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News Article | May 11, 2017
Site: www.eurekalert.org

How do T cells, the beat cops of the immune system, detect signs of disease without the benefit of eyes? Like most cells, they explore their surroundings through direct physical contact, but how T cells feel out intruders rapidly and reliably enough to nip infections and other threats in the bud has remained a mystery to researchers. In a new study, published online May 11, 2017 in Science, UC San Francisco researchers began to address this question by using cutting-edge techniques to capture videos of the surface of living T cells in more detail than ever before. Researchers had previously observed tentacle-like protrusions called microvilli covering the surface of T cells, but the new research revealed that these tentacles are in constant motion: they crawl across the cell surface, each independently searching for signs of danger or infection in a fractal-like pattern that allows T cells to spend the minimum time necessary feeling for a potential threat before moving on. "Previous techniques had allowed us to take snapshots of the surface of T cells, but that's like trying to understand a basketball game by studying a black-and-white photo," said Matthew Krummel, PhD, associate professor of pathology at UCSF and senior author of the new study. "Now we can watch these amazing little fingers of membrane move around in real-time - and it turns out they're incredibly efficient." Among other potential benefits, Krummel says, understanding how T cells efficiently sample their environment to search for invasive pathogens opens up new questions about what countermeasures infectious organisms or even cancer cells may have evolved as a way of avoiding detection, and could suggest new ways for researchers to help T cells see through such a ruse. Efficient search by T cells is key to an effective immune response As they make their rounds through the body, T cells make contact with a network of informants -- other immune cells that scour the body for potential signs of danger and display the protein fragments they find (called "antigens") on their surface for inspection by the T cells. If a T cell meets one of these so-called antigen-presenting cells and recognizes a protein fragment it carries as evidence of danger, the T cell sounds the alarm and triggers a more global immune response to fight off the invaders. Scientists estimate that you have only about 100 T cells in your body at any given moment that can recognize and responding to a specific antigen, such a protein from this year's flu virus, and these few cells each take days to patrol your entire body, Krummel said. "This means the immune system really needs to get ahead of whatever is attacking the body at the very first evidence that there's an intruder on board. If one T cell misses the signs of a virus, the next time a cell that can recognize the threat might come through that tissue, the virus has had hours to make tens of thousands of copies of itself." New imaging techniques reveal how immune cells "talk" using touch In the Science study, Krummel's team was able to study how T cells efficiently interrogate antigen-presenting cells in real time, thanks to a high-resolution cellular imaging technique called lattice light-sheet microscopy, which the team set up at UCSF in collaboration with its inventor, 2014 Nobel prize winner and study co-author Eric Betzig, PhD, of the Howard Hughes Medical Institute's Janelia Research Campus in Virginia. Using this technology, the team studied mouse T cells exploring simulated patches of antigen-presenting cell membrane in laboratory dishes, and found that the T cell microvilli move independently of one another in a fractal-like geometry, such as is often seen in nature as a way of optimizing efficient use of space, such as by plant roots or foraging animals. The researchers calculated that, thanks to this efficient search pattern, in an average minute-long encounter win an antigen-presenting cell, T cell microvilli can thoroughly explore 98 percent of the contact surface between the two cells -- called an "immunological synapse" after the neuronal synapses of the nervous system. This suggests that T cells are tuned to spend the minimum time necessary to get a clear read on the information available at each antigen-presenting cell before moving on, the authors say. To study the details of threat detection by microvilli, the authors devised a new approach that allowed them to simultaneously track microvilli as well as the T cell receptor (TCR) proteins T cells use to detect their target antigens. To do this, the team covered simulated patches of antigen-presenting cell membrane with tiny fluorescent particles called quantum dots, which questing T cell microvilli had to push out of the way to reach the membrane surface. This technique, dubbed synaptic contact mapping, allowed the researchers to visualize the microvilli as holes of negative space in the quantum dot fluorescence, while at the same time visualizing TCRs with a different-colored fluorescent marker. They found that normally, individual microvilli poke and prod at the antigen-presenting cell membrane for an average of about four seconds at a time. But when the microvilli found the antigen they were searching for, they stayed in contact with the antigen-presenting cell membrane for 20 seconds or more and accumulated large rafts of TCRs, suggesting that they were likely signaling the T cell to trigger its immune response. "These videos give me a much more visceral understanding of what's happening when T cells and antigen-presenting cells come into contact," Krummel said. "T cells have these anemone-like sensory organs, and when they want to get information from another cell, their only chance appears to be during this short period of intimate contact. If they don't detect a strong signal during that contact, they move on." Real-time imaging technology opens new opportunities to study immunity and disease Krummel's team also briefly studied the surfaces of other types of immune cells, such as dendritic cells and B cells, which play different roles in pathogen detection and immune response. They found that each cell type appears to use distinct patterns of surface protrusions -- such as tentacles, waves, or curtain-like ripples -- to probe and communicate with their environments, though more research is needed to understand these diverse patterns and how they interact with one another. (See video.) "Understanding how the immune system reliably detects and responds to the huge range of potential threats it has to deal with is one of the key questions we still face as immunologists," Krummel said. "Of course, the immune system also makes mistakes -- like when it attacks the body's own cells in autoimmune disease or fails to recognize cancerous cells as a threat. Understanding the mechanics and constraints of how the immune system recognizes threats in the first place could potentially help us correct those errors." En Cai, PhD, Kyle Marchuk, PhD, Peter Beemiller, PhD, and Casey Beppler, BS, of UCSF, were co-first authors of the new study. Other authors were Matthew G. Rubashkin, PhD, Valerie M. Weaver, PhD, and Audrey Gérard, PhD, of UCSF; Tsung-Li Liu, PhD, and Bi-Chang Chen, PhD, of Janelia; and Frederic Bartumeus, PhD, of the Center for Advanced Studies of Blanes in Girona, Spain and Institut Català de Recerca i Estudis Avançats (ICREA) in Barcelona. Funding for this research was provided by the National Institutes of Health (AI052116), National Cancer Institute (U01CA202241), a US Department of Defense National Defense Science and Engineering Graduate Fellowship, and a National Science Foundation Graduate Research Fellowship (1650113). Betzig is an inventor on patent application US 20130286181 A1, submitted by Howard Hughes Medical Institute (HHMI), which covers LLS imaging. The authors declare no competing financial interests. About UCSF: UC San Francisco (UCSF) is a leading university dedicated to promoting health worldwide through advanced biomedical research, graduate-level education in the life sciences and health professions, and excellence in patient care. It includes top-ranked graduate schools of dentistry, medicine, nursing and pharmacy; a graduate division with nationally renowned programs in basic, biomedical, translational and population sciences; and a preeminent biomedical research enterprise. It also includes UCSF Health, which comprises top-ranked hospitals, UCSF Medical Center and UCSF Benioff Children's Hospitals in San Francisco and Oakland - and other partner and affiliated hospitals and healthcare providers throughout the Bay Area. Please visit http://www. .


