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2019 -
Grant Awardees - Program Grants

Single-molecule protein sequencing

JOO Chirlmin (KOREA, REPUBLIC OF (SOUTH KOREA))

Dept. of BioNanoScience - Kavli Institute of NanoScience - Delft University of Technology - Delft - NETHERLANDS

LEE Sang Wook (KOREA, REPUBLIC OF (SOUTH KOREA))

Dept. of Physics - Ewha Womans University - Seoul - KOREA, REPUBLIC OF (SOUTH KOREA)

Protein sequencing remains a challenge for small samples. A sensitive sequencing technology will create the opportunity for single-cell proteomics and real-time screening for on-site medical diagnostics. We will use our expertise of single-molecule protein detection and material sciences to develop novel sequencing tools. In particular, we will use graphene mass sensors to measure the mass of proteins with sub-Dalton sensitivity. Utilizing this high sensitivity, we will measure the mass of protein fragments and identify the sequence of the fragments. We will also apply this method for detecting post-translational modifications of single proteins. Ultimately we aim to achieve sequencing of full-length proteins. This proof of concept will open the door to single-molecule protein sequencing and pave the road toward the development of a new, fast, and reliable diagnostic tool.

2019 -
Grant Awardees - Program Grants

Tracking trade across symbiotic networks

KIERS Toby (NETHERLANDS)

Institute of Ecological Science - Faculty of Earth and Life Sciences - Amsterdam - NETHERLANDS

STONE Howard A. (USA)

Dept. of Mechanical and Aerospace Engineering - Complex Fluids Group - Princeton - USA

SHIMIZU Thomas (USA)

Dept. of Living Matter - AMOLF Institute - Amsterdam - NETHERLANDS

TOJU Hirokazu (JAPAN)

Center for Ecological Research - Kyoto University - Shiga - JAPAN

The world is characterized by an unequal distribution of resources. To cope, many organisms evolve symbiotic trade partnerships to exchange commodities they can provide at low cost, for resources more difficult to access. Such trade partnerships allow species to colonize extreme environments and survive resource fluctuations. While the ubiquity and importance of trade partnerships has been established, we do not understand the chemical, physical, and environmental stimuli mediating trade strategies, nor how organisms integrate this information to execute trade ‘decisions’. This is largely because of the lack of tools to quantify symbiotic trade across space and time.
Combining biophysics, fluid mechanics, network theory and evolution, we will develop techniques to track, quantify and predict trade strategies in symbiotic networks formed between plants and their arbuscular mycorrhizal fungal partners – a globally ubiquitous trade partnership fundamental to all terrestrial ecosystems. By visually monitoring the trade of nutrients tagged with fluorescent quantum-dot nanoparticles across scales - from within individual fungal hyphae up to complex plant-fungal networks - we will ask: (1) how do oscillatory flow patterns within fungal networks act to regulate fungal trade decisions; (2) can the fungus manipulate its chemistry and physical architecture to maximize nutrient transport and trade benefits; (3) can trade strategies be predicted by environmental stimuli; (4) what is the influence of the external microbiome on trade behaviors.
Using high-resolution video to track fluorescently tagged nutrients within hyphae, we will be the first to test how the fungal symbiont regulates internal flows to mediate trade. We will develop 2D and 3D time-lapse imaging of network topologies to test the factors driving the optimization of fungal transport routes. We will use transformed in-vitro root systems with precisely controlled nutrient landscapes to correlate specific trade strategies with environmental conditions. We will push the frontiers of tracking trade in whole plant mesocosms by growing plant-fungal networks on transparent farming film, characterizing how synthetic microbiomes affect trade strategies. By integrating the state of the art in imaging, fluid mechanics, and ecological manipulations, we will achieve a quantitative and predictive understanding of organismal trade.

2019 -
Grant Awardees - Program Grants

Do hydrocarbons induce membrane curvature in photosynthetic organisms?

LEA-SMITH David (UK)

School of Biological Sciences - University of East Anglia - Norwich - UK

CES Oscar (SPAIN)

Dept. of Chemistry - Imperial College London - London - UK

SHARP Melissa (DENMARK)

Instrument Division - European Spallation Source ERIC - Lund - SWEDEN

ALLISON Jane (NEW ZEALAND)

School of Biological Sciences - University of Auckland - Auckland - NEW ZEALAND

The cell membrane is a double layer of lipid molecules. It plays a critical role in protecting the cell from its environment and in separating the different processes that take place within its interior. Membranes must change their shape in order for the cell to function, especially during cell division, and this depends on membrane curvature. At present, cells are only known to induce curvature by accumulating lipids in one of the layers or using specialised proteins. Our goal is to investigate a new mechanism of inducing membrane curvature by accumulation of hydrocarbons in the middle of the lipid layers that has not been observed before in nature.
These hydrocarbons are like the components of diesel fuel, and are found in photosynthetic cyanobacteria and algae – some of the most abundant and widespread organisms on Earth. Production of hydrocarbons in cyanobacteria or other microbes could substitute for liquid fuels derived from petroleum. As well, cyanobacteria and algae release hydrocarbons into the environment, where they are degraded by other bacteria that clean up oil spills. However despite their environmental and biotechnological importance, the exact cellular role of hydrocarbons has not been determined.
We recently discovered that hydrocarbons are essential for maintaining optimal cell size, growth and division, processes that require cell membranes to curve and bend, and found that cells lacking hydrocarbons have lipid membranes that are less curved or flexible. We showed that hydrocarbons integrate into the cell membranes, and used computer simulations to predict that this induces membrane curvature. To investigate this further, we have assembled a team of scientists from the UK, Sweden and New Zealand. By combining our different skills, we will analyse how hydrocarbons affect the physical properties of algal and cyanobacterial membranes by 1) running computer simulations; 2) studying membranes purified from algae and cyanobacteria; and 3) carrying out experiments on live cells. Together, these simulations and experiments will allow us to explore and quantify how hydrocarbons affect curvature and other membrane properties, and so conclusively establish the role of hydrocarbons in cells. As well as improving our understanding of biology, this information will assist the use of microbes for biofuel production and oil spill cleanup.

