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- 2019
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Tidskriftsartikel (refereegranskat)
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| 3. |
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| 4. |
- Callaway, EM, et al.
(författare)
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A multimodal cell census and atlas of the mammalian primary motor cortex
- 2021
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Ingår i: Nature. - : Springer Science and Business Media LLC. - 1476-4687 .- 0028-0836. ; 598:7879, s. 86-102
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Tidskriftsartikel (refereegranskat)abstract
- Here we report the generation of a multimodal cell census and atlas of the mammalian primary motor cortex as the initial product of the BRAIN Initiative Cell Census Network (BICCN). This was achieved by coordinated large-scale analyses of single-cell transcriptomes, chromatin accessibility, DNA methylomes, spatially resolved single-cell transcriptomes, morphological and electrophysiological properties and cellular resolution input–output mapping, integrated through cross-modal computational analysis. Our results advance the collective knowledge and understanding of brain cell-type organization1–5. First, our study reveals a unified molecular genetic landscape of cortical cell types that integrates their transcriptome, open chromatin and DNA methylation maps. Second, cross-species analysis achieves a consensus taxonomy of transcriptomic types and their hierarchical organization that is conserved from mouse to marmoset and human. Third, in situ single-cell transcriptomics provides a spatially resolved cell-type atlas of the motor cortex. Fourth, cross-modal analysis provides compelling evidence for the transcriptomic, epigenomic and gene regulatory basis of neuronal phenotypes such as their physiological and anatomical properties, demonstrating the biological validity and genomic underpinning of neuron types. We further present an extensive genetic toolset for targeting glutamatergic neuron types towards linking their molecular and developmental identity to their circuit function. Together, our results establish a unifying and mechanistic framework of neuronal cell-type organization that integrates multi-layered molecular genetic and spatial information with multi-faceted phenotypic properties.
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| 5. |
- O'Connor, M. I., et al.
(författare)
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A general biodiversity-function relationship is mediated by trophic level
- 2017
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Ingår i: Oikos. - : Wiley. - 0030-1299. ; 126:1, s. 18-31
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Tidskriftsartikel (refereegranskat)abstract
- Species diversity affects the functioning of ecosystems, including the efficiency by which communities capture limited resources, produce biomass, recycle and retain biologically essential nutrients. These ecological functions ultimately support the ecosystem services upon which humanity depends. Despite hundreds of experimental tests of the effect of biodiversity on ecosystem function (BEF), it remains unclear whether diversity effects are sufficiently general that we can use a single relationship to quantitatively predict how changes in species richness alter an ecosystem function across trophic levels, ecosystems and ecological conditions. Our objective here is to determine whether a general relationship exists between biodiversity and standing biomass. We used hierarchical mixed effects models, based on a power function between species richness and biomass production (Y = a x S-b), and a database of 374 published experiments to estimate the BEF relationship (the change in biomass with the addition of species), and its associated uncertainty, in the context of environmental factors. We found that the mean relationship (b = 0.26, 95% CI: 0.16, 0.37) characterized the vast majority of observations, was robust to differences in experimental design, and was independent of the range of species richness levels considered. However, the richness-biomass relationship varied by trophic level and among ecosystems; in aquatic systems b was nearly twice as large for consumers (herbivores and detritivores) compared to primary producers; in terrestrial ecosystems, b for detritivores was negative but depended on few studies. We estimated changes in biomass expected for a range of changes in species richness, highlighting that species loss has greater implications than species gains, skewing a distribution of biomass change relative to observed species richness change. When biomass provides a good proxy for processes that underpin ecosystem services, this relationship could be used as a step in modeling the production of ecosystem services and their dependence on biodiversity.
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| 6. |
- Schwandt, Melanie L., et al.
