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- ItemAn Innovative Protocol for Metaproteomic Analyses of Microbial Pathogens in Cystic Fibrosis Sputum(Lausanne : Frontiers Media, 2021) Graf, Alexander C.; Striesow, Johanna; Pané-Farré, Jan; Sura, Thomas; Wurster, Martina; Lalk, Michael; Pieper, Dietmar H.; Becher, Dörte; Kahl, Barbara C.; Riedel, KatharinaHallmarks of cystic fibrosis (CF) are increased viscosity of mucus and impaired mucociliary clearance within the airways due to mutations of the cystic fibrosis conductance regulator gene. This facilitates the colonization of the lung by microbial pathogens and the concomitant establishment of chronic infections leading to tissue damage, reduced lung function, and decreased life expectancy. Although the interplay between key CF pathogens plays a major role during disease progression, the pathophysiology of the microbial community in CF lungs remains poorly understood. Particular challenges in the analysis of the microbial population present in CF sputum is (I) the inhomogeneous, viscous, and slimy consistence of CF sputum, and (II) the high number of human proteins masking comparably low abundant microbial proteins. To address these challenges, we used 21 CF sputum samples to develop a reliable, reproducible and widely applicable protocol for sputum processing, microbial enrichment, cell disruption, protein extraction and subsequent metaproteomic analyses. As a proof of concept, we selected three sputum samples for detailed metaproteome analyses and complemented and validated metaproteome data by 16S sequencing, metabolomic as well as microscopic analyses. Applying our protocol, the number of bacterial proteins/protein groups increased from 199-425 to 392-868 in enriched samples compared to nonenriched controls. These early microbial metaproteome data suggest that the arginine deiminase pathway and multiple proteases and peptidases identified from various bacterial genera could so far be underappreciated in their contribution to the CF pathophysiology. By providing a standardized and effective protocol for sputum processing and microbial enrichment, our study represents an important basis for future studies investigating the physiology of microbial pathogens in CF in vivo – an important prerequisite for the development of novel antimicrobial therapies to combat chronic recurrent airway infection in CF.
- ItemNonlinear Optical Investigation of Microbial Chromoproteins(Lausanne : Frontiers Media, 2020) Krekic, Szilvia; Zakar, Tomás; Gombos, Zoltán; Valkai, Sándor; Mero, Mark; Zimányi, László; Heiner, Zsuzsanna; Dér, AndrásMembrane-bound or cytosolic light-sensitive proteins, playing a crucial role in energy- and signal-transduction processes of various photosynthetic microorganisms, have been optimized for sensing or harvesting light by myriads of years of evolution. Upon absorption of a photon, they undergo a usually cyclic reaction series of conformations, and the accompanying spectro-kinetic events assign robust nonlinear optical (NLO) properties for these chromoproteins. During recent years, they have attracted a considerable interest among researchers of the applied optics community as well, where finding the appropriate NLO material for a particular application is a pivotal task. Potential applications have emerged in various branches of photonics, including optical information storage and processing, higher-harmonic and white-light continuum generation, or biosensorics. In our earlier work, we also raised the possibility of using chromoproteins, such as bacteriorhodopsin (bR), as building blocks for the active elements of integrated optical (IO) circuits, where several organic and inorganic photonic materials have been considered as active components, but so far none of them has been deemed ideal for the purpose. In the current study, we investigate the linear and NLO properties of biofilms made of photoactive yellow protein (PYP) and bR. The kinetics of the photoreactions are monitored by time-resolved absorption experiments, while the refractive index of the films and its light-induced changes are measured using the Optical Waveguide Lightmode Spectroscopy (OWLS) and Z-scan techniques, respectively. The nonlinear refractive index and the refractive index change of both protein films were determined in the green spectral range in a wide range of intensities and at various laser repetition rates. The nonlinear refractive index and refractive index change of PYP were compared to those of bR, with respect to photonics applications. Our results imply that the NLO properties of these proteins make them promising candidates for utilization in applied photonics, and they should be considered as valid alternatives for active components of IO circuits. © Copyright © 2020 Krekic, Zakar, Gombos, Valkai, Mero, Zimányi, Heiner and Dér.
