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Memory is Stored by Turning on Genes in Neurons (to Alter Connection Between Neurons)

Posted on December 28, 2011  Comments (0)

I find these kind of stories so interesting. I really have so little understanding of genes. I knew memory had something to do with altering connections between neurons. I had no idea that required turning on many genes in those neurons. Life really is amazing.

Neuroscientists identify a master controller of memory

When you experience a new event, your brain encodes a memory of it by altering the connections between neurons. This requires turning on many genes in those neurons.
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Lin and her colleagues found that Npas4 turns on a series of other genes that modify the brain’s internal wiring by adjusting the strength of synapses, or connections between neurons. “This is a gene that can connect from experience to the eventual changing of the circuit,” says [Yingxi] Lin

So far, the researchers have identified only a few of the genes regulated by Npas4, but they suspect there could be hundreds more. Npas4 is a transcription factor, meaning it controls the copying of other genes into messenger RNA — the genetic material that carries protein-building instructions from the nucleus to the rest of the cell. The MIT experiments showed that Npas4 binds to the activation sites of specific genes and directs an enzyme called RNA polymerase II to start copying them.

“Npas4 is providing this instructive signal,” Ramamoorthi says. “It’s telling the polymerase to land at certain genes, and without it, the polymerase doesn’t know where to go. It’s just floating around in the nucleus.”

When the researchers knocked out the gene for Npas4, they found that mice could not remember their fearful conditioning. They also found that this effect could be produced by knocking out the gene just in the CA3 region of the hippocampus. Knocking it out in other parts of the hippocampus, however, had no effect.

One of the things I aim to do in 2012 is read a few more books on biology and genes. I find it incredible what are genes actually are doing to allow us to live our lives. And I am also very ignorant on the whole area. So hopefully I can have some fun next year learning about it.

Related: Epigenetic Effects on DNA from Living Conditions in Childhood Persist Well Into Middle Age – Antigen Shift in Influenza Viruses – 8 Percent of the Human Genome is Old Virus Genes – Brain Reorganizes As It Learns Math

Using a Virus to Improve Solar-cell Efficiency Over 30%

Posted on December 13, 2011  Comments (0)

Solar and wind energy are making great strides, and are already contributing significantly to providing relatively clean energy.

Researchers at MIT have found a way to make significant improvements to the power-conversion efficiency of solar cells by enlisting the services of tiny viruses to perform detailed assembly work at the microscopic level.

In a solar cell, sunlight hits a light-harvesting material, causing it to release electrons that can be harnessed to produce an electric current. The research, is based on findings that carbon nanotubes — microscopic, hollow cylinders of pure carbon — can enhance the efficiency of electron collection from a solar cell’s surface.

Previous attempts to use the nanotubes, however, had been thwarted by two problems. First, the making of carbon nanotubes generally produces a mix of two types, some of which act as semiconductors (sometimes allowing an electric current to flow, sometimes not) or metals (which act like wires, allowing current to flow easily). The new research, for the first time, showed that the effects of these two types tend to be different, because the semiconducting nanotubes can enhance the performance of solar cells, but the metallic ones have the opposite effect. Second, nanotubes tend to clump together, which reduces their effectiveness.

And that’s where viruses come to the rescue. Graduate students Xiangnan Dang and Hyunjung Yi — working with Angela Belcher, the W. M. Keck Professor of Energy, and several other researchers — found that a genetically engineered version of a virus called M13, which normally infects bacteria, can be used to control the arrangement of the nanotubes on a surface, keeping the tubes separate so they can’t short out the circuits, and keeping the tubes apart so they don’t clump.

The system the researchers tested used a type of solar cell known as dye-sensitized solar cells, a lightweight and inexpensive type where the active layer is composed of titanium dioxide, rather than the silicon used in conventional solar cells. But the same technique could be applied to other types as well, including quantum-dot and organic solar cells, the researchers say. In their tests, adding the virus-built structures enhanced the power conversion efficiency to 10.6% from 8% — almost a one-third improvement.

Read the full press release

Related: Using Virus to Build Batteries – Using Viruses to Construct Electrodes – Using Bacteria to Carry Nanoparticles Into Cells

Synthetic Biologists Design a Gene that Forces Cancer Cells to Commit Suicide

Posted on September 4, 2011  Comments (2)

Killing a cancer cell from the inside out

To create their tumor-killing program, the researchers designed a logic circuit — a system that makes a decision based on multiple inputs. In this case, the circuit is made of genes that detect molecules specific to a type of cervical cancer cell. If the right molecules are present, the genes initiate production of a protein that stimulates apoptosis, or programmed cell death. If not, nothing happens.