(författare)
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Gene-Environment Interactions and Response to Social Intrusion in Male and Female Rhesus Macaques
- 2010
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Ingår i: Biological Psychiatry. - : Elsevier BV. - 0006-3223 .- 1873-2402. ; 67:4, s. 323-330
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Tidskriftsartikel (refereegranskat)abstract
- Background: Genetic factors interact with environmental stressors to moderate risk for human psychopathology, but sex may also be an important mediating factor. Different strategies for coping with environmental stressors have evolved in males and females, and these differences may underlie the differential prevalence of certain types of psychopathology in the two sexes. In this study, we investigated the possibility of sex-specific gene-environment interactions in a nonhuman primate model of response to social threat. Methods: Rhesus macaques (77 males and 106 females) were exposed to an unfamiliar conspecific. Using factor analysis, we identified three behavioral factors characterizing the response to social threat. Monkeys were genotyped for the serotonin transporter-linked polymorphism (5-HTTLPR), and the effects of genotype, early life stress, and sex on behavioral responses were evaluated. Results: Factor analysis produced five factors: High-Risk Aggression, Impulsivity/Novelty-Seeking, Gregariousness/Boldness, Harm Avoidance, and Redirected Aggression. Overall, males displayed higher levels of High-Risk Aggression and Gregariousness/Boldness than females. Levels of High-Risk Aggression in males carrying the s allele were significantly higher if they were also exposed to early adversity in the form of peer rearing. Conclusions: Our findings support those from studies in humans suggesting that males are more vulnerable to externalizing or aggression-related disorders. The results highlight the importance of interactions that exist among behavior, genes, and the environment and suggest that sex differences in vulnerability to psychopathology may be grounded in our evolutionary history.
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| 7. |
- Smerdon, J. E., et al.
(författare)
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Comparing proxy and model estimates of hydroclimate variability and change over the Common Era
- 2017
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Ingår i: Climate of the Past. - : Copernicus GmbH. - 1814-9324 .- 1814-9332. ; 13:12, s. 1851-1900
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Tidskriftsartikel (refereegranskat)abstract
- Water availability is fundamental to societies and ecosystems, but our understanding of variations in hydroclimate (including extreme events, flooding, and decadal periods of drought) is limited because of a paucity of modern instrumental observations that are distributed unevenly across the globe and only span parts of the 20th and 21st centuries. Such data coverage is insufficient for characterizing hydroclimate and its associated dynamics because of its multidecadal to centennial variability and highly regionalized spatial signature. High-resolution (seasonal to decadal) hydroclimatic proxies that span all or parts of the Common Era (CE) and paleoclimate simulations from climate models are therefore important tools for augmenting our understanding of hydroclimate variability. In particular, the comparison of the two sources of information is critical for addressing the uncertainties and limitations of both while enriching each of their interpretations. We review the principal proxy data available for hydroclimatic reconstructions over the CE and highlight the contemporary understanding of how these proxies are interpreted as hydroclimate indicators. We also review the available last-millennium simulations from fully coupled climate models and discuss several outstanding challenges associated with simulating hydroclimate variability and change over the CE. A specific review of simulated hydroclimatic changes forced by volcanic events is provided, as is a discussion of expected improvements in estimated radiative forcings, models, and their implementation in the future. Our review of hydroclimatic proxies and last-millennium model simulations is used as the basis for articulating a variety of considerations and best practices for how to perform proxy-model comparisons of CE hydroclimate. This discussion provides a framework for how best to evaluate hydroclimate variability and its associated dynamics using these comparisons and how they can better inform interpretations of both proxy data and model simulations. We subsequently explore means of using proxy-model comparisons to better constrain and characterize future hydroclimate risks. This is explored specifically in the context of several examples that demonstrate how proxy-model comparisons can be used to quantitatively constrain future hydroclimatic risks as estimated from climate model projections.
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| 8. |
- Bodin, Örjan, et al.
