FAU researchers are the first to show that cells in close proximity to each other can sense when a cell is dying due to environmental stressors like UV light and smoke, and eat the cell before it becomes toxic. In much the same way PAC-MAN gobbles through an intense maze of dots eating and destroying its aggressors, researchers from the Charles E. Schmidt College of Medicine at Florida Atlantic University have revealed for the first time how a similar mechanism in the eye lens does exactly the same thing. They have discovered that cells in close proximity to each other can sense when a cell is dying due to environmental stressors like UV light, smoke and other pollutants, and eat the cell before it becomes toxic. In a study just published in the Journal of Biochemistry and Molecular Biology, these researchers not only demonstrate that this happens with lens cells, but they uncover the molecules that are required to do it. They also reveal that the molecules needed for the cells to eat each other are degraded by UV light. And when that happens, the cells lose the ability to eat each other. Since these systems are not confined to the eye lens and diseases of the eye such as cataracts, uncovering the mechanisms and functions will provide important information in more complex tissues and disease states. It has long been known that environmental damage is associated with cell death and that it kills tissue because it is toxic. Yet, the eye lens, which does not have a blood supply, gets hit by UV light and other stressors that continuously kill cells. Consistently, the eye lens has evolved multiple protective and repair systems to preserve its transparent function in the face of environmental insults. So how does it do that? That’s exactly what these researchers sought to understand in this novel study. They were able to establish that the intact eye lens is indeed capable of removing apoptopic lens cell debris and worked to identify a molecular mechanism for this process by lens cells. By using the eye lens as a model, they searched to understand how other cells and tissues might operate in a different way than by using blood cells. “Accumulation of apoptopic material is toxic to epithelial cell populations, which include the cornea, skin, lungs and other tissue, and is associated with the development of multiple autoimmune, inflammatory, aging and degenerative diseases,” said Marc Kantorow, Ph.D., author of the paper and a professor and director of graduate studies in FAU’s College of Medicine. “Identifying the cell systems that protect against the effects of apoptosis-inducing insults is an important step toward understanding and developing therapies to treat these diseases.” Using embryonic chicken lenses, Kantorow and his collaborators Lisa Brennan, Ph.D., associate research professor; Daniel Chauss, a Ph.D. candidate; and Olya Bakina, a Fulbright scholar and graduate student all in FAU’s College of Medicine, engineered the eye lens cells to be either fluorescent red or fluorescent green – instead of what would normally be a clear lens cell. They created artificial dead green cells and fed them to the red cells. When the green cells ate the red cells, they turned yellow. They observed this mechanism in real-time using microscopy to track the digesting cells and utilized antibodies to specific molecules to determine which molecules were needed for the cells to eat each other. “It is widely known that cells have very specific functions and that environmental damage is associated with cell death,” said Brennan. “Before this study, the common knowledge was that what removed these dead cells were specialized immune cells that literally go into the tissue and eat these dead cells and that’s how your body got rid of them. We looked at the eye lens as a model to try to search for alternate ways to get rid of these dead cells to keep a tissue alive.” The eye lens is one of the most environmentally challenged tissues of the body since it lacks protective pigmentation and resides just behind the transparent and surface exposed cornea. Damage to the lens and its components causes age-related cataract formation that remains a leading cause of visual disability despite advances in surgical treatment options. “Twenty percent of all cataracts are associated with UV light exposure and at some point in their lifetime, most people will get cataracts,” said Kantorow. “Our work has the potential to lead to the development of treatments and therapies that would eliminate the need for surgery, which is the only way to treat cataracts today.”
