Paz E.A.,Arizona Cancer Center |
Paz E.A.,University of Arizona |
Lafleur B.,Arizona Cancer Center |
Lafleur B.,University of Arizona |
And 4 more authors.
Molecular Carcinogenesis | Year: 2014
Polyamine metabolism is a highly coordinated process that is essential for normal development and neoplastic growth in mammals. Although polyamine metabolism is a validated pathway for prevention of carcinogenesis, the mechanisms by which polyamines elicit their tumorigenic effects are poorly understood. In this study, we investigated the role of polyamine metabolism in colon cancer by screening a non-coding RNA (ncRNA) platform to identify polyamine responsive signaling nodes. We report that multiple non-coding RNAs are altered by polyamine depletion including induction of microRNA (miRNA) let-7i, a member of the tumor suppressive let-7 family. The let-7 family targets several RNAs for translational repression, including the growth-associated transcription factor HMGA2 and is negatively regulated by the pluripotency factor LIN28. Depletion of polyamines using difluoromethylornithine (DFMO) or genetic knockdown of the polyamine-modified eukaryotic translation initiation factor 5A isoforms 1 and 2 (eIF5A1/2) resulted in robust reduction of both HMGA2 and LIN28. Locked nucleic acid (LNA) oligonucleotides targeting the seed region of the let-7 family rescued the expression of HMGA2, but not LIN28, in both DFMO-treated and eIF5A1/2 knockdown cultures. Our findings suggest that polyamines are oncometabolites that influence specific aspects of tumorigenesis by regulating pluripotency associated factors, such as LIN28, via an eIF5A-dependent but let-7-independent mechanism while the expression of proliferation-related genes regulated by let-7, such as HMGA2, is mediated through microRNA mediated repression. Therefore, manipulating polyamine metabolism may be a novel method of targeting the LIN28/let-7 pathway in specific disease states. © 2013 Wiley Periodicals, Inc.
Yu Z.,Kent State University |
Gaerig V.,University of Arizona |
Cui Y.,Kent State University |
Kang H.,University of Arizona |
And 6 more authors.
Journal of the American Chemical Society | Year: 2012
The discovery of G-quadruplexes and other DNA secondary elements has increased the structural diversity of DNA well beyond the ubiquitous double helix. However, it remains to be determined whether tertiary interactions can take place in a DNA complex that contains more than one secondary structure. Using a new data analysis strategy that exploits the hysteresis region between the mechanical unfolding and refolding traces obtained by a laser-tweezers instrument, we now provide the first convincing kinetic and thermodynamic evidence that a higher order interaction takes place between a hairpin and a G-quadruplex in a single-stranded DNA fragment that is found in the promoter region of human telomerase. During the hierarchical unfolding or refolding of the DNA complex, a 15-nucleotide hairpin serves as a common species among three intermediates. Moreover, either a mutant that prevents this hairpin formation or the addition of a DNA fragment complementary to the hairpin destroys the cooperative kinetic events by removing the tertiary interaction mediated by the hairpin. The coexistence of the sequential and the cooperative refolding events provides direct evidence for a unifying kinetic partition mechanism previously observed only in large proteins and complex RNA structures. Not only does this result rationalize the current controversial observations for the long-range interaction in complex single-stranded DNA structures, but also this unexpected complexity in a promoter element provides additional justification for the biological function of these structures in cells. © 2012 American Chemical Society.
Cui Y.,Kent State University |
Koirala D.,Kent State University |
Kang H.,University of Arizona |
Dhakal S.,Kent State University |
And 5 more authors.
