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Institute
- Institut für Biochemie und Biologie (250) (remove)
Research on novel and advanced biomaterials is an indispensable step towards their applications in desirable fields such as tissue engineering, regenerative medicine, cell culture, or biotechnology. The work presented here focuses on such a promising material: polyelectrolyte multilayer (PEM) composed of hyaluronic acid (HA) and poly(L-lysine) (PLL). This gel-like polymer surface coating is able to accumulate (bio-)molecules such as proteins or drugs and release them in a controlled manner. It serves as a mimic of the extracellular matrix (ECM) in composition and intrinsic properties. These qualities make the HA/PLL multilayers a promising candidate for multiple bio-applications such as those mentioned above. The work presented aims at the development of a straightforward approach for assessment of multi-fractional diffusion in multilayers (first part) and at control of local molecular transport into or from the multilayers by laser light trigger (second part).
The mechanism of the loading and release is governed by the interaction of bioactives with the multilayer constituents and by the diffusion phenomenon overall. The diffusion of a molecule in HA/PLL multilayers shows multiple fractions of different diffusion rate. Approaches, that are able to assess the mobility of molecules in such a complex system, are limited. This shortcoming motivated the design of a novel evaluation tool presented here.
The tool employs a simulation-based approach for evaluation of the data acquired by fluorescence recovery after photobleaching (FRAP) method. In this approach, possible fluorescence recovery scenarios are primarily simulated and afterwards compared with the data acquired while optimizing parameters of a model until a sufficient match is achieved. Fluorescent latex particles of different sizes and fluorescein in an aqueous medium are utilized as test samples validating the analysis results. The diffusion of protein cytochrome c in HA/PLL multilayers is evaluated as well.
This tool significantly broadens the possibilities of analysis of spatiotemporal FRAP data, which originate from multi-fractional diffusion, while striving to be widely applicable. This tool has the potential to elucidate the mechanisms of molecular transport and empower rational engineering of the drug release systems.
The second part of the work focuses on the fabrication of such a spatiotemporarily-controlled drug release system employing the HA/PLL multilayer. This release system comprises different layers of various functionalities that together form a sandwich structure. The bottom layer, which serves as a reservoir, is formed by HA/PLL PEM deposited on a planar glass substrate. On top of the PEM, a layer of so-called hybrids is deposited. The hybrids consist of thermoresponsive poly(N-isopropylacrylamide) (PNIPAM) -based hydrogel microparticles with surface-attached gold nanorods. The layer of hybrids is intended to serve as a gate that controls the local molecular transport through the PEM–solution-interface. The possibility of stimulating the molecular transport by near-infrared (NIR) laser irradiation is being explored.
From several tested approaches for the deposition of hybrids onto the PEM surface, the drying-based approach was identified as optimal. Experiments, that examine the functionality of the fabricated sandwich at elevated temperature, document the reversible volume phase transition of the PEM-attached hybrids while sustaining the sandwich stability. Further, the gold nanorods were shown to effectively absorb light radiation in the tissue- and cell-friendly NIR spectral region while transducing the energy of light into heat. The rapid and reversible shrinkage of the PEM-attached hybrids was thereby achieved. Finally, dextran was employed as a model transport molecule. It loads into the PEM reservoir in a few seconds with the partition constant of 2.4, while it spontaneously releases in a slower, sustained manner. The local laser irradiation of the sandwich, which contains the fluorescein isothiocyanate tagged dextran, leads to a gradual reduction of fluorescence intensity in the irradiated region.
The release system fabricated employs renowned photoresponsivity of the hybrids in an innovative setting. The results of the research are a step towards a spatially-controlled on-demand drug release system that paves the way to spatiotemporally controlled drug release.
The approaches developed in this work have the potential to elucidate the molecular dynamics in ECM and to foster engineering of multilayers with properties tuned to mimic the ECM. The work aims at spatiotemporal control over the diffusion of bioactives and their presentation to the cells.
We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.
We recently demonstrated that the sympathetic nervous system can be voluntarily activated following a training program consisting of cold exposure, breathing exercises, and meditation. This resulted in profound attenuation of the systemic inflammatory response elicited by lipopolysaccharide (LPS) administration. Herein, we assessed whether this training program affects the plasma metabolome and if these changes are linked to the immunomodulatory effects observed. A total of 224 metabolites were identified in plasma obtained from 24 healthy male volunteers at six timepoints, of which 98 were significantly altered following LPS administration. Effects of the training program were most prominent shortly after initiation of the acquired breathing exercises but prior to LPS administration, and point towards increased activation of the Cori cycle. Elevated concentrations of lactate and pyruvate in trained individuals correlated with enhanced levels of anti-inflammatory interleukin (IL)-10. In vitro validation experiments revealed that co-incubation with lactate and pyruvate enhances IL-10 production and attenuates the release of pro-inflammatory IL-1 beta and IL-6 by LPS-stimulated leukocytes. Our results demonstrate that practicing the breathing exercises acquired during the training program results in increased activity of the Cori cycle. Furthermore, this work uncovers an important role of lactate and pyruvate in the anti-inflammatory phenotype observed in trained subjects.
The Fram Strait is an area with a relatively low and irregular distribution of diatom microfossils in surface sediments, and thus microfossil records are scarce, rarely exceed the Holocene, and contain sparse information about past richness and taxonomic composition. These attributes make the Fram Strait an ideal study site to test the utility of sedimentary ancient DNA (sedaDNA) metabarcoding. Amplifying a short, partial rbcL marker from samples of sediment core MSM05/5-712-2 resulted in 95.7% of our sequences being assigned to diatoms across 18 different families, with 38.6% of them being resolved to species and 25.8% to genus level. Independent replicates show a high similarity of PCR products, especially in the oldest samples. Diatom sedaDNA richness is highest in the Late Weichselian and lowest in Mid- and Late Holocene samples. Taxonomic composition is dominated by cold-water and sea-ice-associated diatoms and suggests several reorganisations - after the Last Glacial Maximum, after the Younger Dryas, and after the Early and after the Mid-Holocene. Different sequences assigned to, amongst others, Chaetoceros socialis indicate the detectability of intra-specific diversity using sedaDNA. We detect no clear pattern between our diatom sedaDNA record and the previously published IP25 record of this core, although proportions of pennate diatoms increase with higher IP25 concentrations and proportions of Nitzschia cf. frigida exceeding 2% of the assemblage point towards past sea-ice presence.
Ranging behavior of European rabbits (Oryctolagus cuniculus) in urban and suburban landscapes
(2020)
Various mammals, particularly carnivores, reportedly establish smaller home ranges in urban compared with rural areas. This may be because urban environments provide optimal resources within a small area, negating the requirement to range further, or because habitat fragmentation constrains ranging behavior. Comparable information on urban populations of herbivorous mammalian species (such as European rabbits) is scarce. To fill this knowledge gap, we radio-tracked 13 individuals (seven females and six males) equipped with radio collars in a suburban and an urban study site in the city of Frankfurt am Main in Germany during the reproductive season (March to September) of 2012. The study sites differed in levels of habitat fragmentation. We report the smallest home ranges ever described for this species, with mean 95% minimum convex polygons (MCPs) covering 0.50 ha, while no consistent differences between sites were uncovered. We occasionally tracked individuals crossing streets underground (in burrows), suggesting that streets may restrict the ranging behavior of rabbits-and possibly other burrowing species-to a much lesser extent than previously thought. We conclude that heterogeneous landscape structures, made up of a diverse mosaic of buildings, parks, and gardens, provide sufficient food and shelter in close proximity to burrows at both study sites. Therefore, our data support the hypothesis that optimal resources constrain ranges in this case rather than habitat fragmentation.
Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.
Although the use of stable transformation technology has led to great insight into gene function, its application in high-throughput studies remains arduous. Agro-infiltration have been widely used in species such as Nicotiana benthamiana for the rapid detection of gene expression and protein interaction analysis, but this technique does not work efficiently in other plant species, including Arabidopsis thaliana. As an efficient high-throughput transient expression system is currently lacking in the model plant species A. thaliana, we developed a method that is characterized by high efficiency, reproducibility, and suitability for transient expression of a variety of functional proteins in A. thaliana and 7 other plant species, including Brassica oleracea, Capsella rubella, Thellungiella salsuginea, Thellungiella halophila, Solanum tuberosum, Capsicum annuum, and N. benthamiana. Efficiency of this method was independently verified in three independent research facilities, pointing to the robustness of this technique. Furthermore, in addition to demonstrating the utility of this technique in a range of species, we also present a case study employing this method to assess protein-protein interactions in the sucrose biosynthesis pathway in Arabidopsis.
Completely water-based systems are of interest for the development of novel material for various reasons: On one hand, they provide benign environment for biological systems and on the other hand they facilitate effective molecular transport in a membrane-free environment. In order to investigate the general potential of aqueous two-phase systems (ATPSs) for biomaterials and compartmentalized systems, various solid particles were applied to stabilize all-aqueous emulsion droplets. The target ATPS to be investigated should be prepared via mixing of two aqueous solutions of water-soluble polymers, which turn biphasic when exceeding a critical polymer concentration. Hydrophilic polymers with a wide range of molar mass such as dextran/poly(ethylene glycol) (PEG) can therefore be applied. Solid particles adsorbed at the interfaces can be exceptionally efficient stabilizers forming so-called Pickering emulsions, and nanoparticles can bridge the correlation length of polymer solutions and are thereby the best option for water-in-water emulsions.
The first approach towards the investigation of ATPS was conducted with all aqueous dextran-PEG emulsions in the presence of poly(dopamine) particles (PDP) in Chapter 4. The water-in-water emulsions were formed with a PEG/dextran system via utilizing PDP as stabilizers. Studies of the formed emulsions were performed via laser scanning confocal microscope (CLSM), optical microscope (OM), cryo-scanning electron microscope (SEM) and tensiometry. The stable emulsions (at least 16 weeks) were demulsified easily via dilution or surfactant addition. Furthermore, the solid PDP at the water-water interface were crosslinked in order to inhibit demulsification of the Pickering emulsion. Transmission electron microscope (TEM) and scanning electron microscope (SEM) were used to visualize the morphology of PDP before and after crosslinking. PDP stabilized water-in-water emulsions were utilized in the following Chapter 5 to form supramolecular compartmentalized hydrogels. Here, hydrogels were prepared in pre-formed water-in-water emulsions and gelled via α-cyclodextrin-PEG (α-CD-PEG) inclusion complex formation. Studies of the formed complexes were performed via X-ray powder diffraction (XRD) and the mechanical properties of the hydrogels were measured with oscillatory shear rheology. In order to verify the compartmentalized state and its triggered decomposition, hydrogels and emulsions were assessed via OM, SEM and CLSM. The last chapter broadens the investigations from the previous two systems by utilizing various carbon nitrides (CN) as different stabilizers in ATPS. CN introduces another way to trigger demulsification, namely irradiation with visible light. Therefore, emulsification and demulsification with various triggers were probed. The investigated all aqueous multi-phase systems will act as model for future fabrication of biocompatible materials, cell micropatterning as well as separation of compartmentalized systems.
