to simpler and more

robust computer network systems

Over the years science has gleaned an enormous amount of knowledge from the humble fruit fly. Drosophila melanogaster was used to provide the post-Mendelian foundations for our understanding of genetics and has also been used extensively in neuroscience research. The latest fruit fly-inspired innovation could simplify how wireless sensor networks communicate and stands to have wider applications for computing.

This is not the first time computing systems have been compared to biological systems. Learning from a comparison between Linux and E.coli and using fly’s eyes to help develop faster visual receivers for robots are just two examples. This time round researchers at Carnegie Mellon University (CMU), Pittsburgh, Pennsylvania, have discovered a highly efficient system of organizing cells in the fruit fly’s nervous system develops that stands to have applications in computer networking.

Without communication with surrounding cells or prior knowledge of what these other cells are doing the fly’s developing nervous system is able to organize itself so that a small number become leader cells or sensory organ precursor cells (SOP), while the rest become ordinary nerve cells. The SOPs which connect to adjoining nerve cells do not connect with other SOPs, but instead to the ends of the nervous system that are attached to tiny hairs for interacting with the outside world. What is extraordinary about how this hierarchy of cells organizes itself is the fact that the right number and combination of SOP cells and nerve cells form without the need for complicated information exchange.

The fly’s nervous system uses a probabilistic method to select the cells that will become SOPs. The cells have no information about how they are connected to each other but as various cells self-select themselves as SOPs, they send out chemical signals to neighboring cells that inhibit those cells from also becoming SOPs. This process continues for three hours, until all of the cells are either SOPs or are neighbors to an SOP, and the fly emerges from the pupal stage.

Ziv Bar-Joseph, associate professor of machine learning and computational biology at CMU and author of the report noted that the probability that any cell will self-select increases not as a function of connections, as with a maximal independent set (MIS) algorithm used in computer networking, but as a function of time. The researchers believe that computer networks could be developed using this innovative system creating networks which are much simpler and more robust.

“It is such a simple and intuitive solution, I can’t believe we did not think of this 25 years ago,” said co-author Noga Alon, a mathematician and computer scientist at Tel Aviv University and the Institute for Advanced Study in Princeton, N.J.

Bar-Joseph, Alon and their co-authors – Yehuda Afek of Tel Aviv University and Naama Barkai, Eran Hornstein and Omer Barad of the Weizmann Institute of Science in Rehovot, Israel – developed a new distributed computing algorithm using their findings. The resulting network was shown to have qualities that are well suited for networks in which the number and position of the nodes is not completely certain including wireless sensor networks, such as environmental monitoring, or where sensors are dispersed. They also believe this could be used in systems for controlling swarms of robots.

“The run time was slightly greater than current approaches, but the biological approach is efficient and more robust because it doesn’t require so many assumptions,” Bar-Joseph said. “This makes the solution applicable to many more applications.”

The research was supported in part by grants from the National Institutes of Health and the National Science Foundation.

Sourced & published by Henry Sapiecha

Metabolically Engineered Bacteria

Science (July 27, 2010) — Researchers have long envied spiders’ ability to manufacture silk that is light-weighted while as strong and tough as steel or Kevlar. Indeed, finer than human hair, five times stronger by weight than steel, and three times tougher than the top quality man-made fiber Kevlar, spider dragline silk is an ideal material for numerous applications. Suggested industrial applications have ranged from parachute cords and protective clothing to composite materials in aircrafts. Also, many biomedical applications are envisioned due to its biocompatibility and biodegradability.

Unfortunately, natural dragline silk cannot be conveniently obtained by farming spiders because they are highly territorial and aggressive. To develop a more sustainable process, can scientists mass-produce artificial silk while maintaining the amazing properties of native silk? That is something Sang Yup Lee at the Korea Advanced Institute of Science and Technology (KAIST) in Daejeon, the Republic of Korea, and his collaborators, Professor Young Hwan Park at Seoul National University and Professor David Kaplan at Tufts University, wanted to figure out. Their method is very similar to what spiders essentially do: first, expression of recombinant silk proteins; second, making the soluble silk proteins into water-insoluble fibers through spinning.

