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Proteins and cellular adaptation to stress

Posted in Curation, De novo synthesis, Discovery process, Evolutionary cognition, Experimental validation, Federal Budget Appropriations, Genome Biology, Healthcare costs and reimbursement, Historical relevance, Innovations in Neurophysiology & Neuropsychology, Medicare and Medicaid, Metabolomics, Molecular Genetics & Pharmaceutical, Neurodegenerative Diseases, Nitric Oxide in Health and Disease, Pharmaceutical R&D Investment, Prescription Drugs Costs, Proteomics, Regenerative Biology and Medicine, Translational Science, tagged Alzheimers Disease, Apoptosis, CHOP, ER stress, neurodegeneration, pERK, proapoptotic RD5, Protein folding, REST, TF-XBP1, UPR, UPR-IRE1a on July 8, 2014| Leave a Comment »

Larry H Bernstein, MD, FCAP, Curator

http://pharmaceuticalintelligence/7/8/2014/Proteins and cellular adaptation to stress

There are two recent articles that are, if not interesting, possibly important in the direction of cellular regulation, adaptation, and decline.  One deals with apoptosis, or cell death, which is synchronized with recovery of membrane and protein breakdown for reuse in synthesis and maintenance.  The other is a new perspective to Alzhemier’s Disease, for which there is no effective pharmacotherapy. In both cases, the stresses of the cell are critical to the responce to the environment.  This is not just about the classical transcriptomics story. This is a perfect followup to the just posted research on the regulatory role of a small RNA that is related to, but distinct from silencing RNA, and also the revelations about lncRNA.

Protein Helps Cells Adapt—or Die

Scientists show how cell stress both prevents and promotes cell suicide in a study that’s equally divisive.

By Ruth Williams | July 3, 2014

A cellular stress pathway called the unfolded-protein-response (UPR) both activates and degrades death receptor 5 protein (DR5), which can promote or prevent cell suicide, according to a paper published in Science today (July 3). The theory is that initial stress blocks cell suicide, or apoptosis, to give the cell a chance to adapt, but that if the stress persists, it eventually triggers apoptosis.

“This work has made the most beautiful simplification of all this big complex mess. Basically, they identified and pinpointed the specific protein involved in the switching decision and explain how the decision is made,” said Alexei Korennykh, a professor of molecular biology at Princeton University, who was not involved in the work.

But Randal Kaufman of the Sanford-Burnham Medical Research Institute in La Jolla, California, was not impressed. He questioned the physiological relevance of the experiments supporting the authors’ main conclusions about this key cellular process.

Protein folding in a cell takes place largely in the endoplasmic reticulum (ER), but if the process goes awry, unfolded proteins accumulate, stressing the ER. This triggers the UPR, which shuts down translation, degrades unfolded proteins, and increases production of protein-folding machinery. If ER stress is not resolved, however, the UPR can also induce apoptosis.

Two main factors control the UPR—IRE1a and PERK. IRE1a promotes cell survival by activating the transcription factor XBP1, which drives expression of cell-survival genes. PERK, on the other hand, activates a transcription factor called CHOP, which in turn drives expression of the proapoptotic factor DR5.

Peter Walter of the University of California, San Francisco, and his colleagues have now confirmed that CHOP activates DR5, showing that it is a cell-autonomous process. But they have also found that IRE1a suppresses DR5, directly degrading its mRNA through a process called regulated IRE1a-dependent degradation (RIDD). Inhibition of IRE1a in a human cancer cell line undergoing ER stress both prevented DR5 mRNA decay and increased apoptosis.

However, in an e-mail to The Scientist, Kaufman expressed concern that “the significance of RIDD has not been demonstrated in a physiologically-relevant context.”

Walter insisted that the evidence for RIDD’s existence is “crystal clear.” His only concession was that “the effects aren’t 100 percent,” he said, because “RIDD degrades mRNA by a few-fold,” making it difficult to measure.

