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Biochemist brothers identify “RNA Chaperone”

Anonymous — Fri, 10 Jan 2020 18:50:02 +0000

Biochemist brothers identify “RNA Chaperone” Anonymous (not verified) Fri, 01/10/2020 - 11:50

Giulia Corbet

Stress granules comprised of RNA (red) and protein assemblies (green) formed in part through RNA-RNA interactions.

A recent study from �� Boulder researchers shows that cells must actively work to keep sticky molecules, known as ribonucleic acid (RNA), apart, or they may form large assemblies that could cause problems for the cell. RNA is the biomolecule that serves as the template for protein synthesis in cells. Protein synthesis halts when cells become stressed, and RNAs assemble into complexes known as “stress granules” with other RNAs and proteins. Not much is known about the function of stress granules. However, aggregates that resemble stress granules are commonly found in neurodegenerative diseases, suggesting a possible role for stress granules in these diseases.

“While proteins have long been recognized to form aberrant complexes that can trigger disease, RNA has generally not been thought to form promiscuous assemblies that might have functional roles in cells as well as cause problems in some contexts,” said Roy Parker, Distinguished Professor of Biochemistry at �� Boulder.

The study, published recently in Cell, highlights how energetically favorable RNA self-assembly is and identifies one way to actively prevent this assembly from growing out of control. Parker has long studied the properties of stress granules and has pioneered the model that RNA-RNA interactions are a significant contributor to stress granule assembly.

This study, spearheaded by two brothers in the Parker research group at �� Boulder, presents two meaningful conclusions. First, stress granules and other ribonucleoprotein (RNP) complexes readily form favorable interactions with free RNAs. These interactions recruit new RNAs onto the surface of the RNP, thereby growing and stabilizing the complex. Second, a highly abundant enzyme within cells, known as eIF4A1, functions as an “RNA chaperone” to prevent the unregulated growth of RNPs within cells by binding to RNAs.

Devin (L) and Gabriel (R) Tauber, Parker Research Group, University of Colorado Boulder

Co-first authors and brothers Devin and Gabriel Tauber used their complementary expertise in Parker’s lab to understand RNA recruitment to RNPs both in a test tube and in living cells. Devin is a Ph.D. student, and Gabriel was an undergraduate at the time of the study. While unplanned, the brotherly collaboration resulted in an elegant characterization of RNA self-assembly and uncovered the role of the enzyme eIF4A1 in limiting this process in cells.

“Gabe and I have always been interested in science, but we never thought we’d publish a research article together, let alone work in the same lab. Yet, we both fell in love with RNA research and became engaged in understanding the many ways in which RNA can function in the cell beyond simply serving as a middle-man between DNA and protein synthesis,” said Devin. “Since we are brothers, when one of us comes up with an off the wall idea, we are comfortable letting each other have it without the risk of endangering a professional relationship.”

Gabriel sought to understand RNA recruitment into RNPs by watching fluorescently-labeled RNA species assemble under the microscope. Gabriel observed robust recruitment of RNAs with every type of RNP tested. This result raised the question – how do cells limit the growth of RNPs such as stress granules?

The authors believed that the enzyme eIF4A1 was the most likely mechanism to prevent aberrant RNA assembly. eIF4A1 is one of the most abundant RNA binding proteins in the cell and uses energy in the form of ATP to disrupt RNA-RNA interactions. Using fluorescence microscopy to view individual cells, they saw that eIF4A1 is concentrated at the periphery of stress granules, providing further support for the idea that eIF4A1 disrupts RNA-RNA interactions at the surface of RNPs. Thus, Devin sought out to ask whether modulating the levels of eIF4A1 in the cell would affect stress granule assembly.

The Tauber brothers observed that depleting the cell of eIF4A1 can induce stress granule assembly under conditions where they typically do not form. Conversely, they found that increasing the amount of eIF4A1 in the cell is sufficient to prevent stress granule formation under conditions where they would normally develop. However, a mutant form of eIF4A1 which cannot bind to RNA was unable to repress stress granule formation. Together, these experiments solidified the role of eIF4A1 as an inhibitor of RNA recruitment to stress granules and helped to shape the model of RNP assembly as a highly favorable process which requires the cell to use energy to limit it.

