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News Article | April 27, 2017
Site: www.eurekalert.org

Researchers have developed a personalized algorithm that predicts the impact of particular foods on an individual's blood sugar levels, according to a new study published in PLOS Computational Biology. The algorithm has been integrated into an app, Glucoracle, which will allow individuals with type 2 diabetes to keep a tighter rein on their glucose levels -- the key to preventing or controlling the major complications of a disease that affects 8 percent of Americans. Medications are often prescribed to help patients with type 2 diabetes manage their blood sugar levels, but exercise and diet also play an important role. "While we know the general effect of different types of food on blood glucose, the detailed effects can vary widely from one person to another and for the same person over time," said lead author David Albers, PhD, associate research scientist in Biomedical Informatics at Columbia University Medical Center (CUMC). "Even with expert guidance, it's difficult for people to understand the true impact of their dietary choices, particularly on a meal-to-meal basis. Our algorithm, integrated into an easy-to-use app, predicts the consequences of eating a specific meal before the food is eaten, allowing individuals to make better nutritional choices during mealtime." The algorithm uses a technique called data assimilation, in which a mathematical model of a person's response to glucose is regularly updated with observational data--blood sugar measurements and nutritional information--to improve the model's predictions, explained co-study leader George Hripcsak, MD, MS, the Vivian Beaumont Allen Professor and chair of Biomedical Informatics at CUMC. Data assimilation is used in a variety of applications, notably weather forecasting. "The data assimilator is continually updated with the user's food intake and blood glucose measurements, personalizing the model for that individual," said co-study leader Lena Mamykina, PhD, assistant professor of biomedical informatics at CUMC, whose team has designed and developed the Glucoracle app. Glucoracle allows the user to upload fingerstick blood measurements and a photo of a particular meal to the app, along with a rough estimate of the nutritional content of the meal. This estimate provides the user with an immediate prediction of post-meal blood sugar levels. The estimate and forecast are then adjusted for accuracy. The app begins generating predictions after it has been used for a week, allowing the data assimilator has learned how the user responds to different foods. The researchers initially tested the data assimilator on five individuals using the app, including three with type 2 diabetes and two without the disease. The app's predictions were compared with actual post-meal blood glucose measurements and with the predictions of certified diabetes educators. For the two non-diabetic individuals, the app's predictions were comparable to the actual glucose measurements. For the three subjects with diabetes, the apps forecasts were slightly less accurate, possibly due to fluctuations in the physiology of patients with diabetes or parameter error, but were still comparable to the predictions of the diabetes educators. "There's certainly room for improvement," said Dr. Albers. "This evaluation was designed to prove that it's possible, using routine self-monitoring data, to generate real-time glucose forecasts that people could use to make better nutritional choices. We have been able to make an aspect of diabetes self-management that has been nearly impossible for people with type 2 diabetes more manageable. Now our task is to make the data assimilation tool powering the app even better." Encouraged by these early results, the research team is preparing for a larger clinical trial. The researchers estimate that the app could be ready for widespread use within two years. This release is based on text provided by the authors. In your coverage please use this URL to provide access to the freely available article in PLOS Computational Biology: http://journals. Funding: GH, ML, and DJA are supported by a grant from the National Library of Medicine LM006910. LM, DJA and ML are supported by a grant from the Robert Wood Johnson Foundation RWJF 73070. LM is supported by a grant from the National Institute of Diabetes and Digestive Kidney diseases R01DK090372. Competing Interests: The authors have declared that no competing interests exist.


