Enhancers display constrained sequence flexibility and context-specific modulation of motif function

The information about when and where each gene is to be expressed is mainly encoded in the DNA sequence of enhancers, sequence elements that comprise binding sites (motifs) for different transcription factors (TFs). Most of the research on enhancer sequences has been focused on TF motif presence, whereas the enhancer syntax, that is, the flexibility of important motif positions and how the sequence context modulates the activity of TF motifs, remains poorly understood. Here, we explore the rules of enhancer syntax by a two-pronged approach in Drosophila melanogaster S2 cells: we (1) replace important TF motifs by all possible 65,536 eight-nucleotide-long sequences and (2) paste eight important TF motif types into 763 positions within 496 enhancers. These complementary strategies reveal that enhancers display constrained sequence flexibility and the context-specific modulation of motif function. Important motifs can be functionally replaced by hundreds of sequences constituting several distinct motif types, but these are only a fraction of all possible sequences and motif types. Moreover, TF motifs contribute with different intrinsic strengths that are strongly modulated by the enhancer sequence context (the flanking sequence, the presence and diversity of other motif types, and the distance between motifs), such that not all motif types can work in all positions. The context-specific modulation of motif function is also a hallmark of human enhancers, as we demonstrate experimentally. Overall, these two general principles of enhancer sequences are important to understand and predict enhancer function during development, evolution, and in disease.

Mechanisms driving plant functional trait variation in a tropical forest

Plant functional trait variation in tropical forests results from taxonomic differences in phylogeny and associated genetic differences, as well as, phenotypic plastic responses to the environment. Accounting for the underlying mechanisms driving plant functional trait variation is important for understanding the potential rate of change of ecosystems since trait acclimation via phenotypic plasticity is very fast compared to shifts in community composition and genetic adaptation. We here applied a statistical technique to decompose the relative roles of phenotypic plasticity, genetic adaptation, and phylogenetic constraints. We examined typically obtained plant functional traits, such as wood density, plant height, specific leaf area, leaf area, leaf thickness, leaf dry mass content, leaf nitrogen content, and leaf phosphorus content. We assumed that genetic differences in plant functional traits between species and genotypes increase with environmental heterogeneity and geographic distance, whereas trait variation due to plastic acclimation to the local environment is independent of spatial distance between sampling sites. Results suggest that most of the observed trait variation could not be explained by the measured environmental variables, thus indicating a limited potential to predict individual plant traits from commonly assessed parameters. However, we found a difference in the response of plant functional traits, such that leaf traits varied in response to canopy-light regime and nutrient availability, whereas wood traits were related to topoedaphic factors and water availability. Our analysis furthermore revealed differences in the functional response of coexisting neotropical tree species, which suggests that endemic species with conservative ecological strategies might be especially prone to competitive exclusion under projected climate change.

Drought and recovery effects on belowground respiration dynamics and the partitioning of recent carbon in managed and abandoned grassland

The supply of soil respiration with recent photoassimilates is an important and fast pathway for respiratory loss of carbon (C). To date it is unknown how drought and land-use change interactively influence the dynamics of recent C in soil-respired CO₂ . In an in situ common-garden experiment, we exposed soil-vegetation monoliths from a managed and a nearby abandoned mountain grassland to an experimental drought. Based on two ¹³ CO₂ pulse-labelling campaigns, we traced recently assimilated C in soil respiration during drought, rewetting and early recovery. Independent of grassland management, drought reduced the absolute allocation of recent C to soil respiration. Rewetting triggered a respiration pulse, which was strongly fuelled by C assimilated during drought. In comparison to the managed grassland, the abandoned grassland partitioned more recent C to belowground respiration than to root C storage under ample water supply. Interestingly, this pattern was reversed under drought. We suggest that these different response patterns reflect strategies of the managed and the abandoned grassland to enhance their respective resilience to drought, by fostering their resistance and recovery respectively. We conclude that while severe drought can override the effects of abandonment of grassland management on the respiratory dynamics of recent C, abandonment alters strategies of belowground assimilate investment, with consequences for soil-CO₂ fluxes during drought and drought-recovery.

Biodiversity policy beyond economic growth

Increasing evidence-synthesized in this paper-shows that economic growth contributes to biodiversity loss via greater resource consumption and higher emissions. Nonetheless, a review of international biodiversity and sustainability policies shows that the majority advocate economic growth. Since improvements in resource use efficiency have so far not allowed for absolute global reductions in resource use and pollution, we question the support for economic growth in these policies, where inadequate attention is paid to the question of how growth can be decoupled from biodiversity loss. Drawing on the literature about alternatives to economic growth, we explore this contradiction and suggest ways forward to halt global biodiversity decline. These include policy proposals to move beyond the growth paradigm while enhancing overall prosperity, which can be implemented by combining top-down and bottom-up governance across scales. Finally, we call the attention of researchers and policy makers to two immediate steps: acknowledge the conflict between economic growth and biodiversity conservation in future policies; and explore socioeconomic trajectories beyond economic growth in the next generation of biodiversity scenarios.

