Posts tagged biology

Posts tagged biology

Real Angry Birds Flip ‘the Bird’ Before a Fight
Male sparrows are capable of fighting to the death. But a new study shows that they often wave their wings wildly first in an attempt to avoid a dangerous brawl.
"For birds, wing waves are like flipping the bird or saying ‘put up your dukes. I’m ready to fight,’" said Duke biologist Rindy Anderson.
Male swamp sparrows use wing waves as an aggressive signal to defend their territories and mates from intruding males, Anderson said. The findings also are a first step toward understanding how the birds use a combination of visual displays and songs to communicate with other males.
Anderson and her colleagues published the results online Jan. 28 in the journal Behavioral Ecology and Sociobiology.
Scientists had assumed the sparrows’ wing-waving behavior was a signal intended for other males, but testing the observations was difficult, Anderson said. So she and her co-author, former Duke engineering undergraduate student David Piech (‘12), built a miniature computer and some robotics, which the team then stuffed into the body cavity of a deceased bird. The result was a ‘robosparrow’ that looked just like a male swamp sparrow, which could flip its wings just like a live male.
Anderson took the wing-waving robosparrow to a swamp sparrow breeding ground in Pennsylvania and placed it in the territories of live males. The robotic bird “sang” swamp sparrow songs using a nearby sound system to let the birds know he was intruding, while Anderson and her colleagues crouched in the swampy grasses and watched the live birds’ responses. She also performed the tests with a stuffed sparrow that stayed stationary and one that twisted from side to side. These tests showed that wing waves combined with song are more potent than song on its own, and that wing waves in particular, not just any movement, evoked aggression from live birds.
The live birds responded most aggressively to the invading, wing-waving robotic sparrow, which Anderson said she expected. “What I didn’t expect to see was that the birds would give strikingly similar aggressive wing-wave signals to the three types of invaders,” she said. That means that if a bird wing-waved five times to the stationary stuffed bird, he would also wing-wave five times to the wing-waving robot.
Anderson had hypothesized that the defending birds would match the signals of the intruding robots, but her team’s results suggest that the males are more individualistic and consistent in the level of aggressiveness that they want to signal, she said.
"That response makes sense, in retrospect, since attacks can be devastating," Anderson said. Because of the risk, the real males may only want to signal a certain level of aggression to see if they could scare off an intruder without the conflict coming to a fight and possible death.

Visualizing Biological Networks in 4D
Every great structure, from the Empire State Building to the Golden Gate Bridge, depends on specific mechanical properties to remain strong and reliable. Rigidity—a material’s stiffness—is of particular importance for maintaining the robust functionality of everything from colossal edifices to the tiniest of nanoscale structures. In biological nanostructures, like DNA networks, it has been difficult to measure this stiffness, which is essential to their properties and functions. But scientists at the California Institute of Technology (Caltech) have recently developed techniques for visualizing the behavior of biological nanostructures in both space and time, allowing them to directly measure stiffness and map its variation throughout the network.
The new method is outlined in the February 4 early edition of the Proceedings of the National Academy of Sciences (PNAS).
"This type of visualization is taking us into domains of the biological sciences that we did not explore before," says Nobel Laureate Ahmed Zewail, the Linus Pauling Professor of Chemistry and professor of physics at Caltech, who coauthored the paper with Ulrich Lorenz, a postdoctoral scholar in Zewail’s lab. "We are providing the methodology to find out—directly—the stiffness of a biological network that has nanoscale properties."
Knowing the mechanical properties of DNA structures is crucial to building sturdy biological networks, among other applications. According to Zewail, this type of visualization of biomechanics in space and time should be applicable to the study of other biological nanomaterials, including the abnormal protein assemblies that underlie diseases like Alzheimer’s and Parkinson’s.
Zewail and Lorenz were able to see, for the first time, the motion of DNA nanostructures in both space and time using the four-dimensional (4D) electron microscope developed at Caltech’s Physical Biology Center for Ultrafast Science and Technology. The center is directed by Zewail, who created it in 2005 to advance understanding of the fundamental physics of chemical and biological behavior.
To get a clear picture of what’s happening inside a cell, scientists need to know the locations of thousands of proteins and other molecules. MIT chemists have now developed a technique that can tag all of the proteins in a particular region of a cell, allowing them to more accurately map those proteins.