This RIDD debate aside, the researchers have also sparked a rumpus with their finding that IRE1a expression switches off just 24 hours after ER stress initiation, leaving PERK to drive the cell toward apoptosis. “We and others have evidence that suggests another model,” said Scott Oakes, a professor of pathology at the University of California, San Francisco, “which is that both PERK and IRE1a under high stress will send out death signals.”

Whether IRE1a promotes or inhibits apoptosis under extreme stress “is controversial,” said Ira Tabas, a professor at Columbia University in New York City. But it’s essential that scientists figure it out. Cell death from ER stress is a pathological process in many major diseases, Tabas said, and there are IRE1a inhibitors in pharmaceutical development. “It is very important because under high stress you have two different views here,” said Oakes. “One is that you want to keep IRE1a on, the other is that you want to shut it off.”

Because ER stress is central to many diseases, “a lot of people are passionate about it,” said Tabas, explaining the polemic views. “Who’s right? . . . I think it depends on the context in which the experiments are done—one pathway may be important in some settings, and another pathway may be important in different settings,” he suggested. What might help to resolve the issues, he said, will be “in vivo causation studies using actual disease models.”

Researchers will continue to debate. So, said Walter, “we’ll have to see what holds-up five years from now.”

M. Lu et al., “Opposing unfolded-protein-response signals converge on death receptor 5 to control apoptosis,” Science, 345:98-101, 2014.

Tags stress response, protein folding, disease/medicine, cell & molecular biology and apoptosis

 

Protein May Hold the Key to Who Gets Alzheimer’s

 

By PAM BELLUCK     MARCH 19, 2014

 

It is one of the big scientific mysteries of Alzheimer’s disease: Why do some people whose brains accumulate the plaques and tangles so strongly associated with Alzheimer’s not develop the disease?

 

Now, a series of studies by Harvard scientists suggests a possible answer, one that could lead to new treatments if confirmed by other research.

 

The memory and thinking problems of Alzheimer’s disease and other dementias, which affect an estimated seven million Americans, may be related to a failure in the brain’s stress response system, the new research suggests. If this system is working well, it can protect the brain from abnormal Alzheimer’s proteins; if it gets derailed, critical areas of the brain start degenerating.

“This is an extremely important study,” said Li-Huei Tsai, director of the Picower Institute for Learning and Memory at the Massachusetts Institute of Technology, who was not involved in the research but wrote a commentary accompanying the study. “This is the first study that is really starting to provide a plausible pathway to explain why some people are more vulnerable to Alzheimer’s than other people.”

An image of tau tangles in the brain, often a hallmark of Alzheimer’s disease.

 

 

 

The research, published on Wednesday in the journal Nature, focuses on a protein previously thought to act mostly in the brains of developing fetuses. The scientists found that the protein also appears to protect neurons in healthy older people from aging-related stresses. But in people with Alzheimer’s and other dementias, the protein is sharply depleted in key brain regions.

Experts said if other scientists could replicate and expand upon the findings, the role of the protein, called REST, could spur development of new drugs for dementia, which has so far been virtually impossible to treat. But they cautioned that much more needed to be determined, including whether the decline of REST was a cause, or an effect, of brain deterioration, and whether it was specific enough to neurological diseases that it could lead to effective therapies.

“You’re going to see a lot of papers now following up on it,” said Dr. Eric M. Reiman, executive director of the Banner Alzheimer’s Institute in Phoenix, who was not involved in the study. “While it’s a preliminary finding, it raises an avenue that hasn’t been considered before. And if this provides a handle on which to understand normal brain aging, that will be great, too.”

REST, a regulator that switches off certain genes, is primarily known to keep fetal neurons in an immature state until they develop to perform brain functions, said Dr. Bruce A. Yankner, a professor of genetics at Harvard Medical School and the lead author of the new study. By the time babies are born, REST becomes inactive, he said, except in some areas outside the brain like the colon, where it seems to suppress cancer.

