TY - JOUR A1 - Nitze, Ingmar A1 - Grosse, Guido A1 - Jones, Benjamin M. A1 - Romanovsky, Vladimir E. A1 - Boike, Julia T1 - Remote sensing quantifies widespread abundance of permafrost region disturbances across the Arctic and Subarctic JF - Nature Communications N2 - Local observations indicate that climate change and shifting disturbance regimes are causing permafrost degradation. However, the occurrence and distribution of permafrost region disturbances (PRDs) remain poorly resolved across the Arctic and Subarctic. Here we quantify the abundance and distribution of three primary PRDs using time-series analysis of 30-m resolution Landsat imagery from 1999 to 2014. Our dataset spans four continental-scale transects in North America and Eurasia, covering similar to 10% of the permafrost region. Lake area loss (-1.45%) dominated the study domain with enhanced losses occurring at the boundary between discontinuous and continuous permafrost regions. Fires were the most extensive PRD across boreal regions (6.59%), but in tundra regions (0.63%) limited to Alaska. Retrogressive thaw slumps were abundant but highly localized (< 10(-5)%). Our analysis synergizes the global-scale importance of PRDs. The findings highlight the need to include PRDs in next-generation land surface models to project the permafrost carbon feedback. Y1 - 2018 U6 - https://doi.org/10.1038/s41467-018-07663-3 SN - 2041-1723 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Fritz, Michael Andre A1 - Rosa, Stefanie A1 - Sicard, Adrien T1 - Mechanisms Underlying the Environmentally Induced Plasticity of Leaf Morphology JF - Frontiers in genetics N2 - The primary function of leaves is to provide an interface between plants and their environment for gas exchange, light exposure and thermoregulation. Leaves have, therefore a central contribution to plant fitness by allowing an efficient absorption of sunlight energy through photosynthesis to ensure an optimal growth. Their final geometry will result from a balance between the need to maximize energy uptake while minimizing the damage caused by environmental stresses. This intimate relationship between leaf and its surroundings has led to an enormous diversification in leaf forms. Leaf shape varies between species, populations, individuals or even within identical genotypes when those are subjected to different environmental conditions. For instance, the extent of leaf margin dissection has, for long, been found to inversely correlate with the mean annual temperature, such that Paleobotanists have used models based on leaf shape to predict the paleoclimate from fossil flora. Leaf growth is not only dependent on temperature but is also regulated by many other environmental factors such as light quality and intensity or ambient humidity. This raises the question of how the different signals can be integrated at the molecular level and converted into clear developmental decisions. Several recent studies have started to shed the light on the molecular mechanisms that connect the environmental sensing with organ-growth and patterning. In this review, we discuss the current knowledge on the influence of different environmental signals on leaf size and shape, their integration as well as their importance for plant adaptation. KW - plants KW - leaf morphology KW - environment KW - developmental plasticity KW - gene regulatory networks KW - sensory system KW - gene responsiveness Y1 - 2018 U6 - https://doi.org/10.3389/fgene.2018.00478 SN - 1664-8021 VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Walther, Sophia A1 - Guanter, Luis A1 - Heim, Birgit A1 - Jung, Martin A1 - Duveiller, Gregory A1 - Wolanin, Aleksandra A1 - Sachs, Torsten T1 - Assessing the dynamics of vegetation productivity in circumpolar regions with different satellite indicators of greenness and photosynthesis JF - Biogeosciences N2 - High-latitude treeless ecosystems represent spatially highly heterogeneous landscapes with small net carbon fluxes and a short growing season. Reliable observations and process understanding are critical for projections of the carbon balance of the climate-sensitive tundra. Space-borne remote sensing is the only tool to obtain spatially continuous and temporally resolved information on vegetation greenness and activity in remote circumpolar areas. However, confounding effects from persistent clouds, low sun elevation angles, numerous lakes, widespread surface inundation, and the sparseness of the vegetation render it highly challenging. Here, we conduct an extensive analysis of the timing of peak vegetation productivity as shown by satellite observations of complementary indicators of plant greenness and photosynthesis. We choose to focus on productivity during the peak of the growing season, as it importantly affects the total annual carbon uptake. The suite of indicators are as follows: (1) MODIS-based vegetation indices (VIs) as proxies for the fraction of incident photosynthetically active radiation (PAR) that is absorbed (fPAR), (2) VIs combined with estimates of PAR as a proxy of the total absorbed radiation (APAR), (3) sun-induced chlorophyll fluorescence (SIF) serving as a proxy for photosynthesis, (4) vegetation optical depth (VOD), indicative of total water content and (5) empirically upscaled modelled gross primary productivity (GPP). Averaged over the pan-Arctic we find a clear order of the annual peak as APAR <= GPP < SIF < VIs/VOD. SIF as an indicator of photosynthesis is maximised around the time of highest annual temperatures. The modelled GPP peaks at a similar time to APAR. The time lag of the annual peak between APAR and instantaneous SIF fluxes indicates that the SIF data do contain information on light-use efficiency of tundra vegetation, but further detailed studies are necessary to verify this. Delayed peak greenness compared to peak photosynthesis is consistently found across years and land-cover classes. A particularly late peak of the normalised difference vegetation index (NDVI) in regions with very small seasonality in greenness and a high amount of lakes probably originates from artefacts. Given the very short growing season in circumpolar areas, the average time difference in maximum annual photosynthetic activity and greenness or growth of 3 to 25 days (depending on the data sets chosen) is important and needs to be considered when using satellite observations as drivers in vegetation models. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-6221-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 20 SP - 6221 EP - 6256 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Kaboth-Bahr, Stefanie A1 - Bahr, André A1 - Zeeden, Christian A1 - Yamoah, Kweku A. A1 - Lone, Mahjoor Ahmad A1 - Chuang, Chih-Kai A1 - Löwemark, Ludvig A1 - Wei, Kuo-Yen T1 - A tale of shifting relations BT - East Asian summer and winter monsoon variability during the Holocene JF - Scientific Reports N2 - Understanding the dynamics between the East Asian summer (EASM) and winter monsoon (EAWM) is needed to predict their variability under future global warming scenarios. Here, we investigate the relationship between EASM and EAWM as well as the mechanisms driving their variability during the last 10,000 years by stacking marine and terrestrial (non-speleothem) proxy records from the East Asian realm. This provides a regional and proxy independent signal for both monsoonal systems. The respective signal was subsequently analysed using a linear regression model. We find that the phase relationship between EASM and EAWM is not time-constant and significantly depends on orbital configuration changes. In addition, changes in the Atlantic Meridional Overturning circulation, Arctic sea-ice coverage, El Niño-Southern Oscillation and Sun Spot numbers contributed to millennial scale changes in the EASM and EAWM during the Holocene. We also argue that the bulk signal of monsoonal activity captured by the stacked non-speleothem proxy records supports the previously argued bias of speleothem climatic archives to moisture source changes and/or seasonality. KW - Environmental sciences KW - Ocean sciences KW - Solid Earth sciences Y1 - 2020 U6 - https://doi.org/10.1038/s41598-021-85444-7 SN - 2045-2322 VL - 11 PB - Macmillan Publishers Limited, part of Springer Nature CY - London ER - TY - JOUR A1 - Schaal, Frederik A1 - Rutloh, Michael A1 - Weidenfeld, Susanne A1 - Stumpe, Joachim A1 - Michler, Peter A1 - Pruss, Christof A1 - Osten, Wolfgang T1 - Optically addressed modulator for tunable spatial polarization control JF - Optics express : the international electronic journal of optics N2 - We present an optically addressed non-pixelated spatial light modulator. The system is based on reversible photoalignment of a LC cell using a red light sensitive novel azobenzene photoalignment layer. It is an electrode-free device that manipulates the liquid crystal orientation and consequently the polarization via light without artifacts caused by electrodes. The capability to miniaturize the spatial light modulator allows the integration into a microscope objective. This includes a miniaturized 200 channel optical addressing system based on a VCSEL array and hybrid refractive-diffractive beam shapers. As an application example, the utilization as a microscope objective integrated analog phase contrast modulator is shown. (C) 2018 Optical Society of America under the terms of the OSA Open Access Publishing Agreement Y1 - 2018 U6 - https://doi.org/10.1364/OE.26.028119 SN - 1094-4087 VL - 26 IS - 21 SP - 28119 EP - 28130 PB - Optical Society of America CY - Washington ER - TY - JOUR A1 - Pourteau, Amaury A1 - Scherer, Erik E. A1 - Schorn, Simon A1 - Bast, Rebecca A1 - Schmidt, Alexander A1 - Ebert, Lisa T1 - Thermal evolution of an ancient subduction interface revealed by Lu-Hf garnet geochronology, Halilbagi Complex (Anatolia) JF - Geoscience Frontiers N2 - The thermal structure of subduction zones exerts a major influence on deep-seated mechanical and chemical processes controlling arc magmatism, seismicity, and global element cycles. Accretionary complexes exposed inland may comprise tectonic blocks with contrasting pressure-temperature (P-T) histories, making it possible to investigate the dynamics and thermal evolution of former subduction interfaces. With this aim, we present new Lu-Hf geochronological results for mafic rocks of the Halilbagi Complex (Anatolia) that evolved along different thermal gradients. Samples include a lawsonite-epidote blueschist, a lawsonite-epidote eclogite, and an epidote eclogite (all with counter-clockwise P-T paths), a prograde lawsonite blueschist with a "hairpin"-type P-T path, and a garnet amphibolite from the overlying sub-ophiolitic metamorphic sole. Equilibrium phase diagrams suggest that the garnet amphibolite formed at similar to 0.6-0.7 GPa and 800-850 degrees C, whereas the prograde lawsonite blueschist records burial from 2.1 GPa and 420 degrees C to 2.6 GPa and 520 degrees C. Well-defined Lu-Hf isochrons were obtained for the epidote eclogite (92.38 +/- 0.22 Ma) and the lawsonite-epidote blueschist (90.19 +/- 0.54 Ma), suggesting rapid garnet growth. The lawsonite-epidote eclogite (87.30 +/- 0.39 Ma) and the prograde lawsonite blueschist (ca. 86 Ma) are younger, whereas the garnet amphibolite (104.5 +/- 3.5 Ma) is older. Our data reveal a consistent trend of progressively decreasing geothermal gradient from granulite-facies conditions at similar to 104 Ma to the