For the successful expression of high molecular weight spider silk protein, Professor Lee and his colleagues pieced together the silk gene from chemically synthesized oligonucleotides, and then inserted it into the expression host (in this case, an industrially safe bacterium Escherichia coli which is normally found in our gut). Initially, the bacterium refused to the challenging task of producing high molecular weight spider silk protein due to the unique characteristics of the protein, such as extremely large size, repetitive nature of the protein structure, and biased abundance of a particular amino acid glycine. “To make E. coli synthesize this ultra high molecular weight (as big as 285 kilodalton) spider silk protein having highly repetitive amino acid sequence, we helped E. coli overcome the difficulties by systems metabolic engineering,” says Sang Yup Lee, Distinguished Professor of KAIST, who led this project. His team boosted the pool of glycyl-tRNA, the major building block of spider silk protein synthesis. “We could obtain appreciable expression of the 285 kilodalton spider silk protein, which is the largest recombinant silk protein ever produced in E. coli. That was really incredible.” says Dr. Xia.

But this was only step one. The KAIST team performed high-cell-density cultures for mass production of the recombinant spider silk protein. Then, the team developed a simple, easy to scale-up purification process for the recombinant spider silk protein. The purified spider silk protein could be spun into beautiful silk fiber. To study the mechanical properties of the artificial spider silk, the researchers determined tenacity, elongation, and Young’s modulus, the three critical mechanical parameters that represent a fiber’s strength, extensibility, and stiffness. Importantly, the artificial fiber displayed the tenacity, elongation, and Young’s modulus of 508 MPa, 15%, and 21 GPa, respectively, which are comparable to those of the native spider silk.

“We have offered an overall platform for mass production of native-like spider dragline silk. This platform would enable us to have broader industrial and biomedical applications for spider silk. Moreover, many other silk-like biomaterials such as elastin, collagen, byssus, resilin, and other repetitive proteins have similar features to spider silk protein. Thus, our platform should also be useful for their efficient bio-based production and applications,” concludes Professor Lee.

This work is published on July 26 in the Proceedings of the National Academy of Sciences (PNAS) online

Sourced & published by Henry Sapiecha

Mimicking Insects to Avoid Sinking

Using Surface Tension

July 1, 2006 — A new robot made of ultralight carbon-fiber can stand or slowly walk on water. The principle it uses is borrowed from insects — surface tension tends to prevent the water’s surface from breaking, and the robot’s legs from sinking in.

PITTSBURGH — Nature inspires many things, from fashion to perfume to furniture. Now, technology gets a little inspiration.

After watching tiny bugs like these walk on water, Carnegie Mellon University mechanical engineer Metin Sitti wanted one of his own.

“We tried to make a robot to simulate the insect,” he tells DBIS. He tried and succeeded. This new tiny, lightweight, spindly legged creature is a robot that can propel itself across water in all directions. It can turn even sharp corners like the insect does, so it’s very agile.

The robot’s body is made of a super-light carbon fiber material. Its steel legs are coated with non-stick Teflon to repel water. A tiny battery gives it power.

“Right now we move by five centimeters per second, and the real insect can go up to one meter per second. So we are like around 20-times less speed,” Sitti says.

It might be slower, but just like insects, the robot doesn’t float. It stands on top of water thanks to the physics of surface tension. The surface is so strong that the robot’s feet only dent the water without breaking the surface while supporting the weight of the robot without sinking.

“When they put their legs on the surface of the water surface, they repel each other,” Sitti says. “And that repulsion can lift the body because it’s so light bodyweight.”

In the near future, Sitti says his creation could carry sensors to detect toxins in water supplies. “We can make many of them, like tens or hundreds of them, and cover a wide range and give you constant, continuous, water quality report,” he says.

Researchers have already received interest in the robot as an educational toy, to educate students and the public about water surface effects, and to provide entertainment.