2019 -
Grant Awardees - Program Grants

Decoding the biomechanics of flight-tone based acoustic communication in mosquitoes

MITTAL Rajat (USA)

Dept. of Mechanical Engineering - Johns Hopkins University - Baltimore - USA

GIBSON Gabriella (USA)

Dept. of Agriculture, Health and Environment - University of Greenwich - London - UK

The aerial courtship “dance” of mosquitoes has fascinated entomologists for over 150 years. This dance involves highly controlled variations in the frequency and intensity of flight-tones (i.e. sounds generated by the flapping wings) with concurrent changes in flight speed and direction, and enables recognition of conspecifics, display of fitness and transmission of mating interest. However, despite over a century and a half of research, significant knowledge gaps continue to exist in our understanding of this behavior. To decipher this courtship dance, entomologists have to integrate acoustic, energetic and flight information for untethered, free-flying mosquitoes, but the tools that can provide these data have, so far, not been available. In the current project, the two investigators combine their respective expertise in computational biomechanics and acoustics, and behavioral entomology, to generate unprecedented data and insights into the biomechanics and physics of courtship-associated acoustic communication in mosquitoes. In particular, by combining computational modeling with biological assays, the team will generate six-dimensional soundscapes of free-flying mosquitoes engaged in courtship and determine how these soundscapes are actively modified during courtship. We will also estimate for the first time, the energetic costs of courtship and mate-chasing, and the potential constraints this places on courtship behavior. Finally, the team will characterize the degree to which, carefully tailored exogenous sounds can alter and even disrupt courtship. The success of this novel approach could be transformative for future research into comparative auditory mechanisms of communication across a wide range of flying insects. In addition, the insights gleaned here could form the scientific foundation for novel insecticidal/surveillance traps and also lead to environmentally friendly strategies for diminishing mating success in mosquito species that are vectors for malaria, Zika fever and other devastating mosquito-borne diseases.

2019 -
Grant Awardees - Program Grants

Unravelling an unusual biomineralization from nano to macro scale using advanced technologies

MOAZEN Mehran (UK)

Dept. of Mechanical Engineering - University College London - London - UK

VICKARYOUS Matthew (CANADA)

Dept. of Biomedical Sciences - University of Guelph - Guelph - CANADA

ABZHANOV Arkhat (USA)

Dept. of Life Sciences - Imperial College London - Ascot - UK

HERREL Anthony (BELGIUM)

Dépt. Adaptations du Vivant - UMR 7179 C.N.R.S/M.N.H.N - Paris - FRANCE

Osteoderms are hard calcified tissues that form within the skin of some animals. They resemble bone, hence the name, but are fundamentally different in several respects. Crocodile and armadillo skin plates, and turtle shells are among the most familiar examples, reportedly forming a protective armour against external predators and aiding locomotion. However, although less visible, osteoderms are also present in many lizards.
In terms of their shape, spatial distribution, and interaction, lizard osteoderms show the highest diversity in the animal kingdom, yet we know little about what drives this extraordinary diversity, how it is controlled, or how it originated. It could be a biproduct of other genetic differences or, more likely, a natural optimization to enhance osteoderm function, protective or otherwise, under conditions specific to each lizard type.
This project brings together a multidisciplinary team of expert engineers, developmental and evolutionary biologists from the UK, Canada and France to investigate the mechanisms underlying the development, patterning, and evolution of osteoderms in lizards. The team will use a range of advanced techniques (e.g. genetic analysis, material testing, imaging, and computer simulations) to investigate lizard osteoderms from the first molecular signalling events and cellular interactions, through to organismal level. Osteoderm mechanical properties will be characterised both as single units and as sheets so as to understand their function during feeding and locomotion.
This is a basic science project focused on a novel biological tissue and its evolutionary implications, but with a systems approach that may shed light on pathological calcifications, as well as aiding the development of biomimetic materials and structures. Most importantly it will train the next generation of scientists, in a multidisciplinary and international setting, providing them with a fundamental knowledge of biological tissues and a diverse skillset with which to address the global challenges of 21st century.

