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Potato (Solanum tuberosum L.) is one of the most important food crops worldwide. Current potato varieties are highly susceptible to drought stress. In view of global climate change, selection of cultivars with improved drought tolerance and high yield potential is of paramount importance. Drought tolerance breeding of potato is currently based on direct selection according to yield and phenotypic traits and requires multiple trials under drought conditions. Marker‐assisted selection (MAS) is cheaper, faster and reduces classification errors caused by noncontrolled environmental effects. We analysed 31 potato cultivars grown under optimal and reduced water supply in six independent field trials. Drought tolerance was determined as tuber starch yield. Leaf samples from young plants were screened for preselected transcript and nontargeted metabolite abundance using qRT‐PCR and GC‐MS profiling, respectively. Transcript marker candidates were selected from a published RNA‐Seq data set. A Random Forest machine learning approach extracted metabolite and transcript markers for drought tolerance prediction with low error rates of 6% and 9%, respectively. Moreover, by combining transcript and metabolite markers, the prediction error was reduced to 4.3%. Feature selection from Random Forest models allowed model minimization, yielding a minimal combination of only 20 metabolite and transcript markers that were successfully tested for their reproducibility in 16 independent agronomic field trials. We demonstrate that a minimum combination of transcript and metabolite markers sampled at early cultivation stages predicts potato yield stability under drought largely independent of seasonal and regional agronomic conditions.
Primary progressive multiple sclerosis (PPMS) shows a highly variable disease progression with poor prognosis and a characteristic accumulation of disabilities in patients. These hallmarks of PPMS make it difficult to diagnose and currently impossible to efficiently treat. This study aimed to identify plasma metabolite profiles that allow diagnosis of PPMS and its differentiation from the relapsing remitting subtype (RRMS), primary neurodegenerative disease (Parkinson’s disease, PD), and healthy controls (HCs) and that significantly change during the disease course and could serve as surrogate markers of multiple sclerosis (MS)-associated neurodegeneration over time. We applied untargeted high-resolution metabolomics to plasma samples to identify PPMS-specific signatures, validated our findings in independent sex- and age-matched PPMS and HC cohorts and built discriminatory models by partial least square discriminant analysis (PLS-DA). This signature was compared to sex- and age-matched RRMS patients, to patients with PD and HC. Finally, we investigated these metabolites in a longitudinal cohort of PPMS patients over a 24-month period. PLS-DA yielded predictive models for classification along with a set of 20 PPMS-specific informative metabolite markers. These metabolites suggest disease-specific alterations in glycerophospholipid and linoleic acid pathways. Notably, the glycerophospholipid LysoPC(20:0) significantly decreased during the observation period. These findings show potential for diagnosis and disease course monitoring, and might serve as biomarkers to assess treatment efficacy in future clinical trials for neuroprotective MS therapies.
Primary progressive multiple sclerosis (PPMS) shows a highly variable disease progression with poor prognosis and a characteristic accumulation of disabilities in patients. These hallmarks of PPMS make it difficult to diagnose and currently impossible to efficiently treat. This study aimed to identify plasma metabolite profiles that allow diagnosis of PPMS and its differentiation from the relapsing remitting subtype (RRMS), primary neurodegenerative disease (Parkinson’s disease, PD), and healthy controls (HCs) and that significantly change during the disease course and could serve as surrogate markers of multiple sclerosis (MS)-associated neurodegeneration over time. We applied untargeted high-resolution metabolomics to plasma samples to identify PPMS-specific signatures, validated our findings in independent sex- and age-matched PPMS and HC cohorts and built discriminatory models by partial least square discriminant analysis (PLS-DA). This signature was compared to sex- and age-matched RRMS patients, to patients with PD and HC. Finally, we investigated these metabolites in a longitudinal cohort of PPMS patients over a 24-month period. PLS-DA yielded predictive models for classification along with a set of 20 PPMS-specific informative metabolite markers. These metabolites suggest disease-specific alterations in glycerophospholipid and linoleic acid pathways. Notably, the glycerophospholipid LysoPC(20:0) significantly decreased during the observation period. These findings show potential for diagnosis and disease course monitoring, and might serve as biomarkers to assess treatment efficacy in future clinical trials for neuroprotective MS therapies.
