Animal code: our favorite Genomes

Every part of our bodies and every action of our cells is exquisitely controlled by the billion base pairs that make up our DNA. These nucleotides are the building blocks of genes, the part of the genome that holds the information our cells turn into proteins.

Since the first gene was suggested by Gregor Mendel in the 1860s, scientists have been searching for ways to decode them, to figure out how this code creates the end product: An organism. That organism can be an animal, plant, virus or bacteria that lives, reproduces and spreads its genome. Uncovering the secrets locked in each species' genomes will teach researchers how to harness the power of genes, from the longevity of the naked mole rate and the fat processing abilities of the orangutan.

Dozens of animal, plant and microbe genomes have been sequenced. Here are  favorite 10 genome projects.

1-Culturing cow

 

Itching for a tastier slice of beef? Look no further than the cow's genome. After being sequenced in 2009, analysis of the cow's genes could lead to higher quality milk and better beef and tells an interesting tale of how human domestication has impacted the evolution of the once-wild animal.

The analysis of the cow's 22,000 genes has also shown that while we humans are more closely related to rodents than to cows in terms of the family tree, our genome more closely resembles those of cows because the tiny lifespan of rodents requires them to have many more babies in a much quicker timeframe, accelerating evolution.

The cows also have many additional immune system genes, ones that could defend against pathogens that live in their extra stomachs. Analysis of other breeds also determined that the cows showed specific patterns of genetic changes depending on whether they were breed for meat or milk.

2-First amphibian, the African clawed frog

 

The first amphibian genome to be sequenced belongs to the frog Xenopus tropicalis, a slimy rotund amphibian also known as the African clawed frog. The genome study enables researchers to compare genes in mammals to those of the amphibians to see which genes stay the same and which have changed since mammals and amphibians parted 360 million years ago, which pinpoints the important basic genes that all complex life needs, including genes involved in the heart and lungs.

3-The tasty turkey

 

The turkey genome was published in the journal PLoS One in November of 2010, just in time for the Thanksgiving meal! The turkey clocked in at 1.1 billion base pairs, about a third the size of the human genome, and bears a close resemblance to its relative, the chicken, whose genome was completed in 2004.

This work could lead to meatier, healthier birds, according to the researchers, by providing a better understanding of the turkey's muscles and taste and can help farmers improve disease resistance and treatment.

4-Our cousin the orangutan

 

A study in the journal Nature in 2011 released the genes of the orangutan Susie (and five of her wild brethren) of the Texas Zoo. The genes revealed that orangutans have been evolving much more slowly than chimps and humans; their genes change around much less frequently. This could mean that chimps and humans have accelerated their evolution since separating from the rest of the primates.

The orangutans were evolving in one respect: Their fat breakdown molecules were changing quicker than expected. This is probably why they make better use of the energy they take in.

5-Spiny, spineless sea urchin

 

Humanity's evolutionary cousin, the spiny but spineless sea urchin, received the honor of having its genome sequenced in 2006 and published in the journal Science. Seventy percent of the urchins' 23,300 genes (made from 814 million pairs of genetic bases) are similar to those in humans, more than many other lab organisms like fruit flies.

The urchins' genes also hold details where the urchins get their unique immune system, and the secrets of their 100-year-long lives. The genes of the innate immune system, our body's first line of defense, multiplied in the urchin, giving them a larger toolbox to combat infections.

Though they lack eyes and ears, the researchers discovered that the urchins sport genes associated with vision and hearing as well as taste, smell and even balance.

6-Rhesus monkey

 

The first primate to get rocketed into space and to be cloned, the rhesus monkey, had its genome sequenced in 2007. The rhesus monkey genome has about 93 percent similarity with that of humans, which is important since it is often used in medical testing for human drugs and therapies.

The researchers identified roughly 200 genes that appear to be key players in what defines the differences between our species. These include genes involved in hair formation, sperm-egg fusion, immune response and changes to cell membrane proteins.

The rhesus monkey shows the same mysterious rearrangements that are seen in the human lineage's X chromosome following the branching off of the chimpanzee which gives us new evidence of the unusual role of this sex chromosome in primate evolution.

