News Article | January 20, 2016
Published in the prestigious journal Plant Cell, Professor Maria Hrmova, a structural biology researcher from the University of Adelaide, led a team of scientists from Australia, Germany and USA. According to Professor Hrmova, this research is fundamental to the agricultural industry, as boric acid toxicity affects crop yields in Australia and around the world, and results in significant revenue losses. The research has led to a better understanding of how to protect vulnerable vegetation to secure higher yields of edible crops and improve their nutritional properties. "The transport of nutrients and toxins in plants is critical for their survival. It is regulated by transporter proteins that are responsible for directing water and nutrients into plants, and removing toxins, but until now only a handful of these proteins had been characterised and we don't know how the majority of proteins function," says Professor Hrmova, from the University's School of Agriculture, Food and Wine and the Australian Centre for Plant Functional Genomics. "Manipulating the function of transporters for the benefit of edible plants is no mean feat, since transporters are embedded in plasma membranes (outer cell layers), which makes them very difficult to handle. "To understand how these transporters work, we have designed an integrated platform encompassing computational, biophysical and biochemical tools. We then used molecular biology, electrophysiology and bioinformatics, to describe the function of the transporter underlying boric acid toxicity tolerance. "Using this platform, we discovered that the transporter function relies on the presence of sodium (which is ever present in soils) and that the origin of the transport function is related to the presence of hydrated sodium in a particular location of the transporter. "This creates an energy barrier that permits an efficient exclusion of borate from plant cells back to soil, possibly through a quantum tunnelling process," she says. According to Professor Hrmova, developing this understanding at a molecular level will aid significant advances in agriculture. "The transport protein that we studied plays a key role in how tolerant a crop, like barley, is to high levels of boric acid in soils. These findings can be used to develop more resilient crops," says Professor Hrmova. "This study also presents a platform for deciphering the molecular function of other transporters in plants, like water permeating aquaporins (for the transport of water), and nitrogen, phosphorus and sugar transporters," she says. "And now that we know how to influence the transport of boric acid in plants, we can commence developing crops that have improved nutritional properties and higher yields in a variety of sub-optimal soil conditions." Explore further: Proteins called membrane transporters will be key to sustainable food production More information: Na+-Dependent Anion Transport by a Barley Efflux Protein Revealed through an Integrative Platform. Plant Cell December 15, 2015 TPC2015-00625-RA doi: dx.doi.org/10.1105/tpc.15.00625
News Article | November 4, 2016
A study led by investigators at Massachusetts General Hospital (MGH), the Broad Institute of MIT and Harvard, and two academic medical centers in the Netherlands has begun to elucidate how differences in the gut microbiome -- the microbial population of the gastrointestinal tract -- affect the immune response in healthy individuals. The study is one of three related papers published in this week's issue of Cell, the other two looking at genetic and environmental influences, as part of the Human Functional Genomics Project (HFGP). "The underlying premise of the HFGP is that the immune system is a perfect target for studying human variation and the intersection of genes and the environment," says Ramnik Xavier, MD, PhD, chief of the MGH Gastrointestinal Unit, an institute member at the Broad and a principal investigator of the HFGP. "We know that some people are more susceptible to infections than others; some develop autoimmune diseases while most don't. In these studies we wanted to see how genes affect the immune system, how environmental factors affect susceptibility and in this investigation, whether and how the gut microbiome influences the immune system's response to various pathogens." The microbiome study -- led by Xavier and Mihai Netea, MD, PhD, of Radboud University Medical Center in the Netherlands -- analyzed blood and stool samples from 500 healthy Western European HFGP participants to look for individual variations in immune responses to pathogens, represented by production of molecules called cytokines; variations in the gut microbiome, and how those two factors relate to each other. Immune cells from individual participants were exposed to three bacterial stimulants -- the commensal microbe B. fragilis, the common pathogen S. aureus, and a toxin produced by E. coli -- and two forms of the Candida fungus. Their response was reflected in the production of cytokines, proteins through which immune cells exert many of their effects. Looking at possible relationships between immune responses and the microbiome in individual participants, the investigators found clear patterns by which both the population of the microbiome and its function, reflected in the production of proteins called metabolites, interact with the immune response. Some of those interactions depended on the particular pathogen, some on the cytokines, and some on both. Among the team's observations was how, depending on the specific pathogenic stimulus, breakdown of the amino acid tryptophan into the metabolite tryptophol can inhibit production of the cytokine TNF-alpha. They also identified an effect of palmitoleic acid -- a fatty acid found in several dietary oils and known to suppress some immune activities -- on production of the cytokine gamma interferon, although the precise mechanism is yet to be discovered. The Isselbacher Professor of Medicine in Gastroenterology at Harvard Medical School and a member of the MGH Center for Computational and Integrative Biology, Xavier says, "We still don't have all the components, but the overall picture suggests that variations in the gut microbiome change production of the metabolites that go on to educate or influence immune cells, leading to differential outcomes when immune cells are exposed to various infections." The accompanying studies, on which he is a co-author, found similar influences on immune response by environmental factors -- including the season of the year as well as participants' age and gender -- and most powerfully, by genetic differences. Among the next steps, Xavier notes, will be conducting similar studies in individuals with specific diseases and in participants from other parts of the world. "By understanding how all of these complex mechanisms -- genetics, microbiome and environment -- drive variations in the immune response, we may be able to identify factors responsible for individual patients' susceptibilities and better target therapies," he says.
