Meet the Bugs. The Victoria Bug Zoo is extremely small. In 1997, the Zoo's founder, Carol Maier, started the collection, which now includes more than 50 insect species, after completing her entomology degree from the University of Guelph. Giant golden orb weaver, Nephila sp. Found in Malaysia and the tropics, the female orb weavers are far larger than the males. prevnextexpand Meet the Bugs Image Gallery The Victoria Bug Zoo is extremely small. Read the full story. [gallery] Filling in the Missing Letters. A new algorithm brings together data from second - and third - generation genome sequencers. A new algorithm published yesterday (July 2) in Nature Biotechnology takes the best of second- and third-generation sequencing technologies to produce fuller and more accurate whole genome sequences. Second-generation sequencers read short DNA snippets—between 100 and 700 base pairs long—then stitch them together to produce a full genome.
However, stitching them in the correct order remains a challenge. Third-generation sequencers, on the other hand, can read long stretches of DNA at once, but are more prone to errors. The researchers tested the new algorithm on the Escherichia coli and yeast genomes, and found it increased accuracy by up to 99.9 percent. This new approach may be useful for researchers interested in sequences that lie beyond gene-coding regions, Adam Phillippy, the bioinformatics researcher who led the study, told Nature. 3-D Printing. Is printing out your own lab equipment, molecular models, and drug compounds the wave of the future?
DESIGNING IN THREE DIMENSIONS: Adam Gardner, technician in Arthur Olson’s lab, holds molecular models made by the lab’s 3-D printer.Adam Gardner DESIGNING IN THREE DIMENSIONS: Adam Gardner, technician in Arthur Olson’s lab, holds molecular models made by the lab’s 3-D printer. ADAM GARDNER If you’ve worn out the spike on your stiletto, misplaced your kazoo, or you need a cheap little centrifuge, three-dimensional printing and a growing community of designers devoted to open-source software have the solutions for you. Once considered the realm of tinkerers and toy makers, 3-D printing is providing scientists with a treasure trove of opportunities to custom-design equipment and experiments. Kevin Lance, a graduate student at the University of California, San Francisco, once fixed a broken Pipetboy by simply drawing up the dimensions of the disabled part and printing it out.
[gallery] Jumping Genes a Cause of Cancer? Genome sequence analysis confirms mobile genetic elements are a mutagenic mechanism in a variety of cancers. Double helix showing coplanar alignment of standard base pairs. Wikimedia Commons, Mushii Double helix showing coplanar alignment of standard base pairs.WIKIMEDIA COMMONS, MUSHII Within the human genome, small DNA elements called retrotransposons have the potential to wreak mutational havoc by copying themselves and reinserting into the genome at multiple locations. Normal adult cells have suppressive mechanisms to stop these elements from jumping about, but according to a report published today (June 28) in Science, those mechanisms can break down in certain cancers. “The paper is very important,” said Keith Slotkin a molecular geneticist at Ohio State University in Columbus, who did not participate in the study.
But a handful of reports documenting retrotransposon insertions in tumor cells suggest that these suppressive mechanisms might go awry in some cancers. Patent War for Prenatal Tests. Four companies who have developed noninvasive genetic prenatal tests are fighting over who has the patent rights to the new and revolutionary techniques. stock.xchng, bsilder This year alone has seen the arrival of three noninvasive tests for analyzing the DNA of a fetus, with a fourth expected to become available in the coming months. These new tests can detect genetic abnormalities, such as Down syndrome, as early as 10 weeks into the pregnancy, and could soon represent a market of more than $1 billion, according to Nature.
With such high financial stakes, the four companies that have made these tests available are currently embroiled in a legal battle over who can patent the underlying technique, which involves scanning maternal blood for fetal DNA. Back in January, Sequenom, a genetic diagnostics manufacturer based in San Diego, California, filed a lawsuit against San Jose-based Ariosa for patent infringement. Toying with RNA. A new online game challenges users to design RNA sequences with the opportunity to have them brought to life. Noncoding RNA folds into intricate shapes that determine its function, but the rules of nucleotide patterns that determine these shapes are largely unknown. Now, an online game that tasks users to manipulate nucleotides until they fit real RNA shapes is rapidly uncovering those rules, using the brain’s innate ability to recognize patterns and its flare for intuition.