News Article | April 6, 2017
Site: www.scientificcomputing.com

The American Heart Association Precision Medicine Platform -- a global, secure data discovery platform, recently developed in collaboration with Amazon Web Services (AWS) -- is now open for use. Researchers, physicians, computational biologists, computer engineers and trainees from around the globe can leverage this cloud-based resource to access and analyze volumes of cardiovascular and stroke data to accelerate the care of patients at risk of the number one killer in the United States and a leading global health threat. The AHA Institute for Precision Cardiovascular MedicineTM is calling on all cardiovascular and stroke dataset owners and stewards to share their data as the first step in acquiring all the pieces needed to treat and prevent heart failure, stroke, coronary artery disease, atrial fibrillation and other cardiovascular diseases. Data from clinical trials, long-running epidemiologic studies, registries and real-time health data acquired through wearable devices and technology is sought. "We have blown away the barriers and welcome all to join this game-changing platform that promotes us working together as one community to ultimately benefit patients worldwide," said Jennifer Hall, PhD, the AHA's Chief of the Institute for Precision Cardiovascular Medicine. "The platform provides an opportunity to learn, search and discover in new and efficient ways, and we will keep working with the community to weave in new diverse data to help us drill deeper and enrich our understanding." Several organizations are leading the way toward the future of open data by contributing their information to the secure platform, including AstraZeneca, Cedars-Sinai Heart Institute, Dallas Heart Study, Duke Cardiovascular Research Institute, Intermountain Health, the International Stroke Genetics Consortium, the National Heart, Lung and Blood Institute (NHLBI) and Stanford University. "The increasing breadth and depth of medical data presents a tremendous opportunity to generate more nuanced and precise pre-diagnoses. However, leveraging this data requires tools capable of integrating data of diverse origin. The AHA Precision Medicine Platform can empower researchers with both the framework and tools to ease the burdens of data harmonization, amplifying the insight available from their own data." Said Gabriel Musso, PhD, VP Life Sciences, BioSymetrics Inc., who has been actively using the platform during the initial phase. The AHA Precision Medicine Platform is the only resource of its kind focused on cardiovascular diseases and stroke. "I am so excited for the potential the AHA Precision Medicine Platform brings for doing research across data sets to find consistent research results, and replicate and confirm research," said early adaptor Laura M. Stevens, a Predoctoral National Library of Medicine Fellow in the computational biosciences program at the University of Colorado Anschutz Medical School. "The platform makes big data analyses much quicker and easier. It's a great foundation for implementing precision medicine and research in a clinical setting. I can't wait to see where this will take us as a research community." Researchers are not charged for accessing the data but will pay a fee for cloud computing capabilities based on the current AWS model. Any revenue from cloud-based computing will be used to fund AHA's research initiatives. "By working together on datasets we have the ability to test the speed, agility and transparency of research," said Hall. "With your data and your efforts, the AHA Precision Medicine Platform can help enable your discoveries of novel underlying causal factors of heart failure, new diagnostic biomarkers to predict stroke, or exponential new approaches to precision care for those with cardiovascular diseases and stroke." Through the tool, the AHA reaches across the government, academic, industry, and patient communities to deepen data resources and spur research opportunities with an aim to transform cardiovascular research and patient care. To further foster research aimed at reversing and preventing cardiovascular diseases and stroke, the AHA Institute for Precision Cardiovascular Medicine also offers a variety of grant opportunities for scientists and researchers from many different fields of study. The application process for several grants is currently open.


News Article | May 4, 2017
Site: www.biosciencetechnology.com

Two years ago, former President Barack Obama announced the Precision Medicine initiative in his State of the Union Address. The initiative aspired to a “new era of medicine” where disease treatments could be specifically tailored to each patient’s genetic code. This resonated soundly in cancer medicine. Patients can already manage their cancer with therapies that target the specific genes that are altered in their particular tumor. For example, women with a type of breast cancer caused by the amplification of gene HER2 are often treated with a therapeutic called herceptin. Because these targeted therapeutics are specific to cancer cells, they tend to have fewer side effects than traditional cancer treatments with chemotherapy or radiation. However, such treatments are not available for most cancer patients. In many cancers, the specific genetic alterations that are responsible for a cancer remain unknown. To create individualized cancer treatments, we must know more about the functional genetic alterations. With data on cancer genetics growing rapidly, mathematics and statistics can now help unlock the hidden patterns in this data to find the genes that are responsible for an individual’s cancer. With this knowledge, physicians can select appropriate treatments that block the action of these genes to personalize therapies for individual patients. My research aims to improve precision medicine in cancer – by building on the same methods that have been used to find patterns in Netflix movie ratings. Today, there is unprecedented public access to cancer genetics data. These data come from generous patients who donate their tumor samples for research. Scientists then apply sequencing technologies to measure the mutations and activity in each of the 20,000 genes in the human genome. All these data are a direct result of the Human Genome Project in 2003. That project determined the sequence for all the genes that make up healthy human DNA. Since the completion of that project, the cost of sequencing the human genome has more than halved every year, surpassing the growth of computing power described in Moore’s Law. This cost reduction enables researches