Autophagy 101

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Every well-run house needs someone to clean up the clutter, prune the hedges, and rake up the leaves, even whip up something to eat when the refrigerator is empty. In the life of a cell, those kinds of jobs are handled by an incredible process called autophagy.

Biologists first observed autophagy in the early 1960s as a mechanism by which cells break down their own components and recycle the parts. Autophagy, which literally means “to eat oneself,” is essential to cell survival, particularly when food is scarce.

But there’s a much larger role for autophagy than just helping a cell survive starvation. The process helps cells dispose of malfunctioning parts, clean up clutter, and defend against invading pathogens.

Mitochondria 101

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“In the depths of history, a free-living bacterium was engulfed by a larger cell and was neither digested nor destroyed. Instead, it was domesticated. It forged a unique and fateful partnership with its host, eventually becoming the mitochondria of today.” – Ed Yong, Not Exactly Rocket Science, Discover Magazine

Mitochondria are the parts of our cells that we often call the “powerhouse.” Without them, animal cells wouldn’t have the energy they need to sustain life. A mitochondrion is surrounded by two membrane layers, kind of like a little pillow encased in two pillowcases. The inner pillowcase is where most of the action takes place. It’s ruffled, which provides more surface area for the series of chemical reactions that generate ATP, the cell’s currency. Like money, you have to have ATP in order to do things. Cells can cash in ATP to divide, make new proteins, process cellular waste, store fat or do anything else they need to survive (see DNA 101 and Proteins 101).

Because of their role in maintaining a cell’s fuel and energy balance, mitochondria are the subject of intense scrutiny by scientists interested in the molecular underpinnings of metabolism, obesity, diabetes and cancer. But mitochondria also play a role in cell death. Some cells are long-lived (like neurons in the brain), while others turn over quickly (think skin cells). Either way, the process of cellular suicide – called apoptosis – has to be carefully managed in order to both avoid untimely demise and prevent cells from living too long. When called upon, mitochondrial proteins leak out through the outer membrane and into the cell’s cytosol, where they remove the molecular brakes that normally promote survival and activate caspases, enzymes that execute apoptosis. When mitochondrial function or apoptosis go awry, disease can develop – too much cell death causes neurodegenerative diseases like Alzheimer’s, while too little allows cancer cells to avoid destruction.

The couch potato effect

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A surprising new model for studying muscle function was unveiled this week: the couch potato mouse. While these mice maintain normal activity and body weight, they don’t have the energy to exercise. In the December 1 issue of the journal Cell Metabolism, Dr. Daniel Kelly, Dr. Christoph Zechner and their colleagues reportwhat happens when muscle tissue lacks PGC-1, a protein coactivator that muscles need to convert fuel into energy.“Part of our interest in understanding the factors that allow muscles to exercise is the knowledge that whatever this machinery is, it becomes inactive in obesity, aging, diabetes and other chronic conditions that affect mobility,” explains Dr. Kelly, scientific director at Sanford-Burnham’s Lake Nona campus.

Normally, physical stimulation boosts PGC-1 activity in muscle cells, which switches on genes that increase fuel storage, ultimately leading to “trained” muscle (the physical condition most people hope to attain through exercise). In obese people, PGC-1 levels drop, possibly further reducing a person’s capacity to exercise – creating a vicious cycle. In this study, mice without muscle PGC-1 looked normal and walked around without difficulty, but could not run on a treadmill.

Super-sized Fruit Flies

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It’s no secret that being overweight is hard on the heart – many studies have shown that heavier people are more likely to suffer from heart disease. But why, exactly? What does fat have to do with your heart?

There are numerous causes of obesity and other risk factors for heart disease, making it difficult to tease them apart. So a team led by Drs. Sean Oldham, Rolf Bodmer and Ryan Birse created a simple model to study the genes linking high-fat diet, obesity and heart dysfunction. Using fruit flies, they discovered that a protein called TOR influences fat accumulation in the heart. Their study, published November 3 in the journal Cell Metabolism, also demonstrates that manipulating TOR protects the hearts of obese flies from damage caused by high-fat diets.

Mitochondria Lovers Unite!