Science (July 17, 2010) — In the battle between insect predators and their prey, chemical signals called kairomones serve as an early-warning system. Pervasively emitted by the predators, the compounds are detected by their prey, and can even trigger adaptations, such a change in body size or armor, that help protect the prey. But as widespread as kairomones are in the insect world, their chemical identity has remained largely unknown. New research by Rockefeller University’s Joel E. Cohen and colleagues at the University of Haifa in Israel has identified two compounds emitted by mosquito predators that make the mosquitoes less inclined to lay eggs in pools of water.

The findings, published in the July issue of Ecology Letters, may provide new environmentally friendly tactics for repelling and controlling disease-carrying insects.

Many animals use chemicals to communicate with each other. Pheromones, which influence social and reproductive behaviors within a particular species, are probably the best known and studied. Kairomones are produced by an individual of one species and received by an individual of a different species, with the receiving species often benefiting at the expense of the donor.

Cohen and his Israeli colleagues focused on the interaction between two insect species found in temporary pools of the Mediterranean and the Middle East: larvae of the mosquito C. longiareolata and its predator, the backswimmer N. maculata. When the arriving female mosquitoes detect a chemical emitted by the backswimmer, they are less likely to lay eggs in that pool.

To reproduce conditions of temporary pools in the field, the researchers used aged tap water with fish food added as a source of nutrients. Individual backswimmers were then placed in vials containing samples of the temporary pools, and air samples were collected from the headspace within the vials. The researchers used gas chromatography-mass spectrometry to analyze the chemicals emitted by the backswimmers.

Cohen and his colleagues identified two chemicals, hydrocarbons called n-heneicosane and n-tricosane, which repelled egg-laying by mosquitoes at the concentrations of those compounds found in nature. Together, the two chemicals had an additive effect.

Since the mosquitoes can detect the backswimmer’s kairomones from above the water’s surface, predator-released kairomones can reduce the mosquito’s immediate risk of predation, says Cohen. But they also increase the female mosquito’s chance of dying from other causes before she finds a pool safe for her to lay her eggs in.

“That’s why we think these chemicals could be a useful part of a strategy to control the population size of mosquitoes,” says Cohen, who is the Abby Mauzé Rockefeller Professor and head of the Laboratory of Populations. “We started this work from very basic curiosity about how food webs and predator-prey interactions work, but we now see unexpected practical applications. These newly identified compounds, and others that remain to be discovered, might be effective in controlling populations of disease-carrying insects. It’s far too soon to say, but there’s the possibility of an advance in the battle against infectious disease.”

Sourced & published by Henry Sapiecha

Robots Designed With Insect Instincts

Science (June 28, 2010) — A swarm of flying robots soars into a blazing forest fire. With insect-like precision and agility, the machines land on tree trunks and bound over rough terrain before deploying crucial sensors and tools to track the inferno and its effects. This is a scenario that Mirko Kovac, from EPFL’s Laboratory of Intelligent Systems, thinks may not be so far off.

Swarm robotics is offering innovative solutions to real-world problems by creating a new form of artificial intelligence based on insect-like instincts. Mirko Kovac, from EPFL’s Laboratory of Intelligent Systems, is a young robotics engineer who has already made leaps forward in the field with his grasshopper-inspired jumping robot. He and his collaborators have created an innovative perching mechanism where the robot flies head first into the object, a tree for example — without being destroyed — and attaches to almost any type of surface using sharp prongs. It then detaches on command. The goal is to create robots that can travel in swarms over rough terrain to come to the aide of catastrophe victims.

“We are not blindly imitating nature, but using the same principles to possibly improve on it,” explains Kovac, who recently finished his doctoral studies as EPFL. “Simple behavioral laws such as jumping, flying and perching lead to complex control over movement without the need for high computational power.”

Jumping, gliding and perching allow for mobility over rocky territory or destroyed urban areas. This new form of AI takes its inspiration from the insect world, but is more as an abstract reflection on their instincts and design principles than merely imitating their morphology. This simplicity allows for greater mobility since the robots are not bogged down with heavy batteries. Kovac imagines swarms of his robots equipped with different sensors and small cameras that could be deployed over devastated areas to transmit essential information back to rescue command centers.