2019 -
Grant Awardees - Program Grants

Imaging viral RNA genome assembly with high spatial and temporal resolutions inside infected cells

NAFFAKH Nadia (FRANCE)

Dept. of Virology - Institut Pasteur - Paris - FRANCE

CISSE Ibrahim (NIGER)

Dept. of Physics - Massachusetts Institute of Technology - Cambridge - USA

FONTANA Juan (SPAIN)

Faculty of Biology and Astbury Centre for Structural Molecular Biology - University of Leeds - Leeds - UK

Sporadically, novel and potentially devastating pandemic influenza A viruses (IAVs) are generated through genome reassortment between human and animal co-infecting IAVs. Such pandemic viruses emerge as a consequence of the segmentation of IAVs genome into a bundle made of 8 distinct viral RNAs (vRNAs). However the molecular mechanisms of vRNA intracellular transport and assembly into vRNAs bundles, which are critical for reassortment, remain largely unknown. Our project aims to elucidate these fundamental aspects of IAV life cycle by developing innovative approaches.
We challenge the original model that newly synthesized vRNAs, in the form of viral ribonucleoproteins (vRNPs), are transported across the cytoplasm on Rab11-dependent recycling endosomes. Based on our recent work, we hypothesize that the concomitant transport and assembly of vRNPs is driven by their physical association with remodelled endoplasmic reticulum (ER) membranes and Rab11-dependent transport vesicles distinct from recycling endosomes.
We will set up a cellular system which resembles the natural respiratory tissue targeted by IAVs, while being amenable to simultaneous imaging of the endogenous Rab11 protein and tagged vRNAs. We will develop two cutting-edge and complementary imaging methods: dual-color single molecule fluorescence in situ hybridization (FISH) in live cells for the tracking of distinct vRNAs that diffuse concomitantly, and cryo-Focused Ion Beam combined with electron microscopy in situ hybridization (EMISH) to image individual vRNPs and their transport vesicles at molecular resolution. We will further assess the role of cellular ER-shaping proteins by performing CRISPR/Cas9-mediated knockdowns, and by monitoring changes in the viral-induced remodelling of ER and biogenesis of vRNP transport vesicles by live fluorescence imaging and cellular EM.
The proposed research will require the very close collaboration between three partners with distinct but complementary expertise. The approaches developed jointly are poised to revolutionize our understanding of IAV multi-RNA genome transport and bundling, and thus help in the broader goal of achieving better prevention and treatment of influenza disease. Additionally, the proposed technical developments in live cell FISH and cellular EM, will have impact on other fields of studies well beyond the scope of the proposed project.

2019 -
Grant Awardees - Program Grants

The repeatability of the genetic mechanisms underlying behavioral evolution

ANDERSEN Erik C. (USA)

Dept. of Molecular Biosciences - Northwestern University - Evanston - USA

BROWN Andre (CANADA)

MRC London Institute of Medical Sciences - Imperial College London - London - UK

HODGINS Kathryn (CANADA)

School of Biological Sciences - Monash University - Clayton - AUSTRALIA

Keen observers of nature have often wondered why diverse species seem to behave similarly. For example, different species of Hawaiian spiders spin similar web architectures, diverse anoles lizard species bob their heads with the same styles and speeds, and distinct species of damselflies avoid predators using the same techniques. These and many other striking examples are thought to represent the convergent evolution of behaviors. Does this convergence reflect changes in the same genes or does evolution act through many genetic routes to create the same behaviors? Genetic differences clearly play a role in behavioral variation, but it remains challenging to identify the genes that underlie evolution of behaviors. However, convergence in the genetic basis of developmental or physiological traits has been discovered with many specific examples of genes and mechanisms, so it is possible to use studies of convergence to discover how behaviors evolve. Therefore, we will use a powerful comparative system to discover the genes and molecular mechanisms that underlie convergent evolution of behaviors for the first time across divergent animals.
The Caenorhabditis nematodes offer a unique experimental platform to connect behavioral differences to genetic differences. Starting with the keystone model organism, C. elegans, and existing data, we will characterize and classify genetic differences across wild isolates from three species of Caenorhabditis - C. briggsae, C. elegans, and C. tropicalis. Whole-genome genotype data combined with high-throughput, high-content imaging of behaviors from these same wild isolates will be input into unsupervised machine learning algorithms to create a high-resolution genotype-phenotype map for a range of natural behaviors and examples of convergence. This map will be queried for signatures of shared genetic changes at orthologous genes to identify which variants are most important evolutionarily. The result will provide the first systematic glimpse into the genomic “knobs” that control behaviors at single-variant resolution across species and insights into the repeatability of the evolution of behaviors.

2019 -
Grant Awardees - Program Grants

Studying sea urchin dermal photoreception to unravel principles of decentralized spherical vision

ARNONE Maria Ina (ITALY)

Dept. of Biology and Evolution of Marine Organisms - Stazione Zoologica Anton Dohrn - Napoli - ITALY

NILSSON Dan-Eric (SWEDEN)

Lund Vision Group, Dept. of Biology - Lund University - Lund - SWEDEN

LUETER Carsten (GERMANY)

Dept. of Evolutionary Morphology (FB1) - Museum fuer Naturkunde - Berlin - GERMANY

LA CAMERA Giancarlo (ITALY)

Dept. of Neurobiology and Behavior - Stony Brook University - Stony Brook - USA

Sea urchins are marine animals genetically close to the vertebrate lineage. Being eye-less and lacking a central nervous system (NS), these animals instead feature dermal photoreceptors dispersed over their spherical body surface and feeding into a decentralized NS. However, sea urchins can visually resolve objects and move towards them, and they can detect looming visual stimuli from any direction and accurately point their spines towards them. Such performance is normally associated with proper eyes feeding information into a brain. Sea urchins thus offer access to a unique visual system of a type that to date has not been studied in terms of its information processing. This alternative solution to vision may also have potential biomimetic applications for robotic miniaturization, smart probes, and intelligent materials where dispersed light detectors control the properties of the material.
The core of the proposed project is to investigate and model the neural mechanisms of information processing, which enables sea urchins to perform spherical vision by deploying an obviously very different mechanism from today's technology, and also very different from visually guided behavior in most other animals. Our study includes molecular and morphological identification of cell types, measurements of behavioral responses and electrophysiological photoreceptor responses, mapping the connectome of sea urchin photoreceptors and NS, and theoretical modelling of the information processing underlying visually guided behavior. We will map the connectomics of the NS and record the activity from key positions in the processing of visual information and generation of locomotory responses. The data will be used for computational modelling of the entire process from visual input to motor control. Special focus will be given to behavioral decisions where small changes in stimuli cause behavioral switches. We will also use genetic approaches to test the agreement between theoretical models and actual behavior.

