Researchers from the University of Chicago have developed a high-throughput RNA sequencing strategy to study the activity of the gut microbiome. The new tools analyze transfer RNA (tRNA), a molecular Rosetta Stone that translates the genetic information encoded in DNA into proteins that perform basic biological functions. Developing a clear picture of tRNA dynamics will allow scientists to understand the activity of naturally occurring microbiomes, and study their responses to environmental changes, such as varying temperatures or changing availability of nutrients. In a new study published in Nature Communications, a team of scientists led by Tao Pan, PhD, professor of biochemistry and molecular biology, and A. Murat Eren, PhD, assistant professor of medicine at UChicago, demonstrated the application of tRNA sequencing to gut microbiome samples from mice that were fed either a low-fat or high-fat diet. The new software and computational strategy described in the study created a catalog of tRNA molecules recovered from the gut samples, traced them back to the bacteria responsible for their expression, and measured chemical modifications in tRNA that take place after transcription. Each tRNA in bacteria has an average of eight chemical modifications that can tune its function. The new high-throughput sequencing and analysis strategy detects two of them, but it can also measure the amount of modification on a scale from 0 to 100 percent at each site. The level of one of the modifications, called m1A, was higher in the gut microbiome of mice that were fed a high-fat diet. This is the first time scientists have been able to see any modification level change in tRNA in any microbiome. "We were working backwards," Pan said. "We had no preconceived notion of why the m1A tRNA modifications were actually there or what they were doing, but to see any modification change at all in the microbiome is unprecedented." The m1A modification helps synthesize certain types of proteins that may be more abundant in a high-fat diet. The researchers don't know yet if these modification differences occur in response to that diet, or if they are already present and become active to enhance the synthesis of those proteins. The study is the first of a series of microbiome projects from UChicago funded by a grant from the Keck Foundation. Pan has pioneered the use of tRNA sequencing tools, and the grant will fund continuing work to make them widely accessible through new computational strategies that Eren develops. Large sets of data generated by tRNA sequencing can provide critical insights into microbiomes associated with humans or the environment at a low cost. "The molecular and computational advances that have emerged during the last two decades have only helped us scratch the surface of microbial life and their influence on their surroundings," Eren said. "By providing quick and affordable insights into the core of the translational machinery, tRNA sequencing may become not only a way to gain insights into microbial responses to subtle environmental changes that can't be easily measured by other means, but also bring more RNA biology and RNA epigenetics into the rapidly developing field of the microbiome." Pan and Eren agree that there is much room to improve this novel strategy, and they hope that it will happen quickly. "There are a number of ways to examine microbiome activities, but nothing is faster and gets you more volume of data than sequencing," Pan said. "Here we have developed a new method that reports activity of the microbiome through tRNA and does so at high throughput. That's really the value." The study, "Microbiome characterization by high-throughput transfer RNA sequencing and modification analysis," was supported by the National Natural Science Foundation of China, Shandong Provincial Natural Science Foundation, China Scholarship Council, the National Institutes of Health, the University of Chicago and the Keck Foundation.
The most important features of the EtherCAT real-time Ethernet fieldbus system include its diagnostic hardware and software options: the system not only detects faults in the EtherCAT network, but also locates them, including loose plug connections. This makes the approach ideal for building a robust industrial network environment. The fault diagnosis allows potential downtimes in a production plant to be prevented. Third-party vendors who can work with any EtherCAT master implementation without additional hardware customization can now use the software-based, low-memory diagnostic interface. Integrating the interface into the in-house diagnostic tool allows the direct retrieval of information about the network topology, comparison with the expected configuration as well as the detection of transmission disturbances and unexpected status changes of the slave devices used. The EtherCAT communication protocol is used to connect a wide range of peripherals and is supported, for example, by the PCRM robot control module from Pilz .