The common dentex (Dentex dentex) is a voracious and aggressive predator that eats fish, crabs and cephalopods. It plays an essential role in the activity of marine benthic ecosystems and it is a target species with great economic value in trade and sports fisheries. According to Professor Bernat Hereu from the Department of Evolutionary Biology, Ecology and Environmental Sciences of the UB and IRBio, "Knowing the movement patterns of the dentex is essential to better understand their biology and ecology as well as to determine the role of marine reserves in the recovery of populations and exportation of models (biomass) that can be captured by fisheries out of the reserves." "Acoustic telemetry, together with new analytical and computational methods in the framework of movement ecology, are revolutionizing marine biology and will allow us to understand the effects of climate change and fishery pressure on key species, as well as the search for solutions for their preservation," added Frederic Bartumeus, ICREA researcher from CEAB-CSIC and CREAF, and expert in animal dispersal and movement patterns. The experts studied dentex populations in the Medes Islands with acoustic telemetry techniques based on tagging with acoustic transmitters that send periodic signals. These signals are received by a network of receivers in the study region and track the fish movement. After more than 15 months of research, the researchers registered the position and depth of all individuals tagged in the study in two-minute intervals. According to Eneko Aspillaga (UB-IRBio and CEAB-CSIC), first author of the article, "The study shows a clear pattern of dentex movement depending on the temperature of the water. In winter, temperatures around 12º C do not alter the whole water column, and dentex move in a depth range between 10 and 40 meters, without any defined pattern." "The thermal pattern of water mass in the Medes Islands is the typical northwestern Mediterranean one. After April, the surface gets warmer, and between May and June, two different water masses appear—shallow ones, which are warm and less dense, and deep, cold ones separated by a frontier called the thermocline. When the thermocline is formed in summer, dentex are found only over this limit, regardless of its depth." Why do dentex move to warmer waters? The new study, published in Scientific Reports, finds that dentex is a thermophile species, with dispersal patterns and activity conditioned to summer due the depth and period the thermocline lasts in the water column. Since the dentex is poikilothermal, with an internal temperature fully dependent on the climate, it would move through the water column until finding warmer and better conditions for its physiology, especially in summer, when they are more active. The population growth of dentex, observed in preserved areas and fishery areas in the Medes Islands, could occur due the rise in the sea temperatures (more than 0.5ºC over the last 30 years in the area). The thermocline temperature and distribution, which lasts until late October, could also have an important impact on the spread of other fish, both predators and others of lower trophic levels, according to data by Josep Pascual, from the Weather Station in Estartit. Climate change, a threat to biodiversity in the Medes Islands The archipelago of the Medes Islands has exceptional ecological value as a natural ecosystem, with a great diversity of habitats and related species. The special orography of the Montgrí mountains, the rivers and the positive effect of marine ecosystem preservation have benefited the richness and biodiversity of the islands, part of the Natural Park of Montgrí, Medes Islands and Baix Ter. Despite being one of the areas less affected by climate change in the Mediterranean, this reserve is also sensitive to global warming due its richness in species and habitats. Gorgonians, coral reefs, sponges or shellfish, filtering organisms that live fixed in marine depths, are highly vulnerable to climate change, especially if they are above the thermocline. Fish and other mobile species are also sensitive to temperature changes during some stages in their life cycles (reproduction, nutrition, etc.). Some thermopile species could widen their distribution range and force other marine organisms to move. Moreover, species that are more prone to move around colder waters could disappear. The authors warn that in this global climate change scenario, the introduction of tropical species is particularly worrying, since they can deeply influence the balance in marine ecosystems. Explore further: Ghost fishing net removed in the Medes Islands marine reserve in Catalonia More information: Eneko Aspillaga et al. Thermal stratification drives movement of a coastal apex predator, Scientific Reports (2017). DOI: 10.1038/s41598-017-00576-z