News Article | February 27, 2017
Research and Markets has announced the addition of the "Global Drug Discovery Technologies Market Analysis & Trends - Industry Forecast to 2025" report to their offering. The Global Drug Discovery Technologies Market is poised to grow at a CAGR of around 12.2% over the next decade to reach approximately $160 billion by 2025. This industry report analyzes the market estimates and forecasts for all the given segments on global as well as regional levels presented in the research scope. The study provides historical market data for 2013, 2014 revenue estimations are presented for 2015 and forecasts from 2016 till 2025. The study focuses on market trends, leading players, supply chain trends, technological innovations, key developments, and future strategies. Some of the prominent trends that the market is witnessing include growing identification of combinatorial chemistry technology, regulatory initiatives fostering demand for pharmacogenomics technology, proteomics in anticancer drug discovery and human protein microarray for various protein analysis. Based on technology the market is categorized into pharmacogenomics, high throughput screening, genomics, bioinformatics, biochips, bioanalytical Instruments, nanotechnology, metabolomics and other technologies. Depending on the end users the market is segmented by research institutes, pharmaceutical companies, biotech companies, biopharmaceutical companies and other end users. Depending on the Applications the market is segmented by cardiovascular diseases, cancer Parkinson's disease, central nervous system disorders and other applications. - The report provides a detailed analysis on current and future market trends to identify the investment opportunities - Market forecasts till 2025, using estimated market values as the base numbers - Key market trends across the business segments, Regions and Countries - Key developments and strategies observed in the market - Market Dynamics such as Drivers, Restraints, Opportunities and other trends - In-depth company profiles of key players and upcoming prominent players - Growth prospects among the emerging nations through 2025 - Market opportunities and recommendations for new investments 3 Market Overview 3.1 Current Trends 3.1.1 Growing identification of combinatorial chemistry technology 3.1.2 Regulatory initiatives fostering demand for pharmacogenomics technology 3.1.3 Proteomics in anticancer drug discovery 3.1.4 Human protein microarray for various protein analysis 3.2 Drivers 3.3 Constraints 3.4 Industry Attractiveness 4 Drug Discovery Technologies Market, By Technology Type 4.1 Pharmacogenomics 4.2 High Throughput Screening 4.3 Genomics 184.108.40.206 Structural Genomics 220.127.116.11 Functional Genomics 18.104.22.168 Other Genomics technologies 22.214.171.124.1.1 Clinical Medicine 126.96.36.199.1.2 New Antibiotics 4.4 Bioinformatics 188.8.131.52 Computer-Aided Drug Design 4.5 Biochips 184.108.40.206 Lab on a chip 220.127.116.11 Proteomics microarrays 18.104.22.168 DNA and Protein microarrays 4.6 Bioanalytical Instruments 22.214.171.124 Chemotherapy instruments 126.96.36.199 Mass spectrometry 188.8.131.52 Microplate readers 184.108.40.206 Nuclear magnetic resonance 4.7 Nanotechnology 220.127.116.11 Nano-mass spectroscopy 18.104.22.168 Dip-pen Nanolithography 22.214.171.124 Atomic force microscopy (AFM) 4.8 Metabolomics 126.96.36.199 Target Identification 188.8.131.52 Target Validation 184.108.40.206 Lead Optimization 220.127.116.11 Mode of Action 18.104.22.168 Preclinical Studies 22.214.171.124 Clinical Studies 126.96.36.199 Post-Approval Studies 188.8.131.52 Diagnostics 4.9 Other Technologies 184.108.40.206 RNAi (RNA interference) 220.127.116.11.1.1 MiRNAS (MicroRNA sequencing) 18.104.22.168.1.2 SiRNA (Small interfering RNA) 22.214.171.124.1.3 Other RNAi technologies 126.96.36.199 Combinatorial chemistry 188.8.131.52.1.1 Chemical Encoding 184.108.40.206.1.2 Positional Encoding 220.127.116.11.1.3 Electronic Encoding 18.104.22.168 Synthetic Biology 22.214.171.124 Proteomic 126.96.36.199.1.1 Two dimensional gel electrphoresis- 2DGE 188.8.131.52.1.2 Two-hybrid systems 184.108.40.206 Cell Based Assays 220.127.116.11 Epigenetics 18.104.22.168 Systems Biology 22.214.171.124.1.1 Computer Modelling 126.96.36.199 Quantitative polymerase chain reaction (QPCR) 188.8.131.52 Laboratory information management systems 184.108.40.206 Microfluidics 220.127.116.11 Chromatography 18.104.22.168 Protein and nucleic acid isolation 6 Drug Discovery Technologies Market, By Application 6.1 Cardiovascular Diseases 6.2 Cancer 6.3 Parkinson's disease 6.4 Central Nervous System Disorders 6.5 Other Applications 6.5.1 Other Applications Market Forecast to 2025 (US$ MN) 7 Drug Discovery Technologies Market, By Geography - Affymetrix Inc. - Tecan Group Ltd. - Sigma-Aldrich Corp - Shimadzu Corp - Perkinelmer Inc. - Thermo Fisher Scientific Inc. - Incyte Corp - Gyros AB - F. Hoffmann-La Roche Ltd. - Evotec AG - Chembridge Corp - Abbott Laboratories Inc. - Celera Corp - Caliper Life Sciences Inc. - Bio-Rad Laboratories Inc. - Astrazeneca Plc. - Albany Molecular Research Inc. - Agilent Technologies Inc. - Charles River Laboratories International Inc. - Life Technologies Corp For more information about this report visit http://www.researchandmarkets.com/research/n5klng/global_drug
News Article | February 5, 2016