2019 -
Grant Awardees - Program Grants

nFlare: an innovative light approach to study and modulate neuronal activity in vitro and in vivo

BALLERINI Laura (ITALY)

Dept. of Neurobiology- neuron physiology and technology lab - International School for Advanced Studies SISSA-ISAS - Trieste - ITALY

TIAN Bozhi (CHINA, PEOPLE'S REPUBLIC OF)

Dept. of Chemistry - The University of Chicago - Chicago - USA

FRUK Ljiljana (CROATIA)

Dept. of Chemical Engineering and Biotechnology - University of Cambridge - Cambridge - UK

To understand how the brain represents the world is a central theme in neuroscience. Neural circuits encode information in terms of rate, timing and synchrony of action potentials arising from the activity of a complex spatial organization of excitatory/inhibitory neurons. The identity of the active neurons at any given time has a profound effect onto the final outcome and regulates fundamental human psychophysical behavior. Attempts to decode the complex behaviors in neurons has led to development of several neuromodulation and sensing tools, by which neural activity can be controlled by microelectrodes or through genetically altering specific neural circuits, ultimately to deliver electrical impulses. Unfortunately, these techniques introduce strong perturbations to the observed system, without reaching the desired spatio-temporal resolution. Experimental approaches that allow non-invasive activation of specific phenotypic groups of neurons could introduce systematic variation of the timing of signals revealing how neural ensembles encode information. Here we propose a novel (nano)tool to alter membrane potential in specific neuronal phenotypes in a spatiotemporally controlled manner.
The nFlare project will develop a novel research paradigm in neuroscience based on a new class of injectable nanodevices delivered to neurons and anchored to their membranes. These nanotools have the ability to depolarize cell membranes or to deliver active biomolecules. Electric or chemical stimulation of single cells will be achieved using deep-penetration near infrared excitation light, to reduce invasiveness.
nFlare core aims are: i) the development of nanodevice components able to generate photoelectrochemical current upon illumination with light; ii) state-of-the-art biochemical functionalization of the nanodevice to target specific neurons and to reduce inflammatory response; iii) applicability of such nanoscale devices as high spatio-temporal neuronal activity modulators in 2D and 3D in vitro neuronal networks followed by in vivo validation.
Selective modulation of neural circuits by artificial stimulation of neuronal membrane or controlled delivery of environmental factors could help answering fundamental neurobiological questions.

2019 -
Grant Awardees - Program Grants

An integrative approach to decipher flowering time dynamics under drought stress

CONTI Lucio (ITALY)

Dept. of Biosciences - Università degli studi di Milano - Milano - ITALY

JUENGER Thomas (USA)

Dept. of Integrative Biology - University of Texas at Austin - Austin - USA

IZAWA Takeshi (JAPAN)

Dept. of Agricultural and Environmental Biology/Lab of Plant Breeding and Genetics - The University of Tokyo - Tokyo - JAPAN

Plants live in an ever-changing environment which is not always compatible with their survival. A major life threatening condition is drought stress. While most plants can deploy an array of physiological countermeasures to endure remarkable levels of stress, there is a huge variability in the different strategies that plants choose to adopt to deal with drought stress. Many plants evade detrimental stress conditions by activating their reproductive development (flowering) earlier compared to non-stress conditions, a strategy known as drought escape (DE). Notably, even in the most water-rich environments plants face unpredictable dry periods, yet how this information affects the floral network at the molecular levels is unknown.
We will address this question with a blend of molecular and genetics-based approaches. We will leverage known mutants with altered DE to identify candidate mechanisms that are drought sensitive and can act as molecular switch to activate flowering. To comprehensively define DE mechanisms utilized under natural conditions we will assess the variability of the DE response in natural plant populations and in crops, which were selected by human intervention for the different field scenarios. Our targeted large-scale screens will allow us to identify naturally occurring variants in the DE process and decipher the molecular mechanism responsible for DE activation. This information will provide breakthroughs in our understanding of novel regulatory mechanisms that play a role in driving developmental adaptations across extremely variable environmental conditions, their natural genetic variation and the selective forces that maintain such variation in populations, an important aspect for predicting and dealing with the effects of climate change. Finally, because flowering time is a major component of yield potential in crops, the defined mechanisms will help us develop breeding strategies targeted for sub-optimal irrigation scenarios to produce crops with ameliorated performances under drought conditions.

