Hotspots for biogenesis of small RNA molecules in plant cells discovered. Throughout their life, plants form leaves and side roots. These two types of organs have something in common: their development is finely tuned by small regulatory RNA molecules, the trans-acting short interfering RNAs (ta-siRNAs). Scientists Dr. Alexis Maizel and Virginie Jouannet at Heidelberg University's Centre for Organismal Studies were able to demonstrate how and where within the plant cell these ta-siRNAs are produced. They succeeded in identifying hotspots for the biogenesis of these special RNA molecules. The results of this study have been published in the EMBO Journal. The formation of plant organs depends on the presence of proteins that allow cells to divide and take on new shapes and characteristics.
Ta-siRNAs are created from longer RNA molecules that are whittled down by a complex of other molecules. Two other observations caught the attention of the researchers. Dr. New technique sheds light on RNA. When researchers sequence the RNA of cancer cells, they can compare it to normal cells and see where there is more RNA. That can help lead them to the gene or protein that might be triggering the cancer. But other than spotting a few known instigators, what does it mean? Is there more RNA because it's synthesizing too quickly or because it's not degrading fast enough? What part of the biological equilibrium is off? After more than a decade of work, researchers at the University of Michigan Comprehensive Cancer Center have developed a technique to help answer those questions.
The method involves a compound called bromouridine, which can be used to tag or label newly created RNA. Researchers apply the bromouridine for 30 minutes then isolate the RNA to see where the new RNA was made. On the other hand, the researchers can follow up the bromouridine labeling with a rinse with the chemical uridine for different periods of time. Early evolution of life: Study of ribosome evolution challenges 'RNA World' hypothesis. In the beginning -- of the ribosome, the cell's protein-building workbench -- there were ribonucleic acids, the molecules we call RNA that today perform a host of vital functions in cells. And according to a new analysis, even before the ribosome's many working parts were recruited for protein synthesis, proteins also were on the scene and interacting with RNA.
This finding challenges a long-held hypothesis about the early evolution of life. The study appears in the journal PLoS ONE. The "RNA world" hypothesis, first promoted in 1986 in a paper in the journal Nature and defended and elaborated on for more than 25 years, posits that the first stages of molecular evolution involved RNA and not proteins, and that proteins (and DNA) emerged later, said University of Illinois crop sciences and Institute for Genomic Biology professor Gustavo Caetano-Anollés, who led the new study.
"I'm convinced that the RNA world (hypothesis) is not correct," Caetano-Anollés said. Retrovirus in the human genome is active in pluripotent stem cells. A retrovirus called HERV-H, which inserted itself into the human genome millions of years ago, may play an important role in pluripotent stem cells, according to a new study published in the journal Retrovirology by scientists at UMass Medical School. Pluripotent stem cells are capable of generating all tissue types, including blood cells, brain cells and heart cells. The discovery, which may help explain how these cells maintain a state of pluripotency and are able to differentiate into many types of cells, could have profound implications for therapies that would use pluripotent stem cells to treat a range of human diseases.
"What we've observed is that a group of endogenous retroviruses called HERV-H is extremely busy in human embryonic stem cells," said Jeremy Luban, MD, the David L. Freelander Memorial Professor in HIV/AIDS Research, professor of molecular medicine and lead author of the study. In the study, Dr. First artificial enzyme created by evolution in a test tube. There's a wobbly new biochemical structure in Burckhard Seelig's lab at the University of Minnesota that may resemble what enzymes looked like billions of years ago, when life on earth began to evolve -- long before they became ingredients for new and improved products, from detergents to foods and fuels. Seelig created the fledgling enzyme by using directed evolution in the laboratory.
Working with colleague Gianluigi Veglia, graduate student Fa-An Chao, and other team members, he subsequently determined its structure, which made its debut December 9 as an advance online publication in Nature Chemical Biology. Lab tests show that the enzyme (a type of RNA ligase, which connects two RNA molecules) functions like natural enzymes although its structure looks very different and it is flexible rather than rigid. Seelig speculates the new protein resembles primordial enzymes, before their current structures evolved. "It's kind of like giving typewriters to monkeys," he says.
Turning off small RNA: New tool designed for breaking the epigenetic code. For the last dozen years, scientists have known that minuscule strings of genetic material called small RNA are critically important to our genetic makeup. But finding out what they do hasn't been easy. Now a scientist from Michigan Technological University and his team have developed a way to turn off small RNAs and find out just how important they can be. When it comes to inheritance, DNA is just the half of it. What we are is also driven by the epigenetic world of RNA: the countless, twisting molecules that DNA churns out. There's more than one kind of RNA, however. Now, Guiliang Tang, an associate professor of biological sciences, has developed a way to put a single small RNA out of commission and observe what happens when it can't do its job.
To do this, Tang and his team threw a wrench into a well-understood process that controls leaf symmetry and the tendency of plants to grow upright. The results were dramatic. New dinosaur fossil challenges bird flight origins theories. The discovery of a new bird-like dinosaur from the Jurassic period challenges widely accepted theories on the origin of flight. Co-authored by Dr Gareth Dyke, Senior Lecturer in Vertebrate Palaeontology at the University of Southampton, the paper describes a new feathered dinosaur about 30 cm in length which pre-dates bird-like dinosaurs that birds were long thought to have evolved from.
Over many years, it has become accepted among palaeontologists that birds evolved from a group of dinosaurs called theropods from the Early Cretaceous period of Earth's history, around 120-130 million years ago. Recent discoveries of feathered dinosaurs from the older Middle-Late Jurassic period have reinforced this theory. The new 'bird-dinosaur' Eosinopteryx described in Nature Communications this week provides additional evidence to this effect. "Our findings suggest that the origin of flight was much more complex than previously thought. " Cellular switches: From the RNA world to the 'modern' protein world.
