Tag Archives: organism

Latest JBEI Startup to Speed Up Biotech Industry

By Guest PostOctober 3, 2012Scienceautocad, berkeley lab, biofuels, biology, chemicals, cutting edge, design, DNA, dna manipulation, eduardo abeliuk, electrical engineering, expressing, inertia, iso27001, j5 software, jbei, majed abolfazli, medicine, metabolic pathway, mike fero, modern cloning, molecular biology, nathan hillson, organism, pharmchem, protocol, qb3, san francisco, Science, sequencing, splicing, stanford university, teselagen

TeselaGen’s DNA construction technology makes genetic engineering cheaper and faster.

Sequencing, splicing and expressing DNA may seem to be the quintessence of cutting-edge science—indeed DNA manipulation has revolutionized fields such as biofuels, chemicals and medicine. But in fact, the actual process can still be tedious and labor-intensive, something Lawrence Berkeley National Laboratory (Berkeley Lab) scientist Nathan Hillson learned the hard way.

After struggling for two days to design a protocol to put together a genetic circuit with 10 pieces of DNA—using a spreadsheet as his primary tool—he was dismayed to discover that an outside company could have done the whole thing, including parts and labor, for lower cost than him ordering the oligonucleotides himself. “I learned two things: one, I never wanted to go through that process again, and two, it’s extremely important to do the cost-effectiveness calculation,” said Hillson, a biochemist who also directs the synthetic biology program at the Berkeley Lab-led Joint BioEnergy Institute (JBEI). “So that was the genesis of the j5 software. This is the perfect thing to teach a computer to do.” (more…)

Evolution is as Complicated as 1-2-3

By Guest PostSeptember 20, 2012Scienceanalysis, bacteria, bacterial evolution, biological function, citrate, citrate molecule, DNA, e coli, evolution, function, genomics, glucose, jeff barrick, michigan, module, mutation, mutational piece, organism, oxygen, potentiation, puzzle, richard lenski, state university, traditional diet, zachary blount

EAST LANSING, Mich. — A team of researchers at Michigan State University has documented the step-by-step process in which organisms evolve new functions.

The results, published in the current issue of Nature, are revealed through an in-depth, genomics-based analysis that decodes how E. coli bacteria figured out how to supplement a traditional diet of glucose with an extra course of citrate. (more…)

Salt Seeds Clouds in the Amazon Rainforest

By Guest PostSeptember 13, 2012Environmentabsorption, aerosol particle, airborne particle, als beamline, Amazon, amazon jungle, amazonian, asci, ballistospores, berkeley lab, biomass, brazil, chemistry, christopher pohlker, david kilcoyne, deep, emission, fine particle, fog, forest canopy, fungi fire, gas phase, Germany, graphitic, institute, isoprene, leaves, liquid droplet, manaus, mary gilles, max planck, meinrat andreae, microscopy, moisture, morning, mpic, natural forest, nexafs, organic carbon, organism, osmosis, photon, potassium level, potassium salt, rainforest, sacs, seed, soluble particle, stxm, sugar alcohol, terpenes, tree resin, trees, ulrich pöschl, water vapor, xray

It’s morning, deep in the Amazon jungle. In the still air innumerable leaves glisten with moisture, and fog drifts through the trees. As the sun rises, clouds appear and float across the forest canopy … but where do they come from? Water vapor needs soluble particles to condense on. Airborne particles are the seeds of liquid droplets in fog, mist, and clouds.

To learn how aerosol particles form in the Amazon, Mary Gilles of the Chemical Sciences Division at the U.S. Department of Energy’s Lawrence Berkeley National Laboratory (Berkeley Lab) and David Kilcoyne of the Lab’s Advanced Light Source (ALS) worked with Christopher Pöhlker of Germany’s Max Planck Institute for Chemistry (MPIC) as part of an international team of scientists led by MPIC’s Meinrat Andreae and Ulrich Pöschl. They analyzed samples of naturally formed aerosols collected above the forest floor, deep in the rainforest. (more…)

Why Do Organisms Build Tissues They Seemingly Never Use?

By Guest PostAugust 12, 2012Sciencebeacon center, charles ofria, computational evolution, computer program, cornell university, Environment, evolution, evolutionary reason, jeff clune, michigan state university, mutate, mutation, organism, richard lenski, robert pennock, skyscraper, tissue

EAST LANSING, Mich. — Why, after millions of years of evolution, do organisms build structures that seemingly serve no purpose?

A study conducted at Michigan State University and published in the current issue of The American Naturalist investigates the evolutionary reasons why organisms go through developmental stages that appear unnecessary.