While investigating how different genes in the brain change as people age, Dr. Yankner’s team was startled to find that REST was the most active gene regulator in older brains. The researchers have found that this protein, normally active in fetuses, may also protect the neurons in older people.  It is not yet possible to measure the levels of this protein that is a gene regulator called REST, in living people.

“Why should a fetal gene be coming on in an aging brain?” he wondered. He hypothesized that it was because in aging, as in birth, brains encounter great stress, threatening neurons that cannot regenerate if harmed.

His team discovered that REST appears to switch off genes that promote cell death, protecting neurons from normal aging processes like energy decrease, inflammation and oxidative stress.

Analyzing brains from brain banks and dementia studies, the researchers found that brains of young adults ages 20 to 35 contained little REST, while healthy adults between the ages of 73 and 106 had plenty. REST levels grew the older people got, so long as they did not develop dementia, suggesting that REST is related to longevity.

But in people with Alzheimer’s, mild cognitive impairment, frontotemporal dementia and Lewy body dementia, the brain areas affected by these diseases contained much less REST than healthy brains.

This was true only in people who actually had memory and thinking problems. People who remained cognitively healthy, but whose brains had the same accumulation of amyloid plaques and tau tangles as people with Alzheimer’s, had three times more REST than those suffering Alzheimer’s symptoms. About a third of people who have such plaques will not develop Alzheimer’s symptoms, studies show.

REST levels dropped as symptoms worsened, so people with mild cognitive impairment had more REST than Alzheimer’s patients. And only key brain regions were affected. In Alzheimer’s, REST steeply declined in the prefrontal cortex and hippocampus, areas critical to learning, memory and planning. Other areas of the brain not involved in Alzheimer’s showed no REST drop-off.

It is not yet possible to analyze REST levels in the brains of living people, and several Alzheimer’s experts said that fact limited what the new research could prove.

John Hardy, an Alzheimer’s researcher at University College London, cautioned in an email that information from post-mortem brains could not prove that a decline in REST caused dementia because death might produce unrelated damage to brain cells.

To investigate further, the team conducted what both Dr. Tsai and Dr. Reiman called a “tour de force” of research, examining REST in mice, roundworms and cells in the lab.

“We wanted to make sure the story was right,” Dr. Yankner said. “It was difficult to believe at first, to be honest with you.”

Especially persuasive was that mice genetically engineered to lack REST lost neurons as they aged in brain areas afflicted in Alzheimer’s.

Dr. Yankner said REST appeared to work by traveling to a neuron’s nucleus when the brain was stressed. In dementia, though, REST somehow gets diverted, traveling with toxic dementia-related proteins to another part of the neuron where it is eventually destroyed.

Experts said the research, while intriguing, left many unanswered questions. Bradley Wise of the National Institute on Aging’s neuroscience division, which helped finance the studies, said REST’s role needed further clarification. “I don’t think you can really say if it’s a cause of Alzheimer’s or a consequence of Alzheimer’s” yet, he said.

Dr. Samuel E. Gandy, an Alzheimer’s researcher at Mount Sinai Medical Center, wondered if REST figured only in neurodegenerative diseases or in other diseases, too, which could make it difficult to use REST to develop specific treatments or diagnostic tests for dementia.

“My ambivalence is, is this really a way that advances our understanding of the disease or does this just tell us this is even more complicated than we thought?” he said.

Dr. Yankner’s team is looking at REST in other neurological diseases, like Parkinson’s. He also has thoughts about a potential treatment, lithium, which he said appears to stimulate REST function, and is considered relatively safe.

But he and other experts said it was too early. “I would hesitate to start rushing into lithium treatment” unless rigorous studies showed that it could forestall dementia, said Dr. John C. Morris, an Alzheimer’s researcher at Washington University in St. Louis.

Still, Dr. Morris said, the REST research the team conducted so far is “very well done, and certainly helps support this idea that we’ve all tried to understand about why Alzheimer’s is age-associated and why, while amyloid is necessary for the development of Alzheimer’s disease, it certainly is not sufficient.”

