Nature Chemistry: Paper here:... Darwinian evolution of an alternative genetic system provides support for TNA as an RNA progenitor : Nature Chemistry. The pre-RNA world hypothesis postulates that RNA was preceded in the evolution of life by a simpler genetic material, but it is not known if such systems can fold into structures capable of eliciting a desired function. Presumably, whatever chemistry gave rise to RNA would have produced other RNA analogues, some of which may have preceded or competed directly with RNA.
Threose nucleic acid (TNA), a potentially natural derivative of RNA, has received considerable interest as a possible RNA progenitor due to its chemical simplicity and ability to exchange genetic information with itself and RNA. Here, we have applied Darwinian evolution methods to evolve, in vitro, a TNA receptor that binds to an arbitrary target with high affinity and specificity. This demonstration shows that TNA has the ability to fold into tertiary structures with sophisticated chemical functions, which provides evidence that TNA could have served as an ancestral genetic system during an early stage of life. Figures. Nature Chemistry: RT @newscientist: It's not... Scientific American: RT @ChemistryWorld: A TNA...
PhysOrg Science News: Simpler times: Did an earl... Simpler times: Did an earlier genetic molecule predate DNA and RNA? (PhysOrg.com) -- In the chemistry of the living world, a pair of nucleic acids—DNA and RNA—reign supreme. As carrier molecules of the genetic code, they provide all organisms with a mechanism for faithfully reproducing themselves as well as generating the myriad proteins vital to living systems. Yet according to John Chaput, a researcher at the Center for Evolutionary Medicine and Informatics, at Arizona State University’s Biodesign Institute®, it may not always have been so. Chaput and other researchers studying the first tentative flickering of life on earth have investigated various alternatives to familiar genetic molecules. These chemical candidates are attractive to those seeking to unlock the still-elusive secret of how the first life began, as primitive molecular forms may have more readily emerged during the planet’s prebiotic era.
Nearly every organism on earth uses DNA to encode chunks of genetic information in genes, which are then copied into RNA. PhysOrg Science News: RNA editing responsible fo... RNA editing responsible for colder water survival in octopus. (PhysOrg.com) -- Researchers have discovered that when it comes to the survival of an octopus living in frigid waters, the reasoning is not a difference in the gene DNA but rather a difference in the RNA editing. The new study, led by molecular neurophysiologist Joshua Rosenthal and his graduate student, Sandra Garrett, from the University of Puerto Rico Medical Sciences Campus in San Juan was published in Science. When it comes to cold temperatures, certain proteins that are responsible for nerve signals can be hampered. As a nerve cell fires, protein channels open or close to allow potassium ions in or out.
Cold temperatures can delay the channels’ closing and stop the neurons ability to fire. Rosenthal and Garrett believed that in order for an octopus to survive in the frigid cold waters of the Arctic and Antarctic seas, they would have had to have changes in the DNA sequence. They realized that RNA editing must be in play. Explore further: Plants evolve ways to control embryo growth. Katherine Harmon: Octopus reveals 1st RNA ed... ResearchBlogging.org: miRNA special reprint in N... MiRNA special reprint in Nature. Foresight Institute: CAD tools to engineer meta...
Sciam: Green Glow Shows RNA Editi... Green Glow Shows RNA Editing in Real Time. Glowing genes: White arrows show hot spots of ADAR activation; courtesy of Reenan Lab/Brown University It’s a long way from gene to protein. The dogmatic scenario is: DNA gets transcribed into RNA, which gets translated into protein. But in real life, and in real living things, the workings aren’t quite that simple. One example: individual units of RNA sometimes need to be converted, in what’s called RNA editing, into related entities for the ultimate formation of the right proteins.
