ENID, Oklahoma (Reuters) – To the untrained eye, Pollard Farms looks much like any other cattle ranch. Similar looking cows are huddled in similar looking pens. But some of the cattle here don’t just resemble each other. They are literally identical — clear down to their genes.

Of the 400-some cattle in Barry Pollard’s herd of mostly Black Angus cattle there are 22 clones, genetic copies of some of the most productive livestock the world has ever known.

Pollard, a neurosurgeon and owner of Pollard Farms, says such breeding technology is at the forefront of a new era in animal agriculture. “We’re trying to stay on the very top of the heap of quality, genetically, with animals that will gain well and fatten well, produce well and reproduce well,” Pollard told a reporter during a recent visit to his farm.

The U.S. Food and Drug Administration in 2008 approved the sale of food from clones and their offspring, stating the products are indistinguishable from that of their non-clone counterparts. Japan, the European Union, and others have followed suit.

The moves have stirred controversy about whether tinkering with nature is safe, or even ethical, prompting major food companies to swear off food products from cloned animals. But consumers are likely already eating meat and drinking milk from the offspring of clones, which are technically not clones, without even knowing it.

Farmers can now use cloning and other assisted breeding technologies to breed cows that produce bigger, better steaks or massive amounts of milk, and animals that resist diseases or reproduce with clockwork precision. Premier genes can translate to improved feeding efficiency, meaning the ability to convert the least amount of feed into the most meat or milk, which results in a smaller environmental footprint.

“If you don’t need as much corn to feed your cattle, you might be able to cut back on the amount of fertilizer put out there on the countryside that might end up in a river. You can cut the amount of diesel that’s spent raising that corn,” Pollard said. “Just like they improve the genetics of corn, so they can produce more bushels per acre, we’re trying to do that same type of thing by using cloning and superior genetics to produce more meat with less input.”

RISING FOOD DEMAND

The United Nations’ Food and Agriculture Organization has said food production will need to double by mid-century to meet demand from a growing world population, with 70 percent of that growth coming from efficiency-improving technologies. Such forecasts have prompted calls for a second Green Revolution, a rethinking of the movement championed by Norman Borlaug, who won the 1970 Nobel Peace Prize for his work in boosting grain production for starving nations.

Biotechnological advances in grain production will remain at the forefront of the global fight to alleviate hunger, although animal agriculture will likely contribute in the longer term.

“When people talk about feeding the world, reducing or eliminating hunger, I don’t think animal agriculture has much of a role to play. But, as people successfully move out of that extreme poverty, that’s when you get the growth in demand for animal protein and potentially cloning could have positive benefits,” said Robert Thomson, professor of agricultural policy at the University of Illinois.

Some animal breeds, ideally suited for arid climates, could be propagated to utilize grazing pastures unsuitable for crop production. Others may be bred to resist local maladies, like the Nguni cattle breed, which can develop resistance to ticks and immunity to tick-borne diseases.

Meanwhile, a growing and more affluent population in the developing world is seen boosting demand for meat and dairy products. Meat consumption in developing countries more than doubled from about 10 kilograms (22 pounds) per person per year in the 1960s to around 26 kg near the turn of the century, according to the FAO. By 2030, that was expected to rise to 37 kg per person. Milk and dairy product consumption has made similarly rapid growth.

SLOW ACCEPTANCE

Supporters say cloning will no doubt play a role in accelerating production, but the technology has been slow to take, primarily because of the high cost and resistance on ethical grounds. Of the more than 2.4 million Angus cattle that have been registered with the American Angus Association since 2001, only 56 were clones, according to Bryce Schumann, the group’s chief executive.

It costs at least $15,000 to clone a cow and $4,000 to clone a sow, although improving efficiencies will likely lower those costs in coming years, said Mark Walton, president of ViaGen, a company in Austin, Texas, that provides animal cloning and genomics services.

ViaGen owns the intellectual property rights to the technology that in 1996 produced Dolly the sheep, the world’s first animal cloned from an adult cell, at Scotland’s Roslin Institute. ViaGen, along with its partner company, Trans Ova Genetics of Sioux Center, Iowa, produces the vast majority of the clones in the United States. Other cloning companies are in Brazil, Argentina, Australia, and China.

Of the roughly 102 million cattle and 66 million hogs in the United States, “no more than a few thousand” are clones, according to Walton. Global numbers are around 6,000.

The most common cloning technique is called somatic cell nuclear transfer, a process in which a donor egg cell’s nucleus is removed and replaced with the nucleus (and genes) of a cell from the animal that scientists aim to duplicate. That cell is then stimulated and later implanted in a surrogate mother.