“This work will trigger a new set of studies on understanding how cells control RNA-RNA interactions to keep RNAs in the proper balance between functional and specific interactions while limiting inappropriate interactions,” said Parker.

eIF4A’s “RNA chaperone” function could be considered analogous to heat shock proteins, which prevent protein aggregation by binding to unfolded proteins. Protein aggregates that may contain RNA are commonly found in neurodegenerative diseases such as Alzheimer’s disease and Amyotrophic lateral sclerosis. Identifying the respective roles of RNA and protein in the formation of these aggregates could provide critical insight into the cause of these diseases.

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The unexpected complexities of TERT, a key cancer driver

Anonymous — Wed, 11 Sep 2019 06:00:00 +0000

The unexpected complexities of TERT, a key cancer driver Anonymous (not verified) Wed, 09/11/2019 - 00:00

Cu Boulder Today

Telomerase reverse transcriptase (TERT), an enzyme associated with nearly all malignant human cancers, is even more diverse and unconventional than previously realized, new University of Colorado Boulder research finds.

Telomeres, the protective ends of chromosomes, help to maintain genomic stability. In most normal adult human cells, the telomeres eventually shorten beyond a critical length, bringing a cell’s life to its natural end. In almost all human cancers, however, telomerase reactivates, leading to cell proliferation and tumor formation. This is a key part of what makes cancer cells “immortal.”

As TERT is the component of telomerase that is required for cancer development, it has become an attractive target for cancer therapeutics in recent decades.

“TERT has great importance in cancer progression and hence there is a great interest in studying its expression regulation,” said Gabrijela Dumbovic, a post-doctoral researcher in the Department of Biochemistry and co-lead author of the �� Boulder study.

The study, published recently in the journal Proceedings of the National Academy of Sciences, used powerful, high-magnification imaging techniques to reveal differences in how TERT is produced on the single-cell level, in individual cancer cells. Previously, studies relied on general averages of TERT production within whole tissue samples or large cell populations, without investigating potential cell-to-cell variation.

�� a year ago, researchers at the BioFrontiers Institute began discussing ways to apply ribonucleic acid (RNA) localization imaging protocols to better classify how TERT RNA was being made within individual cancer cells. (RNA typically serves as a messenger for turning DNA genetic information into proteins, though it is also important for coding and regulating gene expression and catalyzing certain biochemical reactions.) What began as a casual conversation grew into an interdisciplinary effort, combining experience in RNA imaging from the laboratory of Professor John Rinn of �� Boulder’s Department of Biochemistry and the BioFrontiers Institute with innovative telomerase research led by Distinguished Professor Thomas Cech, a Howard Hughes Medical Institute (HHMI) Investigator and Nobel laureate.

“We have a great community of scholars in the Caruthers Biotechnology Building,” Cech explained. “Our students and postdoctoral fellows are encouraged to talk freely about their work, so collaborations are forged naturally and frequently.”

The researchers used a microscopy technique known as single-molecule RNA fluorescent in situ hybridization (“smFISH,” for short) to visualize individual RNA molecules that coded for TERT in separate cancer cells. Looking at the microscope images, they counted the number of TERT RNA molecules – which appeared as tiny fluorescent spots – in different locations within each cell.

“Previous studies were mostly focused on studying TERT expression in a population of cells. We took a different approach and actually could visualize TERT RNA levels, and RNA distribution on a single-cell level,” said Dumbovic.

The authors also found that while most cells in our bodies have two copies of a given gene (one from our mother and one from our father), the cancer cells frequently had more than two copies of the TERT gene. Such gene amplification is common in cancer cells, which have relatively unstable genomes.

“The TERT gene has made all these extra copies of itself,” Rinn said. “Selfishly, it wants to replicate itself, and cancer wants to hijack that mechanism to keep the its cells alive indefinitely. That’s something we can only see with this kind of imaging.”

