When American scientist Carl Woese passed away Dec. 30, 2012 at the age of 84, he left behind an outsized legacy built on the study of the world’s smallest living things. In the past several years, this field has provided dramatic new insights into the pervasive influence of microorganisms on human health, global climate and the evolution of all life on earth.

By pioneering analytical methods that have since become commonplace at biological research centers such as UC Davis, Woese and his colleagues at the University of Illinois discovered in 1977 a hitherto unrecognized third domain of life — known as the Archaea — distinct from what had been the conventional two-fold division of the living world into bacteria (prokaryotes) and everything else (eukaryotes). Not only did the discovery spark an upheaval in the scientific community, but Woese’s methods also established for the first time a tree of life that fully incorporated microbes, which occupy virtually every branch on the tree.

“He just brought a lot of order to a lot of chaos in dealing with microbes,” said John Ingraham, an emeritus professor in UC Davis’ microbiology department and who is currently writing a book on the relationships among organisms in which Woese figures prominently.

The chaos stemmed largely from the challenges microorganisms present to traditional classification schemes: Many are virtually indistinguishable when viewed through the microscope, and they have left little in the way of a fossil record of evolutionary descent. Woese’s key insight was to look deep into the molecular makeup of organisms for an identifying marker. He found it in a type of gene shared by all organisms, which codes for a component of the cell called ribosomal RNA (rRNA).

Woese compared the slight variations in the composition of rRNA gene sequences of dozens of microorganisms in order to determine their evolutionary relationships, known as phylogeny. In the course of this painstaking work, Woese found that not everything that looks like bacteria is bacteria. A special kind of microbe known to produce methane, for example, turned out to belong to an entirely new class of organisms, later named the Archaea, which then took their place on a newly established universal tree of life built entirely from genetic information.

“What’s most astounding about Carl’s discovery is that it was done in a time when sequencing was really laborious and time consuming, and so this was really a labor of love that Carl did to put these organisms on a tree and [go] out on a limb to say there’s a new domain of life,” said UC Davis microbiologist Scott Dawson, who worked with Woese last year on a study of cellular evolution. “It took a lot of courage to do that.”

At first, scientists by and large ignored or disputed Woese’s controversial results, which were first published in the November 1977 issue of the Proceedings of the National Academies of Sciences. But as Woese and his collaborators continued and refined their studies, the new methods eventually became fundamental to the study of the microbial world.

Advances in rRNA sequencing have allowed researchers to begin compiling vast libraries of genetic information on microbes sampled from environments as diverse as the human gut, sulfurous ocean vents and the inside of clouds. Jonathan Eisen, a UC Davis microbiologist who studies microbial ecology and evolution, said Woese easily deserved the Nobel Prize in Medicine or Physiology given the profound application of his work for classifying pathogenic microbes by analyzing their phylogeny.

“What he did is transform classification of microbes into a very rigorous, useful tool where you could say something about the organism and it meant something,” Eisen said. “That single-handedly led to revolutions in understanding causative agents of hundreds to thousands of diseases.”

And then there’s that third domain of life. Follow-up studies to Woese’s 1977 paper have shown that the Archaea, which are often found in extreme environments such as boiling hydrothermal pools, are more closely related to the eukaryotes — which includes the plant and animal lineages — than bacteria. Dawson said that these implications of archaeal biology are still being absorbed by the scientific community.

“[Woese] opened up a whole world of biology we didn’t know about,” Dawson said. “Still now, a lot of people don’t understand the distinction or the implications of it. When you have something that really pokes at the foundation of what we think we know, it can take a generation to get the ideas solidified.”
More information on Woese’s life and work can be found on Eisen’s blog,
phylogenomics.blogspot.com/2012/12/rip-carl-woese-collecting-posts-notes.html.

OYANG TENG can be reached at science@theaggie.org.