Cellulose as well as xylan and xyloglucan are important components of plant cell walls. All walking sticks (Phasmatodea) inherited multiple copies of cellulase genes, whose enzymes can attack the glucose backbone of cellulose. However, some of these enzymes can also break down the xylose-backbone of xylan, and others the xylose-glucose backbone of xyloglucan. This discovery marks the first known xyloglucanase of any kind to be found in multicellular animals. Such enzymes in animals were previously not thought to exist. Researchers in the Department of Entomology isolated the cellulase genes from seven species of stick insect, including the Australian Extatosoma tiaratum, the Vietnamese Ramulus artemis, and the Bornean Aretaon asperrimus. All express multiple different cellulase enzymes from the glycoside hydrolase family 9 (GH9). Maintaining redundant enzymes does not make sense if all have the same function, so the researchers hypothesized some had lost their function or evolved to do something new. To test what these enzymes were capable of, the genes were expressed in a stable insect cell line, and the activities of the isolated proteins tested against different plant cell wall polymers. The results showed that one groups of enzymes were active against cellulose and xylan, and another cellulose and xyloglucan, and several in each group could also degrade glucomannan. These abilities held in all families of stick insects, present in the Vietnamese Medauroidea extradentata (Family Phasmatidae), the Madagascan Sipyloidea sipylus (Diapheromeridae), and the Peruvian Peruphasma schultei (Peruphasmatidae). The researchers even got samples of the Californian Timema cristinae (Timematidae), considered the sister group to all other Phasmatodea, and found the same enzymes with the same new abilities. Such multifunctionality is almost unheard of from glycoside hydrolases 9, and xyloglucanases of any family were never discovered in animals before. "If we hadn't tested these enzymes on other substrates besides cellulose, there was no way we could have discovered these functions," said Dr. Matan Shelomi, a postdoctoral fellow at the Max Planck Institute for Chemical Ecology and lead author of the study. "It was good that we did: nobody found these kind of powerful enzymes in an animal before." A new twist on an old gene family Most importantly, the enzyme functions matched the evolutionary relationships between the insects. Xylanase-cellulases from different species were closely related, and the xyloglucanase-cellulases also formed a monophyletic group. Because T. cristinae also had these activities, this means an ancestral, insect cellulase gene duplicated into several genes, some of which were then able to evolve new abilities. This happened before the Phasmatodea evolved. Next the researchers are testing other insects related to the stick insects, to see if they have multifunctional cellulases too. The ability to break down different polymers with the same enzymes means the Phasmatodea gut is unusually efficient. Along with other enzymes such as cellobiases and xylobiases, their guts can fully degrade nearly all the plant cell wall into its component sugars, using them for nutrition as well as having more access to the easily digested cytoplasm within the cells. This means they can derive more nutrition from the same leafy diet than other herbivores. Theoretically, they could even digest wood. "There is a big community in Germany of people with stick insects as pets," says Shelomi, "and they report them nibbling on sticks, moss, bark, and even Styrofoam and electric cables… but leaves are still their main food. Maybe their gut can break down wood, but their jaws are better suited for leaves, which probably taste better too." Explore further: Garbage bug may help lower the cost of biofuel More information: Matan Shelomi et al. Ancestral gene duplication enabled the evolution of multifunctional cellulases in stick insects (Phasmatodea), Insect Biochemistry and Molecular Biology (2016). DOI: 10.1016/j.ibmb.2016.02.003
There are only 125 of the native parrots left, but now researchers may have discovered the secret to keeping the birds breeding. Dr Pamela von Hurst, from Massey's School of Food and Nutrition, has just had a paper published on the study linking vitamin D in rimu fruit with the endangered parrot's nutritional needs and breeding habits, in the Journal of Steroid Biochemistry and Molecular Biology. The research was carried out in collaboration with Professor David Raubenheimer from the University of Sydney, and staff from the Department of Conservation. Kākāpō breed only in years when the local trees are full with fruit, which they feed to their chicks. This includes Rimu, which this new study has revealed produces berries rich in vitamin D – a nutrient essential for laying eggs and the growth of chicks. Previous attempts to encourage breeding during years of poor fruit supply by providing supplementary food have failed. But Dr von