(författare)
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Improving network approaches to the study of complex social–ecological interdependencies
- 2019
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Ingår i: Nature Sustainability. - : Springer Science and Business Media LLC. - 2398-9629. ; 2:7, s. 551-559
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Tidskriftsartikel (refereegranskat)abstract
- Achieving effective, sustainable environmental governance requires a better understanding of the causes and consequences of the complex patterns of interdependencies connecting people and ecosystems within and across scales. Network approaches for conceptualizing and analysing these interdependencies offer one promising solution. Here, we present two advances we argue are needed to further this area of research: (i) a typology of causal assumptions explicating the causal aims of any given network-centric study of social–ecological interdependencies; (ii) unifying research design considerations that facilitate conceptualizing exactly what is interdependent, through what types of relationships and in relation to what kinds of environmental problems. The latter builds on the appreciation that many environmental problems draw from a set of core challenges that re-occur across contexts. We demonstrate how these advances combine into a comparative heuristic that facilitates leveraging case-specific findings of social–ecological interdependencies to generalizable, yet context-sensitive, theories based on explicit assumptions of causal relationships.
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| 9. |
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| 10. |
- Baker, Maggie, et al.
(författare)
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Early rearing history influences oxytocin receptor epigenetic regulation in rhesus macaques
- 2017
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Ingår i: Proceedings of the National Academy of Sciences of the United States of America. - : NATL ACAD SCIENCES. - 0027-8424 .- 1091-6490. ; 114:44, s. 11769-11774
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Tidskriftsartikel (refereegranskat)abstract
- Adaptations to stress can occur through epigenetic processes and may be a conduit for informing offspring of environmental challenge. We employed ChIP-sequencing for H3K4me3 to examine effects of early maternal deprivation (peer-rearing, PR) in archived rhesus macaque hippocampal samples (male, n = 13). Focusing on genes with roles in stress response and behavior, we assessed the effects of rearing on H3K4me3 binding by ANOVA. We found decreased H3K4me3 binding at genes critical to behavioral stress response, the most robust being the oxytocin receptor gene OXTR, for which we observed a corresponding decrease in RNA expression. Based on this finding, we performed behavioral analyses to deter mine whether a gain-of-function nonsynonymous OXTR SNP inter acted with early stress to influence relevant behavioral stress reactivity phenotypes (n = 194), revealing that this SNP partially rescued the PR phenotype. PR infants exhibited higher levels of separation anxiety and arousal in response to social separation, but infants carrying the alternative OXTR allele did not exhibit as great a separation response. These data indicate that the oxytocin system is involved in social-separation response and suggest that epigenetic down-modulation of OXTR could contribute to behavior al differences observed in PR animals. Epigenetic changes at OXTR may represent predictive adaptive responses that could impart readiness to respond to environmental challenge or maintain proximity to a caregiver but also contribute to behavioral pathology. Our data also demonstrate that OXTR polymorphism can permit animals to partially overcome the detrimental effects of early maternal deprivation, which could have translational implications for human psychiatric disorders.
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| 11. |
- Braae, Ellen, et al.
(författare)
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A conversation on education
- 2018
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Ingår i: Routledge Research Companion to Landscape Architecture. - : Routledge. ; , s. 324-334
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Bokkapitel (övrigt vetenskapligt/konstnärligt)abstract
- Landscape architecture today is becoming increasingly professionalized as a quasi-global profession—not least through the successful expansion of academic research efforts within the discipline. This includes the kinds of effort to which this volume as a whole contributes, and this chapter broadens our understanding of the institutional structures within which we operate. Indeed, education may be one of the most important realms for the engagement and transmission of knowledge that moves back and forth and connects practice and research in intricate ways—with the added benefit that education remains a dialogical and personal setting for exchange, not least in studio-driven design programmes. We therefore have asked significant educators from Landscape Architecture programmes in Europe and North America to reflect on the tensions and challenges the profession currently faces, and on what we can do to prepare new generations of landscape architects who are now part of the educational system or will be so in the future. Moreover, we wished to inspire a discussion of how the aesthetic and ethical dimensions of landscape architecture potentially impact on the discipline, and of the role they should play in future landscape architecture education.
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| 12. |
- Byrnes, J. E. K., et al.