The labs most recent innovation, perching a robot, saves valuable energy by allowing the robot to rest like insects or birds do. Many previous perching mechanisms include a complicated swooping maneuver to decrease momentum and land on legs, often without the ability of detaching. The mechanism developed by Dr Kovac and Jürg Markus Germann, recently published in the Journal of Micro-Nano Mechatronics, avoids this problem by using two spring-loaded arms fitted with pins that dig into the surface, whether it is wood or concrete. The snapping of the arms creates a forward momentum, allowing for a soft deceleration of the glider and avoiding mechanical damage. A remotely controlled mini-motor then detracts the pins and allows the robot to continue on its way.

“I am fascinated by the creative process,” says Kovac, “and how it is possible to use the sophistication found in nature to create something completely new.” The perching mechanism can be easily adapted to other robots. His previous robot, a quarter-gram jumping robot that can achieve heights of up to four and a half feet, could now be fitted with the new perching mechanism as well as wings, thus creating a hybrid creature that gets around much like a flying grasshopper.

Sourced & published by Henry Sapiecha

from Predators:

Researchers Look for

Small Control Organism

Science (June 21, 2010) — One way to keep from getting eaten is to run. But recent research at the University of Guam’s Western Pacific Tropical Research Center shows that sometimes it’s better to just hide.

“The small size of an alien insect that feeds on a native tree from the western Pacific island of Guam allows it to hide in cracks and other locations that are out of reach for its only local natural enemy,” said UOG entomologist Aubrey Moore.

Moore has teamed up with UOG ecologist Thomas Marler to study the relationship between the native cycad tree, known as “fadang” in the Chamorro language, and a minute alien insect pest called cycad aulacaspis scale (CAS). The pest arrived on Guam in 2003, and then spread to Rota 50 miles north and Palau 800 miles southwest of Guam. The pest has killed 90% of Guam’s wild cycads. Findings about the ability of CAS to go undetected in secretive locations on cycad plants were published by Marler and Moore in the May issue of the journal HortScience.

The researchers have been interested in using biological control efforts to save the native fadang populations on Guam, Rota, and Palau. A predatory lady beetle that feeds on CAS was introduced to the three islands to control the pest. “Our initial Guam release was in early 2005 and the beetle established quickly and appeared to be doing a good job of controlling the scale insects by preying on them,” said Moore. But then a second epidemic outbreak of the scale pest occurred in late 2008 on Guam and early 2010 on Rota. Ecologists call this type of population behavior an “irruption” and it was this secondary increase in the pest population that caught the attention of the researchers.

“We wanted to know how the insect pest population could increase to such a serious threat level after the initial threat was brought under reasonable control by the predatory beetle,” said Marler. When some of the tiny insects find a hiding spot where they can feed and make babies without fear of being eaten by the beetle, all it takes for a sudden increase in the pest population is for the beetles to migrate away from the area after they run out of accessible scale insects.

The HortScience article also explains a more insidious outcome of this ability to hide. Cycads are valuable landscaping plants. Many species of cycads are susceptible to the pest, and the out-of-sight crannies on the plants can harbor a few undetectable scale insects. “We believe this is one of the reasons the insect has been so successful in spreading throughout many countries in recent years, as visual inspection of imported plants cannot detect the hiding insects,” said Marler.

Most programs for control of a pest that causes major agricultural or ecological damage do not rely on a single biological control organism. So the Guam team is making plans to introduce a second natural enemy of CAS. They contend that the findings about the secretive nature of the scale pest help inform what sort of natural enemy is needed on Guam and Rota. “Our work has shown that we need to find a biological control organism that is small enough to follow CAS into its tiny hiding places,” concluded Moore.

Sourced and published by Henry Sapiecha

ITHACA, N.Y. (UPI) — Spit from a caterpillar helps Colombian Andes potatoes grow larger, a finding that could benefit farmers worldwide, scientists said.