epidote-eclogite facies around 92 Ma, and the lawsonite blueschist-facies between 90 Ma and 86 Ma. Three Lu-Hf garnet dates (between 92 Ma and 87 Ma) weighted toward the growth of post-peak rims (as indicated by Lu distribution in garnet) suggest that the HP/LT rocks were exhumed continuously and not episodically. We infer that HP/LT metamorphic rocks within the Halilbagi Complex were subjected to continuous return flow, with "warm" rocks being exhumed during the tectonic burial of "cold" ones. Our results, combined with regional geological constraints, allow us to speculate that subduction started at a transform fault near a mid-oceanic spreading centre. Following its formation, this ancient subduction interface evolved thermally over more than 15 Myr, most likely as a result of heat dissipation rather than crustal underplating. (C) 2018, China University of Geosciences (Beijing) and Peking University. Production and hosting by Elsevier B.V. KW - Subduction KW - Lu/Hf dating of garnet KW - Metamorphic sole KW - Eclogite KW - Blueschist KW - Lawsonite Y1 - 2019 U6 - https://doi.org/10.1016/j.gsf.2018.03.004 SN - 1674-9871 VL - 10 IS - 1 SP - 127 EP - 148 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Foster, William J. A1 - Heindel, Katrin A1 - Richoz, Sylvain A1 - Gliwa, Jana A1 - Lehrmann, Daniel J. A1 - Baud, Aymon A1 - Kolar-Jurkovsek, Tea A1 - Aljinovic, Dunja A1 - Jurkovsek, Bogdan A1 - Korn, Dieter A1 - Martindale, Rowan C. A1 - Peckmann, Jörn T1 - Suppressed competitive exclusion enabled the proliferation of Permian/Triassic boundary microbialites JF - The Depositional Record : the open access journal of the International Association of Sedimentologists N2 - During the earliest Triassic microbial mats flourished in the photic zones of marginal seas, generating widespread microbialites. It has been suggested that anoxic conditions in shallow marine environments, linked to the end-Permian mass extinction, limited mat-inhibiting metazoans allowing for this microbialite expansion. The presence of a diverse suite of proxies indicating oxygenated shallow sea-water conditions (metazoan fossils, biomarkers and redox proxies) from microbialite successions have, however, challenged the inference of anoxic conditions. Here, the distribution and faunal composition of Griesbachian microbialites from China, Iran, Turkey, Armenia, Slovenia and Hungary are investigated to determine the factors that allowed microbialite-forming microbial mats to flourish following the end-Permian crisis. The results presented here show that Neotethyan microbial buildups record a unique faunal association due to the presence of keratose sponges, while the Palaeotethyan buildups have a higher proportion of molluscs and the foraminifera Earlandia. The distribution of the faunal components within the microbial fabrics suggests that, except for the keratose sponges and some microconchids, most of the metazoans were transported into the microbial framework via wave currents. The presence of both microbialites and metazoan associations were limited to oxygenated settings, suggesting that a factor other than anoxia resulted in a relaxation of ecological constraints following the mass extinction event. It is inferred that the end-Permian mass extinction event decreased the diversity and abundance of metazoans to the point of significantly reducing competition, allowing photosynthesis-based microbial mats to flourish in shallow water settings and resulting in the formation of widespread microbialites. KW - Competitive exclusion KW - Permian KW - Triassic KW - mass extinction KW - microbialites KW - palaeoecology Y1 - 2019 U6 - https://doi.org/10.1002/dep2.97 SN - 2055-4877 VL - 6 IS - 1 SP - 62 EP - 74 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Schmälzlin, Elmar Gerd A1 - Moralejo, Benito A1 - Gersonde, Ingo A1 - Schleusener, Johannes A1 - Darvin, Maxim E. A1 - Thiede, Gisela A1 - Roth, Martin M. T1 - Nonscanning large-area Raman imaging for ex vivo/in vivo skin cancer discrimination JF - Journal of biomedical optics N2 - Imaging Raman spectroscopy can be used to identify cancerous tissue. Traditionally, a step-by-step scanning of the sample is applied to generate a Raman image, which, however, is too slow for routine examination of patients. By transferring the technique of integral field spectroscopy (IFS) from astronomy to Raman imaging, it becomes possible to record entire Raman images quickly within a single exposure, without the need for a tedious scanning procedure. An IFS-based Raman imaging setup is presented, which is capable of measuring skin ex vivo or in vivo. It is demonstrated how Raman images of healthy and cancerous skin biopsies were recorded and analyzed. (C) The Authors. Published by SPIE under a Creative Commons Attribution 3.0 Unported License. KW - Raman spectroscopy KW - cancer diagnosis KW - Raman imaging KW - multichannel KW - astronomy KW - epidermis KW - dermis Y1 - 2018 U6 - https://doi.org/10.1117/1.JBO.23.10.105001 SN - 1083-3668 SN - 1560-2281 VL - 23 IS - 10 PB - SPIE CY - Bellingham ER - TY - JOUR A1 - Mann, Michael E. A1 - Rahmstorf, Stefan A1 - Kornhuber, Kai A1 - Steinman, Byron A. A1 - Miller, Sonya K. A1 - Petri, Stefan A1 - Coumou, Dim T1 - Projected changes in persistent extreme summer weather events BT - The role of quasi-resonant amplification JF - Science Advances N2 - Persistent episodes of extreme weather in the Northern Hemisphere summer have been associated with high-amplitude quasi-stationary atmospheric Rossby waves, with zonal wave numbers 6 to 8 resulting from the phenomenon of quasi-resonant amplification (QRA). A fingerprint for the occurrence of QRA can be defined in terms of the zonally averaged surface temperature field. Examining state-of-the-art [Coupled Model Intercomparison Project Phase 5 (CMIP5)] climate model projections, we find that QRA events are likely to increase by similar to 50% this century under business-as-usual carbon emissions, but there is considerable variation among climate models. Some predict a near tripling of QRA events by the end of the century, while others predict a potential decrease. Models with amplified Arctic warming yield the most pronounced increase in QRA events. The projections are strongly dependent on assumptions regarding the nature of changes in radiative forcing associated with anthropogenic aerosols over the next century. One implication of our findings is that a reduction in midlatitude aerosol loading could actually lead to Arctic de-amplification this century, ameliorating potential increases in persistent extreme weather events. Y1 - 2018 U6 - https://doi.org/10.1126/sciadv.aat3272 SN - 2375-2548 VL - 4 IS - 10 PB - American Assoc. for the Advancement of Science CY - Washington ER - TY - GEN A1 - Kleuser, Burkhard T1 - The enigma of sphingolipids in health and disease T2 - International journal of molecular sciences Y1 - 2018 U6 - https://doi.org/10.3390/ijms19103126 SN - 1422-0067 VL - 19 IS - 10 PB - MDPI CY - Basel ER - TY - JOUR A1 - Mainka, Stefan A1 - Wissel, Jörg A1 - Völler, Heinz A1 - Evers, Stefan T1 - The Use of Rhythmic Auditory Stimulation to Optimize Treadmill Training for Stroke Patients BT - a randomized controlled trial JF - Frontiers in Neurology N2 - The use of functional music in gait training termed rhythmic auditory stimulation (RAS) and treadmill training (TT) have both been shown to be effective in stroke patients (SP). The combination of RAS and treadmill training (RAS-TT) has not been clinically evaluated to date. The aim of the study was to evaluate the efficacy of RAS-TT on functional gait in SR The protocol followed the design of an explorative study with a rater-blinded three arm prospective randomized controlled parallel group design. Forty-five independently walking SP with a hemiparesis of the lower limb or an unsafe and asymmetrical walking pattern were recruited. RAS-TT was carried out over 4 weeks with TT and neurodevelopmental treatment based on Bobath approach (NDT) serving as control interventions. For RAS-TT functional music was adjusted individually while walking on the treadmill. Pre and post-assessments consisted of the fast gait speed test (FGS), a gait analysis with the locometre (LOC), 3 min walking time test (3MWT), and an instrumental evaluation of balance (IEB). Raters were blinded to group assignments. An analysis of covariance (ANCOVA) was performed with affiliated measures from pre-assessment and time between stroke and start of study as covariates. Thirty-five participants (mean age 63.6 +/- 8.6 years, mean time between stroke and start of study 42.1 +/- 23.7 days) completed the study (11 RAS-TT, 13 TT, 11 NDT). Significant group differences occurred in the FGS for adjusted post-measures in gait velocity [F-(2,F- (34)) = 3.864, p = 0.032; partial eta(2) = 0.205] and cadence [F-(2,F- 34) = 7.656, p = 0.002; partial eta(2) = 0.338]. Group contrasts showed significantly higher values for RAS-TT. Stride length results did not vary between the groups. LOC, 3MWT, and IEB did not indicate group differences. One patient was withdrawn from TT because of pain in one arm. The study provides first evidence for a higher efficacy of RAS-TT in comparison to the standard approaches TT and NDT in restoring functional gait in SP. The results support the implementation of functional music in neurological gait rehabilitation and its use in combination with treadmill training. KW - stroke rehabilitation KW - exercise movement techniques KW - music therapy KW - music KW - gait Y1 - 2018 U6 - https://doi.org/10.3389/fneur.2018.00755 SN - 1664-2295 VL - 9 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Pauly, Maren A1 - Helle, Gerhard A1 - Miramont, Cecile A1 - Buentgen, Ulf A1 - Treydte, Kerstin A1 - Reinig, Frederick A1 - Guibal, Frederic A1 - Sivan, Olivier A1 - Heinrich, Ingo A1 - Riedel, Frank A1 - Kromer, Bernd A1 - Balanzategui, Daniel A1 - Wacker, Lukas A1 - Sookdeo, Adam A1 - Brauer, Achim T1 - Subfossil trees suggest enhanced Mediterranean hydroclimate variability at the onset of the Younger Dryas JF - Scientific reports N2 - Nearly 13,000 years ago, the warming trend into the Holocene was sharply interrupted by a reversal to near glacial conditions. Climatic causes and ecological consequences of the Younger Dryas (YD) have been extensively studied, however proxy archives from the Mediterranean basin capturing this period are scarce and do not provide annual resolution. Here, we report a hydroclimatic reconstruction from stable isotopes (delta O-18, delta C-13) in subfossil pines from southern France. Growing before and during the transition period into the YD (12 900-12 600 cal BP), the trees provide an annually resolved, continuous sequence of atmospheric change. Isotopic signature of tree sourcewater (delta O-18(sw)) and estimates of relative air humidity were reconstructed as a proxy for variations in air mass origin and precipitation regime. We find a distinct increase in inter-annual variability of sourcewater isotopes (delta O-18(sw)), with three major downturn phases of increasing magnitude beginning at 12 740 cal BP. The observed variation most likely results from an amplified intensity of North Atlantic (low delta O-18(sw)) versus Mediterranean (high delta O-18(sw)) precipitation. This marked pattern of climate variability is not seen in records from higher latitudes and is likely a consequence of atmospheric circulation oscillations at the margin of the southward