- ItemThermal Impact on the Culturable Microbial Diversity Along the Processing Chain of Flour From Crickets (Acheta domesticus)(Lausanne : Frontiers Media, 2020) Fröhling, Antje; Bußler, Sara; Durek, Julia; Schlüter, Oliver K.The role of insects for human consumption has lately increased in interest and in order to deliver safe and high-quality raw materials and ingredients for food and feed applications, processing of insects is a major pre-requisite. For edible insects a thermal treatment and appropriate storage conditions are recommended to minimize the microbiological risk and the impact of processing methods on the microbial contamination needs to be considered and determined. Based on standard process conditions for the production of Acheta domesticus flour, different heating treatments were used to reduce the microbial load of A. domesticus. In addition, the drying temperature and drying time were varied to determine whether the required residual moisture of <5% can be achieved more quickly with consistent microbial quality. The influence of the process conditions on the microbial community of A. domesticus along the processing chain was finally investigated under optimized process conditions. The total viable count was reduced from 9.24 log10 CFU/gDM to 1.98 log10 CFU/gDM along the entire processing chain. While Bacillaceae, Enterobacteriaceae, Enterococcaceae, and yeast and molds were no longer detectable in the A. domesticus flour, Staphylococcaceae and mesophilic spore forming bacteria were still found in the flour. The results indicate that the steaming process is essential for effectively increasing microbial safety since this processing step showed the highest inactivation. It is recommended to not only evaluate the total viable count but also to monitor changes in microbial diversity during processing to ensure microbial safety of the final product. © Copyright © 2020 Fröhling, Bußler, Durek and Schlüter.
- ItemThe bleaching limits of IRSL signals at various stimulation temperatures and their potential inference of the pre-burial light exposure duration(Lausanne : Frontiers Media, 2023) Zhang, Jingran; Guralnik, Benny; Tsukamoto, Sumiko; Ankjærgaard, Christina; Reimann, TonyInfrared Stimulated Luminescence (IRSL) techniques are being increasingly used for dating sedimentary feldspars in the middle to late Quaternary. By employing several subsequent stimulations at increasing temperatures, a series of post-IR IRSL (pIRIR) signals with different characteristics (stability and bleachability) can be obtained for an individual sample. It has been experimentally demonstrated that higher-temperature pIRIR signals are more stable, but they tend to exhibit larger residual doses up to few tens of Gy, potentially causing severe age overestimation in young samples. In this study we conducted comprehensive bleaching experiments of IRSL and pIRIR signals using a loess sample from China, and demonstrated that non-bleachable components in the IR (and possibly pIRIR) signals do exist. The level of such non-bleachable signal shows clearly positive correlation with preheat/stimulation temperature, which further supports the notion that lower temperature pIRIR are advantageous to date young samples and sediments especially from difficult-to-bleach environments. These results display a potential in constrain the pre-burial light exposure history of sediment utilizing multiple feldspar post-IR IRSL (pIRIR) signals. For the studied loess sample, we infer that prior to its last burial, the sample has received an equivalent of >264 h exposure to the SOL2 simulator (more than 2,000 h of natural daylight).
- ItemEditorial: Climatic and Associated Cryospheric and Hydrospheric Changes on the Third Pole(Lausanne : Frontiers Media, 2021) Wang, Lei; Song, Chunqiao; Conradt, Tobias; Rasmy, Mohamed; Li, Xiuping[No abstract available]
- ItemThe future is now: Climate displacement and human rights obligations—a note on recent developments in the UN Human Rights Committee(Lausanne : Frontiers Media, 2022) Thornton, FannyAlthough climate litigation—or the pursuit of legal resolve of matters stemming from anthropogenic climate change—has been growing around the world, climate mobility is seldom at the heart of relevant case law. It is human rights law bodies, in particular, which have nevertheless begun to progress legal developments in the sphere of climate mobility. This note looks at a 2022 determination by the UN Human Rights Committee concerning the habitability of a small island setting—Australia's Torres Strait Islands—under climate change conditions and the legal responsibilities of nation states to abide by their international human rights obligations in implementing timely adaptation measures now which could help to ensure continued habitation.
- ItemDepression, anxiety, and burnout in academia: topic modeling of PubMed abstracts(Lausanne : Frontiers Media, 2023) Lezhnina, OlgaThe problem of mental health in academia is increasingly discussed in literature, and to extract meaningful insights from the growing amount of scientific publications, text mining approaches are used. In this study, BERTopic, an advanced method of topic modeling, was applied to abstracts of 2,846 PubMed articles on depression, anxiety, and burnout in academia published in years 1975–2023. BERTopic is a modular technique comprising a text embedding method, a dimensionality reduction procedure, a clustering algorithm, and a weighing scheme for topic representation. A model was selected based on the proportion of outliers, the topic interpretability considerations, topic coherence and topic diversity metrics, and the inevitable subjectivity of the criteria was discussed. The selected model with 27 topics was explored and visualized. The topics evolved differently with time: research papers on students' pandemic-related anxiety and medical residents' burnout peaked in recent years, while publications on psychometric research or internet-related problems are yet to be presented more amply. The study demonstrates the use of BERTopic for analyzing literature on mental health in academia and sheds light on areas in the field to be addressed by further research.