Genome streamlining is frequently observed in free-living aquatic microorganisms and results in physiological dependencies between microorganisms. However, we know little about the specificity of these microbial associations. In order to examine the specificity and extent of these associations, we established mixed cultures from three different freshwater environments and analyzed the cooccurrence of organisms using a metagenomic time series. Free-living microorganisms with streamlined genomes lacking multiple biosynthetic pathways showed no clear recurring pattern in their interaction partners. Free-living freshwater bacteria form promiscuous cooperative associations. This notion contrasts with the well-documented high specificities of interaction partners in host-associated bacteria. Considering all data together, we suggest that highly abundant free-living bacterial lineages are functionally versatile in their interactions despite their distinct streamlining tendencies at the single-cell level. This metabolic versatility facilitates interactions with a variable set of community members.
Although hydrologic models provide hypothesis testing of complex dynamics occurring at catchments, fresh-water quality modeling is still incipient at many subtropical headwaters. In Brazil, a few modeling studies assess freshwater nutrients, limiting policies on hydrologic ecosystem services. This paper aims to compare freshwater quality scenarios under different land-use and land-cover (LULC) change, one of them related to ecosystem-based adaptation (EbA), in Brazilian headwaters. Using the spatially semi-distributed Soil and Water Assessment Tool (SWAT) model, nitrate, total phosphorous (TP) and sediment were modeled in catchments ranging from 7.2 to 1037 km(2). These head-waters were eligible areas of the Brazilian payment for ecosystem services (PES) projects in the Cantareira water supply system, which had supplied water to 9 million people in the Sao Paulo metropolitan region (SPMR). We considered SWAT modeling of three LULC scenarios: (i) recent past scenario (S1), with historical LULC in 1990; (ii) current land-use scenario (S2), with LULC for the period 2010-2015 with field validation; and (iii) future land-use scenario with PES (S2 + EbA). This latter scenario proposed forest cover restoration through EbA following the river basin plan by 2035. These three LULC scenarios were tested with a selected record of rainfall and evapotranspiration observed in 2006-2014, with the occurrence of extreme droughts. To assess hydrologic services, we proposed the hydrologic service index (HSI), as a new composite metric comparing water pollution levels (WPL) for reference catchments, related to the grey water footprint (greyWF) and water yield. On the one hand, water quality simulations allowed for the regionalization of greyWF at spatial scales under LULC scenarios. According to the critical threshold, HSI identified areas as less or more sustainable catchments. On the other hand, conservation practices simulated through the S2 + EbA scenario envisaged not only additional and viable best management practices (BMP), but also preventive decision-making at the headwaters of water supply systems.
The desiccation-tolerant plant Haberlea rhodopensis can withstand months of darkness without any visible senescence. Here, we investigated the molecular mechanisms of this adaptation to prolonged (30 d) darkness and subsequent return to light. H. rhodopensis plants remained green and viable throughout the dark treatment. Transcriptomic analysis revealed that darkness regulated several transcription factor (TF) genes. Stress-and autophagy-related TFs such as ERF8, HSFA2b, RD26, TGA1, and WRKY33 were up-regulated, while chloroplast-and flowering-related TFs such as ATH1, COL2, COL4, RL1, and PTAC7 were repressed. PHYTOCHROME INTERACTING FACTOR4, a negative regulator of photomorphogenesis and promoter of senescence, also was down-regulated. In response to darkness, most of the photosynthesis-and photorespiratory-related genes were strongly down-regulated, while genes related to autophagy were up-regulated. This occurred concomitant with the induction of SUCROSE NON-FERMENTING1-RELATED PROTEIN KINASES (SnRK1) signaling pathway genes, which regulate responses to stress-induced starvation and autophagy. Most of the genes associated with chlorophyll catabolism, which are induced by darkness in dark-senescing species, were either unregulated (PHEOPHORBIDE A OXYGENASE, PAO; RED CHLOROPHYLL CATABOLITE REDUCTASE, RCCR) or repressed (STAY GREEN-LIKE, PHEOPHYTINASE, and NON-YELLOW COLORING1). Metabolite profiling revealed increases in the levels of many amino acids in darkness, suggesting increased protein degradation. In darkness, levels of the chloroplastic lipids digalactosyldiacylglycerol, monogalactosyldiacylglycerol, phosphatidylglycerol, and sulfoquinovosyldiacylglycerol decreased, while those of storage triacylglycerols increased, suggesting degradation of chloroplast membrane lipids and their conversion to triacylglycerols for use as energy and carbon sources. Collectively, these data show a coordinated response to darkness, including repression of photosynthetic, photorespiratory, flowering, and chlorophyll catabolic genes, induction of autophagy and SnRK1 pathways, and metabolic reconfigurations that enable survival under prolonged darkness.