Ecosystems with highly pulsed water supply must be better understood as climate change may increase frequency and severity of intense storms, droughts and floods. Here we collected data over 3 years (2016-2018) in the episodic wetland outflow channel (Aluize), Banhine National Park, in which the system state changed from dry to wet to dry. Field sampling included vegetation records, small-scale vegetation zoning, the seed bank and water and soil quality. The same main plant species were found in both dry and wet conditions across the riverbed of the outflow channel. We found only very few diaspores of plants in the soil after prolonged drought. In the subsequent flooded state, we examined very dense vegetation on the water surface, which was dominated by the gramineous species Paspalidium obtusifolium. This species formed a compact floating mat that was rooted to the riverbed. The Cyperaceae Bolboschoenus glaucus showed high clonal growth in the form of root tubers, which likely serve as important food reservoir during drought. Soil and water analyses do not indicate a limitation by nutrients. We outline how resident people may change the plant community structure with an increasing practice of setting fire to the meadows in the dried-up riverbed to facilitate plant regrowth as food for their livestock.
Ecosystems with highly pulsed water supply must be better understood as climate change may increase frequency and severity of intense storms, droughts and floods. Here we collected data over 3 years (2016-2018) in the episodic wetland outflow channel (Aluize), Banhine National Park, in which the system state changed from dry to wet to dry. Field sampling included vegetation records, small-scale vegetation zoning, the seed bank and water and soil quality. The same main plant species were found in both dry and wet conditions across the riverbed of the outflow channel. We found only very few diaspores of plants in the soil after prolonged drought. In the subsequent flooded state, we examined very dense vegetation on the water surface, which was dominated by the gramineous species Paspalidium obtusifolium. This species formed a compact floating mat that was rooted to the riverbed. The Cyperaceae Bolboschoenus glaucus showed high clonal growth in the form of root tubers, which likely serve as important food reservoir during drought. Soil and water analyses do not indicate a limitation by nutrients. We outline how resident people may change the plant community structure with an increasing practice of setting fire to the meadows in the dried-up riverbed to facilitate plant regrowth as food for their livestock.
Mitochondrial genomes of Late Pleistocene caballine horses from China belong to a separate clade
(2020)
There were several species of Equus in northern China during the Late Pleistocene, including Equus przewalskii and Equus dalianensis. A number of morphological studies have been carried out on E. przewalskii and E. dalianensis, but their evolutionary history is still unresolved. In this study, we retrieved near-complete mitochondrial genomes from E. dalianensis and E. przewalskii specimens excavated from Late Pleistocene strata in northeastern China. Phylogenetic analyses revealed that caballoid horses were divided into two subclades: the New World and the Old World caballine horse subclades. The Old World caballine horses comprise of two deep phylogenetic lineages, with modern and ancient Equus caballus and modern E. przewalskii forming lineage I, and the individuals in this study together with one Yakut specimen forming lineage II. Our results indicate that Chinese Late Pleistocene caballoid horses showed a closer relationship to other Eurasian caballine horses than that to Pleistocene horses from North America. In addition, phylogenetic analyses suggested a close relationship between E. dalianensis and the Chinese fossil E. przewalskii, in agreement with previous researches based on morphological analyses. Interestingly, E. dalianensis and the fossil E. przewalskii were intermixed rather than split into distinct lineages, suggesting either that gene flow existed between these two species or that morphology-based species assignment of palaeontological specimens is not always correct. Moreover, Bayesian analysis showed that the divergence time between the New World and the Old World caballoid horses was at 1.02 Ma (95% CI: 0.86-1.24 Ma), and the two Old World lineages (I & II) split at 0.88 Ma (95% CI: 0.69-1.13 Ma), which indicates that caballoid horses seem to have evolved into different populations in the Old World soon after they migrated from North America via the Bering Land Bridge. Finally, the TMRCA of E. dalianensis was estimated at 0.20 Ma (95% CI: 0.15-0.28 Ma), and it showed a relative low genetic diversity compared with other Equus species.
Electrochemical methods offer the simple characterization of the synthesis of molecularly imprinted polymers (MIPs) and the readouts of target binding. The binding of electroinactive analytes can be detected indirectly by their modulating effect on the diffusional permeability of a redox marker through thin MIP films. However, this process generates an overall signal, which may include nonspecific interactions with the nonimprinted surface and adsorption at the electrode surface in addition to (specific) binding to the cavities. Redox-active low-molecular-weight targets and metalloproteins enable a more specific direct quantification of their binding to MIPs by measuring the faradaic current. The in situ characterization of enzymes, MIP-based mimics of redox enzymes or enzyme-labeled targets, is based on the indication of an electroactive product. This approach allows the determination of both the activity of the bio(mimetic) catalyst and of the substrate concentration.
Biogenic greenhouse gas emissions, e.g., of methane (CH4) and carbon dioxide (CO2) from inland waters, contribute substantially to global warming. In aquatic systems, dissolved greenhouse gases are highly heterogeneous in both space and time. To better understand the biological and physical processes that affect sources and sinks of both CH4 and CO2, their dissolved concentrations need to be measured with high spatial and temporal resolution. To achieve this goal, we developed the Fast-Response Automated Gas Equilibrator (FaRAGE) for real-time in situ measurement of dissolved CH4 and CO2 concentrations at the water surface and in the water column. FaRAGE can achieve an exceptionally short response time (t(95%) = 12 s when including the response time of the gas analyzer) while retaining an equilibration ratio of 62.6% and a measurement accuracy of 0.5% for CH4. A similar performance was observed for dissolved CO2 (t(95%) = 10 s, equilibration ratio 67.1 %). An equilibration ratio as high as 91.8% can be reached at the cost of a slightly increased response time (16 s). The FaRAGE is capable of continuously measuring dissolved CO2 and CH4 concentrations in the nM-to-submM (10(-9)-10(-3) mol L-1) range with a detection limit of subnM (10(-10) mol L-1), when coupling with a cavity ring-down greenhouse gas analyzer (Picarro GasScouter). FaRAGE allows for the possibility of mapping dissolved concentration in a "quasi" three-dimensional manner in lakes and provides an inexpensive alternative to other commercial gas equilibrators. It is simple to operate and suitable for continuous monitoring with a strong tolerance for suspended particles. While the FaRAGE is developed for inland waters, it can be also applied to ocean waters by tuning the gas-water mixing ratio. The FaRAGE is easily adapted to suit other gas analyzers expanding the range of potential applications, including nitrous oxide and isotopic composition of the gases.
Xenikoudakis et al. report a partial mitochondrial genome of the extinct giant beaver Castoroides and estimate the origin of aquatic behavior in beavers to approximately 20 million years. This time estimate coincides with the extinction of terrestrial beavers and raises the question whether the two events had a common cause.
Synthesis and purification of peptide drugs for medical applications is a challenging task. The leech-derived factor hirudin is in clinical use as an alternative to heparin in anticoagulatory therapies. So far, recombinant hirudin is mainly produced in bacterial or yeast expression systems. We describe the successful development and application of an alternative protocol for the synthesis of active hirudin based on a cell-free protein synthesis approach. Three different cell lysates were compared, and the effects of two different signal peptide sequences on the synthesis of mature hirudin were determined. The combination of K562 cell lysates and the endogenous wild-type signal peptide sequence was most effective. Cell-free synthesized hirudin showed a considerably higher anti-thrombin activity compared to recombinant hirudin produced in bacterial cells.
Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (R-S). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions.
Dual glucagon-like peptide-1/glucagon receptor agonists have emerged as promising candidates for the treatment of diabetes and obesity. Issues of degradation sensitivity and rapid renal clearance are addressed, for example, by the conjugation of peptides to fatty acid chains, promoting reversible albumin binding. We use combined dynamic and static light scattering to directly measure the self-assembly of a set of dual peptide agonists based on the exendin-4 structure with varying fatty acid chain lengths in terms of apparent molecular mass and hydrodynamic radius (R-S). We use NMR spectroscopy to gain an insight into the molecular architecture of the assembly. We investigate conformational changes of the monomeric subunits resulting from peptide self-assembly and assembly stability as a function of the fatty acid chain length using circular dichroism and fluorescence spectroscopy. Our results demonstrate that self-assembly of the exendin-4-derived dual agonist peptides is essentially driven by hydrophobic interactions involving the conjugated acyl chains. The fatty acid chain length affects assembly equilibria and the assembly stability, although the peptide subunits in the assembly retain a dynamic secondary structure. The assembly architecture is characterized by juxtaposition of the fatty acyl side chains and a hydrophobic cluster of the peptide moiety. This cluster experiences local conformational changes in the assembly compared to the monomeric unit leading to a reduction in solvent exposure. The N-terminal half of the peptide and a C-terminal loop are not in contact with neighboring peptide subunits in the assemblies. Altogether, our study contributes to a thorough understanding of the association characteristics and the tendency toward self-assembly in response to lipidation. This is important not only to achieve the desired bioavailability but also with respect to the physical stability of peptide solutions.
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
External temperature change has been shown to modify epigenetic patterns, such as DNA methylation, which regulates gene expression. DNA methylation is heritable, and as such provides a mechanism to convey environmental information to subsequent generations. Studies on epigenetic response to temperature increase are still scarce in wild mammals, even more so studies that compare tissue-specific epigenetic responses. Here, we aim to address differential epigenetic responses on a gene and gene pathway level in two organs, liver and testis. We chose these organs, because the liver is the main metabolic and thermoregulation organ, and epigenetic modifications in testis are potentially transmitted to the F2 generation. We focused on the transmission of DNA methylation changes to naive male offspring after paternal exposure to an ambient temperature increase of 10 degrees C, and investigated differential methylated regions of sons sired before and after the paternal exposure using Reduced Representation Bisulfite Sequencing. We detected both a highly tissue-specific epigenetic response, reflected in genes involved in organ-specific metabolic pathways, and a more general regulation of single genes epigenetically modified in both organs. We conclude that genomes are context-specifically differentially epigenetically regulated in response to temperature increase. These findings emphasize the epigenetic relevance in cell differentiation, which is essential for the specific function(s) of complex organs, and is represented in a diverse molecular regulation of genes and gene pathways. The results also emphasize the paternal contribution to adaptive processes.
Epigenetic histone modulation contributes to improvements in inflammatory bowel disease via EBI3
(2020)
Ulcerative colitis (UC) is characterized by relapsing-remitting inflammatory episodes paralleled by varying cytokine levels, suggesting that switching epigenetic processes might be involved. However, the epigenetic impact on cytokine levels in colitis is mostly unexplored. The heterodimeric interleukin (IL)-12 cytokine family have various functions in both pro- and anti-inflammatory processes. The family member IL-35 (EBI3/IL-12p35) was recently reported to play an anti-inflammatory role in UC. Therefore, we aimed to investigate a possible epigenetic regulation of the IL-35 subunits in vitro and in vivo, and to examine the epigenetic targeting of EBI3 expression as a therapeutic option for UC. Exposure to either the pro-inflammatory TNF alpha or to histone deacetylase inhibitors (HDACi) significantly increased EBI3 expression in Human Colon Epithelial Cells (HCEC) generated from healthy tissue. When applied in combination, a drastic upregulation of EBI3 expression occurred, suggesting a synergistic mechanism. Consequently, IL-35 was increased as well. In vivo, the intestines of HDACi-treated wild-type mice exhibited reduced pathological signs of colitis compared to non-treated colitic mice. However, the improvement by HDACi treatment was completely lost in Ebi3-deficient mice (Ebi3(-/-)). In fact, HDACi appeared to exacerbate the disease phenotype in Ebi3(-/-). In conclusion, our results reveal that under inflammatory conditions, EBI3 is upregulated by the epigenetic mechanism of histone acetylation. The in vivo data show that the deficiency of EBI3 plays a key role in colitis manifestation. Concordantly, our data suggest that conditions promoting histone acetylation, such as upon HDACi application, improve colitis by a mechanism involving the local formation of the anti-inflammatory cytokine IL-35.