- ItemAre Conference Posters Being Cited?(Lausanne : Frontiers Media, 2021) Haupka, Nick; Schröer, Cäcilia; Hauschke, ChristianWe present a small case study on citations of conference posters using poster collections from both Figshare and Zenodo. The study takes into account the years 2016-2020 according to the dates of publication on the platforms. Citation data was taken from DataCite, Crossref and Dimensions. Primarily, we want to know to what extent scientific posters are being cited and thereby which impact posters potentially have on the scholarly landscape and especially on academic publications. Our data-driven analysis reveals that posters are rarely cited. Citations could only be found for 1% of the posters in our dataset. A limitation in this study however is that the impact of academic posters was not measured empirical but rather descriptive.
- ItemModeling of Individual Fruit-Bearing Capacity of Trees Is Aimed at Optimizing Fruit Quality of Malus x domestica Borkh. 'Gala'(Lausanne : Frontiers Media, 2021) Penzel, Martin; Herppich, Werner B.; Weltzien, Cornelia; Tsoulias, Nikos; Zude-Sasse, ManuelaThe capacity of apple trees to produce fruit of a desired diameter, i.e., fruit-bearing capacity (FBC), was investigated by considering the inter-tree variability of leaf area (LA). The LA of 996 trees in a commercial apple orchard was measured by using a terrestrial two-dimensional (2D) light detection and ranging (LiDAR) laser scanner for two consecutive years. The FBC of the trees was simulated in a carbon balance model by utilizing the LiDAR-scanned total LA of the trees, seasonal records of fruit and leaf gas exchanges, fruit growth rates, and weather data. The FBC was compared to the actual fruit size measured in a sorting line on each individual tree. The variance of FBC was similar in both years, whereas each individual tree showed different FBC in both seasons as indicated in the spatially resolved data of FBC. Considering a target mean fruit diameter of 65 mm, FBC ranged from 84 to 168 fruit per tree in 2018 and from 55 to 179 fruit per tree in 2019 depending on the total LA of the trees. The simulated FBC to produce the mean harvest fruit diameter of 65 mm and the actual number of the harvested fruit >65 mm per tree were in good agreement. Fruit quality, indicated by fruit's size and soluble solids content (SSC), showed enhanced percentages of the desired fruit quality according to the seasonally total absorbed photosynthetic energy (TAPE) of the tree per fruit. To achieve a target fruit diameter and reduce the variance in SSC at harvest, the FBC should be considered in crop load management practices. However, achieving this purpose requires annual spatial monitoring of the individual FBC of trees.
- ItemUnspecific CTL Killing Is Enhanced by High Glucose via TNF-Related Apoptosis-Inducing Ligand(Lausanne : Frontiers Media, 2022) Yang, Wenjuan; Denger, Andreas; Diener, Caroline; Küppers, Frederic; Soriano-Baguet, Leticia; Schäfer, Gertrud; Yanamandra, Archana K.; Zhao, Renping; Knörck, Arne; Schwarz, Eva C.; Hart, Martin; Lammert, Frank; Roma, Leticia Prates; Brenner, Dirk; Christidis, Grigorios; Helms, Volkhard; Meese, Eckart; Hoth, Markus; Qu, BinTNF-related apoptosis inducing ligand (TRAIL) is expressed on cytotoxic T lymphocytes (CTLs) and TRAIL is linked to progression of diabetes. However, the impact of high glucose on TRAIL expression and its related killing function in CTLs still remains largely elusive. Here, we report that TRAIL is substantially up-regulated in CTLs in environments with high glucose (HG) both in vitro and in vivo. Non-mitochondrial reactive oxygen species, NFκB and PI3K/Akt are essential in HG-induced TRAIL upregulation in CTLs. TRAILhigh CTLs induce apoptosis of pancreatic beta cell line 1.4E7. Treatment with metformin and vitamin D reduces HG-enhanced expression of TRAIL in CTLs and coherently protects 1.4E7 cells from TRAIL-mediated apoptosis. Our work suggests that HG-induced TRAILhigh CTLs might contribute to the destruction of pancreatic beta cells in a hyperglycemia condition.