One important organizational property of morphology is competition. Different means of expression are in conflict with each other for encoding the same grammatical function. In the current study, we examined the nature of this control mechanism by testing the formation of comparative adjectives in English during language production. Event-related brain potentials (ERPs) were recorded during cued silent production, the first study of this kind for comparative adjective formation. We specifically examined the ERP correlates of producing synthetic relative to analytic comparatives, e.g. angriervs. more angry. A frontal, bilaterally distributed, enhanced negative-going waveform for analytic comparatives (vis-a-vis synthetic ones) emerged approximately 300ms after the (silent) production cue. We argue that this ERP effect reflects a control mechanism that constrains grammatically-based computational processes (viz. more comparative formation). We also address the possibility that this particular ERP effect may belong to a family of previously observed negativities reflecting cognitive control monitoring, rather than morphological encoding processes per se.
Stable isotope ratios delta O-18 and delta D in polar ice provide a wealth of information about past climate evolution. Snow-pit studies allow us to relate observed weather and climate conditions to the measured isotope variations in the snow. They therefore offer the possibility to test our understanding of how isotope signals are formed and stored in firn and ice. As delta O-18 and delta D in the snowfall are strongly correlated to air temperature, isotopes in the near-surface snow are thought to record the seasonal cycle at a given site. Accordingly, the number of seasonal cycles observed over a given depth should depend on the accumulation rate of snow. However, snow-pit studies from different accumulation conditions in East Antarctica reported similar isotopic variability and comparable apparent cycles in the delta O-18 and delta D profiles with typical wavelengths of similar to 20 cm. These observations are unexpected as the accumulation rates strongly differ between the sites, ranging from 20 to 80mmw.e.yr(-1) (similar to 6-21 cm of snow per year). Various mechanisms have been proposed to explain the isotopic variations individually at each site; however, none of these are consistent with the similarity of the different profiles independent of the local accumulation conditions.
Here, we systematically analyse the properties and origins of delta O-18 and delta D variations in high-resolution firn profiles from eight East Antarctic sites. First, we confirm the suggested cycle length (mean distance between peaks) of similar to 20 cm by counting the isotopic maxima. Spectral analysis further shows a strong similarity between the sites but indicates no dominant periodic features. Furthermore, the appar-ent cycle length increases with depth for most East Antarctic sites, which is inconsistent with burial and compression of a regular seasonal cycle. We show that these results can be explained by isotopic diffusion acting on a noise-dominated isotope signal. The firn diffusion length is rather stable across the Antarctic Plateau and thus leads to similar power spectral densities of the isotopic variations. This in turn implies a similar distance between isotopic maxima in the firn profiles. Our results explain a large set of observations discussed in the literature, providing a simple explanation for the interpretation of apparent cycles in shallow isotope records, without invoking complex mechanisms. Finally, the results underline previous suggestions that isotope signals in single ice cores from low-accumulation regions have a small signal-to-noise ratio and thus likely do not allow the reconstruction of interannual to decadal climate variations.
