Scientists discover double meaning in genetic code:
Scientists have discovered a second code hiding within DNA. This second code contains information that changes how scientists read the instructions contained in DNA and interpret mutations to make sense of health and disease.
A research team led by Dr. John Stamatoyannopoulos, University of Washington associate professor of genome sciences and of medicine, made the discovery. The findings are reported in the Dec. 13 issue of Science. The work is part of the Encyclopedia of DNA Elements Project, also known as ENCODE. The National Human Genome Research Institute funded the multi-year, international effort. ENCODE aims to discover where and how the directions for biological functions are stored in the human genome.
Since the genetic code was deciphered in the 1960s, scientists have assumed that it was used exclusively to write information about proteins. UW scientists were stunned to discover that genomes use the genetic code to write two separate languages. One describes how proteins are made, and the other instructs the cell on how genes are controlled. One language is written on top of the other, which is why the second language remained hidden for so long.
“For over 40 years we have assumed that DNA changes affecting the genetic code solely impact how proteins are made,” said Stamatoyannopoulos. “Now we know that this basic assumption about reading the human genome missed half of the picture. These new findings highlight that DNA is an incredibly powerful information storage device, which nature has fully exploited in unexpected ways.”
The genetic code uses a 64-letter alphabet called codons. The UW team discovered that some codons, which they called duons, can have two meanings, one related to protein sequence, and one related to gene control. These two meanings seem to have evolved in concert with each other. The gene control instructions appear to help stabilize certain beneficial features of proteins and how they are made.
The discovery of duons has major implications for how scientists and physicians interpret a patient’s genome and will open new doors to the diagnosis and treatment of disease.
“The fact that the genetic code can simultaneously write two kinds of information means that many DNA changes that appear to alter protein sequences may actually cause disease by disrupting gene control programs or even both mechanisms simultaneously,” said Stamatoyannopoulos.
Our galaxy may hold 100M complex-life-supporting planets:
The number of planets in the Milky Way galaxy which could harbor complex life may be as high as 100 million, Washington State University astrobiologist Dirk Schulze-Makuch writes in a column posted this week on the Air & Space/Smithsonian magazine website.
The estimate, which assumes an average of one planet per star in the Milky Way, is drawn from a study believed to be the first quantitative assessment of the number of worlds in our galaxy that could harbor life above the microbial level.
Schulze-Makuch said the study is significant because it is the first to rely on observable data from actual planetary bodies beyond the solar system, rather than making educated guesses about the frequency of life on other worlds based on hypothetical assumptions.
The research was published recently in the journal Challenges by a group of scientists that includes Louis Irwin, of the University of Texas at El Paso; Alberto Fairen of Cornell University; Abel Mendez of the Planetary Habitability Laboratory at the University of Puerto Rico at Arecibo; and Schulze-Makuch.
The researchers surveyed the growing list of more than 1,000 known planets outside the solar system. Using a formula that considers planetary density, temperature, substrate (liquid, solid or gas), chemistry, distance from its central star and age, they computed a “Biological Complexity Index (BCI),” which rates planets on a scale of 0 to 1.0 according to the number and degree of characteristics assumed to be important for supporting various forms of multicellular life.
“The BCI calculation revealed that 1 to 2 percent of exoplanets showed a BCI rating higher than Europa, a moon of Jupiter thought to have a subsurface global ocean which could harbor different forms of life,” writes Schulze-Makuch. “Based on an estimate of 10 billion stars in the Milky Way Galaxy, and assuming an average of one planet per star, this yields the figure of 100 million. Some scientists believe the number could be 10 times higher.”
He emphasizes that the study should not be taken as an indication that complex life actually exists on as many as 100 million planets, but rather that the figure is the best estimate to date of the number of planets in our galaxy likely to exhibit conditions supportive to such life.
“Also, it should be understood that complex life doesn’t mean intelligent life or even animal life, although it doesn’t rule either out,” Schulze-Makuch said. “It means simply that organisms larger and more complex than microbes could exist in a number of different forms, quite likely forming stable food webs like those found in ecosystems on Earth.