Players of the game EteRNA are given a real-world RNA shape and asked to manipulate a chain of nucleotides to fit that shape, by observing how different patterns of nucleotides form certain structures, like loops or tails. Then, every week, a few molecules are selected for synthesis in a lab at Stanford to see how closely they match the desired shape. Before EteRNA came along, software algorithms for predicting RNA folding patterns were primitive. Hat tip to Wired Science. Next Generation: Separation Two Ways. Researchers designed a microfluidics chip to separate cells using gravity and a force field. An artist's rendering of tumor cells flowing over an array of physical barriers. Martin Rietveld/Johns Hopkins University An artist's rendering of tumor cells flowing over an array of physical barriers.
MARTIN RIETVELD/JOHNS HOPKINS UNIVERSITY The Device: Researchers at Johns Hopkins University have developed a simple microfluidics chip to separate biological particles, like cells or proteins, by speed and location. Developed by graduate student Jorge Bernate with professor German Drazer, the strategy is a twist on chromatography, wherein separation of particles, like cells or peptides, occurs over time, with fast-moving particles being collected first and slow-moving particles being picked up later.
Instead of relying on the single dimension of time, however, Bernate uses a strategy termed vector chromatography, which also uses space to separate biological entities. J. Natural Antidepressant Discovered. A newly recognized chemical factor in the brain, called neuritin, regulates plasticity and may play a role in depression. Flickr, MikeBlogs Researchers have identified a nerve growth factor that regulates synaptic plasticity and appears to have antidepressant effects.
In new research, published today (June 25) in Proceedings of the National Academy of Sciences, scientists show that neuritin, which increases synaptic connections in the hippocampus, can alleviate stress-induced depressive symptoms. The findings give insight into the molecular mechanisms underlying depression, as well as identifying a possible target for therapeutics.
“The work does a really good job of convincing me that neuritin is involved in depression,” said Scott Russo, who studies the brain’s response to stress at Mount Sinai Medical School in New York, and was not involved in the research. Duman hopes that more insight into neuritin and BDNF could lead to the development of therapeutics that mimic their effects. H. Honey Bee Killer. A parasitic mite helps spread a deadly virus among honey bee colonies. A parasitic mite (Varroa destructor) that feeds on the blood of honeybees has helped spread a deadly strain of the virus implicated in the deaths of millions of honeybees worldwide. Known as deformed wing virus (DWV), the RNA virus causes wing and abdominal deformities, suppresses the immune system, and affects the behavior of infected bees. The mite was accidentally brought over to Hawaii 5 years ago and quickly began affecting honeybee populations, though it has yet to reach all bees on the islands—affording researchers, led by Stephen Martin from the University of Sheffield, the unique opportunity to study infected and uninfected bee colonies.
They found that the mite drastically altered the normal viral landscape of bees, which typically carry billions of different viral strains, and specifically selected for deformed wing virus—increasing its frequency in infected colonies from 10 percent to 100 percent. Memory Tools for Plants. How plants pass defenses to offspring through a complex molecular network Flickr, Daniel Ocampo Just last week, we covered findings that show plants can transfer acquired defenses against pests and pathogens on to their offspring—a finding that may have implications in crop pest management. Now, a new study published in Plant Signaling and Behavior describes how three molecular mechanisms interact to create an inheritable signal. “To connect the dots, we recently tested a group of Arabidopsis mutants that are affected by all three of the mechanisms suggested in prior research,” said Jurriaan Ton of the University of Sheffield, including small interfering RNAs (siRNAs), DNA methylation, and histone modification.
The current findings suggest that all three signals work together, but that only one factor is likely passed to offspring—methylation of the CHG motif, a common DNA sequence in the genome. The researchers also confirmed a role for siRNAs in defense inheritance. Best in Industry, 2012. Whether working for a pharmaceutical giant or a biotech start-up with a unique vision, researchers who responded to this year’s Best Places to Work in Industry survey are translating society’s most pressing scientific needs into a new generation of drugs, research tools, and cutting-edge innovations.