“That’s a holy grail for biology — to be able to get spatially and temporally resolved molecular maps of living cells,” says Alice Ting, the Ellen Swallow Richards Associate Professor of Chemistry at MIT. “We’re still really far from that goal, but the overarching motivation is to get closer to that goal.”
Ting’s new method, developed with researchers from the Broad Institute and Harvard Medical School, combines the strengths of two existing techniques — microscopic imaging and mass spectrometry — to tag proteins in a specific cell location and generate a comprehensive list of all the proteins in that area.
In a paper appearing in the Jan. 31 online edition of Science, Ting and colleagues used the new technique to identify nearly 500 proteins located in the mitochondrial matrix — the innermost compartment of the cellular organelle where energy is generated.
Using fluorescence or electron microscopy, scientists can determine protein locations with high resolution, but only a handful of a cell’s approximately 20,000 proteins can be imaged at once. “It’s a bandwidth problem,” Ting says. “You certainly couldn’t image all the proteins in the proteome at once in a single cell, because there’s no way to spectrally separate that many channels of information.”
With mass spectrometry, which uses ionization to detect the mass and chemical structure of a compound, scientists can analyze a cell’s entire complement of proteins in a single experiment. However, the process requires dissolving the cell membrane to release a cell’s contents, which jumbles all of the proteins together. By purifying the mixture and extracting specific organelles, it is then possible to figure out which proteins were in those organelles, but the process is messy and often unreliable.
The new MIT approach tags proteins within living cells before mass spectrometry is done, allowing spatial information to be captured before the cell is broken apart. This information is then reconstructed during analysis by noting which proteins carry the location tag.
The Living Lab: Navigating into cells
How do viruses attach to cells? How do proteins interact and mediate infection? How do molecular machines organize themselves in healthy cells? How do they differ in diseased cells? These are the types of questions National Institutes of Health researchers ask in the recently established Living Lab for Structural Biology, questions they strive to answer through the most sophisticated of imaging techniques.
The Living Lab is an innovative partnership between NIH and FEI, an Oregon-based instrumentation company that manufactures advanced microscopes. FEI brings to the table invaluable assistance in developing and customizing electron microscopes for biological applications. Using that cutting edge technology, scientists in the Living Lab, unencumbered by any pressure to patent or otherwise protect discoveries for commercial purposes, can proceed purely driven by scientific and biomedical puzzles. Success of the Living Lab, which is on the NIH campus in Bethesda, Md., will rest on that collaboration between the government and the private sector—and the idea that answering scientific questions and technical advancement go hand in hand.
“We want to navigate our way into cells and into viruses,” said Sriram Subramaniam, Ph. D., director of the NIH component of the Living Lab. “We would like to be able to describe the function of complex things, such as whole cells or infectious viruses, in terms of their molecular make-up, and try to figure out how they work.”
The Living Lab’s advanced imaging technology allows researchers to tackle previously unanswered questions in structural biology by creating three-dimensional shapes of various molecular machines. Visualizing tiny details is a step toward understanding the molecular origins of disease. “The prospects for studying structures of a broad spectrum of medically relevant complexes at minute resolutions has changed dramatically in recent years with advances in structural biology,” said Subramaniam. “Our goal with the Living Lab is to capture the synergy between all of these methods including the latest advances in cryo-electron microscopy to extend these advances to key scientific challenges in modern structural biology.”
Subramaniam, who earned his doctorate at Stanford University and did post-doctoral work at the Massachusetts Institute of Technology in chemistry and biology, directs the research activities of the Living Lab, in close consultation with other team members from FEI and from the National Institute of Diabetes and Digestive and Kidney Diseases.
Strange behavior: new study exposes living cells to synthetic protein
One approach to understanding components in living organisms is to attempt to create them artificially, using principles of chemistry, engineering and genetics. A suite of powerful techniques—collectively referred to as synthetic biology—have been used to produce self-replicating molecules, artificial pathways in living systems and organisms bearing synthetic genomes.
In a new twist, John Chaput, a researcher at Arizona State University’s Biodesign Institute and colleagues at the Department of Pharmacology, Midwestern University, Glendale, AZ have fabricated an artificial protein in the laboratory and examined the surprising ways living cells respond to it.
“If you take a protein that was created in a test tube and put it inside a cell, does it still function,” Chaput asks. “Does the cell recognize it? Does the cell just chew it up and spit it out?” This unexplored area represents a new domain for synthetic biology and may ultimately lead to the development of novel therapeutic agents.