moving polar front. Y1 - 2018 U6 - https://doi.org/10.1038/s41598-018-32251-2 SN - 2045-2322 VL - 8 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Thapa, Samudrajit A1 - Wyłomańska, Agnieszka A1 - Sikora, Grzegorz A1 - Wagner, Caroline E. A1 - Krapf, Diego A1 - Kantz, Holger A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Leveraging large-deviation statistics to decipher the stochastic properties of measured trajectories JF - New Journal of Physics N2 - Extensive time-series encoding the position of particles such as viruses, vesicles, or individualproteins are routinely garnered insingle-particle tracking experiments or supercomputing studies.They contain vital clues on how viruses spread or drugs may be delivered in biological cells.Similar time-series are being recorded of stock values in financial markets and of climate data.Such time-series are most typically evaluated in terms of time-averaged mean-squareddisplacements (TAMSDs), which remain random variables for finite measurement times. Theirstatistical properties are different for differentphysical stochastic processes, thus allowing us toextract valuable information on the stochastic process itself. To exploit the full potential of thestatistical information encoded in measured time-series we here propose an easy-to-implementand computationally inexpensive new methodology, based on deviations of the TAMSD from itsensemble average counterpart. Specifically, we use the upper bound of these deviations forBrownian motion (BM) to check the applicability of this approach to simulated and real data sets.By comparing the probability of deviations fordifferent data sets, we demonstrate how thetheoretical bound for BM reveals additional information about observed stochastic processes. Weapply the large-deviation method to data sets of tracer beads tracked in aqueous solution, tracerbeads measured in mucin hydrogels, and of geographic surface temperature anomalies. Ouranalysis shows how the large-deviation properties can be efficiently used as a simple yet effectiveroutine test to reject the BM hypothesis and unveil relevant information on statistical propertiessuch as ergodicity breaking and short-time correlations. KW - diffusion KW - anomalous diffusion KW - large-deviation statistic KW - time-averaged mean squared displacement KW - Chebyshev inequality Y1 - 2020 U6 - https://doi.org/10.1088/1367-2630/abd50e SN - 1367-2630 VL - 23 PB - Dt. Physikalische Ges. ; IOP CY - Bad Honnef ; London ER - TY - JOUR A1 - Berry, Scott A1 - Rosa, Stefanie A1 - Howard, Martin A1 - Buhler, Marc A1 - Dean, Caroline T1 - Disruption of an RNA-binding hinge region abolishes LHP1-mediated epigenetic repression JF - Genes & Development N2 - Epigenetic maintenance of gene repression is essential for development. Polycomb complexes are central to this memory, but many aspects of the underlying mechanism remain unclear. LIKE HETEROCHROMATIN PROTEIN 1 (LHP1) binds Polycomb-deposited H3K27me3 and is required for repression of many Polycomb target genes in Arabidopsis. Here we show that LHP1 binds RNA in vitro through the intrinsically disordered hinge region. By independently perturbing the RNA-binding hinge region and H3K27me3 (trimethylation of histone H3 at Lys27) recognition, we found that both facilitate LHP1 localization and H3K27me3 maintenance. Disruption of the RNAbinding hinge region also prevented formation of subnuclear foci, structures potentially important for epigenetic repression. KW - chromatin KW - epigenetics KW - plant biology KW - Polycomb KW - RNA Y1 - 2017 U6 - https://doi.org/10.1101/gad.305227.117 SN - 0890-9369 SN - 1549-5477 VL - 31 SP - 2115 EP - 2120 PB - Cold Spring Harbor Laboratory Press CY - Cold Spring Harbor, NY ER - TY - JOUR A1 - Huck, Stefan A1 - Wohlwend, Stephan A1 - Coimbra, Rute A1 - Christ, Nicolas A1 - Weissert, Helmut T1 - Disentangling shallow-water bulk carbonate carbon isotope archives with evidence for multi-stage diagenesis BT - an in-depth component-specific petrographic and geochemical study from Oman (mid-Cretaceous) JF - The depositional record N2 - Disentangling shallow‐water bulk carbonate carbon isotope archives into primary and diagenetic components is a notoriously difficult task and even diagenetically screened records often provide chemostratigraphic patterns that significantly differ from global signals. This is mainly caused by the polygenetic nature of shallow‐water carbonate substrates, local carbon cycle processes causing considerable neritic–pelagic isotope gradients and the presence of hiatal surfaces resulting in extremely low carbonate preservation rates. Provided here is an in‐depth petrographic and geochemical evaluation of different carbonate phases of a mid‐Cretaceous (Barremian–Aptian) shallow‐water limestone succession (Jabal Madar section) deposited on the tropical Arabian carbonate platform in Oman. The superposition of stable isotope signatures of identified carbonate phases causes a complex and often noisy bulk carbon isotope pattern. Blocky sparite cements filling intergranular pores and bioclastic voids evidence intermediate to (arguably) deep burial diagenetic conditions during their formation, owing to different timing or differential faulting promoting the circulation of fluids from variable sources. In contrast, sparite cements filling sub‐vertical veins reveal a rock‐buffered diagenetic fluid composition with an intriguing moderate enrichment in 13C, probably due to fractionation during pressure release in the context of the Miocene exhumation of the carbonate platform under study. The presence of abundant, replacive dedolomite in mud‐supported limestone samples forced negative carbon and oxygen isotope changes that are either associated with the thermal breakdown of organic matter in the deep burial realm or the expulsion of buried meteoric water in the intermediate burial realm. Notwithstanding the documented stratigraphically variable and often facies‐related impact of different diagenetic fluids on the bulk‐rock stable isotope signature, the identification of diagenetic end‐members defined δ13C and δ18O threshold values that allowed the most reliable ‘primary’ bulk carbon isotope signatures to be extracted. Most importantly, this approach exemplifies how to place regional shallow‐water stable isotope patterns with evidence for a complex multi‐stage diagenetic history into a supraregional or even global context. KW - Arabian carbonate platform KW - Barremian-Aptian KW - multi-stage diagenesis KW - shallow-water chemostratigraphy Y1 - 2017 U6 - https://doi.org/10.1002/dep2.35 SN - 2055-4877 VL - 3 SP - 233 EP - 257 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Wendler, Petra A1 - Enenkel, Cordula T1 - Nuclear Transport of Yeast Proteasomes JF - Frontiers in molecular biosciences N2 - Proteasomes are key proteases in regulating protein homeostasis. Their holo-enzymes are composed of 40 different subunits which are arranged in a proteolytic core (CP) flanked by one to two regulatory particles (RP). Proteasomal proteolysis is essential for the degradation of proteins which control time-sensitive processes like cell cycle progression and stress response. In dividing yeast and human cells, proteasomes are primarily nuclear suggesting that proteasomal proteolysis is mainly required in the nucleus during cell proliferation. In yeast, which have a closed mitosis, proteasomes are imported into the nucleus as immature precursors via the classical import pathway. During quiescence, the reversible absence of proliferation induced by nutrient depletion or growth factor deprivation, proteasomes move from the nucleus into the cytoplasm. In the cytoplasm of quiescent yeast, proteasomes are dissociated into CP and RP and stored in membrane-less cytoplasmic foci, named proteasome storage granules (PSGs). With the resumption of growth, PSGs clear and mature proteasomes are transported into the nucleus by Blm10, a conserved 240 kDa protein and proteasome-intrinsic import receptor. How proteasomes are exported from the nucleus into the cytoplasm is unknown. KW - proteasome KW - nuclear transport KW - importin KW - karyopherin KW - Blm10 KW - proteasome storage granules Y1 - 2019 U6 - https://doi.org/10.3389/fmolb.2019.00034 SN - 2296-889X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Möser, Christin A1 - Lorenz, Jessica S. A1 - Sajfutdinow, Martin A1 - Smith, David M. T1 - Pinpointed Stimulation of EphA2 Receptors via DNA-Templated Oligovalence JF - International journal of molecular sciences N2 - DNA nanostructures enable the attachment of functional molecules to nearly any unique location on their underlying structure. Due to their single-base-pair structural resolution, several ligands can be spatially arranged and closely controlled according to the geometry of their desired target, resulting in optimized binding and/or signaling interactions. Here, the efficacy of SWL, an ephrin-mimicking peptide that binds specifically to EphrinA2 (EphA2) receptors, increased by presenting up to three of these peptides on small DNA nanostructures in an oligovalent manner. Ephrin signaling pathways play crucial roles in tumor development and progression. Moreover, Eph receptors are potential targets in cancer diagnosis and treatment. Here, the quantitative impact of SWL valency on binding, phosphorylation (key player for activation) and phenotype regulation in EphA2-expressing prostate cancer cells was demonstrated. EphA2 phosphorylation was significantly increased by DNA trimers carrying three SWL peptides compared to monovalent SWL. In comparison to one of EphA2’s natural ligands ephrin-A1, which is known to bind promiscuously to multiple receptors, pinpointed targeting of EphA2 by oligovalent DNA-SWL constructs showed enhanced cell retraction. Overall, we show that DNA scaffolds can increase the potency of weak signaling peptides through oligovalent presentation and serve as potential tools for examination of complex signaling pathways. KW - DNA nanostructure KW - ephrin KW - EphA2 KW - SWL KW - PC-3 cells KW - multivalence Y1 - 2018 U6 - https://doi.org/10.3390/ijms19113482 SN - 1422-0067 VL - 19 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Schwanhold, Nadine A1 - Iobbi-Nivol, Chantal A1 - Lehmann, Angelika A1 - Leimkühler, Silke T1 - Same but different BT - Comparison of two system-specific molecular chaperones for the maturation of formate dehydrogenases JF - PLoS one N2 - The maturation of bacterial molybdoenzymes is a complex process leading to the insertion of the bulky bis-molybdopterin guanine dinucleotide (bis-MGD) cofactor into the apoenzyme. Most molybdoenzymes were shown to contain a specific chaperone for the insertion of the bis-MGD cofactor. Formate dehydrogenases (FDH) together with their molecular chaperone partner seem to display an exception to this specificity rule, since the chaperone FdhD has been proven to be involved in the maturation of all three FDH enzymes present in Escherichia colt. Multiple roles have been suggested for FdhD-like chaperones in the past, including the involvement in a sulfur transfer reaction from the L-cysteine desulfurase IscS to bis-MGD by the action of two cysteine residues present in a conserved CXXC motif of the chaperones. However, in this study we show by phylogenetic analyses that the CXXC motif is not conserved among FdhD-like chaperones. We compared in detail the FdhD-like homologues from Rhodobacter capsulatus and E. colt and