to collect unprecedented genetics data from cancer patients. Most scientific studies on cancer genetics performed worldwide release their data to a centralized, public database provided by the U.S. National Institutes of Health (NIH) National Library of Medicine. The NIH National Cancer Institute and National Human Genome Research Institute have also freely released genetic data from over 11,000 tumors in 33 cancer types through a project called The Cancer Genome Atlas. Every biological function – from extracting energy from food to healing a wound – results from activity in different combinations of genes. Cancers hijack the genes that enable people to grow to adulthood and that protect the body from the immune system. Researchers dub these the “hallmarks of cancer.” This so-called gene dysregulation enables a tumor to grow uncontrollably and form metastases in distant organs from the original tumor site. Researchers are actively using these public data to find the set of gene alterations that are responsible for each tumor type. But this problem is not as simple is identifying a single dysregulated gene in each tumor. Hundreds, if not thousands, of the 20,000 genes in the human genome are dysregulated in cancer. The group of dysregulated genes varies in each patient’s tumor, with smaller sets of commonly reused genes enabling each cancer hallmark. Precision medicine relies on finding the smaller groups of dysregulated genes that are responsible for biological function in each patient’s tumor. But, genes may have multiple biological functions in different contexts. Therefore, researchers must uncover a set of “overlapping” genes that have common functions in a set of cancer patients. Linking gene status to function requires complex mathematics and immense computing power. This knowledge is essential to predict of outcome to therapies that would block the function of these genes. So, how can we uncover those overlapping features to predict individual outcomes for patients? Fortunately for us, this problem has already been solved in computer science. The answer is a class of techniques called “matrix factorization” – and you’ve likely already interacted with these techniques in your everyday life. In 2009, Netflix held a challenge to personalize movie ratings for each Netflix user. On Netflix, each user has a distinct set of ratings of different movies. While two users may have similar tastes in movies, they may vary wildly in specific genres. Therefore, you cannot rely on comparing ratings from similar users. Instead, a matrix factorization algorithm finds movies with similar ratings among a smaller group of users. The group of users will vary for each movie. The computer associates each user with a group of movies to a different extent, based upon their individual tastes. The relationships among users are referred to as “patterns.” These patterns are learned from the data, and may find common rankings unforeseen by movie genre alone – for example, users may share a preference for a particular director or actor. The same process can work in cancer. In this case, the measurements of gene dysregulation are analogous to movie ratings, movie genres to biological function and users to patients’ tumors. The computer searches across patient tumors to find patterns in gene dysregulation that cause the malignant biological function in each tumor. The analogy between movie ratings and cancer genetics breaks down in the details. Unless they are minors, Netflix users are not constrained in the movies they watch. But, our bodies instead prefer to minimize the number of genes used for any single function. There are also substantial redundancies between genes. To protect a cell, one gene may easily substitute for another to serve a common function. Gene functions in cancer are even more complex. Tumors are also highly complex and rapidly evolving, depending upon random interactions between the cancer cells and the adjacent healthy organ. To account for these complexities, we have developed a matrix factorization approach called Coordinated Gene Activity in Pattern Sets – or CoGAPS for short. Our algorithm accounts for biology’s minimalism by incorporating as few genes as possible into the patterns for each tumor. Different genes can also substitute for one another, each serving a similar function in a different context. To account for this, CoGAPS simultaneously estimates a statistic for the so-called “patterns” of gene function. This allows us to compute the probability of each gene being used in each biological function in a tumor. For example, many patients take a targeted therapeutic called cetuximab to prolong survival in colorectal, pancreatic, lung and oral cancers. Our recent work found that these patterns can distinguish gene function in cancer cells that respond to the targeted therapeutic agent cetuximab from those that do not. Unfortunately, cancer therapies that target genes usually cannot cure a patient’s disease. They can only delay progression for a few years. Most patients then relapse, with tumors that are no longer responsive to the treatment. Our own recent work found that the patterns that distinguish gene function in cells that are responsive to cetuximab include the very genes that give rise to resistance. Emerging immunotherapies are promising and appear to cure some cancers. Yet, far too often, patients with these treatments also relapse. New data that track the cancer genetics after treatment is essential to determine why patients no longer respond. Along with these data, cancer biology also requires a new generation of scientists who can bridge mathematics and statistics to determine the genetic changes occurring over time in drug resistance. In other fields of mathematics, computer programs are able to forecast long-term outcomes. These models are used commonly in weather prediction and investment strategies. In these fields and my own previous research, we have found that updates to the models from large datasets – such as satellite data in the case of weather – improve long-term forecasts. We have all seen the effect of these updates, with weather predictions improving the closer that we are to a storm. Just as tools from computer science used can be adapted to both movie recommendations and cancer, the future generation of computational scientists will adopt prediction tools from an array of fields for precision medicine. Ultimately, with these computational tools, we hope to predict tumors’ response to therapy as commonly as we predict the weather, and perhaps more reliably. This article was originally published on The Conversation.


