Prions can trigger 'stuck' wine fermentations, researchers find

A chronic problem in winemaking is "stuck fermentation," when yeast that should be busily converting grape sugar into alcohol and carbon dioxide prematurely shuts down, leaving the remaining sugar to instead be consumed by bacteria that can spoil the wine.

A team of researchers including UC Davis yeast geneticist Linda Bisson has discovered a biochemical communication system behind this problem. Working through a prion -- an abnormally shaped protein that can reproduce itself -- the system enables bacteria in fermenting wine to switch yeast from sugar to other food sources without altering the yeast's DNA.

"The discovery of this process really gives us a clue to how stuck fermentations can be avoided," said Bisson, a professor in the Department of Viticulture and Enology. "Our goal now is to find yeast strains that essentially ignore the signal initiated by the bacteria and do not form the prion, but instead power on through the fermentation."

She suggests that the discovery of this biochemical mechanism, reported Aug. 28 in the journal Cell, may also have implications for better understanding metabolic diseases, such as Type 2 diabetes, in humans.

Bacteria, yeast and fermentation

Biologists have known for years that an ancient biological circuit, based in the membranes of yeast cells, blocks yeast from using other carbon sources when the sugar glucose is present.

This circuit, known as "glucose repression," is especially strong in the yeast species Saccharomyces cerevisiae, enabling people to use that yeast for practical fermentation processes in winemaking, brewing and bread making, because it causes such efficient processing of sugar.

Prions play key role

In this study, the researchers found that the glucose repression circuit is sometimes interrupted when bacteria jump-start the replication of the prions in membranes of yeast cells. The interference of the prions causes the yeast to process carbon sources other than glucose and become less effective in metabolizing sugar, dramatically slowing down the fermentation until it, in effect, becomes "stuck."

"This type of prion-based inheritance is useful to organisms when they need to adapt to environmental conditions but not necessarily permanently," Bisson said. "In this case, the heritable changes triggered by the prions enable the yeast to also change back to their initial mode of operation if environmental conditions should change again."

The researchers demonstrated in this study that the process leading to a stuck fermentation benefits both the bacteria and the yeast. As sugar metabolism slows down, conditions in the fermenting wine become more conducive to bacterial growth, and the yeast benefit by gaining the ability to metabolize not only glucose but also other carbon sources as well -- maintaining and extending their lifespan.

Solutions for winemakers

Now that this communication mechanism between the bacteria and yeast is more clearly understood, winemakers should be better able to avoid stuck fermentations.

"Winemakers may want to alter the levels of sulfur dioxide used when pressing or crushing the grapes, in order to knock out bacteria that can trigger the processes that we now know can lead to a stuck fermentation," Bisson said. "They also can be careful about blending grapes from vineyards known to have certain bacterial strains or they could add yeast strains that have the ability to overpower these vineyard bacteria."

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The above story is based on materials provided by University of California - Davis . Note: Materials may be edited for content and length.

Cicada study discovers two genomes that function as one

Two is company, three is a crowd. But in the case of the cicada, that's a good thing.

Until a recent discovery by a University of Montana research lab, it was thought that cicadas had a symbiotic relationship with two important bacteria that live within the cells of its body. Since the insect eats a simple diet consisting solely of plant sap, it relies on these bacteria to produce the nutrients it needs for survival.

In exchange, those two bacteria, Hodgkinia and Sulcia, live comfortably inside the cicada. Since all three divvy up the nutritional roles, each member of the symbiosis is completely dependent on the others for survival.

So, where does this third-wheel bacterium come into play? That is exactly what UM microbiologist John McCutcheon and his team of colleagues stumbled upon once they started delving deeper into the genome sequence of the essential bacteria. Instead of two bacterial symbionts, they actually identified three. Sulcia was predictably still there, but they found two different kinds of Hodgkinia. What previously was thought to be a tripartite, or a three-way symbiosis, is now proven to actually be a four-way symbiosis.

Their work was published in the Aug. 28 issue of Cell, a scientific journal in an article titled "Sympatric speciation in a bacterial endosymbiont results in two genomes with the functionality of one."

The researchers discovered that Hodgkinia had subtly become more complex in what McCutcheon explained as a speciation event, in which the original lineage split to produce two separate but interdependent species of Hodgkinia.

"We just didn't expect it," McCutcheon said of this discovery. "I had thought my student made a mistake, but he proved me wrong."

It took a keen eye to identify what were actually two separate versions of the bacteria that were acting as one.