News Article | May 16, 2017
Site: www.eurekalert.org

Energy dissipation is a key ingredient in understanding many physical phenomena in thermodynamics, photonics, chemical reactions, nuclear fission, photon emissions, or even electronic circuits, among others. In a vibrating system, the energy dissipation is quantified by the quality factor. If the quality factor of the resonator is high, the mechanical energy will dissipate at a very low rate, and therefore the resonator will be extremely accurate at measuring or sensing objects thus enabling these systems to become very sensitive mass and force sensors, as well as exciting quantum systems. Take, for example, a guitar string and make it vibrate. The vibration created in the string resonates in the body of the guitar. Because the vibrations of the body are strongly coupled to the surrounding air, the energy of the string vibration will dissipate more efficiently into the environment bath, increasing the volume of the sound. The decay is well known to be linear, as it does not depend on the vibrational amplitude. Now, take the guitar string and shrink it down to nano-meter dimensions to obtain a nano-mechanical resonator. In these nano systems, energy dissipation has been observed to depend on the amplitude of the vibration, described as a non-linear phenomenon, and so far no proposed theory has been proven to correctly describe this dissipation process. In a recent study, published in Nature Nanotechnology, ICFO researchers Johannes Güttinger, Adrien Noury, Peter Weber, Camille Lagoin, Joel Moser, led by Prof. at ICFO Adrian Bachtold, in collaboration with researchers from Chalmers University of Technology and ETH Zurich, have found an explanation of the non-linear dissipation process using a nano-mechanical resonator based on multilayer graphene. In their work, the team of researchers used a graphene based nano-mechanical resonator, well suited for observing nonlinear effects in energy decay processes, and measured it with a superconducting microwave cavity. Such a system is capable of detecting the mechanical vibrations in a very short period of time as well as being sensitive enough to detect minimum displacements and over a very broad range of vibrational amplitudes. The team took the system, forced it out-of-equilibrium using a driving force, and subsequently switched the force off to measure the vibrational amplitude as the energy of the system decayed. They carried out over 1000 measurements for every energy decay trace and were able to observe that as the energy of a vibrational mode decays, the rate of decay reaches a point where it changes abruptly to a lower value. The larger energy decay at high amplitude vibrations can be explained by a model where the measured vibration mode "hybridizes" with another mode of the system and they decay in unison. This is equivalent to the coupling of the guitar string to the body although the coupling is nonlinear in the case of the graphene nano resonator. As the vibrational amplitude decreases, the rate suddenly changes and the modes become decoupled, resulting in comparatively low decay rates, thus in very giant quality factors exceeding 1 million. This abrupt change in the decay has never been predicted or measured until now. Therefore, the results achieved in this study have shown that nonlinear effects in graphene nano-mechanical resonators reveal a hybridization effect at high energies that, if controlled, could open up new possibilities to manipulate vibrational states, engineer hybrid states with mechanical modes at completely different frequencies, and to study the collective motion of highly tunable systems. ICFO - The Institute of Photonic Sciences, member of The Barcelona Institute of Science and Technology, is a research center located in a specially designed, 14.000 m2-building situated in the Mediterranean Technology Park in the metropolitan area of Barcelona. It currently hosts 400 people, including research group leaders, post-doctoral researchers, PhD students, research engineers, and staff. ICFOnians are organized in 27 research groups working in 60 state-of-the-art research laboratories, equipped with the latest experimental facilities and supported by a range of cutting-edge facilities for nanofabrication, characterization, imaging and engineering. The Severo Ochoa distinction awarded by the Ministry of Science and Innovation, as well as 14 ICREA Professorships, 25 European Research Council grants and 6 Fundació Cellex Barcelona Nest Fellowships, demonstrate the centre's dedication to research excellence, as does the institute's consistent appearance in top worldwide positions in international rankings. From an industrial standpoint, ICFO participates actively in the European Technological Platform Photonics21 and is also very proactive in fostering entrepreneurial activities and spin-off creation. The center participates in incubator activities and seeks to attract venture capital investment. ICFO hosts an active Corporate Liaison Program that aims at creating collaborations and links between industry and ICFO researchers. To date, ICFO has created 5 successful start-up companies.