News Article | April 17, 2017
Site: www.prweb.com

Hypertension, or high blood pressure, may come with a plus side, at least for a subset of women with ovarian cancer. New research from epidemiologists at Roswell Park Cancer Institute, published in the journal Cancer Causes & Control, provides evidence that hypertension and diabetes and the use of medications to treat these common conditions may influence the survival of ovarian cancer patients — sometimes in a detrimental way, but in the case of hypertension medications, perhaps as a benefit. Using pooled data from 15 studies that were part of the Ovarian Cancer Association Consortium, an international team of collaborators led by Kirsten Moysich, PhD, MS, and Albina Minlikeeva, PhD, MPH, retroactively examined the associations between survival among patients diagnosed with invasive epithelial ovarian cancer and those patients’ history of hypertension, heart disease, diabetes, and medications taken for those conditions. They found that while a history of diabetes was associated with a 112% higher risk of mortality across more than 7,600 cases, no significant mortality associations were observed for hypertension or heart disease. In fact, the authors report, among women with endometrioid ovarian cancer, a subtype of epithelial ovarian cancer typically associated with better outcomes, hypertension — a condition that applied to nearly 26% of women in the pooled analysis — was associated with 46% lower risk of ovarian cancer progression. “This is a coincidental and unintended consequence of hypertension and its treatment, but it’s a silver lining to a serious but largely manageable medical condition that has reached epidemic prevalence in the U.S. and many other countries worldwide,” says Dr. Moysich, Distinguished Professor of Oncology in the departments of Cancer Prevention and Control and Immunology at the Buffalo cancer center. This study is the first to highlight the role of comorbidities in relation to ovarian cancer survival by histological subtype, and confirmed previous findings linking a history of diabetes to increased risk of death among ovarian cancer patients. It’s possible that commonly prescribed antihypertensive medications, including beta blockers, may influence the growth of ovarian tumors. But the team also documented a higher overall risk of death for patients who had ever taken beta blockers, and notes that further study is needed to better understand these processes and interactions. “Our results suggest that it is important to investigate factors that explain the difference in cancer outcomes among women with different types of ovarian cancer. Most studies only consider clinical characteristics at diagnosis, such as stage and histology in relation to ovarian cancer prognosis,” adds Dr. Minlikeeva, a postdoctoral Research Affiliate with Roswell Park’s Department of Cancer Prevention and Control. “Our findings emphasize the importance of understanding the full clinical profile for women with ovarian cancer in order to predict ovarian cancer outcomes.” Approximately 22,300 new cases of ovarian cancer are diagnosed each year in the U.S., with an estimated 14,200 women dying from the disease each year. Endometrioid carcinoma accounts for about 20% of all epithelial ovarian cancers. The study, “History of hypertension, heart disease, and diabetes and ovarian cancer patient survival: evidence from the ovarian cancer association consortium,” is available at link.springer.com. This work was funded in part by grants and contracts from the National Cancer Institute (project nos. K07CA080668, K07CA095666, K22CA138563, N01CN55424 P30CA072720, P50CA105009, P50CA159981, R01CA074850, R01CA080742, R01CA095023, R01CA112523, R01CA126841, R01CA188900, R01CA54419, R01CA58598, R01CA61107, R01CA76016, R01CA87538, R25CA113951 and T32CA108456), National Library of Medicine (project no. K01LM012100), Division of Cancer Control and Population Sciences (project no. N01PC67001) and Roswell Park Alliance Foundation. A full list of funders is available in the Acknowledgments section at that link. For an online version of this release, please visit: https://www.roswellpark.org/media/news/epidemiological-analysis-shows-unexpected-benefit-related-high-blood-pressure-many The mission of Roswell Park Cancer Institute (RPCI) is to understand, prevent and cure cancer. Founded in 1898, RPCI is one of the first cancer centers in the country to be named a National Cancer Institute-designated comprehensive cancer center and remains the only facility with this designation in Upstate New York. The Institute is a member of the prestigious National Comprehensive Cancer Network, an alliance of the nation’s leading cancer centers; maintains affiliate sites; and is a partner in national and international collaborative programs. For more information, visit http://www.roswellpark.org, call 1-877-ASK-RPCI (1-877-275-7724) or email askrpci(at)roswellpark(dot)org. Follow Roswell Park on Facebook and Twitter.


