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Sanford-Burnham Science Blog

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Seeing is believing

by Heather Buschman, Ph.D. on April 6, 2011 at 10:01 am | 1 comment
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Left: traditional electron microscopy view of actin filaments. Right: Dr. Dorit Hanein's 3-D view of actin.

Left: electron microscopy view of actin. Right: Dr. Dorit Hanein's 3-D view.

Life is complicated. Even one tiny cell has a lot going on at any given time, even when things are running smoothly. Normal cellular functions and their emergency responses (like to injury or infection) are mostly carried out by proteins. Proteins tell other proteins what to do by carrying signals, tagging one another with chemical groups, chewing up other proteins or helping assemble new ones, and so on. They also help orchestrate which genes are turned on or off and when.

The cell itself is constantly sensing and reacting to constant environmental fluctuations, as are the individual proteins and other molecules. So how do you connect these two things?

“You can see a cell by eye, using a standard microscope. But you can’t see individual molecules that way,” explains Sanford-Burnham’s Dr. Dorit Hanein. “A cell is on the micrometer scale (one-thousandth of a millimeter), while an individual molecule is on the nanometer scale (one-millionth of a millimeter). That’s like the difference between walking the 500 miles from here [San Diego] to San Francisco, versus walking from here to the moon.”

What Dr. Hanein and other scientists need are techniques that allow them to look not just at the moon, but at the earth, the moon and everything in between.

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Glycobiology 101

by Heather Buschman, Ph.D. on February 24, 2011 at 12:44 pm | 1 comment
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Glia cells in the brain secrete the glycan Dkk (shown in green) to regulate cell growth and development. (Nakamura et al., BMC Cell Biology 2007, image from Wikimedia Commons)

Glia cells in the brain secrete the glycoprotein Dkk (shown in green), which influences cell growth and development. (Image adapted from Nakamura et al., BMC Cell Biology 2007, available from Wikimedia Commons)

Glycobiologyand glycomics are the scientific fields that study carbohydrates (sugars) in the cell – their chemical structure, how they’re made, where they’re located, and how they influence protein and cell function. Glycomics is to carbohydrates what genomics is to genes and proteomics is to proteins. Glycobiologists study glycans – carbohydrate chains and carbohydrate-coated proteins – and the proteins that bind them.

Read below for more on glycans, glycan-binding proteins and their roles in human health.

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Got MELK?

by Heather Buschman, Ph.D. on January 19, 2011 at 2:51 pm | 3 Comments
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Not all cells in a tumor are equal. They have different genes, proteins and behaviors and while some are easily killed, others are more resistant to cell-destroying therapies. In some cancers, a few of these hardier cells are cancer stem cells and they may be the culprits behind tumor formation and drug resistance. Much like other types of stem cells, cancer stem cells can do two things: self-renew (generating more new stem cells) and differentiate (giving rise to a variety of cell types). The trick to better understanding tumor formation, and designing drugs that specifically target cancer at its root, is figuring out how to pick the stem cell needle out of the tumor haystack. Sanford-Burnham researchers Dr. Alexey Terskikh and Dr. Robert Oshima think a protein called MELK, short for maternal embryonic leucine zipper kinase, might allow them to do just that.

Dr. Terskikh has studied MELK for almost 10 years, but it hasn’t been easy. Early on,  researchers would disrupt MELK in mice but see no consequences from that disruption. Now, in a recent paper published in the journal Cancer Research, Dr. Terskikh, Dr. Oshima, and their colleagues show that MELK protein levels are particularly high in tumor-initiating cells found in a mouse model of breast cancer.

“Previous studies provided evidence that high MELK levels correlate with poor prognosis in breast and brain tumors,” Dr. Terskikh says. “Now we show for the first time that MELK does actually play a role in mammary tumor initiation and progression in a relevant animal model of breast cancer.”

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Mitochondria 101

by Heather Buschman, Ph.D. on December 3, 2010 at 7:24 am | 5 Comments
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Cartoon diagram of a mitochondrion, peeled back to reveal the inner membrane and inner workings of the cell's "powerhouse". (Image courtesy of Wikimedia Commons)

Cartoon diagram of a mitochondrion, the "powerhouse" of the cell. (Image courtesy of Wikimedia Commons)

“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.

Fraydoon Rastinejad & a home for orphan receptors

by Heather Buschman, Ph.D. on November 8, 2010 at 2:50 pm | 0 Comments
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Nuclear receptors are proteins that directly bind DNA to turn genes on or off in response to outside signals. For some of the 48 members of this protein family, it’s well known what sets them in motion and what genes they activate or inactivate. The estrogen receptor, for example, is a nuclear receptor that receives estrogen, the female hormone, and switches on genes that drive female characteristics. For other nuclear receptors, the orphans, all we really know is that they resemble other family members. Their function and their binding partners remain a mystery.