Over the past 40 years, microelectronics have advanced by leaps and bounds thanks to silicon and CMOS (Complementary metal-oxide semiconductors) technology, making possible computing, smartphones, compact and low-cost digital cameras, as well as most of the electronic gadgets we rely on today. However, the diversification of this platform into applications other than microcircuits and visible light cameras has been impeded by the difficulty to combine semiconductors other than silicon with CMOS. This obstacle has now been overcome. ICFO researchers have shown for the first time the monolithic integration of a CMOS integrated circuit with graphene, resulting in a high-resolution image sensor consisting of hundreds of thousands of photodetectors based on graphene and quantum dots (QD). They operated it as a digital camera that is highly sensitive to UV, visible and infrared light at the same time. This has never been achieved before with existing imaging sensors. In general, this demonstration of monolithic integration of graphene with CMOS enables a wide range of optoelectronic applications, such as low-power optical data communications and compact and ultra sensitive sensing systems. The study was published in Nature Photonics, and highlighted on the front cover image. The work was carried out by ICFO researchers Stijn Goossens, Gabriele Navickaite, Carles Monasterio, Schuchi Gupta, Juan Jose Piqueras, Raul Perez, Gregory Burwell, Ivan Nitkitsky, Tania Lasanta, Teresa Galan, Eric Puma, and led by ICREA Professors Frank Koppens and Gerasimos Konstantatos, in collaboration with the company Graphenea. The graphene-QD image sensor was fabricated by taking PbS colloidal quantum dots, depositing them onto the CVD graphene and subsequently depositing this hybrid system onto a CMOS wafer with image sensor dies and a read-out circuit. As Stijn Goossens comments, "No complex material processing or growth processes were required to achieve this graphene-quantum dot CMOS image sensor. It proved easy and cheap to fabricate at room temperature and under ambient conditions, which signifies a considerable decrease in production costs. Even more, because of its properties, it can be easily integrated on flexible substrates as well as CMOS-type integrated circuits." As ICREA Prof. at ICFO Gerasimos Konstantatos, expert in quantum dot-graphene research comments, "we engineered the QDs to extend to the short infrared range of the spectrum (1100-1900nm), to a point where we were able to demonstrate and detect the night glow of the atmosphere on a dark and clear sky enabling passive night vision. This work shows that this class of phototransistors may be the way to go for high sensitivity, low-cost, infrared image sensors operating at room temperature addressing the huge infrared market that is currently thirsty for cheap technologies". "The development of this monolithic CMOS-based image sensor represents a milestone for low-cost, high-resolution broadband and hyperspectral imaging systems" ICREA Prof. at ICFO Frank Koppens highlights. He assures that "in general, graphene-CMOS technology will enable a vast amount of applications, that range from safety, security, low cost pocket and smartphone cameras, fire control systems, passive night vision and night surveillance cameras, automotive sensor systems, medical imaging applications, food and pharmaceutical inspection to environmental monitoring, to name a few". This project is currently incubating in ICFO's Launchpad. The team is working with the institute's tech transfer professionals to bring this breakthrough along with its full patent portfolio of imaging and sensing technologies to the market. This research has been partially supported by the European Graphene Flagship, European Research Council, the Government of Catalonia, Fundació Cellex and the Severo Ochoa Excellence program of the Government of Spain. Link to the video of the sensor: https:/ Link to the research group led by ICREA Prof. Gerasimos Konstantatos: https:/ Link to the research group led by ICREA Prof. Frank Koppens: https:/ Video: ICFO researchers have developed the first graphene -- quantum dots -- CMOS integrated based camera, capable of imaging visible and infrared light at the same time. The camera will be useful for many applications that include night vision, food inspection, fire control, vision under extreme weather conditions, to name a few. The imaging system is based on the first monolithic integration of graphene and quantum dot photodetectors with a CMOS read-out integrated circuit. It has proven to be easy and cheap to fabricate at room temperature and under ambient conditions, allowing for low-cost mass-production. ICFO was created in 2002 by the government of Catalonia and the Technical University of Catalonia as a centre of research excellence devoted to the science and technologies of light with a triple mission: to conduct frontier research, train the next generation of scientists, and provide knowledge and technology transfer. Today, it is one of the top research centres worldwide in its category as measured by international rankings. Research at ICFO targets the forefront of science and technology based on light with programs directed at applications in Health, Renewable Energies, Information Technologies, Security and Industrial processes, among others. The institute hosts 400 professionals based in a dedicated building situated in the Mediterranean Technology Park in the metropolitan area of Barcelona. ICFO participates in a large number of projects and international networks of excellence and is host to the NEST program that is financed by Fundación Privada Cellex Barcelona. Ground-breaking research in graphene is being carried out at ICFO and through key collaborative research partnerships such as the FET Graphene Flagship. ICREA Professor at ICFO and NEST Fellow Frank Koppens is the leader of the Optoelectonics work package within the Flagship program.