Because the genes used to create the circuits can be easily swapped in and out, this approach could also yield new treatments or diagnostics for many other diseases, according to Ron Weiss, an MIT associate professor of biological engineering and one of the leaders of the research team. “This is a general technology for disease-state detection,” he says.
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the researchers created a synthetic gene for a protein, called hBax, that promotes cell death. They designed the gene with two separate safeguards against the killing of healthy, non-HeLa cells: It can be turned off by high levels of microRNAs that are ordinarily low in HeLa, and can also be deactivated by low levels of microRNAs that are normally plentiful in HeLa. A single discrepancy from the target microRNA profile is enough to shut off production of the cell-death protein.

If all microRNA levels match up with the HeLa profile, the protein is produced and the cell dies. In any other cell, the protein never gets made, and the synthetic genes eventually break down.

More very cool research. It is exciting to see how much can be done when we invest in science and engineering research. Of course the path from initial research to implemented solutions is long and complex and often fails to deliver on the initial hopes. But some remarkable breakthroughs achieve spectacular results that we benefit from every day.

Related: Cancer Vaccines – Researchers Find Switch That Allows Cancer Cells to Spread – Global Cancer Deaths to Double by 2030 – Cloned Immune Cells Clear Patient’s Cancer

MIT Scientists Find New Drug That Could Cure Nearly Any Viral Infection

Posted on August 17, 2011  Comments (1)

New drug could cure nearly any viral infection

The drug works by targeting a type of RNA produced only in cells that have been infected by viruses. “In theory, it should work against all viruses,” says Todd Rider, a senior staff scientist in Lincoln Laboratory‘s Chemical, Biological, and Nanoscale Technologies Group who invented the new technology.
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There are a handful of drugs that combat specific viruses, such as the protease inhibitors used to control HIV infection, but these are relatively few in number and susceptible to viral resistance.

Rider drew inspiration for his therapeutic agents, dubbed DRACOs (Double-stranded RNA Activated Caspase Oligomerizers), from living cells’ own defense systems. When viruses infect a cell, they take over its cellular machinery for their own purpose — that is, creating more copies of the virus. During this process, the viruses create long strings of double-stranded RNA (dsRNA), which is not found in human or other animal cells.

As part of their natural defenses against viral infection, human cells have proteins that latch onto dsRNA, setting off a cascade of reactions that prevents the virus from replicating itself. However, many viruses can outsmart that system by blocking one of the steps further down the cascade.

Rider had the idea to combine a dsRNA-binding protein with another protein that induces cells to undergo apoptosis (programmed cell suicide) — launched, for example, when a cell determines it is en route to becoming cancerous. Therefore, when one end of the DRACO binds to dsRNA, it signals the other end of the DRACO to initiate cell suicide.

Combining those two elements is a “great idea” and a very novel approach, says Karla Kirkegaard, professor of microbiology and immunology at Stanford University. “Viruses are pretty good at developing resistance to things we try against them, but in this case, it’s hard to think of a simple path pathway to drug resistance,” she says.

Each DRACO also includes a “delivery tag,” taken from naturally occurring proteins, that allows it to cross cell membranes and enter any human or animal cell. However, if no dsRNA is present, DRACO leaves the cell unharmed.

Very cool stuff and potentially hugely beneficial. Just a reminder: this works against viruses – not bacteria (just as antibiotics do not work against viruses).

image showing the results of cultures treated with DRACO v. those not treated

Related: Science Explained: RNA Interference – 8 Percent of the Human Genome is Old Virus Genes – Virus Engineered To Kill Deadly Brain Tumors
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MIT Engineering Design Workshop for Boston High School Students

Posted on August 7, 2011  Comments (3)

This summer, a few dozen Boston-area high school students chose to spend their mornings toiling away with a variety of materials to create working marvels of engineering in the Engineering Design Workshop, a month-long program that gives teenagers a hands-on experience with the joys and challenges of engineering.

None of the activities are prescribed; instead, students take part in brainstorming sessions on the first day, and things develop from there. Typically, the “counselors” — a mix of undergraduate and graduate students from MIT and other local universities — present a few ideas, and the high school students decide which projects they’d most like to work on. I really like the idea of involving the college students.

This year, the 22 students divided themselves into five projects: a modified Razor scooter, equipped with a motor and brakes; a sound system of giant tower speakers; remote-controlled “anything” (which ended up including cars, fish, birds and even a flying turtle); a mosaic tiger meticulously assembled from pieces of stained glass; and an electric cello.

Each student is allotted $100 to spend on materials for his or her group’s project; this way, projects that attract more students have a larger budget to work with. Counselors help them purchase supplies online and work with them on the construction from the ground up.

There are probably thousands of similar type activities throughout the year to help engage students in engineering. I think it is great, but we need to do more. We need to let young students know what they are missing. If people know the wonders of engineering and choose something else for their career path, that is fine. It is a shame when people don’t get to decide, because they never experience what engineering has to offer.