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
Plant roots control uptake of water and nutrients and cope with environmental challenges. The root epidermis provides the first selective interface for nutrient absorption, while the endodermis produces the main apoplastic diffusion barrier in the form of a structure called the Casparian strip. The positioning of root hairs on epidermal cells, and of the Casparian strip around endodermal cells, requires asymmetries along cellular axes (cell polarity). Cell polarity is termed planar polarity, when coordinated within the plane of a given tissue layer. Here, we review recent molecular advances towards understanding both the polar positioning of the proteo-lipid membrane domain instructing root hair initiation, and the cytoskeletal, trafficking and polar tethering requirements of proteins at outer or inner plasma membrane domains. Finally, we highlight progress towards understanding mechanisms of Casparian strip formation and underlying endodermal cell polarity.
Subduction zone magmas are more oxidised on eruption than those at mid-ocean ridges. This is attributed either to oxidising components, derived from subducted lithosphere (slab) and added to the mantle wedge, or to oxidation processes occurring during magma ascent via differentiation. Here we provide direct evidence for contributions of oxidising slab agents to melts trapped in the sub-arc mantle. Measurements of sulfur (S) valence state in sub-arc mantle peridotites identify sulfate, both as crystalline anhydrite (CaSO4) and dissolved SO42− in spinel-hosted glass (formerly melt) inclusions. Copper-rich sulfide precipitates in the inclusions and increased Fe3+/∑Fe in spinel record a S6+–Fe2+ redox coupling during melt percolation through the sub-arc mantle. Sulfate-rich glass inclusions exhibit high U/Th, Pb/Ce, Sr/Nd and δ34S (+ 7 to + 11‰), indicating the involvement of dehydration products of serpentinised slab rocks in their parental melt sources. These observations provide a link between liberated slab components and oxidised arc magmas.
Lifestyle-related disorders, such as the metabolic syndrome, have become a primary risk factor for the development of liver pathologies that can progress from hepatic steatosis, hepatic insulin resistance, steatohepatitis, fibrosis and cirrhosis, to the most severe condition of hepatocellular carcinoma (HCC). While the prevalence of liver pathologies is steadily increasing in modern societies, there are currently no approved drugs other than chemotherapeutic intervention in late stage HCC. Hence, there is a pressing need to identify and investigate causative molecular pathways that can yield new therapeutic avenues. The transcription factor p53 is well established as a tumor suppressor and has recently been described as a central metabolic player both in physiological and pathological settings. Given that liver is a dynamic tissue with direct exposition to ingested nutrients, hepatic p53, by integrating cellular stress response, metabolism and cell cycle regulation, has emerged as an important regulator of liver homeostasis and dysfunction. The underlying evidence is reviewed herein, with a focus on clinical data and animal studies that highlight a direct influence of p53 activity on different stages of liver diseases. Based on current literature showing that activation of p53 signaling can either attenuate or fuel liver disease, we herein discuss the hypothesis that, while hyper-activation or loss of function can cause disease, moderate induction of hepatic p53 within physiological margins could be beneficial in the prevention and treatment of liver pathologies. Hence, stimuli that lead to a moderate and temporary p53 activation could present new therapeutic approaches through several entry points in the cascade from hepatic steatosis to HCC.
Development of a multiple-chambered heart from the linear heart tube is inherently linked to cardiac looping. Although many molecular factors regulating the process of cardiac chamber ballooning have been identified, the cellular mechanisms underlying the chamber formation remain unclear. Here, we demonstrate that cardiac chambers remodel by cell neighbour exchange of cardiomyocytes guided by the planar cell polarity (PCP) pathway triggered by two non-canonical Wnt ligands, Wnt5b and Wnt11. We find that PCP signalling coordinates the localisation of actomyosin activity, and thus the efficiency of cell neighbour exchange. On a tissue-scale, PCP signalling planar-polarises tissue tension by restricting the actomyosin contractility to the apical membranes of outflow tract cells. The tissue-scale polarisation of actomyosin contractility is required for cardiac looping that occurs concurrently with chamber ballooning. Taken together, our data reveal that instructive PCP signals couple cardiac chamber expansion with cardiac looping through the organ-scale polarisation of actomyosin-based tissue tension.