Home > Press > Graphene and quantum dots put in motion a CMOS-integrated camera that can see the invisible Abstract: Over the past 40 years, microelectronics have advanced by leaps and bounds thanks to silicon and CMOS (Complementary metal-oxide semiconductors) technology, making possible computing, smartphones, compact and low-cost digital cameras, as well as most of the electronic gadgets we rely on today. ICFO researchers have developed the first graphene -- quantum dots -- CMOS integrated based camera, capable of imaging visible and infrared light at the same time. The camera will be useful for many applications that include night vision, food inspection, fire control, vision under extreme weather conditions, to name a few. The imaging system is based on the first monolithic integration of graphene and quantum dot photodetectors with a CMOS read-out integrated circuit. It has proven to be easy and cheap to fabricate at room temperature and under ambient conditions, allowing for low-cost mass-production. Credit: ICFO-The Institute of Photonic Sciences However, the diversification of this platform into applications other than microcircuits and visible light cameras has been impeded by the difficulty to combine semiconductors other than silicon with CMOS. This obstacle has now been overcome. ICFO researchers have shown for the first time the monolithic integration of a CMOS integrated circuit with graphene, resulting in a high-resolution image sensor consisting of hundreds of thousands of photodetectors based on graphene and quantum dots (QD). They operated it as a digital camera that is highly sensitive to UV, visible and infrared light at the same time. This has never been achieved before with existing imaging sensors. In general, this demonstration of monolithic integration of graphene with CMOS enables a wide range of optoelectronic applications, such as low-power optical data communications and compact and ultra sensitive sensing systems. The study was published in Nature Photonics, and highlighted on the front cover image. The work was carried out by ICFO researchers Stijn Goossens, Gabriele Navickaite, Carles Monasterio, Schuchi Gupta, Juan Jose Piqueras, Raul Perez, Gregory Burwell, Ivan Nitkitsky, Tania Lasanta, Teresa Galan, Eric Puma, and led by ICREA Professors Frank Koppens and Gerasimos Konstantatos, in collaboration with the company Graphenea. The graphene-QD image sensor was fabricated by taking PbS colloidal quantum dots, depositing them onto the CVD graphene and subsequently depositing this hybrid system onto a CMOS wafer with image sensor dies and a read-out circuit. As Stijn Goossens comments, "No complex material processing or growth processes were required to achieve this graphene-quantum dot CMOS image sensor. It proved easy and cheap to fabricate at room temperature and under ambient conditions, which signifies a considerable decrease in production costs. Even more, because of its properties, it can be easily integrated on flexible substrates as well as CMOS-type integrated circuits." As ICREA Prof. at ICFO Gerasimos Konstantatos, expert in quantum dot-graphene research comments, "we engineered the QDs to extend to the short infrared range of the spectrum (1100-1900nm), to a point where we were able to demonstrate and detect the night glow of the atmosphere on a dark and clear sky enabling passive night vision. This work shows that this class of phototransistors may be the way to go for high sensitivity, low-cost, infrared image sensors operating at room temperature addressing the huge infrared market that is currently thirsty for cheap technologies". "The development of this monolithic CMOS-based image sensor represents a milestone for low-cost, high-resolution broadband and hyperspectral imaging systems" ICREA Prof. at ICFO Frank Koppens highlights. He assures that "in general, graphene-CMOS technology will enable a vast amount of applications, that range from safety, security, low cost pocket and smartphone cameras, fire control systems, passive night vision and night surveillance cameras, automotive sensor systems, medical imaging applications, food and pharmaceutical inspection to environmental monitoring, to name a few". This project is currently incubating in ICFO's Launchpad. The team is working with the institute's tech transfer professionals to bring this breakthrough along with its full patent portfolio of imaging and sensing technologies to the market. ### This research has been partially supported by the European Graphene Flagship, European Research Council, the Government of Catalonia, Fundació Cellex and the Severo Ochoa Excellence program of the Government of Spain. About ICFO-The Institute of Photonic Sciences ICFO was created in 2002 by the government of Catalonia and the Technical University of Catalonia as a centre of research excellence devoted to the science and technologies of light with a triple mission: to conduct frontier research, train the next generation of scientists, and provide knowledge and technology transfer. Today, it is one of the top research centres worldwide in its category as measured by international rankings. Research at ICFO targets the forefront of science and technology based on light with programs directed at applications in Health, Renewable Energies, Information Technologies, Security and Industrial processes, among others. The institute hosts 400 professionals based in a dedicated building situated in the Mediterranean Technology Park in the metropolitan area of Barcelona. ICFO participates in a large number of projects and international networks of excellence and is host to the NEST program that is financed by Fundación Privada Cellex Barcelona. Ground-breaking research in graphene is being carried out at ICFO and through key collaborative research partnerships such as the FET Graphene Flagship. ICREA Professor at ICFO and NEST Fellow Frank Koppens is the leader of the Optoelectonics work package within the Flagship program. For more information, please click If you have a comment, please us. Issuers of news releases, not 7th Wave, Inc. or Nanotechnology Now, are solely responsible for the accuracy of the content.