2019 -
Grant Awardees - Program Grants

Regrowing the brain: evolution and mechanisms of seasonal reversible size changes in a mammal

DECHMANN Dina (SWITZERLAND)

Dept. of Migration and Immunoecology - Max Planck Institute for Ornithology - Radolfzell - GERMANY

DAVALOS Liliana (COLOMBIA)

Dept. of Ecology and Evolution - SUNY Stony Brook - Stony Brook - USA

NIELAND John (NETHERLANDS)

Dept. of Health Science and Technology - Aalborg University - Aalborg - DENMARK

Organisms need strategies to survive when conditions are hard. For mammals, winter is particularly difficult - they have to invest large amounts of energy into keeping warm, while food availability is low. For this reason, many mammals migrate or hibernate. However, what to do if you are too small to migrate long distance, burn your energy fast, and cannot hibernate? The common shrew is such a mammal and has evolved an astonishing strategy: each individual shrinks in winter by up to 20% and then regrows in the spring by about 13%. This size change, thought to allow shrews to survive on fewer resources because of the smaller size and linked lower energy requirements, include not just overall size, but specifically organs that do not usually change size in fully grown animals, such as the brain, heart and liver.
The process of neurological degeneration and regeneration is of great interest, since many central nervous system diseases (e.g., Alzheimer’s, multiple sclerosis) involve degeneration, but ongoing research for therapies to reverse this process has been of limited success. As one of only a few recorded examples of mammalian brain regeneration, understanding how the shrew regrows its brain can accelerate research that leads to future therapies.
To answer the question of how the shrew shrinks and then regrows its brain, we will establish this unusual species as a new model, by studying the biological, molecular, biochemical and genetic processes behind this reversible size change. Besides establishing a database of information that can be mined and researched in years to come to discover the pathways that generate this cycle in the shrew, we will test a metabolic model of neurological change by artificially blocking molecular access to fats. Thus, the cross-disciplinary study of this wintering adaptation may help us understand more about regeneration in mammals in general, and the brain in particular.

2019 -
Grant Awardees - Program Grants

Navigating the waters – A neural systems approach to spatial cognition in fish

ENGELMANN Jacob (GERMANY)

Dept. of Active Sensing - Bielefeld University - Bielefeld - GERMANY

SEGEV Ronen (ISRAEL)

Dept of Biomedical Engineering and Dept. of Life Sciences - Ben-Gurion University - Beer-Sheva - ISRAEL

BURT DE PERERA Theresa (UK)

Dept. of Zoology - University of Oxford - Oxford - UK

MUELLER Thomas (GERMANY)

Division of Biology / Mueller-lab - Kansas State University - Manhattan (Kansas) - USA

In 2014, the Nobel Prize in Physiology was awarded for the discovery of place and grid cells that process spatial cues in the mammalian hippocampal formation;, the key structure for both navigation and episodic memory1. Place and grid cells, and additional cell types form the central building blocks in the current circuit models of navigation in mammals. However, a cohesive picture of how these circuits compute space and enable navigation has not been achieved. In fact, emerging evidence suggest that these navigation circuits are highly diverse in cellular phenotypes and functionality; they do not only map aspects of space but also elements like sound, time, and reward. How neural systems of spatial cognition have evolved outside of the mammalian clade is not clear, and comparative studies are critically needed to gain insights to basic functional constraints and structural requirements underlying these neural circuits.
The international research team of four PIs proposes a broad comparative systems neurobiological approach using teleost fish for integrative studies on higher navigation circuits. These fish are ideal models because they have conquered diverse spatial ecologies and show highly specialized sensory adaptions. Also, their brains exhibit an overall lower complexity to mammals, and are highly accessible to experimental manipulation. To establish systematic research on teleostean spatial cognition, the project combines neuroethological, electrophysiological, neuroimaging, and computational methodologies. Introducing a powerful electrophysiological recording technology in freely-moving fish and generating long-needed anatomical atlas resources, the project analyzes four teleost species with differing spatial ecologies. The team will uncover how different sensory modalities like vision, perception of depth, and active electrolocation are integrated during spatial navigation tasks, thereby investigating how top-down mechanisms modulate sensory integration of spatial learning.
Finally, the team will test specific hypotheses developed in small-scaled laboratory setups in an unconstrained natural environment. Here, the group will measure the activity of neurons in freely moving fish that explore a coral reef habitat. This will be the first ever attempt to analyze brain activity underlying navigation in the wild. Altogether, the project will provide new perspectives on the evolution, function, and mechanism of memory systems in animal navigation.

2019 -
Grant Awardees - Program Grants

In vitro reconstitution of synaptic plasticity: a minimalist approach

HAYASHI Yasunori (JAPAN)

Dept. of Pharmacology - Graduate School of Medicine - Kyoto - JAPAN

ZHANG Mingjie (HONG KONG, CHINA)

Division of Life Science - Hong Kong University of Science and Technology - Kowloon - HONG KONG, CHINA

LUCIC Vladan (SERBIA)

Dept. of Molecular Structural Biology - Max Planck Institute of Biochemistry - Martinsried - GERMANY

Neuronal circuits store information through the mechanism of synaptic plasticity, a process where synaptic transmission is strengthened or weakened. Long-term potentiation (LTP) is a major form of synaptic plasticity. It requires both activation of CaMKII and subsequent trafficking of receptors and other proteins to the postsynaptic site. Despite extensive research, the causative relationship linking these two processes is still unknown. Here, Hayashi (live imaging and electrophysiology), Zhang (structure biology), and Lucic (cryoelectron tomography) will team up and take a unique minimalist approach to reconstitute synaptic plasticity from purified proteins. We will reconstitute postsynaptic density (reconstituted PSD or rPSD) on a glass substrate using a group of key scaffold proteins (PSD-95, SynGAP, SAPAP, Shank, and Homer) and receptor such as NR2B. Once a key process is found in minimal system, we will test if the same mechanisms work in intact neurons. Finally, we will investigate the persistent modification of the rPSD induced by the activation of CaMKII, which is expected to act as a hub for trafficking of various proteins. The network organization of the resulting complexes in vitro and in situ will be determined by cryo-electron tomography. The final goal of this proposal is to understand the minimum essential machinery for activity dependent delivery of postsynaptic proteins.