Read the full press release.

Related: Infinity Project: Engineering Education for Today’s Classroom – Rutgers Initiative to Help Disadvantaged Children – Inspirational Engineer – What Kids can Learn on Their Own

MIT Engineers Design New Type of Nanoparticle for Vacines

Posted on February 22, 2011  Comments (5)

MIT engineers have designed a new type of nanoparticle that could safely and effectively deliver vaccines for diseases such as HIV and malaria. The new particles, described in the Feb. 20 issue of Nature Materials, consist of concentric fatty spheres that can carry synthetic versions of proteins normally produced by viruses. These synthetic particles elicit a strong immune response – comparable to that produced by live virus vaccines – but should be much safer, says Darrell Irvine, author of the paper and an associate professor of materials science and engineering and biological engineering.

Such particles could help scientists develop vaccines against cancer as well as infectious diseases. In collaboration with scientists at the Walter Reed Army Institute of Research, Irvine and his students are now testing the nanoparticles’ ability to deliver an experimental malaria vaccine in mice.

Vaccines protect the body by exposing it to an infectious agent that primes the immune system to respond quickly when it encounters the pathogen again. In many cases, such as with the polio and smallpox vaccines, a dead or disabled form of the virus is used. Other vaccines, such as the diphtheria vaccine, consist of a synthetic version of a protein or other molecule normally made by the pathogen.

When designing a vaccine, scientists try to provoke at least one of the human body’s two major players in the immune response: T cells, which attack body cells that have been infected with a pathogen; or B cells, which secrete antibodies that target viruses or bacteria present in the blood and other body fluids.

For diseases in which the pathogen tends to stay inside cells, such as HIV, a strong response from a type of T cell known as “killer” T cell is required. The best way to provoke these cells into action is to use a killed or disabled virus, but that cannot be done with HIV because it’s difficult to render the virus harmless.

To get around the danger of using live viruses, scientists are working on synthetic vaccines for HIV and other viral infections such as hepatitis B. However, these vaccines, while safer, do not elicit a very strong T cell response. Recently, scientists have tried encasing the vaccines in fatty droplets called liposomes, which could help promote T cell responses by packaging the protein in a virus-like particle. However, these liposomes have poor stability in blood and body fluids.

Irvine, who is a member of MIT’s David H. Koch Institute for Integrative Cancer Research, decided to build on the liposome approach by packaging many of the droplets together in concentric spheres. Once the liposomes are fused together, adjacent liposome walls are chemically “stapled” to each other, making the structure more stable and less likely to break down too quickly following injection. However, once the nanoparticles are absorbed by a cell, they degrade quickly, releasing the vaccine and provoking a T cell response.

read the full press release

Related: New and Old Ways to Make Flu Vaccines – Engineering Mosquitoes to be Flying Vaccinators – New nanoparticles could improve cancer treatment – Vaccines Can’t Provide Miraculous Results if We Don’t Take Them

Solar-Powered Desalination

Posted on April 12, 2010  Comments (0)

Solar-Powered Desalination

Saudi Arabia meets much of its drinking water needs by removing salt and other minerals from seawater. Now the country plans to use one of its most abundant resources to counter its fresh-water shortage: sunshine.
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KACST’s main goal is to reduce the cost of desalinating water. Half of the operating cost of a desalination plant currently comes from energy use, and most current plants run on fossil fuels.
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Reducing cost isn’t the only reason that people have dreamed of coupling renewable energy with desalination for decades, says Lisa Henthorne, a director at the International Desalination Association. “Anything we can do to lower this cost over time or reduce the greenhouse gas emissions associated with that power is a good thing,” Henthorne says. “This is truly a demonstration in order to work out the bugs, to see if the technologies can work well together.”
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Saudi Arabia, the top desalinated water producer in the world, uses 1.5 million barrels of oil per day at its plants, according to Arab News.
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In a concentrated PV system, lenses or mirrors focus sunlight on ultra-efficient solar cells that convert the light into electricity. The idea is to cut costs by using fewer semiconductor solar cell materials. But multiplying the sun’s power by hundreds of times creates a lot of heat. “If you don’t cool [the device], you end up overheating the circuits and killing them,” says Sharon Nunes, vice president of IBM Big Green Innovations. IBM’s solution is to use a highly conducting liquid metal–an indium gallium alloy–on the underside of silicon computer chips to ferry heat away. Using this liquid metal, the researchers have been able to concentrate 2,300 times the sun’s power onto a one-square-centimeter solar device. That is three times higher than what’s possible with current concentrator systems, says Nunes.

Finding good desalination solution could help many other locations (including southern California). But there is still a long way to go.