Nucleic Acids Research | Year: 2014
Minute difference in free energy change of unfolding among structures in an oligonucleotide sequence can lead to a complex population equilibrium, which is rather challenging for ensemble techniques to decipher. Herein, we introduce a new method, molecular population dynamics (MPD), to describe the intricate equilibrium among non-B deoxyribonucleic acid (DNA) structures. Using mechanical unfolding in laser tweezers, we identified six DNA species in a cytosine (C)-rich bcl-2 promoter sequence. Population patterns of these species with and without a small molecule (IMC-76 or IMC-48) or the transcription factor hnRNP LL are compared to reveal the MPD of different species. With a pattern recognition algorithm, we found that IMC-48 and hnRNP LL share 80% similarity in stabilizing i-motifs with 60 s incubation. In contrast, IMC-76 demonstrates an opposite behavior, preferring flexible DNA hairpins. With 120-180 s incubation, IMC-48 and hnRNP LL destabilize i-motifs, which has been previously proposed to activate bcl-2 transcriptions. These results provide strong support, from the population equilibrium perspective, that small molecules and hnRNP LL can modulate bcl-2 transcription through interaction with i-motifs. The excellent agreement with biochemical results firmly validates the MPD analyses, which, we expect, can be widely applicable to investigate complex equilibrium of biomacromolecules. © 2014 The Author(s) 2014.
News Article | February 22, 2017
Quick! Name the top-performing athletes in the animal kingdom. Cheetah? Try again. Blue whale? Nope. Here's a clue: If you take a walk in the desert on a moonlit night, you might see them, darting from flower to flower and hovering in midair: moths of the hawkmoth family (Sphingidae). Nectar-feeding moths, pollinating bats and hummingbirds are masters in sustaining the most intense exercise of all animals. To extract nectar from a flower, they must hover in front of the flower before darting off to the next one. But how can these organisms perform such feats on a diet that's mostly sugar? New research by University of Arizona biologists not only offers an explanation, but also suggests that these animals stay healthy not despite, but because of, their sugary diet. Oxygen, while necessary for life to exist, is a double-edged sword. The more we engage in intense aerobic exercise, such as hovering, the more oxygen reveals its ugly side in the form of reactive oxygen species -- small reactive molecules that wreak havoc on cells. Researchers in the lab of Goggy Davidowitz in the Department of Entomology in the UA's College of Agriculture and Life Sciences discovered that hawkmoths (also known as Manduca moths) have evolved a strategy that helps them minimize the muscle damage inflicted by the oxidative stress generated during sustained flight. The results are published in the journal Science. "If you wanted to consume the equivalent amount of sugar that a moth takes up in one meal, you'd have to drink 80 cans of soda," says Eran Levin, who led the research as a postdoctoral fellow in Davidowitz's group. "It's amazing that an animal can process such an amount of sugar in such a short time." Nectar-feeding moths and hummingbirds don't take up any antioxidants with their diet, which begs the question of how they deal with the oxidative damage their muscles are suffering during the moths' nightly foraging flights. Two sophisticated pieces of equipment set up to work in tandem made it possible to study in great detail the metabolism of Manduca moths during sustained flight. The team found that the insects actually use the sugar in their diet to make their own antioxidants. They accomplish this by shunting the carbohydrates they consume to a metabolic pathway that evolved early on in the evolution of life: the pentose phosphate pathway. Humans, too, have this pathway, but it cannot, on its own, produce all the antioxidants needed, which is why athletes drink antioxidant-laced sports drinks and parents tell their children to eat their veggies. Fitting this pattern, migrating birds often are observed eating berries and fruit -- both rich in antioxidants -- during stopovers. "Manduca is a well-suited model system to study this metabolic pathway, which is the same for bacteria and sequoia trees," Levin explains. "If we understand how the moth is doing it, you can find out how we do it. And we can learn about what goes wrong with our sugar consumption." During the flight experiments, the researchers noticed something strange: The measurements tracking how much oxygen the moths consumed and how much carbon dioxide they produced didn't add up. "If you burn all the sugar you're eating, you expect the same ratio of carbon dioxide exhaled to oxygen consumed," Levin says. "This is normal when you feed on carbohydrates, but we obtained results that shouldn't have been possible according to the scientific literature." Reluctant to trust the data their moths were generating, Davidowitz contacted the manufacturer of the flight measurement apparatus. The CEO of the company came out, and after much troubleshooting, tinkering and adjusting, the readings still did not