2019 -
Grant Awardees - Program Grants

Phase separation of glycolytic machinery as a fundamental mechanism in energy metabolism

HYMAN Anthony (UK)

Dept. of Cell division - Max Planck Institute of Molecular Cell Biology and Genetics - Dresden - GERMANY

COLÓN-RAMOS Daniel A. (PUERTO RICO)

Dept. of Cell Biology; Program in Cellular Neuroscience, Neurodegeneration and Repair - Yale School of Medicine - New Haven - USA

Glycolysis is a fundamental energy metabolic pathway which consists of ten enzymatic steps. Unlike the mitochondrion, which is a membrane-bound organelle, glycolytic enzymes are soluble proteins in the cytosol. Based on biochemical evidence, glycolytic enzymes have long been hypothesized to form functional complexes to sustain the rates of glycolysis. This purported complex, called the glycolytic metabolon, was a subject of intense study and debate thirty years ago. Still today we do not yet understand how these purported complexes are organized in cells to sustain local energy metabolism, or their physiological importance. This gap in knowledge results from the fact that when glycolysis was being rigorously examined forty years ago, the techniques did not exist to conclusively answer these questions. The main challenge in addressing these questions lay then, as now, in the ability to both examine the localization of the glycolytic enzymes in living cells, while understanding the biophysical and biochemical mechanisms of their association, and its implications in cellular physiology. We have established a collaboration to address these fundamental questions by making use of our joint expertise in vitro reconstitution and C.elegans physiology, using the energy demands of the C.elegans synapse as a model system.

2019 -
Grant Awardees - Program Grants

Synthetic biocompounds to direct neuronal circuit assembly

JABAUDON Denis (SWITZERLAND)

Dept. of Basic Neuroscience - University of Geneva - Geneva - SWITZERLAND

LIM Wendell (USA)

Dept. of Cellular and Molecular Pharmacology - University of California, San Francisco - San Francisco - USA

The cerebral cortex is composed of distinct subtypes of neurons organized in circuits allowing high-order functions such as integration of sensory stimuli and sensorimotor transformations. These different neuronal subtypes are connected with neurons located both within and outside of the cortex. Intracortical connectivity is mostly mediated by layer (L) 2/3 neurons, which form synapses with other cortical neurons within and across areas; instead neurons located in L5B project to sub-cerebral targets and are responsible for cortical output.
While the molecular diversity of cortical neurons and their circuit organization is increasingly understood, it is still difficult to genetically manipulate cortical neurons based on which circuits they belong to; the ability to do so would, however, be a critical skill to repair circuits when they are affected by injuries or neurodegenerative diseases. To address this challenge, here we combine our expertise in developmental neurobiology (DJ) and in bioengineering (WL) to develop a strategy to manipulate gene expression in cortical neurons in a circuit-dependent manner. We do so by engineering artificial synaptic contact-dependent signaling cascades to drive new cellular features.
Specifically, we will:
1. Assess the in vitro molecular identity and connectivity of pure populations of L2/3 and L5B cortical neuronal types and manipulate these cellular features by direct reprogramming of L2/3 neurons into L5B neurons (Aim 1).
2. Manipulate gene expression and cellular features of L2/3 neurons in vitro in a synaptic-contact dependent manner by developing a synaptic version of the synthetic notch (synNotch) receptor system (synsynNotch) (Aim 2).
3. Manipulate axonal projections of specific populations of intracortically-projecting neurons in vivo using the synsynNotch system (Aim 3).
Together, these experiments will increase our understanding of the mechanisms controlling cell-type specific circuit assembly and allow us to functionally interrogate this process through circuit-specific manipulation of gene expression.

2019 -
Grant Awardees - Program Grants

Imaging sensory processing and memory storage in the octopus brain

NIELL Cristopher M. (USA)

Institute of Neuroscience - University of Oregon - Eugene - USA

HOCHNER Binyamin (ISRAEL)

Dept. of Neurobiology, Silberman Institute of Life Sciences - Hebrew University - Jerusalem - ISRAEL

Octopuses have highly complex brains and are capable of many advanced behaviors that involve cognitive abilities. However, their brains and nervous system evolved completely independently from those of vertebrates, and it is largely unknown how the brains of such seemingly “alien” animals perform vertebrate-like sensory and cognitive functions with this distinct brain organization. In this proposal, we will study how visual sensory information is processed and stored in the octopus memory system. In order to overcome the technical obstacles to achieve this, we will bring together two labs with complementary expertise. The Niell lab studies the visual system of mouse, using calcium imaging of neural activity to understand how cortical circuits perform the computations that underlying visual perception and behavior. The Hochner lab studies learning and memory in the octopus vertical lobe. They have used electrophysiological tools and behavior to show that the vertical lobe is organized in a simple fan-out fan-in architecture and demonstrates robust activity-dependent synaptic plasticity. However, these current experimental methods are not sufficient for understanding how learning and memory networks store sensory features that are likely represented sparsely in the activity of many individual neurons.

