Europe against GMO crops! Please, sign the Avaaz petition! I already did.
It's us who decide, not Monsanto!!!

Thursday, 1 April 2010

Biology gone crazy, 03, 2010

First:

Evolution caught in the act: Scientists measure how quickly genomes change (in plants)
Chimp and human Y chromosomes evolving faster than expected (in mammals) - and this is 2nd or 3d article on evolution in humans I read. We change and slowly evolve. That much is a fact.
Giant bizarre deep sea fish filmed in Gulf of Mexico (videos) - amazing footage and amazing fishes.

Today:

  1. New RNA interference technique can silence up to five
  2. Machine Translates Thoughts into Speech in Real
  3. Scientists show 'lifeless' prions capable of evolutionary change and adaptation
  4. Viral phenomenon: Ancient microbe invaded human DNA
  5. For this microbe, cousins not particularly welcome
  6. Punishment important in plant-pollinator relationship

New RNA interference technique can silence up to five genes

December 28, 2009 by Anne Trafton
Researchers at MIT and Alnylam Pharmaceuticals report this week that they have successfully used RNA interference to turn off multiple genes in the livers of mice, an advance that could lead to new treatments for diseases of the liver and other organs.

The new delivery method, described in the Proceedings of the National Academy of Sciences, is orders of magnitude more effective than previous methods, says Daniel Anderson, senior author of the paper and a biomedical engineer at the David H. Koch Institute for Integrative at MIT.

The key to success with is finding a safe and effective way to deliver the short strands of RNA that can bind with and destroy , which carries instructions from the nucleus.

Anderson and his colleagues believe the best way to do that is to wrap short interfering RNA (siRNA) in a layer of fat-like molecules called lipidoids, which can cross cells' fatty . Using one such lipidoid, the researchers were able to successfully deliver five snippets of RNA at once, and Anderson believes the lipidoids have the potential to deliver as many as 20.

The team at MIT, along with Alnylam researchers, have developed methods to rapidly produce, assemble and screen a variety of different lipidoids, allowing them to pick out the most effective ones.

Using C12-200, the researchers achieved effective gene silencing with a dose of less than 0.01 milligrams of siRNA per kilogram of solution, and 0.01 milligrams per kilogram in non-human primates. If the same dosing were translated to humans, a potential therapy would only require an injection of less than 1 milliliter to specifically inhibit a gene, compared with previous formulations that would have required hundreds of milliliters, says Anderson.

The MIT/Alnylam team hopes to start clinical trials within the next couple of years. source

My comment: Wow, that's great! Just imagine what this method could do for people with genes the cause cancers or other diseases. Of course, on should be careful with gene therapies, but they are the future, we only have to figure how to keep them safe and efficient.

Machine Translates Thoughts into Speech in Real Time

December 21, 2009 By Lisa Zyga
(PhysOrg.com) -- By implanting an electrode into the brain of a person with locked-in syndrome, scientists have demonstrated how to wirelessly transmit neural signals to a speech synthesizer. The "thought-to-speech" process takes about 50 milliseconds - the same amount of time for a non-paralyzed, neurologically intact person to speak their thoughts. The study marks the first successful demonstration of a permanently installed, wireless implant for real-time control of an external device.

“The results of our study show that a brain-machine interface (BMI) user can control sound output directly, rather than having to use a (relatively slow) typing process,” Guenther told PhysOrg.com.

In their study, the researchers tested the technology on a 26-year-old male who had a brain stem at age 16. The brain stem stroke caused a lesion between the volunteer’s that carry out actions and the rest of the brain; while his consciousness and cognitive abilities are intact, he is paralyzed except for slow vertical movement of the eyes. The rare condition is called locked-in syndrome.

Five years ago, when the volunteer was 21 years old, the scientists implanted an electrode near the boundary between the speech-related premotor and primary motor cortex (specifically, the left ventral premotor cortex). Neurites began growing into the electrode and, in three or four months, the neurites produced signaling patterns on the electrode wires that have been maintained indefinitely.

Three years after implantation, the researchers began testing the brain-machine interface for real-time synthetic production. The system is “telemetric” - it requires no wires or connectors passing through the skin, eliminating the risk of infection. Instead, the electrode amplifies and converts neural signals into frequency modulated (FM) radio signals. These signals are wirelessly transmitted across the scalp to two coils, which are attached to the volunteer’s head using a water-soluble paste. The coils act as receiving antenna for the RF signals. The implanted electrode is powered by an induction power supply via a power coil, which is also attached to the head.