"When we looked at the genes, they were clearly closely related to each other," McCutcheon said. "If there was a broken gene in one version of Hodgkinia, it would be complete and functional on the other and visa-versa. So, the functional genes in each, when working together, seem to operate as one."

Because they only are complete when they operate as a team, they are reliant on each other just as the Sulcia, and ultimately the cicada, is reliant on their contributions to the symbiotic ecosystem.

"This is an obligate symbiosis -- all of the organisms in there need each other," McCutcheon said. "We've shown that what was once a three-way symbiosis is now a four-way symbiosis."

This unexpected discovery piqued the interest of McCutcheon, who theorizes that this evolutionary development is a result of "slop and chance." However, this accidental evolution may answer some questions about how other organisms have evolved and become more sophisticated over time.

Hodgkinia's development closely parallels that of a path of some organelles. Essentially, organelles are to cells what an organ is to the human body. Mitochondria of our own cells are organelles, and like Hodgkinia, are derived from symbiotic bacteria.

In the case of the cicada, Hodgkinia's speciation event added a new member to the symbiotic team but it did not add any new functionality to the symbiosis. McCutcheon writes in the paper that, "this process parallels what is observed in some organelles, where massive genome expansions result in little if any observable increase in function."

Understanding the development of organelles is fundamental to understanding the development of life. Because organelles arose such a long time ago, it's impossible to trace back to the specific events that allowed the organelle to become what it is today. By examining Hodgkinia's evolution, researchers in McCutcheon's lab are hoping to gain insight into the storied pasts of organelles whose history has since been erased.


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The above story is based on materials provided by The University of Montana . Note: Materials may be edited for content and length.

Zombie bacteria are nothing to be afraid of

A cell is not a soap bubble that can simply pinch in two to reproduce. The ability to faithfully copy genetic material and distribute it equally to daughter cells is fundamental to all forms of life. Even seemingly simple single-celled organisms must have the means to meticulously duplicate their DNA, carefully separate the newly copied genetic material, and delicately divide in two to ensure their offspring survive.

In eukaryotic cells such as those in plants and animals, an elaborate molecular circuitry coordinates duplication and separation of genetic material with division, much as the control knob on a washing machine coordinates agitation, rinsing and spinning. And the cellular control system, like the washing machine control system, has sensors that detect anomalies and shut things down if something is wrong.

What about bacteria? In the August 28 issue of Current Biology, Heidi A. Arjes, a doctoral student in the lab of Petra Levin, PhD, associate professor of biology in Arts & Sciences at Washington University in St. Louis, presents the first experimental data that show there are at least two fail-safe points in the bacterial cell cycle that tie DNA replication to cell division.

A cell that stumbles at either division or DNA replication can repair itself and re-enter the cell cycle. But if it does not do so quickly, the fail-safes are activated, forcing the cell to exit the cell cycle forever. It then enters a zombie-like state and is unable to reproduce even under the most favorable of conditions.

When nutrients are scarce, bacteria grow slowly, working through the cell cycle step-by-step. In nutrient rich conditions, however, bacteria take advantage of the situation to multiply as rapidly as possible, overlapping two of the steps: cell division and DNA replication -- something that never happens in eukaryotic cells.

Because of their ability to overlap these two essential processes, bacteria have been thought to lack the fail-safe mechanisms that ensure stepwise progression through reproduction in eukaryotic cells.

Understanding the mechanisms of bacterial cell-cycle control may have major payoffs for medicine. Drugs that shut down the cell cycle could be used to fight bacterial infections. Not only would they prevent bacteria from multiplying, they would prevent them from passing on resistance genes or recovering once the drug had been metabolized.

Dividing at top speed

The bacterial cell cycle begins when a newborn daughter cell elongates and begins to make another copy of its DNA. As DNA replication proceeds, a division ring, called the Z-ring, starts to assemble at mid-cell. The Z-ring recruits other molecules to form a contractile ring and, once there are at least two complete copies of the DNA, pinches the bacterial cell in two to form daughter cells.

So far the bacterial cell cycle isn't all that different from the eukaryotic cell cycle. But when bacteria find themselves in nutrient-rich conditions, they shift into high gear, doubling in size and dividing as often as once every 20 minutes. Since it takes a bacterium 40 minutes to completely copy its DNA, how can it divide once every 20 minutes?

