Category Archives: Science

Science and Engineering Lectures Online

VideoLectures.Net offers free and open access of a high quality video lectures presented by distinguished scholars and scientists at events like conferences, summer schools, workshops and science promotional events. The portal is aimed at promoting science, exchanging ideas and fostering knowledge sharing by providing high quality didactic contents not only to a scientific community but also to a general public.

Enjoy the great lectures they provide. Also see the Curious Cat directory of science and engineering webcast web sites. There are lots of great presentations available now. The last several years has really seen a huge increase in the valuable webcasts available online.

The Only Known Cancerless Animal

Unlike any other mammal, naked mole rate communities consist of queens and workers more reminiscent of bees than rodents. Naked mole rats can live up to 30 years, which is exceptionally long for a small rodent. Despite large numbers of naked mole-rats under observation, there has never been a single recorded case of a mole rat contracting cancer, says Gorbunova. Adding to their mystery is the fact that mole rats appear to age very little until the very end of their lives.

The mole rat’s cells express p16, a gene that makes the cells “claustrophobic,” stopping the cells’ proliferation when too many of them crowd together, cutting off runaway growth before it can start. The effect of p16 is so pronounced that when researchers mutated the cells to induce a tumor, the cells’ growth barely changed, whereas regular mouse cells became fully cancerous.

“It’s very early to speculate about the implications, but if the effect of p16 can be simulated in humans we might have a way to halt cancer before it starts.” says Vera Gorbunova, associate professor of biology at the University of Rochester and lead investigator on the discovery.

In 2006, Gorbunova discovered that telomerase—an enzyme that can lengthen the lives of cells, but can also increase the rate of cancer—is highly active in small rodents, but not in large ones.

Until Gorbunova and Seluanov’s research, the prevailing wisdom had assumed that an animal that lived as long as we humans do needed to suppress telomerase activity to guard against cancer. Telomerase helps cells reproduce, and cancer is essentially runaway cellular reproduction, so an animal living for 70 years has a lot of chances for its cells to mutate into cancer, says Gorbunova. A mouse’s life expectancy is shortened by other factors in nature, such as predation, so it was thought the mouse could afford the slim cancer risk to benefit from telomerase’s ability to speed healing.

While the findings were a surprise, they revealed another question: What about small animals like the common grey squirrel that live for 24 years or more? With telomerase fully active over such a long period, why isn’t cancer rampant in these creatures?

Engineered Circuits That can Count Cellular Events

Engineered circuits can count cellular events by Anne Trafton

MIT and Boston University engineers have designed cells that can count and “remember” cellular events, using simple circuits in which a series of genes are activated in a specific order.
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The first counter, dubbed the RTC (Riboregulated Transcriptional Cascade) Counter, consists of a series of genes, each of which produces a protein that activates the next gene in the sequence.

With the first stimulus — for example, an influx of sugar into the cell — the cell produces the first protein in the sequence, an RNA polymerase (an enzyme that controls transcription of another gene). During the second influx, the first RNA polymerase initiates production of the second protein, a different RNA polymerase.

The number of steps in the sequence is, in theory, limited only by the number of distinct bacterial RNA polymerases. “Our goal is to use a library of these genes to create larger and larger cascades,” said Lu.

The counter’s timescale is minutes or hours, making it suitable for keeping track of cell divisions. Such a counter would be potentially useful in studies of aging.

The RTC Counter can be “reset” to start counting the same series over again, but it has no way to “remember” what it has counted. The team’s second counter, called the DIC (DNA Invertase Cascade) Counter, can encode digital memory, storing a series of “bits” of information.

The process relies on an enzyme known as invertase, which chops out a specific section of double-stranded DNA, flips it over and re-inserts it, altering the sequence in a predictable way.

The DIC Counter consists of a series of DNA sequences. Each sequence includes a gene for a different invertase enzyme. When the first activation occurs, the first invertase gene is transcribed and assembled. It then binds the DNA and flips it over, ending its own transcription and setting up the gene for the second invertase to be transcribed next.

When the second stimulus is received, the cycle repeats: The second invertase is produced, then flips the DNA, setting up the third invertase gene for transcription. The output of the system can be determined when an output gene, such as the gene for green fluorescent protein, is inserted into the cascade and is produced after a certain number of inputs or by sequencing the cell’s DNA.

This circuit could in theory go up to 100 steps (the number of different invertases that have been identified). Because it tracks a specific sequence of stimuli, such a counter could be useful for studying the unfolding of events that occur during embryonic development, said Lu.

Other potential applications include programming cells to act as environmental sensors for pollutants such as arsenic. Engineers would also be able to specify the length of time an input needs to be present to be counted, and the length of time that can fall between two inputs so they are counted as two events instead of one.