An enzyme called ADAR (adenosine deaminase, RNA-specific) is responsible for a specific such alteration important for good nervous system function. Now researchers have devised a technique for seeing this particular RNA editing process in real time—the corrected strand gives off a green glow—and even for the restoration of functionality. Reenan and colleagues produced fruit flies that included an altered version of the gene for the oft-used lab tool green fluorescent protein. PhysOrg Science News: A radar for ADAR: Altered... A radar for ADAR: Altered gene tracks RNA editing in neurons. To track what they can't see, pilots look to the green glow of the radar screen. Now biologists monitoring gene expression, individual variation, and disease have a glowing green indicator of their own: Brown University biologists have developed a "radar" for tracking ADAR, a crucial enzyme for editing RNA in the nervous system. The advance gives scientists a way to view when and where ADAR is active in a living animal and how much of it is operating.
In experiments in fruit flies described in the journal Nature Methods, the researchers show surprising degrees of individual variation in ADAR's RNA editing activity in the learning and memory centers of the brains of individual flies. "We designed this molecular reporter to give us a fluorescent readout from living organisms," said Robert Reenan, professor of biology and senior author of the paper, which appears Dec. 25, 2011. "When it comes to gene expression and regulation, the devil is in the details. " A reporter of an editor. E! Science News: CAD for RNA... CAD for RNA. Related images(click to enlarge) Image by Zosia Rostomian, Berkeley Lab Photo by Roy Kaltschmidt, Berkeley Lab The computer assisted design (CAD) tools that made it possible to fabricate integrated circuits with millions of transistors may soon be coming to the biological sciences.
Researchers at the U.S. Keasling, who also holds appointments with the Lawrence Berkeley National Laboratory (Berkeley Lab) and the University of California (UC) Berkley, is the corresponding author of a paper in the journal Science that describes this work. Synthetic biology is an emerging scientific field in which novel biological devices, such as molecules, genetic circuits or cells, are designed and constructed, or existing biological systems, such as microbes, are re-designed and engineered. Keasling, Carothers and their co-authors focused their design-driven approach on RNA sequences that can fold into complicated three dimensional shapes, called ribozymes and aptazymes. Sciencedaily: Computer assisted design (... PhysOrg Science News: Researchers develop CAD-Ty...
PhysOrg Science News: Built-in 'self-destruct ti... Natureblogs: Video animation: RNA inter... Video animation: RNA interference. Scientific American: cool MT @NatureRevGenet: V... Scientific Reports: Cdc14b regulates mammalian... PhysOrg Science News: Acquired traits can be inh... Acquired traits can be inherited via small RNAs. Columbia University Medical Center (CUMC) researchers have found the first direct evidence that an acquired trait can be inherited without any DNA involvement. The findings suggest that Lamarck, whose theory of evolution was eclipsed by Darwin's, may not have been entirely wrong. The study is slated to appear in the December 9 issue of Cell. "In our study, roundworms that developed resistance to a virus were able to pass along that immunity to their progeny for many consecutive generations," reported lead author Oded Rechavi, PhD, associate research scientist in biochemistry and molecular biophysics at CUMC.
"The immunity was transferred in the form of small viral-silencing agents called viRNAs, working independently of the organism's genome. " In an early theory of evolution, Jean Baptiste Larmarck (1744-1829) proposed that species evolve when individuals adapt to their environment and transmit those acquired traits to their offspring. Dr. E! Science News: Study identifies mechanism... PhysOrg Science News: Study identifies mechanism... ResearchBlogging.org: Transposome-based RNA-Seq... PhysOrg Science News: Just the two of us: Stable...
E! Science News: Cancer drug cisplatin foun... Cancer drug cisplatin found to bind like glue in cellular RNA. Related images(click to enlarge) University of Oregon An anti-cancer drug used extensively in chemotherapy binds pervasively to RNA -- up to 20-fold more than it does to DNA, a surprise finding that suggests new targeting approaches might be useful, according to University of Oregon researchers. Medical researchers have long known that cisplatin, a platinum compound used to fight tumors in nearly 70 percent of all human cancers, attaches to DNA. Its attachment to RNA had been assumed to be a fleeting thing, says UO chemist Victoria J. DeRose, who decided to take a closer look due to recent discoveries of critical RNA-based cell processes. "We're looking at RNA as a new drug target," she said. The National Institutes of Health- and UO-funded research is detailed in a paper placed online ahead of regular publication in ACS Chemical Biology, a journal of the American Chemical Society.