Intriguingly, the study also found that when looking at where TERT messenger RNA resides within a given cell, a high amount (over 80 percent in some instances) stays quarantined in the nucleus, rather than the expected cytoplasm, raising yet another mystery for future study. Typically, messenger RNA, which is made in the cell’s nucleus, is exported from the nucleus to be turned into protein in the cell’s cytoplasm.

“RNA imaging has continually shed new insights into biology by providing an important layer of information of where a gene is in the cell. When we took the ‘molecular picture’ of the TERT gene, we’re struck by the unexpected and sometimes substantial amount of TERT RNA in the nucleus where it can’t function to make protein,” explained Rinn. “This opens up a new layer of regulation where the molecules of TERT RNA are when considering its abundance in cancer and other disease states.”

This surprising pattern of nuclear localization was also observed in healthy cells that produce TERT, specifically human induced pluripotent stem cells (iPSCs). “This suggests that the nuclear localization is not a behavior specific to the diseased cancer cells,” said Teisha Rowland, co-lead author of the study and former post-doctoral research in the lab of Thomas Cech. Rowland is now Director of the new Stem Cell Research and Technology Resource Center in the Department of Molecular, Cellular, and Developmental Biology.

“It was generally assumed that TERT mRNA localizes to the cytoplasm, which is needed for it to make a protein product, but now we have a different perspective. Now, we want to understand why TERT RNA is retained in the nucleus,” Dumbovic said. “Is there a stimulus that causes it to move, or to stay?”

The research adds to the increasingly complex picture of TERT’s role in making cancer cells immortal, nuances that could lead to more effective therapeutic solutions for cancer in the future.

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Mimicking the heart's microenvironment

Anonymous — Wed, 11 Sep 2019 06:00:00 +0000

Mimicking the heart's microenvironment Anonymous (not verified) Wed, 09/11/2019 - 00:00

Trent Knoss

�� Boulder engineers and faculty from the Consortium for Fibrosis Research & Translation (CFReT) at the �� Anschutz Medical Campus have teamed up to develop biomaterial-based “mimics” of heart tissues to measure patients’ responses to an aortic valve replacement procedure, offering new insight into the ways that cardiac tissue re-shapes itself post-surgery.

Aortic valve stenosis (AVS), a progressive disease characterized by heart valve tissue stiffening and obstructed blood flow from the heart, is known as a “silent killer,” affecting 12.4 percent of the population over 75 years old with a mortality range of 2-5 years if left untreated. Transcatheter aortic valve replacement (TAVR) procedures, which place an artificial valve at the site of the blockage, have been widely and successfully adopted as a remedy in recent decades.

Details of the broader biological reaction to the valve replacement have remained largely unknown, but nevertheless hold significant ramifications for quantifying the quality of recovery, the risk of complications and the assessment of overall patient outcomes.

During AVS disease progression, tissue-specific cells known as fibroblasts transition into myofibroblasts, which promote tissue stiffening. The researchers were interested in understanding how and why, post TAVR, myofibroblasts revert to the more benign fibroblasts.

“Previous studies have shown significant remodeling of cardiac tissues post-intervention,” said Dr. Brian Aguado, lead author of the study and a post-doctoral researcher in �� Boulder’s Department of Chemical and Biological Engineering. “Our hypothesis was that perhaps there are biochemical cues in a patient’s blood that may revert myofibroblasts back to fibroblasts.”

Modeling such a transformation in the lab is one thing, Aguado said, but the key to the new study was obtaining blood samples from real AVS patients and then using biomaterials to replicate the microenvironment of the heart.

“The heart is not made of plastic like a petri dish is,” he said. “We needed to engineer materials that could reflect the various stiffnesses of both healthy and diseased valve and cardiac tissue.”

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A key ‘kill switch’ in a gene-regulating protein group

Anonymous — Mon, 09 Sep 2019 06:00:00 +0000

A key ‘kill switch’ in a gene-regulating protein group Anonymous (not verified) Mon, 09/09/2019 - 00:00

Trent Knoss

�� Boulder and Howard Hughes Medical Institute (HHMI) biochemists have revealed a key regulatory process in a gene-suppressing protein group that could hold future applications for drug discovery and clinical treatment of diseases, including cancer.