Walton said cloning is costly because it is a relatively tedious process and the technology is relatively immature, comparable to the production inefficiencies to that of the early automobile industry. Years ago, scientists were able to achieve success in only 2 or 3 percent of attempts, but ViaGen now boasts 10 to 15 percent efficiency in producing a calf. It’s aim is nearer to 60 percent, about the same as traditional in-vitro fertilization, Walton said.

CONSUMER ACCEPTANCE

Despite the steady improvement in the technology, consumer acceptance of cloning as a viable means to produce human food remains the top hurdle for breeders and cloning companies.

A survey conducted by the International Food Information Council found that half of Americans surveyed viewed animal cloning as “not very favorable” or “not at all favorable.” A similar number said they were unlikely to buy meat, milk, or eggs from offspring of cloned animals, even if the FDA says the products are safe. Other surveys have found that nearly half of consumers have moral objections to cloning.

“When you’re genetically modifying a plant, creating a seed that perhaps has a resistance to insects, that’s different than cloning, and maybe modifying a sentient being,” said Chris Waldrop, director of the Food Policy Institute at the Consumer Federation of America. “There are different ethical, religious, and moral issues that a society has to grapple with before they move forward on such a technology.”

Despite cloning’s gradually improving rate of success in producing healthy animals, the process still has a high rate of failure. Some animals are born with abnormalities and have to be euthanized and some have more health problems at birth than conventionally bred animals.

Large Offspring Syndrome also occurs more often with assisted breeding technologies like cloning. The syndrome causes the fetus to grow too large, causing problems for both the clone and the surrogate.

Opponents also say the FDA’s risk assessment was not thorough enough and a long-term, multi-generational study of cloning’s effects on food products is needed. At the very least, the products should be labeled as derived from cloning, they say.

“The largest study looked at milk from only 15 cows. Only one study used standard methods of toxicology, and that study looked at the effects of feeding 20 rats products from clones for 14 weeks,” said Jaydee Hanson, policy analyst at the Center for Food Safety, a nonprofit advocacy and research group. “We don’t think that cloning is a technology that’s ready yet, and we certainly don’t think it’s ready to be on your plate.”

The only way to definitively avoid food from clones is to buy organic products, which by the Organic Trade Association’s definition are from only traditionally bred animals, he said.

The U.S. Agriculture Department has asked the livestock industry to voluntarily keep clones out of the food supply for the moment, but the moratorium does not apply to progeny of clones. Major meat and dairy companies, such as Tyson Foods, Smithfield Foods, and Dean Foods, have said they will not accept products from clones, citing the desires of their customers.

BREEDERS, NOT FOOD

ViaGen’s Walton said cloned animals are far too valuable as breeding stock to be used for food, but that the progeny of clones are “undoubtedly already in the food chain.” However, he said, “the proportion is infinitesimally small compared to the total meat supply, a tiny little drop in the ocean.”

Still, ViaGen and the Biotechnology Industry Organization have helped to create a supply chain management program to track clones from birth to death. ViaGen also gives farmers the incentive to disclose when and where they cull a clone by holding a deposit until the clone’s owner can verify that the animal has been euthanized or slaughtered for meat.

In time, Walton said, consumers and food producers will become more comfortable with cloning, much like they have with genetically modified crops, but it will take time and it will take openness from cloning providers.

“Companies have a bottom line to protect, so they are cautious about new technologies and they are cautious about listening to their customers,” he said. “No scientist can say definitively that nothing will be different tomorrow. But, given the body of knowledge and the amount of work that’s been done, you can be extremely confident that the probability of something untoward happening is incredibly small.”

Researchers in Australia and the UK are flying the idea that insect wings could act as a model for making self-cleaning, frictionless, and superhydrophobic materials. They discuss the latest developments in their laboratories in a forthcoming issue of the International Journal of Nanomanufacturing.

Insects are incredible nanotechnologists. The surfaces of many insect wings have evolved properties materials scientists only dream of for their creations. For instance, some wings are superhydrophobic, due to a clever combination of natural chemistry and their detailed structure at the nanoscopic scale. This means that the wing cannot become wet, the tiniest droplet of water is instantly repelled. Likewise, other insect wing surfaces are almost frictionless, so that any tiny dust particles that might stick are sloughed away with minimal force.