News Article | February 27, 2017
Site: www.rdmag.com

In movies and TV shows, dolphins are often portrayed as heroes who save humans through remarkable feats of strength and tenacity. Now dolphins could save the day for humans in real life, too - with the help of emerging technology that can measure thousands of proteins and an improved database full of genetic data. "Dolphins and humans are very, very similar creatures," said NIST's Ben Neely, a member of the Marine Biochemical Sciences Group and the lead on a new project at the Hollings Marine Laboratory, a research facility in Charleston, South Carolina that includes the National Institute of Standards and Technology (NIST) as one of its partner institutions. "As mammals, we share a number of proteins and our bodies function in many similar ways, even though we are terrestrial and dolphins live in the water all their lives." Neely and his colleagues have just finished creating a detailed, searchable index of all the proteins found in the bottlenose dolphin genome. A genome is the complete set of genetic material present in an organism. Neely's project is built on years of marine mammal research and aims to provide a new level of bioanalytical measurements. The results of this work will aid wildlife biologists, veterinary professionals and biomedical researchers. Protein Maps Could Help Dolphins and Humans Although a detailed map of the bottlenose dolphin (Tursiops truncatus) genome was first compiled in 2008, recent technological breakthroughs enabled the creation of a new, more exhaustive map of all of the proteins produced by the dolphins' DNA. Neely led the process to generate the new genome with the help of colleagues at the Hollings Marine Laboratory. For this project, the initial genomic sequencing and assembly were completed by Dovetail Genomics, a private U.S.-based company. Next, the genome was annotated by the National Center for Biotechnology Information at the National Library of Medicine (NCBI) using previously deposited data generated in large part by the National Oceanic and Atmospheric Administration's National Centers for Coastal Ocean Science Marine Genomics Core. "Once you can identify all of the proteins and know their amounts as expressed by the genome," Neely explained, "you can figure out what's going on in the bottlenose dolphin's biological systems in this really detailed manner." Neely's study is part of an emerging field called proteomics. In the case of dolphins, proteomic work has a wide variety of potential applications. The zoo and aquarium industry, which generates revenues of approximately $16 billion a year, could use it to improve the care of bottlenose dolphins. In addition, improved dolphin proteomics could improve assessments of wild dolphin populations, and provide an immense amount of data on environmental contaminants and the safety and health of the world's oceanic food web. Comparing the proteins of humans and these other mammals is already providing researchers with a wealth of new information about how the human body works. Those findings could eventually be used to develop new, more precise treatment methods for common medical problems. As marine mammals descend, they shut off the blood flow to many of their organs, which has long puzzled and intrigued biologists. In contrast, if blood stops flowing to the organs of a human's body for even a few seconds, the result can be a stroke, kidney failure, or even death. Studies have recently revealed that lesser-known proteins in the blood of marine mammals may be playing a big role in the dives by protecting bottlenose dolphins' kidneys and hearts from damage when blood flow and oxygen flow start and stop repeatedly during those underwater forays. One of these proteins is known as vanin-1. Humans produce vanin-1, but in much smaller amounts. Researchers would like to gather more information on whether or not elevating levels of vanin-1 may offer protection to kidneys. "There's this gap in the knowledge about genes and the proteins they make. We are missing a huge piece of the puzzle in how these animals do what they do," said Mike Janech from the Medical University of South Carolina. His group has been researching vanin-1 (link is external) and has identified numerous other potential biomedical applications for the dolphin genome just created by NIST. "Genes carry the information of life," Janech said. "But proteins execute the functions." Vanin-1 is just one example of how genomic information about this mammalian cousin might prove useful. There may be hundreds of other similar applications, including some related to the treatment of high blood pressure and diabetes. This represents another avenue for biomimicry, which seeks solutions to human problems by examining and imitating nature's patterns and strategies. In the past, biomimicry was solely focused on the structural aspects of animal body parts such as arms and legs or functional patterns of things like noses and sniffing. But as the study of DNA has evolved, so too has our ability to examine the things happening at the most minute levels within another mammal's body. "We are now entering what could be called the post-model-organism era," Neely said. Instead of looking only for a structure to model, imitate or learn from, scientists are looking at the complete molecular landscape of genes and proteins of these creatures for model processes, too. "With abundant genomic resources it is now possible to study non-model organisms with similar molecular machinery in order to tackle difficult biomedical problems." To gather the needed protein information, Neely and his team used a specimen provided by the National Marine Mammal Tissue Bank (link is external) (NMMTB), the longest running project of NIST's Marine Environmental Specimen Bank. Half of the approximately 4,000 marine mammal specimens in the NMMTB are collected as a part of the Marine Mammal Health and Stranding Response Program (link is external). The specimen provided for Neely's study was known to originate very close to the Hollings Marine Lab. The new, state-of-the-art genome immediately began providing new biochemical insights. Studies at NIST are ongoing to validate the updated protein maps using an ultra-high-resolution tribrid mass spectrometer, which is the most powerful tool available to identify and quantify proteins. Other Mammal Proteins Seem Promising, Too Neely said the results demonstrate the utility of re-mapping genomes with the improved bioanalytical capabilities provided by new genomic sequencing technology coupled to high-resolution mass spectrometers. The data from this project will also be available in the public domain so that the results will be easy for others to access and use for diverse applications and research. This is the first of many such projects to be undertaken by the Charleston group whereby new analytical techniques could be applied to marine animals. Studying other diving marine mammals can improve our understanding of the molecular mechanisms involved in diving. Also, sea lion proteins may have much to tell us about metastatic cancer, which especially intrigues Neely and his colleagues. As a research chemist, Neely says he has not really spent much time before now observing marine mammals as a part of his work hours. He does encounter dolphins when he goes out surfing along the Carolina coastline, though. "It's amazing to think that we are at a point where cutting-edge research in marine mammals can directly advance human biomedical discoveries," he said.