7-Marsupials versus mammals

 

Marsupials, our mammalian brethren, are found mostly in Australia and New Guinea. They have many weird features that separate them from other mammals, including a very short pregnancy, after which they shelter their very immature offspring in a pouch.

Sequences of the kangaroo and other marsupials have shed light on how these features have developed after the placental mammal-marsupial split 150 million years ago. The genome sequencing of an opossum and a small kangaroo species called the tammar wallaby show that the group may have evolved in South America, not Australia.

Analysis of the tammar wallaby genome indicates that large areas of the marsupial genome are similar to the genome of normal, placental mammals.

8-Nematodes

 

One of the first multi-cellular organisms to have its genome decoded, way back in 1998, the nematode is a staple in many research labs. The nematode and its simple-minded cousins have about 20,000 genes. While similar in number to those of other animals, the nematode's genome contains only 100 million base pairs of DNA; one tenth the size of an average mammalian genome.

This is because more evolved organisms tend to have more non protein coding regions that regulate how, when and how much of a gene is expressed in different types of cells, and not necessarily have more genes. This fine-tuned regulation seems to play an important part in what makes mammals and other organisms unique.

9-Human

 

The first human genome was sequenced in 2001, and currently over 60 complete human genomes have been sequenced. These include the genome of researcher J Craig Venter, James Watson (who helped discover the double helix shape of DNA), a Han Chinese, a Yoruban Nigerian, a female leukemia patient and a Korean individual.

Comparison of these genomes to the genome of the chimpanzee and other organisms and looked at which seem to disappear in humans. These genes are likely to play an important role in what makes us humans, though only one held the code for an actual protein, the rest were involved in regulation or had other functions.

They found differences in the handling of several proteins, including ones in the brain, and ones that respond to male hormones. These changes resulted in bigger brains and changes in penis shape in response to a decrease in polyandry in humans. (Many other species have specially shaped penises, sometimes with spines, to compete with the sperm of other males.)

10-The enigmatic naked mole rat

 

The newly deciphered genome of the hairless, underground-dwelling, long-lived and cancer-resistant naked mole rat could help researchers unravel the creature's secrets, and may help improve human health along the way.

The researchers found that the naked mole rat had turned off several genes related to vision since they live in the dark. They also saw a mutation in the gene dubbed "hairless," previously seen to cause baldness in mice and humans, which could explain how they lost their fur.

While a quick cursory look at the genome sequencing is already shedding light on changes that may lead to the naked mole rat's exquisite uniqueness, the information is also useful for human health. Stroke and heart attack deprive parts of the body from oxygen. Discovering how the mole rats survive in their low-oxygen burrows can help scientists design treatments to improve outcomes.

By comparing this genome with those of other mole rats, including solitary ones, scientists could also tease out how the animal's genes influence their behaviors.

Gussas monkey








In the thin mountain air of the Guassa plateau in the Ethiopian Highlands, ecologist and photographer Jeff Kerby joined anthropologist Vivek Venkataraman expedition to study the interactions between gelada monkeys and Ethiopian wolves.

"The open expanses of Ethiopia’s Afro-alpine grasslands make perfect playgrounds for juvenile gelada monkeys. Their constant chattering, play fighting, and terrible coordination are enough to divert the attention of even the most hardened field observer away from more pressing project goals.

"This young male caught my attention at the end of a long day Vivek and I had spent searching for wolves. Sitting atop a giant lobelia plant he was uncharacteristically relaxed as he gnawed on an unpalatable, latex-filled leaf. We shared a brief moment, captured here, where a mature gaze eclipsed his youthful playfulness. As soon as I clicked the shutter he promptly flopped backward off the plant, rolled awkwardly after falling about a meter, and then ran off to bite his sister."

—Jeff Kerby, photographer on expedition with Young Explorer grantee Vivek Venkataraman

New vineyards could create conservation challenges

 

How will vineyards cope with climate challenges caused by global warming?
A kangaroo stands among grapevines in a vineyard.   

Inland Australia is one of many grape-growing regions facing warmer-than-optimal temperatures due to climate change.


Could wine lovers soon be sipping Montana merlots or Beaujolais clones grown on the shores of the Baltic (map)?