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.
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.
To meet the demands of a growing world population while reducing carbon dioxide (CO2) emissions, it is necessary to capture CO2 and convert it into value-added compounds. In recent years, metabolic engineering of microbes has gained strong momentum as a strategy for the production of valuable chemicals. As common microbial feedstocks like glucose directly compete with human consumption, the one carbon (C1) compound formate was suggested as an alternative feedstock. Formate can be easily produced by various means including electrochemical reduction of CO2 and could serve as a feedstock for microbial production, hence presenting a novel entry point for CO2 to the biosphere and a storage option for excess electricity. Compared to the gaseous molecule CO2, formate is a highly soluble compound that can be easily handled and stored. It can serve as a carbon and energy source for natural formatotrophs, but these microbes are difficult to cultivate and engineer. In this work, I present the results of several projects that aim to establish efficient formatotrophic growth of E. coli – which cannot naturally grow on formate – via synthetic formate assimilation pathways. In the first study, I establish a workflow for growth-coupled metabolic engineering of E. coli. I demonstrate this approach by presenting an engineering scheme for the PFL-threonine cycle, a synthetic pathway for anaerobic formate assimilation in E. coli. The described methods are intended to create a standardized toolbox for engineers that aim to establish novel metabolic routes in E. coli and related organisms. The second chapter presents a study on the catalytic efficiency of C1-oxidizing enzymes in vivo. As formatotrophic growth requires generation of both energy and biomass from formate, the engineered E. coli strains need to be equipped with a highly efficient formate dehydrogenase, which provides reduction equivalents and ATP for formate assimilation. I engineered a strain that cannot generate reducing power and energy for cellular growth, when fed on acetate. Under this condition, the strain depends on the introduction of an enzymatic system for NADH regeneration, which could further produce ATP via oxidative phosphorylation. I show that the strain presents a valuable testing platform for C1-oxidizing enzymes by testing different NAD-dependent formate and methanol dehydrogenases in the energy auxotroph strain. Using this platform, several candidate enzymes with high in vivo activity, were identified and characterized as potential energy-generating systems for synthetic formatotrophic or methylotrophic growth in E. coli. In the third chapter, I present the establishment of the serine threonine cycle (STC) – a synthetic formate assimilation pathway – in E. coli. In this pathway, formate is assimilated via formate tetrahydrofolate ligase (FtfL) from Methylobacterium extorquens (M. extorquens). The carbon from formate is attached to glycine to produce serine, which is converted into pyruvate entering central metabolism. Via the natural threonine synthesis and cleavage route, glycine is regenerated and acetyl-CoA is produced as the pathway product. I engineered several selection strains that depend on different STC modules for growth and determined key enzymes that enable high flux through threonine synthesis and cleavage. I could show that expression of an auxiliary formate dehydrogenase was required to achieve growth via threonine synthesis and cleavage on pyruvate. By overexpressing most of the pathway enzymes from the genome, and applying adaptive laboratory evolution, growth on glycine and formate was achieved, indicating the activity of the complete cycle. The fourth chapter shows the establishment of the reductive glycine pathway (rGP) – a short, linear formate assimilation route – in E. coli. As in the STC, formate is assimilated via M. extorquens FtfL. The C1 from formate is condensed with CO2 via the reverse reaction of the glycine cleavage system to produce glycine. Another carbon from formate is attached to glycine to form serine, which is assimilated into central metabolism via pyruvate. The engineered E. coli strain, expressing most of the pathway genes from the genome, can grow via the rGP with formate or methanol as a sole carbon and energy source.
Methane is an important greenhouse gas contributing to global climate change. Natural environments and restored wetlands contribute a large proportion to the global methane budget. Methanogenic archaea (methanogens) and methane oxidizing bacteria (methanotrophs), the biogenic producers and consumers of methane, play key roles in the methane cycle in those environments. A large number of studies revealed the distribution, diversity and composition of these microorganisms in individual habitats. However, uncertainties exist in predicting the response and feedback of methane-cycling microorganisms to future climate changes and related environmental changes due to the limited spatial scales considered so far, and due to a poor recognition of the biogeography of these important microorganisms combining global and local scales.
With the aim of improving our understanding about whether and how methane-cycling microbial communities will be affected by a series of dynamic environmental factors in response to climate change, this PhD thesis investigates the biogeographic patterns of methane-cycling communities, and the driving factors which define these patterns at different spatial scales. At the global scale, a meta-analysis was performed by implementing 94 globally distributed public datasets together with environmental data from various natural environments including soils, lake sediments, estuaries, marine sediments, hydrothermal sediments and mud volcanos. In combination with a global biogeographic map of methanogenic archaea from multiple natural environments, this thesis revealed that biogeographic patterns of methanogens exist. The terrestrial habitats showed higher alpha diversities than marine environments. Methanoculleus and Methanosaeta (Methanothrix) are the most frequently detected taxa in marine habitats, while Methanoregula prevails in terrestrial habitats. Estuary ecosystems, the transition zones between marine and terrestrial/limnic ecosystems, have the highest methanogenic richness but comparably low methane emission rates. At the local scale, this study compared two rewetted fens with known high methane emissions in northeastern Germany, a coastal brackish fen (Hütelmoor) and a freshwater riparian fen (Polder Zarnekow). Consistent with different geochemical conditions and land-use history, the two rewetted fens exhibit dissimilar methanogenic and, especially, methanotrophic community compositions. The methanotrophic community was generally under-represented among the prokaryotic communities and both fens show similarly low ratios of methanotrophic to methanogenic abundances. Since few studies have characterized methane-cycling microorganisms in rewetted fens, this study provides first evidence that the rapid and well re-established methanogenic community in combination with the low and incomplete re-establishment of the methanotrophic community after rewetting contributes to elevated sustained methane fluxes following rewetting.
Finally, this thesis demonstrates that dispersal limitation only slightly regulates the biogeographic distribution patterns of methanogenic microorganisms in natural environments and restored wetlands. Instead, their existence, adaption and establishment are more associated with the selective pressures under different environmental conditions. Salinity, pH and temperature are identified as the most important factors in shaping microbial community structure at different spatial scales (global versus terrestrial environments). Predicted changes in climate, such as increasing temperature, changes in precipitation patterns and increasing frequency of flooding events, are likely to induce a series of environmental alterations, which will either directly or indirectly affect the driving environmental forces of methanogenic communities, leading to changes in their community composition and thus potentially also in methane emission patterns in the future.
Resilience trinity
(2020)
Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
Resilience trinity
(2020)
Ensuring ecosystem resilience is an intuitive approach to safeguard the functioning of ecosystems and hence the future provisioning of ecosystem services (ES). However, resilience is a multi-faceted concept that is difficult to operationalize. Focusing on resilience mechanisms, such as diversity, network architectures or adaptive capacity, has recently been suggested as means to operationalize resilience. Still, the focus on mechanisms is not specific enough. We suggest a conceptual framework, resilience trinity, to facilitate management based on resilience mechanisms in three distinctive decision contexts and time-horizons: 1) reactive, when there is an imminent threat to ES resilience and a high pressure to act, 2) adjustive, when the threat is known in general but there is still time to adapt management and 3) provident, when time horizons are very long and the nature of the threats is uncertain, leading to a low willingness to act. Resilience has different interpretations and implications at these different time horizons, which also prevail in different disciplines. Social ecology, ecology and engineering are often implicitly focussing on provident, adjustive or reactive resilience, respectively, but these different notions of resilience and their corresponding social, ecological and economic tradeoffs need to be reconciled. Otherwise, we keep risking unintended consequences of reactive actions, or shying away from provident action because of uncertainties that cannot be reduced. The suggested trinity of time horizons and their decision contexts could help ensuring that longer-term management actions are not missed while urgent threats to ES are given priority.
Large-scale crop yield failures are increasingly associated with food price spikes and food insecurity and are a large source of income risk for farmers. While the evidence linking extreme weather to yield failures is clear, consensus on the broader set of weather drivers and conditions responsible for recent yield failures is lacking. We investigate this for the case of four major crops in Germany over the past 20 years using a combination of machine learning and process-based modelling. Our results confirm that years associated with widespread yield failures across crops were generally associated with severe drought, such as in 2018 and to a lesser extent 2003. However, for years with more localized yield failures and large differences in spatial patterns of yield failures between crops, no single driver or combination of drivers was identified. Relatively large residuals of unexplained variation likely indicate the importance of non-weather related factors, such as management (pest, weed and nutrient management and possible interactions with weather) explaining yield failures. Models to inform adaptation planning at farm, market or policy levels are here suggested to require consideration of cumulative resource capture and use, as well as effects of extreme events, the latter largely missing in process-based models. However, increasingly novel combinations of weather events under climate change may limit the extent to which data driven methods can replace process-based models in risk assessments.
Context Cities are a challenging habitat for obligate nocturnal mammals because of the ubiquitous use of artificial light at night (ALAN). How nocturnal animals move in an urban landscape, particularly in response to ALAN is largely unknown. Objectives We studied the movement responses, foraging and commuting, of common noctules (Nyctalus noctula) to urban landscape features in general and ALAN in particular. Methods We equipped 20 bats with miniaturized GPS loggers in the Berlin metropolitan area and related spatial positions of bats to anthropogenic and natural landscape features and levels of ALAN. Results Common noctules foraged close to ALAN only next to bodies of water or well vegetated areas, probably to exploit swarms of insects lured by street lights. In contrast, they avoided illuminated roads, irrespective of vegetation cover nearby. Predictive maps identified most of the metropolitan area as non-favoured by this species because of high levels of impervious surfaces and ALAN. Dark corridors were used by common noctules for commuting and thus likely improved the permeability of the city landscape. Conclusions We conclude that the spatial use of common noctules, previously considered to be more tolerant to light than other bats, is largely constrained by ALAN. Our study is the first individual-based GPS tracking study to show sensitive responses of nocturnal wildlife to light pollution. Approaches to protect urban biodiversity need to include ALAN to safeguard the larger network of dark habitats for bats and other nocturnal species in cities.