National Institutes of Health researchers have identified a striking signature in tumor DNA that occurs in five different types of cancer. They also found evidence that this methylation signature may be present in many more types of cancer. The specific signature results from a chemical modification of DNA called methylation, which can control the expression of genes like a dimmer on a light switch. Higher amounts of DNA methylation (hypermethylation), like that found by the researchers in some tumor DNA, decreases a gene's activity. Based on this advance, the researchers hope to spur development of a blood test that can be used to diagnose a variety of cancers at early stages, when treatments can be most effective. The study appeared February 5, 2016, in The Journal of Molecular Diagnostics. "Finding a distinctive methylation-based signature is like looking for a spruce tree in a pine forest," said Laura Elnitski, Ph.D., a computational biologist in the Intramural Research Program at NIH's National Human Genome Research Institute (NHGRI). "It's a technical challenge to identify, but we found an elevated methylation signature around the gene known as ZNF154 that is unique to tumors." Dr. Elnitski is head of the Genomic Functional Analysis Section and senior investigator in the Translational and Functional Genomics Branch at NHGRI. In 2013, her research group discovered a methylation mark (or signature) around ZNF154 in 15 tumor types in 13 different organs and deemed it a possible universal cancer biomarker. Biomarkers are biological molecules that indicate the presence of disease. Dr. Elnitski's group identified the methylation mark using DNA taken from solid tumors. "No one in my group slept the night after that discovery," Dr. Elnitski said. "We were so excited when we found this candidate biomarker. It's the first of its kind to apply to so many types of cancer." In this new study, they developed a series of steps that uncovered telltale methylation marks in colon, lung, breast, stomach and endometrial cancers. They showed that all the tumor types and subtypes consistently produced the same methylation mark around ZNF154. "Finding the methylation signature was an incredibly arduous and valuable process," said NHGRI Scientific Director Dan Kastner, M.D., Ph.D. "These findings could be an important step in developing a test to identify early cancers through a blood test." The NIH Intramural Sequencing Center sequenced the tumor DNA that had been amplified using a technique called polymerase chain reaction (PCR). Dr. Elnitski and her group then analyzed the results, finding elevated levels of methylation at ZNF154 across the different tumor types. To verify the connection between increased methylation and cancer, Dr. Elnitski's group developed a computer program that looked at the methylation marks in the DNA of people with and without cancer. By feeding this information into the program, they were able to predict a threshold for detecting tumor DNA. Even when they reduced the amount of methylated molecules by 99 percent, the computer could still detect the cancer-related methylation marks in the mixture. Knowing that tumors often shed DNA into the bloodstream, they calculated the proportions of circulating tumor DNA that could be found in the blood. Dr. Elnitski will next begin screening blood samples from patients with bladder, breast, colon, pancreatic and prostate cancers to determine the accuracy of detection at low levels of circulating DNA. Tumor DNA in a person with cancer typically comprises between 1 and 10 percent of all DNA circulating in the bloodstream. The group noted that when 10 percent of the circulating DNA contains the tumor signature, their detection rate is quite good. Because the methylation could be detected at such low levels, it should be adequate to detect advanced cancer as well as some intermediate and early tumors, depending on the type. Dr. Elnitski's group will also collaborate with Christina Annunziata, M.D., Ph.D., an investigator in the Women's Malignancies Branch and head of the Translational Genomics Section at NIH's National Cancer Institute (NCI). They will test blood samples from women with ovarian cancer to validate the process over the course of treatment and to determine if this type of analysis leads to improved detection of a recurrence and, ultimately, improved outcomes. "Ovarian cancer is difficult to detect in its early stages, and there are no proven early detection methods," said Dr. Annunziata. "We need a reliable biomarker for detecting the disease when a cure is more likely. We are looking forward to testing Dr. Elnitski's novel approach using DNA methylation signatures." Current blood tests are specific to a known tumor type. In other words, clinicians must first find the tumor, remove a sample of it and determine its genome sequence. Once the tumor-specific mutations are known, they can be tracked for appearance in the blood. The potential of the new approach is that no prior knowledge of cancer is required, it would be less intrusive than other screening approaches like colonoscopies and mammograms and it could be used to follow individuals at high risk for cancer or to monitor the activity of a tumor during treatment. Once the blood test is developed, the scientific community must conduct studies to ensure that it does not indicate the presence of cancer when it is not there or miss cancer when it is there. Dr. Elnitski does not yet understand the connection between tumors and elevated DNA methylation. It may represent derailment of normal processes in the cell, or it may have something to do with the fact that tumors consume a lot of energy and circumvent the cellular processes that keep growth in check. Researchers also don't know exactly what the gene ZNF154 does. "We have laid the groundwork for developing a diagnostic test, which offers the hope of catching cancer earlier and dramatically improving the survival rate of people with many types of cancer," Dr. Elnitski said.