“Many animals build tissues and structures they don’t appear to use, and then they disappear,” said Jeff Clune, lead author and former doctoral student at MSU’s BEACON Center of Evolution in Action. “It’s comparable to building a roller coaster, razing it and building a skyscraper on the same ground. Why not just skip ahead to building the skyscraper?” (more…)

Division of Labor Offers Insight into the Evolution of Multicellular Life

By Guest PostAugust 8, 2012Scienceann dornhaus, avida, beacon center, beacon researchers, ben kerr, charles ofria, communication system, digital organism, evolution, evolution platform, evolutionary history, genetic material, heather goldsby, human economies, michigan state university, multi celled, multicellular life, organism, single celled, university of arizona, university of washington

EAST LANSING, Mich. — Dividing tasks among different individuals is a more efficient way to get things done, whether you are an ant, a honeybee or a human.

A new study by researchers at Michigan State University’s BEACON Center for the Study of Evolution in Action suggests that this efficiency may also explain a key transition in evolutionary history, from single-celled to multi-celled organisms.

The results, which can be found in the current issue of the Proceedings of the National Academy of Sciences, demonstrate that the cost of switching between different tasks gives rise to the evolution of division of labor in digital organisms. In human economies, these costs could be the mental shift or the travel time required to change from activity to another. (more…)

Melting Sea Ice Threatens Emperor Penguins, Study Finds

By Guest PostJuly 1, 2012Environment, Natureantarctic peninsula, antarctic sea ice, Antarctica, christophe barbraud, climate models, climate variable, demographic model, dion islets, east antarctica, emperor penguins, food web, global temperature, happy feet, henri weimerskirch, ipev, krill, life cycle, marika holland, mark serreze, melting sea ice, nutrient cycle, organism, penguin colony, penguin population, sea bird, sea ice forecasts, shrimplike animal, squid, stephanie jenouvrier, terre adelie, warming temperature, whoi

At nearly four feet tall, the Emperor penguin is Antarctica’s largest sea bird—and thanks to films like “March of the Penguins” and “Happy Feet,” it’s also one of the continent’s most iconic. If global temperatures continue to rise, however, the Emperor penguins in Terre Adélie, in East Antarctica may eventually disappear, according to a new study by led by researchers from the Woods Hole Oceanographic Institution (WHOI). The study was published in the June 20th edition of the journal Global Change Biology.

“Over the last century, we have already observed the disappearance of the Dion Islets penguin colony, close to the West Antarctic Peninsula,” says Stephanie Jenouvrier, WHOI biologist and lead author of the new study. “In 1948 and the 1970s, scientists recorded more than 150 breeding pairs there. By 1999, the population was down to just 20 pairs, and in 2009, it had vanished entirely.” Like in Terre Adélie, Jenouvrier thinks the decline of those penguins might be connected to a simultaneous decline in Antarctic sea ice due to warming temperatures in the region. (more…)

Not a One-Way Street: Evolution Shapes Environment of Connecticut Lakes

By Guest PostMay 24, 2012Environment, Naturealewife, atlantic coast, bosminia, colonial settlers, colonial times, connecticut, daphnia, david post, ecology, environmental change, evolution, evolutionary change, evolutionary feedback, fish, force, genetic changes, john delong, lake, loop, matthew r walsh, organism, plankton, population growth, predator, prey, torrance hanley, water fleas, yale university, zooplankton

Environmental change is the selective force that preserves adaptive traits in organisms and is a primary driver of evolution. However, it is less well known that evolutionary change in organisms also trigger fundamental changes in the environment.

Yale University researchers found a prime example of this evolutionary feedback loop in a few lakes in Connecticut, where dams built 300 years ago in Colonial times trapped a fish called the alewife.

In a study published May 23 in the journal Proceedings of the Royal Academy B, the Yale team describes how this event fundamentally changed the structure of the alewife and, with it, the water flea that the alewife feeds upon and the food chain that supports them both. (more…)

Locked RNA Editing Yields Odd Fly Behavior

By Guest PostApril 26, 2012Scienceabiotic factor, als, arthur sugden, asli sahin, brown university, cell, charles lawrence, dadar, enzyme adar, epilepsy, factor, fruit fly, function, genetic, jacquelyn dorsky, james jepson, lauren alpert, locking down, lou gehrigs disease, nucleus, organism, phenomenon, protein, rna, robert reenan, suicidal depression, temperature, wallflowers, yiannis savva

At the level of proteins, organisms can adapt by editing their RNA — and an editor can even edit itself. Brown University scientists working with fruit flies found that “locking down” the self-editing process at two extremes created some strange behaviors. They also found that the process is significantly affected by temperature.

PROVIDENCE, R.I. [Brown University] — Because a function of RNA is to be translated as the genetic instructions for the protein-making machinery of cells, RNA editing is the body’s way of fine-tuning the proteins it produces, allowing us to adapt. The enzyme ADAR, which does this editing job in the nervous system of creatures ranging from mice to men, even edits itself. In a new study that examined the self-editing process and locked it down at two extremes in fruit flies, Brown University scientists found some surprising insights into how this “fine-tuning of the fine-tuner” happens, including bizarre behavioral effects that come about when the self-editor can’t edit. (more…)