 

Changing climate may well redraw the familiar map of world wine production, making it harder to grow grapes in some traditional regions while opening up new frontiers for vineyards. But satisfying our thirst for wine in a warmer world could take a toll on biodiversity, a new study suggests, if vineyard changes aren't managed carefully.

Lee Hannah, a climate change ecologist with Conservation International, and his colleagues modeled the impacts of changing climate on winemaking, an art that's fine-tuned to local climate conditions, in a study published this week in the journal Proceedings of the National Academy of Sciences.

Today's top wine-producing regions from Chile to Tuscany could see their suitable growing area reduced by as much as 20 to 70 percent by the year 2050, the study suggests.

That means some growers will likely adjust by planting new vines in previously undisturbed ecosystems at higher latitudes or higher elevations—displacing the plant and animal species currently residing there.

“This can lead to serious impacts on wildlife habitat as new areas become suitable for wine production and open up to planting,” Hannah said.

Intersection

Making matters worse is the intersection between tasty wine territory and prime habitat. Some of the top terrain for wine production is located in Mediterranean climate regions around the world boasting warm, dry summers and wet, cool winters with infrequent freezes.

These same spots are home to some of the world's greatest natural biodiversity, which may be put increasingly at risk as vineyards expand into higher elevations in search of cooler climes.

The Mediterranean Basin (map), for example, is home to more than 12,000 plants that grow nowhere else in the world. Two-thirds of its amphibians, half of its reptiles, and a quarter of its mammals are also unique to the region. (Learn more about the Mediterranean as a biodiversity hotspot.)

After native vegetation is plowed under and fields are fertilized, doused with fungicide, and prepared for planting, vineyards, on the whole, are not hospitable habitats for many native plants or animals, Hannah added.

The study's models suggest that places including northern North America and Europe, New Zealand, Tasmania, and central Chile could become newly desirable locations for vineyards by mid-century.

“The real detriment will be to those on the extremes,” said Southern Oregon University's Gregory Jones, a leading expert on wine and viticulture who was not involved in the study.

“Those growing grapes in the hotter climates where you know it's marginal, like large areas of southern Spain, parts of inland Australia, some of these places are at the limit of being too hot right now.” (Related: "Earliest Known Winery Found in Armenian Cave.")

Wine on the Range?
Indeed, the changes charted in the study aren't entirely projections, Hannah stressed—they've already begun. “Vineyards are already expanding into places like the Okanagan Valley in British Columbia,” he said.

The Rocky Mountain region near the U.S.-Canadian border is home to the ambitious Yellowstone to Yukon conservation plan that patches together habitat corridors for the region's grizzlies, wolves, pronghorn antelope, and other iconic animals. It has no real history of wine production—but a few degrees warmth could make it very enticing to growers, the study suggests.

“Right now you're looking at open ranch land which can be quite friendly to wildlife movement,” Hannah explained. “But if you start getting vineyards put in that area, bears would love to come in and eat wine grapes and browsers will eat the vines. So that's a concern for the growers, and if vineyards are fenced or animals shot, a potential barrier to wildlife movement.” (Learn about other effects climate change will have on wildlife.)

Another surprising concern is China, Hannah noted, which doesn't come to mind as a wine superpower but is already a top producer and the fastest growing of all winemaking nations. Their vineyard expansion may come at the expense of panda habitat, as the two share the same mountain ranges.

Making Preparations

Jones, who has authored studies mapping the world of wine under projected climate change, noted that while some areas didn't shift too much in his projections, others moved dramatically.

And the wine industry is already taking some steps to prepare, he said.

The industry's major corporate players, like E. & J. Gallo, Constellation, Diageo and others, use their own strategies to counter climate uncertainty.

“Big companies are probably trying to hedge their economic bets to some degree,” Jones said. “You do that by having a portfolio of wines across different regions and different climates." That way, if a hailstorm or drought hits one region, it's not likely to affect another area and your production is protected, he explained.

Jones also noted that individual growers have already begun to source vineyard locations a bit closer to the poles, a bit higher up mountainous slopes, and, in some cases, a bit closer to coastlines, which can also provide a cooling impact for their grapes.