Undergraduate Student Discovers Herbivorous Spider

Herbivory Discovered in a Spider

A jumping spider from Central America eats mostly plants, according to new research. Spiders were thought to be strictly predators on animals. The spider, Bagheera kiplingi, was described scientifically in the late 1800s, but its vegetarian tendencies were not observed until the 21st century.

“This is the first spider in the world known to deliberately hunt plant parts. It is also the first found to go after plants as a primary food source,” said lead author Christopher Meehan.
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Of the approximately 40,000 species of spiders known, Bagheera kiplingi is the only species known to be primarily herbivorous. Ironically, the vegetarian spider is named after the panther in Rudyard Kipling’s “The Jungle Book.” The spider inhabits several species of acacia shrubs involved in a well-known mutualism between the acacias and several species of ants.
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Previously, very few spiders had been seen consuming plants at all. Some spiders had been observed occasionally eating nectar and pollen, although the bulk of their diet was insects and other small animals.

Dennis Bray Podcast on Microbes As Computers

Carl Zimmer interviews Dennis Bray in an interesting podcast:

Dennis Bray is an active professor emeritus in both the Department of Physiology and Department of Neuroscience at the University of Cambridge. He studies the behavior of microbes–how they “decide” where to swim, when to divide, and how best to manage the millions of chemical reactions taking place inside their membranes. For Bray, microbes are tiny, living computers, with genes and proteins serving the roles of microprocessors.

William Kamkwamba on the Daily Show

Pointy haired bosses removed the video. Argh!

William Kamkwamba on the Daily show. I first posted about William’s great work in 2007 – Home Engineering: Windmill for Electricity. What a great example of what can be done by sharing scientific and engineering ideas with those who will make the effort to create workable solutions.

William has written a book on his life: The Boy Who Harnessed the Wind.

Learning Design of Experiments with Paper Helicopters

Photo showing the helicopter test track by Brad

Dr. George E.P. Box wrote a great paper on Teaching Engineers Experimental Design With a Paper Helicopter that can be used to learn principles of experimental design, including – conditions for validity of experimentation, randomization, blocking, the use of factorial and fractional factorial designs and the management of experimentation.

I ran across an interesting blog post on a class learning these principles today – Brad’s Hella-Copter:

For our statistics class, we have been working hard on a Design of Experiments project that optimizes a paper helicopter with respect to hang time an accuracy of a decent down a stairwell.
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We were to design a helicopter that would drop 3 stories down within the 2ft gap between flights of stairs.
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[design of experiments is] very powerful when you have lots of variables (ie. paper type, helicopter blade length, blade width, body height, body width, paperclip weights, etc) and not a lot of time to vary each one individually. If we were to individually change each variable one at a time, we would have made over 256 different helicopters. Instead we built 16, tested them, and got a feel for which variables were most important. We then focused on these important variables for design improvement through further testing and optimization.

The Nobel Prize in Physics 2009

The 2009 Nobel Prize in Physics honors three scientists, who have had important roles in shaping modern information technology, with one half to Charles Kuen Kao and with Willard Sterling Boyle and George Elwood Smith sharing the other half. Kao’s discoveries have paved the way for optical fiber technology, which today is used for almost all telephony and data communication. Boyle and Smith have invented a digital image sensor – CCD, or charge-coupled device – which today has become an electronic eye in almost all areas of photography. The Nobel prize site includes great information on the science behind the research that has been honored:

The first ideas of applications of light guiding in glass fibers (i.e. small glass rods) date from the late 1920’s. They were all about image transmission through a bundle of fibers. The motivation was medicine (gastroscope), defense (flexible periscope, image scrambler) and even early television. Bare glass fibers were, however, quite leaky and did not transmit much light. Each time the fibers were touching each other, or when the surface of the fibers was scratched, light was led away from the fibers. A breakthrough happened in the beginning of the 1950’s with the idea and demonstration that cladding the fibers would help light transmission, by facilitating total internal reflection.
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Optical communication of today has reached its present status thanks to a number of breakthroughs. Light emitting diodes (LEDs) and especially diode lasers, first based on GaAs (800-900 nm) and later on InGaAsP (1-1.7 ïm), have been essential. The optical communication window has evolved from 870 nm to 1.3 ïm and, finally, to 1.55 ïm where fiber losses are lowest. Gradient-index fibers were used in the first optical communication lines. However, when moving towards longer wavelengths and longer communication distances, single-mode fibers have become more advantageous.

