Project acronym FunKeyGut
Project Illuminating Functional Networks and Keystone Species in the Gut
Researcher (PI) David Michael BERRY
Host Institution (HI) UNIVERSITAT WIEN
Call Details Starting Grant (StG), LS8, ERC-2016-STG
Summary We live in an intimate symbiosis with our gut microbiota, which provides us services such as vitamin production, breakdown of dietary compounds, and immune training. Sequencing-based approaches that have been applied to catalogue the gut microbiota have revealed intriguing discoveries associating the microbiome with diet and disease. The next outstanding challenge is to unravel the many activities and interactions that define gut microbiota function.
The gut microbiota is a diverse community of cooperating and competing microbes. These interactions form a network that links organisms with each other and their environment. Interactions in such a “functional network” are based partially, though not exclusively, on food webs. Certain “keystone species”, such as Rumonicoccus bromii, are thought to play a major role in these networks. Though some evidence exists for the presence of keystone species, their identity and activity remains largely unknown. As keystone species are vital to networks they are ideal targets for manipulating the gut microbiota to improve metabolic health and protect against enteropathogen infection.
Given the complexity of the gut microbiota, networks can only be elucidated directly in the native community. This project aims to identify functional networks and keystone species in the human gut using novel approaches that are uniquely and ideally suited for studying microbial activity in complex communities. Using state-of-the-art methods such as stable isotope labeling, Raman microspectroscopy, and secondary ion mass spectrometry (NanoSIMS) we will illuminate functional networks in situ. This will allow us to identify what factors shape gut microbiota activity, reveal important food webs, and ultimately use network knowledge to target the microbiota with prebiotic/probiotic treatments rationally designed to promote health.
Summary
We live in an intimate symbiosis with our gut microbiota, which provides us services such as vitamin production, breakdown of dietary compounds, and immune training. Sequencing-based approaches that have been applied to catalogue the gut microbiota have revealed intriguing discoveries associating the microbiome with diet and disease. The next outstanding challenge is to unravel the many activities and interactions that define gut microbiota function.
The gut microbiota is a diverse community of cooperating and competing microbes. These interactions form a network that links organisms with each other and their environment. Interactions in such a “functional network” are based partially, though not exclusively, on food webs. Certain “keystone species”, such as Rumonicoccus bromii, are thought to play a major role in these networks. Though some evidence exists for the presence of keystone species, their identity and activity remains largely unknown. As keystone species are vital to networks they are ideal targets for manipulating the gut microbiota to improve metabolic health and protect against enteropathogen infection.
Given the complexity of the gut microbiota, networks can only be elucidated directly in the native community. This project aims to identify functional networks and keystone species in the human gut using novel approaches that are uniquely and ideally suited for studying microbial activity in complex communities. Using state-of-the-art methods such as stable isotope labeling, Raman microspectroscopy, and secondary ion mass spectrometry (NanoSIMS) we will illuminate functional networks in situ. This will allow us to identify what factors shape gut microbiota activity, reveal important food webs, and ultimately use network knowledge to target the microbiota with prebiotic/probiotic treatments rationally designed to promote health.
Max ERC Funding
1 498 279 €
Duration
Start date: 2017-04-01, End date: 2022-03-31
Project acronym SexAntag
Project Prevalence and Influence of Sexual Antagonism on Genome Evolution
Researcher (PI) Beatriz Barahona Pena Vicoso
Host Institution (HI) INSTITUTE OF SCIENCE AND TECHNOLOGYAUSTRIA
Call Details Starting Grant (StG), LS8, ERC-2016-STG
Summary Males and females display profound differences in phenotype, physiology and behavior, and understanding the evolutionary forces driving this diversity is a long-standing goal in evolutionary biology. Sexually antagonistic conflict, resulting from traits and/or mutations that are beneficial to one sex but harmful to the other, can in theory lead to strong dimorphism, and has been invoked to explain many evolutionary features, including the large number of genes that acquire sex-biased expression. Quantifying it, however, has proved difficult, and only a few experimental studies have attempted to systematically identify genes under sexual conflict. Species groups with both sexual and asexual populations offer a promising approach to tackle this question, as they allow for a direct comparison of gene expression when selection occurs ½ of the time in females and ½ of the time in males (in sexual species), versus a female-only selective regime (asexual species).
Here, we will test the hypothesis that widespread sexual conflict maintains sex-biased gene expression, using the brine shrimp Artemia as a model. Specifically, we will:
1. Compare gene expression levels of closely related Artemia sexual and asexual species, to test if the absence of selection on males (in the female-only species) leads to general shifts in expression, and if these changes are consistent with predictions made under sexual antagonism.
2. Characterize the Z (sex) chromosome of the sexual and asexual species, to test if this chromosome is particularly prone to maintaining genes under sexual conflict, as predicted by theory.
3. Investigate the population genomics profile of genes under sexual conflict, to find signatures of sexual conflict that may be diagnostic for sexually antagonistic genes in other systems.
Together, these analyses will provide us with a global overview of the prevalence of sexual antagonism, and of its influence on gene expression and genome evolution.
