Research suggesting genetic elements from plants make it into eater's bloodstream turns out to be a 'false positive' In 2011 and 2012, research from China's Nanjing University made international headlines with reports that after mice ate, bits of genetic material from the plants they'd ingested could make it into their bloodstreams intact and turn the animals' own genes off. The surprising results from Chen-Yu Zhang's group led to speculation that genetic illness might one day be treated with medicinal food, but also to worry that genetically modified foods might in turn modify consumers in unanticipated ways.
Now, though, a research team at Johns Hopkins reports that Zhang's results were likely a false positive that resulted from the technique his group used. The new study, the Johns Hopkins group says, bolsters the case of skeptics who argued that genetic material from food would have little chance of surviving the digestive system, much less crossing the intestinal lining to enter the bloodstream. The study appears in the July issue of RNA Biology. Edited RNA + invasive DNA add individuality. The story of why we are all so different goes well beyond the endless mixing and matching of DNA through breeding. A new study in the journal Nature Communications, for instance, reports a new molecular mechanism of individual variation found in fruit flies that uses components operating in a wide variety of species, including humans. The new mechanism is based in a surprising genetic oddity.
Nearly all genomes—those of humans, fruit flies, and even corn and rice—are constantly grappling with parasitic snippets of genetic material called "transposons. " These snippets copy themselves, move around, and embed themselves within DNA. In the new paper, scientists show that an enzyme called ADAR, which edits RNA in humans, flies, and many other creatures, edits double-stranded RNAs. Since the amount of ADAR varies from one individual to the next, the amount of jailbreaking from those chromatin prison varies too, and that should lead to altered gene expression. Picking the double strand. Hairpin turn: Micro-RNA plays role in wood formation. For more than a decade, scientists have suspected that hairpin-shaped chains of micro-RNA regulate wood formation inside plant cells. Now, scientists at NC State University have found the first example and mapped out key relationships that control the process.
The research, published online in Proceedings of the National Academy of Sciences the week of June 10, describes how one strand of micro-RNA reduced by more than 20 percent the formation of lignin, which gives wood its strength. Understanding how to reduce lignin at the cellular level could lead to advances in paper and biofuels production, where harsh chemicals and costly treatments are used to remove lignin from wood. "This is the first time that we have proof that a micro-RNA controls lignin biosynthesis," said Dr.
Vincent Chiang, who co-directs NC State's Forest Biotechnology Group with Dr. The network illustrates the hierarchy of gene control and narrows the transcription factors of interest from approximately 2,000 to 20. Enhancing RNA interference. Nanoparticles that deliver short strands of RNA offer a way to treat cancer and other diseases by shutting off malfunctioning genes. Although this approach has shown some promise, scientists are still not sure exactly what happens to the nanoparticles once they get inside their target cells. A new study from MIT sheds light on the nanoparticles' fate and suggests new ways to maximize delivery of the RNA strands they are carrying, known as short interfering RNA (siRNA). "We've been able to develop nanoparticles that can deliver payloads into cells, but we didn't really understand how they do it," says Daniel Anderson, the Samuel Goldblith Associate Professor of Chemical Engineering at MIT.
"Once you know how it works, there's potential that you can tinker with the system and make it work better. " Through a process called RNA interference, siRNA targets messenger RNA (mRNA), which carries genetic instructions from a cell's DNA to the rest of the cell. Molecular traffic jam. Sensitive technique for taking RNA inventory of individual cells offers powerful tool. Every cell is a hectic messaging center, with thousands of genes churning out messenger RNA (mRNA) transcripts for translation into functional proteins. Accordingly, sequencing the mRNA content of an individual cell can reveal critical insights into that cell's health and physiological state.
Unfortunately, as cells contain only tiny amounts of mRNA, on the order of ten trillionths of a gram, accurate quantitation is a major challenge. By introducing critical improvements to existing techniques, however, a research team led by Hiroki Ueda and Yohei Sasagawa at the RIKEN Center for Developmental Biology has now devised a robust and reproducible approach for surveying the mRNA content of individual cells. Several whole-transcriptome shotgun sequencing methods are available for performing RNA analyses on large numbers of cells. The Quartz-Seq method is already proving valuable for exploring genetic differences among individual cells.