Enter Dr. Fraydoon Rastinejad, new professor in Sanford-Burnham’s Diabetes and Obesity Research Center in Lake Nona and caretaker of orphan receptors.

“We are interested in how a subset of the nuclear receptor family works – the orphans.  Even though some of these receptors have thousands of publications already, there are still dozens that very few people work on,” Dr. Rastinejad explains. “We don’t have a clue what their natural binding partners are or what genes they regulate. But they’re all part of the nuclear receptor family, so there’s a lot of excitement every time a new one is uncovered.”

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Nuclear Receptors 101

by Heather Buschman, Ph.D. on October 27, 2010 at 8:51 am | 0 Comments
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Cartoon representation of an orphan nuclear receptor

Cartoon representation of an orphan nuclear receptor

When the human genome project was completed in 2003, it revealed that we have roughly 22,000 different genes (see DNA 101). But not every gene is active in every cell at all  times. A skin cell doesn’t need to express the same genes as a liver cell. And a liver cell doesn’t always need to express the genes necessary to process alcohol, unless triggered to do so. To conserve resources and function properly, cells have many ways to control which genes are on, which are off and when to switch that up.

One way to regulate gene expression is with nuclear receptors – proteins that directly bind to DNA to turn genes on or off in response to outside signals. There are 48 known nuclear receptor family members. For some, it’s well known what turns them on or off and what genes they activate or inactivate in response. The estrogen receptor is a nuclear receptor that receives estrogen, the female hormone, and switches on genes that drive female characteristics. For other nuclear receptors, the orphan receptors, all we really know is that they resemble other family members. Their function and their binding partners remain a mystery.

Nuclear receptors make good drug targets because they have open pockets just waiting to hold a signaling molecule. Drug compounds can also be made to fit these pockets, switching the nuclear receptor on or off to alter gene expression. The breast cancer drug tamoxifen, for example, targets the estrogen receptor.

Proteins 101

by Heather Buschman, Ph.D. on October 15, 2010 at 12:00 pm | 32 Comments
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Proteins are the molecules that do the majority of the work in a cell. They make up most of the cell’s structure, facilitate chemical reactions, carry molecular signals in and out of the cell, turn genes on and off and much more. A cell’s genes provide the recipe for assembling the correct building blocks – called amino acids – to make specific proteins (see DNA 101).

A short sequence of amino acids is called a peptide; a chain of many amino acids is a polypeptide. But a protein is more than just the sum of its parts – how it folds, the shape it takes and its interactions with other proteins also influence its identity and function. Those factors are determined not only by the amino acid sequence, but also by other chemical modifications made to the protein as it’s being built, or even later. Protein modifications are named for the type of chemical group added. For example, a phosphate group is added in a process called phosphorylation, which can alter a protein’s function.

Once assembled, the best-known proteins are those that perform specialized functions, such as enzymes, antibodies, toxins or hormones.

Where Structure Meets Function

by Heather Buschman, Ph.D. on September 30, 2010 at 10:06 am | 2 Comments
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The human genome project taught us a lot about the number and sequences of our genes, but not a whole lot about what they do. In the years since, scientists have been using that genomic information to examine the structures of proteins, the molecules that carry out our genes’ instructions (see DNA 101). Structural information is being used to answer biological questions about protein function – how they facilitate chemical reactions, carry molecular signals in and out of cells and control cellular movements. There’s a growing need to understand how multiple proteins work together to accomplish all that and more.As part of their Protein Structure Initiative (PSI), the National Institute of General Medical Sciences (NIGMS) at the National Institutes of Health has awarded a five-year, $6.8 million grant to a team led by Sanford-Burnham’s Dr. Robert Liddington and Stanford University’s Dr. W. James Nelson. PSI was formed in 1999 to help researchers establish the structure of more proteins, faster. Now in its third phase, called PSI:Biology, PSI structure determination centers are partnering with scientists like Dr. Liddington and Dr. Nelson to address important biological questions linking a protein’s structure and its function.

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A balance of fat and sugar

by Heather Buschman, Ph.D. on August 17, 2010 at 3:57 pm | 1 comment
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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.