change. One day, a colleague suggested flying a bumblebee in place of a moth, because bumblebees are known to burn only carbohydrates during flight. Sure enough, the machine spat out the expected values. "That told us our data were correct," Levin says. "They indicated that 40 percent of the carbon in our moth flight experiments had to come from something other than carbohydrates, so we looked for an explanation, and the only such pathway that would produce those results is the pentose phosphate pathway." While flying, it turned out the moths were not only burning carbohydrates, but fat as well. As soon as they rested, within seconds, they shunted their metabolism to the pentose phosphate pathway. In addition to solving the issue of the higher-than-what-theory-allows measurements, the results provided the answer to the mystery of how a nectar-feeding organism avoids killing itself from oxidative stress. "On our flight apparatus, moths fly about three miles a night on average," Davidowitz says. "We don't know how much they are actually flying in the wild." When moths burn lipids during intense exercise, they produce more reactive oxygen species that pose further danger to their flight muscles. "We think the tissue repair occurs when they rest, but we haven't measured that," Davidowitz says. If You Rest, You Rust Moths that were frequent and intense flyers were found to have less oxidative cell damage than those that did not, which seemed counterintuitive, Levin says. "There is this common notion out there where we tend to think that all animals that feed on sugar are very active and fast-living creatures," he says. "But our experiments suggest that this is actually not the case. In fact, there is much more energy to be gained by burning fats, so we suggest these high-performing animals consume a sugar-heavy diet to protect their muscles from damage." Levin says he thinks the principles observed in Manduca moths apply to all animals, as similar respiratory values have been measured in marsupials, mammals and birds. "But because they seemed to contradict theory, those measurements usually didn't make it into the paper, or they were ascribed to lipid synthesis," Levin says. Adds Davidowitz: "We think the ability to shunt glucose through an ancient metabolic pathway has allowed animals that only feed on nectar to embark on long migrations, such as monarch butterflies, hummingbirds and bats." The co-authors on the paper are Giancarlo López-Martinez at New Mexico State University in Las Cruces, New Mexico, and Bentley Fane, in the UA School of Plant Sciences and the UA's BIO5 Institute.
News Article | February 23, 2017
If you take a walk in the desert on a moonlit night, you might see the animal kingdom’s top-performing athletes darting from flower to flower and hovering in midair: moths of the hawkmoth family. Nectar-feeding moths, pollinating bats, and hummingbirds are masters in sustaining the most intense exercise of all animals. To extract nectar from a flower, they must hover in front of the flower before darting off to the next one. But how can these organisms perform such feats on a diet that’s mostly sugar? New research not only offers an explanation, but also suggests that these animals stay healthy not despite, but because of, their sugary diet. Oxygen, while necessary for life to exist, is a double-edged sword. The more we engage in intense aerobic exercise, such as hovering, the more oxygen reveals its ugly side in the form of reactive oxygen species—small reactive molecules that wreak havoc on cells. Researchers in the lab of Goggy Davidowitz in the entomology department in the University of Arizona’s College of Agriculture and Life Sciences discovered that hawkmoths (also known as Manduca moths) have evolved a strategy that helps them minimize the muscle damage inflicted by the oxidative stress generated during sustained flight. The results appear in the journal Science. “If you wanted to consume the equivalent amount of sugar that a moth takes up in one meal, you’d have to drink 80 cans of soda,” says Eran Levin, who led the research as a postdoctoral fellow in Davidowitz’s group. “It’s amazing that an animal can process such an amount of sugar in such a short time.” Nectar-feeding moths and hummingbirds don’t take up any antioxidants with their diet, which begs the question of how they deal with the oxidative damage their muscles are suffering during the moths’ nightly foraging flights. Two sophisticated pieces of equipment set up to work in tandem made it possible to study in great detail the metabolism of Manduca moths during sustained flight. The team found that the insects actually use the sugar in their diet to make their own antioxidants. They accomplish this by shunting the carbohydrates they consume to a metabolic pathway that evolved early on in the evolution of life: the pentose phosphate pathway. Humans, too, have this pathway, but it cannot, on its own, produce all the antioxidants needed, which is why athletes drink antioxidant-laced sports drinks and parents tell their children to eat their veggies. Fitting this pattern, migrating birds often are observed eating berries and fruit—both rich in