Developmental success of sea turtle clutches depends on incubation temperature, which also determines sex ratio of hatchlings. As global temperatures are rising, several studies have proposed mitigation strategies such as irrigation and shading to increase hatching success. Our study expands upon this research and measures the effects of using boxes with different degrees of shade coverage (50%, 80%, and 90%) on sand temperature and water content. Boxes were fully covered with fabric in 2017/2018 (top and sides) but were side open in 2018/2019. We took measurements at olive ridley (Lepidochelys olivacea) and leatherback (Dermochelys coriacea) turtle nest depths (45 and 75 cm) at Playa Grande, Costa Rica. Shading reduced temperature by up to 0.8 degrees C and up to 0.4 degrees C at 45 cm and 75 cm, respectively. There were statistically significant differences between shading and control treatments at both depths, but differences between shade treatments were only significant when using side open boxes, possibly due to air flow. Shading had no effect on water content. While the impact of using shaded boxes on temperature was low, the potential impact on primary sex ratios was large. If shading were applied to leatherback clutches, the percentage of female hatchlings could vary by up to 50%, with a maximum difference around the pivotal temperature (temperature with 1:1 sex ratio). Shading can be useful to increase hatching success, but we recommend avoiding it at temperatures within the transitional range (temperatures that produce both sexes), or using it only during the last third of incubation, when sex is already determined. As global warming will likely continue, understanding potential impact and effectiveness of mitigation strategies may be critical for the survival of threatened sea turtle populations.
The competitive exclusion principle is one of the oldest ideas in ecology and states that without additional self-limitation two predators cannot coexist on a single prey. The search for mechanisms allowing coexistence despite this has identified niche differentiation between predators as crucial: without this, coexistence requires the predators to have exactly the same R* values, which is considered impossible. However, this reasoning misses a critical point: predators' R* values are not static properties, but affected by defensive traits of their prey, which in turn can adapt in response to changes in predator densities. Here I show that this feedback between defense and predator dynamics enables stable predator coexistence without ecological niche differentiation. Instead, the mechanism driving coexistence is that prey adaptation causes defense to converge to the value where both predators have equal R* values ("fitness equalization"). This result is highly general, independent of specific model details, and applies to both rapid defense evolution and inducible defenses. It demonstrates the importance of considering long-standing ecological questions from an eco-evolutionary viewpoint, and showcases how the effects of adaptation can cascade through communities, driving diversity on higher trophic levels. These insights offer an important new perspective on coexistence theory.
Plans are currently being drafted for the next decade of action on biodiversity-both the post-2020 Global Biodiversity Framework of the Convention on Biological Diversity (CBD) and Biodiversity Strategy of the European Union (EU). Freshwater biodiversity is disproportionately threatened and underprioritized relative to the marine and terrestrial biota, despite supporting a richness of species and ecosystems with their own intrinsic value and providing multiple essential ecosystem services. Future policies and strategies must have a greater focus on the unique ecology of freshwater life and its multiple threats, and now is a critical time to reflect on how this may be achieved. We identify priority topics including environmental flows, water quality, invasive species, integrated water resources management, strategic conservation planning, and emerging technologies for freshwater ecosystem monitoring. We synthesize these topics with decades of first-hand experience and recent literature into 14 special recommendations for global freshwater biodiversity conservation based on the successes and setbacks of European policy, management, and research. Applying and following these recommendations will inform and enhance the ability of global and European post-2020 biodiversity agreements to halt and reverse the rapid global decline of freshwater biodiversity.
Alkylphospholipids are a novel class of antineoplastic drugs showing remarkable therapeutic potential. Among them, erufosine (EPC3) is a promising drug for the treatment of several types of tumors. While EPC3 is supposed to exert its function by interacting with lipid membranes, the exact molecular mechanisms involved are not known yet. In this work, we applied a combination of several fluorescence microscopy and analytical chemistry approaches (i.e., scanning fluorescence correlation spectroscopy, line-scan fluorescence correlation spectroscopy, generalized polarization imaging, as well as thin layer and gas chromatography) to quantify the effect of EPC3 in biophysical models of the plasma membrane, as well as in cancer cell lines. Our results indicate that EPC3 affects lipid–lipid interactions in cellular membranes by decreasing lipid packing and increasing membrane disorder and fluidity. As a consequence of these alterations in the lateral organization of lipid bilayers, the diffusive dynamics of membrane proteins are also significantly increased. Taken together, these findings suggest that the mechanism of action of EPC3 could be linked to its effects on fundamental biophysical properties of lipid membranes, as well as on lipid metabolism in cancer cells.
Alkylphospholipids are a novel class of antineoplastic drugs showing remarkable therapeutic potential. Among them, erufosine (EPC3) is a promising drug for the treatment of several types of tumors. While EPC3 is supposed to exert its function by interacting with lipid membranes, the exact molecular mechanisms involved are not known yet. In this work, we applied a combination of several fluorescence microscopy and analytical chemistry approaches (i.e., scanning fluorescence correlation spectroscopy, line-scan fluorescence correlation spectroscopy, generalized polarization imaging, as well as thin layer and gas chromatography) to quantify the effect of EPC3 in biophysical models of the plasma membrane, as well as in cancer cell lines. Our results indicate that EPC3 affects lipid–lipid interactions in cellular membranes by decreasing lipid packing and increasing membrane disorder and fluidity. As a consequence of these alterations in the lateral organization of lipid bilayers, the diffusive dynamics of membrane proteins are also significantly increased. Taken together, these findings suggest that the mechanism of action of EPC3 could be linked to its effects on fundamental biophysical properties of lipid membranes, as well as on lipid metabolism in cancer cells.
The development of bioinspired self-assembling materials, such as hydrogels, with promising applications in cell culture, tissue engineering and drug delivery is a current focus in material science. Biogenic or bioinspired proteins and peptides are frequently used as versatile building blocks for extracellular matrix (ECM) mimicking hydrogels. However, precisely controlling and reversibly tuning the properties of these building blocks and the resulting hydrogels remains challenging. Precise control over the viscoelastic properties and self-healing abilities of hydrogels are key factors for developing intelligent materials to investigate cell matrix interactions. Thus, there is a need to develop building blocks that are self-healing, tunable and self-reporting. This thesis aims at the development of α-helical peptide building blocks, called coiled coils (CCs), which integrate these desired properties. Self-healing is a direct result of the fast self-assembly of these building blocks when used as material cross-links. Tunability is realized by means of reversible histidine (His)-metal coordination bonds. Lastly, implementing a fluorescent readout, which indicates the CC assembly state, self-reporting hydrogels are obtained.
Coiled coils are abundant protein folding motifs in Nature, which often have mechanical function, such as in myosin or fibrin. Coiled coils are superhelices made up of two or more α-helices wound around each other. The assembly of CCs is based on their repetitive sequence of seven amino acids, so-called heptads (abcdefg). Hydrophobic amino acids in the a and d position of each heptad form the core of the CC, while charged amino acids in the e and g position form ionic interactions. The solvent-exposed positions b, c and f are excellent targets for modifications since they are more variable. His-metal coordination bonds are strong, yet reversible interactions formed between the amino acid histidine and transition metal ions (e.g. Ni2+, Cu2+ or Zn2+). His-metal coordination bonds essentially contribute to the mechanical stability of various high-performance proteinaceous materials, such as spider fangs, Nereis worm jaws and mussel byssal threads. Therefore, I bioengineered reversible His-metal coordination sites into a well-characterized heterodimeric CC that served as tunable material cross-link. Specifically, I took two distinct approaches facilitating either intramolecular (Chapter 4.2) and/or intermolecular (Chapter 4.3) His-metal coordination.
Previous research suggested that force-induced CC unfolding in shear geometry starts from the points of force application. In order to tune the stability of a heterodimeric CC in shear geometry, I inserted His in the b and f position at the termini of force application (Chapter 4.2). The spacing of His is such that intra-CC His-metal coordination bonds can form to bridge one helical turn within the same helix, but also inter-CC coordination bonds are not generally excluded. Starting with Ni2+ ions, Raman spectroscopy showed that the CC maintained its helical structure and the His residues were able to coordinate Ni2+. Circular dichroism (CD) spectroscopy revealed that the melting temperature of the CC increased by 4 °C in the presence of Ni2+. Using atomic force microscope (AFM)-based single molecule force spectroscopy, the energy landscape parameters of the CC were characterized in the absence and the presence of Ni2+. His-Ni2+ coordination increased the rupture force by ~10 pN, accompanied by a decrease of the dissociation rate constant. To test if this stabilizing effect can be transferred from the single molecule level to the bulk viscoelastic material properties, the CC building block was used as a non-covalent cross-link for star-shaped poly(ethylene glycol) (star-PEG) hydrogels. Shear rheology revealed a 3-fold higher relaxation time in His-Ni2+ coordinating hydrogels compared to the hydrogel without metal ions. This stabilizing effect was fully reversible when using an excess of the metal chelator ethylenediaminetetraacetate (EDTA). The hydrogel properties were further investigated using different metal ions, i.e. Cu2+, Co2+ and Zn2+. Overall, these results suggest that Ni2+, Cu2+ and Co2+ primarily form intra-CC coordination bonds while Zn2+ also participates in inter-CC coordination bonds. This may be a direct result of its different coordination geometry.
Intermolecular His-metal coordination bonds in the terminal regions of the protein building blocks of mussel byssal threads are primarily formed by Zn2+ and were found to be intimately linked to higher-order assembly and self-healing of the thread. In the above example, the contribution of intra-CC and inter-CC His-Zn2+ cannot be disentangled. In Chapter 4.3, I redesigned the CC to prohibit the formation of intra-CC His-Zn2+ coordination bonds, focusing only on inter-CC interactions. Specifically, I inserted His in the solvent-exposed f positions of the CC to focus on the effect of metal-induced higher-order assembly of CC cross-links. Raman and CD spectroscopy revealed that this CC building block forms α-helical Zn2+ cross-linked aggregates. Using this CC as a cross-link for star-PEG hydrogels, I showed that the material properties can be switched from viscoelastic in the absence of Zn2+ to elastic-like in the presence of Zn2+. Moreover, the relaxation time of the hydrogel was tunable over three orders of magnitude when using different Zn2+:His ratios. This tunability is attributed to a progressive transformation of single CC cross-links into His-Zn2+ cross-linked aggregates, with inter-CC His-Zn2+ coordination bonds serving as an additional, cross-linking mode.
Rheological characterization of the hydrogels with inter-CC His-Zn2+ coordination raised the question whether the His-Zn2+ coordination bonds between CCs or also the CCs themselves rupture when shear strain is applied. In general, the amount of CC cross-links initially formed in the hydrogel as well as the amount of CC cross-links breaking under force remains to be elucidated. In order to more deeply probe these questions and monitor the state of the CC cross-links when force is applied, a fluorescent reporter system based on Förster resonance energy transfer (FRET) was introduced into the CC (Chapter 4.4). For this purpose, the donor-acceptor pair carboxyfluorescein and tetramethylrhodamine was used. The resulting self-reporting CC showed a FRET efficiency of 77 % in solution. Using this fluorescently labeled CC as a self-reporting, reversible cross-link in an otherwise covalently cross-linked star-PEG hydrogel enabled the detection of the FRET efficiency change under compression force. This proof-of-principle result sets the stage for implementing the fluorescently labeled CCs as molecular force sensors in non-covalently cross-linked hydrogels.