DeRose is now pursuing the ramifications of the findings. Source: University of Oregon. PhysOrg Science News: Cancer drug cisplatin foun... Cancer drug cisplatin found to bind like glue in cellular RNA. An anti-cancer drug used extensively in chemotherapy binds pervasively to RNA -- up to 20-fold more than it does to DNA, a surprise finding that suggests new targeting approaches might be useful, according to University of Oregon researchers. Medical researchers have long known that cisplatin, a platinum compound used to fight tumors in nearly 70 percent of all human cancers, attaches to DNA.
Its attachment to RNA had been assumed to be a fleeting thing, says UO chemist Victoria J. DeRose, who decided to take a closer look due to recent discoveries of critical RNA-based cell processes. "We're looking at RNA as a new drug target," she said. "We think this is an important discovery because we know that RNA is very different in tumors than it is in regular healthy cells. The National Institutes of Health-supported research is detailed in a paper placed online ahead of regular publication in ACS Chemical Biology, a journal of the American Chemical Society.
ResearchBlogging.org: The case of "junk DNA" and... RNA. This is part 5 of 5 in a series dedicated to the concept of "junk DNA". Links to the previous parts: Part 1, Part 2 (redundancy), Part 3 (epigenetics), and Part 4 (topology). I recently discovered the work of John S. Mattick (who's written many beautiful reviews on RNA) and learned a new concept, which he discusses in [1]: while the number of protein-coding genes is relatively constant across complex species, non-coding DNA increases with developmental complexity.
Isn't it intriguing? In [2], Mattick and colleagues list examples of non-coding RNA that was later identified to encode a functional protein (in a different context), and they hypothesize that this may be the case for many more non-coding RNA regions, as they may be "translated in very specific contexts or at very low levels. " All this suggests that DNA alone is only one part of the picture, and together with DNA, we should be sequencing RNA as well to see whether or not putative mutations are indeed expressed. Natureblogs: RNA pioneer H. Gobind Khor... RNA pioneer H. Gobind Khorana dies, aged 89. Har Gobind Khorana, a biochemist who rose from humble origins in rural India to win the Nobel Prize in physiology or medicine in 1968, died on 9 November at the age of 89. He won the prize while working at the University of Wisconsin–Madison for working out how RNA codes for the synthesis of proteins.
Khorana was born in Raipur, a small village in the Punjab region of India, around 9 January 1922 (he was never sure of the date). His Hindu father was an agriculture taxation clerk for the British colonial government and was dedicated to educating his five children. “We were practically the only literate family in the village inhabited by about 100 people,” Khorana wrote. Khorana received a fellowship to study at the University of Liverpool, UK, and received his PhD there in 1948.
His work earned him the 1968 Nobel Prize, which he shared with Robert Holley of Cornell University in Ithaca, New York, and Marshall Nirenberg of the National Institutes of Health in Bethesda, Maryland. Image: MIT. PhysOrg Science News: Non-coding RNA relocates g... Non-coding RNA relocates genes when it's time to go to work. Cells develop and thrive by turning genes on and off as needed in a precise pattern, a process known as regulated gene transcription.
In a paper published in the Nov. 9 issue of the Journal of Neuroscience, researchers at the University of California, San Diego School of Medicine say this process is even more complex than previously thought, with regulated genes actually relocated to other, more conducive places in the cell nucleus. "When regulated gene transcription goes awry, many human diseases result, such as diabetes, atherosclerosis, cancer and growth defects in children," said Michael G. Rosenfeld, MD, a professor in the UC San Diego Department of Medicine, Howard Hughes Medical Institute investigator and senior author of the study. "We've shown that rather than being activated at certain, random locations within the cell nucleus, regulated genes can dynamically relocate. NcRNA are molecules that are not translated into proteins. Foresight Institute: Controlling artificial mol... PhysOrg Science News: Study links Fragile X Synd... Natureblogs: Argument over RNA editing...