News Article | December 22, 2016
Making muscles burn more fat and less glucose can increase exercise endurance, but could simultaneously cause diabetes, says a team of scientists from Baylor College of Medicine and other institutions. Mouse muscles use glucose (carbohydrate) as fuel when the animals are awake and active and switch to fat (lipid) when they are asleep. The team discovered that disrupting this natural cycle may lead to diabetes but, surprisingly, also can enhance exercise endurance. The switch is controlled by a molecule called histone deacetylase 3, or HDAC3. This finding opens the possibility of selecting the right time to exercise for losing body fat but also raises the concern of using HDAC inhibitors as doping drugs for endurance exercise. The study appears in Nature Medicine. "How the muscle uses glucose is regulated by its internal circadian clock that anticipates the level of its activity during the day and at night," said senior author Dr. Zheng Sun, assistant professor of medicine - diabetes, endocrinology and metabolism, and of molecular and cellular biology at Baylor. "The circadian clock works by turning certain genes on and off as the 24-hour cycle progresses. HDAC3 is a key connection between the circadian clock and gene expression. Our previous work showed that HDAC3 helps the liver alternate between producing glucose and producing lipid. In this work, we studied how HDAC3 controls the use of different fuels in skeletal muscle." Skeletal muscles, the voluntary muscles, are important in the control of blood glucose in the body. They consume most of the glucose, and if they develop insulin resistance and consequently are not able to use glucose, then diabetes likely will develop. To study the role of HDAC3 in mouse skeletal muscle, Sun and colleagues genetically engineered laboratory mice to deplete HDAC3 only in the skeletal muscles. Then they compared these knocked out mice with normal mice regarding how their muscles burn fuel. When normal mice eat, their blood sugar increases and insulin is released, which stimulates muscles to take in and use glucose as fuel. "When the knocked out mice ate, their blood sugar increased and insulin was released just fine, but their muscles refused to take in and use glucose," said Sun. "Lacking HDAC3 made the mice insulin resistant and more prone to develop diabetes." Yet, when the HDAC3-knocked out mice ran on a treadmill, they showed superior endurance, "which was intriguing because diabetes is usually associated with poor muscle performance," said Sun. "Glucose is the main fuel of muscle, so if a condition limits the use of glucose, the expectation is low performance in endurance exercises. That's the surprise." The researchers then studied what fueled the HDAC3-knocked out mice's stellar performance using metabolomics approaches and found that their muscles break down more amino acids. This changed the muscles' preference from glucose to lipids and allowed them to burn lipid very efficiently. This explains the high endurance, because the body carries a much larger energy reservoir in the form of lipid than carbohydrate. The finding challenges the widely-used carbohydrate-loading (carbo-loading) strategy for improving endurance performance. "Carbo-loading didn't make evolutionary sense before the invention of agriculture," said Sun. "Switching muscles from using carbohydrates to lipids could increase exercise endurance, especially for low-intensity exercise." The study suggests that HDAC inhibitors, a class of small molecule drugs currently being tested for treating several diseases, could potentially be used to manipulate such fuel switch in muscle and therefore raises concern of doping. The team performed a number of functional genomics studies that established the link between HDAC3 and the circadian clock. "In normal mice, when the mouse is awake, the clock in the muscle anticipates a feeding cycle and uses HDAC3 to turn off many metabolic genes. This leads the muscles to use more carbohydrate," said Sun. "When the animal is about to go to sleep and anticipates a fasting cycle, the clock removes HDAC3. This leads the muscles to use more lipid." Although these studies were done in mice, the researchers speculate that human muscles most likely will follow the same cycle. The study opens the possibility of promoting body fat burning by increasing exercise activity during the periods in which muscles use lipid, which is at night for people. "Losing body fat would be easier by exercising lightly and fasting at night," said Sun. "It's not a bad idea to take a walk after dinner." Other contributors to this work include Sungguan Hong, Wenjun Zhou, Bin Fang, Wenyun Lu, Emanuele Loro, Manashree Damle, Guolian Ding, Jennifer Jager, Sisi Zhang, Yuxiang Zhang, Dan Feng, Qingwei Chu, Brian D Dill, Henrik Molina, Tejvir S Khurana, Joshua D Rabinowitz and Mitchell A Lazar. The authors are affiliated with one or more of the following institutions: Baylor College of Medicine, University of Pennsylvania, Princeton University, Shanghai Jiao Tong University and Rockefeller University. Financial support was provided by the National Institutes of Health grants DK043806 and DK099443. The study was also supported by multiple core facilities including the Penn Diabetes Center (DK19525) Functional Genomics Core and Mouse Metabolic Phenotyping Core, Rockefeller University Proteomics Center, Princeton/Penn Regional Metabolomics Core, Vanderbilt MMPC (DK59637) and the Baylor Diabetes Center (DK079638) Mouse Metabolism Core.
