 |
|
Carnegie Mellon algorithm charts evolution of genetic networks during fruit fly life cycle
June 23, 2009PITTSBURGH-A new algorithm developed by Carnegie Mellon University computer scientists has revealed for the first time how genetic networks in the fruit fly, Drosophila melanogaster, evolve during the insect's life cycle.
Scientists have known that the relationships between fruit fly genes change over time, but existing experimental approaches can not capture the details of those changes as they occur. The new algorithm, called Tesla, incorporates machine learning techniques that now enable researchers to figure out how the rewiring of those networks takes place as the insect develops.
"Many problems in biological, social and engineering systems require us to understand the interconnections between genes, people or other entities, but directly observing the evolution of these interconnections has often been impossible because of experimental or computational limitations," said Eric P. Xing, associate professor of computer science, machine learning and language technology in Carnegie Mellon's School of Computer Science. "Researchers typically could identify only a static 'average' network within each system over a period of time, but had no way to capture time-specific 'snapshots' of the actual rewiring network topology at consecutive clock-ticks within the period.
"Our new method exploits the information sharing between the evolving networks, and makes it possible to uncover interconnections that exist for a short moment in time," Xing said. "These findings help us to understand how these networks evolve over time, respond to stimuli and sometimes become dysfunctional."
In a paper to be published online this week in the Early Edition of the Proceedings of the National Academy of Sciences, Xing and Amr Ahmed, a Ph.D. student in the Language Technology Institute, detail how the Tesla algorithm can be used to analyze not only evolving gene networks in fruit flies, but also changes in voting alliances in the U.S. Senate and shifts in the social network of the machine learning academic community.
"Once we understand the dynamics of a network, we can build models that predict how it will respond to stimuli and identify its vulnerabilities," said Xing, a member of the Ray and Stephanie Lane Center for Computational Biology at Carnegie Mellon. "In the context of cancer genetics, for instance, this dynamic network analysis could help us identify new targets for drug therapy."
In analyzing the gene networks of the fruit fly, Xing and Ahmed began with an existing database that measured the activity of 4,028 genes at 66 intervals spanning the embryonic, larval, pupal and adult periods of the fruit fly life cycle. Each of the samplings, performed with microarrays, provided a snapshot of which genes were active at the time in the large, evolving networks. The Tesla algorithm was used to determine the links between the genes in those networks at the time of the snapshot. Using a novel extension of the sparse regression technique popular in statistical inference, Tesla was able to reverse engineer the rewiring of those links, figuring out exactly how one network related to the next network in the progression. The result is the first "movie" of fruit fly gene network aging.
Because the original data set may have missed important developmental genes, it isn't yet possible to draw any strong biological conclusion from the resulting movie of gene network evolution, Xing said, but the analysis nevertheless illustrates the promising utility of Tesla.
"To our knowledge, Tesla represents the first practical and scalable method for recovering large-scale, time-varying networks underlying sociocultural and biological processes at arbitrary temporal resolutions," the authors concluded in their report.
Xing and Ahmed also used Tesla to analyze the voting record for 642 bills before the U.S. Senate in 2005 and 2006, and see how relationships between senators changed over time. Democratic and Republican senators tended to bunch together (with then-Sen. Barack Obama always connected only to other Democrats) in their voting, though there were anomalies. For instance, Sen. James Jeffords, then an independent senator from Vermont, had a voting record that was closely tied to Democrats, though around January 2006 his voting began to reflect slightly more connections with the Republicans, his original party. The votes of then-Sen. Lincoln Chafee (R-R.I.) can be seen to progressively change toward the Democrats; he subsequently became an Independent after losing re-election in 2006. The work was supported by grants from the National Science Foundation, the Defense Advanced Research Projects Agency and the Alfred P. Sloan Foundation.
Carnegie Mellon University
"Our new method exploits the information sharing between the evolving networks, and makes it possible to uncover interconnections that exist for a short moment in time," Xing said. "These findings help us to understand how these networks evolve over time, respond to stimuli and sometimes become dysfunctional."
In a paper to be published online this week in the Early Edition of the Proceedings of the National Academy of Sciences, Xing and Amr Ahmed, a Ph.D. student in the Language Technology Institute, detail how the Tesla algorithm can be used to analyze not only evolving gene networks in fruit flies, but also changes in voting alliances in the U.S. Senate and shifts in the social network of the machine learning academic community.