He added, “There have to be some other processes and triggers that result in Alzheimer’s.”

Correction: March 19, 2014 
Because of an editing error, an earlier version of this article misstated the gender of Dr. Li-Huei Tsai. Dr. Tsai is a woman.

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Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

Posted in Affordable Care Act, Cerebrovascular and Neurodegenerative Diseases, Chemical Biology and its relations to Metabolic Disease, Curation, Discovery process, Evolutionary cognition, Explanatory, Health Economics and Outcomes Research, Health Law & Patient Safety, Indigent Nutrition, Innovations in Neurophysiology & Neuropsychology, Liver & Digestive Diseases Research, Medicare and Medicaid, Metabolomics, Nephrology, Neurodegenerative Diseases, Nutrigenomics, Nutrition, Nutritional Supplements: Atherogenesis, lipid metabolism, Population Health Management, Nutrition and Phytochemistry, Proteomics, Skilled Nursing Facilities, Uninsured and Underinsured, tagged fish, memory loss, muscle wasting, omega-3 PUFA, sarcopenia, stage 3 & 4 renal disease on July 6, 2014| Leave a Comment »

Larry H. Bernstein, MD, FCAP, Curator

http://pharmaceuticalinnovation/6/7/2014/Omega-3 fatty acids, depleting the source, and protein insufficiency in renal disease

 

This article is concerned only with updating the importance of key nutrients for maintenance of health. Nutritional losses are associated with memory loss, impaired immunity, and loss of lean body mass.

 

Low levels of omega-3 fatty acids may cause memory problems

Disease and Conditions, General Diet • Tags: Alzheimer’s disease, American Academy of Neurology, Docosahexaenoic acid, Magnetic resonance imaging, Neurology, Omega-3 fatty acid, United States Environmental Protection Agency, University of California Los Angeles

09 Mar 2012

 

ST. PAUL, Minn. – A diet lacking in omega-3 fatty acids, nutrients commonly found in fish, may cause your brain to age faster and lose some of its memory and thinking abilities, according to a study published in the February 28, 2012, print issue of Neurology®, the medical journal of the American Academy of Neurology. Omega-3 fatty acids include the nutrients called docosahexaenoic acid (DHA) and eicosapentaenoic acid (EPA).

salmon dinner

 

 

 

 

 

 

 

 

 

“People with lower blood levels of omega-3 fatty acids had lower brain volumes that were equivalent to about two years of structural brain aging,” said study author Zaldy S. Tan, MD, MPH, of the Easton Center for Alzheimer’s Disease Research and the Division of Geriatrics, University of California at Los Angeles.

For the study, 1,575 people with an average age of 67 and free of dementia underwent MRI brain scans. They were also given tests that measured mental function, body mass and the omega-3 fatty acid levels in their red blood cells.

The researchers found that people whose DHA levels were among the bottom 25 percent of the participants had lower brain volume compared to people who had higher DHA levels. Similarly, participants with levels of all omega-3 fatty acids in the bottom 25 percent also scored lower on tests of visual memory and executive function, such as problem solving and multi-tasking and abstract thinking.

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Mechanisms of muscle wasting in chronic kidney disease.

Xiaonan H Wang, William E Mitch

Nature Reviews Nephrology (Impact Factor: 7.94). 07/2014; DOI: 10.1038/nrneph.2014.112