Researchers from ICN2's Phononic and Photonic Nanostructures (P2N) Group at the UAB campus have published a study in which the complex dynamics, including chaos, of optical nonlinearities, are controlled by using optomechanical crystals and changing the parameters of the excitation laser. This discovery might allow the codification of information by introducing chaos into the signal. Optomechanical crystals are designed at nanoscale to allow the confinement of photons and mechanical motion in a common physical volume. Such structures are being studied in complex experimental setups and might have an impact in the future of telecommunications. The interaction of the photons and the mechanical motion is mediated by optical forces leading to a strongly modulated beam of continuous-wave light after interacting with an optomechanical crystal. In optomechanics, optical nonlinearities are usually regarded as detrimental and efforts are made to minimise their effects. ICN2 researchers suggest using them to transport codified information. Initiatives such as PHENOMEN, a European project led by ICN2, lay the foundations of a new information technology combining photonics, radio-frequency (RF) signal processing and phononics. Researchers from the Phononic and Photonic Nanostructures (P2N) Group, led by the ICREA Research Prof. Dr Clivia Sotomayor-Torres at the Institut Català de Nanociència i Nanotecnologia (ICN2), published an article in Nature Communications presenting the complex non-linear dynamics observed in a silicon optomechanical crystal. Dr Daniel Navarro-Urrios is the first author of this study describing how a continuous-wave, low-power laser source is altered after traveling through one of these structures combining optical and mechanical properties of light and matter. The paper reports on the nonlinear dynamics of an optomechanical cavity system. The stable intensity of a laser beam was affected by factors such as thermo-optic effects, free-carrier dispersion and optomechanical coupling. The number of photons stored in the cavity affects and is affected by these factors, creating a chaotic effect that researchers were able to modulate by smoothly changing the parameters of the excitation laser. The authors demonstrate accurate control to activate a heterogeneous variety of stable dynamical solutions. The results of this work set the foundations of a low-cost technology reaching high security levels in optical communications using chaos-based optomechanical cryptographic systems. It is possible to introduce dynamical changes in the light beam traveling through an optical fiber by using an optomechanical crystal. The original light conditions could be reestablished if the parameters of the excitation laser and the optomechanical crystal that introduced those dynamical changes are known. Thus, by linking via optical fibers two integrated chips containing equivalent optomechanical cavities, it is possible to secure information by introducing chaos into the light beam at the emitting point and suppressing it at the reception point. Explore further: An optomechanical crystal to study interactions among colocalized photons and phonons More information: Daniel Navarro-Urrios et al. Nonlinear dynamics and chaos in an optomechanical beam, Nature Communications (2017). DOI: 10.1038/ncomms14965


