Violaxanthin cycle kinetics analysed in vivo with resonance Raman spectroscopy

Measuring the kinetics of the violaxanthin cycle imposes an experimental challenge. Traditionally, carotenoid analysis was carried out laboriously with high-performance liquid chromatography. In this work, we present the first in vivo approach to directly measure the kinetics of the violaxanthin cycle, using resonance Raman spectroscopy in combination with baseline correction and principal component analysis. Applying the new approach allows measuring thousands of data points as opposed to the few possible with chemical analysis over the course of a violaxanthin cycle kinetics experiment. In vivo analysis of the violaxanthin cycle is necessary to fully understand adaptation kinetics to varying light conditions, the knowledge of which is especially important for assessing the stress tolerance of plants in the wake of the increasing climate change. Three experiments on the green alga Dunaliella salina were performed, featuring both the light-to-dark and dark-to-light transitions response of the algae. This is the peer reviewed version of the following article: Koch, M. et al.: Violaxanthin cycle kinetics analysed in vivo with resonance Raman spectroscopy. In: Journal of Raman Spectroscopy (2017), which has been published in final form at http://onlinelibrary.wiley.com/doi/10.1002/jrs.5102/abstract. This article may be used for non-commercial purposes in accordance with Wiley Terms and Conditions for Self-Archiving

Existence and Stability of a Spike in the Central Component for a Consumer Chain Model

We study a three-component consumer chain model which is based on Schnakenberg type kinetics. In this model there is one consumer feeding on the producer and a second consumer feeding on the first consumer. This means that the first consumer (central component) plays a hybrid role: it acts both as consumer and producer. The model is an extension of the Schnakenberg model suggested in \cite{gm,schn1} for which there is only one producer and one consumer. It is assumed that both the producer and second consumer diffuse much faster than the central component. We construct single spike solutions on an interval for which the profile of the first consumer is that of a spike. The profiles of the producer and the second consumer only vary on a much larger spatial scale due to faster diffusion of these components. It is shown that there exist two different single spike solutions if the feed rates are small enough: a large-amplitude and a small-amplitude spike. We study the stability properties of these solutions in terms of the system parameters. We use a rigorous analysis for the linearized operator around single spike solutions based on nonlocal eigenvalue problems. The following result is established: If the time-relaxation constants for both producer and second consumer vanish, the large-amplitude spike solution is stable and the small-amplitude spike solution is unstable. We also derive results on the stability of solutions when these two time-relaxation constants are small. We show a new effect: if the time-relaxation constant of the second consumer is very small, the large-amplitude spike solution becomes unstable. To the best of our knowledge this phenomenon has not been observed before for the stability of spike patterns. It seems that this behavior is not possible for two-component reaction-diffusion systems but that at least three components are required. Our main motivation to study this system is mathematical since the novel interaction of a spike in the central component with two other components results in new types of conditions for the existence and stability of a spike. This model is realistic if several assumptions are made: (i) cooperation of consumers is prevalent in the system, (ii) the producer and the second consumer diffuse much faster than the first consumer, and (iii) there is practically an unlimited pool of producer. The first assumption has been proven to be correct in many types of consumer groups or populations, the second assumption occurs if the central component has a much smaller mobility than the other two, the third assumption is realistic if the consumers do not feel the impact of the limited amount of producer due to its large quantity. This chain model plays a role in population biology, where consumer and producer are often called predator and prey. This system can also be used as a model for a sequence of irreversible autocatalytic reactions in a container which is in contact with a well-stirred reservoir

TERT Promoter Mutation Detection in Cell-Free Tumor-Derived DNA in Patients with IDH Wild-Type Glioblastomas: A Pilot Prospective Study

Purpose: We conducted a pilot study to assess the feasibility and the potential implications of detecting TERT promoter (TERTp)–mutant cell-free tumor-derived DNA (tDNA) in the cerebrospinal fluid (CSF) and plasma of glioblastoma patients. Experimental Design: Matched CSF and plasma samples were collected in 60 patients with glial tumors. The CSF collection was obtained during surgery, before any surgical manipulation of the tumor. The extracted tDNA and corresponding tumor DNA samples were analyzed for TERTp and isocitrate dehydrogenase (IDH) hotspot mutations. In addition, the variant allele frequency (VAF) of TERTp mutation in the CSF-tDNA was correlated with tumor features and patients’ outcome. Results: Thirty-eight patients had TERTp-mutant/IDH wild-type glioblastomas. The matched TERTp mutation in the CSF-tDNA was successfully detected with 100% specificity (95% CI, 87.6–100%) and 92.1% sensitivity (95% CI, 78.6–98.3%) (n = 35/38). In contrast, the sensitivity in the plasma-tDNA was far lower [n = 3/38, 7.9% (95% CI, 1.6–21.4%)]. We concordantly observed a longer overall survival of patients with low VAF in the CSF-tDNA when compared with patients with high VAF, irrespective of using the lower quartile VAF [11.45%; 14.0 mo. (95% confidence interval, CI, 10.3–17.6) vs. 8.6 mo. (95% CI, 4.1–13.2), P = 0.035], the lower third VAF [13%; 15.4 mo. (95% CI, 11.6–19.2) vs. 8.3 mo. (95% CI, 2.3–14.4), P = 0.008], or the median VAF [20.3%; 14.0 mo. (95% CI, 9.2–18.7) vs. 8.6 mo. (95% CI, 7.5–9.8), P = 0.062] to dichotomize the patients. Conclusions: This pilot study highlights the value of CSF-tDNA for an accurate and reliable detection of TERTp mutations. Furthermore, our findings suggest that high TERTp mutation VAF levels in the CSF-tDNA may represent a suitable predictor of poor survival in glioblastoma patients. Further studies are needed to complement the findings of our exploratory analysis