Source: PubMed

ABSTRACT In patients with chronic kidney disease (CKD), loss of cellular proteins increases the risks of morbidity and mortality. Persistence of muscle protein catabolism in CKD results in striking losses of muscle proteins as whole-body protein turnover is great; even small but persistent imbalances between protein synthesis and degradation cause substantial protein loss. No reliable methods to prevent CKD-induced muscle wasting currently exist, but mechanisms that control cellular protein turnover have been identified, suggesting that therapeutic strategies will be developed to suppress or block protein loss. Catabolic pathways that cause protein wasting include activation of the ubiquitin-proteasome system (UPS), caspase-3, lysosomes and myostatin (a negative regulator of skeletal muscle growth). These pathways can be initiated by complications associated with CKD, such as metabolic acidosis, defective insulin signalling, inflammation, increased angiotensin II levels, abnormal appetite regulation and impaired microRNA responses. Inflammation stimulates cellular signalling pathways that activate myostatin, which accelerates UPS-mediated catabolism. Blocking this pathway can prevent loss of muscle proteins. Myostatin inhibition could yield new therapeutic directions for blocking muscle protein wasting in CKD or disorders associated with its complications.

 

We’re Fishing the Oceans Dry. It’s Time to Reconsider Fish Farms.

Food and Agriculture Organization of the United Nations -State of World Fisheries and Aquaculture 2014

 

 

 

 

 

 

 

 

 

 

 

 

Aquaculture has gotten much greener, with American innovators leading the way.

— Text by Maddie Oatman; video by Brett Brownell

| Wed Jul. 2, 2014 6:00 AM EDT    MotherJones.com

 

When I meet Kenny Belov mid-morning at San Francisco’s Fisherman’s Wharf, the boats that would normally be out at sea chasing salmon sit tethered to their docks. The steady breeze coursing through the bay belies choppier conditions farther out—so rough that the local fishermen threw in the towel for the fifth morning in a row. Belov scans the horizon as he explains this, feet away from the warehouse of his sustainable seafood company, TwoXSea. Because his business hinges on what local fishermen can bring in, he’s used to coping with wild fish shortages.

If we continue to fish at the current pace, some scientists predict we’ll be facing oceans devoid of edible marine creatures by 2050.

But unlike these fishermen, Belov has a stash of treasure in his warehouse, as he soon shows me: a golf-cart-size container of plump trout, their glossy bodies still taut from rigor mortis. The night before, Belov drove north to Humboldt to help “chill kill” the fish by submerging them live into barrels of slushy ice water. Belov can count on shipments of these McFarland Springs trout every week—because he helped grow them himself on a farm.

For many consumers, aquaculture lost its appeal after unappetizing news spread about commercial fish farms—like fish feed’s pressure on wild resources, overflowing waste, toxic buildup in the water, and displacement of natural species. But consider this: Our appetite for seafood continues to rise. Globally, we’ve hungered for 3.2 percent more seafood every year for the last five decades, double the rate of our population. Yet more than four-fifths of the world’s wild fisheries are overexploited or fully exploited (yielding the most fish possible with no expected room for growth). Only 3 percent of stocks are considered underexploited—meaning they have any significant room for expansion. If we continue to fish at the current pace, some scientists predict we’ll be facing oceans devoid of edible marine creatures by 2050.

Aquaculture could come to the rescue. The Food and Agriculture Organization of the United Nations predicts that farmed fish will soon surpass wild-caught; by 2030, aquaculture may produce more than 60 percent of fish we consume as food.

Food and Agriculture Organization of the United Nations “State of World Fisheries and Aquaculture” 2014 report

One of the most pressing concerns about aquaculture, though, is that many farmed fish are raised on a diet of 15 million tons a year of smaller bait fish—species like anchovies and menhaden. These bait—also known as forage fish—are ground up and converted into a substance called fishmeal. It takes roughly five pounds of them to produce one pound of farmed salmon. Bait fish are also used for nonfood products like pet food, makeup, farm animal feed, and fish oil supplements.

Forage fish are a “finite resource that’s been fully utilized.”

It may appear as though the ocean enjoys endless schools of these tiny fish, but they too have been mismanaged, and their populations are prone to collapse. They’re a “finite resource that’s been fully utilized,” says Mike Rust of NOAA’s fisheries arm. Which is disturbing, considering that researchers like those at Oceana argue that forage fish may play an outsize role in maintaining the ocean’s ecological balance, including by contributing to the abundance of bigger predatory fish.