In summary, this thesis highlights that rationally designed CCs are excellent reversibly tunable, self-healing and self-reporting hydrogel cross-links with high application potential in bioengineering and biomedicine. For the first time, I demonstrated that His-metal coordination-based stabilization can be transferred from the single CC level to the bulk material with clear viscoelastic consequences. Insertion of His in specific sequence positions was used to implement a second non-covalent cross-linking mode via intermolecular His-metal coordination. This His-metal binding induced aggregation of the CCs enabled for reversibly tuning the hydrogel properties from viscoelastic to elastic-like. As a proof-of-principle to establish self-reporting CCs as material cross-links, I labeled a CC with a FRET pair. The fluorescently labelled CC acts as a molecular force sensor and first preliminary results suggest that the CC enables the detection of hydrogel cross-link failure under compression force. In the future, fluorescently labeled CC force sensors will likely not only be used as intelligent cross-links to study the failure of hydrogels but also to investigate cell-matrix interactions in 3D down to the single molecule level.
A shelter for the future
(2020)
Plant development in its majority occurs post-embryonically
through the activity of local meristems that provide daughter cells
for the development of new organs. It has long been acknowledged
that the shoot apical meristem (SAM), which holds the stem cells
that will form above-ground organs, is recalcitrant to infection by
multiple pathogens, a crucial strategy to safeguard normal devel-
opment and subsequent generations. However, the molecular
mechanisms underlying SAM immunity remain largely unknown.
Induced point mutations are important genetic resources for their ability to create hypo- and hypermorphic alleles that are useful for understanding gene functions and breeding. However, such mutant populations have only been developed for a few temperate maize varieties, mainly B73 and W22, yet no tropical maize inbred lines have been mutagenized and made available to the public to date. We developed a novel Ethyl Methanesulfonate (EMS) induced mutation resource in maize comprising 2050 independent M2 mutant families in the elite tropical maize inbred ML10. By phenotypic screening, we showed that this population is of comparable quality with other mutagenized populations in maize. To illustrate the usefulness of this population for gene discovery, we performed rapid mapping-by-sequencing to clone a fasciated-ear mutant and identify a causal promoter deletion in ZmCLE7 (CLE7). Our mapping procedure does not require crossing to an unrelated parent, thus is suitable for mapping subtle traits and ones affected by heterosis. This first EMS population in tropical maize is expected to be very useful for the maize research community. Also, the EMS mutagenesis and rapid mapping-by-sequencing pipeline described here illustrate the power of performing forward genetics in diverse maize germplasms of choice, which can lead to novel gene discovery due to divergent genetic backgrounds.
Highly efficient and accurate selection of elite genotypes can lead to dramatic shortening of the breeding cycle in major crops relevant for sustaining present demands for food, feed, and fuel. In contrast to classical approaches that emphasize the need for resource-intensive phenotyping at all stages of artificial selection, genomic selection dramatically reduces the need for phenotyping. Genomic selection relies on advances in machine learning and the availability of genotyping data to predict agronomically relevant phenotypic traits. Here we provide a systematic review of machine learning approaches applied for genomic selection of single and multiple traits in major crops in the past decade. We emphasize the need to gather data on intermediate phenotypes, e.g. metabolite, protein, and gene expression levels, along with developments of modeling techniques that can lead to further improvements of genomic selection. In addition, we provide a critical view of factors that affect genomic selection, with attention to transferability of models between different environments. Finally, we highlight the future aspects of integrating high-throughput molecular phenotypic data from omics technologies with biological networks for crop improvement.
The current trends of crop yield improvements are not expected to meet the projected rise in demand. Genomic selection uses molecular markers and machine learning to identify superior genotypes with improved traits, such as growth. Plant growth directly depends on rates of metabolic reactions which transform nutrients into the building blocks of biomass. Here, we predict growth of Arabidopsis thaliana accessions by employing genomic prediction of reaction rates estimated from accession-specific metabolic models. We demonstrate that, comparing to classical genomic selection on the available data sets for 67 accessions, our approach improves the prediction accuracy for growth within and across nitrogen environments by 32.6% and 51.4%, respectively, and from optimal nitrogen to low carbon environment by 50.4%. Therefore, integration of molecular markers into metabolic models offers an approach to predict traits directly related to metabolism, and its usefulness in breeding can be examined by gathering matching datasets in crops. An increase in genomic selection (GS) accuracy can accelerate genetic gain by shortening the breeding cycles. Here, the authors introduce a network-based GS method that uses metabolic models and improves the prediction accuracy of Arabidopsis growth within and across environments.
In nature, plants are constantly exposed to many transient, but recurring, stresses. Thus, to complete their life cycles, plants require a dynamic balance between capacities to recover following cessation of stress and maintenance of stress memory. Recently, we uncovered a new functional role for macroautophagy/autophagy in regulating recovery from heat stress (HS) and resetting cellular memory of HS inArabidopsis thaliana. Here, we demonstrated that NBR1 (next to BRCA1 gene 1) plays a crucial role as a receptor for selective autophagy during recovery from HS. Immunoblot analysis and confocal microscopy revealed that levels of the NBR1 protein, NBR1-labeled puncta, and NBR1 activity are all higher during the HS recovery phase than before. Co-immunoprecipitation analysis of proteins interacting with NBR1 and comparative proteomic analysis of annbr1-null mutant and wild-type plants identified 58 proteins as potential novel targets of NBR1. Cellular, biochemical and functional genetic studies confirmed that NBR1 interacts with HSP90.1 (heat shock protein 90.1) and ROF1 (rotamase FKBP 1), a member of the FKBP family, and mediates their degradation by autophagy, which represses the response to HS by attenuating the expression ofHSPgenes regulated by the HSFA2 transcription factor. Accordingly, loss-of-function mutation ofNBR1resulted in a stronger HS memory phenotype. Together, our results provide new insights into the mechanistic principles by which autophagy regulates plant response to recurrent HS.
Aldehyde oxidases (AOXs) are a small group of enzymes belonging to the larger family of molybdo-flavoenzymes, along with the well-characterized xanthine oxidoreductase. The two major types of reactions that are catalyzed by AOXs are the hydroxylation of heterocycles and the oxidation of aldehydes to their corresponding carboxylic acids. Different animal species have different complements of AOX genes. The two extremes are represented in humans and rodents; whereas the human genome contains a single active gene (AOX1), those of rodents, such as mice, are endowed with four genes (Aox1-4), clustering on the same chromosome, each encoding a functionally distinct AOX enzyme. It still remains enigmatic why some species have numerous AOX enzymes, whereas others harbor only one functional enzyme. At present, little is known about the physiological relevance of AOX enzymes in humans and their additional forms in other mammals. These enzymes are expressed in the liver and play an important role in the metabolisms of drugs and other xenobiotics. In this review, we discuss the expression, tissue-specific roles, and substrate specificities of the different mammalian AOX enzymes and highlight insights into their physiological roles.
Carrion plays an essential role in shaping the structure and functioning of ecosystems and has far‐reaching implications for biodiversity conservation. The change in availability and type of carcasses throughout ecosystems can involve negative effects for scavenging communities. To address this issue, there have been recent conservation management measures of carrion provision in natural systems. However, the optimal conditions under which exposing carcasses to optimize conservation outcomes are still limited. Here, we used camera traps throughout elevational and vegetational gradients to monitor the consumption of 48 deer carcasses over a study period of six years by evaluating 270,279 photographs resulting out of 15,373 trap nights. We detected 17 species visiting carcass deployments, including five endangered species. Our results show that large carcasses, the winter season, and a heterogeneous surrounding habitat enhanced the frequency of carcass visits and the species richness of scavenger assemblages. Contrary to our expectations, carcass species, condition (fresh/frozen), and provision schedule (continuous vs single exposure) did not influence scavenging frequency or diversity. The carcass visitation frequency increased with carcass mass and lower temperatures. The effect of large carcasses was especially pronounced for mesopredators and the Eurasian lynx (Lynx lynx ). Lynx were not too influenced in its carrion acquisition by the season, but exclusively preferred remote habitats containing higher forest cover. Birds of prey, mesopredators, and top predators were also positively influenced by the visiting rate of ravens (Corvus corax ), whereas no biotic or abiotic preferences were found for wild boars (Sus scrofa ). This study provides evidence that any ungulate species of carrion, either in a fresh or in previously frozen condition, attracts a high diversity of scavengers especially during winter, thereby supporting earlier work that carcass provisions may support scavenger communities and endangered species.
Carrion plays an essential role in shaping the structure and functioning of ecosystems and has far‐reaching implications for biodiversity conservation. The change in availability and type of carcasses throughout ecosystems can involve negative effects for scavenging communities. To address this issue, there have been recent conservation management measures of carrion provision in natural systems. However, the optimal conditions under which exposing carcasses to optimize conservation outcomes are still limited. Here, we used camera traps throughout elevational and vegetational gradients to monitor the consumption of 48 deer carcasses over a study period of six years by evaluating 270,279 photographs resulting out of 15,373 trap nights. We detected 17 species visiting carcass deployments, including five endangered species. Our results show that large carcasses, the winter season, and a heterogeneous surrounding habitat enhanced the frequency of carcass visits and the species richness of scavenger assemblages. Contrary to our expectations, carcass species, condition (fresh/frozen), and provision schedule (continuous vs single exposure) did not influence scavenging frequency or diversity. The carcass visitation frequency increased with carcass mass and lower temperatures. The effect of large carcasses was especially pronounced for mesopredators and the Eurasian lynx (Lynx lynx ). Lynx were not too influenced in its carrion acquisition by the season, but exclusively preferred remote habitats containing higher forest cover. Birds of prey, mesopredators, and top predators were also positively influenced by the visiting rate of ravens (Corvus corax ), whereas no biotic or abiotic preferences were found for wild boars (Sus scrofa ). This study provides evidence that any ungulate species of carrion, either in a fresh or in previously frozen condition, attracts a high diversity of scavengers especially during winter, thereby supporting earlier work that carcass provisions may support scavenger communities and endangered species.
Infectious pathogens are a global issue. Global air travel offers an easy and fast opportunity not only for people but also for infectious diseases to spread around the world within a few days. Also, large public events facilitate increasing infection numbers. Therefore, rapid on-site screening for infected people is urgently needed. Due to the small size and easy handling, ion mobility spectrometry coupled with a multicapillary column (MCC-IMS) is a very promising, sensitive method for the on-site identification of infectious pathogens based on scents, representing volatile organic compounds (VOCs). The purpose of this study was to prospectively assess whether identification of Influenza-A-infection based on VOCs by MCC-IMS is possible in breath. Nasal breath was investigated in 24 consecutive persons with and without Influenza-A-infection by MCC-IMS. In 14 Influenza-A-infected patients, infection was proven by PCR of nasopharyngeal swabs. Four healthy staff members and six patients with negative PCR result served as controls. For picking up relevant VOCs in MCC-IMS spectra, software based on cluster analysis followed by multivariate statistical analysis was applied. With only four VOCs canonical discriminant analysis was able to distinguish Influenza-A-infected patients from those not infected with 100% sensitivity and 100% specificity. This present proof-of-concept-study yields encouraging results showing a rapid diagnosis of viral infections in nasal breath within 5 min by MCC-IMS. The next step is to validate the results with a greater number of patients with Influenza-A-infection as well as other viral diseases, especially COVID-19. Registration number at ClinicalTrials.gov NCT04282135.