A socio-ecological model for predicting impacts of land-use and climate change on regional plant diversity in the Austrian Alps

Climate and land-use change jointly affect the future of biodiversity. Yet, biodiversity scenarios have so far concentrated on climatic effects because forecasts of land use are rarely available at appropriate spatial and thematic scales. Agent-based models (ABMs) represent a potentially powerful but little explored tool for establishing thematically and spatially fine-grained land-use scenarios. Here, we use an ABM parameterized for 1,329 agents, mostly farmers, in a Central European model region, and simulate the changes to land-use patterns resulting from their response to three scenarios of changing socio-economic conditions and three scenarios of climate change until the mid of the century. Subsequently, we use species distribution models to, first, analyse relationships between the realized niches of 832 plant species and climatic gradients or land-use types, respectively, and, second, to project consequent changes in potential regional ranges of these species as triggered by changes in both the altered land-use patterns and the changing climate. We find that both drivers determine the realized niches of the studied plants, with land use having a stronger effect than any single climatic variable in the model. Nevertheless, the plants' future distributions appear much more responsive to climate than to land-use changes because alternative future socio-economic backgrounds have only modest impact on land-use decisions in the model region. However, relative effects of climate and land-use changes on biodiversity may differ drastically in other regions, especially where landscapes are still dominated by natural or semi-natural habitat. We conclude that agent-based modelling of land use is able to provide scenarios at scales relevant to individual species distribution and suggest that coupling ABMs with models of species' range change should be intensified to provide more realistic biodiversity forecasts.

Analytic Framework to Determine Proximity in Relationship Coffee Models

In conventional food systems, there are often large social and geographical distances between production and consumption. Alternative food networks (AFNs) like relationship coffee models aim to shorten these distances through direct contacts, communication, trust, transparency or commitment to improve farmers' livelihoods. These relationship coffee models appear in diverse shapes with various implications for producers. Therefore, we deductively develop a framework to conceptualise proximity in four dimensions (organisational, institutional, cognitive and social) with subdimensions and three transversal dimensions ((temporary) geographical proximity, power, and communication). The analytic framework is complemented by an illustrative case to empirically test it, showing high geographical, organisational, institutional and cognitive proximity but low social proximity between coffee producer and restaurant owner. For future research, the framework can help to conceptualise proximity or to distinguish different types of relationship coffee models and to unpack conditions under which relationship coffees can increase proximity between coffee producers and buyers, often located far apart.

Long-term monitoring of sporadic permafrost at the eastern margin of the European Alps (Hochreichart, Seckauer Tauern range, Austria)

Delineating the spatial extent and the altitudinal lower limit of mountain permafrost is difficult due to complex topo-climatic and variable ground thermal conditions within short distances. Little information exists regarding sporadic permafrost existence, its thermal characteristics and its long-term changes at the eastern margin of the European Alps. To reduce this gap, permafrost monitoring was initiated in 2004 in the Seckauer Tauern mountains, Austria. Research was carried out in the summit region of Mt Hochreichart (2416 m a.s.l.) and at several nearby cirques and valleys, all with rock glaciers. Geomorphic mapping, numerical permafrost modeling, measurements of the bottom temperature of the winter snow cover, continuous ground temperature monitoring, electrical resistivity tomography and optical snow cover monitoring were applied. Results indicate sporadic permafrost occurrence in the summit region with mean annual ground temperatures slightly below 0°C at the surface and -1.4°C at 2.5 m depth. Permafrost lenses also exist in the transition zone between the rock glacier and the talus slope behind attributed to coarse-grained, blocky material causing additional ground cooling. Thanks to long-term data, statistically significant trends of atmospheric and ground warming were observed in 2000-2018. Permafrost at this site will presumably disappear within the next few decades.

Nonadiabatic Dynamics Simulation Predict Intersystem Crossing in Nitroaromatic Molecules on a Picosecond Time Scale

Previous time-resolved spectroscopic experiments and static quantum-chemical calculations attributed nitronaphthalene derivatives one of the fastest time scales for intersystem crossing within organic molecules, reaching the 100 fs mark. Nonadiabatic dynamics simulations on three nitronaphthalene derivatives challenge this view, showing that the experimentally observed ∼100 fs process corresponds to internal conversion in the singlet manifolds. Intersystem crossing, instead, takes place on a longer time scale of ∼1 ps. The dynamics simulations further reveal that the spin transitions occur via two distinct pathways with different contribution for the three systems, which are determined by electronic factors and the torsion of the nitro group. This study, therefore, indicates that the existence of sub-picosecond intersystem crossing in other nitroaromatic molecules should be questioned.

Robust presurgical functional MRI at 7 T using response consistency

Functional MRI is valuable in presurgical planning due to its non-invasive nature, repeatability, and broad availability. Using ultra-high field MRI increases the specificity and sensitivity, increasing the localization reliability and reducing scan time. Ideally, fMRI analysis for this application should identify unreliable runs and work even if the patient deviates from the prescribed task timing or if there are changes to the hemodynamic response due to pathology. In this study, a model-free analysis method-UNBIASED-based on the consistency of fMRI responses over runs was applied, to ultra-high field fMRI localizations of the hand area. Ten patients with brain tumors and epilepsy underwent 7 Tesla fMRI with multiple runs of a hand motor task in a block design. FMRI data were analyzed with the proposed approach (UNBIASED) and the conventional General Linear Model (GLM) approach. UNBIASED correctly identified and excluded fMRI runs that contained little or no activation. Generally, less motion artifact contamination was present in UNBIASED than in GLM results. Some cortical regions were identified as activated in UNBIASED but not GLM results. These were confirmed to show reproducible delayed or transient activation, which was time-locked to the task. UNBIASED is a robust approach to generating activation maps without the need for assumptions about response timing or shape. In presurgical planning, UNBIASED can complement model-based methods to aid surgeons in making prudent choices about optimal surgical access and resection margins for each patient, even if the hemodynamic response is modified by pathology. Hum Brain Mapp 38:3163-3174, 2017. © 2017 The Authors Human Brain Mapping Published by Wiley Periodicals, Inc.