The saliva of the potato moth larvae, Tecia solanivora, increases the rate of photosynthesis in the Colombian Andes potato plant, Solanum tuberosum, researchers from Cornell University said.

More photosynthesis means more carbon is drawn into the plant, which creates more starch and larger tubers, said co-author Andre Kessler, who teaches ecology and evolutionary biology at Cornell.

The plant may be compensating for tubers lost to damage from the caterpillar, a major pest, researchers from Cornell and the National University of Colombia said in a release Thursday.

“This could be an example where the co-evolutionary arms race led to a beneficial outcome for both,” Kessler said.

Future experiments will test more commercial varieties of potatoes, as well as wild potatoes, Kessler and his team wrote in a recent issue of the journal Ecological Applications.

Received and published by Henry Sapiecha 7th June 2010

Transfer of Genetic Material

Between Blood-Sucking Insect

and Mammals

Science(Apr. 30, 2010) — Researchers at The University of Texas at Arlington have found the first solid evidence of horizontal DNA transfer, the movement of genetic material among non-mating species, between parasitic invertebrates and some of their vertebrate hosts.

The findings are published in the April 28 issue of the journal Nature, one of the world’s foremost scientific journals.

Genome biologist Cédric Feschotte and postdoctoral researchers Clément Gilbert and Sarah Schaack found evidence of horizontal transfer of transposon from a South American blood-sucking bug and a pond snail to their hosts. A transposon is a segment of DNA that can replicate itself and move around to different positions within the genome. Transposons can cause mutations, change the amount of DNA in the cell and dramatically influence the structure and function of the genomes where they reside.

“Since these bugs frequently feed on humans, it is conceivable that bugs and humans may have exchanged DNA through the mechanism we uncovered. Detecting recent transfers to humans would require examining people that have been exposed to the bugs for thousands of years, such as native South American populations,” Feschotte said.

Data on the insect and the snail provide strong evidence for the previously hypothesized role of host-parasite interactions in facilitating horizontal transfer of genetic material. Additionally, the large amount of DNA generated by the horizontally transferred transposons supports the idea that the exchange of genetic material between hosts and parasites influences their genomic evolution.

“It’s not a smoking gun, but it is as close to it as you can get,” Feschotte said

The infected blood-sucking triatomine, causes Chagas disease by passing trypanosomes (parasitic protozoa) to its host. Researchers found the bug shared transposon DNA with some hosts, namely the opossum and the squirrel monkey. The transposons found in the insect are 98 percent identical to those of its mammal hosts.

The researchers also identified members of what Feschotte calls space invader transposons in the genome of Lymnaea stagnalis, a pond snail that acts as an intermediate host for trematode worms, a parasite to a wide range of mammals.

The long-held theory is that mammals obtain genes vertically, or handed down from parents to offspring. Bacteria receive their genes vertically and also horizontally, passed from one unrelated individual to another or even between different species. Such lateral gene transfers are frequent in bacteria and essential for rapid adaptation to environmental and physiological challenges, such as exposure to antibiotics.

Until recently, it was not known horizontal transfer could propel the evolution of complex multicellular organisms like mammals. In 2008, Feschotte and his colleagues published the first unequivocal evidence of horizontal DNA transfer.

Millions of years ago, tranposons jumped sideways into several mammalian species. The transposon integrated itself into the chromosomes of germ cells, ensuring it would be passed onto future generations. Thus, parts of those mammals’ DNA did not descend from their common ancestors, but were acquired laterally from another species.

The actual means by which transposons can spread across widely diverse species has remained a mystery.

“When you are trying to understand something that occurred over thousands or millions of years ago, it is not possible to set up a laboratory experiment to replicate what happened in nature,” Feschotte said.

Instead, the researchers made their discovery using computer programs designed to compare the distribution of mobile genetic elements among the 102 animals for which entire genome sequences are currently available. Paul J. Brindley of George Washington University Medical Center in Washington, D.C., contributed tissues and DNA used to confirm experimentally the computational predictions of Feschotte’s team.