News Article | February 23, 2017
Site: www.eurekalert.org

In movies and TV shows, dolphins are often portrayed as heroes who save humans through remarkable feats of strength and tenacity. Now dolphins could save the day for humans in real life, too - with the help of emerging technology that can measure thousands of proteins and an improved database full of genetic data. "Dolphins and humans are very, very similar creatures," said NIST's Ben Neely, a member of the Marine Biochemical Sciences Group and the lead on a new project at the Hollings Marine Laboratory, a research facility in Charleston, South Carolina that includes the National Institute of Standards and Technology (NIST) as one of its partner institutions. "As mammals, we share a number of proteins and our bodies function in many similar ways, even though we are terrestrial and dolphins live in the water all their lives." Neely and his colleagues have just finished creating a detailed, searchable index of all the proteins found in the bottlenose dolphin genome. A genome is the complete set of genetic material present in an organism. Neely's project is built on years of marine mammal research and aims to provide a new level of bioanalytical measurements. The results of this work will aid wildlife biologists, veterinary professionals and biomedical researchers. Although a detailed map of the bottlenose dolphin (Tursiops truncatus) genome was first compiled in 2008, recent technological breakthroughs enabled the creation of a new, more exhaustive map of all of the proteins produced by the dolphins' DNA. Neely led the process to generate the new genome with the help of colleagues at the Hollings Marine Laboratory. For this project, the initial genomic sequencing and assembly were completed by Dovetail Genomics, a private U.S.-based company. Next, the genome was annotated by the National Center for Biotechnology Information at the National Library of Medicine (NCBI) using previously deposited data generated in large part by the National Oceanic and Atmospheric Administration's National Centers for Coastal Ocean Science Marine Genomics Core. "Once you can identify all of the proteins and know their amounts as expressed by the genome," Neely explained, "you can figure out what's going on in the bottlenose dolphin's biological systems in this really detailed manner." Neely's study is part of an emerging field called proteomics. In the case of dolphins, proteomic work has a wide variety of potential applications. The zoo and aquarium industry, which generates revenues of approximately $16 billion a year, could use it to improve the care of bottlenose dolphins. In addition, improved dolphin proteomics could improve assessments of wild dolphin populations, and provide an immense amount of data on environmental contaminants and the safety and health of the world's oceanic food web. Comparing the proteins of humans and these other mammals is already providing researchers with a wealth of new information about how the human body works. Those findings could eventually be used to develop new, more precise treatment methods for common medical problems. As marine mammals descend, they shut off the blood flow to many of their organs, which has long puzzled and intrigued biologists. In contrast, if blood stops flowing to the organs of a human's body for even a few seconds, the result can be a stroke, kidney failure, or even death. Studies have recently revealed that lesser-known proteins in the blood of marine mammals may be playing a big role in the dives by protecting bottlenose dolphins' kidneys and hearts from damage when blood flow and oxygen flow start and stop repeatedly during those underwater forays. One of these proteins is known as vanin-1. Humans produce vanin-1, but in much smaller amounts. Researchers would like to gather more information on whether or not elevating levels of vanin-1 may offer protection to kidneys. "There's this gap in the knowledge about genes and the proteins they make. We are missing a huge piece of the puzzle in how these animals do what they do," said Mike Janech from the Medical University of South Carolina. His group has been researching vanin-1 (link is external) and has identified numerous other potential biomedical applications for the dolphin genome just created by NIST. "Genes carry the information of life," Janech said. "But proteins execute the functions." Vanin-1 is just one example of how genomic information about this mammalian cousin might prove useful. There may be hundreds of other similar applications, including some related to the treatment of high blood pressure and diabetes. This represents another avenue for biomimicry, which seeks solutions to human problems by examining and imitating nature's patterns and strategies. In the past, biomimicry was solely focused on the structural aspects of animal body parts such as arms and legs or functional patterns of things like noses and sniffing. But as the study of DNA has evolved, so too has our ability to examine the things happening at the most minute levels within another mammal's body. "We are now entering what could be called the post-model-organism era," Neely said. Instead of looking only for a structure to model, imitate or learn from, scientists are looking at the complete molecular landscape of genes and proteins of these creatures for model processes, too. "With abundant genomic resources it is now possible to study non-model organisms with similar molecular machinery in order to tackle difficult biomedical problems." To gather the needed protein information, Neely and his team used a specimen provided by the National Marine Mammal Tissue Bank (link is external) (NMMTB), the longest running project of NIST's Marine Environmental Specimen Bank. Half of the approximately 4,000 marine mammal specimens in the NMMTB are collected as a part of the Marine Mammal Health and Stranding Response Program (link is external). The specimen provided for Neely's study was known to originate very close to the Hollings Marine Lab. The new, state-of-the-art genome immediately began providing new biochemical insights. Studies at NIST are ongoing to validate the updated protein maps using an ultra-high-resolution tribrid mass spectrometer, which is the most powerful tool available to identify and quantify proteins. Neely said the results demonstrate the utility of re-mapping genomes with the improved bioanalytical capabilities provided by new genomic sequencing technology coupled to high-resolution mass spectrometers. The data from this project will also be available in the public domain so that the results will be easy for others to access and use for diverse applications and research. This is the first of many such projects to be undertaken by the Charleston group whereby new analytical techniques could be applied to marine animals. Studying other diving marine mammals can improve our understanding of the molecular mechanisms involved in diving. Also, sea lion proteins may have much to tell us about metastatic cancer, which especially intrigues Neely and his colleagues. As a research chemist, Neely says he has not really spent much time before now observing marine mammals as a part of his work hours. He does encounter dolphins when he goes out surfing along the Carolina coastline, though. "It's amazing to think that we are at a point where cutting-edge research in marine mammals can directly advance human biomedical discoveries," he said.