Now, Gregory Watson of the James Cook University, in Townsville, Queensland, working with colleagues there and at Griffith University, and the universities of Queensland, and Oxford, are hoping to mimic these properties by using the surface of insect wings as a template for producing plastics, or polymeric, materials with novel surface properties.

If they are successful, they might then develop self-cleaning, water-resistant, and friction-free coatings for a wide range of machine components, construction materials, and other applications, including nano- and micro-electromechanical systems (NEMS and MEMS) and lab-on-a-chip devices for medical diagnostics and environmental sensing.

The team has carried out atomic force microscopy analysis of the surface of insect wings in order to determine the forces with which fine dust particles stick, or rather don’t stick to the wing. That work confirms that only very small forces, just a few billionths of a Newton (2 to 20 nanonewtons) are needed to shed nanoscopic dust particles. 10 Newtons is the approximate force exerted by a 1 kg bag of sugar sitting on a kitchen work surface because of gravity. 2 nN is equivalent to the downward force of 100th imposed by a single grain of sugar.

“Many of the surfaces demonstrate superhydrophobic properties and will not only reduce the effects of contact with surfaces but also promote a self-cleaning function for removing foreign bodies,” the team explains.

With that data in hand, they then used wing membrane as a “natural template” to cast a polymer surface and so duplicate the surface structure of the wing in PDMS, polydimethylsiloxane, the same type of silicone gel used in breast implants. One of the advantages of this approach is that no prior “design” of the surface of the material is needed and so the team can exploit the enormous diversity of surface types from different insects and so produce materials with specific characteristics.

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Researchers in Australia and the UK are flying the idea that insect wings could act as a model for making self-cleaning, frictionless, and superhydrophobic materials. They discuss the latest developments in their laboratories in a forthcoming issue of the International Journal of Nanomanufacturing.

Insects are incredible nanotechnologists. The surfaces of many insect wings have evolved properties materials scientists only dream of for their creations. For instance, some wings are superhydrophobic, due to a clever combination of natural chemistry and their detailed structure at the nanoscopic scale. This means that the wing cannot become wet, the tiniest droplet of water is instantly repelled. Likewise, other insect wing surfaces are almost frictionless, so that any tiny dust particles that might stick are sloughed away with minimal force.

Now, Gregory Watson of the James Cook University, in Townsville, Queensland, working with colleagues there and at Griffith University, and the universities of Queensland, and Oxford, are hoping to mimic these properties by using the surface of insect wings as a template for producing plastics, or polymeric, materials with novel surface properties.

If they are successful, they might then develop self-cleaning, water-resistant, and friction-free coatings for a wide range of machine components, construction materials, and other applications, including nano- and micro-electromechanical systems (NEMS and MEMS) and lab-on-a-chip devices for medical diagnostics and environmental sensing.

The team has carried out atomic force microscopy analysis of the surface of insect wings in order to determine the forces with which fine dust particles stick, or rather don’t stick to the wing. That work confirms that only very small forces, just a few billionths of a Newton (2 to 20 nanonewtons) are needed to shed nanoscopic dust particles. 10 Newtons is the approximate force exerted by a 1 kg bag of sugar sitting on a kitchen work surface because of gravity. 2 nN is equivalent to the downward force of 100th imposed by a single grain of sugar.

“Many of the surfaces demonstrate superhydrophobic properties and will not only reduce the effects of contact with surfaces but also promote a self-cleaning function for removing foreign bodies,” the team explains.

With that data in hand, they then used wing membrane as a “natural template” to cast a polymer surface and so duplicate the surface structure of the wing in PDMS, polydimethylsiloxane, the same type of silicone gel used in breast implants. One of the advantages of this approach is that no prior “design” of the surface of the material is needed and so the team can exploit the enormous diversity of surface types from different insects and so produce materials with specific characteristics.

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It’s official: the only thing certain in this world is taxes. That’s because death, for a tiny sea creature, is not inevitable.Turritopsis nutricul, a jellyfish-like hydrazoan, is the only animal known to be potentially immortal.

Once it reaches sexual maturity, Turritopsis looks like a tiny, transparent, many-tentacled parachute (only about 5mm in diameter) that floats freely in warm ocean waters. But when times get tough, Turritopsis can turn into a blob, anchor itself to a surface, and undergo a sort of reverse methamorphosisback to its youthful form as a stalk-like polyp. That’s like a butterfly turning back into a caterpillar. Scientists, who firstdescribed this phenomenon [pdf] in the 1990s, believeTurritopsis can repeat its life cycle indefinitely.