News Article | November 4, 2016
It is estimated that in Germany alone around 150,000 people fall ill with sepsis every year; despite medical advances, between 30 and 50 percent of the patients still die of the consequences (see box). One of the reasons for the high mortality rate: the diagnosis often comes too late for the lifesaving therapy with antibiotics that only combat the specific causative pathogen. In general the sepsis pathogens are detected by means of so-called blood cultures in which the pathogenic organism from blood samples of the patients are cultivated in the laboratory. Here, two to five days pass before the pathogens have multiplied and a result is available. Due to rapid progress in nucleic acid analysis, the currently available high-throughput technologies (NGS, Next-Generation Sequencing) make it possible to sequence the complete genome of organisms within just a few hours and to check them against known gene sequences (see box). On the basis of these technologies researchers at the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB have developed an alternative diagnostic platform for sepsis. This enables them to identify bacteria, fungi or viruses directly by means of a sequence analysis of their DNA – without having to cultivate the pathogens beforehand in the laboratory. In a clinical study that the researchers carried out in cooperation with Heidelberg University Hospital, they have now validated their diagnostic method with blood samples from sepsis patients. Here, they identified the infectious microorganisms by means of the high-throughput sequencing of DNA circulating freely in the blood (CNAPS, Circulating Nucleic Acids in Plasma and Serum). "With our next-generation sequencing diagnostic method we were able to determine within just 24 hours which pathogens the patients were infected with," Dr. Kai Sohn, head of the "Functional Genomics" working group at Fraunhofer IGB, explains. "As a result of the direct sequencing of the DNA of a blood sample, the time-consuming step of cultivating the microorganisms in the lab is no longer necessary. In this way we can also identify those pathogens that are more difficult to grow under laboratory conditions," says Dr. Sohn. A further advantage: If the samples contain not only the DNA of bacteria, but also that of viruses or fungi, these are sequenced, analyzed and identified as well. "For example, in our study we were able to identify a viral pathogen as the cause of a patient's illness. Yet the patient's blood culture showed a negative result because here only bacteria can be detected," the scientist explains. The method provides both qualitative and quantitative results at the same time. "With our technology, we can recognize on the basis of the number of genome fragments which pathogens have greatly multiplied in the patient and which are already responding to the therapy," Dr. Sohn points out. This permits the physician to immediately implement further targeted therapeutic measures instead of allowing valuable time to pass employing incorrect medication. Over 99 percent of the DNA freely circulating in the blood plasma is of human origin – thus identifying the sepsis pathogens resembles the proverbial search for a needle in a haystack. The researchers therefore use special software programs to compare the sequenced fragments with a genome database into which they have entered publicly available DNA sequences of bacteria, fungi and viruses. However, not every microorganism that is identified is necessarily also the cause of the sepsis. One of the greatest challenges in the evaluation of the sequencing data is therefore to assess whether the finding differs from the statistically expected result. In order to be able to answer this decisive question, Philip Stevens, the bioinformatics specialist in the team, developed a special algorithm in his doctoral thesis at the Center for Integrative Bioinformatics Vienna (CIBIV) and the Institute of Interfacial Process Engineering and Plasma Technology (IGVP) of the University of Stuttgart. The centerpiece of the diagnostic method, for which a patent is pending, compares the sequencing results with sequenced fragments from the blood of healthy test persons. "In this way the algorithm provides us with a score with which we can assess the significance of the data and can exclude the microbial "background noise", i.e. harmless bacteria of our skin or intestinal flora, as diagnostically relevant pathogens," Stevens explains. The clinical study showed that the computed diagnoses correlated closely with those of the blood culture. The resistance of bacteria to commonly used antibiotics such as methicillin, vancomycin or tetracycline is acquired via corresponding resistance genes. Therefore high-throughput sequencing makes it possible, in the same analysis, to identify both the biological species of the pathogen and its resistance genes. This also helps the physician treating the patient to set in motion a targeted therapy. In order to further shorten the time from sample to final diagnosis, the scientists are examining how the method can be transferred to more recently developed sequencing platforms. With nanopore-based sequencing, for example, which is currently in the test phase, DNA can be sequenced in an even shorter time than previously. Thus in future the specific diagnosis of infections would be possible within a period of six to eight hours. For 2017 the Fraunhofer scientists are planning to carry out a multicenter validation study together with leading clinical partners. Explore further: UTI testing technology cuts screening time to four hours More information: Silke Grumaz et al. Next-generation sequencing diagnostics of bacteremia in septic patients, Genome Medicine (2016). DOI: 10.1186/s13073-016-0326-8
News Article | November 2, 2016