Hurst says this latest research might be a game changer. "This could change the way we encourage breeding. Rimu berries provide kākāpō with high levels of vitamin D and calcium, meaning they are the perfect food package for breeding and nesting birds. "The study challenges previous beliefs there are no food sources with a naturally high concentration of vitamin D. Kākāpō are forest-dwelling, nocturnal and flightless, which means minimal sun exposure, so we assumed there must be a dietary source. This confirms that." From the beginning of the breeding season in spring, female kākāpō consume Rimu berries, which at that time are unripe. Dr von Hurst says while the vitamin D content of the unripe berries isn't yet known, it's possible that vitamin D in the fruit triggers nesting in the female bird. "We know that kākāpō breed in response to rimu fruiting; this result may tell us why, and help us identify which other trees stimulate breeding." "The next step will include measuring the vitamin D levels of adult birds during breeding, growing chicks and rimu fruit throughout the ripening process, to see if the vitamin D content changes over time, and with it, the levels in the birds". The Department of Conservation's Kākāpō Recovery Team is keen to build on this research. Dr Andrew Digby says, "This potential link between vitamin D in rimu fruit and kākāpō breeding is an exciting finding, and is a high priority for us to explore further. We have a collaborative programme in place to expand on this research in the upcoming breeding season, to further understand the link between vitamin D and kākāpō health and fertility." Explore further: Geometric model could mean breakthrough in saving endangered kakapo
As Barack Obama prepares to leave office, Nature examines the scientific highs and lows of his presidency. Read the other stories in this series about his policies on space, research integrity and climate change. When president-elect Barack Obama chose physicist John Holdren as his top science adviser in December 2008, some biomedical researchers worried that the pick signalled a White House bias towards physical science. Obama quickly put those fears to rest. Within weeks of his inauguration, he had overturned restrictions on research using embryonic stem cells. He has gone on to launch major initiatives to map the brain, develop personalized medical treatments and cure cancer. But faced with a penny-pinching Congress, Obama’s strong support for biomedical science has not translated into significant funding gains for the US National Institutes of Health (NIH). The agency has seen the purchasing power of flat research budgets eroded by inflation (see ‘Budget battles’). “The life sciences were a significant priority for the Obama administration,” says Gregory Petsko, a biochemist at Weill Cornell Medical College in New York City. “But with Congress being the way that it is, there was a limit to what Obama could do as far as increasing support of biomedical research.” It is the big initiatives that will probably form Obama’s lasting biomedical legacy, says Benjamin Corb, head of public affairs at the American Society for Biochemistry and Molecular Biology in Rockville, Maryland. In 2013, Obama announced the Brain Research Through Advancing Innovative Neurotechnologies (BRAIN) initiative to map the human brain. In 2015, he unveiled the Precision Medicine Initiative, which includes an ambitious study of health records and genomic information from one million people in the United States. And in January, he introduced the Cancer Moonshot, a US$1-billion proposal to double the pace of cancer research in five years. NIH director Francis Collins, who led the Human Genome Project in the 1990s, likens Obama to a player who scores three goals in the same game: “I said to him, basically, ‘Mr President, you have achieved a hat-trick.’” But such programmes may come at a cost to basic research funding, even as they draw attention to areas of science that may be overlooked or underfunded. “These big initiatives tend to cast a really large shadow,” says Corb. “They can overshadow some of those basic research needs.” And it’s not clear whether Obama’s major initiatives will survive under the next president. Democratic presidential candidate Hillary Clinton has said that she would continue the Cancer Moonshot initiative. She also supports Alzheimer’s disease research, which bodes well for the BRAIN initiative if she is elected, Corb says. Republican candidate Donald Trump has no clear policy on biomedical research. But the next president won’t be making that decision alone. Patient advocates drive major changes in biomedical research priorities and funding over time, and will probably ensure that Obama’s big-science initiatives continue, says Mary Woolley, president of the science-advocacy organization Research!America in Arlington, Virginia. “Determined advocates are not going to take ‘no’ for an answer,” she says. “They’ll be the ones that bridge administrations.”