Since March 2010, necropsies have revealed raccoons with a significant similarity. These specimens, studied by the scientists at the UC Davis School of Veterinary Medicine and UC Davis-led California Animal Health and Food Safety Laboratory (CAHFS), all had tumors. Raccoons, with their short lives, are not known for getting tumors so it was rare to find cancer in multiple cases as the cause of death.

Through study of the tumors, researchers discovered a new virus that is believed to be the cause of these tumors. This newly described virus was named raccoon polyomavirus. Polyomaviruses are known to cause cancer under lab conditions, but since cancer usually takes time to form, little is known about their effects in natural environments.

Besides the raccoon polyomavirus virus, Linlin Li, a doctor at the Blood Systems Research Institute, also identified other animal viruses including dog kobuvirus, dog sapovirus, dog bocavirus, dog circovirus, bovine astrovirus and gray fox amdovirus.

These viruses affect many parts of the animal, including multiple parts of the intestinal tract.
“Raccoons have short life spans and generally speaking cancer is a disease more likely with age,” said Patty Pesavento, associate professor of anatomic pathology at UC Davis. “In humans the exposure to polyomavirus precedes cancer by decades. We’re not sure whether this is a transformative event caused by the virus or whether these raccoons are in some way immunocompromised (have weakened immune systems) or exposed to anthropogenic (human-made) pollutants.”

The majority of these raccoons were found in the North Coast and one in Oregon. Eleven so far were found in Northern California, including Marin and Yolo County.

“The tumor types described in these raccoons, which are tumors of the olfactory system, have never been reported in this species,” said Federico Giannitti, a researcher at the UC Davis School of Veterinary Medicine. “We can consider this a new species of emerging disease.”

However, this does not mean that it is restricted to just this area.

“Raccoons are not necropsied unless they are seen with nervous signs (signs of rabies) and there is a chance of human exposure. Necropsy with diagnostic testing is expensive and funding has to be available for disease surveillance in wildlife, which it is not in many states,” said Leslie W. Woods, professor of clinical anatomic pathology at UC Davis. “Some of the raccoons with neurologic disease are sent to veterinary diagnostic labs, and those get a full necropsy, including rabies testing. There may be many more tumors out there, but surveillance is spotty and infrequent.”

There could be other cases that simply were not fully studied due to these reasons, but it is thought that this virus remains in the West Coast.

Of course, concern arises if this is a disease capable of spreading to other species, especially humans, but according to Pesavento, this spread is doubtful.

“[It’s] very difficult to say ‘at all’ when it comes to natural disease. Viruses are very clever,” she said.

Further studies will be needed to see the connection between the virus and the formation of tumors.
Luckily, raccoons are ideal to study in this case since they have short life spans, about 2 to 3 years, which means they can provide a good model for studying the virus. Also, more research will be needed to see if humans had a part in propagating the new virus. Since raccoons exist in habitats very close to us, our actions can easily influence their lives.

These studies could be a great part of our steps toward a better understanding of cancer and how it forms.
“We finally got the complete genome of the [racoon polyomavirus], which was the basis of the following study,” Li said.

KELLY MITCHELL can be reached at science@theaggie.org.

I want to talk about something today, and I hope that it does not result in my office getting burned down. But I work in a basement, so I guess its not that much of an issue. Genetically modified crops — devil incarnate or world savior? Solution to the hunger problem, or a capitalist venture? Each of these holds a little bit of truth, and I want to explore a side of the debate that isn’t normally discussed in the press — GM crops as the good guys.