To make everything come out right, bacteria employ "multifork replication": they initiate new rounds of DNA copying before the first round finishes. Getting a head start on DNA replication ensures at least one set of genetic material will be ready before they divide. Only the most mature DNA round must be complete before the cell divides. The other replication forks will finish in subsequent generations.

It was this overlap between replication and division that led to the traditional view that the bacterial cell cycle consists of parallel processes that are only loosely linked.

It was common sense that the processes had to be connected somehow, Levin said. After all, bacteria wait until one set of chromosomes is complete to divide. Dividing across incomplete or mingled DNA is usually lethal. "But until Heidi's data, people spoke of the bacterial cell cycle as somehow magically coordinated even though there was no mechanism for doing so. Things just somehow worked out fine even though no control system had been identified."

Blocking division blocks DNA replication

In the Current Biology article, Arjes and coworkers describe experiments that show cell division and DNA replication are not independent. New rounds of DNA replication depend on the successful completion of cell division and assembly of the division machinery at midcell depends on the initiation of DNA replication.

One set of experiments showed that after division is blocked, DNA replication gradually diminishes and, after about five generations, the bacterium reached the point of no return. In other experiments DNA replication was blocked directly. In this case, it took about three generations for the bacterium to reach the point of no return. The timing suggests DNA replication might be the event that shunts bacteria into the state of suspended animation.

What is the benefit of terminal arrest in a single-celled organism, whose main goal in life is to divide?

"It might actually be a form of altruism," Arjes said. "In nature, bacteria often exist not in isolation, but in communities. An aged or unhealthy cell that removed itself from the population would benefit the community as a whole because it would no longer compete for nutrients or produce defective daughter cells."

Zombifying bacteria Although the research firmly establishes the existence of two fail-safe points in the bacterial cell cycle, the mechanisms that ensure proper cell-cycle progression are still a mystery.

"That's the next thing we have to do," Levin said. "Figure out how the division machinery is telling the DNA replication machinery something is wrong," and how the "information that DNA replication isn't working is communicated to the division machinery."

These signaling pathways will be great targets for new antibiotic therapies. Drugs that drove bacteria past the point of no return would prevent them from proliferating, stalling an infection. Blocking DNA replication would prevent bacteria from sharing mutations that confer antibiotic resistance. "Most importantly," says Arjes, "if a bacterium has encountered a terminal cell-cycle arrest, it cannot recover even after the drug has been metabolized."

"People are already working on drugs that hit the division machinery," said Arjes. "They've done a lot of screens; in fact in our experiments we used a new drug called PC190723 that blocks division in Staphyloccus aureus. It was synthesized for us by Jared Shaw, a chemist at the University of California at Davis, and is being tested against MRSA (methicillin-resistant Staphylococcus aureus) isolates.

"Combination therapy with PC190723 and other drugs such as methicillin, an extended-spectrum penicillin antibiotic, appear to be effective against MRSA even though methicillin alone is no longer effective. The division blocker somehow sensitizes the bacteria to drugs to which they have become resistant."

The eukaryotic cell cycle has been studied for more than a century. Three scientists won the Nobel Prize for Physiology and Medicine in 2001 for figuring out the regulators that prevent the cell from dividing promiscuously and endlessly. It's even possible to play a cell cycle control game at the Nobel site,

"When I talk to people who study eukaryotic cells about our work with the bacterial cell cycle, they say, 'What? This is new? People don't know this?'" said Arjes. "But when I talk to people who study bacterial cells, they're astonished. It's a completely novel idea."

Saturday Morning Mushrooms [Aardvarchaeology]

blandsvamp Mushroom picking again this morning, this time in the area between Lakelets Skinnmossen and Knipträsket. Found more velvet and birch boletes than we cared to pick.

  • King bolete, Stensopp/Karl Johan, Boletus edulis

  • Bay bolete, Brunsopp, Boletus badius

  • Orange birch bolete, Tegelsopp, Leccinum versepelle

  • Velvet bolete, Sandsopp, Suillus variegatus

  • Chanterelle, Kantarell, Cantharellus cibarius

  • Gypsy mushroom, Rynkad tofsskivling, Rozites caperata

  • False saffron milkcap, Blodriska, Lactarius deterrimus

Why Jumper Remains the Ultimate Sci-Fi Teleportation Adventure


Ellen Datlow

Steven Gould is the author of the classic 1992 novel Jumper , about a teenage boy who discovers that he can teleport or “jump.” Whereas the 2008 film adaptation discards most of the original story in order to focus instead on action and spectacle, the book uses jumping as a powerful metaphor for needing to escape from unbearable circumstances. Moreover, the story’s frank treatment of physical and sexual abuse have made it both one of the country’s most banned books and also a favorite among many readers who identify with its young protagonist, Davy.