Bacteriophages use a large number of different bacterial cell envelope structures as receptors for surface attachment. As a consequence, bacterial surfaces represent a major control point for the defense against phage attack. One strategy for phage population control is the production of outer membrane vesicles (OMVs). In Gram-negative host bacteria, O-antigen-specific bacteriophages address lipopolysaccharide (LPS) to initiate infection, thus relying on an essential outer membrane glycan building block as receptor that is constantly present also in OMVs. In this work, we have analyzed interactions ofSalmonella(S.) bacteriophage P22 with OMVs. For this, we isolated OMVs that were formed in large amounts during mechanical cell lysis of the P22 S. Typhimurium host.In vitro, these OMVs could efficiently reduce the number of infective phage particles. Fluorescence spectroscopy showed that upon interaction with OMVs, bacteriophage P22 released its DNA into the vesicle lumen. However, only about one third of the phage P22 particles actively ejected their genome. For the larger part, no genome release was observed, albeit the majority of phages in the system had lost infectivity towards their host. With OMVs, P22 ejected its DNA more rapidly and could release more DNA against elevated osmotic pressures compared to DNA release triggered with protein-free LPS aggregates. This emphasizes that OMV composition is a key feature for the regulation of infective bacteriophage particles in the system.
One of the strongest determinants of behavioural variation is the tradeoff between resource gain and safety. Although classical theory predicts optimal foraging under risk, empirical studies report large unexplained variation in behaviour. Intrinsic individual differences in risk-taking behaviour might contribute to this variation. By repeatedly exposing individuals of a small mesopredator to different experimental landscapes of risks and resources, we tested 1) whether individuals adjust their foraging behaviour according to predictions of the general tradeoff between energy gain and predation avoidance and 2) whether individuals differ consistently and predictably from each other in how they solve this tradeoff. Wild-caught individuals (n = 42) of the jumping spiderMarpissa muscosa, were subjected to repeated release and open-field tests to quantify among-individual variation in boldness and activity. Subsequently, individuals were tested in four foraging tests that differed in risk level (white/dark background colour) and risk variation (constant risk/variable risk simulated by bird dummy overflights) and contained inaccessible but visually perceivable food patches. When exposed to a white background, individuals reduced some aspects of movement and foraging intensity, suggesting that the degree of camouflage serves as a proxy of perceived risk in these predators. Short pulses of acute predation risk, simulated by bird overflights, had only small effects on aspects of foraging behaviour. Notably, a significant part of variation in foraging was due to among-individual differences across risk landscapes that are linked to consistent individual variation in activity, forming a behavioural syndrome. Our results demonstrate the importance of among-individual differences in behaviour of animals that forage under different levels of perceived risk. Since these differences likely affect food-web dynamics and have fitness consequences, future studies should explore the mechanisms that maintain the observed variation in natural populations.
Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection.
Polynucleobacter asymbioticus strain QLW-P1DMWA-1T represents a group of highly successful heterotrophic ultramicrobacteria that is frequently very abundant (up to 70% of total bacterioplankton) in freshwater habitats across all seven continents. This strain was originally isolated from a shallow Alpine pond characterized by rapid changes in water temperature and elevated UV radiation due to its location at an altitude of 1300 m. To elucidate the strain’s adjustment to fluctuating environmental conditions, we recorded changes occurring in its transcriptomic and proteomic profiles under contrasting experimental conditions by simulating thermal conditions in winter and summer as well as high UV irradiation. To analyze the potential connection between gene expression and regulation via methyl group modification of the genome, we also analyzed its methylome. The methylation pattern differed between the three treatments, pointing to its potential role in differential gene expression. An adaptive process due to evolutionary pressure in the genus was deduced by calculating the ratios of non-synonymous to synonymous substitution rates for 20 Polynucleobacter spp. genomes obtained from geographically diverse isolates. The results indicate purifying selection.
Redox signalling in plants
(2020)
Once proteins are synthesized, they can additionally be modified by post-translational modifications (PTMs). Proteins containing reactive cysteine thiols, stabilized in their deprotonated form due to their local environment as thiolates (RS-), serve as redox sensors by undergoing a multitude of oxidative PTMs (Ox-PTMs). Ox-PTMs such as S-nitrosylation or formation of inter- or intra-disulfide bridges induce functional changes in these proteins. Proteins containing cysteines, whose thiol oxidation state regulates their functions, belong to the so-called redoxome. Such Ox-PTMs are controlled by site-specific cellular events that play a crucial role in protein regulation, affecting enzyme catalytic sites, ligand binding affinity, protein-protein interactions or protein stability. Reversible protein thiol oxidation is an essential regulatory mechanism of photosynthesis, metabolism, and gene expression in all photosynthetic organisms. Therefore, studying PTMs will remain crucial for understanding plant adaptation to external stimuli like fluctuating light conditions. Optimizing methods suitable for studying plants Ox-PTMs is of high importance for elucidation of the redoxome in plants. This study focusses on thiol modifications occurring in plant and provides novel insight into in vivo redoxome of Arabidopsis thaliana in response to light vs. dark. This was achieved by utilizing a resin-assisted thiol enrichment approach. Furthermore, confirmation of candidates on the single protein level was carried out by a differential labelling approach. The thiols and disulfides were differentially labelled, and the protein levels were detected using immunoblot analysis. Further analysis was focused on light-reduced proteins. By the enrichment approach many well studied redox-regulated proteins were identified. Amongst those were fructose 1,6-bisphosphatase (FBPase) and sedoheptulose-1,7-bisphosphatase (SBPase) which have previously been described as thioredoxin system targeted enzymes. The redox regulated proteins identified in the current study were compared to several published, independent results showing redox regulated proteins in Arabidopsis leaves, root, mitochondria and specifically S-nitrosylated proteins. These proteins were excluded as potential new candidates but remain as a proof-of-concept to the enrichment experiments to be effective. Additionally, CSP41A and CSP41B proteins, which emerged from this study as potential targets of redox-regulation, were analyzed by Ribo-Seq. The active translatome study of csp41a mutant vs. wild-type showed most of the significant changes at end of the night, similarly as csp41b. Yet, in both mutants only several chloroplast-encoded genes were altered. Further studies of CSP41A and CSP41B proteins are needed to reveal their functions and elucidate the role of redox regulation of these proteins.
Biochemical food quality constraints affect the performance of consumers and mediate trait variation among and within consumer species. To assess inter- and intraspecific differences in fatty acid retention and conversion in freshwater rotifers, we provided four strains of two closely related rotifer species,Brachionus calyciflorussensustricto andBrachionus fernandoi, with food algae differing in their fatty acid composition. The rotifers grazed for 5 days on eitherNannochloropsis limneticaorMonoraphidium minutum, two food algae with distinct polyunsaturated fatty acid (PUFA) profiles, before the diets were switched to PUFA-freeSynechococcus elongatus, which was provided for three more days. We found between- and within-species differences in rotifer fatty acid compositions on the respective food sources and, in particular, highly specific acclimation reactions to the PUFA-free diet. The different reactions indicate inter- but also intraspecific differences in physiological traits, such as PUFA retention, allocation and bioconversion capacities, within the genusBrachionusthat are most likely accompanied by differences in their nutritional demands. Our data suggest that biochemical food quality constraints act differently on traits of closely related species and of strains of a particular species and thus might be involved in shaping ecological interactions and evolutionary processes. This article is part of the theme issue 'The next horizons for lipids as 'trophic biomarkers': evidence and significance of consumer modification of dietary fatty acids'.
The earth’s ecosystems undergo considerable changes characterized by human-induced alterations of environmental factors. In order to develop conservation goals for vulnerable ecosystems, research on ecosystem functioning is required.. Therefore, it is crucial to explore organismal interactions, such as trophic interaction or competition, which are decisive for key processes in ecosystems. These interactions are determined by the performance responses of organisms to environmental changes, which in turn, are shaped by the organism’s functional traits. Exploring traits, their variation, and the environmental factors that act on them may provide insights on how ecological interactions affect
populations, community structures and dynamics, and thus ecosystem
functioning. In aquatic ecosystems, global warming intensifies
phytoplankton blooms, which are more frequently dominated by
cyanobacteria. As cyanobacteria are poor in polyunsaturated fatty acids
(PUFA) and sterols, this compositional change alters the biochemical
food quality of phytoplankton for consumer species with potential
effects on ecological interactions. Within this thesis, I studied the
effects of biochemical food quality on consumer traits and performance responses at the phytoplankton-zooplankton interface using different strains of two closely related generalist rotifer species Brachionus calyciflorus and Brachionus fernandoi and three phytoplankton species that differ in their biochemical food quality, i.e. in their content and composition of PUFA and sterols. In a series of laboratory feeding experiments I found that biochemical food quality affected rotifer’s performance, i.e. fecundity, survival, and population growth, across a broad range of food quantities. Biochemical food quality constraints,
which are often underestimated as influencing environmental factors, had strong impacts on performance responses. I further explored the potential of biochemical food quality in mediating consumer response variation between species and among strains of one species. Co-limitation by food quantity and biochemical food quality resulted in differences in performance responses, which were more pronounced within than between rotifer species. Furthermore, I demonstrated that the body PUFA compositions of rotifer species and strains were differently affected by the dietary PUFA supply, which indicates inter- and intraspecific differences in physiological traits, such as PUFA retention, allocation, and/or bioconversion capacity, within the genus Brachionus. This indicates that dietary PUFA are involved in shaping traits and performance responses of rotifers. This thesis reveals that biochemical food quality is an environmental factor with strong effects on individual traits and performance responses of consumers. Biochemical food quality constraints can further mediate trait and response variation among species or strains. Consequently, they carry the potential to shape ecological interactions and evolutionary processes with effects on community structures and dynamics. Trait-based approaches, which include food quality research, thus may provide further insights into the linkage between functional diversity and the maintenance of crucial ecosystem functions.
Chloroplasts are the photosynthetic organelles in plant and algae cells that enable photoautotrophic growth. Due to their prokaryotic origin, modern-day chloroplast genomes harbor 100 to 200 genes. These genes encode for core components of the photosynthetic complexes and the chloroplast gene expression machinery, making most of them essential for the viability of the organism. The regulation of those genes is predominated by translational adjustments. The powerful technique of ribosome profiling was successfully used to generate highly resolved pictures of the translational landscape of Arabidopsis thaliana cytosol, identifying translation of upstream open reading frames and long non-coding transcripts. In addition, differences in plastidial translation and ribosomal pausing sites were addressed with this method. However, a highly resolved picture of the chloroplast translatome is missing. Here, with the use of chloroplast isolation and targeted ribosome affinity purification, I generated highly enriched ribosome profiling datasets of the chloroplasts translatome for Nicotiana tabacum in the dark and light. Chloroplast isolation was found unsuitable for the unbiased analysis of translation in the chloroplast but adequate to identify potential co-translational import. Affinity purification was performed for the small and large ribosomal subunit independently. The enriched datasets mirrored the results obtained from whole-cell ribosome profiling. Enhanced translational activity was detected for psbA in the light. An alternative translation initiation mechanism was not identified by selective enrichment of small ribosomal subunit footprints. In sum, this is the first study that used enrichment strategies to obtain high-depth ribosome profiling datasets of chloroplasts to study ribosome subunit distribution and chloroplast associated translation.