The new research, recently published in the journal Genes & Development, centered on a protein group known as Polycomb Repressive Complex 2 (PRC2), which acts as a gatekeeper for gene expression as cells differentiate and tissues develop.

“PRC2 plays a critical role in stem cell differentiation to make sure that irrelevant genes are switched off,” said Yicheng Long, an HHMI post-doctoral fellow and a co-author of the study. “If you have a muscle cell, for example, PRC2 shuts off genes that are specific to the brain.”

When that regulation goes awry, however, abnormal PRC2 activation is suspected to play a role in the development of diseases such as cardiac hypertrophy, Huntington’s Disease and multiple types of cancer.

Researchers from HHMI and �� Boulder’s Department of Biochemistry began by re-examining exactly how PRC2 achieves methylation, a complex epigenetic process by which proteins modify the structure of regions of chromosomes.

While examining the activity of human PRC2, the scientists began to notice a “mystery band” appearing in the data. As PRC2 was previously known to modify an important histone protein that is a fundamental unit of human chromosome, the scientists indeed observed this modification in vitro. Surprisingly, the scientists noticed another modification event indicated by this “mystery band.” Although other scientists had seen this band before, nobody could understand how and why it was happening.

“This unexpected band caught our attention and we suspect that this could represent a novel activity and function of PRC2,” said Xueyin Wang, one of the two co-first authors of the study and a then-�� Boulder graduate student now with A2 Biotherapeutics Inc. in California.

Further investigation revealed that this “mystery band” is a self-modification event (named “automethylation”) which have important physiological functions. Using mass spectrometry, it became apparent that PRC2 automethylates three lysines of a flexible, evolutionarily conserved loop. The loop essentially holds the key to its own lock within its own structure and remains poised in an inhibited state. Automethylation of the three lysines unlocks this loop from PRC2’s catalytic center and thus relieves PRC2 from the poised state.

“The interesting question is why nature would devise such a mechanism,” Long said.

The researchers hypothesize that with abundant level of PRC2 in stem cell, the flexible loop ensures that most of it stays inactive until needed, like a fire sprinkler that stays closed during normal operations, only opening when a fire needs to be extinguished. If that sprinkler ever malfunctions and remains open (as in a cancerous mutation), biochemists can now foresee a means of re-closing it to prevent unwanted flooding.

“Others have found the way to activate PRC2,” Long said. “We found a key to turning it off.”

“I expect that many other examples of automethylation will be found,” said Nobel Laureate and Distinguished Professor Thomas Cech, the senior author of the study and an HHMI Investigator. “Many enzymes that regulate our genes do so by adding methyl groups to their target proteins. So they’re also primed to add methyl groups to themselves, allowing them to self-regulate their own activity.”

With greater knowledge of PRC2’s form and function, the research could one day lead to more specific clinical focus on inhibiting activations associated with tumor formation and other known disease pathways.

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Pedigree and Productivity

Anonymous — Thu, 02 May 2019 06:00:00 +0000

Pedigree and Productivity Anonymous (not verified) Thu, 05/02/2019 - 00:00

Colleen Flaherty

A 2015 study found that “social inequality” across a range of disciplines was so bad that just 25 percent of Ph.D. institutions produced 71 to 86 percent of tenured and tenure-track professors, depending on field.

The effect was more extreme the farther up the chain the researchers looked, based on their own program ranking system: the top 10 programs in each discipline produced 1.6 to three times more faculty than even the next 10 programs. The top 11 to 20 programs produced 2.3 to 5.6 times more professors than the next 10. In theory, this reflects the quality of those programs. But critics say in-group hiring is also about snobbery.

Now computer scientists at the University of Colorado at Boulder who led that earlier study say academic pedigree isn’t destiny after all -- at least in terms of future productivity.

“Our results show that the prestige of faculty’s current work environment, not their training environment, drives their future scientific productivity,” says the new paper in Proceedings of the National Academy of Sciences. Current and past locations, meanwhile, "drive prominence.”

That is, when it comes to actual research output, where one works is more important than where one trained.