Together, we will implement two-photon calcium imaging techniques for the octopus brain, to directly observe how sensory information from the eye is processed and represented in the visual system as it is conveyed into the central brain. We will then measure how this information is stored in patterns of activity across the large population of small neurons in the memory centers of the octopus brain, within a learning paradigm. In other words, we will watch memories being formed from a visual input. We will also perform manipulations that will allow us to determine the role of synaptic mechanisms and neuromodulation that enable this storage and its modulation by reward and punishment signals. The result of this collaborative endeavor will be a comprehensive view of neural information processing, from sensory input to memory formation, in the unique and enigmatic brain of the octopus.

2019 -
Grant Awardees - Program Grants

A spatiotemporal map of signalling processes controlling human stem cell renewal and differentiation

PERTZ Olivier (SWITZERLAND)

Institute of Cell Biology - University of Bern - Bern - SWITZERLAND

CARAZO SALAS Rafael Edgardo (UK)

School of Cellular and Molecular Medicine - University of Bristol - Bristol - UK

COHEN Andrew (USA)

Dept. of Electrical & Computer Engineering - Drexel University - Philadelphia - USA

The Personalized, Regenerative Medicine of the future will rely on being able to make replacement cells and tissues of choice at will and in a robust, predictive manner. However, key challenges have to be overcome before the promise of personalized stem cell therapeutics becomes a reality. This is because stem cell renewal/differentiation are stochastic processes, precluding the differentiation of a stem cell population into a homogeneously differentiated desired cell type, but also leading to spurious differentiation during renewal. This is thought to partly arise from heterogeneous single-cell signaling states among different cells of a population, which are not measurable using classical ‘population-average’ biochemical methods. A mechanistic understanding of how dynamic signaling processes control differentiation/renewal fates at the single-cell level might therefore significantly improve our capacity to robustly and precisely manipulate cell fates for tissue engineering purposes. We propose to use an integrated interdisciplinary strategy to map the dynamic, single-cell signaling programs that control differentiation/renewal using human Pluripotent Stem Cell (hPSC) differentiation into neural stem cells as a differentiation paradigm. Using multiplexed, genetically-encoded biosensors, we will quantitate hPSC single-cell dynamic signaling states by large-scale, multi-color, multi-day timelapse microscopy across millions of cells, to reveal with unparalleled precision how heterogeneous signaling states correlate with renewal/differentiation fates. Using computer vision approaches, we will automatically segment, track and lineage at scale each of the cells that were induced to self-renew or differentiate, and we will extract a panel of signaling, cell-cycle, pluripotency state, and cell morphodynamics features that quantify these dynamic processes. We will then mine these high-dimensional feature sets to build computational models that identify dynamic single-cell signaling patterns associated with robust fate transitions and predict actionable interventions that might cause those transitions. Lastly, using drug perturbations, and/or microfluidic/optogenetic actuators, we will quantitatively test those predictions by evoking synthetic dynamic signaling states that induce robust fate transitions. Our approach will help to significantly clarify the mechanistic basis of signaling-mediated human stem cell fate decisions, providing new avenues to robustly control stem cell fate. This might help establish a larger framework, broadly applicable to other hPSC lines and differentiation routes.

2019 -
Grant Awardees - Program Grants

Elucidating the development of biological optical nanostructures

SHAWKEY Matthew (USA)

Dept. of Evolution and Optics of Nanostructures - Ghent University - Ghent - BELGIUM

YEO Jong-Souk (KOREA, REPUBLIC OF (SOUTH KOREA))

School of Integrated Technology/Nano Convergence Systems Group - Yonsei University - Incheon - KOREA, REPUBLIC OF (SOUTH KOREA)

MANCEAU Marie (FRANCE)

Center for Interdisciplinary Research in Biology - College de France - Paris - FRANCE

Optical nanostructures are highly organized composites of materials with varying refractive indices (e.g. keratin, melanin and air) that produce some of the brightest colors found in nature through coherent light scattering. How these tissues organise themselves at the nanometer scale to produce colors is poorly understood, despite its fundamental significance to developmental and evolutionary biology and potential to spark advances in the biomimetic design and "green" commercial manufacture of self-assembling optical materials.
We thus propose to use both transcriptomic, laser diffraction and microscopy-based tools of developmental biology to elucidate the mechanisms by which these nanostructures self-assemble in a subsample of birds (Class Aves), a group with incredibly diverse structural colors and mechanisms. Our working hypothesis is that iridescent colors form through depletion-attraction, phase separation and other self-assembly mechanisms. Because most developmental biology is done at larger size scales, testing these hypotheses will require the use and development of methods such as wet cell TEM and in situ laser diffraction analysis to adequately resolve nanometer-scale changes in developing tissue. We will then test these proposed mechanisms using biomimetic approaches that replicate natural conditions as closely as possible (e.g. at room temperature,at biological pH) using natural or semi-natural materials. Use of optical techniques including angle-resolved spectrophotometry and microspectrophotometry will enable us to compare these properties between the natural and synthetic versions. This approach will enable us to not only experimentally test modes of development but also generate and test new materials and/or processes to produce them.
There are three highly innovative aspects to this proposal. First, it attempts to unlock the developmental pathways producing nanostructured tissues. This is a long-standing question with few answers thus far. Second, it uses biomimicry in novel ways to test developmental hypotheses and pushes the technical boundaries of developmental biology by focusing on nanometer-scale organisation of tissues. Finally, the use of biologically realistic chemistry in our biomimetic approaches is a huge leap forward in this field where most work is done at high temperature or with non-biocompatible materials. This work will therefore significantly advance both our fundamental understanding of these materials and the tools to study them and other nanoscale materials.