The trick to Turritopsis‘ infinite do-overs is a process called transdifferentiation, which turns one type of cell into another. While other animals can undergo limited transdifferentiation to regenerate organs (salamandars can regrow limbs, for example), Turritopsi is the only one that can regenerate its entire body.

Not surprisingly, the immortal Turritopsi are spreading. Native to the Caribbean oceans, Turritopsi have now been identified in waters near Spain, Italy, Japan, and the Atlantic side of Panama. Even though specimens from different locations have different numbers of tentacles (from 8 to 24), genetic tests confirm that they are of the same species. Researchers believe the creatures are criss-crossing the oceans by hitchhiking in the ballast tanks of large ships.

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It’s official: the only thing certain in this world is taxes. That’s because death, for a tiny sea creature, is not inevitable.Turritopsis nutricul, a jellyfish-like hydrazoan, is the only animal known to be potentially immortal.

Once it reaches sexual maturity, Turritopsis looks like a tiny, transparent, many-tentacled parachute (only about 5mm in diameter) that floats freely in warm ocean waters. But when times get tough, Turritopsis can turn into a blob, anchor itself to a surface, and undergo a sort of reverse methamorphosisback to its youthful form as a stalk-like polyp. That’s like a butterfly turning back into a caterpillar. Scientists, who firstdescribed this phenomenon [pdf] in the 1990s, believeTurritopsis can repeat its life cycle indefinitely.

The trick to Turritopsis‘ infinite do-overs is a process called transdifferentiation, which turns one type of cell into another. While other animals can undergo limited transdifferentiation to regenerate organs (salamandars can regrow limbs, for example), Turritopsi is the only one that can regenerate its entire body.

Not surprisingly, the immortal Turritopsi are spreading. Native to the Caribbean oceans, Turritopsi have now been identified in waters near Spain, Italy, Japan, and the Atlantic side of Panama. Even though specimens from different locations have different numbers of tentacles (from 8 to 24), genetic tests confirm that they are of the same species. Researchers believe the creatures are criss-crossing the oceans by hitchhiking in the ballast tanks of large ships.

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An entry at the WAN Awards 2009, the Frame Hotel is a simple yet modern structure that pioneers a new form of architectural design to create an imposing aesthetics while sustaining the environment. Designed for Villamoda Galleries in Dubai, UAE, the structure accommodates a vast vertical garden enclosed in a huge frame, which apart from limiting the built-up areas also determines the exterior facade of the massive hotel building. Featuring a plant-like structure cut out from the constructive frame, the architecture is covered by perpendicular planes of solar protected dark glass to create a dynamic parallaxical vision, while protecting the structure from sun and wind.

Housing various restaurants, showrooms, a cigar lounge, all connected by mechanical pathways and vertigo-inspiring escalators, the structure looks like an urban jungle and invites guests to enjoy fresh and green surroundings in the desert.