Development of a multiple-chambered heart from the linear heart tube is inherently linked to cardiac looping. Although many molecular factors regulating the process of cardiac chamber ballooning have been identified, the cellular mechanisms underlying the chamber formation remain unclear. Here, we demonstrate that cardiac chambers remodel by cell neighbour exchange of cardiomyocytes guided by the planar cell polarity (PCP) pathway triggered by two non-canonical Wnt ligands, Wnt5b and Wnt11. We find that PCP signalling coordinates the localisation of actomyosin activity, and thus the efficiency of cell neighbour exchange. On a tissue-scale, PCP signalling planar-polarises tissue tension by restricting the actomyosin contractility to the apical membranes of outflow tract cells. The tissue-scale polarisation of actomyosin contractility is required for cardiac looping that occurs concurrently with chamber ballooning. Taken together, our data reveal that instructive PCP signals couple cardiac chamber expansion with cardiac looping through the organ-scale polarisation of actomyosin-based tissue tension.
Polysulfobetaines in aqueous solution show upper critical solution temperature (UCST) behavior. We investigate here the representative of this class of materials, poly (N,N-dimethyl-N-(3-methacrylamidopropyl) ammonio propane sulfonate) (PSPP), with respect to: (i) the dynamics in aqueous solution above the cloud point as function of NaBr concentration; and (ii) the swelling behavior of thin films in water vapor as function of the initial film thickness. For PSPP solutions with a concentration of 5 wt.%, the temperature dependence of the intensity autocorrelation functions is measured with dynamic light scattering as function of molar mass and NaBr concentration (0-8 mM). We found a scaling of behavior for the scattered intensity and dynamic correlation length. The resulting spinodal temperatures showed a maximum at a certain (small) NaBr concentration, which is similar to the behavior of the cloud points measured previously by turbidimetry. The critical exponent of susceptibility depends on NaBr concentration, with a minimum value where the spinodal temperature is maximum and a trend towards the mean-field value of unity with increasing NaBr concentration. In contrast, the critical exponent of the correlation length does not depend on NaBr concentration and is lower than the value of 0.5 predicted by mean-field theory. For PSPP thin films, the swelling behavior was found to depend on film thickness. A film thickness of about 100 nm turns out to be the optimum thickness needed to obtain fast hydration with H2O.
Polysulfobetaines in aqueous solution show upper critical solution temperature (UCST) behavior. We investigate here the representative of this class of materials, poly (N,N-dimethyl-N-(3-methacrylamidopropyl) ammonio propane sulfonate) (PSPP), with respect to: (i) the dynamics in aqueous solution above the cloud point as function of NaBr concentration; and (ii) the swelling behavior of thin films in water vapor as function of the initial film thickness. For PSPP solutions with a concentration of 5 wt.%, the temperature dependence of the intensity autocorrelation functions is measured with dynamic light scattering as function of molar mass and NaBr concentration (0–8 mM). We found a scaling of behavior for the scattered intensity and dynamic correlation length. The resulting spinodal temperatures showed a maximum at a certain (small) NaBr concentration, which is similar to the behavior of the cloud points measured previously by turbidimetry. The critical exponent of susceptibility depends on NaBr concentration, with a minimum value where the spinodal temperature is maximum and a trend towards the mean-field value of unity with increasing NaBr concentration. In contrast, the critical exponent of the correlation length does not depend on NaBr concentration and is lower than the value of 0.5 predicted by mean-field theory. For PSPP thin films, the swelling behavior was found to depend on film thickness. A film thickness of about 100 nm turns out to be the optimum thickness needed to obtain fast hydration with H 2 O.