Immersing deeper and deeper into cells with the microscope. Imaging the nucleus and other structures more and more accurately. Getting the most detailed views of cellular multi-protein complexes. All of these are goals pursued by the microscopy expert Markus Sauer at the Biocenter of Julius-Maximilians-Universität Würzburg (JMU) in Bavaria, Germany. Together with researchers from Geneva and Lausanne in Switzerland, he has now shown that a hitherto doubted method of super-resolution microscopy is reliable. We are talking about ultrastructural expansion microscopy (U-ExM). In a nutshell, it works like this: The cell structures to be imaged, in this case multi-protein complexes, are anchored in a polymer – just like decorating a Christmas tree. Then the interactions between the proteins are destroyed and the polymer is swelled with liquid. "The polymer then expands uniformly in all spatial directions by a factor of four. The antigens are retained and can subsequently be stained with dye-labeled antibodies," says Professor Sauer. So far, many scientists have been of the opinion that the expansion of the polymer does not proceed uniformly and one gets a distorted representation in the end. "With U-ExM, we can really depict ultrastructural details, the method is reliable," says Sauer. "And it delivers a picture that is four times higher resolved than with standard methods of microscopy." The research team is currently proving this in the journal "Nature Methods" using the example of the centrioles. These cylindrical protein structures play an important role in cell division; the Würzburg biologist Theodor Boveri first described it in 1888. The centrioles were chosen for the experiment because their structure is already well known. "This enabled us to see, in comparison to electron micrographs, that U-ExM works reliably and even preserves the chirality of the microtubule triplets that make up the centrioles," explains Sauer. Next, the JMU researchers want to use this method of microscopy to analyze cell structures of which one has not yet had such a precise picture. "These are, for example, substructures of the centrioles, the nuclear pore complexes or synaptonemal complexes. All of them are now accessible for the first time with molecular resolution by light microscopy, "said Sauer.
Eccrine Systems, Inc., an advanced sweat sensor company, today announced that a key patent, US10136831, has been issued to Dr. Jason Heikenfeld, Co-Founder & CSO, and prominent University of Cincinnati researcher. The company holds exclusive rights to the UC patent. he patented invention covers the use of on-body sweat devices that are capable of electronically correlating two or more measurements of an analyte with the time at which the analyte emerged in newly excreted sweat. Without the use of the invention it is likely not possible to correlate sweat analyte data trends with chronological blood values or similar physiological measurements. Heikenfeld developed his invention over four years ago at a time when continuous on-body measurement of sweat analytes was at its inception. Heikenfeld is a well-known scientific leader of the wearable sweat sensor space with many of its most prescient and important advances to his credit. The company uses Heikenfeld's invention to time correlate the data derived from its sweat sensor devices, including data and algorithms that will define the pharmacokinetic (PK) profile of medications that are excreted in locally stimulated sweat. "Non-invasive medication monitoring is a great example of the utility of Jason's invention," says Dr. Gavi Begtrup, CEO of Eccrine Systems. "You can't devise an on-body device to derive a sweat pharmacokinetic curve, and then correlate that curve to a drug's blood PK curve, without using this invention. This is a big deal given the estimated $500 billion dollar annual healthcare cost of non-optimized medication therapy, a significant portion of which can result from individual PK differences that cause failed treatment outcomes."