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Start uga_preg_callback: Array Get tracker for full url Start uga_track_full_url: www.worldarchitecturenews.com/index.php?fuseaction=wanappln.showawardinformations Start uga_is_url_internal: www.worldarchitecturenews.com/index.php?fuseaction=wanappln.showawardinformations Start uga_get_option: internal_domains uga_options: array ( 'internal_domains' => 'www.humacon.org,humacon.org', 'account_id' => 'UA-10399907-2', 'enable_tracker' => true, 'track_adm_pages' => false, 'ignore_users' => true, 'max_user_level' => '8', 'footer_hooked' => true, 'filter_content' => true, 'filter_comments' => true, 'filter_comment_authors' => true, 'track_ext_links' => true, 'prefix_ext_links' => '/outgoing/', 'track_files' => true, 'prefix_file_links' => '/downloads/', 'track_extensions' => 'gif,jpg,jpeg,bmp,png,pdf,mp3,wav,phps,zip,gz,tar,rar,jar,exe,pps,ppt,xls,doc', 'track_mail_links' => true, 'prefix_mail_links' => '/mailto/', 'debug' => true, 'check_updates' => true, 'version_sent' => '1.6.0', 'advanced_config' => true, ) Ending uga_get_option: internal_domains (www.humacon.org,humacon.org) Checking hostname www.humacon.org Checking hostname humacon.org Ending uga_is_url_internal: Get tracker for external URL Start uga_track_external_url: www.worldarchitecturenews.com/index.php?fuseaction=wanappln.showawardinformations Start uga_get_option: track_ext_links uga_options: array ( 'internal_domains' => 'www.humacon.org,humacon.org', 'account_id' => 'UA-10399907-2', 'enable_tracker' => true, 'track_adm_pages' => false, 'ignore_users' => true, 'max_user_level' => '8', 'footer_hooked' => true, 'filter_content' => true, 'filter_comments' => true, 'filter_comment_authors' => true, 'track_ext_links' => true, 'prefix_ext_links' => '/outgoing/', 'track_files' => true, 'prefix_file_links' => '/downloads/', 'track_extensions' => 'gif,jpg,jpeg,bmp,png,pdf,mp3,wav,phps,zip,gz,tar,rar,jar,exe,pps,ppt,xls,doc', 'track_mail_links' => true, 'prefix_mail_links' => '/mailto/', 'debug' => true, 'check_updates' => true, 'version_sent' => '1.6.0', 'advanced_config' => true, ) Ending uga_get_option: track_ext_links (1) Tracking external links enabled Start uga_get_option: prefix_ext_links uga_options: array ( 'internal_domains' => 'www.humacon.org,humacon.org', 'account_id' => 'UA-10399907-2', 'enable_tracker' => true, 'track_adm_pages' => false, 'ignore_users' => true, 'max_user_level' => '8', 'footer_hooked' => true, 'filter_content' => true, 'filter_comments' => true, 'filter_comment_authors' => true, 'track_ext_links' => true, 'prefix_ext_links' => '/outgoing/', 'track_files' => true, 'prefix_file_links' => '/downloads/', 'track_extensions' => 'gif,jpg,jpeg,bmp,png,pdf,mp3,wav,phps,zip,gz,tar,rar,jar,exe,pps,ppt,xls,doc', 'track_mail_links' => true, 'prefix_mail_links' => '/mailto/', 'debug' => true, 'check_updates' => true, 'version_sent' => '1.6.0', 'advanced_config' => true, ) Ending uga_get_option: prefix_ext_links (/outgoing/) Ending uga_track_external_url: www.worldarchitecturenews.com/index.php?fuseaction=wanappln.showawardinformations Ending uga_track_full_url: /outgoing/www.worldarchitecturenews.com/index.php?fuseaction=wanappln.showawardinformations Adding onclick attribute for /outgoing/www.worldarchitecturenews.com/index.php?fuseaction=wanappln.showawardinformations Ending uga_preg_callback: WAN Awards 2009 Ending uga_filter:

An entry at the WAN Awards 2009, the Frame Hotel is a simple yet modern structure that pioneers a new form of architectural design to create an imposing aesthetics while sustaining the environment. Designed for Villamoda Galleries in Dubai, UAE, the structure accommodates a vast vertical garden enclosed in a huge frame, which apart from limiting the built-up areas also determines the exterior facade of the massive hotel building. Featuring a plant-like structure cut out from the constructive frame, the architecture is covered by perpendicular planes of solar protected dark glass to create a dynamic parallaxical vision, while protecting the structure from sun and wind.

Housing various restaurants, showrooms, a cigar lounge, all connected by mechanical pathways and vertigo-inspiring escalators, the structure looks like an urban jungle and invites guests to enjoy fresh and green surroundings in the desert.

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Emory University researchers have identified the first fish known to have switched from ultraviolet vision to violet vision, or the ability to see blue light. The discovery is also the first example of an animal deleting a molecule to change its visual spectrum.

The scabbardfish (Lepidopus fitchi) is now the only fish known to have switched from ultraviolet to violet vision, or the ability to see blue light. (Credit: Carol Clark, Emory University)

Their findings on scabbardfish, linking molecular evolution to functional changes and the possible environmental factors driving them, were published Oct. 13 in the Proceedings of the National Academy of Sciences.

“This multi-dimensional approach strengthens the case for the importance of adaptive evolution,” says evolutionary geneticist Shozo Yokoyama, who led the study. “Building on this framework will take studies of natural selection to the next level.”

The research team included Takashi Tada, a post-doctoral fellow in biology, and Ahmet Altun, a post-doctoral fellow in biology and computational chemistry.

Vision ‘like a painting’

For two decades, Yokoyama has done groundbreaking work on the adaptive evolution of vision in vertebrates. Vision serves as a good study model, since it is the simplest of the sensory systems. For example, only four genes are involved in human vision.

“It’s amazing, but you can mix together this small number of genes and detect a whole color spectrum,” Yokoyama says. “It’s just like a painting.”

The common vertebrate ancestor possessed UV vision. However, many species, including humans, have switched from UV to violet vision, or the ability to sense the blue color spectrum.