show that their roles in the maturation of FDH enzymes from different subgroups can be exchanged. We reveal that bis-MGDbinding is a common characteristic of FdhD-like proteins and that the cofactor is bound with a sulfido-ligand at the molybdenum atom to the chaperone. Generally, we reveal that the cysteine residues in the motif CXXC of the chaperone are not essential for the production of active FDH enzymes. Y1 - 2018 U6 - https://doi.org/10.1371/journal.pone.0201935 SN - 1932-6203 VL - 13 IS - 11 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Siddiqui, Tarique Adnan A1 - Maute, Astrid A1 - Pedatella, Nick A1 - Yamazaki, Yosuke A1 - Lühr, Hermann A1 - Stolle, Claudia T1 - On the variability of the semidiurnal solar and lunar tides of the equatorial electrojet during sudden stratospheric warmings JF - Annales geophysicae N2 - The variabilities of the semidiurnal solar and lunar tides of the equatorial electrojet (EEJ) are investigated during the 2003, 2006, 2009 and 2013 major sudden stratospheric warming (SSW) events in this study. For this purpose, ground-magnetometer recordings at the equatorial observatories in Huancayo and Fuquene are utilized. Results show a major enhancement in the amplitude of the EEJ semidiurnal lunar tide in each of the four warming events. The EEJ semidiurnal solar tidal amplitude shows an amplification prior to the onset of warmings, a reduction during the deceleration of the zonal mean zonal wind at 60 degrees N and 10 hPa, and a second enhancement a few days after the peak reversal of the zonal mean zonal wind during all four SSWs. Results also reveal that the amplitude of the EEJ semidiurnal lunar tide becomes comparable or even greater than the amplitude of the EEJ semidiurnal solar tide during all these warming events. The present study also compares the EEJ semidiurnal solar and lunar tidal changes with the variability of the migrating semidiurnal solar (SW2) and lunar (M2) tides in neutral temperature and zonal wind obtained from numerical simulations at E-region heights. A better agreement between the enhancements of the EEJ semidiurnal lunar tide and the M2 tide is found in comparison with the enhancements of the EEJ semidiurnal solar tide and the SW2 tide in both the neutral temperature and zonal wind at the E-region altitudes. Y1 - 2018 U6 - https://doi.org/10.5194/angeo-36-1545-2018 SN - 0992-7689 SN - 1432-0576 VL - 36 IS - 6 SP - 1545 EP - 1562 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Rosenbaum, Benjamin A1 - Raatz, Michael A1 - Weithoff, Guntram A1 - Fussmann, Gregor F. A1 - Gaedke, Ursula T1 - Estimating parameters from multiple time series of population dynamics using bayesian inference JF - Frontiers in ecology and evolution N2 - Empirical time series of interacting entities, e.g., species abundances, are highly useful to study ecological mechanisms. Mathematical models are valuable tools to further elucidate those mechanisms and underlying processes. However, obtaining an agreement between model predictions and experimental observations remains a demanding task. As models always abstract from reality one parameter often summarizes several properties. Parameter measurements are performed in additional experiments independent of the ones delivering the time series. Transferring these parameter values to different settings may result in incorrect parametrizations. On top of that, the properties of organisms and thus the respective parameter values may vary considerably. These issues limit the use of a priori model parametrizations. In this study, we present a method suited for a direct estimation of model parameters and their variability from experimental time series data. We combine numerical simulations of a continuous-time dynamical population model with Bayesian inference, using a hierarchical framework that allows for variability of individual parameters. The method is applied to a comprehensive set of time series from a laboratory predator-prey system that features both steady states and cyclic population dynamics. Our model predictions are able to reproduce both steady states and cyclic dynamics of the data. Additionally to the direct estimates of the parameter values, the Bayesian approach also provides their uncertainties. We found that fitting cyclic population dynamics, which contain more information on the process rates than steady states, yields more precise parameter estimates. We detected significant variability among parameters of different time series and identified the variation in the maximum growth rate of the prey as a source for the transition from steady states to cyclic dynamics. By lending more flexibility to the model, our approach facilitates parametrizations and shows more easily which patterns in time series can be explained also by simple models. Applying Bayesian inference and dynamical population models in conjunction may help to quantify the profound variability in organismal properties in nature. KW - Bayesian inference KW - chemostat experiments KW - ordinary differential equation KW - parameter estimation KW - population dynamics KW - predator prey KW - time series analysis KW - trait variability Y1 - 2019 U6 - https://doi.org/10.3389/fevo.2018.00234 SN - 2296-701X VL - 6 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Kruse, Julia A1 - Kummer, Volker A1 - Shivas, Roger G. A1 - Thines, Marco T1 - The first smut fungus, Thecaphora anthemidis sp nov (Glomosporiaceae), described from Anthemis (Asteraceae) JF - MycoKeys N2 - There are 63 known species of Thecaphora (Glomosporiaceae, Ustilaginomycotina), a third of which occur on Asteraceae. These smut fungi produce yellowish-brown to reddish-brown masses of spore balls in specific, mostly regenerative, plant organs. A species of Thecaphora was collected in the flower heads of Anthemis chia (Anthemideae, Asteraceae) on Rhodes Island, Greece, in 2015 and 2017, which represents the first smut record of a smut fungus on a host plant species in this tribe. Based on its distinctive morphology, host species and genetic divergence, this species is described as Thecaphora anthemidis sp. nov. Molecular barcodes of the ITS region are provided for this and several other species of Thecaphora. A phylogenetic and morphological comparison to closely related species showed that Th. anthemidis differed from other species of Thecaphora. Thecaphora anthemidis produced loose spore balls in the flower heads and peduncles of Anthemis chia unlike other flower-infecting species. KW - Glomosporiaceae KW - host specificity KW - internal transcribed spacer KW - molecular phylogenetics KW - smut fungi Y1 - 2018 U6 - https://doi.org/10.3897/mycokeys.41.28454 SN - 1314-4057 SN - 1314-4049 IS - 41 SP - 39 EP - 50 PB - Pensoft Publ. CY - Sofia ER - TY - JOUR A1 - Manzoni, Stefano A1 - Capek, Petr A1 - Porada, Philipp A1 - Thurner, Martin A1 - Winterdahl, Mattias A1 - Beer, Christian A1 - Bruchert, Volker A1 - Frouz, Jan A1 - Herrmann, Anke M. A1 - Lindahl, Bjorn D. A1 - Lyon, Steve W. A1 - Šantrůčková, Hana A1 - Vico, Giulia A1 - Way, Danielle T1 - Reviews and syntheses BT - Carbon use efficiency from organisms to ecosystems - definitions, theories, and empirical evidence JF - Biogeosciences N2 - The cycling of carbon (C) between the Earth surface and the atmosphere is controlled by biological and abiotic processes that regulate C storage in biogeochemical compartments and release to the atmosphere. This partitioning is quantified using various forms of C-use efficiency (CUE) - the ratio of C remaining in a system to C entering that system. Biological CUE is the fraction of C taken up allocated to biosynthesis. In soils and sediments, C storage depends also on abiotic processes, so the term C-storage efficiency (CSE) can be used. Here we first review and reconcile CUE and CSE definitions proposed for autotrophic and heterotrophic organisms and communities, food webs, whole ecosystems and watersheds, and soils and sediments using a common mathematical framework. Second, we identify general CUE patterns; for example, the actual CUE increases with improving growth conditions, and apparent CUE decreases with increasing turnover. We then synthesize > 5000CUE estimates showing that CUE decreases with increasing biological and ecological organization - from uni-cellular to multicellular organisms and from individuals to ecosystems. We conclude that CUE is an emergent property of coupled biological-abiotic systems, and it should be regarded as a flexible and scale-dependent index of the capacity of a given system to effectively retain C. Y1 - 2018 U6 - https://doi.org/10.5194/bg-15-5929-2018 SN - 1726-4170 SN - 1726-4189 VL - 15 IS - 19 SP - 5929 EP - 5949 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Risbey, James S. A1 - Lewandowsky, Stephan A1 - Cowtan, Kevin A1 - Oreskes, Naomi A1 - Rahmstorf, Stefan A1 - Jokimäki, Ari A1 - Foster, Grant T1 - A fluctuation in surface temperature in historical context BT - reassessment and retrospective on the evidence JF - Environmental research letters N2 - This work reviews the literature on an alleged global warming 'pause' in global mean surface temperature (GMST) to determine how it has been defined, what time intervals are used to characterise it, what data are used to measure it, and what methods used to assess it. We test for 'pauses', both in the normally understood meaning of the term to mean no warming trend, as well as for a 'pause' defined as a substantially slower trend in GMST. The tests are carried out with the historical versions of GMST that existed for each pause-interval tested, and with current versions of each of the GMST datasets. The tests are conducted following the common (but questionable) practice of breaking the linear fit at the start of the trend interval ('broken' trends), and also with trends that are continuous with the data bordering the trend interval. We also compare results when appropriate allowance is made for the selection bias problem. The results show that there is little or no statistical evidence for a lack of trend or slower trend in GMST using either the historical data or the current data. The perception that there was a 'pause' in GMST was bolstered by earlier biases in the data in combination with incomplete statistical testing. KW - climate variability KW - climate trends KW - temperature fluctuation KW - pause hiatus Y1 - 2018 U6 - https://doi.org/10.1088/1748-9326/aaf342 SN - 1748-9326 VL - 13 IS - 12 PB - IOP Publ. Ltd. CY - Bristol ER - TY - JOUR A1 - Perkins, Daniel M. A1 - Perna, Andrea A1 - Adrian, Rita A1 - Cermeno, Pedro A1 - Gaedke, Ursula A1 - Huete-Ortega, Maria A1 - White, Ethan P. A1 - Yvon-Durocher, Gabriel T1 - Energetic equivalence underpins the size structure of tree and phytoplankton communities JF - Nature Communications N2 - The size structure of autotroph communities - the relative abundance of small vs. large individuals - shapes the functioning of ecosystems. Whether common mechanisms underpin the size structure of unicellular and multicellular autotrophs is, however, unknown. Using a global data compilation, we show that individual body masses in tree and phytoplankton communities follow power-law distributions and that the average exponents of these individual size distributions (ISD) differ. Phytoplankton communities are characterized by an average ISD exponent consistent with three-quarter-power scaling of metabolism with body mass and equivalence in energy use among mass classes. Tree communities deviate from this pattern in a manner consistent with equivalence in energy use among diameter size classes. Our findings suggest that whilst universal metabolic constraints ultimately underlie the emergent size structure of autotroph communities, divergent aspects of body size (volumetric vs. linear dimensions) shape the ecological outcome of metabolic scaling in forest vs. pelagic ecosystems. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-018-08039-3 SN - 2041-1723 VL - 10 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Wickert, Andrew D. A1 - Schildgen, Taylor F. T1 - Long-profile evolution of transport-limited gravel-bed rivers JF - Earth surface dynamics N2 - Alluvial and transport-limited bedrock rivers constitute the majority of fluvial systems on Earth. Their long profiles hold clues to their present state and past evolution. We currently possess first-principles-based governing equations for flow, sediment transport, and channel morphodynamics in these systems, which we lack for detachment-limited bedrock rivers. Here we formally couple these equations for transport-limited gravel-bed river long-profile evolution. The result is a new predictive relationship whose functional form and parameters are grounded in theory and defined through experimental data. From this, we produce a power-law analytical solution and a finite-difference numerical solution to long-profile evolution. Steady-state channel concavity and steepness are diagnostic of external drivers: concavity decreases with increasing uplift rate, and steepness increases with an increasing sediment-to-water supply ratio. Constraining free parameters explains common observations of river form: to match observed channel concavities, gravel-sized sediments must weather and fine - typically rapidly - and valleys typically should widen gradually. To match the empirical square-root width-discharge scaling in equilibrium-width gravel-bed rivers, downstream fining must occur. The ability to assign a cause to such observations is the direct result of a deductive approach to developing equations for landscape evolution. Y1 - 2019 U6 - https://doi.org/10.5194/esurf-7-17-2019 SN - 2196-6311 SN - 2196-632X VL - 7 IS - 1 SP - 17 EP - 43 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Uber, Magdalena A1 - Vandervaere, Jean-Pierre A1 - Zin, Isabella A1 - Braud, Isabelle A1 - Heistermann, Maik A1 - Legout, Cedric A1 - Molinie, Gilles A1 - Nord, Guillaume T1 - How does initial soil moisture influence the hydrological response? A case study from southern France JF - Hydrology and earth system sciences : HESS N2 - The phi(ev) is calculated from high-resolution discharge and precipitation data for several rain events with a cumulative precipitation P-cum ranging from less than 5mm to more than 80 mm. Because of the high uncertainty of phi(ev) associated with the hydrograph separation method, phi(ev) is calculated with several methods, including graphical methods, digital filters and a tracer-based method. The results indicate that the hydrological response depends on (theta) over bar (ini): during dry conditions phi(ev) is consistently below 0.1, even for events with high and intense precipitation. Above a threshold of (theta) over bar (ini) = 34 vol % phi(ev) can reach values up to 0.99 but there is a high scatter. Some variability can be explained with a weak correlation of phi(ev) with P-cum and rain intensity, but a considerable part of the variability remains unexplained. It is concluded that threshold-based methods can be helpful to prevent overestimation of the hydrological response during dry catchment conditions. The impact of soil moisture on the hydrological response during wet catchment conditions, however, is still insufficiently understood and cannot be generalized based on the present results. Y1 - 2018 U6 - https://doi.org/10.5194/hess-22-6127-2018 SN - 1027-5606 SN - 1607-7938 VL - 22 IS - 12 SP - 6127 EP - 6146 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Milewski, Robert A1 - Chabrillat, Sabine A1 - Behling, Robert T1 - Analyses of Recent Sediment Surface Dynamic of a Namibian Kalahari Salt Pan Based on Multitemporal Landsat and Hyperspectral Hyperion Data JF - Remote Sensing N2 - This study combines spaceborne multitemporal and hyperspectral data to analyze the spatial distribution of surface evaporite minerals and changes in a semi-arid depositional environment associated with episodic flooding events, the Omongwa salt pan (Kalahari, Namibia). The dynamic of the surface crust is evaluated by a change-detection approach using the Iterative-reweighted Multivariate Alteration Detection (IR-MAD) based on the Landsat archive imagery from 1984 to 2015. The results show that the salt pan is a highly dynamic and heterogeneous landform. A change gradient is observed from very stable pan border to a highly dynamic central pan. On the basis of hyperspectral EO-1 Hyperion images, the current distribution of surface evaporite minerals is characterized using Spectral Mixture Analysis (SMA). Assessment of field and image endmembers revealed that the pan surface can be categorized into three major crust types based on diagnostic absorption features and mineralogical ground truth data. The mineralogical crust types are related to different zones of surface change as well as pan morphology that influences brine flow during the pan inundation and desiccation cycles. These combined information are used to spatially map depositional environments where the more dynamic halite crust concentrates in lower areas although stable gypsum and calcite/sepiolite crusts appear in higher elevated areas. KW - salt pan KW - playa KW - hyperspectral KW - multitemporal KW - change detection KW - evaporite minerals Y1 - 2016 U6 - https://doi.org/10.3390/rs9020170 SN - 2072-4292 VL - 9 IS - 2 PB - MDPI CY - Basel ER - TY - JOUR A1 - Schinköth, Michaela A1 - Brand, Ralf T1 - Automatic associations and the affective valuation of exercise BT - disentangling the type-1 process of the affective–reflective theory of physical inactivity and exercise JF - German Journal of Exercise and Sport Research N2 - The decision to exercise is not only bound to rational considerations but also automatic affective processes. The affective–reflective theory of physical inactivity and exercise (ART) proposes a theoretical framework for explaining how the automatic affective process (type‑1 process) will influence exercise behavior, i.e., through the automatic activation of exercise-related associations and a subsequent affective valuation of exercise. This study aimed to empirically test this assumption of the ART with data from 69 study participants. A single-measurement study, including within-subject experimental variation, was conducted. Automatic associations with exercise were first measured with a single-target implicit association test. The somato-affective core of the participants’ automatic valuation of exercise-related pictures was then assessed via heart rate variability (HRV) analysis, and the affective valence of the valuation was tested with a facial expression (FE; smile and frown) task. Exercise behavior was assessed via self-report. Multiple regression (path) analysis revealed that automatic associations predicted HRV reactivity (β = −0.24, p = .044); the signs of the correlation between automatic associations and the smile FE score was in the expected direction but remained nonsignificant (β = −0.21, p = .078). HRV reactivity predicted self-reported exercise behavior (β = −0.28, p = .013) (the same pattern of results was achieved for the frown FE score). The HRV-related results illustrate the potential role of automatic negative affective reactions to the thought of exercise as a restraining force in exercise motivation. For better empirical distinction between the two ART type‑1 process components, automatic associations and the affective valuation should perhaps be measured separately in the future. The results support the notion that automatic and affective processes should be regarded as essential aspects of the motivation to exercise. KW - Heart rate variability KW - Facial expression KW - Somatic KW - Dual-process KW - Motivation Y1 - 2019 U6 - https://doi.org/10.1007/s12662-020-00664-9 SN - 2509-3150 SN - 2509-3142 VL - 50 IS - 654 SP - 366 EP - 376 PB - Springer CY - Berlin ; Heidelberg ER - TY - JOUR A1 - Mardoukhi, Yousof A1 - Chechkin, Aleksei V. A1 - Metzler, Ralf T1 - Spurious ergodicity breaking in normal and fractional Ornstein–Uhlenbeck process JF - New Journal of Physics N2 - The Ornstein–Uhlenbeck process is a stationary and ergodic Gaussian process, that is fully determined by its covariance function and mean. We show here that the generic definitions of the ensemble- and time-averaged mean squared displacements fail to capture these properties consistently, leading to a spurious ergodicity breaking. We propose to remedy this failure by redefining the mean squared displacements such that they reflect unambiguously the statistical properties of any stochastic process. In particular we study the effect of the initial condition in the Ornstein–Uhlenbeck process and its fractional extension. For the fractional Ornstein–Uhlenbeck process representing typical experimental situations in crowded environments such as living biological cells, we show that the stationarity of the process delicately depends on the initial condition. KW - Ornstein–Uhlenbeck process KW - stationary stochastic process KW - ensemble and time averaged mean squared displacement Y1 - 2020 U6 - https://doi.org/10.1088/1367-2630/ab950b SN - 1367-2630 VL - 22 PB - IOP CY - London ER - TY - JOUR A1 - Lonsdorf, Tina B. A1 - Klingelhöfer-Jens, Maren A1 - Andreatta, Marta A1 - Beckers, Tom A1 - Chalkia, Anastasia A1 - Gerlicher, Anna A1 - Jentsch, Valerie L. A1 - Drexler, Shira Meir A1 - Mertens, Gaetan A1 - Richter, Jan A1 - Sjouwerman, Rachel A1 - Wendt, Julia A1 - Merz, Christian J. T1 - Navigating the garden of forking paths for data exclusions in fear conditioning research JF - eLife N2 - In this report, we illustrate the considerable impact of researcher degrees of freedom with respect to exclusion of participants in paradigms with a learning element. We illustrate this empirically through case examples from human fear conditioning research, in which the exclusion of ‘non-learners’ and ‘non-responders’ is common – despite a lack of consensus on how to define these groups. We illustrate the substantial heterogeneity in exclusion criteria identified in a systematic literature search and highlight the potential problems and pitfalls of different definitions through case examples based on re-analyses of existing data sets. On the basis of these studies, we propose a consensus on evidence-based rather than idiosyncratic criteria, including clear guidelines on reporting details. Taken together, we illustrate how flexibility in data collection and analysis can be avoided, which will benefit the robustness and replicability of research findings and can be expected to be applicable to other fields of research that involve a learning element. Y1 - 2019 U6 - https://doi.org/10.7554/eLife.52465 SN - 2050-084X VL - 8 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Lonsdorf, Tina B. A1 - Klingelhöfer-Jens, Maren A1 - Andreatta, Marta A1 - Beckers, Tom A1 - Chalkia, Anastasia A1 - Gerlicher, Anna Maria Veronika A1 - Jentsch, Valerie L. A1 - Drexler, Shira Meir A1 - Mertens, Gaetan A1 - Richter, Jan A1 - Sjouwerman, Rachel A1 - Wendt, Julia A1 - Merz, Christian J. T1 - Navigating the garden of forking paths for data exclusions in fear conditioning research JF - eLife Y1 - 2019 U6 - https://doi.org/10.7554/eLife.52465 SN - 2050-084X VL - 8 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Günther, Erika A1 - Klauß, André A1 - Toro-Nahuelpan, Mauricio A1 - Schüler, Dirk A1 - Hille, Carsten A1 - Faivre, Damien T1 - The in vivo mechanics of the magnetotactic backbone as revealed by correlative FLIM-FRET and STED microscopy JF - Scientific reports N2 - Protein interaction and protein imaging strongly benefit from the advancements in time-resolved and superresolution fluorescence microscopic techniques. However, the techniques were typically applied separately and ex vivo because of technical challenges and the absence of suitable fluorescent protein pairs. Here, we show correlative in vivo fluorescence lifetime imaging microscopy Forster resonance energy transfer (FLIM-FRET) and stimulated emission depletion (STED) microscopy to unravel protein mechanics and structure in living cells. We use magnetotactic bacteria as a model system where two proteins, MamJ and MamK, are used to assemble magnetic particles called magnetosomes. The filament polymerizes out of MamK and the magnetosomes are connected via the linker MamJ. Our system reveals that bacterial filamentous structures are more fragile than the connection of biomineralized particles to this filament. More importantly, we anticipate the technique to find wide applicability for the study and quantification of biological processes in living cells and at high resolution. Y1 - 2019 U6 - https://doi.org/10.1038/s41598-019-55804-5 SN - 2045-2322 VL - 9 PB - Nature Publ. Group CY - London ER - TY - JOUR A1 - Thomas, Jessica E. A1 - Carvalho, Gary R. A1 - Haile, James A1 - Rawlence, Nicolas J. A1 - Martin, Michael D. A1 - Ho, Simon Y. W. A1 - Sigfusson, Arnor P. A1 - Josefsson, Vigfus A. A1 - Frederiksen, Morten A1 - Linnebjerg, Jannie F. A1 - Castruita, Jose A. Samaniego A1 - Niemann, Jonas A1 - Sinding, Mikkel-Holger S. A1 - Sandoval-Velasco, Marcela A1 - Soares, Andre E. R. A1 - Lacy, Robert A1 - Barilaro, Christina A1 - Best, Juila A1 - Brandis, Dirk A1 - Cavallo, Chiara A1 - Elorza, Mikelo A1 - Garrett, Kimball L. A1 - Groot, Maaike A1 - Johansson, Friederike A1 - Lifjeld, Jan T. A1 - Nilson, Goran A1 - Serjeanston, Dale A1 - Sweet, Paul A1 - Fuller, Errol A1 - Hufthammer, Anne Karin A1 - Meldgaard, Morten A1 - Fjeldsa, Jon A1 - Shapiro, Beth A1 - Hofreiter, Michael A1 - Stewart, John R. A1 - Gilbert, M. Thomas P. A1 - Knapp, Michael T1 - Demographic reconstruction from ancient DNA supports rapid extinction of the great auk JF - eLife N2 - The great auk was once abundant and distributed across the North Atlantic. It is now extinct, having been heavily exploited for its eggs, meat, and feathers. We investigated the impact of human hunting on its demise by integrating genetic data, GPS-based ocean current data, and analyses of population viability. We sequenced complete mitochondrial genomes of 41 individuals from across the species' geographic range and reconstructed population structure and population dynamics throughout the Holocene. Taken together, our data do not provide any evidence that great auks were at risk of extinction prior to the onset of intensive human hunting in the early 16th century. In addition, our population viability analyses reveal that even if the great auk had not been under threat by environmental change, human hunting alone could have been sufficient to cause its extinction. Our results emphasise the vulnerability of even abundant and widespread species to intense and localised exploitation. Y1 - 2019 U6 - https://doi.org/10.7554/eLife.47509 SN - 2050-084X VL - 8 PB - eLife Sciences Publications CY - Cambridge ER - TY - JOUR A1 - Bröker, Katharine A1 - Sinelnikov, Evgeny A1 - Gustavus, Dirk A1 - Schumacher, Udo A1 - Pörtner, Ralf A1 - Hoffmeister, Hans A1 - Lüth, Stefan A1 - Dammermann, Werner T1 - Mass Production of Highly Active NK Cells for Cancer Immunotherapy in a GMP Conform Perfusion Bioreactor JF - Frontiers in Bioengineering and Biotechnology N2 - NK cells have emerged as promising candidates for cancer immunotherapy, especially due to their ability to fight circulating tumor cells thereby preventing metastases formation. Hence several studies have been performed to generate and expand highly cytotoxic NK cells ex vivo, e.g., by using specific cytokines to upregulate both their proliferation and surface expression of distinct activating receptors. Apart from an enhanced activity, application of NK cells as immunotherapeutic agent further requires sufficient cell numbers and a high purity. All these parameters depend on a variety of different factors including the starting material, additives like cytokines as well as the culture system. Here we analyzed PBMC-derived NK cells of five anonymized healthy donors expanded under specific conditions in an innovative perfusion bioreactor system with respect to their phenotype, IFN gamma production, and cytotoxicity in vitro. Important features of the meander type bioreactors used here are a directed laminar flow of medium and control of relevant process parameters. Cells are cultivated under "steady state" conditions in perfusion mode. Our data demonstrate that expansion of CD3(+) T cell depleted PBMCs in our standardized system generates massive amounts of highly pure (>85%) and potent anticancer active NK cells. These cells express a variety of important receptors driving NK cell recruitment, adhesion as well as activation. More specifically, they express the chemokine receptors CXCR3, CXCR4, and CCR7, the adhesion molecules L-selectin, LFA-1, and VLA-4, the activating receptors NKp30, NKp44, NKp46, NKG2D, DNAM1, and CD16 as well as the death ligands TRAIL and Fas-L. Moreover, the generated NK cells show a strong IFN gamma expression upon cultivation with K562 tumor cells and demonstrate a high cytotoxicity toward leukemic as well as solid tumor cell lines in vitro. Altogether, these characteristics promise a high clinical potency of thus produced NK cells awaiting further evaluation. KW - natural killer cells (NK cells) KW - cytotoxicity KW - tumor immunity KW - immunotherapy KW - perfusion bioreactor KW - GMP KW - mass production process Y1 - 2019 U6 - https://doi.org/10.3389/fbioe.2019.00194 SN - 2296-4185 VL - 7 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Löpfe, Moira A1 - Duss, Anja A1 - Zafeiropoulou, Katerina-Alexandra A1 - Bjoergvinsdottir, Oddny A1 - Eglin, David A1 - Fortunato, Giuseppino A1 - Klasen, Jürgen A1 - Ferguson, Stephen J. A1 - Würtz-Kozak, Karin A1 - Krupkova, Olga T1 - Electrospray-Based Microencapsulation of Epigallocatechin 3-Gallate for Local Delivery into the Intervertebral Disc JF - Pharmaceutics N2 - Locally delivered anti-inflammatory compounds can restore the homeostasis of the degenerated intervertebral disc (IVD). With beneficial effects on IVD cells, epigallocatechin 3-gallate (EGCG) is a promising therapeutic candidate. However, EGCG is prone to rapid degradation and/or depletion. Therefore, the purpose of this study was to develop a method for controlled EGCG delivery in the degenerated IVD. Primary IVD cells were isolated from human donors undergoing IVD surgeries. EGCG was encapsulated into microparticles by electrospraying of glutaraldehyde-crosslinked gelatin. The resulting particles were characterized in terms of cytocompatibility and anti-inflammatory activity, and combined with a thermoresponsive carrier to produce an injectable EGCG delivery system. Subsequently, electrospraying was scaled up using the industrial NANOSPIDER (TM) technology. The produced EGCG microparticles reduced the expression of inflammatory (IL-6, IL-8, COX-2) and catabolic (MMP1, MMP3, MMP13) mediators in pro-inflammatory 3D cell cultures. Combining the EGCG microparticles with the carrier showed a trend towards modulating EGCG activity/release. Electrospray upscaling was achieved, leading to particles with homogenous spherical morphologies. In conclusion, electrospray-based encapsulation of EGCG resulted in cytocompatible microparticles that preserved the activity of EGCG and showed the potential to control EGCG release, thus favoring IVD health by downregulating local inflammation. Future studies will focus on further exploring the biological activity of the developed delivery system for potential clinical use. KW - degenerative disc disease KW - inflammation KW - drug delivery KW - EGCG KW - microparticles KW - injectable biomaterial KW - electrospraying Y1 - 2019 U6 - https://doi.org/10.3390/pharmaceutics11090435 SN - 1999-4923 VL - 11 IS - 9 PB - MDPI CY - Basel ER - TY - JOUR A1 - Miele, Vincent A1 - Guill, Christian A1 - Ramos-Jiliberto, Rodrigo A1 - Kéfi, Sonia T1 - Non-trophic interactions strengthen the diversity-functioning relationship in an ecological bioenergetic network model JF - PLoS Computational Biology : a new community journal N2 - Ecological communities are undeniably diverse, both in terms of the species that compose them as well as the type of interactions that link species to each other. Despite this long recognition of the coexistence of multiple interaction types in nature, little is known about the consequences of this diversity for community functioning. In the ongoing context of global change and increasing species extinction rates, it seems crucial to improve our understanding of the drivers of the relationship between species diversity and ecosystem functioning. Here, using a multispecies dynamical model of ecological communities including various interaction types (e.g. competition for space, predator interference, recruitment facilitation in addition to feeding), we studied the role of the presence and the intensity of these interactions for species diversity, community functioning (biomass and production) and the relationship between diversity and functioning. Taken jointly, the diverse interactions have significant effects on species diversity, whose amplitude and sign depend on the type of interactions involved and their relative abundance. They however consistently increase the slope of the relationship between diversity and functioning, suggesting that species losses might have stronger effects on community functioning than expected when ignoring the diversity of interaction types and focusing on feeding interactions only. Y1 - 2020 U6 - https://doi.org/10.1371/journal.pcbi.1007269 SN - 1553-7358 VL - 15 IS - 8 PB - PLoS CY - San Fransisco ER - TY - JOUR A1 - Koetz, Joachim T1 - The Effect of Surface Modification of Gold Nanotriangles for Surface-Enhanced Raman Scattering Performance JF - Nanomaterials N2 - A surface modification of ultraflat gold nanotriangles (AuNTs) with different shaped nanoparticles is of special relevance for surface-enhanced Raman scattering (SERS) and the photo-catalytic activity of plasmonic substrates. Therefore, different approaches are used to verify the flat platelet morphology of the AuNTs by oriented overgrowth with metal nanoparticles. The most important part for the morphological transformation of the AuNTs is the coating layer, containing surfactants or polymers. By using well established AuNTs stabilized by a dioctyl sodium sulfosuccinate (AOT) bilayer, different strategies of surface modification with noble