When the human genome was sequenced a decade ago, researchers found that nearly half of the human genome is derived from transposons, so this new knowledge has important ramifications for understanding the genetics of humans and other mammals.

Feschotte’s research is representative of the cutting edge research that is propelling UT Arlington on its mission of becoming a nationally recognized research institution.

Sourced and published by Henry Sapiecha 2nd May 2010

Research Targets Lethal Chagas’

Disease Spread by Insect

That Bites Lips

Science (Apr. 29, 2010) — It makes your skin crawl — a bug that crawls onto your lips while you sleep, drawn by the exhaled carbon dioxide, numbs your skin, bites, then gorges on your blood. And if that’s not insult enough, it promptly defecates on the wound-and passes on a potentially deadly disease.

Now Jean-Paul Paluzzi, a PhD candidate in biology at the University of Toronto Mississauga, believes that manipulating physiology to prevent the insects from leaving their messy calling card represents the best hope for stopping the transmission of the illness, known as Chagas’ disease.

“This is a disease of the poor,” says Paluzzi, who has visited parts of the world affected by the illness. “The bugs are found in makeshift homes with mud walls and palm tree-like ceilings. Unfortunately, the people of Central and South America that this affects don’t have sufficient voice to get help. Given that there are roughly 15 to 19 million people that are infected-a substantial proportion of that area’s population-it’s a disease that’s been neglected.”

Chagas’ disease is one of the major health problems in South and Central America and is spread by reduvid bugs, also known as “kissing bugs” because of their fondness for lips. The disease they transmit is caused by Trypanosoma cruzi, a parasite that lives in their gut. In the initial acute stage, symptoms are relatively mild, but as the disease progresses over several years, serious chronic symptoms can appear, such as heart disease and malformation of the intestines. Without treatment, it can be fatal. Currently, insecticide sprays are used to control insect populations, and anti-parasitic drugs are somewhat successful at treating acute infections.

Once the disease is chronic, it cannot be cured.

To make matters worse, kissing bugs are particularly “bloodthirsty.” In mosquitoes, which go through four distinct stages of development, only adult females feed on blood (and potentially transmit disease). This means that pest control methods need to target only one out of eight stages (when you include both sexes). But in kissing bugs, each sex feeds on blood through all fives stages of development. “So you have about a ten-fold greater chance of infection just because of the number of times that these insects have to feed,” says Paluzzi.

His research focuses on insect diuresis-more specifically, the genes and peptides that control how the kissing bug eliminates excess fluid in its gut after it gorges on blood. For the insect, the real prize in its meal is the red blood cells, while the water and salt is “excess baggage.” After they feed, the bugs are bloated and sluggish, and must jettison the waste so they can make their escape.

Here’s how it happens: when the kissing bug finds a snoozing victim and feeds, its levels of serotonin and diuretic hormones rise sharply, targeting the insect’s midgut and Malpighian tubules (the equivalent of kidneys), and triggering the release of waste. About four hours later, a peptide named CAP2b is released in the insect’s gut, abolishing the effect of the diuretic hormones.

Paluzzi has identified two genes (RhoprCAPA-alpha and RhoprCAPA-beta) that carry the chemical recipe for the peptides that stop diuresis. With that information, he hopes to create a peptide “agonist”-something that would enhance the activity of the CAP2B peptide and prevent the insect from leaving waste (and the parasite) on the wound. In theory, says Paluzzi, this might be an insecticide-like room spray or topical lotion that is biologically stable and has no effect on humans or other insects. Paluzzi is collaborating with a structural biochemist at the U.S. Food and Drug Administration in Texas, with the ultimate goal of creating a pest control solution, but he cautions that a market-ready product is many years away.

The research was funded by the Natural Sciences and Engineering Research Council of Canada, through a discovery grant to Professor Ian Orchard of the Department of Biology and a Canada Graduate Scholarship to Paluzzi.

Sourced and published by Henry Sapiecha 2nd May 2010

On Butterfly Wings

Inspire More Powerful Solar Cells