“Despite the large absolute number of planets that could harbor complex life, the Milky Way is so vast that, statistically, planets with high BCI values are very far apart,” Schulze-Makuch writes. “One of the closest and most promising extrasolar systems, known as Gliese 581, has possibly two planets with the apparent capacity to host complex biospheres, yet the distance from the Sun to Gliese 581 is about 20 light years.”
And most planets with a high BCI are much farther away, he said.
If the 100 million planets that the team says have the theoretical capacity for hosting complex life were randomly distributed across the galaxy, Schulze-Makuch said they would lie about 24 light years apart, assuming equal stellar density. And he estimates the distance between planets with intelligent life would likely be significantly farther.
“On the one hand it seems highly unlikely that we are alone,” he writes in the article. “On the other hand, we are likely so far away from life at our level of complexity, that a meeting with such alien forms might be improbable for the foreseeable future.”
Tiny Nanomotors Successfully Placed Inside Live Human Cells For The First Time:
Scientists have successfully placed tiny synthetic motors in live human cells through nanotechnology. Using ultrasonic waves as the power source and magnets to steer, the nanomotors can zip around the cell and perform tasks.
The main obstacle for placing nanomotors in cells is the power source. Previous nanomotors needed toxic fuels to propel them. It wouldn’t move in a biological environment.
The researchers at Penn State University and at Weinberg Medical Physics found that ultrasonic waves can be used to power these motors and that magnetic fields can be used to steer them.
The image above is that of a HeLa cell with some gold-ruthenium nanomotors inside it. The arrows indicate the trajectories of the nanomotors, and the solid white line shows its propulsion. There are several nanomotors is spinning at the center. HeLa cells are a line of human cervical cancer cells that are used in research studies. Image credit: Mallouk lab, Penn State University.
Bionanotechnology is fast becoming popular in medical and scientific research. Implants and devices hundreds of times smaller than the width of a human hair, can be integrated into cells. This technology can open up various medical applications such as surgery, deliver medication, and even eradicate cancer cells. Because of its microscopic size, bionanotech devices are non-invasive and results in fewer complications normal open surgery would have.
For the first time, a team of chemists and engineers at Penn State University have placed tiny synthetic motors inside live human cells, propelled them with ultrasonic waves and steered them magnetically. It’s not exactly “Fantastic Voyage,” but it’s close. The nanomotors, which are rocket-shaped metal particles, move around inside the cells, spinning and battering against the cell membrane.
“As these nanomotors move around and bump into structures inside the cells, the live cells show internal mechanical responses that no one has seen before,” said Tom Mallouk, Evan Pugh Professor of Materials Chemistry and Physics at Penn State. “This research is a vivid demonstration that it may be possible to use synthetic nanomotors to study cell biology in new ways. We might be able to use nanomotors to treat cancer and other diseases by mechanically manipulating cells from the inside. Nanomotors could perform intracellular surgery and deliver drugs noninvasively to living tissues.”
The researchers’ findings will be published in Angewandte Chemie International Edition on 10 February 2014. In addition to Mallouk, co-authors include Penn State researchers Wei Wang, Sixing Li, Suzanne Ahmed, and Tony Jun Huang, as well as Lamar Mair of Weinberg Medical Physics in Maryland U.S.A.
Up until now, Mallouk said, nanomotors have been studied only “in vitro” in a laboratory apparatus, not in living human cells. Chemically powered nanomotors first were developed ten years ago at Penn State by a team that included chemist Ayusman Sen and physicist Vincent Crespi, in addition to Mallouk. “Our first-generation motors required toxic fuels and they would not move in biological fluid, so we couldn’t study them in human cells,” Mallouk said. “That limitation was a serious problem.” When Mallouk and French physicist Mauricio Hoyos discovered that nanomotors could be powered by ultrasonic waves, the door was open to studying the motors in living systems.
For their experiments, the team uses HeLa cells, an immortal line of human cervical cancer cells that typically is used in research studies. These cells ingest the nanomotors, which then move around within the cell tissue, powered by ultrasonic waves. At low ultrasonic power, Mallouk explained, the nanomotors have little effect on the cells. But when the power is increased, the nanomotors spring into action, moving around and bumping into organelles — structures within a cell that perform specific functions. The nanomotors can act as egg beaters to essentially homogenize the cell’s contents, or they can act as battering rams to actually puncture the cell membrane.