(författare)
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Investigating the relationship between biodiversity and ecosystem multifunctionality: Challenges and solutions
- 2014
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Ingår i: Methods in Ecology and Evolution. - 2041-210X. ; 5:2, s. 111-124
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Tidskriftsartikel (refereegranskat)abstract
- Summary: Extensive research shows that more species-rich assemblages are generally more productive and efficient in resource use than comparable assemblages with fewer species. But the question of how diversity simultaneously affects the wide variety of ecological functions that ecosystems perform remains relatively understudied. It presents several analytical and empirical challenges that remain unresolved. In particular, researchers have developed several disparate metrics to quantify multifunctionality, each characterizing different aspects of the concept and each with pros and cons. We compare four approaches to characterizing multifunctionality and its dependence on biodiversity, quantifying (i) magnitudes of multiple individual functions separately, (ii) the extent to which different species promote different functions, (iii) the average level of a suite of functions and (iv) the number of functions that simultaneously exceeds a critical threshold. We illustrate each approach using data from the pan-European BIODEPTH experiment and the R multifunc package developed for this purpose, evaluate the strengths and weaknesses of each approach and implement several methodological improvements. We conclude that an extension of the fourth approach that systematically explores all possible threshold values provides the most comprehensive description of multifunctionality to date. We outline this method and recommend its use in future research. © 2013 British Ecological Society.
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| 13. |
- Cox, Michael, et al.
(författare)
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How academic podcasting can change academia and its relationship with society : A conversation and guide
- 2023
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Ingår i: Frontiers in Communication. - 2297-900X. ; 8
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Tidskriftsartikel (refereegranskat)abstract
- In this paper we explore the potential of academic podcasting to e ect positive change within academia and between academia and society. Building on the concept of epistemic living spaces, we consider how podcasting can change how we evaluate what is legitimate knowledge and methods for knowledge production, who has access to what privileges and power, the nature of our connections within academia and with other partners, and how we experience the constraints and opportunities of space and time. We conclude by o ering a guide for others who are looking to develop their own academic podcasting projects and discuss the potential for podcasting to be formalized as amainstream academic output. To listen to an abridged and annotated version of this paper, visit: https://soundcloud.com/conservechange/podcastinginacademia.
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| 14. |
- Denver, Dee R, et al.
(författare)
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Selective sweeps and parallel mutation in the adaptive recovery from deleterious mutation in Caenorhabditis elegans.
- 2010
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Ingår i: Genome Research. - : Cold Spring Harbor Laboratory. - 1088-9051 .- 1549-5469. ; 20:12
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Tidskriftsartikel (refereegranskat)abstract
- Deleterious mutation poses a serious threat to human health and the persistence of small populations. Although adaptive recovery from deleterious mutation has been well-characterized in prokaryotes, the evolutionary mechanisms by which multicellular eukaryotes recover from deleterious mutation remain unknown. We applied high-throughput DNA sequencing to characterize genomic divergence patterns associated with the adaptive recovery from deleterious mutation using a Caenorhabditis elegans recovery-line system. The C. elegans recovery lines were initiated from a low-fitness mutation-accumulation (MA) line progenitor and allowed to independently evolve in large populations (N ∼ 1000) for 60 generations. All lines rapidly regained levels of fitness similar to the wild-type (N2) MA line progenitor. Although there was a near-zero probability of a single mutation fixing due to genetic drift during the recovery experiment, we observed 28 fixed mutations. Cross-generational analysis showed that all mutations went from undetectable population-level frequencies to a fixed state in 10-20 generations. Many recovery-line mutations fixed at identical timepoints, suggesting that the mutations, if not beneficial, hitchhiked to fixation during selective sweep events observed in the recovery lines. No MA line mutation reversions were detected. Parallel mutation fixation was observed for two sites in two independent recovery lines. Analysis using a C. elegans interactome map revealed many predicted interactions between genes with recovery line-specific mutations and genes with previously accumulated MA line mutations. Our study suggests that recovery-line mutations identified in both coding and noncoding genomic regions might have beneficial effects associated with compensatory epistatic interactions.
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| 15. |
- Felipe-Lucia, María R., et al.