Researchers then use DNA- and RNA- sequencing to look at populations of cells, examining which genes are expressed within a sample of cancerous tissue. However, traditional sequencing methods can hide that fact that not all tumor cells necessarily behave in the same way. Not recognizing this means that if you target a tumor with a specific type of drug, some cells may be just different enough to survive and thrive. In a major advance for genomics, it is now possible to look at what one single cell is doing at any given time with a technique called single-cell RNA sequencing (scRNA-seq). This method looks at the amount of messenger RNAs (mRNAs) in a cell and compares those to other cells to look for differences in gene expression. However, what information you find can depend on how your run your experiment and how the data are analyzed. Lana Garmire, Ph.D., associate professor of the department of computational medicine & bioinformatics at Michigan Medicine and her team is studying ways to eliminate some of the biases that can make interpreting scRNA-seq data difficult. "A lot of the noise in this type of sequencing comes from the fact that you have to measure samples in extreme low quantities and in different batches," she explains. Differences that arise due to this split are called batch effects. Genomics researchers must correct for these batch effects, but this process can raise a conundrum: how do you know if a difference is a batch effect or a true difference between cells? Bioinformatics is the term for collecting and analyzing complex biological data using computer programs. It is a relatively new field born out of the ability to gather enormous amounts of biological data, such as DNA and protein sequences. Researchers rely on bioinformatics techniques to determine which genes are expressed in single cells. But they've had to work around the noise introduced through different research protocols and batch effects. Garmire, who recently joined U-M from the University of Hawaii and is the new faculty director University of Michigan Medical School Bioinformatics Core, has discovered a more efficient way of identifying differences between cells using the same set of data produced during sequencing experiments. Instead of relying on gene expression, she found that looking at what are known as single nucleotide variants (SNVs) can eliminate some of this uncertainty. "With SNVs, you are dealing with numbers that are binary, 0 and 1. Either the mutation is there or not." Recall that genes are made up of nucleotides represented by the letters A, T, G and C that make up a code that is translated into a protein. Garmire's method looks for differences in single nucleotides, knowing that an A can only be replaced by a T and a G by a C. This new work, described in Nature Communications, developed a new set of procedures to process scRNA-seq data and retrieve this variant information. Further, using a computer program called SSrGE, they can link this variant information to more traditional gene expression information. "This gives us information on different subpopulations of tumor cells and becomes sort of like a fingerprint that can be marked to identify cell-to-cell differences," says Garmire. Ultimately, drug makers and clinicians use these targets to guide pharmaceutical treatments. "When you want to attack the issue, you go at it by attacking the fundamental features of that issue: the mutations. Clinicians may be able to use this information later on to guide their therapeutics." Garmire looks forward to bringing bioinformatics out of the lab, helping researchers who amass large amounts of data to use them and develop downstream clinical applications. "We divide the body up and specialize but at the end of the day, you need to look holistically and ask, what am I doing and who is this helping?
Contrary to some analyses, according to which German medium-sized enterprises have missed the boat on digitization , a recent study by the consultancy company PAC and the business software provider proALPHA paints a much more positive picture. It is based on a survey of 102 leading IT and departmental managers from the manufacturing industry. This indicates that 71% have at least undertaken initial pilot projects in the context of Industry 4.0. For 90%, implementation of an ERP system is regarded as the basis for successful digitization. However, more than half criticized existing solutions for being too rigid to allow customized process optimization. Of those surveyed, 62% are therefore planning to modernize their existing ERP solutions and have already taken this into account in their budget planning. As other factors connected with successful digital transformation, 89% cite interdepartmental collaboration, 82% mention training and internal staff development, and 82% support from the highest management level. Another striking aspect of the study, which is free to download , is that although digitization of production is well advanced, there is a lack of consistency in the development of additional digital products and services.