For this new study, researchers looked at productivity and prominence (measured in number of published papers and scholarly citations, respectively) for 2,453 tenure-line faculty members in 205 Ph.D.-granting computer science departments. The analysis was based on a matched-pairs experimental design. As opposed to a completely randomized design, matched pairs involve one binary factor and blocks that sort the experimental units into pairs.

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'Pedigree is not destiny' when it comes to scholarly success

Anonymous — Wed, 01 May 2019 17:50:44 +0000

'Pedigree is not destiny' when it comes to scholarly success Anonymous (not verified) Wed, 05/01/2019 - 11:50

By: Sante Fe Institute

What matters more to a scientist’s career success: where they currently work, or where they got their Ph.D.? It’s a question a team of researchers teases apart in a new paper published in PNAS. Their analysis calls into question a common assumption underlying academia: that a researcher’s productivity reflects their scientific skill, which is reflected in the prestige of their doctoral training.

It’s true that faculty at prestigious universities publish more scientific papers and receive more citations and awards than professors at lower-ranked institutions. It’s also true that prestigious schools tend to hire new faculty who hold Ph.D.s from similarly prestigious programs. But according to the authors of the new study, an early career researcher’s current working environment is a better predictor of their future success than is the prestige of their doctoral training.

“Pedigree is not destiny,” says SFI External Professor Aaron Clauset (�� Boulder), a co-author on the paper. “Our analysis supports the fairly radical idea for academia that where you train doesn’t directly impact your future productivity.”

The team looked at two basic measures of academic success — productivity (how many papers a researcher publishes) and prominence (how often their work is cited) — of 2453 tenure-track faculty in all 205 Ph.D.-granting computer science departments in the US and Canada during the five years before and five years following those individual’s first faculty appointment.

“We wanted to disentangle the impact of environment on productivity and prominence, and to isolate the effects of where someone trained versus where they went on to work as faculty,” says lead author Samuel Way (�� Boulder). “On the prominence side, people do retain some benefit from having studied in a prestigious Ph.D. program. They continue to accumulate citations from their doctoral work.”

But the prestige of the training program seems to play little role in how many papers researchers go on to produce once they begin their appointments in a new place. “Someone like me, who trained at Colorado, and someone from MIT… if we both end up at Stanford, our productivity will look the same,” says Way.

The authors identify several possible mechanisms driving the increased productivity of faculty at more prestigious institutions. Selection criteria in hiring, expectations for high productivity once hired, and selective retention of productive faculty were all considered. “We only find weak evidence for each,” says Way. However, the prestige of the current work environment had a strong effect on productivity.

Identifying the underlying “forces that tilt the scientific playing field in favor of some scientists over others,” as Clauset says, is important for identifying and potentially correcting the systemic biases that may be limiting the production of scientific knowledge.

“…our findings have direct implications for research on the science of science, which often assumes, implicitly if not explicitly, that meritocratic principles or mechanisms govern the production of knowledge,” write the authors. “Theories and models that fail to account for the environmental mechanism identified here, and the more general causal effects of prestige on productivity and prominence, will thus be incomplete.”

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Do all networks obey the scale-free law? Maybe not

Anonymous — Mon, 04 Mar 2019 23:22:48 +0000

Do all networks obey the scale-free law? Maybe not Anonymous (not verified) Mon, 03/04/2019 - 16:22

Daniel Strain

As Benjamin Franklin once joked, death and taxes are universal. Scale-free networks may not be, at least according to a new study from �� Boulder.

The research challenges a popular two-decade-old theory that networks of all kinds, from Facebook and Twitter to the interactions of genes in yeast cells, follow a common architecture that mathematicians call “scale-free.”

Such networks fit into a larger category of networks that are dominated by a few hubs with many more connections than the vast majority of nodes—think Twitter where for every Justin Bieber (105 million followers) and Kim Kardashian (60 million followers) out there, you can find thousands of users with just a handful of fans.

Key takeaways

A popular theory claims that all networks are “scale-free”—meaning that the patterns of connections coming into and out of nodes follows a precise mathematical structure called a power law distribution.
�� Boulder researchers set out to test that idea, analyzing more than 900 networks from the realms of biology, technology, transportation and more.
They found that only about 4 percent of networks met the strictest definition for being scale-free—and close to half didn’t fit the bill at all.