The signals are then routed to an electrophysiological recording system that digitizes and sorts them. The sorted spikes, which contain the relevant data, are sent to a neural decoder that runs on a desktop computer. The neural decoder’s output becomes the input to a speech synthesizer, also running on the computer. Finally, the speech synthesizer generates synthetic speech (in the current study, only three vowel sounds were tested). The entire process takes an average of 50 milliseconds.

“The study supported our hypothesis (based on the DIVA model, our neural network model of speech) that the premotor cortex represents intended speech as an ‘auditory trajectory,’ that is, as a set of key frequencies (formant frequencies) that vary with time in the acoustic signal we hear as speech,” Guenther said. “In other words, we could predict the intended sound directly from neural activity in the premotor cortex, rather than try to predict the positions of all the speech articulators individually and then try to reconstruct the intended sound (a much more difficult problem given the small number of neurons from which we recorded). This result provides our first insight into how neurons in the brain represent speech, something that has not been investigated before since there is no animal model for speech.”

To confirm that the neurons in the implanted area were able to carry speech information in the form of formant frequency trajectories, the researchers asked the volunteer to attempt to speak in synchrony with a vowel sequence that was presented auditorily. In later experiments, the volunteer received real-time auditory feedback from the speech synthesizer. During 25 sessions over a five-month period, the volunteer significantly improved the thought-to-speech accuracy. His average hit rate increased from 45% to 70% across sessions, reaching a high of 89% in the last session.

Although the current study focused only on producing a small set of vowels, the researchers think that consonant sounds could be achieved with improvements to the system. While this study used a single three-wire electrode, the use of additional electrodes at multiple recording sites, as well as improved decoding techniques, could lead to rapid, accurate control of a speech synthesizer that could generate a wide range of sounds.

“Our immediate plans involve the implementation of a new synthesizer that can produce consonants as well as vowels but remains simple enough for a BMI user to control,” Guenther said. source

My comment: WOW! I mean it! WOW! This is only a step away from an efficient brain-pc interface. Sure, the goal of the study is to help people with locked-in syndrome, but the applications of the technology are endless. Imagine that by simple implanting of an electrode in your brain, you could control a machine or a computer only with your thoughts. Sure, that means even more obese people, but that's up to us to change. The key moment is that it opens immense possibilities. If you add communication in the other direction - from the computer to our brain, that makes the technology even more exciting. Just imagine! Amazing, simply amazing.

Scientists show 'lifeless' prions capable of evolutionary change and adaptation

December 31, 2009

Scientists from The Scripps Research Institute have determined for the first time that prions, bits of infectious protein devoid of DNA or RNA that can cause fatal neurodegenerative disease, are capable of Darwinian evolution.

The study from Scripps Florida in Jupiter shows that prions can develop large numbers of mutations at the protein level and, through natural selection, these mutations can eventually bring about such evolutionary adaptations as drug resistance, a phenomenon previously known to occur only in bacteria and viruses. These breakthrough findings also suggest that the normal - which occurs naturally in human cells - may prove to be a more effective than its abnormal toxic relation.

Infectious prions (short for proteinaceous infectious particles) are associated with some 20 different diseases in humans and animals, including and a rare human form, Creutzfeldt-Jakob disease. All these diseases are untreatable and eventually fatal.
Prions, which are composed solely of protein, are classified by distinct strains, originally characterized by their incubation time and the disease they cause. Prions have the ability to reproduce, despite the fact that they contain no nucleic acid genome.

Mammalian cells normally produce cellular protein or PrPC. During infection, abnormal or misfolded protein - known as PrPSc - converts the normal host prion protein into its toxic form by changing its conformation or shape. The end-stage consists of large assemblies (polymers) of these misfolded proteins, which cause massive tissue and cell damage. source

My comment: Another cool news which demonstrates the power of evolution. Now we see it in action for prions, which are basically proteins folded in different way. Leaving Darwin aside, prions are so simple, they are a step above the organic molecules we observe in nebulae in the sky. Thus they show how common can life in space be - if they can evolve, and they are so simple, then it becomes even easier to produce life-forms from organic molecules on big scale. Life may be all around us and waiting for us to recognize it!

Viral phenomenon: Ancient microbe invaded human DNA

January 6, 2010
Humans carry in their genome the relics of an animal virus that infected their forerunners at least 40 million years ago, according to research published Wednesday by the British science journal Nature.

The invader is called bornavirus, a brain-infecting pathogen that was first identified in 1970s.