(författare)
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Conceptualizing ecosystem services using social–ecological networks
- 2022
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Ingår i: Trends in Ecology & Evolution. - : Elsevier BV. - 0169-5347 .- 1872-8383. ; 37:3, s. 211-222
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Tidskriftsartikel (refereegranskat)abstract
- Social–ecological networks (SENs) represent the complex relationships between ecological and social systems and are a useful tool for analyzing and managing ecosystem services. However, mainstreaming the application of SENs in ecosystem service research has been hindered by a lack of clarity about how to match research questions to ecosystem service conceptualizations in SEN (i.e., as nodes, links, attributes, or emergent properties). Building from different disciplines, we propose a typology to represent ecosystem service in SENs and identify opportunities and challenges of using SENs in ecosystem service research. Our typology provides guidance for this growing field to improve research design and increase the breadth of questions that can be addressed with SEN to understand human–nature interdependencies in a changing world.
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| 16. |
- Janssens-Maenhout, G., et al.
(författare)
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Toward an operational anthropogenic CO2 emissions monitoring and verification support capacity
- 2020
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Ingår i: Bulletin of the American Meteorological Society. - 0003-0007. ; 101:8, s. 1439-1451
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Tidskriftsartikel (refereegranskat)abstract
- Under the Paris Agreement (PA), progress of emission reduction efforts is tracked on the basis of regular updates to national greenhouse gas (GHG) inventories, referred to as bottom-up estimates. However, only top-down atmospheric measurements can provide observation-based evidence of emission trends. Today, there is no internationally agreed, operational capacity to monitor anthropogenic GHG emission trends using atmospheric measurements to complement national bottom-up inventories. The European Commission (EC), the European Space Agency, the European Centre for Medium-Range Weather Forecasts, the European Organisation for the Exploitation of Meteorological Satellites, and international experts are joining forces to develop such an operational capacity for monitoring anthropogenic CO2 emissions as a new CO2 service under the EC's Copernicus program. Design studies have been used to translate identified needs into defined requirements and functionalities of this anthropogenic CO2 emissions Monitoring and Verification Support (CO2MVS) capacity. It adopts a holistic view and includes components such as atmospheric spaceborne and in situ measurements, bottom-up CO2 emission maps, improved modeling of the carbon cycle, an operational data-assimilation system integrating top-down and bottom-up information, and a policy-relevant decision support tool. The CO2MVS capacity with operational capabilities by 2026 is expected to visualize regular updates of global CO2 emissions, likely at 0.05° x 0.05°. This will complement the PA's enhanced transparency framework, providing actionable information on anthropogenic CO2 emissions that are the main driver of climate change. This information will be available to all stakeholders, including governments and citizens, allowing them to reflect on trends and effectiveness of reduction measures. The new EC gave the green light to pass the CO2MVS from exploratory to implementing phase.
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| 18. |
- Pinty, B, et al.
(författare)
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An Operational Anthropogenic CO₂ Emissions Monitoring & Verification Support Capacity : Needs and High Level Requirements for in situ Measurements
- 2019
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Rapport (övrigt vetenskapligt/konstnärligt)abstract
- This is the third report form the CO2 Monitoring Task Force on the multiple input streams of in-situ observations that are requirement for the Copernicus CO2 Monitoring and Verification Support capacity to: (i) calibrated and validate the space component, (ii) assimilate data in the models and integrate information in the core of the system, and (iii) evaluate the output generated by the system for its end users. The availability of sustained in situ networks is currently a significant factor of risk that needs to be mitigated to establish a European CO 2 support capacity which is fit-for-purpose. The current status of existing networks may be the source of large uncertainties in anthropogenicCO2 emission estimates as well as limited capability in meeting the requirements for country, large city and point source scale assessments. This conclusion results from a risk analysis formulated for four scenarios: 1) maintaining the status quo, 2) assuring sustained funding for the status quo, 3) enhancing network capabilities at European scale with sustained funding and 4) with a significantly improved in situ infrastructure in Europe and beyond. This report substantiates the multifaceted needs and requirements of the European CO2 support capacity with respect to in situ observations. The analysis concerns all