RNA folding: A little cooperation goes a long way. (Phys.org)—The nucleic acid RNA is an essential part of the critical process by which the cells in our bodies manufacture proteins. But noncoding RNAs also exist whose sequences, while not converted into proteins, play important roles in many biological processes.
RNA molecules aggregate into complex three-dimensional (3-D) or "tertiary" structures, producing globular forms stabilized by various interactions. Proteins, ligands, and other RNA molecules recognize these folded RNAs and result in the biochemical pathways that affect all aspects of cellular metabolism. Utilizing synchrotron x-ray scattering at the Biophysics Collaborative Access Team (Bio-CAT) beamline 18-ID at the Argonne Advanced Photon Source (APS), researchers investigated the unique folding behavior of ribozyme, which is an RNA that acts as a catalyst.
RNA is one of two types of nucleic acids found in all cells. Small-angle x-ray scattering (as well as other techniques) at Bio-CAT beamline 18-ID at the U.S. Research sheds light on M.O. of unusual RNA molecules. Jul 05, Biology/Biotechnology The Xist lncrna (red) recruits proteins responsible for modifying chromatin architecture (green) across the x-chromosome. Xist and its associated proteins coat the entire x-chromosome, Forming a distinctive compartment in the nucleus (blue).
Credit: Amy Pandya-Jones and Kathrin Plath (Phys.org) —The genes that code for proteins—more than 20,000 in total—make up only about 1 percent of the complete human genome. That entire thing—not just the genes, but also genetic junk and all the rest—is coiled and folded up in any number of ways within the nucleus of each of our cells.
Now a team of researchers led by newly arrived biologist Mitchell Guttman of the California Institute of Technology (Caltech) and Kathrin Plath of UCLA, has figured out how some RNA molecules take advantage of their position within the three-dimensional mishmash of genomic material to home in on targets. "That's where this got really surprising," Guttman says. New portable device enables RNA detection from ultra-small sample in only 20 minutes. A new power-free microfluidic chip developed by researchers at the RIKEN Advanced Science Institute (ASI) enables detection of microRNA from extremely small sample volume in only 20 minutes. By drastically reducing the time and quantity of sample required for detection, the chip lays the groundwork for early-stage point-of-care diagnosis of diseases such as cancer and Alzheimer's.
MicroRNAs (miRNAs) are small, non-coding RNA molecules that regulate gene expression in a wide range of biological processes including development, cell proliferation, differentiation and cell death (apoptosis). Concentration of certain miRNA in body fluids increases with the progression of diseases such as cancer and Alzheimer's, generating hope that these short RNA may hold the key to faster, more accurate diagnosis.
The research team set out to overcome these obstacles by developing a device that enables fast, easy-to-use point-of-care (POC) diagnosis from only a very small sample. Metals in the genetic forge: Detailed views of RNA splicing. Scientists at Yale University have described in the greatest detail yet aspects of the chemical processes by which RNA carries out the expression of our genes. In a paper published Oct. 26 in the journal Cell, researchers report 14 crystal structures for a group II intron—an enzyme involved in RNA splicing, a critical phase of genetic reproduction. These new views capture the enzyme's working parts and multiple steps in its operation, revealing the chemical mechanisms at work.
"We didn't just get a snapshot—we caught the intron in action," said principal investigator Anna Pyle, the William Edward Gilbert Professor of Molecular, Cellular and Developmental Biology and professor of chemistry at Yale. A major function of RNA is copying all genetic information and making it readable by the cellular protein factories, the ribosomes. Splicing consists of breaking apart the RNA and recombining its pieces in ways that produce just the right protein the organism requires at any given time. Optical tweezers and sub-nanoscale precision: Following the process—and the consequence—of RNA folding. (Phys.org)—In a soundproofed, vibration-stabilized, temperature-controlled room, Stanford biophysicist Steven Block was watching a very small origami project. "The apparatus is so sensitive that, if you talk in the room, the vibrations in the air disturb the movement you're trying to measure," he said quietly.
On a black-and-white monitor, two microscopic plastic beads were being slowly drawn apart. Although we couldn't see it even at this high level of magnification, between the beads was stretched a single strand of RNA, folding up in real time. Because RNA nucleotides are so small – each is only nanometers long – these effects had never been directly observed before. But Block's feat isn't remarkable only for its sensitivity. "Issues of gene control are arguably more important than the genes themselves," Block said. Block, a professor of applied physics and of biology, and graduate student Kirsten Frieda published their findings today in the journal Science.