When talking about genetically modified crops, Monsanto is, for the most part, the centerpiece of conversation. Debates, if they can even be called that, are riddled with hearsay, rumors, myths, “I read this” or “I heard that.” It seems to me that most people simply have absolutely no idea what they are talking about. And those who do have some knowledge on the subject are focusing on all the wrong things.
As bad press and political heat goes, Monsanto is on the sharp end of it more often than not. The “liberal” media paints Monsanto as a mean, heartless company, set on destroying any and all competition.
So Monsanto has some rather shrewd business practices … all successful companies do. They have some of the most consistently stable stock prices on Wall Street, and have earned massive investments from both Bill Gates and Warren Buffet. So what is it about Monsanto that the public finds so appalling? Most of the arguments I have heard against this company are that Monsanto destroys the small farmer. While many small farmers are bankrupt by lawsuits with Monsanto, it is merely the result of Monsanto defending its intellectual property … to the death.

Monsanto makes a large percentage of its money from licensing patented genes to other companies. They have contracts with Dow Chemical, Syngenta, Novartis and many others. Monsanto is truly ruthless in its negotiations when licensing out its patents, and it should be.

No one is forcing these companies to license with Monsanto, no one is forcing farmers to buy Monsanto seeds. But good products cost more, and consumers (farmers and other corporations in this case) are willing to pay the premium that Monsanto charges for good products. Good products cost more. That’s business. That’s how the world works.

There is some humor I find in this situation, and that is the complete hypocrisy of the hoards of internet users who rush to vilify Monsanto. How many of the people writing about this company are typing on a computer made by Apple and manufactured by Foxconn? A computer made in factories with such terrible working conditions that Foxconn had to install bars on the windows to prevent suicides due to low pay and illegal overtime. Employees even need to sign away the right for their family or any of their descendants to sue the company in the case of death. I myself am guilty of owning multiple Apple products. I am willing to pay that premium because Apple products are beautiful and functional.

How many of these writers are wearing Nike shoes, manufactured by children paid pennies per day? I find it completely asinine that these individuals who claim to hold themselves to such a high moral standard are so selective in their moral battles. They buy a $2,000 computer and then blog about the unfairness of big corporations.

Now don’t get me wrong — I do understand that there is a fundamental difference between bad labor practices for something you wear or use, like a computer, and a genetically modified food product that you assimilate into your body. There is an intimacy related to food that does not exist with shoes or computers; the food that you eat is broken down on a molecular level and literally becomes part of you.

After doing my homework for this column, I came to the realization that there are in fact many reasons to hate, or at least avoid, Monsanto.

First, the excessive enforcement of patents. Monsanto has customers sign end-user license agreements (EULAs) that prevent the replication and even the study of their seeds. These EULAs forbid independent research and can block unflattering findings from being published.

Another frowned upon practice is the implementation of the Terminator and the Zombie. The infamous Monsanto patent #5,723,765, a.k.a., the Terminator gene, is for a gene that makes all seeds of Monsanto crops completely sterile. The Zombie gene is similar to the Terminator gene except that sterility can be reversed by spraying a chemical, made by Monsanto, that triggers fertility.

One of the last points I want to make is that the general public has an uncanny knack for remembering every mistake in history and forgetting the good parts. Monsanto is often condemned as as the manufacturer of Agent Orange and the other “Rainbow Herbicides” during the Vietnam War. What surprises me yet again about the public is that they cry murder for a chemical that was meant to kill crops, and had the unfortunate side effect of stillbirths and infant deformations, but that same public seems to develop complete amnesia regarding companies who design products with the sole purpose of taking life. There are easily close to a hundred weapons manufacturers just in the United States.

And finally, I want to talk about consumer stupidity. Hate me, don’t hate me; I really don’t care, but it is my honest opinion that the average consumer is not educated enough to know what a GMO is, or educated enough to make decisions about GMO legislation. I read dozens of bloggers’ posts about GMOs and many of them are under the idiotic impression that GMO is a chemical that is added to plants.

Monsanto may have questionable-at-best legal practices, but they have achieved the ultimate corporate success — government support the likes of which hasn’t been seen since the times of John D. Rockefeller and Standard Oil. Our government turns a relatively blind eye toward Monsanto’s activities because Monsanto has branded itself as “agents of a future prosperity that will trickle down to all.”

