Tag Archives: MIT

Scientists discover new class of RNA

These new RNAs are named after their distinctive features: Each molecule contains 21 chemical building blocks (or nucleotides), and each begins with the chemical uridine, represented by the letter U (the only RNA nucleotide not also found on DNA). In addition, each of the 5,000 different 21U-RNA molecules comes from one of two chromosomal regions.

Further, “we can predict where additional 21U-RNA genes might reside,” says Bartel, who is also a member of the Whitehead Institute for Biomedical Research and a Howard Hughes Medical Institute investigator. “Combining these predictions with the 5,000 (21U-RNAs) that we experimentally identified, we suspect that there are more than 12,000 different 21U-RNA genes in the genome.” Because each gene typically produces a unique 21U-RNA, a very large diversity of molecules is made.

RNA description from the Nobel Prize site:

When an organism needs to use the data stored in the genome, e.g. to build components of a new cell, a copy of the required DNA part is made. This copy is called RNA and is almost identical to DNA. Just like DNA, RNA is an abbreviated form of a chemical name which in the case of RNA is ribonucleic acid. Unlike the double stranded DNA, RNA is only made up of a single strand. Furthermore, the base T, thymine, is replaced by U, uracil in RNA. This RNA string is used by the organism as a template when it builds protein molecules, sometimes called the building blocks of the body. For example, your muscles and hair are mostly made up of proteins.

Related: DNA-RNA-Protein Introduction

Cool Mechanical Simulation System

Cool device from MIT: A Shrewd Sketch Interpretation and Simulation Tool.

We aim to create a tool that allows the engineer to sketch a mechanical system as she would on paper, and then allows her to interact with the design as a mechanical system, for example by seeing a simulation of her drawing. We have built an early incarnation of such a tool, called ASSIST, which allows a user to sketch simple mechanical systems and see simulations of her drawings in a two-dimensional kinematic simulator.

via: Back to the Drawing Board

Using Viruses to Construct Electrodes and More

She harnesses viruses to make things

Manufacturing was once the province of human hands, then of machines. Angela Belcher, professor of materials science and engineering and biological engineering at MIT, has pushed manufacturing in another, much smaller, direction: Her lab has genetically engineered viruses that can construct useful objects like electrodes and wires.
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Her lab employed this method to form an electrode that can be used in a lithium ion battery like the rechargeable ones used in electronics. The result looks like an innocuous length of celluloid tape, the sort you could use to wrap a package.

“It’s self-assembled,” says Belcher. “The viruses make these materials at room temperature.” So there’s little pollution.
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Belcher hopes to be making prototypes within the next two years. “Actual devices are five to 10 years off.”

Protein Knots

graphic of human ubiquitin hydrolase

Knotty problem puzzles protein researchers by Anne Trafton:

Knots are rare in proteins–less than 1 percent of all proteins have any knots, and most are fairly simple. The researchers analyzed 32,853 proteins, using a computational technique never before applied to proteins at this scale.

Of those that had knots, all were enzymes. Most had a simple three-crossing, or trefoil knot, a few had four crossings, and the most complicated, a five-crossing knot, was initially found in only one protein–ubiquitin hydrolase.

That complex knot may hold some protective value for ubiquitin hydrolase, whose function is to rescue other proteins from being destroyed–a dangerous job.

Photo: MIT researchers recently found that human ubiquitin hydrolase, shown here, has the most complicated knot ever observed in a protein. The simplified diagram, inset, shows the knot in the protein, which crosses itself five times. Larger image.

MIT’s molecular sieve advances protein research

Separating proteins from complex biological fluids such as blood is becoming increasingly important for understanding diseases and developing new treatments. The molecular sieve developed by MIT engineers is more precise than conventional methods and has the potential to be much faster.
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The key to the molecular sieve, which is made using microfabrication technology, is the uniform size of the nanopores through which proteins are separated from biological fluids. Millions of pores can be spread across a microchip the size of a thumbnail.
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Juhwan Yoo, a Caltech undergraduate, also participated in the research as a summer visiting student. Funding came from the National Science Foundation, the National Institutes of Health and the Singapore-MIT Alliance.

Open Course Ware from Japan

Soccer Robots from Osaka University

A number of Japanese Universities are creating open courseware, in cooperation with MIT’s OpenCourseWare initiative (which has spawned the OCW Consortium).