The study targeted people aged 60-69 years, and just under a half of the age group, or a little more than 300,000 people, were randomised by late 2011. Half of the population in the study were invited for screening, while the other half of the age cohort served as a control group. Faecal occult blood tests (FOBT) were used in the screening, and patients who tested positive for blood were referred for a colonoscopy. The first study based on the screening results indicated no significant decrease in mortality, so the screenings were discontinued after 2016. However, researchers from the Helsinki University Hospital and the Finnish Cancer Registry wanted to examine whether the screening had offered benefits to patients with colorectal cancer. "Practically no cancer screenings have been found to have an impact on overall mortality. However, they may still be useful in other ways. We wanted to study whether the patients could avoid the more intense treatments if they participated in screening for colorectal cancer," says Dr. Laura Koskenvuo, gastrointestinal surgeon. The study examined the data of approximately 1,400 patients diagnosed with colorectal cancer. The results indicated that among patients from the screening group, the surgical removal of the entire tumour was more commonly successful than it was among the control group patients, and they were less likely to require chemotherapy. The patients from the screening group were also less likely to undergo emergency surgery because of their tumour than the control group patients. "The control group had 50% more emergency surgeries, 40% more incomplete tumour removals and 20% more chemotherapy treatments than patients in the screening group," says Adjunct Prof. Ville Sallinen, gastrointestinal surgeon. Closer inspection of the results showed that these benefits were particularly prevalent among male patients. Similar benefits were not seen among women. Additionally, the researchers found that the screening was most efficient at detecting left-sided colorectal cancer and the screening was found to have no benefit for patients with cancer on the right side, possibly because blood seeping from tumours on the right side becomes so diluted as it travels through the colon that the gFOBT can no longer detect it. "The strength of this Finnish study is that it randomised an enormous number of people in the public health care system, which meant that we could objectively evaluate the benefits of the screening. Similar studies have not been available anywhere else," says Professor Nea Malila, director of the Finnish Cancer Registry. "In the future, we must examine whether different screening techniques could improve the situation of female patients and facilitate the diagnosis of right-sided colorectal cancer," the researchers state.
When used in industrial fans, radial impellers are exposed to high mechanical, thermal and medial loads. They are usually made of metal. At the Institute of Lightweight Engineering and Polymer Technology (ILK) of TU Dresden, researchers have now developed a radial fan impeller with a modular metal-fiber composite design . Because of its low mass, the load is significantly lower than with metal fan impellers. For the same reason and thanks to the high strength of the composite fiber material, scientists have been able to increase the speed of the impellers significantly. In initial centrifuging tests at the ILK, at a maximum rotational speed of 10,266 rpm a circumferential speed of 543 m/s was achieved – about twice as fast as the maximum speed of a comparable metal impeller. The researchers also point out that, with modern metal-fiber composite designs, fan impellers with multiple parts can be made, which cuts manufacturing costs and simplifies maintenance. The project team around Prof. Maik Gude was awarded the AVK Innovation Prize by the Industrievereinigung Verstärkte Kunststoffe (Industrial Association for Reinforced Plastics) for the development at the International Composites Congress 2018 in Stuttgart.
"We compared three novel tau-specific radiopharmaceuticals – 11C-RO-963, 11C-RO-643, and 18F-RO-948 – that showed pre-clinical in vitro and in vivo promise for use in imaging human tau (Honer et al., JNM, April 2018)," explains Dean F. Wong, MD, PhD, Johns Hopkins University professor of radiology, neurology, psychiatry and neurosciences and director of the Division of Nuclear Medicine's Section of High Resolution Brain PET Imaging. In this first human evaluation of these novel radiotracers, healthy humans and patients with Alzheimer's disease (AD) were studied using an innovative study design to perform head-to-head comparisons of the three compounds in a pairwise fashion. Wong states, "This design allowed us to select one radioligand, 18F-R0-948, as the most promising second-generation tau radiopharmaceutical for larger scale use in human PET tau imaging." Over all brain regions and subjects, the trend was for 18F-RO-948 to have the highest standardized uptake value (SUVpeak), followed by 11C-RO-963 and then 11C-RO-643. Regional analysis of SUV ratio and total distribution volume for 11C-RO-643 and 18F-RO-948 clearly discriminated the AD group from the healthy control groups. Compartmental modeling confirmed that 11C-RO-643 had lower brain entry than either 