Functional Genomics

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Functional Genomics

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The Clustered regularly interspaced short palindromic repeats CRISPR and CRISPR-associated (Cas) genes market is anticipated to reach USD 4.09 billion by 2025. This genome editing principle spans almost every industry that involves biological systems. The rising adoption of technology in different areas associated with biotechnology is anticipated to drive industrial growth of the technology substantially in the coming years. Possibility of rewriting the host DNA through the virtue of Cas9 by introduction of major modifications can be attributed for rising adoption of technology. These modifications include inversion, deletions, knockouts, translocations, and gene replacement. Moreover, application of the technology as a qualitative as well as quantitative tool in plant genome editing is expected to propel growth. The technique holds the potential for producing plants with mutations linked to other disciplines of science such as disease resistance, biofuel production, synthetic biology, phytoremediation and abiotic stress tolerance. Combination of clustered regularly interspaced short palindromic repeats and sequencing technology enables high-throughput analysis of gene regulation thereby resulting to enhancement in genomics sector. The aforementioned combination is applicable in the epigenetic study of diseases such as leukemia. However, off-target effects associated with the implementation of CRISPR is anticipated to impede growth in the coming years. These effects include improper concentration ratio between Cas9 and single guide RNA that may result into off-target cleavage. Further Key Findings from the Report Suggest: 3 CRISPR and Cas Genes Market Variables, Trends & Scope 3.1 Market Segmentation & Scope 3.1.1 Market Driver Analysis 3.1.1.1 Rising adoption in diverse fields of biotechnology 3.1.1.1.1 Epigenetics 3.1.1.1.2 Medicine 3.1.1.1.3 Human germline editing 3.1.1.1.4 Tool for qualitative and quantitative plant genome editing 3.1.1.2 Technological advancements in CRISPR technology 3.1.1.3 Introduction of anti-CRISPR protein 3.1.1.4 Ongoing competition for CRISPR commercialization 3.1.2 Market Restraint Analysis 3.1.2.1 Off-target effects of CRISPR technology 3.1.2.2 Intellectual property disputes pertaining to Cas 3.1.2.3 Ethical concerns and implications with respect to human genome editing 3.2 Penetration & Growth Prospect Mapping for Application, 2015 3.3 CRISPR and Cas Genes -Swot Analysis, By Factor (Political & Legal, Economic And Technological) 3.4 Industry Analysis - Porter's 3.5 CRISPR and Cas Genes Market: Pipeline Analysis 3.5.1 Editas Medicine 3.5.2 Intellia Therapeutics, Inc. 3.5.3 CRISPR THERAPEUTICS 3.5.4 Precision Biosciences 3.5.5 Caribou Biosciences 3.5.6 Cibus 3.5.7 Recombinetics, Inc 3.6 CRISPR and Cas Genes Market: Patent Landscape 5 CRISPR and Cas Genes Market: Application Estimates & Trend Analysis 5.1 CRISPR and Cas Genes Market: Application Movement Analysis 5.2 Genome Engineering 5.3 Disease Models 5.4 Functional Genomics 5.5 Knockdown/Activation 5.6 Others For more information about this report visit http://www.researchandmarkets.com/research/bg9lth/crispr_and To view the original version on PR Newswire, visit:http://www.prnewswire.com/news-releases/research-and-markets---global-crispr-and-crispr-associated-cas-genes-market-analysis-2014-2017--2025-focus-on-genome-engineering-disease-models-functional-genomics-300444155.html


