Category Archives: Life Science

Gene Linked to Fish and Human Pigmentation

Until now, the genetics underlying human skin pigmentation have remained a mystery. But while studying the zebrafish–a fish common to household aquariums and research laboratories–a team of interdisciplinary scientists found a gene that plays a major role in human coloration.

Besides unraveling some of the mysteries of human variation, the research, which is featured on the cover of the Dec. 16 issue of Science, has implications for understanding a host of human diseases including cancer, diabetes and rickets.

Our Single-Celled Ancestors

choanoflagellates in water (photo by Melissa Mott)

Our Single-Celled Ancestors by David Pescovitz, ScienceMatters@Berkeley. Photo: propelled by their flagella, choanoflagellates move through water collecting bacteria on a collar of tentacles at the base of the cell body. (photo by Melissa Mott)

Six-hundred million years ago, a pivotal turning point in the history of life occurred. In the ancient sea, multicellular organisms evolved that are now recognized as the world’s first animals. But what was the biology of the single-celled organism that made the transition? And how did it become the common progenitor of all animals?

As always this issue of ScienceMatters@Berkeley includes excellent articles. Other articles from this issue: Extreme Biomaterials and Machines That Learn.

Massive Project Will Reveal How Humans Continue to Evolve

Massive Project Will Reveal How Humans Continue to Evolve by Gregory Mone

By comparing differences among those groups’ DNA, HapMap gives scientists a better shot at distinguishing the genetic factors involved in disease from the environmental ones. Ultimately, it will help them explain why, for instance, some people have a higher or lower risk of certain illnesses. And once scientists understand how deleterious genes affect various populations, they’ll be better equipped to develop more-effective, targeted drugs to combat them.

What Are Viruses?

What Are Viruses?, from the excellent Science In Action blog:

Viruses are small, from about 20 nanometers to about 400 nanometers in size. (A bacterial cell is generally in the range of 0.5 to 5.0 micrometers in size. A micrometer is one thousand times bigger than a nanometer, so bacteria are hundreds of times larger than viruses.)
…
Viruses cannot be killed by antibiotics. Antibiotics kill or stop the growth of bacteria, not viruses. Using antibiotics to try to control viral diseases like colds and flu just hastens the day those antibiotics will be useless against dangerous bacteria, because exposing populations of bacteria to antibiotics gives them a chance to evolve defenses against the drugs.

Adventures in Synthetic Biology

Nature offers its first ever comic: Adventures in Synthetic Biology (via easternblot). Learn more about the creation of the comic. The graphics are nice, though honestly the interface to view the comic could be better. The pdf version is larger and easier to read.

I think it is great to experiment with using different ways to present scientific ideas. This comic is a good example of one of those ways. Also see several books that use cartoons to present ideas: Cartoon Guide to Genetics, Cartoon Guide to Physics and Cartoon Guide to Chemistry (all by Larry Gonick).

2005 intercollegiate Genetically Engineered Machine competition

Davidson College: Kristen DeCelle 2006 and Andrew Drysdale 2007

2005 Intercollegiate Genetically Engineered Machine Competition. Thirteen schools participated in the 2005 Intercollegiate Genetically Engineered Machine competition (iGEM 2005): Berkeley, Caltech, Cambridge, Davidson, ETH Zurich, Harvard, MIT, Oklahoma, Penn State, Princeton, Toronto, UCSF, and UT Austin. Learn about and sign up for the 2006 competition.

Photo of Davidson College students: Kristen DeCelle ’06 and Andrew Drysdale ’07. Davidson Students “Ace” Presentation at MIT Synthetic Biology Competition.

The Davidson team-“The Synth-Aces,” a word play on enzymes called synthases-presented their design of a genetically-engineered, E. coli-based “digital decoder.” The device detects which combination of three common chemicals (with eight combinations possible) is present, and then displays a human-readable number that glows in the dark. The number is produced by genetically customized bacteria that grow in a familiar pattern of a digital numeric display. The resulting readouts of “0” through “7” correspond to the specific chemical combination detected in solution. One real world application of a decoder device might be to monitor water for contaminants or toxins.