From the ocean depths

Fish provide clues for how environmental factors can lead to such vision changes, since the available light at various ocean depths is well quantified. All fish previously studied have retained UV vision, but the Emory researchers found that the scabbardfish has not. To tease out the molecular basis for this difference, they used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.

“Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted,” Yokoyama says.

More examples likely

“The finding implies that we can find more examples of a similar switch to violet vision in different fish lineages,” he adds. “Comparing violet and UV pigments in fish living in different habitats will open an unprecedented opportunity to clarify the molecular basis of phenotypic adaptations, along with the genetics of UV and violet vision.”

Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light.

A framework for evolutionary biology

Last year, Yokoyama and collaborators completed a comprehensive project to track changes in the dim-light vision protein opsin in nine fish species, chameleons, dolphins and elephants, as the animals spread into new environments and diversified over time. The researchers found that adaptive changes occur by a small number of amino acid substitutions, but most substitutions do not lead to functional changes.

Their results provided a reference framework for further research, and helped bring to light the limitations of studies that rely on statistical analysis of gene sequences alone to identify adaptive mutations in proteins.

“Evolutionary biology is filled with arguments that are misleading, at best,” Yokoyama says. “To make a strong case for the mechanisms of natural selection, you have to connect changes in specific molecules with changes in phenotypes, and then you have to connect these changes to the living environment.”

Start uga_in_feed Ending uga_in_feed: Start uga_track_user Start uga_get_option: ignore_users uga_options: array ( 'internal_domains' => 'www.humacon.org,humacon.org', 'account_id' => 'UA-10399907-2', 'enable_tracker' => true, 'track_adm_pages' => false, 'ignore_users' => true, 'max_user_level' => '8', 'footer_hooked' => true, 'filter_content' => true, 'filter_comments' => true, 'filter_comment_authors' => true, 'track_ext_links' => true, 'prefix_ext_links' => '/outgoing/', 'track_files' => true, 'prefix_file_links' => '/downloads/', 'track_extensions' => 'gif,jpg,jpeg,bmp,png,pdf,mp3,wav,phps,zip,gz,tar,rar,jar,exe,pps,ppt,xls,doc', 'track_mail_links' => true, 'prefix_mail_links' => '/mailto/', 'debug' => true, 'check_updates' => true, 'version_sent' => '1.6.0', 'advanced_config' => true, ) Ending uga_get_option: ignore_users (1) Start uga_get_option: max_user_level uga_options: array ( 'internal_domains' => 'www.humacon.org,humacon.org', 'account_id' => 'UA-10399907-2', 'enable_tracker' => true, 'track_adm_pages' => false, 'ignore_users' => true, 'max_user_level' => '8', 'footer_hooked' => true, 'filter_content' => true, 'filter_comments' => true, 'filter_comment_authors' => true, 'track_ext_links' => true, 'prefix_ext_links' => '/outgoing/', 'track_files' => true, 'prefix_file_links' => '/downloads/', 'track_extensions' => 'gif,jpg,jpeg,bmp,png,pdf,mp3,wav,phps,zip,gz,tar,rar,jar,exe,pps,ppt,xls,doc', 'track_mail_links' => true, 'prefix_mail_links' => '/mailto/', 'debug' => true, 'check_updates' => true, 'version_sent' => '1.6.0', 'advanced_config' => true, ) Ending uga_get_option: max_user_level (8) Tracking user with level 0 Ending uga_track_user: 1 Calling preg_replace_callback: ]*?)href\s*=\s*['"](.*?)['"]([^>]*)>(.*?) Ending uga_filter:

Emory University researchers have identified the first fish known to have switched from ultraviolet vision to violet vision, or the ability to see blue light. The discovery is also the first example of an animal deleting a molecule to change its visual spectrum.

The scabbardfish (Lepidopus fitchi) is now the only fish known to have switched from ultraviolet to violet vision, or the ability to see blue light. (Credit: Carol Clark, Emory University)

Their findings on scabbardfish, linking molecular evolution to functional changes and the possible environmental factors driving them, were published Oct. 13 in the Proceedings of the National Academy of Sciences.

“This multi-dimensional approach strengthens the case for the importance of adaptive evolution,” says evolutionary geneticist Shozo Yokoyama, who led the study. “Building on this framework will take studies of natural selection to the next level.”

The research team included Takashi Tada, a post-doctoral fellow in biology, and Ahmet Altun, a post-doctoral fellow in biology and computational chemistry.

Vision ‘like a painting’

For two decades, Yokoyama has done groundbreaking work on the adaptive evolution of vision in vertebrates. Vision serves as a good study model, since it is the simplest of the sensory systems. For example, only four genes are involved in human vision.