Let’s for one moment imagine a world without Monsanto. Without the Golden Rice engineered by Monsanto, millions of malnourished individuals would die every year of Vitamin A deficiency, and nearly half a million more from blindness caused by Vitamin A deficiency.

I am by no means suggesting that Monsanto is a good company. Their level of social standards leave much to be desired. What I am saying is that if you want to launch a campaign of hate and protest against a multinational, multi-billion dollar company, at least educate yourself enough to know what you are talking about.

And ask yourself this: Is it worth sacrificing the hundreds of thousands of lives saved every year by Monsanto’s products just to destroy the company that bankrupt the small farmer down the street?

HUDSON LOFCHIE can be reached at science@theaggie.org.

As a species, humans have historically held a unique relationship with fermented grapes. The ancient Greeks devoted an entire god’s worth of worship to them, Dionysus. For the past few millennia, the French have held the tradition of producing wine very dearly. Even wealthy Northern Californians have a longstanding history of growing, strategically smashing and, after waiting a while, drinking the contents of these berries. Such a long and colorful relationship leaves the medium of wine with a lot to be appreciated. This can be evidenced by the emergence of a multi-billion dollar wine industry. But even with all that being said, what is it about wine that people like so much anyway?

So many first-glass-of-wine stories involve a sip followed by a mild wince and a strained, “It’s really good.” And then, often unfortunately, an, “I guess I just don’t really get wine,” tends to follow. What is it about wine that draws such a large following?

Some might say that wine is an acquired taste. The flavors have nuance and intricacy. It takes a refined palate to appreciate a refined drink. These statements are popular, but don’t tell anybody much about anything, let alone appreciating wine. If anything, the language used is divisive and only associates a layer of stiffness and pomp to the industry and prevents a more widespread enjoyment of the drink.

How about some helpful advice? According to Dongha Luong, a UC Davis alumnus and enologist at Acacia Vineyards, “People generally look for a nice bouquet, nice mouth feel, a strong body that can stand the test of aging without falling apart and finish. Color and clarity are also considered, but usually aren’t as important.”

To break it down, the bouquet is the smell of the wine and the lingering scents after one drinks it. Smell is an important component of wine flavor, since the way the human body detects taste is via chemoreceptors on the tongue that send signals to the brain in the presence of specific molecules. While the thousands of taste buds on the tongue are significant in how people perceive their foods, the millions of olfactory chemoreceptors in the nose also play a crucial role. Try holding your nose the next time you eat and taste the difference.

Mouth feel, as the name would suggest, describes the characteristics of the fluid itself — whether or not a wine is viscous or watery. The mouth feel might make a glass of chardonnay seem “buttery.”

Body is a little harder to explain. When describing the body of a wine, people often refer to the tannic levels. Tannins are molecules often associated with the ripening of fruits.

“Tannins are responsible for that sour puckering taste in wines,” said Lynn Anderson, a local wine enthusiast.

People tend to describe really tannic wines, like Cabernets, as big-bodied and bold-tasting. Less tannic wines, such as Zinfandels, are usually considered semi-sweet and lighter.

Finish is the taste that lingers on after the sip is finished and leaves the drinker with something to reflect on afterwards.

Winemaking comes down to a lot more than crushing grapes, adding yeast, waiting a while and drinking what’s left. Many things like soil type, yeast genetics, even the chemistry happening in the machinery, the packing and the transport methods have to be taken into careful consideration when going from grape in the field to wine in the glass.

This end combination of flavors is the result of a careful production process that starts with growing the right grapes the right way and then processing and fermenting them under carefully monitored conditions. For instance, acids are added to wines that are intended to be crisp to give them tartness. Additionally, selecting for increased potassium carbonate makes some reds feel velvety.

According to Kathleen Go, a UC Davis alumna currently working for the Livingston Winery, the levels of added sulfurous anhydride have to be kept within strict parameters.