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Molecular dominoes tip tumors toward metastasis

by Heather Buschman, Ph.D. on July 12, 2010 at 11:05 am | 2 Comments
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Dr. Jianfei Qi

Dr. Jianfei Qi

Why do some tumors stay put while others metastasize? In particularly aggressive forms of prostate cancer, a handful of dangerous cells (known as neuroendocrine-type cells) are to blame. In a study published in the July 13 issue of Cancer Cell, a team of investigators led by Dr. Ze’ev Ronai and postdoctoral researcher Dr. Jianfei Qi identified a series of molecular events that, like a line of falling dominoes, ultimately leads to the more metastatic neuroendocrine forms of the disease. This study revealed a protein named Siah2 as the first domino to fall – triggering the chain reaction of events that turns a non-malignant tumor into a metastatic neuroendocrine tumor. Members of this Sanford-Burnham research team are now looking for chemical compounds that target Siah2 or other proteins along the chain that leads to the formation of neuroendocrine-type cancer cells. They hope to find a drug that prevents one domino from knocking over the next, halting this series of molecular events and keeping prostate tumors in check.

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Chemical Genomics and the Art of Discovery

by Heather Buschman, Ph.D. on June 30, 2010 at 3:27 pm | 0 Comments
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Inflammation – one of the body’s earliest responses to infection or injury – can help the healing process when it’s closely controlled by the immune system. Mismanaged inflammation, however, can contribute to a variety of disorders, such as autoimmune diseases or allergic reactions. The immune system maintains this careful balance in part through the activity of a protein known as NF-κB. When triggered by cellular damage, infectious bacteria or some other molecular signal, NF-κB binds to DNA and turns on genes that activate inflammation. Since NF-κB acts like a master inflammation regulator, it makes an attractive target for researchers hoping to manipulate the immune response in patients suffering from either too much or too little inflammation.

A bi-coastal Sanford-Burnham research team led by Dr. Greg Roth in Lake Nona, Orlando, Fla. and Dr. John Reed in La Jolla, Calif. recently used the robotic technology in the Conrad Prebys Center for Chemical Genomics (Prebys Center) to screen a collection of more than 100,000 chemical compounds to find that one needle-in-a-haystack (or handful of needles) capable of blocking NF-κB. In a pair of studies published in ACS Chemical Biology (March 19, 2010) and the Journal of Medicinal Chemistry (May 18, 2010), they discovered a chemical compound that selectively impairs NF-κB activity under certain conditions. By inhibiting NF-κB this way, the compound has the potential to dampen potentially harmful inflammation without shutting down the whole immune system.

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Getting a handle on cellular JNK

by Heather Buschman, Ph.D. on June 28, 2010 at 10:01 am | 0 Comments
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Dr. Gustavo Gutierrez

Dr. Gustavo Gutierrez

Some cells divide often (think skin cells), while some, such as most brain cells, almost never do. So it stands to reason that cell division must be precisely regulated – an error at any of several transitions along the way can result in developmental problems or out-of-control cell proliferation, the hallmark of cancer. To assure that the cell cycle – the cell’s process of duplicating its DNA and dividing into two identical ‘daughter’ cells – goes smoothly, a large network of proteins tells other proteins what to do and when to do it. In order to better understand cancerand other diseases, it’s important to map out exactly how the cell cycle works.A new study led by Dr. Ze’ev Ronai, associate director of Sanford-Burnham’s National Cancer Institute-designated Cancer Center, and postdoctoral researcher Dr. Gustavo Gutierrez reveals a new player in cell cycle control. This study, which appeared online in Nature Cell Biology on June 27, showed that JNK, a protein already well known for other reasons, also regulates the cell cycle.

“This was totally unexpected of JNK,” Dr. Gutierrez explained. “We already knew that JNK helps cells respond to stress, such as damage caused by ultraviolet radiation. We thought we already knew how the major components of the cell cycle were regulated. This study really changes the thinking by connecting the two.”

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The Promise of Chemical Genomics

by Josh Baxt on June 22, 2010 at 2:52 pm | 16 Comments
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With the completion of the Human Genome Project in 2003, scientists have a basic blueprint of our DNAand the genes it contains. While the project answered many questions, it also left many unanswered. How and why are genes turned on and off? What proteins do specific genes produce? What do those proteins do, and how does their activity affect our health?The Conrad Prebys Center for Chemical Genomics (Prebys Center) seeks to answer these and other questions by finding small molecule chemical compounds that selectively bind to a specific protein and turn it on or off. Small molecules are valuable because they help scientists determine a protein’s function in a cell. These are the first steps toward understanding how a dysfunctional protein can cause disease—important knowledge that can lead to new treatments.

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Partners, part 1

by Josh Baxt on March 31, 2010 at 4:21 pm | 2 Comments
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Denny Sanford and Malin Burnham are the latest in a long line of partnerships to advance the Institute’s important work, starting with co-founders Dr. William and Lillian Fishman.

In fact, collaboration is one of Sanford-Burnham’s most cherished values and has led to many successes in the laboratory. Biologists, chemists, pharmacologists, physicists, engineers and others routinely cross disciplinary boundaries to find solutions to pressing medical problems.

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