metal nanoparticles are possible. On the one hand undulated superstructures were synthesized by in situ growth of hemispherical gold nanoparticles in the polyethyleneimine (PEI)-coated AOT bilayer of the AuNTs. On the other hand spiked AuNTs were obtained by a direct reduction of Au³⁺ ions in the AOT double layer in presence of silver ions and ascorbic acid as reducing agent. Additionally, crumble topping of the smooth AuNTs can be realized after an exchange of the AOT bilayer by hyaluronic acid, followed by a silver-ion mediated reduction with ascorbic acid. Furthermore, a decoration with silver nanoparticles after coating the AOT bilayer with the cationic surfactant benzylhexadecyldimethylammonium chloride (BDAC) can be realized. In that case the ultraviolet (UV)-absorption of the undulated Au@Ag nanoplatelets can be tuned depending on the degree of decoration with silver nanoparticles. Comparing the Raman scattering data for the plasmon driven dimerization of 4-nitrothiophenol (4-NTP) to 4,4′-dimercaptoazobenzene (DMAB) one can conclude that the most important effect of surface modification with a 75 times higher enhancement factor in SERS experiments becomes available by decoration with gold spikes. KW - undulated KW - spiked and crumble gold nanotriangles KW - SERS enhancement factor KW - dimerization of 4-nitrothiophenol KW - AOT bilayer KW - PEI coating Y1 - 2020 U6 - https://doi.org/10.3390/nano10112187 SN - 2079-4991 VL - 10 IS - 11 PB - MDPI CY - Basel ER - TY - JOUR A1 - Rieck, Christoph Paul Kurt A1 - Geiger, Daniel A1 - Munkert, Jennifer A1 - Messerschmidt, Katrin A1 - Petersen, Jan A1 - Strasser, Juliane A1 - Meitinger, Nadine A1 - Kreis, Wolfgang T1 - Biosynthetic approach to combine the first steps of cardenolide formation in Saccharomyces cerevisiae JF - Microbiologyopen N2 - A yeast expression plasmid was constructed containing a cardenolide biosynthetic module, referred to as CARD II, using the AssemblX toolkit, which enables the assembly of large DNA constructs. The genes cloned into the vector were (a) a Δ5‐3β‐hydroxysteroid dehydrogenase gene from Digitalis lanata, (b) a steroid Δ5‐isomerase gene from Comamonas testosteronii, (c) a mutated steroid‐5β‐reductase gene from Arabidopsis thaliana, and (d) a steroid 21‐hydroxylase gene from Mus musculus. A second plasmid bearing an ADR/ADX fusion gene from Bos taurus was also constructed. A Saccharomyces cerevisiae strain bearing these two plasmids was generated. This strain, termed “CARD II yeast”, was capable of producing 5β‐pregnane‐3β,21‐diol‐20‐one, a central intermediate in 5β‐cardenolide biosynthesis, starting from pregnenolone which was added to the culture medium. Using this approach, five consecutive steps in cardenolide biosynthesis were realized in baker's yeast. Y1 - 2019 U6 - https://doi.org/10.1002/mbo3.925 SN - 2045-8827 VL - 8 IS - 12 PB - Wiley CY - Hoboken ER - TY - JOUR A1 - Werger, Luise A1 - Bergmann, Joana A1 - Weber, Ewald A1 - Heinze, Johannes T1 - Wind intensity affects fine root morphological traits with consequences for plant-soil feedback effects JF - Annals of Botany Plants N2 - Wind influences the development, architecture and morphology of plant roots and may modify subsequent interactions between plants and soil (plant–soil feedbacks—PSFs). However, information on wind effects on fine root morphology is scarce and the extent to which wind changes plant–soil interactions remains unclear. Therefore, we investigated the effects of two wind intensity levels by manipulating surrounding vegetation height in a grassland PSF field experiment. We grew four common plant species (two grasses and two non-leguminous forbs) with soil biota either previously conditioned by these or other species and tested the effect of wind on root:shoot ratio, fine root morphological traits as well as the outcome for PSFs. Wind intensity did not affect biomass allocation (i.e. root:shoot ratio) in any species. However, fine-root morphology of all species changed under high wind intensity. High wind intensity increased specific root length and surface area and decreased root tissue density, especially in the two grasses. Similarly, the direction of PSFs changed under high wind intensity in all four species, but differences in biomass production on the different soils between high and low wind intensity were marginal and most pronounced when comparing grasses with forbs. Because soils did not differ in plant-available nor total nutrient content, the results suggest that wind-induced changes in root morphology have the potential to influence plant–soil interactions. Linking wind-induced changes in fine-root morphology to effects on PSF improves our understanding of plant–soil interactions under changing environmental conditions. KW - Wind KW - root traits KW - root morphology KW - specific root length KW - plant–soil feedback Y1 - 2020 U6 - https://doi.org/10.1093/aobpla/plaa050 SN - 2041-2851 VL - 12 IS - 5 PB - Oxford University Press CY - Oxford ER - TY - JOUR A1 - Knudsen, Erlend Moster A1 - Heinold, Bernd A1 - Dahlke, Sandro A1 - Bozem, Heiko A1 - Crewell, Susanne A1 - Gorodetskaya, Irina V. A1 - Heygster, Georg A1 - Kunkel, Daniel A1 - Maturilli, Marion A1 - Mech, Mario A1 - Viceto, Carolina A1 - Rinke, Annette A1 - Schmithusen, Holger A1 - Ehrlich, Andre A1 - Macke, Andreas A1 - Lüpkes, Christof A1 - Wendisch, Manfred T1 - Meteorological conditions during the ACLOUD/PASCAL field campaign near Svalbard in early summer 2017 JF - Atmospheric chemistry and physics N2 - The two concerted field campaigns, Arctic CLoud Observations Using airborne measurements during polar Day (ACLOUD) and the Physical feedbacks of Arctic planetary boundary level Sea ice, Cloud and AerosoL (PASCAL), took place near Svalbard from 23 May to 26 June 2017. They were focused on studying Arctic mixed-phase clouds and involved observations from two airplanes (ACLOUD), an icebreaker (PASCAL) and a tethered balloon, as well as ground-based stations. Here, we present the synoptic development during the 35-day period of the campaigns, using near-surface and upper-air meteorological observations, as well as operational satellite, analysis, and reanalysis data. Over the campaign period, short-term synoptic variability was substantial, dominating over the seasonal cycle. During the first campaign week, cold and dry Arctic air from the north persisted, with a distinct but seasonally unusual cold air outbreak. Cloudy conditions with mostly low-level clouds prevailed. The subsequent 2 weeks were characterized by warm and moist maritime air from the south and east, which included two events of warm air advection. These synoptical disturbances caused lower cloud cover fractions and higher-reaching cloud systems. In the final 2 weeks, adiabatically warmed air from the west dominated, with cloud properties strongly varying within the range of the two other periods. Results presented here provide synoptic information needed to analyze and interpret data of upcoming studies from ACLOUD/PASCAL, while also offering unprecedented measurements in a sparsely observed region. Y1 - 2018 U6 - https://doi.org/10.5194/acp-18-17995-2018 SN - 1680-7316 SN - 1680-7324 VL - 18 IS - 24 SP - 17995 EP - 18022 PB - Copernicus CY - Göttingen ER - TY - JOUR A1 - Runge, Alexandra A1 - Grosse, Guido T1 - Mosaicking Landsat and Sentinel-2 Data to Enhance LandTrendr Time Series Analysis in Northern High Latitude Permafrost Regions JF - Remote Sensing N2 - Permafrost is warming in the northern high latitudes, inducing highly dynamic thaw-related permafrost disturbances across the terrestrial Arctic. Monitoring and tracking of permafrost disturbances is important as they impact surrounding landscapes, ecosystems and infrastructure. Remote sensing provides the means to detect, map, and quantify these changes homogeneously across large regions and time scales. Existing Landsat-based algorithms assess different types of disturbances with similar spatiotemporal requirements. However, Landsat-based analyses are restricted in northern high latitudes due to the long repeat interval and frequent clouds, in particular at Arctic coastal sites. We therefore propose to combine Landsat and Sentinel-2 data for enhanced data coverage and present a combined annual mosaic workflow, expanding currently available algorithms, such as LandTrendr, to achieve more reliable time series analysis. We exemplary test the workflow for twelve sites across the northern high latitudes in Siberia. We assessed the number of images and cloud-free pixels, the spatial mosaic coverage and the mosaic quality with spectral comparisons. The number of available images increased steadily from 1999 to 2019 but especially from 2016 onward with the addition of Sentinel-2 images. Consequently, we have an increased number of cloud-free pixels even under challenging environmental conditions, which then serve as the input to the mosaicking process. In a comparison of annual mosaics, the Landsat+Sentinel-2 mosaics always fully covered the study areas (99.9–100 %), while Landsat-only mosaics contained data-gaps in the same years, only reaching coverage percentages of 27.2 %, 58.1 %, and 69.7 % for Sobo Sise, East Taymyr, and Kurungnakh in 2017, respectively. The spectral comparison of Landsat image, Sentinel-2 image, and Landsat+Sentinel-2 mosaic showed high correlation between the input images and mosaic bands (e.g., for Kurungnakh 0.91–0.97 between Landsat and Landsat+Sentinel-2 mosaic and 0.92–0.98 between Sentinel-2 and Landsat+Sentinel-2 mosaic) across all twelve study sites, testifying good quality mosaic results. Our results show that especially the results for northern, coastal areas was substantially improved with the Landsat+Sentinel-2 mosaics. By combining Landsat and Sentinel-2 data we accomplished to create reliably high spatial resolution input mosaics for time series analyses. Our approach allows to apply a high temporal continuous time series analysis to northern high latitude permafrost regions for the first time, overcoming substantial data gaps, and assess permafrost disturbance dynamics on an annual scale across large regions with algorithms such as LandTrendr by deriving the location, timing and progression of permafrost thaw disturbances KW - time series analysis KW - data fusion KW - disturbance tracking KW - permafrost KW - permafrost thaw Y1 - 2020 U6 - https://doi.org/10.3390/rs12152471 SN - 2072-4292 VL - 12 IS - 15 PB - MDPI CY - Basel ER - TY - JOUR A1 - He, Hai A1 - Höper, Rune A1 - Dodenhöft, Moritz A1 - Marlière, Philippe A1 - Bar-Even, Arren T1 - An optimized methanol assimilation pathway relying on promiscuous formaldehyde-condensing aldolases in E. coli JF - Metabolic Engineering N2 - Engineering biotechnological microorganisms to use methanol as a feedstock for bioproduction is a major goal for the synthetic metabolism community. Here, we aim to redesign the natural serine cycle for implementation in E. coli. We propose the homoserine cycle, relying on two promiscuous formaldehyde aldolase reactions, as a superior pathway design. The homoserine cycle is expected to outperform the serine cycle and its variants with respect to biomass yield, thermodynamic favorability, and integration with host endogenous metabolism. Even as compared to the RuMP cycle, the most efficient naturally occurring methanol assimilation route, the homoserine cycle is expected to support higher yields of a wide array of products. We test the