Osaka University OpenCourseWare offers courses in English including: Theory in Materials Science | Fluid-Solid Multiphase Flow

Kyoto University OpenCourseWare aims to:

share information in consideration of the fact that sixty percent of visitors to MIT’s OCW project come from Asia. We will make active use of Japanese in building OpenCourseWare, to recruit talented students from all over Asia as well as to promote the Kyoto University education, with Kyoto’s culture and traditions, to the world at large.

Many of the courses are available in Japanese, some are available in English, including: Applied Pharmacology

Tokyo Tech OpenCourseWare courses include: Advanced Signal Processing – Guided Wave Circuit Theory and Mixed Signal systems and Integrated Circuits.

The Nagoya University OpenCourseWare brings free courseware to the Internet. Currently several courses are available in English including, Basics of Bioagricultural Sciences. They aim to post 25 courses initially.
Continue reading →

Berkeley and MIT courses online

Huge amount of University of California Berkely webcasts of course lectures. Subscribe to RSS feeds and listen to podcasts or listen online.

Courses include: General Biology, Solid State Devices and Introductory Physics. Course websites include handouts for the lectures.

A great open access resource.

I can’t believe I have mentioned MIT open courseware before but a search didn’t find anything. MIT’s effort is an excellent resource, many on science and engineering: Brain and Cognitive Sciences, Materials Science and Engineering, etc..

MIT also includes the excellent: Visualizing Cultures – a gateway to seeing history through images that once had wide circulation among peoples of different times and places by John Dower (author of National Book Award and Pulitzer Prize winning: Embracing Defeat: Japan in the Wake of World War II) and Shigeru Miyagawa.

The Future is Engineering

Do Great Engineering Schools Beget Entrepreneurism? by Brent Edwards provides two great links.

How to Kick Silicon Valley’s Butt by Guy Kawasaki:

Focus on educating engineers. The most important thing you can do is establish a world-class school of engineering. Engineering schools beget engineers. Engineers beget ideas. And ideas beget companies. End of discussion.

If I had to point to the single biggest reason for Silicon Valley’s existence, it would be Stanford University—specifically, the School of Engineering. Business schools are not of primary importance because MBAs seldom sit around discussing how to change the world with great products.

Why Startups Condense in America:

You need a great university to seed a silicon valley, and so far there are few outside the US. I asked a handful of American computer science professors which universities in Europe were most admired, and they all basically said “Cambridge” followed by a long pause while they tried to think of others. There don’t seem to be many universities elsewhere that compare with the best in America, at least in technology.

Both essays make many excellent points – read them! Continue reading →

MIT Hosts Student Vehicle Design Summit

Solar concept car drawing

Student summit set on vehicle design by Deborah Halbe

Seventy-three students from 21 universities around the world will gather at MIT this summer to design and build between five and 10 commuter vehicles that exploit human power, biofuels, solar technologies and fuel cells to travel at least 500 miles per gallon of fuel.
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An added goal for the June 13-Aug. 13 program is to lay a foundation for ongoing multidisciplinary transportation research involving all five MIT schools. “We hope to create a project-based, socially conscious engineering curriculum for the ’06-’07 academic year,” said Anna S. Jaffe, a junior in civil and environmental engineering and one of the summit student organizers.

Image by Mitchell Joachim and William Lark, sketch of a concept solar car was created for the MIT Vehicle Design Summit.

Seeing Machine from MIT

View from photo: an image (of a staircase) created to approximate the view through a seeing machine

MIT poet develops ‘seeing machine’ by Elizabeth A. Thomson

The work is led by Elizabeth Goldring, a senior fellow at MIT’s Center for Advanced Visual Studies. She developed the machine over the last 10 years, in collaboration with more than 30 MIT students and some of her personal eye doctors. The new device costs about $4,000, low compared to the $100,000 price tag of its inspiration, a machine Goldring discovered through her eye doctor.
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The pilot clinical trial of the seeing machine involved visually impaired people recruited from the Beetham Eye Institute. All participants had a visual acuity of 20/70 or less in the better-seeing eye. A person with 20/70 vision can see nothing smaller than the third line from the top of most eye charts. Most participants, however, had vision that was considered legally blind, meaning they could see nothing smaller than the “big E” on a standard eye chart.
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Goldring and colleagues are now working toward a large-scale clinical trial of a color seeing machine (the device tested in the pilot trial was black and white).