Summary
Males and females display profound differences in phenotype, physiology and behavior, and understanding the evolutionary forces driving this diversity is a long-standing goal in evolutionary biology. Sexually antagonistic conflict, resulting from traits and/or mutations that are beneficial to one sex but harmful to the other, can in theory lead to strong dimorphism, and has been invoked to explain many evolutionary features, including the large number of genes that acquire sex-biased expression. Quantifying it, however, has proved difficult, and only a few experimental studies have attempted to systematically identify genes under sexual conflict. Species groups with both sexual and asexual populations offer a promising approach to tackle this question, as they allow for a direct comparison of gene expression when selection occurs ½ of the time in females and ½ of the time in males (in sexual species), versus a female-only selective regime (asexual species).
Here, we will test the hypothesis that widespread sexual conflict maintains sex-biased gene expression, using the brine shrimp Artemia as a model. Specifically, we will:
1. Compare gene expression levels of closely related Artemia sexual and asexual species, to test if the absence of selection on males (in the female-only species) leads to general shifts in expression, and if these changes are consistent with predictions made under sexual antagonism.
2. Characterize the Z (sex) chromosome of the sexual and asexual species, to test if this chromosome is particularly prone to maintaining genes under sexual conflict, as predicted by theory.
3. Investigate the population genomics profile of genes under sexual conflict, to find signatures of sexual conflict that may be diagnostic for sexually antagonistic genes in other systems.
Together, these analyses will provide us with a global overview of the prevalence of sexual antagonism, and of its influence on gene expression and genome evolution.
Max ERC Funding
1 444 394 €
Duration
Start date: 2017-03-01, End date: 2022-02-28
Project acronym XSTREAM
Project X-ray-waveforms at the Space-Time Resolution Extreme for Atomic-scale Movies
Researcher (PI) Tenio POPMINTCHEV
Host Institution (HI) TECHNISCHE UNIVERSITAET WIEN
Call Details Starting Grant (StG), PE2, ERC-2016-STG
Summary Nonlinear optics revolutionized the ability to create directed, coherent beams particularly in spectral regions where lasers based on conventional population inversion are not practical. New breakthroughs in extreme nonlinear optics promise a similar revolution in the X-ray regime. In a dramatic and unanticipated breakthrough, an international team lead by the PI demonstrated that the high harmonic generation process (HHG) driven by mid-IR lasers can be used to generate keV photons, implementing a >5000 order nonlinear process, while still maintaining the full phase matching that is necessary for good conversion efficiency. This work represents the most extreme, fully coherent upconversion for electromagnetic waves in the 50 year history of nonlinear optics. Moreover, the limits of HHG are still not understood, either theoretically or experimentally. It may be possible to generate coherent hard X-rays using a tabletop-scale apparatus.
In another surprising breakthrough, the PI showed that UV-driven HHG in multiply ionized plasma can be also highly efficient, representing a 2nd route towards the X-ray region. Remarkably, this regime provides X-rays with contrasting spectral and temporal properties. Furthermore, by shaping the polarization of a bi-color mid-IR driving laser the PI, the JILA team in collaboration with Technion, demonstrated robust phase matching of circularly polarized soft X-rays.
In the proposed work, the fundamental atomic, phase matching plus group velocity matching limits of HHG in the multi-keV X-ray regime will be explored using the 3 most promising, complimentary approaches: 1) mid-IR driven HHG, 2) UV driven HHG, and 3) all-optical quasi phase matching. The knowledge gained as a result of this effort will identify the best path forward for generating bright coherent X-ray beams on a tabletop, at photon energies of 1-10 keV and greater with unprecedented attosecond-to-zeptosecond pulse durations, and arbitrary polarization state.
Summary
Nonlinear optics revolutionized the ability to create directed, coherent beams particularly in spectral regions where lasers based on conventional population inversion are not practical. New breakthroughs in extreme nonlinear optics promise a similar revolution in the X-ray regime. In a dramatic and unanticipated breakthrough, an international team lead by the PI demonstrated that the high harmonic generation process (HHG) driven by mid-IR lasers can be used to generate keV photons, implementing a >5000 order nonlinear process, while still maintaining the full phase matching that is necessary for good conversion efficiency. This work represents the most extreme, fully coherent upconversion for electromagnetic waves in the 50 year history of nonlinear optics. Moreover, the limits of HHG are still not understood, either theoretically or experimentally. It may be possible to generate coherent hard X-rays using a tabletop-scale apparatus.
In another surprising breakthrough, the PI showed that UV-driven HHG in multiply ionized plasma can be also highly efficient, representing a 2nd route towards the X-ray region. Remarkably, this regime provides X-rays with contrasting spectral and temporal properties. Furthermore, by shaping the polarization of a bi-color mid-IR driving laser the PI, the JILA team in collaboration with Technion, demonstrated robust phase matching of circularly polarized soft X-rays.
In the proposed work, the fundamental atomic, phase matching plus group velocity matching limits of HHG in the multi-keV X-ray regime will be explored using the 3 most promising, complimentary approaches: 1) mid-IR driven HHG, 2) UV driven HHG, and 3) all-optical quasi phase matching. The knowledge gained as a result of this effort will identify the best path forward for generating bright coherent X-ray beams on a tabletop, at photon energies of 1-10 keV and greater with unprecedented attosecond-to-zeptosecond pulse durations, and arbitrary polarization state.
Max ERC Funding
1 513 335 €
Duration
Start date: 2017-08-01, End date: 2022-07-31