antioxidants—during stopovers. “Manduca is a well-suited model system to study this metabolic pathway, which is the same for bacteria and sequoia trees,” Levin explains. “If we understand how the moth is doing it, you can find out how we do it. And we can learn about what goes wrong with our sugar consumption.” During the flight experiments, the researchers noticed something strange: The measurements tracking how much oxygen the moths consumed and how much carbon dioxide they produced didn’t add up. “If you burn all the sugar you’re eating, you expect the same ratio of carbon dioxide exhaled to oxygen consumed,” Levin says. “This is normal when you feed on carbohydrates, but we obtained results that shouldn’t have been possible according to the scientific literature.” Reluctant to trust the data their moths were generating, Davidowitz contacted the manufacturer of the flight measurement apparatus. The CEO of the company came out, and after much troubleshooting, tinkering, and adjusting, the readings stayed the same. One day, a colleague suggested flying a bumblebee in place of a moth, because bumblebees are known to burn only carbohydrates during flight. Sure enough, the machine spat out the expected values. “That told us our data were correct,” Levin says. “They indicated that 40 percent of the carbon in our moth flight experiments had to come from something other than carbohydrates, so we looked for an explanation, and the only such pathway that would produce those results is the pentose phosphate pathway.” While flying, it turned out the moths were not only burning carbohydrates, but fat as well. As soon as they rested, within seconds, they shunted their metabolism to the pentose phosphate pathway. In addition to solving the issue of the higher-than-what-theory-allows measurements, the results provided the answer to the mystery of how a nectar-feeding organism avoids killing itself from oxidative stress. “On our flight apparatus, moths fly about three miles a night on average,” Davidowitz says. “We don’t know how much they are actually flying in the wild.” When moths burn lipids during intense exercise, they produce more reactive oxygen species that pose further danger to their flight muscles. “We think the tissue repair occurs when they rest, but we haven’t measured that,” Davidowitz says. Moths that were frequent and intense flyers were found to have less oxidative cell damage than those that did not, which seemed counterintuitive, Levin says. “There is this common notion out there where we tend to think that all animals that feed on sugar are very active and fast-living creatures,” he says. “But our experiments suggest that this is actually not the case. In fact, there is much more energy to be gained by burning fats, so we suggest these high-performing animals consume a sugar-heavy diet to protect their muscles from damage.” Levin says he thinks the principles observed in Manduca moths apply to all animals, as similar respiratory values have been measured in marsupials, mammals, and birds. “But because they seemed to contradict theory, those measurements usually didn’t make it into the paper, or they were ascribed to lipid synthesis,” Levin says. Adds Davidowitz: “We think the ability to shunt glucose through an ancient metabolic pathway has allowed animals that only feed on nectar to embark on long migrations, such as monarch butterflies, hummingbirds, and bats.” Coauthors of the paper from New Mexico State University in Las Cruces, New Mexico, and the University of Arizona’s School of Plant Sciences BIO5 Institute. Funding came from the National Science Foundation.
News Article | October 4, 2016
University of Arizona research assistant professor and immunologist Adam Buntzman used CyVerse data-sharing and analysis capabilities to lead the first team to comprehensively map the human adaptive immune system. Knowing the full potential for our immune systems to protect us from harmful pathogens brings us one huge step closer to finding cures for illnesses such as cancer, infections, autoimmune diabetes and asthma, as well as developing improved diagnostic tests and immune therapies. "Understanding adaptive immunity is one of the grand challenges in science," said Yves Lussier, associate vice president for UA Health Sciences and executive director of the UA Center for Biomedical Informatics and Biostatics. "The unique genetics and massive diversity that occur exclusively in cells of the adaptive immune system has posed a dire need for computer tools created specifically to analyze adaptive immune receptors." Now Buntzman and his collaborators have combined the expertise of immunologists, mathematicians and computer scientists to develop these much-needed computational tools. "If we were on a treasure hunt, where the cure to many illnesses is the buried treasure, then we've just drawn the first map of Treasure Island," said Buntzman, an investigator in the lab of Monica Kraft, a physician-scientist specializing in research of dysfunctional autoimmune response in asthma and chair of the UA Department of Medicine. More Complex Than the Human Genome The adaptive immune system is perhaps the most mysterious — and