Baltimore, MD-- New work led by Carnegie's Steven Farber sheds light on how form follows function for intestinal cells responding to high-fat foods that are rich in cholesterol and triglycerides. Their findings are published in the Journal of Biological Chemistry. Enterocytes are specialized cells that line the insides of our intestines. The intestinal surface is like a toothbrush, with lots of grooves and protrusions that allow the cells there to grab and absorb nutrients from food as it is digested, including the lipid molecules from fatty foods. The cells absorb, process, and package these lipids for distribution throughout our bodies. Clearly they are very important for sustaining good health and keeping us alive, since lipids are necessary for many of the body's functions, including nutrient absorption and hormone production. "When we eat fatty foods, our body's response is coordinated between our digestive organs, our nervous system, and the microbes living in our gut," explained Farber. "Our research used zebrafish to focus on one aspect of this system--how the enterocyte cells inside our intestines respond to a high-fat meal." It turns out that fatty foods cause enterocyte cells to do some interior remodeling. Cells are like tiny factories, where different functions are carried out by highly specialized structures called organelles. In enterocytes, several of these organelles undergo changes in their shape in response to an influx of fats from rich foods. One such shape shift occurs in the nucleus, where the cell's DNA is stored. Farber's team demonstrated that the nucleus takes on a rapid and reversible ruffled appearance after fatty foods are consumed. This is of interest because a cell's genetic material is housed in the nucleus, and this is the location where different genes get turned on and off in response to external stimuli, such as the presence of lipids from fatty foods. So the team examined this issue further and found that the shape shifting in the nucleus coincides with the activation of certain genes that regulate the intestinal cell's ability to package and distribute the lipids to other parts of the body. The team was able to determine that this activation process occurs within an hour of eating high-fat foods. "Our working hypothesis is that the whole response to fat in the enterocyte--the remodeling and gene activation--may be coordinated by an organelle called the endoplasmic reticulum," said lead author Erin Zeituni. If the cell is a factory, then the endoplasmic reticulum it is the assembly line, where various cellular products are synthesized, stored, and packaged for distribution outside of the cell. It is constructed of a series of interconnected tube-like shapes. When the research team used pharmaceuticals to inhibit one function of the endoplasmic reticulum (the building of so-called lipoprotein particles that will export fats out of the cell), the gene activation process was inhibited for many key genes and nuclear ruffling was also altered. This demonstrated that the flux of fat in the endoplasmic reticulum is crucial for initiating the intestinal response to a fatty meal. "So much of the process by which enterocytes prepare and package fats for distribution to the circulatory and lymphatic system is poorly understood," Farber said. "These findings should help increase our understanding of the basic molecular and cellular biology of intestinal cells." This work was supported by the National Institute of Diabetes and Digestive and Kidney, National Institute of General Medicine, and the Zebrafish Functional Genomics Consortium. The Carnegie Institution for Science is a private, nonprofit organization headquartered in Washington, D.C., with six research departments throughout the U.S. Since its founding in 1902, the Carnegie Institution has been a pioneering force in basic scientific research. Carnegie scientists are leaders in plant biology, developmental biology, astronomy, materials science, global ecology, and Earth and planetary science.
News Article | November 6, 2016
Microbial pathogens can be diagnosed unambiguously and within just 24 hours by means of high-throughput sequencing of their genetic makeup and special bioinformatics evaluation algorithms. Fraunhofer researchers have validated this in a clinical study with sepsis patients. The researchers present the NGS diagnosis platform at Medica in Düsseldorf from November 14-17, 2016. It is estimated that in Germany alone around 150,000 people fall ill with sepsis every year; despite medical advances, between 30 and 50 percent of the patients still die of the consequences (see box). One of the reasons for the high mortality rate: the diagnosis often comes too late for the lifesaving therapy with antibiotics that only combat the specific causative pathogen. In general the sepsis pathogens are detected by means of so-called blood cultures in which the pathogenic organism from blood samples of the patients are cultivated in the laboratory. Here, two to five days pass before the pathogens have multiplied and a result is available. Due to rapid progress in nucleic acid analysis, the currently available high-throughput technologies (NGS, Next-Generation Sequencing) make it possible to sequence the complete genome of organisms within just a few hours and to check them against known gene sequences (see box). On the basis of these technologies researchers at the Fraunhofer Institute for Interfacial Engineering and Biotechnology IGB have developed an alternative diagnostic platform for sepsis. This enables them to identify bacteria, fungi or viruses directly by means of a sequence analysis of their DNA -- without having to cultivate the pathogens beforehand in the laboratory. In a clinical study that the researchers carried out in cooperation with Heidelberg University Hospital, they have now validated their diagnostic method with blood samples from sepsis patients. Here, they identified the infectious microorganisms by means of the high-throughput sequencing of DNA circulating freely in the blood (CNAPS, Circulating Nucleic Acids in Plasma and Serum). "With our next-generation sequencing diagnostic method we were able to determine within just 24 hours which pathogens the patients were infected with," Dr. Kai Sohn, head of the "Functional Genomics" working group at Fraunhofer IGB, explains. "As a result of the direct sequencing of the DNA of a blood sample, the time-consuming step of cultivating the microorganisms in the lab is no longer necessary. In this way we can also identify those