While ultrasound pulses control whether the nanomotors spin around or whether they move forward, the researchers can control the motors even further by steering them, using magnetic forces. Mallouk and his colleagues also found that the nanomotors can move autonomously — independently of one another — an ability that is important for future applications. “Autonomous motion might help nanomotors selectively destroy the cells that engulf them,” Mallouk said. “If you want these motors to seek out and destroy cancer cells, for example, it’s better to have them move independently. You don’t want a whole mass of them going in one direction.”
The ability of nanomotors to affect living cells holds promise for medicine, Mallouk said. “One dream application of ours is Fantastic Voyage-style medicine, where nanomotors would cruise around inside the body, communicating with each other and performing various kinds of diagnoses and therapy. There are lots of applications for controlling particles on this small scale, and understanding how it works is what’s driving us.”
Scientists Invent 30 Year Continuous Power Laptop Battery!
Your next laptop could have a continuous power battery that lasts for 30 years without a single recharge thanks to work being funded by the U.S. Air Force Research Laboratory. The breakthrough betavoltaic power cells are constructed from semiconductors and use radioisotopes as the energy source. As the radioactive material decays it emits beta particles that transform into electric power capable of fueling an electrical device like a laptop for years.
Although betavoltaic batteries sound Nuclear they’re not, they’re neither use fission/fusion or chemical processes to produce energy and so (do not produce any radioactive or hazardous waste). Betavoltaics generate power when an electron strikes a particular interface between two layers of material. The Process uses beta electron emissions that occur when a neutron decays into a proton which causes a forward bias in the semiconductor. This makes the betavoltaic cell a forward bias diode of sorts, similar in some respects to a photovoltaic (solar) cell. Electrons scatter out of their normal orbits in the semiconductor and into the circuit creating a usable electric current.
The profile of the batteries can be quite small and thin, a porous silicon material is used to collect the hydrogen isotope tritium which is generated in the process. The reaction is non-thermal which means laptops and other small devices like mobile phones will run much cooler than with traditional lithium-ion power batteries. The reason the battery lasts so long is that neutron beta-decay into protons is the world’s most concentrated source of electricity, truly demonstrating Einstein’s theory E=MC2.
The best part about these cells are when they eventually run out of power they are totally inert and non-toxic, so environmentalists need not fear these high tech scientific wonder batteries. If all goes well plans are for these cells to reach store shelves in about 2 to 3 years.
Plants recognize their siblings, biologists discover:
The next time you venture into your garden armed with plants, consider who you place next to whom. It turns out that the docile garden plant isn’t as passive as widely assumed, at least not with strangers. Researchers at McMaster University have found that plants get fiercely competitive when forced to share their pot with strangers of the same species, but they’re accommodating when potted with their siblings.
The study appears today in the Royal Society journal Biology Letters.
“The ability to recognize and favour kin is common in animals, but this is the first time it has been shown in plants” said Susan Dudley, associate professor of biology at McMaster University in Hamilton, Canada. “When plants share their pots, they get competitive and start growing more roots, which allows them to grab water and mineral nutrients before their neighbours get them. It appears, though, that they only do this when sharing a pot with unrelated plants; when they share a pot with family they don’t increase their root growth. Because differences between groups of strangers and groups of siblings only occurred when they shared a pot, the root interactions may provide a cue for kin recognition.”
Though they lack cognition and memory, the study shows plants are capable of complex social behaviours such as altruism towards relatives, says Dudley. Like humans, the most interesting behaviours occur beneath the surface.
Dudley and her student, Amanda File, observed the behavior in sea rocket (Cakile edentula), a member of the mustard family native to beaches throughout North America, including the Great Lakes.
So should gardeners arrange their plants like they would plan the seating at a dinner party?
“Gardeners have known for a long time that some pairs of species get along better than others, and scientists are starting to catch up with why that happens,” says Dudley. “What I’ve found is that plants from the same mother may be more compatible with each other than with plants of the same species that had different mothers. The more we know about plants, the more complex their interactions seem to be, so it may be as hard to predict the outcome as when you mix different people at a party.”