core elements of the envisaged integrated system with a particular attention on the impact of such observations in achieving the proposed objectives. The specific needs for the validation of products delivered by the space component that is, the Copernicus Sentinels CO2 monitoring constellation, are addressed as another prerequisite for the success of the CO2 support capacity. This European asset will represent a significant contribution to the virtual constellation proposed by the Committee on Earth Observation Satellites (CEOS) and, accordingly, complementary requirements are elaborated in that international frame.The report highlights that although high measurement standards are present within existing networks such as ICOS, in the context of the needs for targeted in situ data for the realization of the operational system, these data are not fully fit-for-purpose. A fundamental prerequisite is to have a good geographical coverage over Europe for evaluating the data assimilation and modeling system over a large variety of environmental conditions such as, for instance, urban areas, agricultural regions, forested zones and industrial complexes. The in situ observations need to be extended under a coordinated European lead with sustained infrastructure and targeted additional and maintained long-term funding.It has been clearly understood from the onset that the international dimension of the European CO2 support capacity would be critical and that these aspects should be developed in parallel to, and in synergy with the definition and implementation of a European contributing system. It was also understood that this international dimension had both strategic, policy relevant and technical dimensions and the Commission and the relevant European institutional partners have started since several years to engage both bilaterally and multilaterally with the relevant stakeholders and counterparts to develop these relations. Specifically, CEOS will undertake, over the next few years,dedicated preparatory work in a coordinated international context, to provide cumulative added value to the specific programmatic activities of their member agencies. Concerted efforts have already begun in the context of the European Commission's Chairmanship of CEOS in 2018. It is recognized in the context of the European efforts, and increasingly by our international counterparts that a broad and holistic system approach is required to address the requirements which are represented by the climate policy, of which the satellite component, whilst important, cannot effectively be developed in isolation. This system indeed includes the satellite observing capability but in addition, the required modelling component and data integration elements, prior information, ancillary data and in situ observations delivered by essential networks.Acknowledging the need for an efficient coordination at international level for instance via the Global Atmosphere Watch programme of the World Meteorological Organisation is a key towards a successful implementation of appropriate actions to ensure the sustainability of essential networks, to enhance current network capabilities with new observations and to propose adequate governance schemes. Such actions to mitigate current network limitations are deemed critical to implementing the Copernicus CO 2 Monitoring & Verification Support capacity in its full strength.
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| 19. |
- Wakelee, Heather A., et al.
(författare)
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Lung cancer incidence in never smokers
- 2007
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Ingår i: Journal of Clinical Oncology. - 0732-183X .- 1527-7755. ; 25:5, s. 472-478
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Tidskriftsartikel (refereegranskat)abstract
- PURPOSE: Lung cancer is a leading cause of cancer death worldwide. Although smoking remains the predominant cause of lung cancer, lung cancer in never smokers is an increasingly prominent public health issue. However, data on this topic, particularly lung cancer incidence rates in never smokers, are limited. METHODS: We reviewed the existing literature on lung cancer incidence and mortality rates among never smokers and present new data regarding rates in never smokers from the following large, prospective cohorts: Nurses' Health Study; Health Professionals Follow-Up Study; California Teachers Study; Multiethnic Cohort Study; Swedish Lung Cancer Register in the Uppsala/Orebro region; and First National Health and Nutrition Examination Survey Epidemiologic Follow-Up Study. RESULTS: Truncated age-adjusted incidence rates of lung cancer among never smokers age 40 to 79 years in these six cohorts ranged from 14.4 to 20.8 per 100,000 person-years in women and 4.8 to 13.7 per 100,000 person-years in men, supporting earlier observations that women are more likely than men to have non-smoking-associated lung cancer. The distinct biology of lung cancer in never smokers is apparent in differential responses to epidermal growth factor receptor inhibitors and an increased prevalence of adenocarcinoma histology in never smokers. CONCLUSION: Lung cancer in never smokers is an important public health issue, and further exploration of its incidence patterns, etiology, and biology is needed.
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