certainly one of the most vital — systems of the human body, protecting us from everything from common cold germs to serious infections. Cells within the human adaptive immune system produce antibodies and T-cell receptors that identify and remove harmful foreign substances from the body. Unfortunately, the immune system can become a powerful enemy when it misidentifies a part of the body as pathogenic, leading to autoimmune diseases, or when it overreacts to foreign materials such as pollen, resulting in allergies such as asthma. The immune system is considered to be "adaptive" because it can respond to our unique environments. Once it has overcome a particular pathogen, the immune system will "remember" and quickly destroy that pathogen if it ever enters our bodies again, thus giving us immunity. Adaptive immune systems also vary from one person to the next, providing immunity depending upon what microbes an individual has been exposed to throughout their lifetime. "Humans have about 25,000 genes in our genome, but there are millions of harmful microbes, which begs the question: How does such a small number of genes code for all of the immune receptors needed to recognize the enormous array of microbes that can hurt us?" Buntzman said. It turns out that immune receptor genes do not code for immune receptors; rather, broken gene fragments combine in novel ways to produce new code. Every time a new antibody or T-cell receptor is created, the adaptive immune system "shuffles the deck" of gene fragments, blending together the broken pieces through a process called VDJ Recombination. "These gene fragments are then modified by enzymes, creating a dizzying array of variation," Buntzman said. The possible variation of immune receptors far exceeds the number of genes in our genome, at roughly 10 million times more than the number of stars in the Milky Way galaxy, he noted. That's also about 100-fold the number of ants on Earth. And therein lies the complication. "How do we study this much diversity? How do we find which receptors cause autoimmune disorders, and which receptors protect us from influenza?" Buntzman said. Genome sequencing instruments have addressed the problem yet remain incapable of handling the enormity of data. Until now. Just as genomics involves sequencing whole genomes, the field of immunomics involves mapping sequences of immune receptors — a mathematical challenge given that the human adaptive immune system swamps the diversity of most genomics studies. Buntzman calculated that using traditional computational methods to generate a complete genetic map of the immunome — all possible receptors the immune system might generate — would take roughly 106 years. "Waiting that long is clearly impractical," he said, "but this is where CyVerse comes in." Headquartered at the UA's BIO5 Institute, CyVerse is a National Science Foundation-funded project to provide computational infrastructure for big-data problems in the life sciences. Buntzman began working with CyVerse collaborator Ali Akoglu of the UA College of Engineering to develop computational tools to map the immunome using high-performance computing, or HPC, techniques. With access to HPC technology and support through CyVerse, Buntzman, Akoglu and Akoglu's graduate student Gregory Striemer developed a program to run the analysis in under 17 days on a computer chip housed inside a simple laptop. "My role was to restructure the algorithm to accelerate the results," Akoglu said. "This was the first study to generate and process terabytes of data exhaustively, going through all possible combinations of sequences, and in a relatively short amount of time. And CyVerse was the catalyzer that brought us together." Armed with the power of computation, Buntzman and his colleagues have developed a software tool capable of comprehensively mapping the adaptive immune system without limitation, and a computer program that is a community-accessible utility to database these complex immunome datasets, as described at the 2016 conference of the American Association of Immunologists and in an upcoming publication to be released in the journal BMC Bioinformatics. In addition, Buntzman's group has developed another computer program to run a novel algorithm called iWAS, or immunome-Wide Association Study, that can mine the immunome for patterns of immune receptors responsible for protecting us from specific diseases or causing autoimmune disorders. Understanding the role of individual immune receptors could pave the way to developing advanced therapies, potentially revolutionizing the field of adaptive immunity. "This work will aid in the study of cancer, autoimmunity, transplantation and vaccination, and assist in developing new precision medical diagnostics and patient-centered immunotherapies, as well as identify biomarkers for inflammatory diseases," Lussier said. "By working across disciplines as immunologists, mathematicians and computer scientists," he said, "we were able to tackle a problem that was untenable to any discipline alone. We've created an analytical infrastructure with CyVerse that allows for all the data to be stored and analyzed by researchers everywhere."