Laser traps. Carnegie Institution and UMASS Medical School granted broad US Patent related to RNA interference. The Carnegie Institution for Science and the University of Massachusetts Medical School (UMMS) have been granted United States Patent 8,283,329, entitled, "Genetic inhibition of double-stranded RNA. " The patent, issued on October 9, 2012, is broadly directed to the use of RNA interference (RNAi) to inhibit expression of a target gene in animal cells, including mammalian cells. The process by which RNA, the cellular material responsible for the transmission of genetic information, can silence a targeted gene within a living cell was discovered in 1998 by Carnegie's Andrew Fire, (now a professor at Stanford University) and Craig C.
Mello, Howard Hughes Medical Institute Investigator, Blais University Chair in Molecular Medicine and distinguished professor of molecular medicine and cell & developmental biology at UMass Medical School. The duo received the 2006 Nobel Prize in Physiology and/or Medicine for this work. This document is subject to copyright. Scientists devise screening method to aid RNA drug development research.
(Phys.org)—Scientists from the Florida campus of The Scripps Research Institute (TSRI) have developed a new method of screening more than three million combinations of interactions between RNA and small molecules to identify the best targets on RNA as well as the most promising potential drug compounds. This novel technology may lead to more efficient drug development. The study was published in the October 9, 2012 issue of the journal Nature Communications.
RNA has multiple biological functions, including encoding and translating proteins from genes and regulating the amount of protein expressed under various cellular conditions. Recent studies have identified RNA as a "molecular switch" that controls cellular events such as gene expression, making RNA an attractive target for small molecules that serve as chemical genetics probes, analytical tools or potential drugs. This document is subject to copyright. Smallest, fastest-known RNA switches provide new drug targets. (Phys.org)—A University of Michigan biophysical chemist and his colleagues have discovered the smallest and fastest-known molecular switches made of RNA, the chemical cousin of DNA. The researchers say these rare, fleeting structures are prime targets for the development of new antiviral and antibiotic drugs. Once believed to merely store and relay genetic information, RNA is now known to be a cellular Swiss Army knife of sorts, performing a wide variety of tasks and morphing into myriad shapes.
Over the past decade, researchers have determined that most of the DNA in our cells is used to make RNA molecules, that RNA plays a central role in regulating gene expression, and that these macromolecules act as switches that detect cellular signals and then change shape to send an appropriate response to other biomolecules in the cell. Al-Hashimi calls these short-lived structures, which were detected using a new imaging technique developed in his laboratory, micro-switches. From vitro to vivo: Fully automated design of synthetic RNA circuits in living cells.
(Phys.org)—Synthetic biology combines science and engineering in the pursuit of two general goals: to design and construct new biological parts, devices, and systems not found in nature; and redesign existing, natural biological systems for useful purposes. For synthetic biologists a key goal is to use RNA to automatically engineer synthetic sequences that encode functional RNA sequences in living cells.
While earlier RNA design attempts have mostly been developed in vitro or needed fragments of natural sequences to be viable, scientists at Institut de biologie systémique et synthétique in France have recently developed a fully automated design methodology and experimental validation of synthetic RNA interaction circuits working in a cellular environment. Their results demonstrate that engineering interacting RNAs with allosteric behavior in living cells can be accomplished using a first-principles computation.
Drs. Alfonso Jaramillo, Guillermo Rodrigo, and Thomas E. New study shows promise in using RNA nanotechnology to treat cancers and viral infections. A new study by University of Kentucky researchers shows promise for developing ultrastable RNA nanoparticles that may help treat cancer and viral infections by regulating cell function and binding to cancers without harming surrounding tissue. The study, published in Nano Today, was carried out in the laboratory of Peixuan Guo, the William S. Farish Endowed Chair in Nanobiotechnology at the UK Markey Cancer Center, in collaboration with Dr. Mark Evers, director of the UK Markey Cancer Center.
The study uses RNA (ribonucleic acid) as a building block for the bottom-up fabrication of nanostructures. Using the RNA nanotechnology pioneered by Guo, the researchers constructed ultrastable X-shaped RNA nanoparticles using re-engineered RNA fragments to carry up to four therapeutic and diagnostic modules. The study demonstrated that regulation of cellular functions progressively increased with the increasing number of functional modules in the nanoparticle.