"Once we understand the dynamics of a network, we can build models that predict how it will respond to stimuli and identify its vulnerabilities," said Xing, a member of the Ray and Stephanie Lane Center for Computational Biology at Carnegie Mellon. "In the context of cancer genetics, for instance, this dynamic network analysis could help us identify new targets for drug therapy."
In analyzing the gene networks of the fruit fly, Xing and Ahmed began with an existing database that measured the activity of 4,028 genes at 66 intervals spanning the embryonic, larval, pupal and adult periods of the fruit fly life cycle. Each of the samplings, performed with microarrays, provided a snapshot of which genes were active at the time in the large, evolving networks. The Tesla algorithm was used to determine the links between the genes in those networks at the time of the snapshot. Using a novel extension of the sparse regression technique popular in statistical inference, Tesla was able to reverse engineer the rewiring of those links, figuring out exactly how one network related to the next network in the progression. The result is the first "movie" of fruit fly gene network aging.
Because the original data set may have missed important developmental genes, it isn't yet possible to draw any strong biological conclusion from the resulting movie of gene network evolution, Xing said, but the analysis nevertheless illustrates the promising utility of Tesla.
"To our knowledge, Tesla represents the first practical and scalable method for recovering large-scale, time-varying networks underlying sociocultural and biological processes at arbitrary temporal resolutions," the authors concluded in their report.
Xing and Ahmed also used Tesla to analyze the voting record for 642 bills before the U.S. Senate in 2005 and 2006, and see how relationships between senators changed over time. Democratic and Republican senators tended to bunch together (with then-Sen. Barack Obama always connected only to other Democrats) in their voting, though there were anomalies. For instance, Sen. James Jeffords, then an independent senator from Vermont, had a voting record that was closely tied to Democrats, though around January 2006 his voting began to reflect slightly more connections with the Republicans, his original party. The votes of then-Sen. Lincoln Chafee (R-R.I.) can be seen to progressively change toward the Democrats; he subsequently became an Independent after losing re-election in 2006. The work was supported by grants from the National Science Foundation, the Defense Advanced Research Projects Agency and the Alfred P. Sloan Foundation.
Carnegie Mellon University
Fruit Fly Current Events and Fruit Fly News RSSDeciphering the regulatory code
Embryonic development is like a well-organised building project, with the embryo's DNA serving as the blueprint from which all construction details are derived.
UM Scientists Create Fruit Fly Model to Help Unravel Genetics of Human Diabetes
As rates of obesity, diabetes, and related disorders have reached epidemic proportions in the US in recent years, scientists are working from many angles to pinpoint the causes and contributing factors involved in this public health crisis.
Circadian surprise: A heat sensor for body-clock synchronization
New research on the fruit-fly brain points to a possible mechanism by which temperature influences the body clock, according to scientists from Queen Mary, University of London.
A solution to Darwin's 'mystery of the mysteries' emerges from the dark matter of the genome
Biological species are often defined on the basis of reproductive isolation. Ever since Darwin pointed out his difficulty in explaining why crosses between two species often yield sterile or inviable progeny (for instance, mules emerging from a cross between a horse and a donkey), biologists have struggled with this question.
Scientists of the UGR obtain a bioinsecticide to control the Mediterranean fruit fly
UGR News The Mediterranean fruit fly, Ceratitis capitata, is a world plague which represents one of the most serious problems for agriculture. However, the control methods currently present in the market for this plague are ineffective.
Happy flies look for a place like home
A happy youth can influence where a fruit fly chooses to live as an adult, according to new research in the American Naturalist. The study, led by Judy Stamps from the University of California at Davis, provides new insight into how animals choose places to live and raise their young.
Fruit fly pest identified in wine grapes
A newly recognized pest in Oregon continues to concern fruit growers and researchers with the recent discovery of a Spotted Wing Drosophila fly in a sample of Willamette Valley wine grapes.
Reactive oxygen in fruit flies acts as a cell signalling mechanism for immune response
For years, health conscious people have been taking antioxidants to reduce the levels of reactive oxygen in their blood and prevent the DNA damage done by free radicals, which are the result of oxidative stress. But could excessive use of antioxidants deplete our immune systems?
Scientists pinpoint protein link to fat storage
A protein found present in all cells in the body could help scientists better understand how we store fat.
Pesky fruit flies learn from experienced females: Study
A common household nuisance, the fruit fly, is capable of intricate social learning much like that used by humans, according to new research from McMaster University.