News Article | October 24, 2016
In his State of the Union address of January 12, 2016, President Barack Obama challenged America to tackle one of the world’s top killers: “For the loved ones we’ve all lost, for the families that we can still save, let’s make America the country that cures cancer once and for all.” In the weeks following the address, Obama announced the White House Cancer Moonshot project, which urges the nation’s scientists, industries, and families to come together to take on cancer. And in the months following the address, they have. University of Arizona (UA) research assistant professor Adam Buntzman and his colleagues are pushing the boundaries of cancer research using CyVerse data sharing and high-performance computing technology. “A staggering number of diseases are linked to the adaptive immune system,” noted Buntzman, an immunologist in the lab of Monica Kraft in the UA College of Medicine – Tucson. “Cancers such as lymphoma, myeloma, leukemia, and solid tumors, viral, bacterial, fungal, and parasitic infections, autoimmune diseases, asthma, inflammation, transplant tolerance or rejection… the list goes on.” Buntzman, who is based in the UA’s BIO5 Institute, and his colleagues recently developed a tool that uses CyVerse supercomputing resources to create the first nearly comprehensive map of the human immunome, all the possible immune receptors our bodies can make. Then, with the immunome at their fingertips, the researchers went on to develop an informatics tool to find patterns denoting which immune receptors may be responsible for protecting us from infectious disease, and which ones may cause autoimmune disorders, tissue rejection, or some types of cancer. “Once we find these receptors, scientists can design unique therapies to enhance the protective response, or add just the right receptors to a patient who may be missing them, or deplete the cells that harbor receptors that cause autoimmune disease.” Buntzman said. “This is the basis of the burgeoning field of immunotherapy.” “The same tools we use to study basic science questions in adaptive immunology can be used clinically,” he continued. Now, Buntzman and his colleagues at the UA Genetics Core(UAGC) and UA Cancer Center are developing methods to test for lymphoma, myeloma, and leukemia tumors. “Buntzman’s technique for immune-profiling with high-throughput informatics will help us to develop better clinical diagnostic tests, and will supplement our current clinical testing so that we can provide the UA clinical community with cutting-edge diagnostics to benefit the patients of the Banner-University Medical Center,” noted Michael Hammer, UA geneticist and UAGC Director. “This is an example of real-world precision diagnostics being developed here on the UA campus.” “The cancer cells of leukemia, myeloma, and lymphoma are unique in that the tumor cells themselves are immune cells,” Buntzman explained. “These three diseases occur when an immune cell gets a mutation and starts to outgrow the healthy immune cells. But the tumor cells harbor a unique biomarker that our tools can follow diagnostically through the course of treatment and, hopefully, into remission.” With the immunome at their fingertips courtesy of Buntzman’s informatics tool, “it’s very easy for us to see an overgrowth of immune receptors. We can sequence immune receptors to count the number of each receptor a person has in their bloodstream or at the site of the tumor. If there is one sequence that occurs out of proportion to the others, that’s a marker for an existing tumor.” A healthy person would have mostly unique immune cell receptors, he said. “Once we know the sequence of a cancerous immune cells, we know the tumor’s bio-signature. We can follow it for the time that the person is being treated and find the faintest trickle of it still remaining in their system. No other technique is as sensitive as this.” Buntzman envisions perfected tests to find cancer and cancerous remissions earlier, giving greater chance of successful treatment. According to one study, immunomic tests could be up to 100 times more sensitive than classical tests. Buntzman believes that immunomic tests, which require only a small genetic sample, could be vital for tracking cancer treatment and remission. A highly sensitive test is more likely to detect if a small amount of cancerous cells remain after treatment: “It’s a better test of the effectiveness of that treatment, and a better indicator of the next steps to take.” Immunomic tests also could be crucial for detecting cancer early by scanning people before they become ill. “When people go to a clinic, it’s usually because they’re already sick," Buntzman said. "If doctors could detect cancerous cells before they grow drastically out of proportion to healthy cells, patients would have much higher odds of successful cancer treatment and survival.”