“Too much would cause problems of color and taste, but too little would spoil the wine,” Go said.

Ultimately, when people taste wines, they‘re looking for something in particular, whether it be a sweetness, a bitterness or even simple alcohol. In the end, the winemaking process yields a great variety of flavors enjoyed by many, once people get an idea of what they’re looking for.

ALAN LIN wants to know more about what to look for in wine and can be contacted at science@theaggie.org.

With the New Year comes resolutions to eat better, make a career change or to just be a better friend. With a high volume of birthdays approaching in the coming months, the thought of getting something for your roommate or distant friend may cross your mind, especially since you are subliminally expecting something from them. People may deny such thoughts and claim that it is all out of the goodness of their heart but studies using primates as models say otherwise.

Adrian Jaeggi, a postdoctoral researcher in anthropology at UC Santa Barbara and a junior research fellow at the campus’ SAGE Center for the Study of the Mind, conducted a study to answer the question of reciprocity — resource exchange between individuals — using chimpanzees and bonobos as his subjects.

“Many primates exchange grooming, social support or even food sharing on a reciprocal basis. Most of this reciprocity happens in the long-term fashion … the evidence for immediate exchanges is much more limited,” Jaeggi said. “This suggests that single events are negligible, and primates balance exchange over longer time frames; they have ‘friendships.’ The function of friendships is to ultimately increase reproductive success by helping the individual to have more surviving offspring.”

The researchers gave food to certain individuals in the chimpanzee and bonobo groups and then observed the success rate of other individuals depending on whether they groomed that individual prior to receiving food as a gift. The chimp group demonstrated a lot of long-term exchange rather than immediate reciprocation. Chimps have long life spans and stable social groups, thus more lasting relationships form between individuals. Because of these friendships, chimps generally shared food with their partners and friends regardless of grooming. Bonobos, however, presented a different result. The bonobo monkeys were much more likely to groom before taking food.

Jaeggi said that bonobos participated in more grooming behavior because they sought the calming effects of the endorphins.

“And there we did see an effect of grooming on sharing,” Jaeggi said in the initial press release. “Chimps would go and take food pretty confidently, but bonobos were more reticent. They’d reach out and then groom. It seemed to be that they’d groom to release tension, and then there would be these short-term reciprocal exchanges.”

As far as what these findings say about humans, they reveal clues about the distant past and why favor exchange has evolved within our society.

“[This study] suggests that friendships are an evolutionarily old feature, going back at least to our last common ancestors with chimpanzees and bonobos … Food is shared between families in order to buffer the risk of coming home empty-handed,” Jaeggi said. “This research indicates that this precondition of reciprocal relationships was already present in our last common ancestor and might have facilitated the evolution of a hunting and gathering lifestyle.”

Chris Swanson, a fourth-year anthropology student at UC Davis, commented on how Native American tribes used gift exchange as a demonstration of wealth. The tradition, known as potlatch, was reciprocated in a grander fashion by the receiving tribe and the cycle started over again.

“The potlatch was a way for leaders to strengthen their social position,” Swanson said.
Studies done on reciprocity are also related to altruism in humans. Altruism, as defined by psychology, is a motivational state with the goal of benefiting someone else’s welfare — though there is a lot of debate among and within the fields concerned with human behavior about what the underlying motive actually is.
“[We] have shown that where monetary rewards are concerned, roughly 20 percent of college students behave altruistically,” said Edmund Fantino, a professor of psychology at UCSD. “[That is] being willing to give up resources in order to give a windfall to an unknown other.”

Whether or not you are fully aware of the subconscious reasoning for why you give gifts, looking at our gift-giving behavior in our closest ancestors has given us detailed insight into the psychology and evolutionary behavior of humans. The practice of giving a cup of sugar to your neighbor may yield more than just a cup of sugar in return.

NICOLE NOGA can be reached at science@theaggie.org.