Ever-changing light intensities are challenging the photosynthetic capacity of photosynthetic organism. Increased light intensities may lead to over-excitation of photosynthetic reaction centers resulting in damage of the photosystem core subunits. Additional to an expensive repair mechanism for the photosystem II core protein D1, photosynthetic organisms developed various features to reduce or prevent photodamage. In the long-term, photosynthetic complex contents are adjusted for the efficient use of experienced irradiation. However, the contribution of chloroplastic gene expression in the acclimation process remained largely unknown. Here, comparative transcriptome and ribosome profiling was performed for the early time points of high-light acclimation in Nicotiana tabacum chloroplasts in a genome-wide scale. The time- course data revealed stable transcript level and only minor changes in translational activity of specific chloroplast genes during high-light acclimation. Yet, psbA translation was increased by two-fold in the high light from shortly after the shift until the end of the experiment. A stress-inducing shift from low- to high light exhibited increased translation only of psbA. This study indicate that acclimation fails to start in the observed time frame and only short-term responses to reduce photoinhibition were observed.
Siberian larch (Larix Mill.) forests dominate vast areas of northern Russia and contribute important ecosystem services to the world. It is important to understand the past dynamics of larches in order to predict their likely response to a changing climate in the future. Sedimentary ancient DNA extracted from lake sediment cores can serve as archives to study past vegetation. However, the traditional method of studying sedimentary ancient DNA-metabarcoding-focuses on small fragments, which cannot resolve Larix to species level nor allow a detailed study of population dynamics. Here, we use shotgun sequencing and hybridization capture with long-range PCR-generated baits covering the complete Larix chloroplast genome to study Larix populations from a sediment core reaching back to 6700 years from the Taymyr region in northern Siberia. In comparison with shotgun sequencing, hybridization capture results in an increase in taxonomically classified reads by several orders of magnitude and the recovery of complete chloroplast genomes of Larix. Variation in the chloroplast reads corroborates an invasion of Larix gmelinii into the range of Larix sibirica before 6700 years ago. Since then, both species have been present at the site, although larch populations have decreased with only a few trees remaining in what was once a forested area. This study demonstrates for the first time that hybridization capture applied directly to ancient DNA of plants extracted from lake sediments can provide genome-scale information and is a viable tool for studying past genomic changes in populations of single species, irrespective of a preservation as macrofossil.
L-(+)-lactic acid from reed
(2020)
Biotechnological production of lactic acid (LA) is based on the so-called first generation feedstocks, meaning sugars derived from food and feed crops such as corn, sugarcane and cassava. The aim of this study was to exploit the potential of a second generation resource: Common reed (Phragmites australis) is a powerfully reproducing sweet grass which grows in wetlands and creates vast monocultural populations. This lignocellulose biomass bears the possibility to be refined to value-added products, without competing with agro industrial land. Besides utilizing reed as a renewable and inexpensive substrate, low-cost nutritional supplementation was analyzed for the fermentation of thermophilicBacilluscoagulans.Various nutritional sources such as baker's and brewer's yeast, lucerne green juice and tryptone were investigated for the replacement of yeast extract. The structure of the lignocellulosic material was tackled by chemical treatment (1% NaOH) and enzymatic hydrolysis (Cellic(R)CTec2).B.coagulansDSM ID 14-300 was employed for the homofermentative conversion of the released hexose and pentose sugars to polymerizable L-(+)-LA of over 99.5% optical purity. The addition of autolyzed baker's yeast led to the best results of fermentation, enabling an LA titer of 28.3 g L(-1)and a yield of 91.6%.
1. We generally assume that animals should maximize information acquisition about their environment to make prudent decisions. But this is a naive assumption, as gaining information typically involves costs. <br /> 2. This is especially so in the social context, where interests between interacting partners usually diverge. The arms race involved in mutual assessment is characterized by the attempt to obtain revealing information from a partner while providing only as much information by oneself as is conducive to one's own intentions. <br /> 3. If obtaining information occasions costs in terms of time, energy and risk, animals should be selected to base their decisions on a cost-benefit ratio that takes account of the trade-off between the risk of making wrong choices and the costs involved in information acquisition, processing and use. <br /> 4. In addition, there may be physiological and/or environmental constraints limiting the ability to obtaining, processing and utilizing reliable information. <br /> 5. Here, we discuss recent empirical evidence for the proposition that social decisions are to an important extent based on the costs that result from acquiring, processing, evaluating and storing information. Using examples from different taxa and ecological contexts, we aim at drawing attention to the often neglected costs of information recipience, with emphasis on the potential role of sensory ecology and cognition in social decisions.
The smell of hunger
(2020)
When individuals exchange helpful acts reciprocally, increasing the benefit of the receiver can enhance its propensity to return a favour, as pay-offs are typically correlated in iterated interactions. Therefore, reciprocally cooperating animals should consider the relative benefit for the receiver when deciding to help a conspecific. Norway rats (Rattus norvegicus) exchange food reciprocally and thereby take into account both the cost of helping and the potential benefit to the receiver. By using a variant of the sequential iterated prisoner's dilemma paradigm, we show that rats may determine the need of another individual by olfactory cues alone. In an experimental food-exchange task, test subjects were provided with odour cues from hungry or satiated conspecifics located in a different room. Our results show that wild-type Norway rats provide help to a stooge quicker when they receive odour cues from a hungry rather than from a satiated conspecific. Using chemical analysis by gas chromatography-mass spectrometry (GC-MS), we identify seven volatile organic compounds that differ in their abundance between hungry and satiated rats. Combined, this "smell of hunger" can apparently serve as a reliable cue of need in reciprocal cooperation, which supports the hypothesis of honest signalling.
Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change.
Anthropogenic changes in climate, land use, and disturbance regimes, as well as introductions of non-native species can lead to the transformation of many ecosystems. The resulting novel ecosystems are usually characterized by species assemblages that have not occurred previously in a given area. Quantifying the ecological novelty of communities (i.e., biotic novelty) would enhance the understanding of environmental change. However, quantification remains challenging since current novelty metrics, such as the number and/or proportion of non-native species in a community, fall short of considering both functional and evolutionary aspects of biotic novelty. Here, we propose the Biotic Novelty Index (BNI), an intuitive and flexible multidimensional measure that combines (a) functional differences between native and non-native introduced species with (b) temporal dynamics of species introductions. We show that the BNI is an additive partition of Rao's quadratic entropy, capturing the novel interaction component of the community's functional diversity. Simulations show that the index varies predictably with the relative amount of functional novelty added by recently arrived species, and they illustrate the need to provide an additional standardized version of the index. We present a detailed R code and two applications of the BNI by (a) measuring changes of biotic novelty of dry grassland plant communities along an urbanization gradient in a metropolitan region and (b) determining the biotic novelty of plant species assemblages at a national scale. The results illustrate the applicability of the index across scales and its flexibility in the use of data of different quality. Both case studies revealed strong connections between biotic novelty and increasing urbanization, a measure of abiotic novelty. We conclude that the BNI framework may help building a basis for better understanding the ecological and evolutionary consequences of global change.
My niche
(2020)
Intraspecific trait variation is an important determinant of fundamental ecological interactions. Many of these interactions are mediated by behaviour. Therefore, interindividual differences in behaviour should contribute to individual niche specialization. Comparable with variation in morphological traits, behavioural differentiation between individuals should limit similarity among competitors and thus act as a mechanism maintaining within-species variation in ecological niches and facilitating species coexistence. Here, we aimed to test whether interindividual differences in boldness covary with spatial interactions within and between two ecologically similar, co-occurring rodent species (Myodes glareolus, Apodemus agrarius). In five subpopulations in northeast Germany, we quantified individual differences in boldness via repeated standardized tests and spatial interaction patterns via capture-mark- recapture (n = 126) and automated VHF telemetry (n = 36). We found that boldness varied with space use in both species. Individuals of the same population occupied different spatial niches, which resulted in non-random patterns of within- and between-species spatial interactions. Behavioural types mainly differed in the relative importance of intra- versus interspecific competition. Within-species variation along this competition gradient could contribute to maintaining individual niche specialization. Moreover, behavioural differentiation between individuals limits similarity among competitors, which might facilitate the coexistence of functionally equivalent species and, thus, affect community dynamics and local biodiversity.
Botulinum neurotoxins (BoNTs) are potent neurotoxins produced by bacteria, which inhibit neurotransmitter release, specifically in their physiological target known as motor neurons (MNs). For the potency assessment of BoNTs produced for treatment in traditional and aesthetic medicine, the mouse lethality assay is still used by the majority of manufacturers, which is ethically questionable in terms of the 3Rs principle. In this study, MNs were differentiated from human induced pluripotent stem cells based on three published protocols. The resulting cell populations were analyzed for their MN yield and their suitability for the potency assessment of BoNTs. MNs produce specific gangliosides and synaptic proteins, which are bound by BoNTs in order to be taken up by receptor-mediated endocytosis, which is followed by cleavage of specific soluble N-ethylmaleimide-sensitive-factor attachment receptor (SNARE) proteins required for neurotransmitter release. The presence of receptors and substrates for all BoNT serotypes was demonstrated in MNs generated in vitro. In particular, the MN differentiation protocol based on Du et al. yielded high numbers of MNs in a short amount of time with high expression of BoNT receptors and targets. The resulting cells are more sensitive to BoNT/A1 than the commonly used neuroblastoma cell line SiMa. MNs are, therefore, an ideal tool for being combined with already established detection methods.
Marine sponges host highly diverse but specific bacterial communities that provide essential functions for the sponge holobiont, including antimicrobial defense. Here, we characterized the bacterial microbiome of the marine sponge Haliclona cnidata that has been in culture in an artificial marine aquarium system. We tested the hypotheses (1) that the long-term aquarium cultured sponge H. cnidata is tightly associated with a typical sponge bacterial microbiota and (2) that the symbiotic Bacteria sustain bioactivity under harmful environmental conditions to facilitate holobiont survival by preventing pathogen invasion. Microscopic and phylogenetic analyses of the bacterial microbiota revealed that H. cnidata represents a high microbial abundance (HMA) sponge with a temporally stable bacterial community that significantly shifts with changing aquarium conditions. A 4-week incubation experiment was performed in small closed aquarium systems with antibiotic and/or light exclusion treatments to reduce the total bacterial and photosynthetically active sponge-associated microbiota to a treatment-specific resilient community. While the holobiont was severely affected by the experimental treatment (i.e., bleaching of the sponge, reduced bacterial abundance, shifted bacterial community composition), the biological defense and bacterial community interactions (i.e., quorum sensing activity) remained intact. 16S rRNA gene amplicon sequencing revealed a resilient community of 105 bacterial taxa, which remained in the treated sponges. These 105 taxa accounted for a relative abundance of 72-83% of the bacterial sponge microbiota of non-treated sponge fragments that have been cultured under the same conditions. We conclude that a sponge-specific resilient community stays biologically active under harmful environmental conditions, facilitating the resilience of the holobiont. In H. cnidata, bacteria are located in bacteriocytes, which may have contributed to the observed phenomenon.