In research published this week in the journal Nature Communications, �� Boulder’s Anna Broido and Aaron Clauset set out to test that trendy theory. They used computational tools to analyze a huge dataset of more than 900 networks, with examples from the realms of biology, transportation, technology and more.

Their results suggest that death and taxes may not have much competition, at least in networks. Based on Broido and Clauset’s analysis, close to 50 percent of real networks didn’t meet even the most liberal definition of what makes a network scale-free.

Those findings matter, Broido said, because the shape of a network determines a lot about its properties, including how susceptible it is to targeted attacks or disease outbreaks.

“It’s important to be careful and precise in defining things like what it means to be a scale-free network,” said Broido, a graduate student in the Department of Applied Mathematics.

Clauset, an associate professor in the Department of Computer Science and the BioFrontiers Institute, agrees.

“The idea of scale-free networks has been a unifying but controversial theme in network theory for nearly 20 years,” he said. “Resolving the controversy has been difficult because we lacked good tools and broad data. What we’ve found now is that there is little evidence for classically scale-free networks except in a few specific places. Most networks don’t look scale-free at all.”

Power law

Deciding whether or not a network is “scale-free,” however, can be tricky. Many types of networks look similar from a distance.

But Scale-free networks are special because the patterns of connections coming into and out of nodes follows a precise mathematical form called a power law distribution.

“If human height followed a power law, you might expect one person to be as tall as the Empire State Building, 10,000 people to be as tall as a giraffe, and more than 150 million to be only about 7-inches-tall,” Clauset said.

Beginning in the late 1990s, a handful of researchers made a bold claim that all real-world networks follow a universal structure represented by such giraffe- and inch-sized disparities.

There was just one problem: “The original claims were mostly based on analyzing a handful of networks with very rough tools,” Clauset said. “The idea was provocative, but also, in retrospect, quite speculative.”

To take scale-free networks out of the realm of speculation, he and Broido turned to the Index of Complex Networks (ICON). This archive, which was assembled by Clauset’s research group at �� Boulder, lists data on thousands of networks from every scientific domain. They include the social links between Star Wars characters, interactions among yeast proteins, friendships on Facebook and Twitter, airplane travel and more.

Their findings were stark. By applying a series of statistical tests of increasing severity, the researchers calculated that only about 4 percent of the networks they studied met the strictest criteria for being scale free, meaning the number of connections that each node carried followed a power-law distribution. These special networks included some types of protein networks in cells and certain kinds of technological networks.

A multitude of shapes

But not all researchers use those exact requirements to decide what makes a scale-free network, Broido said. To account for these alternative definitions, she and Clauset adapted their tests to account for each of the variations.

“Wherever you’re coming from, one of our definitions should be close to what you’re thinking,” Broido said.

Despite the added flexibility, most networks still failed to show evidence even for weakly scale-free structure. Roughly half of all biological networks and all social networks, for example, didn’t look like anything close to a scale-free network, no matter how flexible the definitions were made.

Far from being a let-down, Clauset sees these null findings in a positive light: if scale-free isn’t the norm, then scientists are free to explore new and more accurate structures for the networks people encounter every day.

“The diversity of real networks presents a mystery,” he said. “What are the common shapes of the networks? How do different kinds of networks assemble and maintain their structure over time? I’m excited that our findings open up room to explore new ideas.”

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Muscle-building proteins hold clues to ALS, muscle degeneration

Anonymous — Wed, 31 Oct 2018 06:00:00 +0000

Muscle-building proteins hold clues to ALS, muscle degeneration Anonymous (not verified) Wed, 10/31/2018 - 00:00

Lisa Marshall

Toxic protein assemblies, or "amyloids," long considered to be key drivers in many neuromuscular diseases, also play a beneficial role in the development of healthy muscle tissue, University of Colorado Boulder researchers have found.

"Ours is the first study to show that amyloid-like structures not only exist in healthy skeletal muscle during regeneration, but are likely important for its formation," said co-first author Thomas Vogler, an M.D./PhD candidate in the Department of Molecular, Cellular, and Developmental Biology (MCDB).