Nowadays, long-distance optical communication uses single mode fibers almost exclusively, following Kao’s vision. The first such systems used frequent electronic repeaters to compensate for the remaining losses. Most of these repeaters have now been replaced by optical amplifiers, in particular erbium-doped fiber amplifiers. Optical communication uses wavelength division multiplexing with different wavelengths to carry different signals in the same fiber, thus multiplying the transmission rate. The first non-experimental optical fiber links were installed in 1975 in UK, and soon after in the US and in Japan. The first transatlantic fiber-optic cable was installed in 1988.

2009 Nobel Prize in Chemistry: the Structure and Function of the Ribosome

graphic image of the components of a cell

Cross section of a cell by the Royal Swedish Academy of Sciences. A ribosome is about 25 nanometters (a millionth of a millimeter) in size. A cell contains tens of thousands of ribosomes.

The Nobel Prize in Chemistry for 2009 awards studies of one of life’s core processes: the ribosome’s translation of DNA information into life. Ribosomes produce proteins, which in turn control the chemistry in all living organisms. As ribosomes are crucial to life, they are also a major target for new antibiotics.

This year’s Nobel Prize in Chemistry awards Venkatraman Ramakrishnan, Thomas A. Steitz and Ada E. Yonath for having showed what the ribosome looks like and how it functions at the atomic level. All three have used a method called X-ray crystallography to map the position for each and every one of the hundreds of thousands of atoms that make up the ribosome.

Inside every cell in all organisms, there are DNA molecules. They contain the blueprints for how a human being, a plant or a bacterium, looks and functions. But the DNA molecule is passive. If there was nothing else, there would be no life.

The blueprints become transformed into living matter through the work of ribosomes. Based upon the information in DNA, ribosomes make proteins: oxygen-transporting haemoglobin, antibodies of the immune system, hormones such as insulin, the collagen of the skin, or enzymes that break down sugar. There are tens of thousands of proteins in the body and they all have different forms and functions. They build and control life at the chemical level.

Details from the Nobel Prize site (which continues to do a great job providing scientific information to the public openly).
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2009 Nobel Prize in Physiology or Medicine

This year’s Nobel Prize in Physiology or Medicine is awarded to three scientists who have solved a major problem in biology: how the chromosomes can be copied in a complete way during cell divisions and how they are protected against degradation. The Nobel Laureates have shown that the solution is to be found in the ends of the chromosomes – the telomeres – and in an enzyme that forms them – telomerase.

The long, thread-like DNA molecules that carry our genes are packed into chromosomes, the telomeres being the caps on their ends. Elizabeth Blackburn and Jack Szostak discovered that a unique DNA sequence in the telomeres protects the chromosomes from degradation. Carol Greider and Elizabeth Blackburn identified telomerase, the enzyme that makes telomere DNA. These discoveries explained how the ends of the chromosomes are protected by the telomeres and that they are built by telomerase.

If the telomeres are shortened, cells age. Conversely, if telomerase activity is high, telomere length is maintained, and cellular senescence is delayed. This is the case in cancer cells, which can be considered to have eternal life. Certain inherited diseases, in contrast, are characterized by a defective telomerase, resulting in damaged cells. The award of the Nobel Prize recognizes the discovery of a fundamental mechanism in the cell, a discovery that has stimulated the development of new therapeutic strategies.

Scientists began to investigate what roles the telomere might play in the cell. Szostak’s group identified yeast cells with mutations that led to a gradual shortening of the telomeres. Such cells grew poorly and eventually stopped dividing. Blackburn and her co-workers made mutations in the RNA of the telomerase and observed similar effects in Tetrahymena. In both cases, this led to premature cellular ageing – senescence. In contrast, functional telomeres instead prevent chromosomal damage and delay cellular senescence. Later on, Greider’s group showed that the senescence of human cells is also delayed by telomerase. Research in this area has been intense and it is now known that the DNA sequence in the telomere attracts proteins that form a protective cap around the fragile ends of the DNA strands.

Many scientists speculated that telomere shortening could be the reason for ageing, not only in the individual cells but also in the organism as a whole. But the ageing process has turned out to be complex and it is now thought to depend on several different factors, the telomere being one of them. Research in this area remains intense.

The 3 awardees are citizens of the USA; two were born elsewhere.
Read more about their research at the Nobel Prize web site.

Molecular biologist Elizabeth Blackburn–one of Time magazine’s 100 “Most Influential People in the World” in 2007–made headlines in 2004 when she was dismissed from the President’s Council on Bioethics after objecting to the council’s call for a moratorium on stem cell research and protesting the suppression of relevant scientific evidence in its final report.

Webcast of Dr. Elizabeth Blackburn speaking at Google:
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