“It’s amazing, but you can mix together this small number of genes and detect a whole color spectrum,” Yokoyama says. “It’s just like a painting.”

The common vertebrate ancestor possessed UV vision. However, many species, including humans, have switched from UV to violet vision, or the ability to sense the blue color spectrum.

From the ocean depths

Fish provide clues for how environmental factors can lead to such vision changes, since the available light at various ocean depths is well quantified. All fish previously studied have retained UV vision, but the Emory researchers found that the scabbardfish has not. To tease out the molecular basis for this difference, they used genetic engineering, quantum chemistry and theoretical computation to compare vision proteins and pigments from scabbardfish and another species, lampfish. The results indicated that scabbardfish shifted from UV to violet vision by deleting the molecule at site 86 in the chain of amino acids in the opsin protein.

“Normally, amino acid changes cause small structure changes, but in this case, a critical amino acid was deleted,” Yokoyama says.

More examples likely

“The finding implies that we can find more examples of a similar switch to violet vision in different fish lineages,” he adds. “Comparing violet and UV pigments in fish living in different habitats will open an unprecedented opportunity to clarify the molecular basis of phenotypic adaptations, along with the genetics of UV and violet vision.”

Scabbardfish spend much of their life at depths of 25 to 100 meters, where UV light is less intense than violet light, which could explain why they made the vision shift, Yokoyama theorizes. Lampfish also spend much of their time in deep water. But they may have retained UV vision because they feed near the surface at twilight on tiny, translucent crustaceans that are easier to see in UV light.

A framework for evolutionary biology

Last year, Yokoyama and collaborators completed a comprehensive project to track changes in the dim-light vision protein opsin in nine fish species, chameleons, dolphins and elephants, as the animals spread into new environments and diversified over time. The researchers found that adaptive changes occur by a small number of amino acid substitutions, but most substitutions do not lead to functional changes.

Their results provided a reference framework for further research, and helped bring to light the limitations of studies that rely on statistical analysis of gene sequences alone to identify adaptive mutations in proteins.

“Evolutionary biology is filled with arguments that are misleading, at best,” Yokoyama says. “To make a strong case for the mechanisms of natural selection, you have to connect changes in specific molecules with changes in phenotypes, and then you have to connect these changes to the living environment.”

Start uga_filter:

A 21-year Michigan State University experiment that distills the essence of evolution in laboratory flasks not only demonstrates natural selection at work, but could lead to biotechnology and medical research advances, researchers said.

E. coli cultures in the laboratory of Michigan State University evolutionary biologist Richard Lenski. (Credit: Greg Kohuth, Michigan State University)

Charles Darwin’s seminal Origin of Species first laid out the case for evolution exactly 150 years ago. Now, MSU professor Richard Lenski and colleagues document the process in their analysis of 40,000 generations of bacteria, published this week in the international science journal Nature.

Lenski, Hannah Professor of Microbial Ecology at MSU, started growing cultures of fast-reproducing, single-celled E. coli bacteria in 1988. If a genetic mutation gives a cell an advantage in competition for food, he reasoned, it should dominate the entire culture. While Darwin’s theory of natural selection is supported by other studies, it has never before been studied for so many cycles and in such detail.

“It’s extra nice now to be able to show precisely how selection has changed the genomes of these bacteria, step by step over tens of thousands of generations,” Lenski said.

Lenski’s team periodically froze bacteria for later study, and technology has since developed to allow complete genetic sequencing. By the 20,000-generation midpoint, researchers discovered 45 mutations among surviving cells. Those mutations, according to Darwin’s theory, should have conferred some advantage, and that’s exactly what the researchers found.

The results “beautifully emphasize the succession of mutational events that allowed these organisms to climb toward higher and higher efficiency in their environment,” noted Dominique Schneider, a molecular geneticist at the Université Joseph Fourier in Grenoble, France.

Lenski’s long-running experiment itself is uniquely suited to answer some critical questions — such as whether rates of change in a bacteria’s genome move in tandem with its fitness to survive.

“The coupling between genomic and adaptive evolution is complex and can be counterintuitive,” Lenski concluded. “The genome was evolving along at a surprisingly constant rate, even as the adaptation of the bacteria slowed down a lot. But then suddenly the mutation rate jumped way up, and a new dynamic relationship was established.”

A mutation involved in DNA metabolism arose around generation 26,000, causing the mutation rate everywhere else in the genome to increase dramatically. The number of mutations jumped to 653 by generation 40,000, but researchers surmise that most of the late-evolving mutations were not helpful to the bacteria.