pathogens that are more difficult to grow under laboratory conditions," says Dr. Sohn. A further advantage: If the samples contain not only the DNA of bacteria, but also that of viruses or fungi, these are sequenced, analyzed and identified as well. "For example, in our study we were able to identify a viral pathogen as the cause of a patient's illness. Yet the patient's blood culture showed a negative result because here only bacteria can be detected," the scientist explains. The method provides both qualitative and quantitative results at the same time. "With our technology, we can recognize on the basis of the number of genome fragments which pathogens have greatly multiplied in the patient and which are already responding to the therapy," Dr. Sohn points out. This permits the physician to immediately implement further targeted therapeutic measures instead of allowing valuable time to pass employing incorrect medication. Over 99 percent of the DNA freely circulating in the blood plasma is of human origin -- thus identifying the sepsis pathogens resembles the proverbial search for a needle in a haystack. The researchers therefore use special software programs to compare the sequenced fragments with a genome database into which they have entered publicly available DNA sequences of bacteria, fungi and viruses. However, not every microorganism that is identified is necessarily also the cause of the sepsis. One of the greatest challenges in the evaluation of the sequencing data is therefore to assess whether the finding differs from the statistically expected result. In order to be able to answer this decisive question, Philip Stevens, the bioinformatics specialist in the team, developed a special algorithm in his doctoral thesis at the Center for Integrative Bioinformatics Vienna (CIBIV) and the Institute of Interfacial Process Engineering and Plasma Technology (IGVP) of the University of Stuttgart. The centerpiece of the diagnostic method, for which a patent is pending, compares the sequencing results with sequenced fragments from the blood of healthy test persons. "In this way the algorithm provides us with a score with which we can assess the significance of the data and can exclude the microbial "background noise," i.e. harmless bacteria of our skin or intestinal flora, as diagnostically relevant pathogens," Stevens explains. The clinical study showed that the computed diagnoses correlated closely with those of the blood culture. The resistance of bacteria to commonly used antibiotics such as methicillin, vancomycin or tetracycline is acquired via corresponding resistance genes. Therefore high-throughput sequencing makes it possible, in the same analysis, to identify both the biological species of the pathogen and its resistance genes. This also helps the physician treating the patient to set in motion a targeted therapy. In order to further shorten the time from sample to final diagnosis, the scientists are examining how the method can be transferred to more recently developed sequencing platforms. With nanopore-based sequencing, for example, which is currently in the test phase, DNA can be sequenced in an even shorter time than previously. Thus in future the specific diagnosis of infections would be possible within a period of six to eight hours. For 2017 the Fraunhofer scientists are planning to carry out a multicenter validation study together with leading clinical partners. Fraunhofer IGB presents sepsis diagnostics by means of next-generation sequencing at Medica in Düsseldorf from November 14-17, 2016 at the Fraunhofer joint stand.
News Article | September 23, 2016
Researchers at the University of Toronto's Donnelly Centre have created the first map that shows the global genetic interaction network of a cell. It begins to explain how thousands of genes coordinate with one another to orchestrate cellular life. The study was led by U of T Professors Brenda Andrews and Charles Boone, and Chad Myers of the University of Minnesota-Twin Cities. It opens the door to a new way of exploring how genes contribute to disease with a potential for developing finely-tuned therapies. The findings are published in the journal Science. "We've created a reference guide for how to chart genetic interactions in a cell," said Michael Costanzo, a research associate in the Boone lab and one of the researchers who spearheaded the study. "We can now tell what kind of properties to look for in searching for highly connected genes in human genetic networks with the potential to impact genetic diseases." The study took 15 years to complete and adds to Andrews' rich scientific legacy for which she was awarded a Companion of the Order of Canada. Just as societies in the world are organized from countries down to local communities, the genes in cells operate in hierarchical networks to organize cellular life. Researchers believe that if we are to understand what 20,000 human genes do, we must first find out how they are connected to each other. Studies in yeast cells first showed the need to look farther than a gene's individual effect to understand its role. With 6,000 genes, many of which are also found in humans, yeast cells are a relatively simple but powerful stand-ins for human cells. Over a decade ago, an international consortium of scientists first deleted every yeast gene, one by one. They were surprised to find that only one in five were essential for survival. It wasn't until last year that advances in gene editing technology allowed scientists to tackle the equivalent question in human cells. It revealed the same answer: a mere fraction of genes are essential in human cells too. These findings suggested most genes are "buffered" to protect the cell from mutations and environmental stresses. To understand how this buffering works, scientists had to ask if cells can survive upon losing more than one gene at a time, and they had to test millions of gene pairs. Andrews, Boone and Myers led the pioneering work in yeast cells by deleting two genes at a time in pair combinations. They were trying to look for gene pairs that are essential for survival. This called for custom-built robots and a state-of-the-art automated pipeline to