Argument over RNA editing study deepens. The geneticist whose claimed to find a new mechanism of genetic regulation is defending her work against critics. Vivian Cheung of the University of Pennsylvania in Philadelphia says that her team stands by a May paper in which it reported that it had found more than ten thousand sites where transcribed RNA differed from an individual’s corresponding DNA sequence. The paper raised the possibility of an as-yet unknown mechanism that performs a new form of “RNA editing” in our cells. Cheung also says that new data from her own group and from others (PDF) supports the finding. “We stand by our report that there are many sites in the human genome where RNA sequences differ from their corresponding DNA sequences, and the types of RNA-DNA differences (RDDs) are not restricted to the known A-to-G and C-to-U RNA editing events,” Cheung wrote in an email.
Cheung’s defense comes after Daniel R. Schrider, Jean-Francois Gout and Matthew W. “[T]he language Dr. PhysOrg Science News: New research links common... New research links common RNA modification to obesity. An international research team has discovered that a pervasive human RNA modification provides the physiological underpinning of the genetic regulatory process that contributes to obesity and type II diabetes. European researchers showed in 2007 that the FTO gene was the major gene associated with obesity and type II diabetes, but the details of its physiological and cellular functioning remained unknown. Now, a team led by University of Chicago chemistry professor Chuan He has demonstrated experimentally the importance of a reversible RNA modification process mediated by the FTO protein upon biological regulation. He and 10 co-authors from Chicago, China and England published the details of their finding in the Oct. 16 advance online edition of Nature Chemical Biology.
Scientists already had demonstrated that FTO removes methyl groups from nucleic acids, but only on one rare type of DNA or RNA methylation. Important but mysterious "RNA epigenetics? " Sciencedaily: New role for RNA interfere... PhysOrg Science News: Study reveals new role for... Natureblogs: RNA editing may not be as... Natureblogs: RNA editing may not be as... RNA editing may not be as widespread as claimed. A paper that appeared to find evidence for a new mechanism of genetic regulation has been challenged by an analysis released today. In May, a team led by Vivian Cheung of the University of Pennsylvania in Philadelphia reported that in an analysis of 27 people, it had found 10,210 sites where transcribed RNA differed from an individual’s corresponding DNA sequence. The finding was startling because it implied that there might be an as-yet undiscovered mechanism of ‘RNA editing’ that could disrupt the central dogma, the process whereby DNA is faithfully transcribed into matching sequences of RNA, which are translated into proteins.
But other researchers pointed out that Cheung’s team had not performed some crucial analyses to ensure that it was actually observing mismatches rather than genetic sequencing errors or accurately transcribed regions of DNA. Today, Daniel R. Schrider, Jean-Francois Gout and Matthew W. Hahn says his team did contact Cheung’s group, but did not receive a reply. PhysOrg Science News: Novel technique uses RNA i... Novel technique uses RNA interference to block inflammation. PhysOrg Science News: New technique gives precis... PhysOrg Science News: Team finds stable RNA nano... Team finds stable RNA nano-scaffold within virus core. PhysOrg Science News: New roles emerge for non-c... Scientific Reports: A Non-coding RNA of Insect...
Nature Chemistry: Check out Chuan He's Comme... Nature Chemistry: Super plenary from Chuan H... Natureblogs: Merck shutters RNAi resear... E! Science News: Breakthrough lights way fo... PhysOrg Science News: Breakthrough lights way fo... Nature Chemistry: Our enzyme-free RNA copyin... Efficient enzyme-free copying of all four nucleobases templated by immobilized RNA : Nature Chemistry.
PhysOrg Science News: Talk softly but carry a ti... Foresight Institute: Finding small molecules to... PhysOrg Science News: Hitting moving RNA drug ta... E! Science News: Non-coding RNA has role in... PhysOrg Science News: Non-coding RNA has role in... PhysOrg Science News: New research describes key... Sciencedaily: Removal of a tiny RNA mole...
PhysOrg Science News: Tiny RNA molecule removal... E! Science News: Noncoding RNA may promote... PhysOrg Science News: Noncoding RNA may promote... Scientific American: RNA Editing to Create 'Acq... E! Science News: Researchers uncover a new... Sciencedaily: New level of genetic diver... PhysOrg Science News: RNA dynamics deconstructed... Sciencedaily: RNA nanoparticles construc...