News Article | February 23, 2017
Site: phys.org

"Dolphins and humans are very, very similar creatures," said NIST's Ben Neely, a member of the Marine Biochemical Sciences Group and the lead on a new project at the Hollings Marine Laboratory, a research facility in Charleston, South Carolina that includes the National Institute of Standards and Technology (NIST) as one of its partner institutions. "As mammals, we share a number of proteins and our bodies function in many similar ways, even though we are terrestrial and dolphins live in the water all their lives." Neely and his colleagues have just finished creating a detailed, searchable index of all the proteins found in the bottlenose dolphin genome. A genome is the complete set of genetic material present in an organism. Neely's project is built on years of marine mammal research and aims to provide a new level of bioanalytical measurements. The results of this work will aid wildlife biologists, veterinary professionals and biomedical researchers. Protein Maps Could Help Dolphins and Humans Although a detailed map of the bottlenose dolphin (Tursiops truncatus) genome was first compiled in 2008, recent technological breakthroughs enabled the creation of a new, more exhaustive map of all of the proteins produced by the dolphins' DNA. Neely led the process to generate the new genome with the help of colleagues at the Hollings Marine Laboratory. For this project, the initial genomic sequencing and assembly were completed by Dovetail Genomics , a private U.S.-based company. Next, the genome was annotated by the National Center for Biotechnology Information at the National Library of Medicine (NCBI) using previously deposited data generated in large part by the National Oceanic and Atmospheric Administration's National Centers for Coastal Ocean Science Marine Genomics Core. "Once you can identify all of the proteins and know their amounts as expressed by the genome," Neely explained, "you can figure out what's going on in the bottlenose dolphin's biological systems in this really detailed manner." Neely's study is part of an emerging field called proteomics. In the case of dolphins, proteomic work has a wide variety of potential applications. The zoo and aquarium industry, which generates revenues of approximately $16 billion a year, could use it to improve the care of bottlenose dolphins. In addition, improved dolphin proteomics could improve assessments of wild dolphin populations, and provide an immense amount of data on environmental contaminants and the safety and health of the world's oceanic food web. Comparing the proteins of humans and these other mammals is already providing researchers with a wealth of new information about how the human body works. Those findings could eventually be used to develop new, more precise treatment methods for common medical problems. As marine mammals descend, they shut off the blood flow to many of their organs, which has long puzzled and intrigued biologists. In contrast, if blood stops flowing to the organs of a human's body for even a few seconds, the result can be a stroke, kidney failure, or even death. Studies have recently revealed that lesser-known proteins in the blood of marine mammals may be playing a big role in the dives by protecting bottlenose dolphins' kidneys and hearts from damage when blood flow and oxygen flow start and stop repeatedly during those underwater forays. One of these proteins is known as vanin-1. Humans produce vanin-1, but in much smaller amounts. Researchers would like to gather more information on whether or not elevating levels of vanin-1 may offer protection to kidneys. "There's this gap in the knowledge about genes and the proteins they make. We are missing a huge piece of the puzzle in how these animals do what they do," said Mike Janech from the Medical University of South Carolina. His group has been researching vanin-1 and has identified numerous other potential biomedical applications for the dolphin genome just created by NIST. "Genes carry the information of life," Janech said. "But proteins execute the functions." Vanin-1 is just one example of how genomic information about this mammalian cousin might prove useful. There may be hundreds of other similar applications, including some related to the treatment of high blood pressure and diabetes. This represents another avenue for biomimicry, which seeks solutions to human problems by examining and imitating nature's patterns and strategies. In the past, biomimicry was solely focused on the structural aspects of animal body parts such as arms and legs or functional patterns of things like noses and sniffing. But as the study of DNA has evolved, so too has our ability to examine the things happening at the most minute levels within another mammal's body. "We are now entering what could be called the post-model-organism era," Neely said. Instead of looking only for a structure to model, imitate or learn from, scientists are looking at the complete molecular landscape of genes and proteins of these creatures for model processes, too. "With abundant genomic resources it is now possible to study non-model organisms with similar molecular machinery in order to tackle difficult biomedical problems." To gather the needed protein information, Neely and his team used a specimen provided by the National Marine Mammal Tissue Bank (NMMTB), the longest running project of NIST's Marine Environmental Specimen Bank. Half of the approximately 4,000 marine mammal specimens in the NMMTB are collected as a part of the Marine Mammal Health and Stranding Response Program . The specimen provided for Neely's study was known to originate very close to the Hollings Marine Lab. The new, state-of-the-art genome immediately began providing new biochemical insights. Studies at NIST are ongoing to validate the updated protein maps using an ultra-high-resolution tribrid mass spectrometer, which is the most powerful tool available to identify and quantify proteins. Other Mammal Proteins Seem Promising, Too Neely said the results demonstrate the utility of re-mapping genomes with the improved bioanalytical capabilities provided by new genomic sequencing technology coupled to high-resolution mass spectrometers. The data from this project will also be available in the public domain so that the results will be easy for others to access and use for diverse applications and research. This is the first of many such projects to be undertaken by the Charleston group whereby new analytical techniques could be applied to marine animals. Studying other diving marine mammals can improve our understanding of the molecular mechanisms involved in diving. Also, sea lion proteins may have much to tell us about metastatic cancer, which especially intrigues Neely and his colleagues. As a research chemist, Neely says he has not really spent much time before now observing marine mammals as a part of his work hours. He does encounter dolphins when he goes out surfing along the Carolina coastline, though. "It's amazing to think that we are at a point where cutting-edge research in marine mammals can directly advance human biomedical discoveries," he said. Explore further: Researchers probing the beneficial secrets in dolphins' proteins


Bentolila S.,Cornell University | Stefanov S.,National Library of Medicine
Plant Physiology | Year: 2012

Plant mitochondrial genomes have features that distinguish them radically from their animal counterparts: a high rate of rearrangement, of uptake and loss of DNA sequences, and an extremely low point mutation rate. Perhaps the most unique structural feature of plant mitochondrial DNAs is the presence of large repeated sequences involved in intramolecular and intermolecular recombination. In addition, rare recombination events can occur across shorter repeats, creating rearrangements that result in aberrant phenotypes, including pollen abortion, which is known as cytoplasmic male sterility (CMS). Using nextgeneration sequencing, we pyrosequenced two rice (Oryza sativa) mitochondrial genomes that belong to the indica subspecies. One genome is normal, while the other carries the wild abortive-CMS. We find that numerous rearrangements in the rice mitochondrial genome occur even between close cytotypes during rice evolution. Unlike maize (Zea mays), a closely related species also belonging to the grass family, integration of plastid sequences did not play a role in the sequence divergence between rice cytotypes. This study also uncovered an excellent candidate for the wild abortive-CMS-encoding gene; like most of the CMS-associated open reading frames that are known in other species, this candidate was created via a rearrangement, is chimeric in structure, possesses predicted transmembrane domains, and coopted the promoter of a genuine mitochondrial gene. Our data give new insights into rice mitochondrial evolution, correcting previous reports. © 2011 American Society of Plant Biologists.