And that’s where Belov’s trout come in: Though he swears no one can taste the difference, his fish are vegetarians. That means those five pounds of forage fish can rest easy at sea. It also means that the trout don’t consume some of the other rendered animal proteins in normal fishmeal pellets: bone meal, feather meal, blood meal, and chicken byproducts.

Belov and McFarland Springs’ owner David McFarland were inspired to switch to vegetarian feed in part by Rick Barrows, a USDA researcher. About six years ago, recounts Barrows, several USDA studies confirmed that fish rely on nutrients—vitamins, minerals, fatty acids, and protein—rather than fishmeal or fish oil, to thrive. If those nutrients could be found in other products, including purely plant-based substances, then aquaculture might not be so dependent on feeding fish other smaller fish.

Barrows and team began to test about 50 potential materials a year, and now have a database of 140 that anyone can browse through online. Belov was one of their first commercial partners. The plant-based food fed to McFarland Springs’ trout consists of a hearty blend of marine algae, freshwater micro algae, vitamins, minerals, flax, flax oil, corn, and nut waste. The resulting complete protein means the trout’s omega 3s are high and their omega 6s are low—a ratio that’s said to enhance anti-inflammatory properties. And “they don’t have the concentration of heavy metals that come from the bait fish,” Belov says. I took one of his rosy fillets home and turned it into trout lox; find the recipe here.

McFarland Springs manages the trout’s waste by funneling it out into a natural sagebrush pasture where it composts the soil.

Belov’s fish feed includes California nuts that are too broken or disfigured to be sold.

Barrows thinks region-specific material for this type of feed offers the most potential. For instance, his team learned that around 5 percent of California nuts can’t be sold because they’re broken or disfigured. They realized they could repurpose excess nut parts for the trout feed; the nut bits helped round out the complete protein. Lately, Barrows has become especially excited about turning barley surplus from the beer industry—which comes at a cheap price in Montana, where he’s based—into a feed-grade concentrate for trout feed.

“You can get just as much growth rate out of fishmeal-free feeds as fishmeal,” says Barrows. And his lab has proven as much with eight different fish species: cobia, Florida pompano, coho salmon, Atlantic salmon, walleye, yellowtail, and White seabass.

But the price difference still stands in the way for many fish farmers. Belov pays slightly more than $1/pound for his plant-based feed, whereas fishmeal pellets average around $0.71/pound. He sells his trout for $6.95/pound, about a dollar more than conventional. But he’s well positioned in the affluent Bay Area, and he usually sells out of his McFarland Springs trout well before the end of each week. As innovation continues in the realm of plant-based feeds, he’s hopeful, along with Barrows, that the price of the pellets will continue to drop.

Here in the United States, we consume plenty of farmed fish already, but only 5 percent of it is sourced domestically. “If we didn’t import so much farmed seafood,” implored Four Fish author Paul Greenberg in a recent New York Times op-ed, “we might develop a viable, sustainable aquaculture sector of our own.” It doesn’t just boil down to economics: The locations we generally export from, like China and South Asia, don’t have near the stringent environmental and health regulations as the US. “Growing more seafood at home would help with trade deficit, but also we could control the safety more,” says Barrows.

Though our current aquaculture sector is relatively tiny, US farmers are in a better position to innovate, because we have a sophisticated animal nutrition research center and feed sector, says NOAA’s Rust. “We’re the leading technical country in the world on feed.”

Belov wasn’t always open to aquaculture, and he still feels that fish—such as some salmon—with healthy wild fisheries attached to them should never be farmed. That way, environmentally responsible fishermen can stay in business. His long-term strategy for sustainable seafood? Draw from the “amazing [wild] fisheries that exist, and then you backfill with intelligent aquaculture, and yes, you can feed the planet with sustainable marine products.” Which may take more work, but as he puts it, “We depleted the ocean. It wasn’t anybody else’s fault. So it’s our job to fix it.”

 

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