Stability of cluster solutions in a cooperative consumer chain model

This is the author's accepted manuscript. The final published article is available from the link below. Copyright @ Springer-Verlag Berlin Heidelberg 2012.We study a cooperative consumer chain model which consists of one producer and two consumers. It is an extension of the Schnakenberg model suggested in Gierer and Meinhardt [Kybernetik (Berlin), 12:30-39, 1972] and Schnakenberg (J Theor Biol, 81:389-400, 1979) for which there is only one producer and one consumer. In this consumer chain model there is a middle component which plays a hybrid role: it acts both as consumer and as producer. It is assumed that the producer diffuses much faster than the first consumer and the first consumer much faster than the second consumer. The system also serves as a model for a sequence of irreversible autocatalytic reactions in a container which is in contact with a well-stirred reservoir. In the small diffusion limit we construct cluster solutions in an interval which have the following properties: The spatial profile of the third component is a spike. The profile for the middle component is that of two partial spikes connected by a thin transition layer. The first component in leading order is given by a Green's function. In this profile multiple scales are involved: The spikes for the middle component are on the small scale, the spike for the third on the very small scale, the width of the transition layer for the middle component is between the small and the very small scale. The first component acts on the large scale. To the best of our knowledge, this type of spiky pattern has never before been studied rigorously. It is shown that, if the feedrates are small enough, there exist two such patterns which differ by their amplitudes.We also study the stability properties of these cluster solutions. We use a rigorous analysis to investigate the linearized operator around cluster solutions which is based on nonlocal eigenvalue problems and rigorous asymptotic analysis. The following result is established: If the time-relaxation constants are small enough, one cluster solution is stable and the other one is unstable. The instability arises through large eigenvalues of order O(1). Further, there are small eigenvalues of order o(1) which do not cause any instabilities. Our approach requires some new ideas: (i) The analysis of the large eigenvalues of order O(1) leads to a novel system of nonlocal eigenvalue problems with inhomogeneous Robin boundary conditions whose stability properties have been investigated rigorously. (ii) The analysis of the small eigenvalues of order o(1) needs a careful study of the interaction of two small length scales and is based on a suitable inner/outer expansion with rigorous error analysis. It is found that the order of these small eigenvalues is given by the smallest diffusion constant ε22.RGC of Hong Kon

EGFL7 loss correlates with increased VEGF-D expression, upregulating hippocampal adult neurogenesis and improving spatial learning and memory

Correction: Volume: 80 Issue: 8 DOI: 10.1007/s00018-023-04835-3 Article Number: 201 Published: AUG 2023Neural stem cells reside in the subgranular zone, a specialized neurogenic niche of the hippocampus. Throughout adulthood, these cells give rise to neurons in the dentate gyrus, playing an important role in learning and memory. Given that these core cognitive processes are disrupted in numerous disease states, understanding the underlying mechanisms of neural stem cell proliferation in the subgranular zone is of direct practical interest. Here, we report that mature neurons, neural stem cells and neural precursor cells each secrete the neurovascular protein epidermal growth factor-like protein 7 (EGFL7) to shape this hippocampal niche. We further demonstrate that EGFL7 knock-out in a Nestin-CreERT2-based mouse model produces a pronounced upregulation of neurogenesis within the subgranular zone. RNA sequencing identified that the increased expression of the cytokine VEGF-D correlates significantly with the ablation of EGFL7. We substantiate this finding with intraventricular infusion of VEGF-D upregulating neurogenesis in vivo and further show that VEGF-D knock-out produces a downregulation of neurogenesis. Finally, behavioral studies in EGFL7 knock-out mice demonstrate greater maintenance of spatial memory and improved memory consolidation in the hippocampus by modulation of pattern separation. Taken together, our findings demonstrate that both EGFL7 and VEGF-D affect neurogenesis in the adult hippocampus, with the ablation of EGFL7 upregulating neurogenesis, increasing spatial learning and memory, and correlating with increased VEGF-D expression.Peer reviewe

Synergetic use of IASI and TROPOMI space borne sensors for generating a tropospheric methane profile product