Journal of DST is a Peer-Reviewed Bi-monthly Scientific Journal Indexed in the National Library of Medicine's Database, PubMed. They Publish the Largest Number of Articles on Diabetes Technology of any Journal in the World LOS ANGELES, CA--(Marketwired - February 08, 2017) - ViaDerma, Inc. ( : VDRM), a specialty pharmaceutical company devoted to bringing new products to market, recently announced today that the President, Dr. Christopher Otiko has been invited to write an article in a leading Diabetic publication, the "Journal of Diabetes Science and Technology." Dr. Otiko has also been selected to present his abstract at DFCON or the Diabetic Foot Global Conference in Houston, TX, March 23rd through the 25th. DFCon, website www.dfcon.com, is the premier international, interdisciplinary diabetic foot conference in North America. In its 15th year, the course is designed for the wide spectrum of generalists and specialists who diagnose and manage the diabetic foot. Didactic talks, panel discussions, Q&A sessions, specialty symposia and workshops will delve into diagnostic and interventional strategies for diabetic foot ulcers and amputation prevention. Featuring a world-renowned international faculty, DFCon offers the opportunity to review state-of-the-art concepts and techniques. "Diabetes affects almost a half a billion people globally with 23 million affected in the US. With about 83 million affected with condition designated as pre-diabetes. Of those with diabetes, 50% will develop peripheral neuropathy and/or diabetic ulcers. Of the 23 million people affected with diabetes, 25% will develop diabetic ulcers many will require expensive therapy or invasive surgical amputations. The goal of this study was to evaluate the efficacy and safety of the FDA registered OTC medication Viabecline. A topically applied antibiotic ointment designed to treat infections in cuts, scrapes and burns, we found that Viabecline is very effective as part of a diabetic foot ulcer (DFU) treatment protocol. Clinical investigation (CI) documenting the treatment effectiveness was estimated by enrolling patients in a multi-center outpatient clinic setting," said CEO Dr. Christopher Otiko. "The results conclude Viabecline is more effective than standard care in treating DFU's, including IV antibiotics. The effect was greatest in those with the most severe wounds, i.e., large wounds that affect deeper anatomical structures. These patients were last resort patients that had failed all previous care and were headed to an amputation. In some cases, even an amputation wasn't feasible because of the patient's cardiac status. Viabecline is more than 96% effective in healing diabetic foot ulcers within 4 weeks. This effect is more pronounced in more severe wounds, and the effect is the same whether the wound is infected or not," said CEO Dr. Christopher Otiko. "Our goal is to have Viabecline added to all diabetic foot ulcer treatment protocols." "We are also in the clinical testing stages of an anti-aging topical solution, a topical pain medication, a topical for male-pattern baldness, and a topical designed to boost male libido. The market for our many products is very promising. We are enthusiastic about the results we have achieved to date in terms of the anecdotal feedback we have received from the medical community," said Dr. Otiko. ViaDerma, Inc. ( : VDRM) is a publicly traded specialty pharmaceutical company committed to bringing new products to market and licensing its innovative technology to current leaders in the pharmaceutical industry in a wide variety of therapeutic areas. ViaDerma's lead product, Viabecline, uses an innovative transdermal delivery method that allows for application of active ingredients in a topical form. This patent-pending dual carrier transdermal technology may be applied in products within the medical and cosmetic markets. Also, a patent application using the combination of CBD's and THC with the delivery system was filed in 2014. The use of CBD's is for the reduction of inflammation and for the treatment of several diseases, such as, nicotine addiction, fibromyalgia, Cohn's disease, schizophrenia, migraine headaches, pain management for cancer and Multiple Sclerosis. For more information, please visit: www.viadermalicensing.com Forward-Looking Statements certain statements in this release that are not historical facts are "forward-looking statements" within the meaning of the Private Securities Litigation Reform Act of 1995. Such statements may be identified using words such as "anticipate," "believe," "expect," "future," "may," "will," "would," "should," "plan," "projected," "intend," and similar expressions. Such forward-looking statements involve known and unknown risks, uncertainties and other factors that may cause the actual results, performance or achievements of the Company to be materially different from those expressed or implied by such forward-looking statements. The Company's future operating results are dependent upon many factors, including but not limited to the Company's ability to: (i) obtain sufficient capital or a strategic business arrangement to fund its expansion plans; (ii) build the management and human resources and infrastructure necessary to support the growth of its business; (iii) competitive factors and developments beyond the Company's control; and (iv) other risk factors. We assume no obligation to update the information contained in this news release.

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