The research results, reported in the advanced online edition of the journal ACS Chemical Biology, describe a peculiar set of adaptations exhibited by Escherichia coli bacterial cells exposed to a synthetic protein, dubbed DX. Inside the cell, DX proteins bind with molecules of ATP, the energy source required by all biological entities.
New form of cell division found
Researchers at the University of Wisconsin Carbone Cancer Center have discovered a new form of cell division in human cells.
They believe it serves as a natural back-up mechanism during faulty cell division, preventing some cells from going down a path that can lead to cancer.
"If we could promote this new form of cell division, which we call klerokinesis, we may be able to prevent some cancers from developing," says lead researcher Dr. Mark Burkard, an assistant professor of hematology-oncology in the department of medicine at the UW School of Medicine and Public Health.
Burkard presented the finding on Monday, Dec. 17 at the annual meeting of the American Society for Cell Biology in San Francisco.
(View a short video of the process here)
Trabecular meshwork cells from a pig’s eye
Image by Carmen Laethem (Aerie Pharmaceuticals Research Triangle Park, North Carolina, USA)
(Source: nikonsmallworld.com)
Results: At the moment that someone is suffering a stroke, the immediate concern is getting them stabilized. Once the initial attack has passed, additional treatment and preventive measures can be implemented. Understanding what’s happening during the actual event, and in the subsequent hours and days, will help improve the effectiveness of the post-attack treatment plan, and also help identify methods of neuroprotection—that is, administer treatments to protect against a stroke in advance for potentially at-risk individuals. Computational biology researchers at Pacific Northwest National Laboratory developed a model for predicting what’s happening during a stroke, how the process evolves over time, the potential outcomes, and the effects of different treatment options.
The work was featured in the journal PLOS Computational Biology
Why It Matters: The ability to examine strokes and other biological processes, through the use of computer simulations rather than after the fact on actual organisms, may significantly accelerate how quickly discoveries can be made in fighting diseases. The ability to model and simulate different treatments prior to administering them to a patient can help predict with more certainty which therapeutic approaches may be the most effective.
"This is the first step in being able to suggest {to health care providers} that if you do X and Y, you’d get a much bigger effect than what you’re currently doing,” said Dr. Jason McDermott, a PNNL computational biologist and lead author on the paper.
Methods: The team developed novel mathematical approaches for extending existing methods of determining causal relationships between genes that are driving biological processes. They implemented ordinary differential equations—a process for describing how things change over time—to improve their ability to infer what these gene relationships might look like and to allow more dynamic simulation of these biological processes over time.
What’s Next: The team is looking at improving the model to simulate events that are happening during a biological process for which there isn’t pre-existing data. Additionally, they plan to test the effect of adding drugs to a treatment plan and also will be looking at micro RNA molecules that currently aren’t included in the model.
Separation of a cell
This illustration shows a cell undergoing mitosis or “cell division.” The cell membrane is shown in blue, and the cell’s chromosomes are shown in yellow. Mitosis is a well-studied and well-imaged phenomenon in two-dimensional images, but it’s never before been seen quite like this. What makes this image special is the use of a new fluorescent protein called MiniSOG, shown flying out of the cell.
Image courtesy of Andrew Noske and Thomas Deerinck (National Center for Microscopy and Imaging Research, University of California, San Diego); Horng Ou and Clodagh O’Shea (Salk Institute).
(Source: MSNBC)

Test that can predict death - with a terrifying degree of accuracy
A blood test to determine how fast someone is ageing has been shown to work on a population of wild birds, the first time the ageing test has been used successfully on animals living outside a laboratory setting.
The test measures the average length of tiny structures on the tips of chromosomes called telomeres which are known to get shorter each time a cell divides during an organism’s lifetime.
Telomeres are believed to act like internal clocks by providing a more accurate estimate of a person’s true biological age rather than their actual chronological age.
This has led some experts to suggest that telomere tests could be used to estimate not only how fast someone is ageing, but possibly how long they have left to live if they die of natural causes.
Telomere tests have been widely used on experimental animals and at least one company is offering a £400 blood test in the UK for people interested in seeing how fast they are ageing based on their average telomere length.
Now scientists have performed telomere tests on an isolated population of songbirds living on an island in the Seychelles and found that the test does indeed accurately predict an animal’s likely lifespan.
“We saw that telomere length is a better indicator of life expectancy than chronological age. So by measuring telomere length we have a way of estimating the biological age of an individual – how much of its life it has used up,” said David Richardson of the University of East Anglia.