Scientists led by Keizo Tomonaga of Japan's Osaka University compared the DNA of a range of mammals, including humans, apes, elephants, marsupials and rodents, to look for tell-tale signatures of bornavirus code.

In the , the team found several bornavirus fragments but also in the form of two genes that may be functional, although what they do is unclear.

Until now, the only viruses known to have been handed on in vertebrates were retroviruses, which work by hijacking cellular machinery in order to reproduce.

Retroviruses are effective in infiltrating the germline -- the of , which means their sequence, or part of it, is handed on to ensuing generations.

By some estimates, retroviruses account for as much as eight percent of the human code for life.

Bornavirus has a different stealth tactic, replicating in the nucleus of infected cells.

The impact of bornavirus on the human genetic odyssey is likely to trigger fierce debate.

The big questions are whether it provided a potential cause of genetic mutation or innovation in our species, or whether it provided a source for inherited illness -- or, conversely, protection.

Bornavirus has not been clearly linked to diseases in humans, although some researchers speculate there could be a link with schizophrenia and other mental disorders. source

My comment: Ok, this is even cooler, because it makes you think about the role of viruses in human history and evolution. Because so far, we considered viruses for evil creatures that makes us sick. But if each virus carries away a piece of our DNA and spread it among other people or creatures, that virus is making a part of us to live forever. And it makes us even more connected with each other and the nature. We're all part of the DNA soup :) That's kind of interesting, right? And obviously, the changes the viruses bring to our organisms are not always negative, sometimes they protects us from diseases (as you can read in the article). Then, maybe we have to learn them more carefully before calling them names. Sure, the viruses are masters of infections, but maybe there is a way to keep only the bad ones away? Who knows...

For this microbe, cousins not particularly welcome

January 6, 2010
(PhysOrg.com) -- A bacterial species that depends on cooperation to survive is discriminating when it comes to the company it keeps. Scientists from Indiana University Bloomington and Netherlands' Centre for Terrestrial Ecology have learned Myxococcus xanthus cells are able to recognize genetic differences in one another that are so subtle, even the scientists studying them must go to great lengths to tell them apart.

The scientists' report, which appears in a recent issue of Current Biology, also provides further evidence that cooperation in nature is not always a festival of peace and love. Rather, cooperation may be more of a grudging necessity, in which partners continually compete and undermine one another in a bid for evolutionary dominance.

Myxococcus xanthus is a predatory bacterium that through soil, killing and eating other by secreting toxic and digestive compounds. When food runs out, cells aggregate and exchange chemical signals to form cooperative, multi-cellular "fruiting bodies." Some of the cells create the fruiting body's structure, while other cells are destined to become hardy spores for the purpose of surviving difficult conditions.

Previously, experiments by Velicer and Ph.D. student Francesca Fiegna showed that when different Myxococcus strains isolated from around the globe were mixed together, the number of spores produced was much reduced. This indicated that this social had diverged into many socially conflicting types.

As part of the experimental design for their study, Velicer and Vos paired Myxococcus strains isolated from soil samples taken just centimeters apart to see whether they would behave cooperatively or competitively.

The scientists found that some pairs of strains, inhabiting the same patch of soil and almost identical genetically, had nevertheless diverged enough to inhibit each other's ability to make spores.

In general, however, the scientists found competition was less intense among centimeter-scale pairings than for pairings of more distantly related bacteria isolated from distant locations. These results indicate that social divergence can evolve rapidly within populations, but this divergence can be augmented by geographic isolation.

Another set of experiments revealed that different strains actively avoid each other prior to starvation-induced fruiting body formation. Velicer and Vos argue that this type of exclusion within diverse populations -- in which the probability of social conflict among neighbors is high -- may serve to direct the benefits of cooperation to close kin only. source

My comment: Can you even imagine bacterias being so smart? It's kind of creepy, that they are able to know their friends and hate their enemies, and to "decide" whether to avoid the enemies or to fight them. I mean, this thing is so damn little and yet it has a strategy in life that is successful for the conditions it lives in. Something we, with our huge brains, often don't have!

Punishment important in plant-pollinator relationship

January 14, 2010
Figs and the wasps that pollinate them present one of biologists' favorite examples of a beneficial relationship between two different species. In exchange for the pollination service provided by the wasp, the fig fruit provides room and board for the wasp's developing young. However, wasps do not always pollinate the fig. Fig trees "punish" these "cheaters" by dropping unpollinated fruit, killing the wasp's offspring inside, report researchers working at the Smithsonian Tropical Research Institute. source


My comment: ROFL! The fig punishes the wasp. That's so fun. And it's true!

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