Related: Agricultural Irrigation with Salt Water – Cheap Drinking Water From Seawater

$100,000 Lemelson-MIT Award for Sustainability

Posted on February 10, 2010  Comments (3)

According to the United Nations, more than 40 percent of Africans live in poverty, subsisting on less than US$1 a day. As co-founder and CEO of the nonprofit social enterprise KickStart, Fisher develops and markets moneymaking tools such as low-cost, human-powered irrigation pumps that improve the lives of small-scale rural farmers – the majority of the poor in sub-Saharan Africa.

“These poor rural farmers have one asset: a small plot of land; and one basic skill: farming. The best business they can pursue is irrigated farming,” Fisher explained. “Once they employ irrigation, the farmers can grow and sell high-value crops, like fruits and vegetables. They can grow year-round and reap four or five harvests, instead of waiting for the rain to grow a staple crop once or twice a year.”

Related: High School Inventor Teams @ MIT – Water Pump Merry-go-Round – Appropriate Technology: Self Adjusting Glasses – Fixing the World on $2 a Day
Continue reading →

Siftable Modular Computers

Posted on January 19, 2010  Comments (3)

Pretty cool. I must admit I don’t really see how this would function outside of specifically designed situation. I can imagine it could be very cool for education, especially of young kids. Siftables act in concert to form a single interface: users physically manipulate them – piling, grouping, sorting – to interact with digital information and media. David Merrill and Jeevan Kalanithi originally created Siftables at the MIT Media Lab and have formed a company to commercialize the product and have received a grant from NSF to continue the work.

Related: Cool Mechanical Simulation System – Video Cat Cam – Arduino: Open Source Programmable Hardware – What Kids can Learn

Re-engineering the Food System for Better Health

Posted on November 22, 2009  Comments (6)

Good food nation

According to the Centers for Disease Control, between 1980 and 2006 the percentage of obese teenagers in the United States grew from 5 to 18, while the percentage of pre-teens suffering from obesity increased from 7 to 17.
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Obesity is widespread due to our national-scale system of food production and distribution, which surrounds children – especially lower-income children – with high-calorie products…
90 percent of American food is processed – according to the United States Department of Agriculture – meaning it has been mixed with ingredients, often acting as preservatives, that can make food fattening.
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Now, in another report finished this October after meetings with food-industry leaders, the MIT and Columbia researchers propose a solution: America should increase its regional food consumption.
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Only 1 to 2 percent of all food consumed in the United States today is locally produced. But the MIT and Columbia team, which includes urban planners and architects, believes widespread adoption of some modest projects could change that, by increasing regional food production and distribution.

To help production, the group advocates widespread adoption of small-scale innovations such as “lawn to farm” conversions in urban and suburban areas, and the “10 x 10 project,” an effort to develop vegetable plots in schools and community centers. Lawns require more equipment, labor and fuel than industrial farming nationwide, yet produce no goods. But many vegetables, including lettuce, cucumbers and peppers, can be grown efficiently in small plots.
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As Albright sees it, the effort to produce healthier foods “fits right in with the health-care reform effort right now because chronic diseases are so costly for the nation.” America currently spends $14 billion annually treating childhood obesity, and $147 billion treating all forms of obesity.

Good stuff. We need to improve health in the USA. The current system is unhealthy and needs to be improved. The public good from improving the health of society is huge (both in terms of individual happiness and economic benefits).

Related: Rethinking the Food Production System – Study Finds Obesity as Teen as Deadly as Smoking – Eat food. Not too much. Mostly plants. – Active Amish Avoid Obesity – Obesity Epidemic Explained – Another Strike Against Cola

Science Explained: RNA Interference

Posted on November 13, 2009  Comments (1)

Explained: RNA interference

Every high school biology student learns the basics of how genes are expressed: DNA, the cell’s master information keeper, is copied into messenger RNA, which carries protein-building instructions to the ribosome, the part of the cell where proteins are assembled.

But it turns out the picture is far more complicated than that. In recent years, biologists have discovered a myriad of other molecules that fine-tune this process, including several types of RNA (ribonucleic acid). Through a naturally occurring phenomenon known as RNA interference, short strands of RNA can selectively intercept and destroy messenger RNA before it delivers its instructions.
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Double-stranded RNA molecules called siRNA (short interfering RNA) bind to complementary messenger RNA, then enlist the help of proteins, the RNA-induced silencing complex. Those proteins cleave the chemical bonds holding messenger RNA together and prevent it from delivering its protein-building instructions.

This article from MIT is one, of many, showing MIT’s commitment to science education of the public. Good job, MIT.

Related: Antigen Shift in Influenza Viruses – Posts explaining scientific principles and concepts – DNA Passed to Descendants Changed by Your Life – Why Does Hair Turn Grey as We Age? – Amazing Science: Retroviruses

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