analyze almost all of the mind-blowing 18 million different combinations. The yeast map identified genes that work together in a cell. It shows how, if a gene function is lost, there's another gene in the genome to fill its role. Consider a bicycle analogy: a wheel is akin to an essential gene – without it, you couldn't ride the bike. But front brakes? Well, as long as the back brakes are working, you might be able to get by. But if you were to lose both sets of brakes, you are heading for trouble. Geneticists say that front and back brakes are "synthetic lethal," meaning that losing both – but not one – spells doom. Synthetic lethal gene pairs are relatively rare, but because they tend to control the same process in the cell, they reveal important information about genes we don't know much about. For example, scientists can predict what an unexplored gene does in the cell simply based on its genetic interaction patterns. It's becoming increasingly clear that human genes also have one or more functional backups. So researchers believe that instead of searching for single genes underlying diseases, we should be looking for gene pairs. That is a huge challenge because it means examining about 200 million possible gene pairs in the human genome for association with a disease. Fortunately, with the know-how from the yeast map, researchers can now begin to map genetic interactions in human cells and even expand it to different cell types. Together with whole-genome sequences and health parameters measured by new personal devices, it should finally become possible to find combinations of genes that underlie human physiology and disease. "Without our many years of genetic network analysis with yeast, you wouldn't have known the extent to which genetic interactions drive cellular life or how to begin mapping a global genetic network in human cells," said Boone, who is also a professor in U of T's molecular genetics department and a co-director of the Genetic Networks program at the Canadian Institute for Advanced Research (CIFAR) and holds Canada Research Chair in Proteomics, Bioinformatics and Functional Genomics. We have tested the method to completion in a model system to provide the proof of principle for how to approach this problem in human cells. There's no doubt it will work and generate a wealth of new information." The concept of synthetic lethality is already changing cancer treatment because of its potential to identify drug targets that exist only in tumour cells. Cancer cells differ from normal cells in that they have scrambled genomes littered with mutations. They're like a bicycle without a set of brakes. If scientists could find the highly vulnerable back-up genes in cancer, they could target specific drugs at them to destroy only the cells that are sick, leaving the healthy ones untouched.
News Article | November 5, 2016
People react very differently to an infection with the Borrelia bacterium that causes Lyme disease. Researchers at Radboud university medical center, the University Medical Center Groningen (UMCG) and the Broad Institute of MIT and Harvard have investigated this varying response, and their results will be published on 4 November in Cell Host & Microbe. Age, genetic disposition and previous Lyme infections play an important role. However, despite the large differences observed, the Borrelia bacterium has a clear effect on the immune system's energy regulation, opening up opportunities for research into better detection of Borrelia infections. One million people are bitten by a tick in the Netherlands each year, and about one in five of these ticks are carriers of the Borrelia bacterium. The symptoms after an infection vary widely: for example, many people have a red ring or patch around the bite, but some do not. This can make it difficult to give a correct diagnosis. The variation in immune response can be largely explained by differences in the production of cytokines, the most important signalling molecules in our immune system. The Human Functional Genomics Project, run by professors Mihai Netea and Leo Joosten at Radboud university medical center, UMCG Professor Cisca Wijmenga and Professor Ramnik Xavier at the Broad Institute of MIT and Harvard investigated how differences in cytokine production during a Borrelia infection in 500 healthy volunteers can be explained. Leo Joosten: "Forest rangers, who may receive as many as 35 tick bites per day, also took part in an additional study. Some of them had never had Lyme disease, even though the chance of infection was high." First of all, the immune response to Lyme disease appears to be strongly age-related. Production of the cytokine IL-22 deceases with age, reducing the immune system's defence against the Borrelia bacteria. The researchers also found a genetic variation that increases production of the HIF-1a protein during a Borrelia infection. This protein causes the amount of lactic acid in the cell to increase, which normally only happens at low oxygen levels. This results in an energy deficiency in the immune cells and therefore a reduction in the production of IL-22 and other inflammatory proteins. This effect on the metabolism of immune cells is specific to the Borrelia bacterium, which opens up possibilities for research into the better detection and treatment of a Borrelia infection. Leo Joosten: "It is not possible to measure IL-22 in patient's blood so we have no new test. We do however want to look at whether blocking the lactic acid route could help, but that is difficult to do at cell level. Another way is to strengthen the immune system by raising the levels of IL-22 but we would rather find ways to increase the immune system's ability to kill the Borrelia bacteria." It is interesting that previous Borrelia infections do not seem to provide protection from Lyme disease. Leo Joosten: "We had expected that people with Borrelia antibodies in their blood would have a stronger immune response to the Borrelia bacteria. However, that is not the case. It seems that the Borrelia bacterium does not cause improved resistance. We hope that further research will show how previous Lyme infections specifically affect the immune system."