The surprising finding, published today in the journal Nature, sheds new light on the potential origins of a host of incurable disorders, ranging from amyotrophic lateral sclerosis (ALS) to inclusion body myopathy (which causes debilitating muscle degeneration) to certain forms of muscular dystrophy.

The researchers believe it could ultimately open new avenues for treating musculoskeletal diseases and also lend new understanding to related neurological disorders like Parkinson's and Alzheimer's disease, in which different amyloids play a role.

"Many of these degenerative diseases share a similar scenario in which they have these protein aggregates that accumulate in the cell and gum up the system," said co-first author Joshua Wheeler, also an M.D./PhD candidate in the Department of Biochemistry. "As these aggregates are beneficial for normal regeneration, our data suggest that the cell is just damaged and trying to repair itself."

For the study, Vogler and MCDB professor Brad Olwin, who study muscle generation, teamed up with Wheeler and Roy Parker, who study RNA, to investigate a protein called TDP-43.

TDP-43 has long been suspected to be a culprit in disease, having been found in the skeletal muscle of people with inclusion body myopathy and the neurons of people with ALS. But when the researchers closely examined muscle tissue growing in culture in the lab, they discovered clumps of TDP-43 were present not only in diseased tissue but also in healthy tissue.

"That was astounding," said Olwin. "These amyloid-like aggregates, which we thought were toxic, seemed to be a normal part of muscle formation, appearing at a certain time and then disappearing again once the muscle was formed."

Subsequent studies in muscle tissue growing in culture showed that when the gene that codes for TDP-43 was knocked out, muscles didn't grow. When the researchers looked at human tissue biopsied from healthy people whose muscles were regenerating, they found aggregates, or "myo-granules," of TDP-43. Further RNA-protein mapping analysis showed that the clusters - like shipping trucks traveling throughout the cell - appear to carry instructions for how to build contractile muscle fibers.

Wheeler and Vogler, both competitive runners and long-time friends, came up with the initial idea for the study while on a trail run. Wheeler says the data suggest that when healthy athletes push their muscles hard via things like marathons and ultramarathons, they are probably also forming amyloid-like clusters within their cells.

The key question remains: Why do most people quickly clear these proteins while others do not, with. the granules - like sugar cubes that won't dissolve - clustering together and causing disease?

"If they normally form and go away, something is making them dissolve," said Olwin. "Figuring out the mechanisms involved could potentially open a new avenue for treatments."

The team is also interested in exploring whether a similar process may occur in the brain after injury, kick-starting disease. And subsequent studies will go even further to identify what the protein clusters do.

"This is a great example of how collaboration across disciplines can lead to really important work," said Parker.

As participants in ��'s Medical Science Training Program, which enables students to concurrently pursue a medical degree at the Anschutz Medical Campus and a PhD at �� Boulder, Wheeler and Vogler hope that someday the work they do in the lab will help the patients they see in the clinic.

"The holy grail of all this is to be able to treat devastating and incurable diseases like ALS and to develop therapeutic strategies to improve skeletal muscle and fitness," said Wheeler. "We are just opening the door on this."

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Riboglow improves live cell RNA imaging

Anonymous — Wed, 26 Sep 2018 06:00:00 +0000

Riboglow improves live cell RNA imaging Anonymous (not verified) Wed, 09/26/2018 - 00:00

Jessica Miller

In a multidisciplinary study recently published in Nature Chemical Biology, researchers at the University of Colorado Boulder have developed a novel tool for visualizing RNA. This project centered on a collaboration between the Palmer Lab, with expertise in live cell imaging, the Batey Lab, with expertise in RNA, and the Gryko Lab with expertise in chemical synthesis. Researchers from the Parker and Jimenez labs also contributed to the study.

RNA, or ribonucleic acid, is a macromolecule essential to all forms of life. RNA plays a key role in gene expression and regulation, catalyzes the formation of polypeptides, and facilitates the transformation of genetic information from DNA to protein. Considering the many functions of this diverse molecule, visualizing RNA is essential to understanding a wide array of cellular processes.