in vivo feasibility of the homoserine cycle by constructing several E. coli gene deletion strains whose growth is coupled to the activity of different pathway segments. Using this approach, we demonstrate that all required promiscuous enzymes are active enough to enable growth of the auxotrophic strains. Our findings thus identify a novel metabolic solution that opens the way to an optimized methylotrophic platform. KW - Pathway design KW - Promiscuous enzymes KW - Formaldehyde assimilation KW - Serine cycle KW - Growth selection Y1 - 2020 U6 - https://doi.org/10.1016/j.ymben.2020.03.002 SN - 1096-7176 SN - 1096-7184 VL - 60 SP - 1 EP - 13 PB - Elsevier CY - Amsterdam [u.a.] ER - TY - JOUR A1 - He, Hai A1 - Noor, Elad A1 - Ramos-Parra, Perla A. A1 - García-Valencia, Liliana E. A1 - Patterson, Jenelle A. A1 - Díaz de la Garza, Rocío I. A1 - Hanson, Andrew D. A1 - Bar-Even, Arren T1 - In Vivo Rate of Formaldehyde Condensation with Tetrahydrofolate JF - Metabolites N2 - Formaldehyde is a highly reactive compound that participates in multiple spontaneous reactions, but these are mostly deleterious and damage cellular components. In contrast, the spontaneous condensation of formaldehyde with tetrahydrofolate (THF) has been proposed to contribute to the assimilation of this intermediate during growth on C1 carbon sources such as methanol. However, the in vivo rate of this condensation reaction is unknown and its possible contribution to growth remains elusive. Here, we used microbial platforms to assess the rate of this condensation in the cellular environment. We constructed Escherichia coli strains lacking the enzymes that naturally produce 5,10-methylene-THF. These strains were able to grow on minimal medium only when equipped with a sarcosine (N-methyl-glycine) oxidation pathway that sustained a high cellular concentration of formaldehyde, which spontaneously reacts with THF to produce 5,10-methylene-THF. We used flux balance analysis to derive the rate of the spontaneous condensation from the observed growth rate. According to this, we calculated that a microorganism obtaining its entire biomass via the spontaneous condensation of formaldehyde with THF would have a doubling time of more than three weeks. Hence, this spontaneous reaction is unlikely to serve as an effective route for formaldehyde assimilation. KW - one-carbon metabolism KW - spontaneous reaction KW - auxotrophy KW - serine cycle KW - phenotypic phase plane Y1 - 2019 U6 - https://doi.org/10.3390/metabo10020065 SN - 2218-1989 VL - 10 IS - 65 PB - MDPI CY - Basel ER - TY - JOUR A1 - Shcherbakov, Robert A1 - Zhuang, Jiancang A1 - Zöller, Gert A1 - Ogata, Yosihiko T1 - Forecasting the magnitude of the largest expected earthquake JF - Nature Communications N2 - The majority of earthquakes occur unexpectedly and can trigger subsequent sequences of events that can culminate in more powerful earthquakes. This self-exciting nature of seismicity generates complex clustering of earthquakes in space and time. Therefore, the problem of constraining the magnitude of the largest expected earthquake during a future time interval is of critical importance in mitigating earthquake hazard. We address this problem by developing a methodology to compute the probabilities for such extreme earthquakes to be above certain magnitudes. We combine the Bayesian methods with the extreme value theory and assume that the occurrence of earthquakes can be described by the Epidemic Type Aftershock Sequence process. We analyze in detail the application of this methodology to the 2016 Kumamoto, Japan, earthquake sequence. We are able to estimate retrospectively the probabilities of having large subsequent earthquakes during several stages of the evolution of this sequence. Y1 - 2019 U6 - https://doi.org/10.1038/s41467-019-11958-4 SN - 2041-1723 VL - 10 PB - Nature Publishing Group CY - London ER - TY - JOUR A1 - Figueroa Campos, Gustavo A. A1 - Sagu Tchewonpi, Sorel A1 - Saravia Celis, Pedro A1 - Rawel, Harshadrai Manilal T1 - Comparison of batch and continuous wet-processing of coffee BT - changes in the main compounds in beans, by-products and wastewater JF - Foods N2 - Many technical challenges still need to be overcome to improve the quality of the green coffee beans. In this work, the wet Arabica coffee processing in batch and continuous modus were investigated. Coffee beans samples as well as by-products and wastewaters collected at different production steps were analyzed in terms of their content in total phenols, antioxidant capacity, caffeine content, organic acids, reducing sugars, free amino group and protein content. The results showed that 40% of caffeine was removed with pulp. Green coffee beans showed highest concentration of organic acids and sucrose (4.96 ± 0.25 and 5.07 ± 0.39 g/100 g DW for the batch and continuous processing). Batch green coffee beans contained higher amount of phenols. 5-caffeoylquinic Acid (5-CQA) was the main constituent (67.1 and 66.0% for the batch and continuous processing, respectively). Protein content was 15 and 13% in the green coffee bean in batch and continuous processing, respectively. A decrease of 50 to 64% for free amino groups during processing was observed resulting in final amounts of 0.8 to 1.4% in the processed beans. Finally, the batch processing still revealed by-products and wastewater with high nutrient content encouraging a better concept for valorization. KW - Arabica coffee beans KW - coffee by-products KW - batch process KW - continuous process KW - nutritional characteristics Y1 - 2020 U6 - https://doi.org/10.3390/foods9081135 SN - 2304-8158 VL - 9 IS - 8 PB - MDPI CY - Basel ER - TY - JOUR A1 - Schiro, Gabriele A1 - Colangeli, Pierluigi A1 - Müller, Marina E. H. T1 - A Metabarcoding Analysis of the Mycobiome of Wheat Ears Across a Topographically Heterogeneous Field JF - Frontiers in microbiology KW - Fusarium KW - microclimate KW - canopy KW - fungal community KW - Alternaria KW - spatially induced variance Y1 - 2019 U6 - https://doi.org/10.3389/fmicb.2019.02095 SN - 1664-302X VL - 10 PB - Frontiers Research Foundation CY - Lausanne ER - TY - JOUR A1 - Brust, Henrike A1 - Orzechowski, Slawomir A1 - Fettke, Jörg T1 - Starch and Glycogen Analyses BT - Methods and Techniques JF - Biomolecules N2 - For complex carbohydrates, such as glycogen and starch, various analytical methods and techniques exist allowing the detailed characterization of these storage carbohydrates. In this article, we give a brief overview of the most frequently used methods, techniques, and results. Furthermore, we give insights in the isolation, purification, and fragmentation of both starch and glycogen. An overview of the different structural levels of the glucans is given and the corresponding analytical techniques are discussed. Moreover, future perspectives of the analytical needs and the challenges of the currently developing scientific questions are included KW - starch KW - glycogen KW - analytics Y1 - 2020 U6 - https://doi.org/10.3390/biom10071020 SN - 2218-273X VL - 10 IS - 7 PB - MDPI CY - Basel ER - TY - JOUR A1 - Bielcik, Milos A1 - Aguilar-Trigueros, Carlos A. A1 - Lakovic, Milica A1 - Jeltsch, Florian A1 - Rillig, Matthias C. T1 - The role of active movement in fungal ecology and community assembly JF - Movement Ecology N2 - Movement ecology aims to provide common terminology and an integrative framework of movement research across all groups of organisms. Yet such work has focused on unitary organisms so far, and thus the important group of filamentous fungi has not been considered in this context. With the exception of spore dispersal, movement in filamentous fungi has not been integrated into the movement ecology field. At the same time, the field of fungal ecology has been advancing research on topics like informed growth, mycelial translocations, or fungal highways using its own terminology and frameworks, overlooking the theoretical developments within movement ecology. We provide a conceptual and terminological framework for interdisciplinary collaboration between these two disciplines, and show how both can benefit from closer links: We show how placing the knowledge from fungal biology and ecology into the framework of movement ecology can inspire both theoretical and empirical developments, eventually leading towards a better understanding of fungal ecology and community assembly. Conversely, by a greater focus on movement specificities of filamentous fungi, movement ecology stands to benefit from the challenge to evolve its concepts and terminology towards even greater universality. We show how our concept can be applied for other modular organisms (such as clonal plants and slime molds), and how this can lead towards comparative studies with the relationship between organismal movement and ecosystems in the focus. KW - Filamentous fungi KW - Microbial community KW - Active movement KW - Modular organisms KW - Interference competition KW - Fungal space searching algorithms KW - Fungal foraging KW - Fungal highways KW - Clonal plants KW - Slime molds Y1 - 2019 U6 - https://doi.org/10.1186/s40462-019-0180-6 SN - 2051-3933 VL - 7 IS - 1 PB - BMC CY - London ER - TY - JOUR A1 - Schwarz, Anja T1 - Melancholia JF - Cultural studies review Y1 - 2019 U6 - https://doi.org/10.5130/csr.v25i2.6918 SN - 1837-8692 VL - 25 IS - 2 SP - 259 EP - 261 PB - Melbourne Univ. Press CY - Sydney ER - TY - JOUR A1 - Ziesemer, Florence A1 - Hüttel, Alexandra A1 - Balderjahn, Ingo T1 - Anti-Consumption JF - Sustainability N2 - Transcending the conventional debate around efficiency in sustainable consumption, anti-consumption patterns leading to decreased levels of material consumption have been gaining importance. Change agents are crucial for the promotion of such patterns, so there may be lessons for governance interventions that can be learnt from the every-day experiences of those who actively implement and promote sustainability in the field of anti-consumption. Eighteen social innovation pioneers, who engage in and diffuse practices of voluntary simplicity and collaborative consumption as sustainable options of anti-consumption share their knowledge and personal insights in expert interviews for this research. Our qualitative content analysis reveals drivers, barriers, and governance strategies to strengthen anti-consumption patterns, which are negotiated between the market, the state, and civil society. Recommendations derived from the interviews concern entrepreneurship, municipal infrastructures in support of local grassroots projects, regulative policy measures, more positive communication to strengthen the visibility of initiatives and emphasize individual benefits, establishing a sense of community, anti-consumer activism, and education. We argue for complementary action between top-down strategies, bottom-up initiatives, corporate activities, and consumer behavior. The results are valuable to researchers, activists, marketers, and policymakers who seek to enhance their understanding of materially reduced consumption patterns based on the real-life experiences of active pioneers in the field. KW - social innovation KW - sufficiency KW - collaborative consumption KW - expert interview KW - consumer behavior KW - sustainability KW - innovation policy KW - governance for sustainable development KW - consumer education Y1 - 2019 U6 - https://doi.org/10.3390/su11236663 SN - 2071-1050 VL - 11 IS - 23 PB - MDPI CY - Basel ER -