“I’ve had kids with abusive home lives email me and say, ‘This book saved my life,’” Gould says in Episode 116 of the Geek’s Guide to the Galaxy podcast. “Or, ‘This book let me get away, in a way that wasn’t physical, but it let me know there are other people who are having things happen that are comparable to mine, and that they got through them, and they survived, and they had a life afterward.’”

Another thing that sets Jumper apart is the rigor and consistency with which it explores the idea of teleportation. Why do Davy’s clothes come with him when he jumps? What happens if he jumps while chained to a wall? What happens to his orbital velocity when he jumps from one latitude to another? The rules laid down in Jumper form the basis for much of what happens in subsequent novels. The fourth Jumper book, Exo , explores the question of whether jumping can be used to travel into outer space. The answer is yes, which only leads to more questions, and presumably more books.

“I’m curious about where the energy comes from for jumping, for tearing holes open between various areas,” says Gould. “And if it comes from someplace, where is that, and what’s happening there?”

Listen to our complete interview with Gould in Episode 116 of Geek’s Guide to the Galaxy (above). Then stick around after the interview as guest geeks Alison Haislip, Matt London, and David Wexler join host David Barr Kirtley to discuss the Teenage Mutant Ninja Turtles.

Steven Gould on Jumper being banned:

“The two most objectionable scenes, for a parent, are on page two and on page nine. So they’re able to just pick up this book that their child has brought home from the library and turn to something that they found awful. So on page two we have a scene of impending child abuse by a parent, and then on page nine we have a scene of impending sexual assault by a group of people on that same child, and so in both cases these are the impetus for jumping. But I don’t know, for some reason some parents look at something in a book, and see something awful happening, and think if their child reads that it’s going to happen to them, which to me just doesn’t make sense. In this case we’re reading about a kid who’s run away, and I think it’s a valuable thing for people to know that maybe if you run away as a young teen, you might be subject to predation, and so you might want to think about this.”

Steven Gould on working with James Cameron:

“I was hired to both be in the room while we worked on the plots for the next three Avatar films and then I am currently working on writing corresponding books for the four movies, which includes the first movie, which has never been made into a novel. … You know, there are 12 people who’ve walked on the moon, right? There are only three people who’ve been to the bottom of the Challenger Deep, and one of those was James Cameron, so it’s safe to say that there will be water, there will be oceans, as part of these movies. … We had a lot of conversations about space travel, among other things, and one of the things I noticed was that over and over again, you know, he was talking about the potential Mars stuff, and he never said ‘manned’ mission once. Whenever he was talking about a mission that involved humans on board he would call it a ‘piloted’ mission, and I found that impressive.”

Teenage Mutant Ninja Turtles Panel

Matt London on the original Nintendo game:

“The weird thing about that game is that nothing in it except the characters of the turtles themselves have anything to do with the Ninja Turtles. You’re fighting flying robot bugs, and there are these giant steamrollers that are trying to kill you. It doesn’t make any sense at all. It was an incredibly challenging game. Some of the levels were just near-impossible. I’ve gone back and tried to play it, I still can’t beat that game. … Whoever was helping you on [the underwater bomb defusal] mission, whether it’s April or Splinter or someone, would give you hints, but the hints would always be like, ‘Yeah, you should disarm these bombs quickly,’ and it’s like, ‘Oh, thanks for your help. Appreciate it.’ … There is no reprieve in that game. It’s just punishment after punishment.”

David Wexler on toys and accessories:

“I loved the cartoons as well, clearly, but it was more than that. It was the bedsheets, the lunchboxes, it was just this mass thing. … What was cool about the Halloween costume was that it was just the armbands and the kneepads and then the nose/face mask thing, but it was kind of real. You didn’t have to wear the nose thing. You could kind of be just like a skateboarding ninja and put the kneepads over the rollerblade pads. It was kind of official. And then growing up in New York and skating around the manholes, it really felt like we were Ninja Turtles. You know, I would wear that stuff to school. … I’m embarrassed to say this, but I literally have about 40 of [the action figures] under my bed as we speak.”