Sal Sadoti, one of several engineering technicians at #1-ranked ADInstruments, tests a prototype of a new software-controlled isolated stimulator. prevnextexpand Best in Industry, 2012 Image Gallery Whether working for a pharmaceutical giant or a biotech start-up with a unique vision, researchers who responded to this year’s Best Places to Work in Industry survey are translating society’s most pressing scientific needs into a new generation of drugs, research tools, and cutting-edge innovations.
[gallery] Targeting DNA. The concept is simple: if a mutated gene is causing a problem, replace or supplement it with a new, accurate copy. In theory, such a strategy could not just treat, but cure countless human genetic diseases. In practice, however, developing safe and effective gene therapies has not been easy. Even when identifying a disorder’s genetic basis is fairly straightforward, finding the appropriate delivery vector to target the diseased tissues in the body, while avoiding unintended consequences, has challenged would-be gene therapists for more than 20 years.
But more and more researchers are convinced that the technique is on the brink of becoming a common medical practice. Clearly gene therapy is going to be a therapeutic pathway forward for a whole range of diseases. Fits and starts It hasn’t always been such high times for gene therapy, however. Infographic: Delivering New Genes View full size JPG | PDF But things are looking up. An eye on gene therapy Targeting cancer: pluses and minuses.
Seeds Inherit Memories of Enemies. The Arabidopsis plant on the left received a priming treatment before infection with bacteria and shows no sign of disease. The plant on the right is an untreated control plant. Brigitte Mauch-Mani The Arabidopsis plant on the left received a priming treatment before infection with bacteria and shows no sign of disease. The plant on the right is an untreated control plant. BRIGITTE MAUCH-MANI After plants acquire resistance to pests and pathogens, their offspring shoot up through the soil with better defenses. The findings, published in a recent series of papers in Plant Physiology, are the first to identify small interfering RNAs (siRNAs) as a possible mechanism of this inherited memory response, and suggest a new strategy for managing crop pests. “It’s sort of like giving a vaccine to the parent and seeing immunity in the child,” said Andrei Alyokhin, who studies insect-plant interactions at the University of Maine and was not involved in the research.
The Aging and Inflammation Link. A protein that keeps the immune response in check leads a double life as an anti-aging factor. Scientists studying mice genetically engineered to lack an anti-inflammatory factor have stumbled upon an unexpected secondary function for the protein—it slows down aging. The surprising discovery, which is reported online today (May 24) in Molecular Cell, has implications for inflammatory and age-related diseases, but also for cancer. “We were [shocked], to put it mildly,” said Robert Schneider of New York University, who led the study. “This is certainly not something anybody would have ever anticipated.” Schneider and his team had been analyzing mice that lacked a protein called AUF1 and they'd shown that it was critical for binding to and degrading mRNA transcripts encoding inflammatory proteins. But besides having a dampened inflammatory response, mice lacking AUF1 displayed some unusual characteristics.
“We noticed that they aged very rapidly,” said Schneider. A. Debate over RNA Transcription. Researchers question earlier findings of a new mechanism for gene regulation. Flickr, kyz Results regarding a new type of RNA editing, reported last July by Vivian Cheung at the University of Pennsylvania, were questioned last Thursday (March 15) by three groups publishing technical commentaries in Science. Cheung’s research found more than 10,000 cases in which RNA underwent an additional editing step before being translated into protein, suggesting a possible rewrite of the central dogma, which states that the RNA message usually matches the original gene.
The work was immediately criticized by biologists who questioned Cheung’s interpretation of her results. Now, three independent research groups who reanalyzed Cheung’s data say that up to 94 percent of the reported RNA editing sites were inaccurately assessed. Multiple Strikes Against Autism. Virology Technologist Position. Debate over RNA Transcription.
Coffee Pest Gene Transfer. New Kind of Cellular Suicide. Color Explosion. Eye Trials Give Hope for Stem Cells. Cellular Workout. Smart Drugs. How to Survive Freezing Waters. Before the Genes Jumped, 1930s. All the single (polyandrous) ladies. Celebration of a breakthrough tool for understanding RNA. Tracy Dale at SfN 2011. So long, and thanks… New EMBO Members. Manel Esteller, 2011 EACR Cancer Researcher. RNomics - The Scientist - Magazine of the Life Sciences.