News Article | April 20, 2017
Site: www.chromatographytechniques.com

Scientists at the Centre for Genomic Regulation (CRG) in Barcelona and the Josep Carreras Leukaemia Research Institute and The Institute for Health Science Research Germans Trias i Pujol (IGTP) in Badalona, Spain, have discovered that the impact of environmental change can be passed on in the genes of tiny nematode worms for at least 14 generations—the most that has ever been seen in animals. The findings will be published on Friday, April 21, in the journal Science. Led by Ben Lehner, group leader at the EMBL-CRG Systems Biology Unit and ICREA and AXA professor, together with Tanya Vavouri from the Josep Carreras Leukaemia Research Institute and the Institute for Health Science Research Germans Trias i Pujol (IGTP), the researchers noticed that the impact of environmental change can be passed on in the genes for many generations while studying C. elegans worms carrying a transgene array -- a long string of repeated copies of a gene for a fluorescent protein that had been added into the worm genome using genetic engineering techniques. If the worms were kept at 20 degrees Celsius, the array of transgenes was less active, creating only a small amount of fluorescent protein. But shifting the animals to a warmer climate of 25 degrees significantly increased the activity of the transgenes, making the animals glow brightly under ultraviolet light when viewed down a microscope. When these worms were moved back to the cooler temperature, their transgenes were still highly active, suggesting they were somehow retaining the "memory" of their exposure to warmth. Intriguingly, this high activity level was passed on to their offspring and onwards for seven subsequent generations kept solely at 20 degrees, even though the original animals only experienced the higher temperature for a brief time. Keeping worms at 25 degrees for five generations led to the increased transgene activity being maintained for at least 14 generations once the animals were returned to cooler conditions. Although this phenomenon has been seen in a range of animal species - including fruit flies, worms and mammals including humans - it tends to fade after a few generations. These findings represent the longest maintenance of transgenerational environmental "memory" ever observed in animals to date. "We discovered this phenomenon by chance, but it shows that it's certainly possible to transmit information about the environment down the generations," says Lehner. "We don't know exactly why this happens, but it might be a form of biological forward-planning," adds first author of the study and CRG Alumnus, Adam Klosin. "Worms are very short-lived, so perhaps they are transmitting memories of past conditions to help their descendants predict what their environment might be like in the future," adds Vavouri. Comparing the transgenes that were less active with those that had become activated by the higher temperature, Lehner and his team discovered crucial differences in a type of molecular "tag" attached to the proteins packaging up the genes, known as histone methylation. Transgenes in animals that had only ever been kept at 20 degrees had high levels of histone methylation, which is associated with silenced genes, while those that had been moved to 25 degrees had largely lost the methylation tags. Importantly, they still maintained this reduced histone methylation when moved back to the cooler temperature, suggesting that it is playing an important role in locking the memory into the transgenes. The researchers also found that repetitive parts of the normal worm genome that look similar to transgene arrays also behave in the same way, suggesting that this is a widespread memory mechanism and not just restricted to artificially engineered genes.


News Article | April 20, 2017
Site: www.eurekalert.org

CRG scientists have discovered that the impact of environmental change can be passed on in the genes of tiny nematode worms for at least 14 generations -- the most that has ever been seen in animals Led by Dr Ben Lehner, group leader at the EMBL-CRG Systems Biology Unit and ICREA and AXA Professor, together with Dr Tanya Vavouri from the Josep Carreras Leukaemia Research Institute and the Institute for Health Science Research Germans Trias i Pujol (IGTP), the researchers noticed that the impact of environmental change can be passed on in the genes for many generations while studying C. elegans worms carrying a transgene array - a long string of repeated copies of a gene for a fluorescent protein that had been added into the worm genome using genetic engineering techniques. If the worms were kept at 20 degrees Celsius, the array of transgenes was less active, creating only a small amount of fluorescent protein. But shifting the animals to a warmer climate of 25 degrees significantly increased the activity of the transgenes, making the animals glow brightly under ultraviolet light when viewed down a microscope. When these worms were moved back to the cooler temperature, their transgenes were still highly active, suggesting they were somehow retaining the 'memory' of their exposure to warmth. Intriguingly, this high activity level was passed on to their offspring and onwards for 7 subsequent generations kept solely at 20 degrees, even though the original animals only experienced the higher temperature for a brief time. Keeping worms at 25 degrees for five generations led to the increased transgene activity being maintained for at least 14 generations once the animals were returned to cooler conditions. Although this phenomenon has been seen in a range of animal species - including fruit flies, worms and mammals including humans - it tends to fade after a few generations. These findings, which will be published on Friday 21st April in the journal Science, represent the longest maintenance of transgenerational environmental 'memory' ever observed in animals to date. "We discovered this phenomenon by chance, but it shows that it's certainly possible to transmit information about the environment down the generations," says Lehner. "We don't know exactly why this happens, but it might be a form of biological forward-planning," adds the first author of the study and CRG Alumnus, Adam Klosin. "Worms are very short-lived, so perhaps they are transmitting memories of past conditions to help their descendants predict what their environment might be like in the future," adds Vavouri. Comparing the transgenes that were less active with those that had become activated by the higher temperature, Lehner and his team discovered crucial differences in a type of molecular 'tag' attached to the proteins packaging up the genes, known as histone methylation.* Transgenes in animals that had only ever been kept at 20 degrees had high levels of histone methylation, which is associated with silenced genes, while those that had been moved to 25 degrees had largely lost the methylation tags. Importantly, they still maintained this reduced histone methylation when moved back to the cooler temperature, suggesting that it is playing an important role in locking the memory into the transgenes.** The researchers also found that repetitive parts of the normal worm genome that look similar to transgene arrays also behave in the same way, suggesting that this is a widespread memory mechanism and not just restricted to artificially engineered genes.