2019 -
Grant Awardees - Program Grants

Enhancing mitochondrial DNA fidelity to improve mammalian lifespan and healthspan

STEWART James (CANADA)

Research Group Stewart - Max Planck Institute for Biology of Ageing - Cologne - GERMANY

MACKERETH Cameron (CANADA)

Institut Européen de Chimie et Biologie - Univ. Bordeaux, U1212, CNRS UMR5320 - Pessac - FRANCE

LAVROV Dennis (RUSSIA)

Dept. of Ecology, Evolution and Organismal Biology - Iowa State University - Ames - USA

Animal mitochondrial DNA (mtDNA) has a higher substitution rate than nuclear DNA, with the accumulation of mtDNA mutations being one of the hallmarks of ageing. This discrepancy in the rates of evolution is partially due to the lack of mismatch repair activities in the mitochondria. Octocorals – a group of cnidarians – have a reduced rate of mitochondrial evolution and encode a MUTS-like protein (mt-MutS) in their mtDNA. Previous analyses suggested that this enzyme was acquired from a virus and has been universally retained among octocoral taxa. Its function, however, remains unknown. The project will combine comparative, structural, and experimental approaches to investigate the function of mt-MutS and to test whether mt-MutS expression results in lower mutation rates in mtDNA and improve heath in ageing. Comparative analysis of octocoral mtDNA will be used to identify distinct mutation patterns among its lineages and correlate them with the changes in mt-MutS. Partial mt-MutS sequences will be used to identify clades with unusual or accelerated rates of mtDNA evolution for additional sampling. Site- and taxa-specific evolutionary rates in mt-MutS will be analyzed to infer functional and structural constraints and to optimize the choice of the mt-MutS for transgenesis. Ancestral sequences of mt-MutS for the nodes of interest will also be reconstructed and analyzed. A structure-function approach will be utilized for in vitro dissection of mt-MutS functions. The full-length proteins from several species and a reconstructed ancestral sequence will be tested for stability and for amenable structure determination. Isolated domains will also be used for high-resolution structural analysis by diverse biophysical techniques to probe molecular details of binding and nuclease activity for understanding and improving function. Finally, we will generate transgenic mice that express a mitochondrially-targeted version of this optimized mt-MutS enzyme to test its effects on mtDNA mutation rate. The transgene construct will be knocked-in to mice by directed Easi-CRISPR template repair or BAC-transgenesis. mtDNA mutation rate analyses in wildtype and mice with enhanced mitochondrial mutation rates will be undertaken. An ageing study on mice expressing mt-MutS will determine if enhanced mtDNA fidelity can positively affect organismal lifespan and healthspan.

2019 -
Grant Awardees - Program Grants

Communication and the coordination of collective behavior across spatial scales in animal societies

STRANDBURG-PESHKIN Ariana (GERMANY)

Dept. of Biology - University of Konstanz - Konstanz - GERMANY

MANSER Marta (SWITZERLAND)

Dept. of Evolutionary Biology and Environmental Studies - University of Zurich - Zurich - SWITZERLAND

HIRSCH Ben (AUSTRALIA)

College of Science and Engineering - James Cook University - Townsville - AUSTRALIA

HOLEKAMP Kay (USA)

Dept. of Ecology, Evolutionary Biology and Behavior - Michigan State University - East Lansing - USA

ROCH Marie (USA)

Dept. of Computer Science - San Diego State University - San Diego - USA

We propose to use new tracking technology and computational modeling to determine how vocal communication influences collective behavior in animal societies. Canonical examples of collective movement such as bird flocking and fish schooling involve cohesive groups making short-term decisions in a shared context. However, many animals form stable social groups that coordinate and cooperate over extended time spans, across varying distances, and in diverse contexts. In these stable animal societies, group members must make decisions despite varying access to information and exposure to the costs and benefits of coordinating. Moreover their decisions are likely to be shaped by the long-term social relationships among group members. To achieve coordination in such systems, many species use sophisticated signaling systems, such as vocal communication, that transfer information among group-mates. Animals can flexibly control the vocalizations they produce independent of their movements, resulting in a complex interplay between signaling and movement that ultimately drives group-level outcomes such as collective decisions and coordinated actions.
To understand the mechanisms underlying coordination in animal societies, we will record movements and vocal signals concurrently from all members of wild animal groups at a high resolution, and across varying degrees of spatial dispersion. We will compare three mammal species that face a common set of coordination task, but differ in cohesiveness: meerkats form highly cohesive groups, coatis are moderately cohesive, and spotted hyenas live in fission-fusion societies. In each species, we will 1) fit at least one entire social group in the wild with tags that continuously record fine-scale movements and vocalizations, 2) combine supervised and unsupervised machine learning to identify animal calls and movement states, 3) develop modeling approaches to reveal how animals integrate spatial and acoustic information, how information flows through groups, and how social interactions give rise to collective outcomes, and 4) conduct audio playback experiments to isolate causal factors driving collective dynamics. Combining these approaches with long-term data from field studies will shed light on both unifying features underlying coordination mechanisms across animal societies and differences imposed by distinct constraints.