News Article | April 6, 2016
Over the past decade, University of Chicago professor and INCITE investigator Benoît Roux has made great strides in biochemistry using Argonne Leadership Computing Facility resources. One of his recent discoveries fills in essential information inaccessible to experimentalists, and potentially crucial to new therapeutic drug design. “Molecular machines,” composed of protein components, consume energy in order to perform specific biological functions. The concerted actions of the proteins trigger many of the critical activities that occur in living cells. However, like any machine, the components can break (through various mutations) and then the proteins fail to perform their functions correctly. It is known that malfunctioning proteins can result in a host of diseases, but pinpointing when and how a malfunction occurs is a significant challenge. Usually, very few functional states of molecular machines are determined by experimentalists working in wet laboratories. Therefore, more structure-function information is needed to develop an understanding of disease processes and to design novel therapeutic agents. The research team of Benoît Roux, a professor in the University of Chicago’s Department of Biochemistry and Molecular Biology and a senior scientist in the U.S. Department of Energy’s (DOE) Argonne National Laboratory Center for Nanoscale Materials, relies on an integrative approach to discover and define the basic mechanisms of biomolecular systems — an approach that relies on theory, modeling and running large-scale simulations on some of the fastest open-science supercomputers in the world. Computers have already changed the landscape of biology in considerable ways; modeling and simulation tools are routinely used to fill in knowledge gaps from experiments, and they are used to help design and define research studies. Petascale supercomputing provides a window into something else entirely: the ability to calculate all the interactions occurring between the atoms and molecules in a biomolecular system, such as a molecular machine, and visualize the motion that emerges. Roux’s team recently concluded a three-year Innovative and Novel Computational Impact on Theory and Experiment (INCITE) project at the Argonne Leadership Computing Facility (ALCF), a DOE Office of Science User Facility, to understand how P-type ATPase ion pumps — an important class of membrane transport proteins — operate. Over the past decade, Roux and his collaborators, Avisek Das, Mikolai Fajer, and Yilin Meng, have been developing new computational approaches to simulate virtual models of biomolecular systems with an unprecedented accuracy. The team exploits state-of-the-art developments in molecular dynamics (MD) and protein modeling. The MD simulation approach, frequently used in computational physics and chemistry, calculates the motions of all the atoms in a given molecular system over time — information that’s impossible to access experimentally. In biology, large-scale MD simulations provide a perspective to understand how a biologically important molecular machine functions. For several years, Roux’s research has been focused on membrane proteins, which control the bidirectional flow of material and information in a cell. Now, in a major breakthrough, he and his team have described the complete transport cycle in atomic detail of a large calcium pump called Sarco/endoplasmic reticulum calcium ATPase, or SERCA, which plays an important role in normal muscle contraction. This membrane protein uses the energy from ATP hydrolysis to transport calcium ions against their concentration gradient and, importantly, its malfunction causes cardiac and skeletal muscle diseases. Roux and his team wanted to understand how SERCA functions in a membrane, so he set out to build a complete atomistic picture of the pump in action. Das, a postdoctoral research fellow in Roux’s lab, did that by obtaining all the transition pathways for the entire ion transport cycle using an approach called the string method — essentially capturing a “molecular movie” of the transport process, frame-by-frame, of how different protein components and parts within the proteins communicated with each other. This achievement has yielded an unprecedented level of detail about the pump’s mechanism, which can now be exploited by experimentalists to further probe this important system. A membrane protein, like all protein molecules, consists of a long chain of amino acids. Once fully formed, it folds into a highly specific conformation that enables it to perform its biological function. Membrane proteins change shape and go through many conformational “states” to perform their functions. “From a scientific standpoint, membrane proteins, such as the calcium pump, are very interesting because they undergo complex changes in their three-dimensional conformations,” said Roux. “Ultimately, a better understanding may have a great impact on human health.” Experimentalists understand the structural details of proteins’ stable conformational states, but very little about the process by which a protein changes from one conformational state to another. “Only computer simulation