Bannanas Going Going Gone

Can This Fruit Be Saved? by Dan Koeppel, Popular Science:

The banana as we know it is on a crash course toward extinction. For scientists, the battle to resuscitate the world’s favorite fruit has begun…

. It also turns out that the 100 billion Cavendish bananas consumed annually worldwide are perfect from a genetic standpoint, every single one a duplicate of every other. It doesn’t matter if it comes from Honduras or Thailand, Jamaica or the Canary Islands—each Cavendish is an identical twin to one first found in Southeast Asia, brought to a Caribbean botanic garden in the early part of the 20th century, and put into commercial production about 50 years ago.

That sameness is the banana’s paradox. After 15,000 years of human cultivation, the banana is too perfect, lacking the genetic diversity that is key to species health. What can ail one banana can ail all. A fungus or bacterial disease that infects one plantation could march around the globe and destroy millions of bunches, leaving supermarket shelves empty.
…
What can ail one banana can ail all. A fungus or bacterial disease that infects one plantation could march around the globe and destroy millions of bunches, leaving supermarket shelves empty.

A wild scenario? Not when you consider that there’s already been one banana apocalypse. Until the early 1960s, American cereal bowls and ice cream dishes were filled with the Gros Michel, a banana that was larger and, by all accounts, tastier than the fruit we now eat.

Scientists crack 40-year-old DNA puzzle

Scientist at University of Bath: Stefan Bagby, Jean van den Elsen and Huan-Lin Wu

Scientists crack 40-year-old DNA puzzle and point to ‘hot soup’ at the origin of life:

A new theory that explains why the language of our genes is more complex than it needs to be also suggests that the primordial soup where life began on earth was hot and not cold, as many scientists believe.
…
The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes – but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.

The University of Bath researchers suggest that the primordial ‘doublet’ code was read in threes – but with only either the first two ‘prefix’ or last two ‘suffix’ pairs of bases being actively read.

By combining arrangements of these doublet codes together, the scientists can replicate the table of amino acids – explaining why some amino acids can be translated from groups of 2, 4 or 6 codons. They can also show how the groups of water loving (hydrophilic) and water-hating (hydrophobic) amino acids emerge naturally in the table, evolving from overlapping ‘prefix’ and ‘suffix’ codons.
…
The theory also explains how the structure of the genetic code maximises error tolerance. For instance, ‘slippage’ in the translation process tends to produce another amino acid with the same characteristics, and explains why the DNA code is so good at maintaining its integrity.

“This is important because these kinds of mistakes can be fatal for an organism,” said Dr van den Elsen. “None of the older theories can explain how this error tolerant structure might have arisen.”

Converting Emissions to Biofuels

Converting emissions to biofuels at GreenFuel Technologies:

In the unit, non-toxic photosynthetic algae ‘eat’ the carbon dioxide and break the nitrogen-oxygen bonds. Scrubbed gas vents from the chimneys at the unit apex. Inline sensors monitor system performance and provide remote reporting, and a built-in automated harvesting system gathers algae ‘crops’ on a preprogrammed schedule, typically daily. The bioreactors are even self-cleaning.

The technology was tested at the MIT Cogeneration Plant (delivered 86% NOx reduction under all conditions, along with 50% CO2 reduction on rainy days, and 82% CO2 reduction on sunny day) and is now being tested at a commerical power plant.

Read news reports about the technology: Power Plants and How Algae Clean the Air

Read a more detailed report from the company: Air-Lift Bioreactors for Algal Growth on Flue Gas: Mathematical Modeling and Pilot-Plant Studies

Red Blood Cell’s Amazing Flexibility

Scientists Discover Secret Behind Human Red Blood Cell’s Amazing Flexibility:

The human red blood cell membrane skeleton is a network of roughly 33,000 protein hexagons that looks like a microscopic geodesic dome.
…
a team of UCSD researchers describe a mathematical model that explains how a mesh-like protein skeleton gives a healthy human red blood cell both its rubbery ability to stretch without breaking, and a potential mechanism to facilitate diffusion of oxygen across its membrane. “Red cells are one of the few kinds of cells in the body with no nucleus and only a thin layer of protein skeleton under their membrane: they are living bags of hemoglobin,” said Amy Sung, a professor of bioengineering at UCSD’s Jacobs School of Engineering