Roundup Herbicide 125 Times More Toxic Than Regulators Say:
A highly concerning new study published in the journal Biomedical Research International reveals that despite the still relatively benign reputation of agrochemicals such as Roundup herbicide, many chemical formulations upon which the modern agricultural system depend are far more toxic than present regulatory tests performed on them reveal. Roundup herbicide, for instance, was found to be 125 times more toxic than its active ingredient glyphosate studied in isolation.
Titled, “Major pesticides are more toxic to human cells than their declared active principles,” the study evaluated to what extent the active principle (AP) and the so-called ‘inert ingredients,’ i.e. adjuvants, in globally popular formulations account for the toxicity of 9 major pesticides: 3 herbicides, 3 insecticides, and 3 fungicides.
The Deceptive Semantics of Pesticide Formulations And Their Regulation
The paper describes how the agrochemical industry conceals the true toxicity of their chemical formulations by focusing on the health risks associated with only one so-called ‘active principle’ (AP) in their complex formulations, and sets the public up for mass poisoning through the determination of an ‘acceptable level of harm’ via the calculation of the so-called ‘acceptable daily intake (ADI)’ based on the toxicological risk profile of only a single ingredient:
“Pesticides are used throughout the world as mixtures called formulations. They contain adjuvants, which are often kept confidential and are called inerts by the manufacturing companies, plus a declared active principle (AP), which is the only one tested in the longest toxicological regulatory tests performed on mammals. This allows the calculation of the acceptable daily intake (ADI)—the level of exposure that is claimed to be safe for humans over the long term—and justifies the presence of residues of these pesticides at “admissible” levels in the environment and organisms. Only the AP and one metabolite are used as markers, but this does not exclude the presence of adjuvants, which are cell penetrants.”
The problem of underestimated toxicological risk is so severe that the researchers describe previous research which found unexpected toxicity in so-called ‘inert’ adjuvants that were up to 10,000 times more toxic than the so-called active principle glyphosate itself, revealing them to be a greater source for secondary side effects than the main ingredient itself. They also note that this ‘synergistic toxicity’ may explain the results of previous long-term animal research where glyphosate-based formulations showed toxicity in the parts-per-trillion range (.1 part per billion) that could not be explained by glyphosate alone.
Dr. Kelly Brogan, MD, commented on this phenomena in connection with the study recently on her blog: “Similar to the non-placebo-controlled trials on vaccines, adjuvants and preservatives are considered innocent bystanders in the consideration of risk profile.” According to Dr. Brogan, an understanding of “Toxicant synergy has exploded the simplistic notion of “the dose makes the poison.””
The Test Method and Results
In order to ascertain the toxicity of various chemical formulations and their ingredients, the researchers used embryonic (HEK293), placental (JEG3), and hepatic (HepG2) human cell lines, “because they are well characterized and validated as useful models to test toxicities of pesticides, corresponding to what is observed on fresh tissue or primary cells.” They noted, “these cells lines are even in some instances less sensitive than primary cells, and therefore do not overestimate cellular toxicity.”
The researchers describe the their method of determining toxicity:
We assayed their mitochondrial succinate dehydrogenase (SD) activity (MTT assay) after 24h pesticide exposure, which is one of the most accurate cytotoxicity assays for measuring the toxicity of pesticide adjuvants such as surfactants. Cytotoxicity was confirmed by the measurement of apoptosis and necrosis, respectively, by caspases 3/7 activation and adenylate kinase leakage after membrane alterations
The results of the study were clear. Except for one pesticide (Matin), “All formulations were cytotoxic and far more toxic than their APs [active principles].”
Key findings included:
- On human cells, among the tested products, fungicides were the most toxic, being cytotoxic from doses 300–600 times lower than agricultural dilutions, followed by herbicides (except Matin) and then insecticides.
- In all cell types, fungicides were the most toxic (mean LC50 12ppm).
- The herbicide Roundup (LC50 63ppm) was next in toxicity to fungicides, twice as toxic as Starane, and more than 10 times as toxic as the 3 insecticides, which represent the less toxic group (mean LC50 720ppm).