Baltimore, MD--Studying how our bodies metabolize lipids such as fatty acids, triglycerides, and cholesterol can teach us about cardiovascular disease, diabetes, and other health problems, as well as reveal basic cellular functions. But the process of studying what happens to lipids after being consumed has been both technologically difficult and expensive to accomplish until now. New work from Carnegie's Steven Farber and his graduate student Vanessa Quinlivan debuts a method using fluorescent tagging to visualize and help measure lipids in real time as they are metabolized by living fish. Their work is published by the Journal of Lipid Research. "Lipids play a vital role in cellular function, because they form the membranes that surround each cell and many of the structures inside of it," Quinlivan said. "They are also part of the crucial makeup of hormones such as estrogen and testosterone, which transmit messages between cells." Unlike proteins, the recipes for different lipid-containing molecules are not precisely encoded by DNA sequences. A cell may receive a genetic signal to build a lipid for a certain cellular purpose, but the exact type may not be indicated with a high degree of specificity. Instead, lipid molecules are built from an array of building blocks whose combinations can change depending on the type of food we eat. However, lipid compositions vary between cells and cellular structures within the same organism, so diet isn't the only factor determining which lipids are manufactured. "Understanding the balancing act in what makes up our bodies' lipids--between availability based on what we're eating and genetic guidance--is very important to cell biologists," Farber explained. "There is growing evidence that these differences can affect wide arrays of cellular processes." For example, omega-3 fatty acids, which are lipid building blocks found in foods like salmon and walnuts, are known to be especially good for heart and liver health. There is evidence that when people eat omega-3 fatty acids, the cellular membranes into which they are incorporated are less likely to overreact to signals from the immune system than membranes comprised of other kinds of lipids. This has an anti-inflammatory effect that could prevent heart or liver disease. Farber and Quinlivan's method allowed them to delve into these kinds of connections. They were able to tag different kinds of lipids, feed them to live zebrafish, and then watch what the fish did with them. "If we fed the fish a specific type of fat, our technique allowed us to determine into what molecules these lipids were reassembled after they were broken down in the small intestine and in which organs and cells these molecules ended up," Farber explained. The tags they used were fluorescent. So Farber and Quinlivan and their team were actually able to see the fats that they fed their zebrafish glowing under the microscope as they were broken down and reassembled into new molecules in different organs. Further experiments allowed them to learn into what types of molecules the broken down fat components were incorporated. "Being able to do microscopy and biochemistry in the same experiment made it easier to understand the biological meaning of our results," Quinlivan said. "We hope our method will allow us to make further breakthroughs in lipid biochemistry going forward." The other members of the team were Carnegie's Meredith Wilson, and Josef Ruzicka of Thermo Fisher Scientific. This work was supported by the National Institute on Alcohol Abuse and Alcoholism, the National Institute of Diabetes and Digestive and Kidney Diseases, and the National Institute of General Medicine grant of the Zebrafish Functional Genomics Consortium. The Carnegie Institution for Science (carnegiescience.edu) 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


DUBLIN, April 24, 2017 /PRNewswire/ -- Research and Markets has announced the addition of the "CRISPR And CRISPR-Associated (Cas) Genes Market Analysis By Product (Vector-Based & DNA-Free Cas), By Application (Genome Engineering, Disease Models, Functional Genomics), By End-Use,...


News Article | January 20, 2016
Site: phys.org

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 | December 22, 2016
Site: www.eurekalert.org

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.


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 4.3.1.1 Structural Genomics 4.3.1.2 Functional Genomics 4.3.1.3 Other Genomics technologies 4.3.1.3.1.1 Clinical Medicine 4.3.1.3.1.2 New Antibiotics 4.4 Bioinformatics 4.4.1.1 Computer-Aided Drug Design 4.5 Biochips 4.5.1.1 Lab on a chip 4.5.1.2 Proteomics microarrays 4.5.1.3 DNA and Protein microarrays 4.6 Bioanalytical Instruments 4.6.1.1 Chemotherapy instruments 4.6.1.2 Mass spectrometry 4.6.1.3 Microplate readers 4.6.1.4 Nuclear magnetic resonance 4.7 Nanotechnology 4.7.1.1 Nano-mass spectroscopy 4.7.1.2 Dip-pen Nanolithography 4.7.1.3 Atomic force microscopy (AFM) 4.8 Metabolomics 4.8.1.1 Target Identification 4.8.1.2 Target Validation 4.8.1.3 Lead Optimization 4.8.1.4 Mode of Action 4.8.1.5 Preclinical Studies 4.8.1.6 Clinical Studies 4.8.1.7 Post-Approval Studies 4.8.1.8 Diagnostics 4.9 Other Technologies 4.9.1.1 RNAi (RNA interference) 4.9.1.1.1.1 MiRNAS (MicroRNA sequencing) 4.9.1.1.1.2 SiRNA (Small interfering RNA) 4.9.1.1.1.3 Other RNAi technologies 4.9.1.2 Combinatorial chemistry 4.9.1.2.1.1 Chemical Encoding 4.9.1.2.1.2 Positional Encoding 4.9.1.2.1.3 Electronic Encoding 4.9.1.3 Synthetic Biology 4.9.1.4 Proteomic 4.9.1.4.1.1 Two dimensional gel electrphoresis- 2DGE 4.9.1.4.1.2 Two-hybrid systems 4.9.1.5 Cell Based Assays 4.9.1.6 Epigenetics 4.9.1.7 Systems Biology 4.9.1.7.1.1 Computer Modelling 4.9.1.8 Quantitative polymerase chain reaction (QPCR) 4.9.1.9 Laboratory information management systems 4.9.1.10 Microfluidics 4.9.1.11 Chromatography 4.9.1.12 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 | November 4, 2016
Site: phys.org

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 6, 2016
Site: www.sciencedaily.com

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
Site: www.chromatographytechniques.com

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
Site: www.sciencedaily.com

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."

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