Heidelberg scientists have discovered the molecular mechanism of a G protein family. G proteins play a central role in cellular signal processing. They are described as molecular switches that oscillate between 'on' and 'off', regulated by effectors. Biochemists at Heidelberg University have now gained fundamental insights into the mechanics of these switches.
By studying the flagella, the organelles of locomotion in bacteria, researchers were able to identify an effector that turns a specific G protein 'off'. Bacteria need to be mobile to react to environmental changes, and in the case of pathogens, to reach the site of infection. The G protein FlhF, together with a signal sequence binding protein (SRP54) and its receptor (FtsY), constitutes the ancient family of SRP-GTPases, which consists solely of these three proteins and is responsible for the transport of proteins in or through a biological membrane. Computer sleuthing helps unravel RNA's role in cellular function. Computer engineers may have just provided the medical community a new way of figuring out exactly how one of the three building blocks of life forms and functions. University of Central Florida Engineering Assistant Professor Shaojie Zhang used a complex computer program to analyze RNA motifs -- the subunits that make up RNA (ribonucleic acid).
RNA is one of three building blocks of life along with DNA and proteins. Knowing how all three building blocks work together and how they go awry will go a long way to understanding what causes diseases and how to treat them. While much has been discovered about DNA thanks to the Human Genome Project, not a lot is known about RNA, which like DNA helps encode genes. Some viruses also use RNA as their prime genetic source to replicate. And various types of RNA are involved in everything from protein synthesis, controlling gene expression and communicating cell signals from one part of the body to another. RNA interference cancer treatment? Delivering RNA with tiny sponge-like spheres. For the past decade, scientists have been pursuing cancer treatments based on RNA interference -- a phenomenon that offers a way to shut off malfunctioning genes with short snippets of RNA.
However, one huge challenge remains: finding a way to efficiently deliver the RNA. Most of the time, short interfering RNA (siRNA) -- the type used for RNA interference -- is quickly broken down inside the body by enzymes that defend against infection by RNA viruses. "It's been a real struggle to try to design a delivery system that allows us to administer siRNA, especially if you want to target it to a specific part of the body," says Paula Hammond, the David H. Koch Professor in Engineering at MIT. Hammond and her colleagues have now come up with a novel delivery vehicle in which RNA is packed into microspheres so dense that they withstand degradation until they reach their destinations. Lead author of the paper is Jong Bum Lee, a former postdoc in Hammond's lab. Genetic disruption Targeting tumors.
A radar for ADAR: Altered gene tracks RNA editing in neurons. Jan. 4, 2012 — RNA editing is a key step in gene expression. Scientists at Brown University report in Nature Methods that they have engineered a gene capable of visually displaying the activity of the key enzyme ADAR in living fruit flies. 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. A reporter of an editor A versatile new tool? Story Source:
Simpler times: Did an earlier genetic molecule predate DNA and RNA? 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. Computer assisted design (CAD) for RNA. 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.
Department of Energy (DOE)'s Joint BioEnergy Institute (JBEI) have developed CAD-type models and simulations for RNA molecules that make it possible to engineer biological components or "RNA devices" for controlling genetic expression in microbes. This holds enormous potential for microbial-based sustainable production of advanced biofuels, biodegradable plastics, therapeutic drugs and a host of other goods now derived from petrochemicals.
"Because biological systems exhibit functional complexity at multiple scales, a big question has been whether effective design tools can be created to increase the sizes and complexities of the microbial systems we engineer to meet specific needs," says Jay Keasling, director of JBEI and a world authority on synthetic biology and metabolic engineering. Built-in 'self-destruct timer' causes ultimate death of messenger RNA in cells. Researchers at Albert Einstein College of Medicine of Yeshiva University have discovered the first known mechanism by which cells control the survival of messenger RNA (mRNA) -- arguably biology's most important molecule. The findings pertain to mRNAs that help regulate cell division and could therefore have implications for reversing cancer's out-of-control cell division.
The research was recently described in the journal Cell. "The fate of the mRNA molecules we studied resembles a Greek tragedy," said the study's senior author, Robert Singer, Ph.D., co-director of the Gruss Lipper Biophotonics Center and professor and co-chair of anatomy and structural biology at Einstein. "Their lifespans are determined at the moment of their birth.
" The study was carried out in yeast cells using advanced microscope technology developed previously by Dr. Singer that has allowed scientists, for the first time, to observe single molecules in single cells in real time. Long non-coding RNA prevents the death of maturing red blood cells. A long non-coding RNA (lncRNA) regulates programmed cell death during one of the final stages of red blood cell differentiation, according to Whitehead Institute researchers.
This is the first time a lncRNA has been found to play a role in red blood cell development and the first time a lncRNA has been shown to affect programmed cell death. "Programmed cell death, or apoptosis, is very important, particularly in the hematopoietic (blood forming) system, where inhibition of cell death leads to leukemias," says Whitehead Institute Founding Member Harvey Lodish, who is also a professor of biology and a professor of bioengineering at MIT. "We know a lot about the genes and proteins that regulate apoptosis, but this is the first example of a non-coding RNA that plays a role in blood cells. We would not be surprised to find this lncRNA or others like it upregulated in cancers. " Currently, little is known about the specific function of lncRNAs, despite their abundance in cells. Mechanisms cells use to remove bits of RNA from DNA strands. Acquired traits can be inherited via small RNAs.
Cancer drug cisplatin found to bind like glue in cellular RNA. New technique gives precise picture of how regulatory RNA controls gene activity. New role for RNA interference during chromosomal replication discovered. Team finds stable RNA nano-scaffold within virus core. Key function of enzyme involved in RNA processing described. Hitting moving RNA drug targets: New way to search for novel drugs.