The thermal infrared nadir spectra of IASI (Infrared Atmospheric Sounding Interferometer) are successfully used for retrievals of different atmospheric trace gas profiles. However, these retrievals offer generally reduced information about the lowermost tropospheric layer due to the lack of thermal contrast close to the surface. Spectra of scattered solar radiation observed in the near and/or short wave infrared, for instance by TROPOMI (TROPOspheric Monitoring Instrument) offer higher sensitivity near ground and are used for the retrieval of total column averaged mixing ratios of a variety of atmospheric trace gases. Here we present a method for the synergetic use of IASI profile and TROPOMI total column data. Our method uses the output of the individual retrievals and consists of linear algebra a posteriori calculations (i.e. calculation after the individual retrievals). We show that this approach is largely equivalent to applying the spectra of the different sensors together in a single retrieval procedure, but with the substantial advantage of being applicable to data generated with different individual retrieval processors, of being very time efficient, and of directly benefiting from the high quality and most recent improvements of the individual retrieval processors.This research has largely benefit from funds of the Deutsche Forschungsgemeinschaft (provided for the two projects MOTIV and TEDDY with IDs/Geschäftszeichen 290612604/GZ:SCHN1126/2-1 and 416767181/GZ:SCHN1126/5-1, respectively) and from support by the European Space Agency in the context the "Sentinel-5p+Innovation (S5p+I) - Water Vapour Isotopologues (H2O-ISO)" activities. Furthermore, we acknowledge funds from the Ministerio de Economía y Competividad from Spain for the project INMENSE (CGL2016-80688-P)

Synergetic use of IASI profile and TROPOMI total-column level 2 methane retrieval products

The thermal infrared nadir spectra of IASI (Infrared Atmospheric Sounding Interferometer) are successfully used for retrievals of different atmospheric trace gas profiles. However, these retrievals offer generally reduced information about the lowermost tropospheric layer due to the lack of thermal contrast close to the surface. Spectra of scattered solar radiation observed in the near-infrared and/or shortwave infrared, for instance by TROPOMI (TROPOspheric Monitoring Instrument), offer higher sensitivity near the ground and are used for the retrieval of total-column-averaged mixing ratios of a variety of atmospheric trace gases. Here we present a method for the synergetic use of IASI profile and TROPOMI total-column level 2 retrieval products. Our method uses the output of the individual retrievals and consists of linear algebra a posteriori calculations (i.e. calculation after the individual retrievals). We show that this approach has strong theoretical similarities to applying the spectra of the different sensors together in a single retrieval procedure but with the substantial advantage of being applicable to data generated with different individual retrieval processors, of being very time efficient, and of directly benefiting from the high quality and most recent improvements of the individual retrieval processors. We demonstrate the method exemplarily for atmospheric methane (CH$_4$). We perform a theoretical evaluation and show that the a posteriori combination method yields a total-column-averaged CH$_4$ product (XCH$_4$) that conserves the good sensitivity of the corresponding TROPOMI product while merging it with the high-quality upper troposphere–lower stratosphere (UTLS) CH$_4$ partial-column information of the corresponding IASI product. As a consequence, the combined product offers additional sensitivity for the tropospheric CH$_4$ partial column, which is not provided by the individual TROPOMI nor the individual IASI product. The theoretically predicted synergetic effect is verified by comparisons to CH$_4$ reference data obtained from collocated XCH$_4$ measurements at 14 globally distributed TCCON (Total Carbon Column Observing Network) stations, CH$_4$ profile measurements made by 36 individual AirCore soundings, and tropospheric CH$_4$ data derived from continuous ground-based in situ observations made at two nearby Global Atmospheric Watch (GAW) mountain stations. The comparisons clearly demonstrate that the combined product can reliably detect the actual variations of atmospheric XCH$_4$, CH$_4$ in the UTLS, and CH$_4$ in the troposphere. A similar good reliability for the latter is not achievable by the individual TROPOMI and IASI products

The fingerprint of the summer 2018 drought in Europe on ground-based atmospheric CO2 measurements

During the summer of 2018, a widespread drought developed over Northern and Central Europe. The increase in temperature and the reduction of soil moisture have influenced carbon dioxide (CO2) exchange between the atmosphere and terrestrial ecosystems in various ways, such as a reduction of photosynthesis, changes in ecosystem respiration, or allowing more frequent fires. In this study, we characterize the resulting perturbation of the atmospheric CO2 seasonal cycles. 2018 has a good coverage of European regions affected by drought, allowing the investigation of how ecosystem flux anomalies impacted spatial CO2 gradients between stations. This density of stations is unprecedented compared to previous drought events in 2003 and 2015, particularly thanks to the deployment of the Integrated Carbon Observation System (ICOS) network of atmospheric greenhouse gas monitoring stations in recent years. Seasonal CO2 cycles from 48 European stations were available for 2017 and 2018.The UK sites were funded by the UK Department of Business, Energy and Industrial Strategy (formerly the Department of Energy and Climate Change) through contracts TRN1028/06/2015 and TRN1537/06/2018. The stations at the ClimaDat Network in Spain have received funding from the ‘la Caixa’ Foundation, under agreement 2010-002624

Modelling human choices: MADeM and decision‑making

Research supported by FAPESP 2015/50122-0 and DFG-GRTK 1740/2. RP and AR are also part of the Research, Innovation and Dissemination Center for Neuromathematics FAPESP grant (2013/07699-0). RP is supported by a FAPESP scholarship (2013/25667-8). ACR is partially supported by a CNPq fellowship (grant 306251/2014-0)