Tag Archives: university research

Measuring Protein Bond Strength with Optical Tweezers

Using a light touch to measure protein bonds

MIT researchers have developed a novel technique to measure the strength of the bonds between two protein molecules important in cell machinery: Gently tugging them apart with light beams. “It’s really giving us a molecular-level picture of what’s going on,” said Matthew Lang, an assistant professor of biological and mechanical engineering
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The researchers studied the interactions between the proteins by pinning one actin filament to a surface and controlling the motion of the second one with a beam of light. As the researchers tug on a bead attached to the second filament, the bond mediated by the actin-binding protein eventually breaks.

With this technique, the researchers can get a precise measurement of the force holding the proteins together, which is on the order of piconewtons (10^-12 newtons).

Mapping Where Brains Store Similar Information

CMU finds human brains similarly organized

Based on how one person thinks about a hammer, a computer can identify when another person also is thinking about a hammer. It also can differentiate between items in the same category of tools, be it a hammer or screwdriver.
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The study makes two important scientific advances: “[T]here is an identifiable neural pattern associated with perception and contemplation of individual objects, and that part of the pattern is shared” by people.

The study reveals that patterns of thought extend into different regions of the brain, reflecting its complexity. It proves that a simple image can invoke thoughts in various regions of the brain, including how to use the object and experiences one has had with the object.

The study also helps to explain how the brain organizes thoughts, and the commonality of that process. “I want a complete mapping of brain states and thoughts,” Dr. Just said. “We’re taking tiny baby steps, but anything we can think about is represented in the brain.”

Using Bacteria to Carry Nanoparticles Into Cells

Bacteria ferry nanoparticles into cells for early diagnosis, treatment

Researchers at Purdue University have shown that common bacteria can deliver a valuable cargo of “smart nanoparticles” into a cell to precisely position sensors, drugs or DNA for the early diagnosis and treatment of various diseases. The approach represents a potential way to overcome hurdles in delivering cargo to the interiors of cells, where they could be used as an alterative technology for gene therapy, said Rashid Bashir, a researcher at Purdue’s Birck Nanotechnology Center.

The researchers attached nanoparticles to the outside of bacteria and linked DNA to the nanoparticles. Then the nanoparticle-laden bacteria transported the DNA to the nuclei of cells, causing the cells to produce a fluorescent protein that glowed green. The same method could be used to deliver drugs, genes or other cargo into cells.

“The released cargo is designed to be transported to different locations in the cells to carry out disease detection and treatment simultaneously,” said Bashir, a professor in the Weldon School of Biomedical Engineering and the School of Electrical and Computer Engineering. “Because the bacteria and nanoparticle material can be selected from many choices, this is a delivery system that can be tailored to the characteristics of the receiving cells. It can deliver diagnostic or therapeutic cargo effectively for a wide range of needs.”

Harmless strains of bacteria could be used as vehicles, harnessing bacteria’s natural ability to penetrate cells and their nuclei, Bashir said. “For gene therapy, a big obstacle has been finding ways to transport the therapeutic DNA molecule through the nuclear membrane and into the nucleus,” he said. “Only when it is in the nucleus can the DNA produce proteins that perform specific functions and correct genetic disease conditions.”
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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

Symbiotic relationship between ants and bacteria

Study reveals classic symbiotic relationship between ants, bacteria

Ants that tend and harvest gardens of fungus have a secret weapon against the parasites that invade their crops: antibiotic-producing bacteria that the insects harbor on their bodies.

“Every ant species [that we have examined] has different, highly modified structures to support different types of bacteria,” says Currie. “This indicates the ants have rapidly adapted to maintain the bacteria. It also indicates that the co-evolution between the bacteria and the ants, as well as the fungus and parasites, has been occurring since very early on, apparently for tens of millions of years.”

Furthermore, Currie says, the fact that the species have coexisted for so long means there might be a mechanism in place to decrease the rate of antibiotic resistance – which could help address a significant problem facing modern medicine. “We can learn a lot about our own use of antibiotics from this system,” he says.

Read more about the overuse of antibiotics

Florida State lures Applied Superconductivity Center from Wisconsin

Ching-Jen “Marty” Chen, dean of the College of Engineering, and Chiang Shih, chairman of the college’s department of mechanical engineering, also were heavily involved in negotiations to bring ASC to FSU.

“The College of Engineering joins the National High Magnetic Field Laboratory in welcoming the move of the Applied Superconductivity Center to Tallahassee,” Chen said.

“This is an excellent example of multidisciplinary collaboration between the sciences and engineering. The affiliation of ASC with the College of Engineering amplifies many ongoing efforts in material engineering research in the college and the magnet lab.”

Four top ASC researchers, including Director David C. Larbalestier, will begin relocating by January 2006. They will be followed over the next six months by eight post-doctoral researchers, several highly skilled machinists and a few graduate students. In all, ASC may bring as many as 30 researchers to Tallahassee, along with some $2 million in research grants and another $2.5 million worth of precision laboratory equipment.

Larbalestier is viewed by many of his peers as the leading researcher in the United States, and possibly the world, in the basic research of practical superconducting materials for magnets and power applications. Over a 35-year career, he has profoundly influenced the development of high-field magnets for high-energy physics and other applications, such as magnetic resonance imaging (MRI), that have evolved from them. Among the highlights of his career is his election in 2003 to the prestigious National Academy of Engineering.

“The Economic Development Council of Tallahassee/Leon County (EDC) is excited with this impressive level of investment and ongoing million-dollar payroll that will leave a lasting and positive influence on our regional economy,” said Brad Day, executive director of the ECD. “With the recruitment of research and development activities like this, our community continues to earn its reputation as a technology-rich economy.”

On the ASC site, hosted at Madison, they don’t spin the story quite the same way – Breaking News: ASC will be teaming up with NHMFL in Tallahassee, FL in 2006. Still that headline links directly to the FSU news release.

Self-Assembling Cubes Could Deliver Medicine

Nanocubes photos

Tiny Self-Assembling Cubes Could Carry Medicine, Cell Therapy – News Release from Johns Hopkins (pdf format)

Details of photos: “Scanning electron microscopy images of image of (A) a hollow, open surfaced, biocontainer, and (B) a device loaded with glass microbeads. (C) Fluorescence microscopy images of a biocontainer loaded with cell-ECM-agarose with the cell viability stain, Calcein-AM. (D) Release of viable cells from the biocontainer.”

Johns Hopkins researchers have devised a self- assembling cube-shaped perforated container, no larger than a dust speck, that could serve as a delivery system for medications and cell therapy.

When the process is completed, they form a perforated cube. When the solution is cooled, the solder hardens again, and the containers remain in their box-like shape.

“To make sure it folds itself exactly into a cube, we have to engineer the hinges very precisely,” Gracias said. “The self-assembly technique allows us to make a large number of these microcontainers at the same time and at a relatively low cost.”

Gracias and his colleagues used micropipettes to insert into the cubes a suspension containing microbeads that are commonly used in cell therapy. The lab team showed that these beads could be released from the cubes through agitation. The researchers also inserted human cells, similar to the type used in medical therapy, into the cubes. A positive stain test showed that these cells remained alive in the microcontainers and could easily be released.

And they are “always on the lookout for exceptional and highly creative undergraduate, graduate students and post-doctoral candidates” – maybe you.