China fines Johnson & Johnson and others for price fixing:
Johnson & Johnson, Bausch & Lomb Inc and other major producers have been fined more than 19 million yuan ($3.04 million) for fixing prices in China’s eye glass and contact lens market, China’s top economic regulator said on Thursday.
The companies mandated their dealers to set the price of lenses strictly in accordance to a “suggested level”, the National Development and Reform Commission (NDRC) said in a statement on its website.
They also ordered retailers to jointly launch promotions in major Chinese cities all year around to keep prices stable, the notice said.
Dealers and retailers who do not comply with the order will be subject to unspecified financial penalties, it said. Other penalties may include seeing a halt to their supplies from the overseas manufacturers.
Johnson & Johnson executives could not be reached immediately for comment.
Chinese authorities have charged executives at British drugmaker GlaxoSmithKline over bribery and corruption. Swiss drugmaker Roche Holding AG had also been visited by a unit of China’s anti-trust regulator.
Other overseas eyes lenses brands named by NDRC included Essilor International SA, Nikon Corp, Carl Zeiss Meditec AG.
Japan to Start Building Giant Ice Wall at Fukushima:
Japan Wants to Build an Ice Wall to Contain Fukushima’s Radioactive Water
Radioactive water full of carcinogenic chemicals is leaking out of the Fukushima power plant at a… Read more
Following examination of the Tokyo Electric Power Co (TEPCO) plans to build the gigantic ice wall, the Nuclear Regulation Authority has given the go ahead for construction to commence. While similar techniques have been used in the past, it’s never been undertaken at the same scale as the proposed Fukushima plans. Speaking to PhysOrg, an anonymous official explained that:
“We had some concerns, including the possibility that part of the ground could sink. But there were no major objections to the project during the meeting, and we concluded that TEPCO can go ahead with at least part of the project as proposed after going through further necessary procedures.”
In June, then, engineers will begin building a 0.9-mile frozen wall that should stem the flow of radioactive groundwater. We’ve explained how it will work before:
The idea is to drive vertical pipes spaced about a meter apart between 20 and 40 meters into the ground and to pump coolant through them. This would effectively create a barrier of permafrost around the affected buildings, keeping the contaminated water in and groundwater out.
Despite the fact the plan is to go ahead, TEPCO may have to review other parts of the project as it progresses. There are some concerns that the ice wall may affect existing infrastructure—drains, utilities and the like—which will all have to carefully monitored once the project goes ahead.
Scientists Create 1st Living Organism From Artificial DNA:
A team of researchers from The Scripps Research Institute (TSRI) in La Jolla, Calif., has created a brand-new bacteria based on a genetic structure found nowhere on Earth.
According to lead researcher Floyd Romesberg, the feat involved artificially engineering a unique combination of DNA material — a combination not found in any living creature — and then successfully inserting it into a living cell that usually contains only natural combinations of DNA.
“Life on Earth in all its diversity is encoded by only two pairs of DNA bases, A-T and C-G,” Romesberg explained in an institute news release. “And what we’ve made is an organism that stably contains those two plus a third, unnatural pair of bases.”
“This shows that other solutions to storing [genetic] information are possible,” he added, “and, of course, takes us closer to an expanded-DNA biology that will have many exciting applications — from new medicines to new kinds of nanotechnology.”
Romesberg and his colleagues discuss their handiwork — funded in part by the U.S. National Institutes of Health — in the May 7 online edition of Nature.
The product of more than 15 years of work, the current effort builds on a proof-of-concept study conducted in 2008. At that time, investigators had shown that hooking up natural and unnatural pairings of DNA was possible in a test-tube setting.
The next challenge was to replicate the process inside a living cell. The cell chosen by the TSRI team was the common E. coli bacterium, and into it they inserted what they considered to be the best unnatural DNA pairing they could construct: a combination of two molecules called “d5SICS” and “dNaM”.
After leaping through a series of highly complex technical problems, the study authors finally managed to pull off their goal: the fashioning on a half-synthetic organism that could actually replicate its unnatural self as long as scientists continuously supplied it with the necessary molecular material.
Romesberg said that, in principle, his team’s high-concept work has a very practical purpose: to gain a “greater power than ever” to fashion new treatments by harnessing the power of genetics.