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What’s so great about working at Sanford-Burnham? For many scientists, it boils down to two things: our collaborative spirit and the freedom to pursue new ideas. Here’s my new favorite example of both.

While chatting at a retreat last spring, a few researchers decided they wanted to maintain the small community feeling the Institute is known for, even as we continue to expand. And so the Institute’s postdoctoral association, the Sanford-Burnham Science Network, initiated an effort to promote informal research interest groups—small clubs of scientists studying any number of different systems or diseases, but united by a common interest.

Shortly after tossing around the idea, they held the first meeting of the first club, now called the Sanford-Burnham Mitochondria Research Interest Group (MRIG). (You might remember mitochondria from ninth grade biology – the organelles often referred to as the “powerhouse” because they generate the energy that helps cells survive and function properly.)

“Mitochondria are a growing area of interest at the Institute, more recently for myself and others, and sometimes the right techniques or protocols and reagents can be hard to find. Troubleshooting on your own can be even more frustrating,” explains Dr. Eric Lau, MRIG co-founder and postdoctoral researcher in Dr. Ze’ev Ronai’s laboratory. “So this group calls together all mitochondrial enthusiasts to meet regularly to share their own research stories, their successes, failures, frustrations…..in order to build a stronger mitochondrial research subcommunity here.”

Targeting mitochondria to combat obesity

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How is fat tissue from an obese person different from a thin person’s fat tissue? Dr. Sheila Collins and her colleagues at Sanford-Burnham’s Diabetes and Obesity Research Centerrecently discovered one major distinguishing feature – fat tissue from obese people doesn’t oxidize fatty acids as well as that from thinner people.Fat cells use fatty acids for energy. But in response to adrenaline, fat tissue can also release fatty acids into the bloodstream for use by other tissues, such as heart and muscle. This latest study, published in the journal Diabetes, revealed that obese fat tissue was not as good as non-obese fat tissue at consuming fatty acids for energy. This might be one of the reasons why obese fat tissue releases more fatty acids into the bloodstream.  And although fatty acids are an important source of energy for other tissues, too much of it in the blood – a condition frequently seen in obesity – is believed to lead to type 2 diabetes and cause detrimental heart problems.

A balance of fat and sugar

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Diabetes results from a lack of functioning insulin, a hormone that stimulates cells to take up glucose (a type of sugar) from the bloodstream. Cells need glucose as fuel to produce energy. Type 1 diabetics lack insulin because their immune systems destroy the pancreatic cells that produce it. In type 2 diabetics, cells no longer respond properly to insulin. Either way, without sugar that can be converted to energy, cells starve and glucose levels build up in the blood, which can lead to life-threatening complications such as heart disease.

“When mice – or people – eat too much fat, they become obese and increasingly resistant to insulin, an early sign of type 2 diabetes,” explained Dr. Julio Ayala, assistant professor at Sanford-Burnham’s Lake Nona campus.

“Fat” man

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Dr. Philip Wood is immersed in fat: fat metabolism, fatty acids, fat signaling, fatty liver disease. Dr. Wood, a professor in the Metabolic Signaling and Disease program at Sanford-Burnham’s Lake Nona campus, is trying to unravel the consequences of too much fat.

“I’m interested in how the body reacts to excess fat and how fat metabolism and the genetics of fat metabolism play a role in insulin resistance and fatty liver disease,” says Dr. Wood.

Given that recent statistics show a third of Americans are obese, the research being done by Dr. Wood and others could have a profound impact on the nation’s health. One key focus is the underlying genetics that make certain people susceptible to disease.

Brown fat: not just for babies and bears

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Sanford-Burnham’s Dr. Sheila Collins recently returned from Stockholm, where she attended a meeting on brown fat (also called brown adipose tissue) and obesity, held in conjunction with the XI International Congress on Obesity. Brown fat, which helps generate heat, was historically thought to be limited to small mammals such as rodents, newborns of larger mammals (including humans), and hibernators – in order for them to stay warm. Scientists used to think that brown fat disappeared after infancy, but recent advances in imaging technology led to a rediscovery of brown fat in adult humans. This meeting brought together scientists studying the basic biology of brown fat tissue and its possible role in adults in order to figure out how all this information can be applied to fight obesity.