More Fruit Fly Current Events and Fruit Fly News Articles
 |
Terro 2500 Fruit Fly Trap by Terro .5 OZ, Terro Fruit Fly Trap, Vinegar Base Attractant Is Safe Around Children & Pets, Can Be Used Indoors Or Outdoors, Safe To Use Around Food. |
 |
SpringStar - Kitchen Fruit Fly Trap by SpringStar SpringStar's fruit fly trap is an excellent way to trap fruit flies that invade your home. There are no poisons or pesticides needed to accomplish this, just our unique and innovative trap. The patented lure attracts them into the trap with a combination of food grade scents. Once in the trap, they cannot get out. Safe to use around the house. |
 |
SpringStar - Glass Fruit Fly Trap by SpringStar A stylish way to trap pesky fruit flies without using pesticides or poisons. This glass jar will catch up to 300 fruit flies and is simple to use. Comes with bait and refill bait is available to keep using the trap as long as needed. |
 |
SpringStar - Fruit Fly Lures by SpringStar This fruit fly lure is designed for use in SpringStar fruit fly traps. The food grade ingredients are safe to use and very effective at attracting fruit flies. |
 |
Pest No More Fruit Fly Trap 3 per pack by CMD Products Kills insects naturally. Since adult fruit flies are attracted to ripe or overripe fruit, garbage, etc to lay their eggs. Pest No More fruit fly trap kills adult flies. Pest No More is safe to use in the home or garden. Also effective inside garbage cans, dumpsters or compost bins. 3 traps per box. Easy to follow directions included. |
 |
Fruit Fly by Janice Tucker (Author) Fruit Fly, a light-hearted fictional love story centers around the life and eccentricities of Kate Kendall, a woman in her late forties, and her best friend Alex Renault, a gay man in his thirties. The college town of Northampton, Massachusetts comes to life with its unique setting and colorful array of characters. Kate’s previous history with men has left her untrusting and paranoid of heterosexual relationships until she meets a visiting architect who, against his better judgement, finds himself fascinated with Kate and her friends. Meanwhile, Alex’s flirtatious teasing with a handsome construction worker blossoms into true love. |
 |
Safer Brand 05140 The Pantry Pest Trap by Safer The Pantry Pest Trap uses a powerful attractant that has a strong effect on certain moths. It has been used in commercial pest control to trap a variety of moths. These include many different species: Indian meal moths, seed moths, raisin moths, almond moths, and tobacco moths. |
 |
Contech Fruit Fly Trap- Pack of 2 by Contech Contech Fruit Fly Trap- Pack of 2 Eliminate pesky fruit flies from your kitchen. Catches three times more fruit flies! Fruit flies are a common nuisance in homes, restaurants and supermarkets - anywhere fruit, vegetables or garbage bins offer a tempting place for them to lay their eggs. But now you can keep your kitchen fruit-fly free, with Contechs Fruit Fly Trap. A natural attractant entices fruit flies into the decorative trap, where a disposable sticky pad ensures they dont escape. Safe, effective, and 100% pesticide free, the Contech Fruit Fly Trap is an easy and effective way to eliminate fruit flies from your kitchen, without using harmful sprays or chemicals. The Fruit Fly Trap Features: Non Toxic Pesticide Free Eliminates adult fruit flies without harmful chemicals -... |
 |
BioCare Non-Toxic Kitchen Fruit Fly Trap - 2 Complete Traps by BioCare Kitchen Fruit Fly Trap is designed to discreetly capture the fruit flies that contaminate fruits & vegetables in your home. These effective, non-toxic traps kill fruit flies so they cannot reproduce. Dead flies remain out of sight inside the decorative container, which is similar in appearance to a spice jar and blends in with kitchen or dining room decor. Lure gives off a mild, pleasant, fruity odor that attracts fruit flies into the disposable jar where they become trapped and drown. Use trap near fruit bowls, indoor garbage cans or those places where kitchen scraps are kept. Each disposable trap will work up to six weeks under normal conditions. Completely safe for use around food products. |
 |
Sterling NFT-D Disposable Fly Control TrapWith Attractant by Sterling Say goodbye to pesky flies with the RESCUE! Fly Control Trap. It s designed to encompass the behavioral characteristics on the fly. Just open add water and hang. |
| © 2009 BrightSurf.com |