living breathing example of an organism capable of sustaining it's existence by utilizing a biochemistry unlike any other organism on the planet. As far as the impact this finding will have on astrobiology- The search for life on other worlds has to begin by looking for the conditions necessary to sustain life as we know it and this discovery helps to expand our understanding of the conditions under which life can exist. In short, the space agency made good on it's promise to deliver something which would impact the field of astrobiology and this organism itself is an astonishing discovery well worth the attention it received.
However-
To the average person, this discovery probably doesn't mean much, and it certainly isn't as cool as it would have been if this same discovery had been made on another planet; which is obviously what the majority of people thought was going to be the case. I myself was aware of the existence of organisms capable of surviving on arsenic ( the part about the DNA is new microbes living on arsenic is not) and that the subject of the press conference would most likely focus primarily on some terrestrial finding. But even I assumed that the topic would be somehow tied to a specific discovery on another world and it is, in a fundamental non-specific sort of way. But still, a lot of people were both disappointed and even irritated by the subject of the conference and quite frankly, I don't blame them.
To be fair, 99% of the hype about alien life came from outside NASA. But when the general public(right or wrong) sees your organization's primary mission as the search for extraterrestrials, you have to know that holding a special event to share an announcement relating to astrobiology is GOING to generate hype, speculation, and ultimately resentment when reality doesn't live up to their expectations.
-CAINE-
Source: Bad Astronomy
For more about the true significance of this find check out Nancy Atkinson's article on Universe Tody.
Among those deeply disappointed by the way NASA handled the release of this information, Justin from Weird Things TV:
Posted by YouTube user:weirdthingsTV
Friday, October 29, 2010
Biotech Company Begins First Human Embryonic Stem Cell Trial
Earlier this month the Geron Corporation began the first Human embryonic stem cell trial. This trial, which began October 8th in the Shepherd Center in Atlanta, Georgia, is expected to involve 10 patients, all of whom must have severe spinal cord injuries and begin treatment within 14 days after sustaining their injuries.
Participants in the trial will receive a single injection containing 2 million of Geron's GRNOPC1 cells and will then be monitored for a year to look for any sign of negative side-effects or regained function or sensation in their lower extremities. Assuming this initial group is found to suffer no ill-effect from the treatment, Geron plans to seek FDA approval to extend the study and increase the dose of GRNOPC1 patients receive, as well as including
"as broad a range of severe spinal cord-injured patients as medically appropriate."
Geron ultimately hopes to be able to inject GRNOPC1 directly into the spinal cord lesions of injured patients prompting the regrowth of damaged nerve cells and restoring function and sensation to patients suffering paralysis.
Trials like this one are long overdue and have been unnecessarily delayed due to what I personally view as the largely manufactured controversy surrounding embryonic stem cells. But if treatments like this prove successful, it will no doubt fuel the public's desire to see such treatments made available to patients with debilitating injuries and will help to remove the unfortunate and - in my opinion - completely unjustified bans and restrictions currently placed on embryonic stem cell research here in the US.
-CAINE-
Source:Discovery News
On a semi-related note, it remains impossible for me to hear the words "embryonic cells" without getting this song stuck in my head, but it's one of my absolute favorites, so I'm okay with that.
Posted by YouTube user:roadrunnerrecords
Friday, May 28, 2010
Synthetic Life...sort of
A research team led by Dr Craig Venter of the J Craig Venter Institute(JCVI) in Maryland and California, have successfully created the first Self-Replicating, Synthetic Bacterial Cell, Mycoplasma mycoides JCVI-syn1.0. (Follow the link above or click HERE to read the Institute's official press release.)
While technically correct, I think the over emphasis being placed on the word synthetic in every headline and article about this story gives the average reader the wrong impression. While Dr. Venter's group has achieved something amazing and ground breaking, this so called synthesized life form is not the sc-fi micro-monster that most main stream reporting implies it to be. I'll explain.
Researchers created this "synthetic" cell by first digitally replicating the entire genome of an existing bacteria, M. Mycoides. That digital copy was then artificially synthesized using a sequencer and inserted into another existing species of bacterium whose own genome had been removed, Mycoplasma capricolum. The Mycoplasma in turn followed the new genetic "Software" it had received and turned itself into a M. Mycoides cell, ultimately resulting in the creation of, "Mycoplasma mycoides JCVI-syn1.0", the worlds first "synthetically" created self-replicating cell.
In other words, the only part of the cell that was "artificial" was the genome it received, which was in fact just a copy of an existing genome from a separate species of bacteria. Point being, JCVI-syn 1.0 is not some entirely new and artificially created species of anything as most mainstream articles seem to imply.
But this is an important advancement regardless of the details. Not only could artificially produced bacteria be engineered to carry out worth while tasks like reducing some of the damage to the environment by capturing Carbon monoxide, as suggested by Dr. Venter In an article from the BBC. But the steps that were necessary to successfully synthesize and implant the genome of one species to another, creating a viable copy of the original. Means more exacting work can begin on understanding the genomes themselves, as stated by Dr Venter in the JCVI press release: "We can now begin working on our ultimate objective of synthesizing a minimal cell containing only the genes necessary to sustain life in its simplest form. This will help us better understand how cells work."
-CAINE-
Links and Additional Content
First, if you did not click through to read the article from the BBC should do so now, it has loads of info on this story including video of Dr Venter as well as a Q&A section and was my primary scource of info on this subject outside of the JCVI press release which you should also go read.Next, Dr. Venter's TED talk video. (more on TED another day)
Image Credit:Nate Beeler
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