Genetic studies of the Eurasian brown bear (Ursus arctos) have so far focused on populations from Europe and North America, although the largest distribution area of brown bears is in Asia. In this study, we reveal population genetic parameters for the brown bear population inhabiting the Grand Kaçkar Mountains (GKM) in the north east of Turkey, western Lesser Caucasus. Using both hair (N = 147) and tissue samples (N = 7) collected between 2008 and 2014, we found substantial levels of genetic variation (10 microsatellite loci). Bear samples (hair) taken from rubbing trees worked better for genotyping than those from power poles, regardless of the year collected. Genotyping also revealed that bears moved between habitat patches, despite ongoing massive habitat alterations and the creation of large water reservoirs. This population has the potential to serve as a genetic reserve for future reintroductions in the Middle East. Due to the importance of the GKM population for on-going and future conservation actions, the impacts of habitat alterations in the region ought to be minimized; e.g., by establishing green bridges or corridors over reservoirs and major roads to maintain habitat connectivity and gene flow among populations in the Lesser Caucasus.
The power spectral density (PSD) of any time-dependent stochastic processX (t) is ameaningful feature of its spectral content. In its text-book definition, the PSD is the Fourier transform of the covariance function of X-t over an infinitely large observation timeT, that is, it is defined as an ensemble-averaged property taken in the limitT -> infinity. Alegitimate question is what information on the PSD can be reliably obtained from single-trajectory experiments, if one goes beyond the standard definition and analyzes the PSD of a single trajectory recorded for a finite observation timeT. In quest for this answer, for a d-dimensional Brownian motion (BM) we calculate the probability density function of a single-trajectory PSD for arbitrary frequency f, finite observation time T and arbitrary number k of projections of the trajectory on different axes. We show analytically that the scaling exponent for the frequency-dependence of the PSD specific to an ensemble of BM trajectories can be already obtained from a single trajectory, while the numerical amplitude in the relation between the ensemble-averaged and single-trajectory PSDs is afluctuating property which varies from realization to realization. The distribution of this amplitude is calculated exactly and is discussed in detail. Our results are confirmed by numerical simulations and single-particle tracking experiments, with remarkably good agreement. In addition we consider a truncated Wiener representation of BM, and the case of a discrete-time lattice random walk. We highlight some differences in the behavior of a single-trajectory PSD for BM and for the two latter situations. The framework developed herein will allow for meaningful physical analysis of experimental stochastic trajectories.
Transition metals in inorganic systems and metalloproteins can occur in different oxidation states, which makes them ideal redox-active catalysts. To gain a mechanistic understanding of the catalytic reactions, knowledge of the oxidation state of the active metals, ideally in operando, is therefore critical. L-edge X-ray absorption spectroscopy (XAS) is a powerful technique that is frequently used to infer the oxidation state via a distinct blue shift of L-edge absorption energies with increasing oxidation state. A unified description accounting for quantum-chemical notions whereupon oxidation does not occur locally on the metal but on the whole molecule and the basic understanding that L-edge XAS probes the electronic structure locally at the metal has been missing to date. Here we quantify how charge and spin densities change at the metal and throughout the molecule for both redox and core-excitation processes. We explain the origin of the L-edge XAS shift between the high-spin complexes Mn-II(acac)(2) and Mn-III(acac)(3) as representative model systems and use ab initio theory to uncouple effects of oxidation-state changes from geometric effects. The shift reflects an increased electron affinity of Mn-III in the core-excited states compared to the ground state due to a contraction of the Mn 3d shell upon core-excitation with accompanied changes in the classical Coulomb interactions. This new picture quantifies how the metal-centered core hole probes changes in formal oxidation state and encloses and substantiates earlier explanations. The approach is broadly applicable to mechanistic studies of redox-catalytic reactions in molecular systems where charge and spin localization/delocalization determine reaction pathways.
Properly designed (randomized and/or balanced) experiments are standard in ecological research. Molecular methods are increasingly used in ecology, but studies generally do not report the detailed design of sample processing in the laboratory. This may strongly influence the interpretability of results if the laboratory procedures do not account for the confounding effects of unexpected laboratory events. We demonstrate this with a simple experiment where unexpected differences in laboratory processing of samples would have biased results if randomization in DNA extraction and PCR steps do not provide safeguards. We emphasize the need for proper experimental design and reporting of the laboratory phase of molecular ecology research to ensure the reliability and interpretability of results.