can explore the interactions that occur during these structural transitions,” said Roux. Intermediate conformations along these transitions could potentially provide the essential information needed for the discovery of novel therapeutic agent design. (Drugs are essentially molecules that counteract the effect of bad mutations to help recover the normal functions of the protein.) Because membrane proteins regulate many aspects of cell physiology, they can serve as possible diagnostic tools or therapeutic targets. Roux and his team are trying to obtain detailed knowledge about all of the relevant conformational states that occur during the transport cycle of SERCA. In years one and two of his study, Roux’s team identified two of the conformation transition pathways needed to describe SERCA’s transport cycle. Last year, the project shifted focus to the three remaining pathways. As is the case for much of the domain science research being conducted on DOE leadership supercomputer systems today, biomolecular science relies on advances in methodology, as well as in software and hardware technologies. The usefulness of Roux’s simulations hinges on the accuracy of the modeling parameters and on the efficiency of the MD algorithm enabling the adequate sampling of motions. Computational science teams can spend years refining their application code to do what they need it to do, which is often to simulate a particular physical phenomenon at the necessary space and time scales. Code advancements can push the simulation capabilities and take advantage of the machine’s features, such as high processor counts or advanced chips, to evolve the system for longer and longer periods of time. Roux and his team used a premier MD simulation code, called NAMD, that combines two advanced algorithms — the swarm-of-trajectory string method and multi-dimensional umbrella sampling. NAMD, which was first developed at the University of Illinois at Urbana-Champaign by Klaus Schulten and Laxmikant Kale, is a program used to carry out classical simulations of biomolecular systems. It is based on the Charm++ parallel programming system and runtime library, which provides infrastructure for implementing highly scalable parallel applications. When combined with a machine-specific communication library (such as PAMI, available on the Blue Gene/Q), the string method can achieve extreme scalability on leadership-class supercomputers. ALCF staff provided maintenance and support for NAMD software and helped to coordinate and monitor the jobs running on Mira, ALCF’s 10-petaflops IBM Blue Gene/Q. ALCF computational scientist Wei Jiang has been actively collaborating with Roux’s team since 2012, as part of Mira’s Early Science Program. Jiang worked with IBM’s system software team on early stage porting and optimization of NAMD on the Blue Gene/Q architecture. He is also one of the core developers of NAMD’s multiple copy algorithm, which is the foundation for multiple INCITE projects that use NAMD. Jiang, who has a background in computational biology, considers the recent work a significant breakthrough. “Only in the third year of the project did we begin to see real progress,” said Jiang. “The first and second year of an INCITE project is often accumulated experience.” The computations Roux and his team ran for this breakthrough work will serve as a roadmap for simulating and visualizing the basic mechanisms of biomolecular systems going forward. By studying experimentally well-characterized systems of increasing size and complexity within a unified theoretical framework, Roux’s approach offers a new route for addressing fundamental biological questions. Roux’s team can be considered to be among the bleeding-edge users of the ALCF, the recipient of a steady succession of INCITE awards on Blue Gene systems since 2008, and whose work on supercomputing resources at Argonne dates back to the laboratory’s Blue Gene/L, which the Mathematics and Computer Science Division installed in 2005 for evaluation. When ALCF’s next-generation system Theta arrives later this year, Roux’s team will again be among the early science users. This research is supported by DOE’s Office of Science. Computing time at the ALCF was allocated through DOE’s Innovative and Novel Computational Impact on Theory and Experiment (INCITE) program. Argonne National Laboratory seeks solutions to pressing national problems in science and technology. The nation's first national laboratory, Argonne conducts leading-edge basic and applied scientific research in virtually every scientific discipline. Argonne researchers work closely with researchers from hundreds of companies, universities, and federal, state and municipal agencies to help them solve their specific problems, advance America's scientific leadership and prepare the nation for a better future. With employees from more than 60 nations, Argonne is managed by UChicago Argonne, LLC for the U.S. Department of Energy's Office of Science. The U.S. Department of Energy's Office of Science is the single largest supporter of basic research in the physical sciences in the United States and is working to address some of the most pressing challenges of our time.