11C-RO-963 or 18F-RO-948 and that 18F-RO-948 showed better contrast between areas of high versus low tau accumulation. Subsequent analysis therefore focused on 18F-RO-948. Both voxelwise and region-based analysis of 18F-RO-948 binding in healthy controls versus AD subjects revealed multiple areas where AD subjects significantly differed from healthy controls. Voxelwise analysis also revealed a set of symmetric clusters where AD subjects had higher binding than healthy controls. "Importantly, this new tracer appears to have much less off-target binding than was reported for existing tau tracers," notes Wong. "Especially, it has less binding to the choroid plexus adjacent to the hippocampus, which has confounded interpretation of mesial temporal tau measured by first generation PET Tau tracers." He points out, "The significance of this research and the companion research reported in Kuwabara et al. in this same issue is that they describe in detail the selection and quantification of a second-generation tau PET imaging as a complement to amyloid imaging, allowing us to accurately measure tau pathology in living people and contributing to our understanding of the pathophysiology of Alzheimer's and related dementias. Better Tau PET radiopharmaceuticals also provide the promise of improved target engagement and monitoring of anti-tau treatments in future Alzheimer's clinical trials." Collaboration has been key to this research process. Wong emphasizes, "These findings demonstrate the impact of the complementary strengths of preclinical, translational and clinical research with university PET and memory experts, NIH aging experts and dedicated imaging neuroscientists in the pharmaceutical industry to approach one of the greatest global public health challenges–i.e., Alzheimer's disease, where there is still no definitive cure. Improved biomarkers such as PET imaging of tau and, in the future, other dementia-implicated proteins are vital to reducing the enormous costs of drug development and eventually understanding and treating Alzheimer's."
The research, published in Nature Communications, will help in diagnosing disease and, in future, guiding therapeutic intervention. Each cell in our organism has a roughly 2-meter-long molecule of DNA – our genetic information – that needs to be properly packed inside a few micron nucleus. How the DNA is organised in the nucleus is known to play a key role for normal cellular development and function, since mutations in the mechanisms that control this process lead to developmental disorders or diseases such as cancer. However, the exact role that the organisation of the genome plays in disease is currently unknown, since scientists have lacked the ability to thoroughly examine the 3D organisation of the genome in diseased cells. In this new research, scientists have performed a proof-of-principle study demonstrating that the 3D genome can be directly examined in diseased cells from patients. Subtle improvements implemented in this new technique to measure three-dimensional genome architecture, called Low-C, allowed researchers to lower the amount of biological material initially required to perform the experiments. This enabled them to determine the spatial architecture of a diffuse large B-cell lymphoma genome. “To be able to examine the genome architecture of the specific cells that cause disease is really exciting, since currently we do not know how the 3D genome is altered in these cells”, says Dr Noelia Díaz, a postdoctoral fellow in the Vaquerizas Laboratory who led the experimental part of the project. The researchers then performed an advanced computational analysis of the data that revealed some surprising observations. First, the scientists were able to detect genome rearrangements – changes in the normal sequence arrangement of our genome that are a key feature of many cancers – and detected both novel and known translocations characteristic of the disease, which were then experimentally validated. “It was reassuring to see our computational predictions validated experimentally”, says Dr Kai Kruse, a postdoctoral fellow in the Vaquerizas Laboratory who performed the computational analysis of the data. But the data held more surprises. When the researchers examined a finer level of chromatin organisation into topological domains (short sections of the genome that are folded into compact knots resembling balls of yarn), they observed that new domains were present in disease cells in regions of the genome that would otherwise present no domains in healthy cells. “This was a surprising finding, since the 3D architecture of fully developed cells is thought to be rather invariant”, says Dr Juanma Vaquerizas, a Group Leader at the Max Planck Institute for Molecular Biomedicine in Muenster, who supervised the research. “We could observe that these new structural domains appear in regions that contain genes previously known to be associated with cancer and disease, but the functional role of these new domains is currently unknown”, says Vaquerizas. The researchers aim now to extend their studies to more samples, to be able to determine the impact that changes in the 3D structure of the genome play in disease and to use this information in the design of personalised patient-specific treatment options.