Gene mutations involved in human DNA replication are involved in some cancers. Many of the patterns observed in the experiment also occur in certain microbial infections, “and cancer progression is a fundamentally similar evolutionary process,” observed collaborator Jeffrey Barrick. “So what we learn here can help us better understand the course of these diseases.”

Barrick, a postdoctoral researcher in MSU’s Department of Microbiology and Molecular Genetics, developed computational tools to discover and validate often complex mutations. “We know an astounding amount about the details of evolution in these little Erlenmeyer flasks,” he said.

The Nature paper involved collaboration with scientists from South Korea as well as France and MSU. The research, said genomics team leader Jihyun Kim of the Korea Research Institute of Bioscience and Biotechnology, “is not only useful in understanding the tempo and mode of evolution, but can serve as a nice framework for practical applications in biotechnology, such as improving the performance or productivity of an industrial strain.”

Thousands of generations later, the MSU experiment continues to evolve. “Like a lot of science, our study answers some questions but raises many others,” Lenski said.

The research has been supported by the National Science Foundation and the Defense Advanced Research Projects Agency.

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A 21-year Michigan State University experiment that distills the essence of evolution in laboratory flasks not only demonstrates natural selection at work, but could lead to biotechnology and medical research advances, researchers said.

E. coli cultures in the laboratory of Michigan State University evolutionary biologist Richard Lenski. (Credit: Greg Kohuth, Michigan State University)

Charles Darwin’s seminal Origin of Species first laid out the case for evolution exactly 150 years ago. Now, MSU professor Richard Lenski and colleagues document the process in their analysis of 40,000 generations of bacteria, published this week in the international science journal Nature.

Lenski, Hannah Professor of Microbial Ecology at MSU, started growing cultures of fast-reproducing, single-celled E. coli bacteria in 1988. If a genetic mutation gives a cell an advantage in competition for food, he reasoned, it should dominate the entire culture. While Darwin’s theory of natural selection is supported by other studies, it has never before been studied for so many cycles and in such detail.

“It’s extra nice now to be able to show precisely how selection has changed the genomes of these bacteria, step by step over tens of thousands of generations,” Lenski said.

Lenski’s team periodically froze bacteria for later study, and technology has since developed to allow complete genetic sequencing. By the 20,000-generation midpoint, researchers discovered 45 mutations among surviving cells. Those mutations, according to Darwin’s theory, should have conferred some advantage, and that’s exactly what the researchers found.

The results “beautifully emphasize the succession of mutational events that allowed these organisms to climb toward higher and higher efficiency in their environment,” noted Dominique Schneider, a molecular geneticist at the Université Joseph Fourier in Grenoble, France.

Lenski’s long-running experiment itself is uniquely suited to answer some critical questions — such as whether rates of change in a bacteria’s genome move in tandem with its fitness to survive.

“The coupling between genomic and adaptive evolution is complex and can be counterintuitive,” Lenski concluded. “The genome was evolving along at a surprisingly constant rate, even as the adaptation of the bacteria slowed down a lot. But then suddenly the mutation rate jumped way up, and a new dynamic relationship was established.”

A mutation involved in DNA metabolism arose around generation 26,000, causing the mutation rate everywhere else in the genome to increase dramatically. The number of mutations jumped to 653 by generation 40,000, but researchers surmise that most of the late-evolving mutations were not helpful to the bacteria.

Gene mutations involved in human DNA replication are involved in some cancers. Many of the patterns observed in the experiment also occur in certain microbial infections, “and cancer progression is a fundamentally similar evolutionary process,” observed collaborator Jeffrey Barrick. “So what we learn here can help us better understand the course of these diseases.”

Barrick, a postdoctoral researcher in MSU’s Department of Microbiology and Molecular Genetics, developed computational tools to discover and validate often complex mutations. “We know an astounding amount about the details of evolution in these little Erlenmeyer flasks,” he said.

The Nature paper involved collaboration with scientists from South Korea as well as France and MSU. The research, said genomics team leader Jihyun Kim of the Korea Research Institute of Bioscience and Biotechnology, “is not only useful in understanding the tempo and mode of evolution, but can serve as a nice framework for practical applications in biotechnology, such as improving the performance or productivity of an industrial strain.”

Thousands of generations later, the MSU experiment continues to evolve. “Like a lot of science, our study answers some questions but raises many others,” Lenski said.

The research has been supported by the National Science Foundation and the Defense Advanced Research Projects Agency.

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