David Barr Kirtley on Raphael:

“Did anyone else feel that Raphael really got the short end of the stick on that one? As a kid I always thought his weapon just seemed so much less effectual than all the other Turtles’ weapons. … I always wondered if that was why he was so angry, because he got the crummy weapon. Or if he just had to be so hyper-aggressive to compensate for his lack of range. … It was weird, when I watched the TMNT movie that came out in 2007, the computer-generated one, I walked out of that one and I was like, ‘Wow, I don’t remember Raphael being that much of a dick,’ and my friends were like, ‘No, he was.’ So I’d be curious to go back and watch the older stuff and see if Raphael was really that much of a dick.”

Alison Haislip on the new movie’s script issues:

“Remember there was that whole big controversy when Michael Bay came out and said, ‘They’re actually going to be aliens,’ and everyone’s like, ‘What do you mean they’re going to be aliens? They’re mutants. They’re not supposed to be aliens.’ So I think they shot most of the movie with the Turtles being aliens, and then had to re-adjust it so it’s like, ‘Oh no, they were mutants,’ and I think that’s why the whole backstory doesn’t quite make sense. … But the things that killed me were like, April O’Neil saves them from the lab fire and puts them in the sewer. Why would she put them in the sewer? They were her pets, kind of, and she loved those things. If I saved the four little turtles I would have just taken them home with me and kept them as pets.”

The Man Behind the Most Iconic Portraits of Skaters, Punks, and Rappers

In 1986, photographer Glen Friedman made a photo of Ice-T, his ball cap turned to the side, leaning on a chainlink fence in Hollywood. This was long before Ice-T was a big name, a TV star, a mogul married to CoCo Austin. The photo captures an innocence and vulnerability that’s now long gone.

You see the same thing in Friedman’s photo of Tony Hawk, and even in his gripping photo of Public Enemy’s Chuck D. That’s a hallmark of many of the photos Friedman made of hip-hop, punk and skating personalities in the 1970s and 1980s, just as they were cementing their places in American pop culture. The best of these portraits has been compiled in a new photo anthology called My Rules .

The thing that’s most gripping about these portraits is not how young everyone is, but how passionate they are about what they’re doing. Guy Picciotto or Ian MacKaye are possessed of an energy, an intensity so strong they almost jump out of the frame. “This is a time when people really fucking cared,” Friedman says. “Back then it wasn’t about becoming famous, it was about doing something you love.”

Friedman first photographed skaters like Tony Alva as a teenager growing up in Los Angeles. Then he started photographing punk shows and icons like Black Flag and Minor Threat. Eventually he was turned onto hip-hop by artists like Ice-T, Run DMC and Public Enemy. At the time, Friedman says he was just making pictures of what inspired him. He had no idea he was creating an important historical record of some of the era’s most influential musicians.

“Those scenes were giving vitality to my entire existence and that’s why I documented it,” says Friedman, who is now 52. “Who the fuck had any idea that any of it would be import in a year or two of when it was going down. Shit was progressing so fast you just had to roll with it.”

Over time, his work paid off as many of the people he documented allowed him into their inner circles, leading to even more intimate photos. Even now, Friedman remains friends with most of the people he’s photographed. He plays softball with Adam Horovitz of the Beastie Boys and remains close with producers Russell Simmons and Rick Rubin. Many of the artists contributed essays to My Rules that acknowledge his work.

“GEF, Glen E Friedman, is a special cat,” writes Chuck D. “The capturing of what was going on in my life and head in the times of R&B (Reagan and Bush) culminated in some epic photos at the start of my career in Public Enemy.”

There’s also a forward by friend and artist Shepard Fairy that addresses why Friedman’s photos have endured. People might think was lucky, that he happened to be in the right place at the right time. “They’ve got it wrong,” Fairy writes. “When something becomes successful and a cultural reference point, people lazily assume that greatness was its destiny. Glen was completely dedicated to the scenes he captured, to the point where he often made them the right places and times, propelling them to greatness.”

It’s rare to see the kind of raw images that Friedman made nowadays, even of artists who are just coming up. Thanks to social media, everyone is a self-promoter and all the photos that get made have a certain level of gloss. No hip-hop artist is going to stare into the camera and reveal a little of themselves like Ice-T. Instead they’re going to look exactly how they think they’re supposed to look to sell albums and every photo they take will be splashed across the internet as soon as it’s shot.

Friedman acknowledges that his in-deep approach probably wouldn’t fly in 2014. He had his moment.

“Nobody lets anything marinate anymore,” he says. “You shoot it and it’s gone.”