News Article | November 16, 2015
Researchers at the University of Arizona have invented a device that for the first time allows neurosurgeons, who use microscopes extensively while operating, to see blood flowing inside vessels and more clearly distinguish cancerous from healthy tissue under the microscope. Called augmented microscopy, the technology gives surgeons a much more detailed picture in real time and helps them stay on course in surgeries where being off two millimeters could cause paralysis, blindness and even death. And surgeons get this better view without having to learn new technical skills or adapt to changes in the operating room. "When we started developing this technology, we thought of it like a Google map of a surgical view, providing layers of pertinent information in real time," said Marek Romanowski, UA associate professor of biomedical engineering. "Our augmented technology provides diagnostic information under the microscope on demand and in color, appearing directly over tissue a surgeon is operating on—as if the tissue was painted to help direct the surgeon's work." The new technology overlays an actual, or bright field, image a surgeon sees under a microscope with an electronically processed image using near-infrared fluorescence. NIR fluorescence is a computer-generated imaging technology in which contrast agents are injected in patients to illuminate vital diagnostic information and help surgeons avoid cutting the wrong vessel or removing healthy tissue. Most neurosurgeons must look up from a surgical microscope, or stereomicroscope, to view fluorescence on a display monitor. If they have a microscope adapted to project fluorescence, it switches back and forth between the real and electronic views, the surgeons' field of vision momentarily fading to black in between. Further, the fluorescence shows only contrast in black and white, not anatomical structures or their spatial relationships. So surgeons must visualize how fluorescence lines up with the anatomical structures they see under the microscope. Doctoral student Jeffrey Watson, left, and associate professor Marek Romanowski assemble parts for the prototype microscopy device.Doctoral student Jeffrey Watson, left, and associate professor Marek Romanowski assemble parts for the prototype microscopy device. The new add-on technology developed at the UA removes such interruptions or guesswork by showing surgeons real and fluorescence images simultaneously and in one location. Romanowski describes the invention with lead author Jeffrey Watson, a biomedical engineering doctoral student in the UA Graduate Interdisciplinary Program in Biomedical Engineering; G. Michael Lemole Jr., MD, chief of the division of neurosurgery in the department of surgery at the UA College of Medicine-Tucson; and UA neurosurgery resident Nikolay Martirosyan, MD, in "Augmented microscopy: Real-time overlay of bright-field and near-infrared fluorescence images," published in the Oct. 2015 edition of the SPIE Journal of Biomedical Optics. "Surgeons need more information than can be provided by stereomicroscopes alone," said Jennifer Barton, a UA professor of biomedical engineering and interim director of the UA BIO5 Institute, who specializes in cancer imaging. "Dr. Romanowski's augmented microscopy technology provides critical functional information that can improve surgical accuracy and efficiency." The new device, a small box fitted inside a surgical microscope, combines electronic circuitry and optical technologies to superimpose the fluorescence image on the real one and send the augmented view up through the microscope's right eyepiece to the surgeon. Lemole, a former flight surgeon in the Air Force Reserve, likens the technology to the head-up display in an airplane cockpit. "If you can place your critical gauges directly in the pilot's line of sight, they don't need to look in a different direction while performing critical maneuvers. It won't change the way they fly the plane, but it gives them more information, without distraction." Perhaps the most valuable application for augmented microscopy is treating brain cancer, said Romanowski, who holds appointments with the University of Arizona Cancer Center and BIO5 Institute. More than 20,000 new cases of primary brain cancer are diagnosed in the United States each year, and each year nearly 16,000 patients die from the disease, Romanowski said. Of the half-million patients who die of any other cancer, up to a third has some form of cancer spreading to the brain. "Brain cancer is especially difficult to remove," he said. "Current surgical microscopes limit how much of the cancer tissue surgeons can see and how precisely they can determine its boundaries." Lemole, a skull base neurosurgeon, routinely operates on brain cancer patients, manipulating vessels the width of a pin to remove malignant tumors. He walks a fine line to remove all of the cancer without removing healthy tissue. "Aggressive resection is associated with the risk of removing normal brain tissue and impairing functions of the patient," he and his co-authors write in the Journal of Biomedical Optics. "On the other hand, incomplete resection of tumor results in its immediate relapse in 90 percent of patients. Intraoperative NIR imaging may aid in resection of these challenging tumors." Augmented microscopy also holds promise for aneurysm, a bulging of an artery caused by weakened arterial walls. Neurosurgeons treat aneurysm by sealing it off from connecting vessels to prevent a rupture. Nearly half the patients with ruptured aneurysms die, Lemole said, and at least half the survivors have major mobility and other problems. Augmented technology could improve aneurysm patients' prognosis, by giving surgeons real-time feedback on every delicate and potentially deadly surgical maneuver they make. "When I pick up and clip a vessel, I like to see the implications of what happens in that very moment," he said. Explore further: New high-tech glasses detect cancer cells during surgery More information: Jeffrey R. Watson et al. Augmented microscopy: real-time overlay of bright-field and near-infrared fluorescence images, Journal of Biomedical Optics (2015). DOI: 10.1117/1.JBO.20.10.106002
Ortiz M.,University of Arizona |
Legatzki A.,University of Arizona |
Neilson J.W.,University of Arizona |
Fryslie B.,University of Arizona |
And 5 more authors.