Ancient enzymes function like nanopistons to unwind RNA. Researchers demonstrate how 'interfering' RNA can block bacterial evolution. To cap or not to cap: Scientists find new RNA phenomenon that challenges dogma. Researchers develop new method to detect, analyze DNA and RNA. Study identifies how RNA viruses hijack a host cell to multiply. Simple new method of extracting viral RNA from blood samples allows quick, on-the-spot identification of dengue fever. IU partnership results in faster Trinity RNA sequencing software. Lariats: How RNA splicing decisions are made. Researchers achieve RNA interference, in a lighter package. The cell's 'New World': First complete atlas of RNA-binding proteins. On early Earth, iron may have performed magnesium's RNA folding job. Real-time monitoring of RNA splicing in living cells moves step closer with novel fluorescent probe.
Research uncovers new exception to decades-old rule about RNA splicing. Researchers reveal an RNA modification influences thousands of genes. Locked down, RNA editing yields odd fly behavior. 3-D RNA modeling opens scientific doors. Nanoparticle-delivered RNA interference drug stops head and neck cancer growth. Researchers develop glowing probes to detect germs via RNA. A double ring ceremony prepares telomerase RNA to wed its protein partner. Molecular ticket determines RNA's destination and speed inside egg cell. Study of ribosome evolution challenges 'RNA World' hypothesis. Evolutionarily young protein helps ancient RNA get into shape. Molecular fossil: Crystal structure shows how RNA, one of biology's oldest catalysts, is made. Identifying molecular guardian of cell's RNA. A mystery solved: How genes are selectively silenced. The code for survival: Cells fight stress by reprogramming a system of RNA modifications.
Nature study shows how molecules escape from the nucleus. MicroRNA molecule increases number of blood stem cells, may help improve cancer treatment. Micro-RNA determines malignancy of lung cancer. Human cells can copy not only DNA, but also RNA. Now coming to your iPhone: App that shows 2-D structure of thousands of RNA molecules. Computer sleuthing helps unravel RNA's role in cellular function. New RNA-based therapeutic strategies for controlling gene expression. Scientists create novel RNA repair technology. Simpler times: Did an earlier genetic molecule predate DNA and RNA? RNA editing responsible for colder water survival in octopus.
A radar for ADAR: Altered gene tracks RNA editing in neurons. Researchers develop CAD-Type tools for engineering RNA control systems. Built-in 'self-destruct timer' causes ultimate death of messenger RNA in cells. Long non-coding RNA prevents the death of maturing red blood cells. Study identifies mechanisms cells use to remove bits of RNA from DNA strands.
Just the two of us: Stable dinucleotide-RNA duplexes show promise in biotechnology. Cancer drug cisplatin found to bind like glue in cellular RNA. Researchers find synthetic RNA lessens severity of fatal disease. Non-coding RNA relocates genes when it's time to go to work. TACC supercomputers help researchers find deeper insight into structure and behavior of protein, DNA and RNA. Study links Fragile X Syndrome proteins and RNA editing mistakes at nerve-muscle junction. New research links common RNA modification to obesity. Study reveals new role for RNA interference during chromosomal replication. New technique gives precise picture of how regulatory RNA controls gene activity. A micro-RNA as a key regulator of learning and Alzheimer's disease. BGI develops RNA-Seq (Quantification) from as low as 100 Ng total RNA.
Team finds stable RNA nano-scaffold within virus core. Researchers publish study on neuronal RNA targeting. Breakthrough lights way for RNA discoveries. RNA reactor could have served as a precursor of life. Hitting moving RNA drug targets. Non-coding RNA has role in inherited neurological disorder -- and maybe other brain diseases too. New research describes key function of enzyme involved in RNA processing. Tiny RNA molecule removal can inhibit cancer growth.
Noncoding RNA may promote Alzheimer's disease. Better vaccines thanks to RNA. New level of genetic diversity in human RNA sequences uncovered. Scientists work with RNA silencing and plant stem cells. RNA spurs melanoma development. RNA dynamics deconstructed: Technique offers detailed view of how RNA levels change. Researchers construct RNA nanoparticles to safely deliver long-lasting therapy to cells. UCSD chemists produce first high-resolution RNA 'nano square' Micro-RNA blocks the effect of insulin in obesity. RNA-exporting machine deciphered. Micro-RNA's contribute to risk for panic disorder.