Visualization of U-bodies in live mammalian cells

“As the community continues to discover new functions for coding and non-coding RNAs, the desire to look at them over time in live cells can provide unique functional insights“, commented Esther Braselmann, the lead author on this study and member of the Palmer Lab at the BioFrontiers Institute. Dr. Braselmann recently won a prestigious NIH K99 award, which helps outstanding postdoctoral researchers transition to tenure-track positions.

Established techniques to fluorescently tag and track RNA have several limitations. These tags are not compatible with all types of RNA, perform poorly in live cell studies, and can interfere with normal RNA activity due to their large size. The authors of this study sought to create a versatile imaging platform applicable to real-time experiments in live cells.

The methodology presented in this study relies on a Cobalamin-fluorophore probe which fluoresces upon binding to riboswitch RNA. This system is highly adaptable, allowing researchers to target diverse types of RNA and customize the probe with fluorophores of different colors.

The authors employed this Riboglow technology to visualize mRNA dynamics in live mammalian cells. They were able to record mRNA localization to stress granules, and visualize U1 snRNA in live cells for the first time. When compared to other imaging techniques, Riboglow was less susceptible to photobleaching and demonstrated a robust fluorescent signal.

“We view Riboglow as a complementary platform to existing tools and an addition to the growing toolbox for labeling RNAs,” remarked Dr. Braselmann. The versatility of the Riboglow platform will allow for widespread application to continue illuminating the many roles of RNA in live cells.

This research was supported by the Human Frontiers Science Project, the National Institute of Health, and the National Science Centre.

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Shape-shifting material can morph, reverse itself using heat, light

Anonymous — Fri, 24 Aug 2018 06:00:00 +0000

Shape-shifting material can morph, reverse itself using heat, light Anonymous (not verified) Fri, 08/24/2018 - 00:00

Trent Knoss

A new material developed by �� Boulder engineers can transform into complex, pre-programmed shapes via light and temperature stimuli, allowing a literal square peg to morph and fit into a round hole before fully reverting to its original form.

The controllable shape-shifting material, described today in the journal Science Advances, could have broad applications for manufacturing, robotics, biomedical devices and artificial muscles.

“The ability to form materials that can repeatedly oscillate back and forth between two independent shapes by exposing them to light will open up a wide range of new applications and approaches to areas such as additive manufacturing, robotics and biomaterials”, said Christopher Bowman, senior author of the new study and a Distinguished Professor in �� Boulder’s Department of Chemical and Biological Engineering (CHBE).

Previous efforts have used a variety of physical mechanisms to alter an object’s size, shape or texture with programmable stimuli. However, such materials have historically been limited in size or extent and the object state changes have proven difficult to fully reverse.

The new �� Boulder material achieves readily programmable two-way transformations on a macroscopic level by using liquid crystal elastomers (LCEs), the same technology underlying modern television displays. The unique molecular arrangement of LCEs make them susceptible to dynamic change via heat and light.

To solve this, the researchers installed a light-activated trigger to LCE networks that can set a desired molecular alignment in advance by exposing the object to particular wavelengths of light. The trigger then remains inactive until exposed to the corresponding heat stimuli. For example, a hand-folded origami swan programmed in this fashion will remain folded at room temperature. When heated to 200 degrees Fahrenheit, however, the swan relaxes into a flat sheet. Later, as it cools back to room temperature, it will gradually regain its pre-programmed swan shape.

The ability to change and then change back gives this new material a wide range of possible applications, especially for future biomedical devices that could become more flexible and adaptable than ever before.

“We view this as an elegant foundational system for transforming an object’s properties,” said Matthew McBride, lead author of the new study and a post-doctoral researcher in CHBE. “We plan to continue optimizing and exploring the possibilities of this technology.”

Additional co-authors of the study include Alina Martinez, Marvin Alim, Kimberly Childress, Michael Beiswinger, Maciej Podgorski and Brady Worrell of �� Boulder and Lewis Cox and Jason Killgore of the National Institute of Standards and Technology (NIST). The National Science Foundation provided funding for the research.

[video:https://vimeo.com/286537992]

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