Food, energy, and orexin

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Ever wonder why you feel sleepy after a heavy meal and why it is difficult to catch some Zs when you’re hungry? It’s because our blood glucose levels directly control the amount of a hormone called orexin, which influences hunger and sleep/wake cycles. High glucose after a meal reduces orexin levels and the activity of orexin-producing neurons, making us feel sluggish. Plunging glucose levels following overnight fasting elevates orexin levels, which wakes us up to seek food. In other words, soaring orexin levels trigger wakefulness, vigilance and hunger; reduced levels induce inactivity and somnolence.“Regulation of hunger and consciousness appear to be intimately tied to our metabolic state,” says Dr. Dev Sikder, an assistant professor in the Metabolic Signaling and Disease program at Sanford-Burnham’s Lake Nona campus . “Consistent with this theory, the cyclic waxing and waning of orexin levels appears to be perturbed in metabolic disorders such as type 2 diabetes, obesity and even cancer. These disorders are also a consequence of physical inactivity and sleep/wake disturbances, which are directly influenced by orexin. Indeed, several epidemiological studies have reported a correlation between lower orexin levels and a higher incidence of obesity and type 2 diabetes.”

The skinny on fat resistance

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Dr. Philip Wood, professor in Sanford-Burnham’s Diabetes and Obesity Research Center at Lake Nona, Florida, co-authored a study showing that obesity-resistant mice could be genetically engineered by deleting an enzyme that helps break down fatty acids. The study, which appeared May 5 in the journal Cell Metabolism, was co-led by Dr. Wood and Dr. Gerald Shulman of the Howard Hughes Medical Institute and Yale University.

In the study, mice lacking the gene – called VLCAD – were fed a high-fat diet. Since VLCAD is necessary for normal fatty acid metabolism and the production of cellular energy, the scientists figured that disrupting the gene’s function would inhibit metabolism and lead to weight gain and other ailments. However, instead of packing on extra fat, the mice were actually protected from obesity and insulin resistance (an early stage  of type 2 diabetes). The researchers think that VLCAD deficiency triggers a back-up mechanism that acts like an emergency generator, compensating for the loss of the enzyme.

“This study illustrates the power of a genetic mouse model to tease apart different components of the fat burning process and insulin resistance, a common side effect of obesity,” Dr. Wood explained. “By inactivating this one step in fat burning, we activated two different drug targets currently used to treat problems of excess fat in human patients.”

Dr. Wood was also interviewed in a recent story about obesity by WJRT-TV, the ABC affiliate in Flint, Michigan.

Some like it sweet

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Bacteria need sugars to survive. So they grab sugars where they can – either by making them or by taking them up from the environment – and mold them into a form that can be used nutritionally (to make energy) or structurally (to build a cell wall, for example). In turn, a bacterial cell’s sugar give-and-take can influence its environment, whether that’s water, soil or the human gut. With the long-term goal of developing ways to manipulate bacteria for a desired outcome, like new antibiotics or producing alternative energy, scientists are piecing together the complicated machinery that bacteria use to modulate sugars. In doing so, they face the major challenge of figuring out which genes are involved and what roles they play in sugar processing.

Sanford-Burnham’s Dr. Andrei Osterman addressed this problem in a talk he gave last week at the San Diego Consortium for Systems Biology’s 5th Annual Systems to Synthesis symposium, held at the Salk Institute for Biological Studies. Two types of bacteria that Dr. Osterman uses to study sugar processing pathways, Thermotoga maritime and Shewanella oneidensis, may have potential industrial applications to produce biohydrogen or clean up nuclear waste.

Early in his talk, Dr. Osterman summed up his group’s method for pinpointing what a gene does. “Coming from Russia, I think of it as a very American approach,” he joked. “We try to figure out what’s going on by taking a look around the neighborhood.”

He means the genomic neighborhood, of course.

There’s more to fat

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Sheila Collins, Ph.D., recently joined Sanford-Burnham at Lake Nona as a professor in the Metabolic Signaling and Disease program. Her lab is interested in fat metabolism. Until the mid-1990s, adipose (fat) tissue had been largely considered an inert storage depot for excess metabolic fuel, much like a savings bank. There is now a better understanding of how fat cells secrete key hormones that play help regulate body weight and insulin sensitivity.