News Article | February 24, 2017
Site: www.eurekalert.org

New algorithm helps scientists prioritize binding partners for experimental validation, which will contribute to our understanding of the role of long non-coding RNAs in normal cell function and in disease Far from just reading the information contained in the human genome, and in order to fully understand how it works, researchers aim to know the ins and outs of all the elements in this tiny regulated gear. Many laboratories, consortia and projects are devoted to get a global view of the functional regions of the genome and to know in which cell types genes are active. Intriguingly, only a small fraction of the human genome (around 2%) contains genes encoding for proteins, which are the building blocks of the cell. The remaining 98% is important for regulation, meaning that it is involved in controlling when and where genes are active. This large portion of the genome produces RNA molecules, called non-coding RNAs, which differ in size, structure and function. As the different types of non-coding RNAs can interact with proteins in different ways, big efforts have been put into investigating them. Until now, there were no computational tools available to handle very long RNA sequences and studying them through experimental methods is at present a huge challenge. In a recent article published in Nature Methods, researchers at the Centre for Genomic Regulation in Barcelona (Spain), in collaboration with scientists at EMBL's site in Monterotondo (Italy) and the California Institute of Technology (US), introduced a new computational tool to predict protein interactions with long non-coding RNAs, which they validated using advanced experimental techniques. "Long non-coding RNAs interact with various proteins to mediate important cellular functions. Trying to identify these interactions can be a good starting point in order to understand the role of these molecules in the normal functioning of the cell but also in disease," explains Gian Gaetano Tartaglia, ICREA research professor at the Centre for Genomic Regulation (CRG) and principal investigator of this article. The new computational tool, which is called Global Score, allows scientists to predict where, along the sequence of a non-coding RNA, a protein will establish a physical contact. To do so, this algorithm integrates not only the global propensity of the protein to bind a particular RNA but also the local features of such a binding. "The structure of the RNA is absolutely important when predicting protein interactions. Our main challenge was to be able to work with RNA sequences regardless of their length in order to keep a complete view of their structural properties when looking for protein partners," adds Davide Cirillo, post-doctoral researcher at the CRG and first author of the paper. "The algorithm we have developed integrates this information and allows us not only to predict protein partners but also to prioritize them for experimental validation. This methodological advance will be crucial to better study long non-coding RNAs and their functions", concludes the researcher. This work highlights, again, the relevant contribution of bioinformatics and computational biology to advance knowledge and their key role boosting and accelerating research in the life sciences.


Far from just reading the information contained in the human genome, and in order to fully understand how it works, researchers aim to know the ins and outs of all the elements in this tiny regulated gear. Many laboratories, consortia and projects are devoted to get a global view of the functional regions of the genome and to know in which cell types genes are active. Intriguingly, only a small fraction of the human genome (around 2%) contains genes encoding for proteins, which are the building blocks of the cell. The remaining 98% is important for regulation, meaning that it is involved in controlling when and where genes are active. This large portion of the genome produces RNA molecules, called non-coding RNAs, which differ in size, structure and function. As the different types of non-coding RNAs can interact with proteins in different ways, big efforts have been put into investigating them. Until now, there were no computational tools available to handle very long RNA sequences and studying them through experimental methods is at present a huge challenge. In a recent article published in Nature Methods, researchers at the Centre for Genomic Regulation in Barcelona (Spain), in collaboration with scientists at EMBL's site in Monterotondo (Italy) and the California Institute of Technology (US), introduced a new computational tool to predict protein interactions with long non-coding RNAs, which they validated using advanced experimental techniques. "Long non-coding RNAs interact with various proteins to mediate important cellular functions. Trying to identify these interactions can be a good starting point in order to understand the role of these molecules in the normal functioning of the cell but also in disease," explains Gian Gaetano Tartaglia, ICREA research professor at the Centre for Genomic Regulation (CRG) and principal investigator of this article. The new computational tool, which is called Global Score, allows scientists to predict where, along the sequence of a non-coding RNA, a protein will establish a physical contact. To do so, this algorithm integrates not only the global propensity of the protein to bind a particular RNA but also the local features of such a binding. "The structure of the RNA is absolutely important when predicting protein interactions. Our main challenge was to be able to work with RNA sequences regardless of their length in order to keep a complete view of their structural properties when looking for protein partners," adds Davide Cirillo, post-doctoral researcher at the CRG and first author of the paper. "The algorithm we have developed integrates this information and allows us not only to predict protein partners but also to prioritize them for experimental validation. This methodological advance will be crucial to better study long non-coding RNAs and their functions", concludes the researcher. This work highlights, again, the relevant contribution of bioinformatics and computational biology to advance knowledge and their key role boosting and accelerating research in the life sciences. More information: Davide Cirillo et al, Quantitative predictions of protein interactions with long noncoding RNAs, Nature Methods (2016). DOI: 10.1038/nmeth.4100

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