ISME Journal | Year: 2014
Carbonate caves represent subterranean ecosystems that are largely devoid of phototrophic primary production. In semiarid and arid regions, allochthonous organic carbon inputs entering caves with vadose-zone drip water are minimal, creating highly oligotrophic conditions; however, past research indicates that carbonate speleothem surfaces in these caves support diverse, predominantly heterotrophic prokaryotic communities. The current study applied a metagenomic approach to elucidate the community structure and potential energy dynamics of microbial communities, colonizing speleothem surfaces in Kartchner Caverns, a carbonate cave in semiarid, southeastern Arizona, USA. Manual inspection of a speleothem metagenome revealed a community genetically adapted to low-nutrient conditions with indications that a nitrogen-based primary production strategy is probable, including contributions from both Archaea and Bacteria. Genes for all six known CO 2 -fixation pathways were detected in the metagenome and RuBisCo genes representative of the Calvin-Benson-Bassham cycle were over-represented in Kartchner speleothem metagenomes relative to bulk soil, rhizosphere soil and deep-ocean communities. Intriguingly, quantitative PCR found Archaea to be significantly more abundant in the cave communities than in soils above the cave. MEtaGenome ANalyzer (MEGAN) analysis of speleothem metagenome sequence reads found Thaumarchaeota to be the third most abundant phylum in the community, and identified taxonomic associations to this phylum for indicator genes representative of multiple CO 2 -fixation pathways. The results revealed that this oligotrophic subterranean environment supports a unique chemoautotrophic microbial community with potentially novel nutrient cycling strategies. These strategies may provide key insights into other ecosystems dominated by oligotrophy, including aphotic subsurface soils or aquifers and photic systems such as arid deserts.
Ma C.,BIO5 Institute |
Zhang J.,BIO5 Institute |
Wang J.,BIO5 Institute
Molecular Pharmacology | Year: 2016
Adamantanes (amantadine and rimantadine) are one of the two classes of Food and Drug Administration- Approved antiviral drugs used for the prevention and treatment of influenza A virus infections. They inhibit viral replication by blocking the wild- Type (WT) M2 proton channel, thus preventing viral uncoating. However, their use was discontinued due to widespread drug resistance. Among a handful of drug-resistant mutants, M2-S31N is the predominant mutation and persists in more than 95% of currently circulating influenza A strains. We recently designed two classes of M2-S31N inhibitors, S31N-specific inhibitors and S31N/WT dual inhibitors, which are represented by N-[(5- cyclopropyl-1,2-oxazol-3-yl)methyl]adamantan-1- Amine (WJ379) and N-[(5-bromothiophen-2-yl)methyl]adamantan-1- Amine (BC035), respectively. However, their antiviral activities against currently circulating influenza A viruses and their genetic barrier to drug resistance are unknown. In this report, we evaluated the therapeutic potential of these two classes of M2-S31N inhibitors (WJ379 and BC035) by profiling their antiviral efficacy against multidrug-resistant influenza A viruses, in vitro drug resistance barrier, and synergistic effect with oseltamivir. We found that M2- S31N inhibitors were active against several influenza A viruses that are resistant to one or both classes of Food and Drug Administration- Approved anti-influenza drugs. In addition, M2- S31N inhibitors display a higher in vitro genetic barrier to drug resistance than amantadine. The antiviral effect of WJ379 was also synergistic with oseltamivir carboxylate. Overall, these results reaffirm that M2-S31N inhibitors are promising antiviral drug candidates that warrant further development. © 2016 by The American Society for Pharmacology and Experimental Therapeutics.