Limited Options

But other winemakers face serious limitations on how they can adjust. Many European countries, for example, produce wines under longstanding systems of defined regions and styles.

The protections that ensure a champagne is really a champagne also limit the things winemakers can do if their local climate shifts, like altering grape varieties or moving beyond designated borders.

For this and other economic and traditional reasons, many growers will continue to tend fields even as they become hotter and drier, and Conservation International's Hannah says that could spell trouble for scarce freshwater resources.

“Remarkably, the Mediterranean regions are nearly all projected to undergo declines in rainfall,” Hannah said. “That's not universally true across the planet, but for those major wine growing regions it is true.”

At the same time as water becomes scarcer, he added, rising temperatures may make growers use more of it with increasing irrigation or misting vines to keep grapes cool.

Wine is far from the only agricultural product facing such changes, so similar water and wildlife impacts will likely be linked to many other crops as well.

Win-Win?

But wine's unique relationship with climate made it an ideal subject for study, Hannah said. “We know that this is an industry that's all about getting the climate just right, so it's a perfect place to start looking at the impacts to conservation as agriculture shifts.”

Winemakers also seem unusually capable of making the necessary adjustments to satisfy both wine lovers and wildlife, Hannah added, so consumers may well be able to have their wine and help wildlife too.

“The industry is very environmentally sensitive, very aware, and very clued into climate,” he explained.

“They're concerned about things like carbon footprints and pesticide use. The realm of looking at the wildlife habitat impacts of vineyards hasn't gotten as much attention, but with climate change, that's going to become more prevalent. Planning that in conjunction with wildlife concerns takes collective action.”

Some such action, he added, is already well under way. Chile boasts a Wine, Climate Change, and Biodiversity Program; California has a Sustainable Winegrowing Alliance; and South Africa has a Biodiversity and Wine Initiative.

Hannah suggested that China might be able to use a current forest buyback program to purchase panda habitat that is also zoned for vineyard use, ensuring their preservation.

“If we see unplanned and unchecked growth, it's unfortunately much more likely that there will be negative consequences for wildlife,” Hannah said. “But I think there are positive solutions here. If the industry can plan with conservation, there are ways both wine and wildlife can win.”

Why a Cold Spring Delays Cherry Blossom Blooming

 

It's been a dull spring for cherry blossom watchers so far. Blossoms in Philadelphia did not open until early April. Usually, the flowers appear anywhere from mid- to late March. Festivals in New York and Washington are experiencing a similar delay due to the ongoing cold and wet spring.

"Cherries and other early spring blooming plants are highly variable as to when they bloom, and it's driven totally by warmth," said Paul Meyer, executive director of the Morris Arboretum at the University of Pennsylvania.

This means that in a single city, different cherry trees will flower at different times. Those that are downtown tend to flower earlier than suburban trees — there's more pavement downtown, which creates an "urban island" heating effect when the sun heats the ground up.

Also, plants on the south side of a building tend to bloom earlier than those on the north side, because the south siders receive more sunlight.

Given the variability, "it's always a challenge in scheduling cherry blossom festivals," Meyer said. [Images: Stages of Cherry Blossom Blooming]

Longer blooms

Flowers, like all biological processes, are driven by chemistry. One chemical rule of thumb — true in most cases, but not always — is that for every 18 degrees Fahrenheit (10 degrees Celsius) increase in temperature, the amount of chemical reaction taking place, say, in a plant, doubles as particles interact more frequently. This increase in chemistry makes the flowers bloom.

During the winter, the closed cherry buds can tolerate below-freezing temperatures, Meyer said. "But as things start to warm, they will break dormancy and they will start to swell," he added.

So the lingering cold is a signal to the blossoms to stay closed for a while longer, as the reactions that will make them bloom aren't yet humming along.

The cold spring may at least produce one positive side effect: longer-lasting blooms. If exposed to high temperatures — say, in the 60s or 70s — a flower will bloom quickly and then disappear within four to five days. However, a prolonged colder temperature will cause the flowers to slow their blooms, making them last between seven and 10 days, Meyer said.

Cherry plants are pretty short-lived for trees, typically living around 40 or 50 years. Their longevity, however, depends on the species. There are some types in Japan that have been bred to last more than a century.