Objective:
Stunting (height-for-age < −2 SD) is one of the forms of undernutrition and is frequent among children of low- and middle-income countries. But stunting perSe is not a synonym of undernutrition. We investigated association between body height and indicators of energetic undernutrition at three critical thresholds for thinness used in public health: (1) BMI SDS < −2; (2) mid-upper arm circumference divided by height (MUAC (mm) × 10/height (cm) < 1·36) and (3) mean skinfold thickness (SF) < 7 mm and to question the reliability of thresholds as indicators of undernutrition.
Design:
Cross-sectional study; breakpoint analysis.
Setting:
Rural and urban regions of Indonesia and Guatemala – different socio-economic status (SES).
Participants:
1716 Indonesian children (6·0–13·2 years) and 3838 Guatemalan children (4·0–18·9 years) with up to 50 % stunted children.
Results:
When separating the regression of BMI, MUAC or SF, on height into distinguishable segments (breakpoint analysis), we failed to detect relevant associations between height, and BMI, MUAC or SF, even in the thinnest and shortest children. For BMI and SF, the breakpoint analysis either failed to reach statistical significance or distinguished at breakpoints above critical thresholds. For MUAC, the breakpoint analysis yielded negative associations between MUAC/h and height in thin individuals. Only in high SES Guatemalan children, SF and height appeared mildly associated with R2 = 0·017.
Conclusions:
Currently used lower thresholds of height-for-age (stunting) do not show relevant associations with anthropometric indicators of energetic undernutrition. We recommend using the catch-up growth spurt during early re-feeding instead as immediate and sensitive indicator of past undernourishment. We discuss the primacy of education and social-economic-political-emotional circumstances as responsible factors for stunting.
Flight behaviour characteristics such as flight altitude and avoidance behaviour determine the species-specific collision risk of birds with wind turbines. However, traditional observational methods exhibit limited positional accuracy. High-resolution GPS telemetry represents a promising method to overcome this drawback. In this study, we used three-dimensional GPS tracking data including high-accuracy tracks recorded at 3-s intervals to investigate the collision risk of breeding male Montagu's Harriers Circus pygargus in the Dutch–German border region. Avoidance of wind turbines was quantified by a novel approach comparing observed flights to a null model of random flight behaviour. On average, Montagu's Harriers spent as much as 8.2 h per day in flight. Most flights were at low altitude, with only 7.1% within the average rotor height range (RHR; 45–125 m). Montagu's Harriers showed significant avoidance behaviour, approaching turbines less often than expected, particularly when flying within the RHR (avoidance rate of 93.5%). For the present state, with wind farms situated on the fringes of the regional nesting range, collision risk models based on our new insights on flight behaviour indicated 0.6–2.0 yearly collisions of adult males (as compared with a population size of c. 40 pairs). However, the erection of a new wind farm inside the core breeding area could markedly increase mortality (up to 9.7 yearly collisions). If repowering of the wind farms was carried out using low-reaching modern turbines (RHR 36–150 m), mortality would more than double, whereas it would stay approximately constant if higher turbines (RHR 86–200 m) were used. Our study demonstrates the great potential of high-resolution GPS tracking for collision risk assessments. The resulting information on collision-related flight behaviour allows for performing detailed scenario analyses on wind farm siting and turbine design, in contrast to current environmental assessment practices. With regard to Montagu's Harriers, we conclude that although the deployment of higher wind turbines represents an opportunity to reduce collision risk for this species, precluding wind energy developments in core breeding areas remains the most important mitigation measure.
Escaping the plant cell
(2020)
Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses.
Research synthesis on simple yet general hypotheses and ideas is challenging in scientific disciplines studying highly context-dependent systems such as medical, social, and biological sciences. This study shows that machine learning, equation-free statistical modeling of artificial intelligence, is a promising synthesis tool for discovering novel patterns and the source of controversy in a general hypothesis. We apply a decision tree algorithm, assuming that evidence from various contexts can be adequately integrated in a hierarchically nested structure. As a case study, we analyzed 163 articles that studied a prominent hypothesis in invasion biology, the enemy release hypothesis. We explored if any of the nine attributes that classify each study can differentiate conclusions as classification problem. Results corroborated that machine learning can be useful for research synthesis, as the algorithm could detect patterns that had been already focused in previous narrative reviews. Compared with the previous synthesis study that assessed the same evidence collection based on experts' judgement, the algorithm has newly proposed that the studies focusing on Asian regions mostly supported the hypothesis, suggesting that more detailed investigations in these regions can enhance our understanding of the hypothesis. We suggest that machine learning algorithms can be a promising synthesis tool especially where studies (a) reformulate a general hypothesis from different perspectives, (b) use different methods or variables, or (c) report insufficient information for conducting meta-analyses.
Aim: We aimed to examine the distribution and secular changes of conscript body height in the geographic network of Norway since 1878 and to study its association with the degree of urbanization, and population density. Material and methods: Data on body height of Norwegian military conscripts were provided by the Statistics Norway Department (SSB). The sample comprised eight cohorts with the following measurement years: 1st 1877, 1878 and 1880, 2nd 18951897, 3rd 1915-1917, 4th 1935-1937, 5th 1955-1957, 6th 1975-1977, 7th 1995-1997, and 8th 2009-2011. For determining neighborhood correlations, a network was created consisting of neighboring counties, sharing a common border. Results: Average body height of Norwegian men increased by 10.9 cm between 1878 and 2010, but this trend was heterogeneous. Some counties increased by more than 1 cm per decade (Finmark) others by only 7 mm per decade (Sor-Trondelag). Urban counties and counties with higher population density showed stronger height trends than rural counties. The largest spread in body height between the various counties was observed in 1936 when for the first time people living in the more urban counties got taller than rural people. The height advantage of urban counties however, disappeared after 1996. At this time, also the secular trend in height had come to a halt. The secular trend in height had become obvious after the dissolution of the union between Norway and Sweden in 1905 and World War I, and was strongest between 1936 and 1956. During this period maximum between-county heterogeneity in height existed with body height differences of more than 6 cm between the tallest and the shortest county. The end of this period was characterized by social democratic reforms that flattened the income distribution, eliminated poverty, and ensured social services after World War II. Conclusion: The temporal coincidence between the trends in height, the degree of urbanization and the onset of the political transition of Norway from a Swedish province into an independent democratic wealthy modern European state after World War I and particularly after World War II, and the abatement of this trend after this period of transition had stabilized, suggest social and political components interfering with the regulation of physical growth in humans.
Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57%, similar to 37%, and similar to 6% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23% of the Chaco would have to be protected to safeguard the top 17% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them.
Global biodiversity is under high and rising anthropogenic pressure. Yet, how the taxonomic, phylogenetic, and functional facets of biodiversity are affected by different threats over time is unclear. This is particularly true for the two main drivers of the current biodiversity crisis: habitat destruction and overexploitation. We provide the first long-term assessment of multifaceted biodiversity changes caused by these threats for any tropical region. Focussing on larger mammals in South America's 1.1 million km(2) Gran Chaco region, we assessed changes in multiple biodiversity facets between 1985 and 2015, determined which threats drive those changes, and identified remaining key areas for all biodiversity facets. Using habitat and threat maps, we found, first, that between 1985 and 2015 taxonomic (TD), phylogenetic (PD) and functional (FD) diversity all declined drastically across over half of the area assessed. FD declined about 50% faster than TD and PD, and these declines were mainly driven by species loss, rather than species turnover. Second, habitat destruction, hunting, and both threats together contributed similar to 57%, similar to 37%, and similar to 6% to overall facet declines, respectively. However, hunting pressure increased where TD and PD declined most strongly, whereas habitat destruction disproportionally contributed to FD declines. Third, just 23% of the Chaco would have to be protected to safeguard the top 17% of all three facets. Our findings uncover a widespread impoverishment of mammal species richness, evolutionary history, and ecological functions across broad areas of the Chaco due to increasing habitat destruction and hunting. Moreover, our results pinpoint key areas that should be preserved and managed to maintain all facets of mammalian diversity across the Chaco. More generally, our work highlights how long-term changes in biodiversity facets can be assessed and attributed to specific threats, to better understand human impacts on biodiversity and to guide conservation planning to mitigate them.
Deep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3,474 m) in two transects of about 1,500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). We distinguished a cluster composed mainly by yeasts, and a second cluster by filamentous fungi, but we were unable to detect a strong effect of depth and the overlying water temperature, salinity, dissolved oxygen (DO), and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.
Deep waters represent the largest biome on Earth and the largest ecosystem of Costa Rica. Fungi play a fundamental role in global biogeochemical cycling in marine sediments, yet, they remain little explored. We studied fungal diversity and community composition in several marine sediments from 16 locations sampled along a bathymetric gradient (from a depth of 380 to 3,474 m) in two transects of about 1,500 km length in the Eastern Tropical Pacific (ETP) of Costa Rica. Sequence analysis of the V7-V8 region of the 18S rRNA gene obtained from sediment cores revealed the presence of 787 fungal amplicon sequence variants (ASVs). On average, we detected a richness of 75 fungal ASVs per sample. Ascomycota represented the most abundant phylum with Saccharomycetes constituting the dominant class. Three ASVs accounted for ca. 63% of all fungal sequences: the yeast Metschnikowia (49.4%), Rhizophydium (6.9%), and Cladosporium (6.7%). We distinguished a cluster composed mainly by yeasts, and a second cluster by filamentous fungi, but we were unable to detect a strong effect of depth and the overlying water temperature, salinity, dissolved oxygen (DO), and pH on the composition of fungal communities. We highlight the need to understand further the ecological role of fungi in deep-sea ecosystems.
When running a lab we do not think about calamities, since they are rare events for which we cannot plan while we are busy with the day-to-day management and intellectual challenges of a research lab. No lab team can be prepared for something like a pandemic such as COVID-19, which has led to shuttered labs around the globe. But many other types of crises can also arise that labs may have to weather during their lifetime. What can researchers do to make a lab more resilient in the face of such exterior forces? What systems or behaviors could we adjust in 'normal' times that promote lab success, and increase the chances that the lab will stay on its trajectory? We offer 10 rules, based on our current experiences as a lab group adapting to crisis.
An increase in zoonotic infections in humans in recent years has led to a high level of public interest. However, the extent of infestation of free-living small mammals with pathogens and especially parasites is not well understood. This pilot study was carried out within the framework of the "Rodent-borne pathogens" network to identify zoonotic parasites in small mammals in Germany. From 2008 to 2009, 111 small mammals of 8 rodent and 5 insectivore species were collected. Feces and intestine samples from every mammal were examined microscopically for the presence of intestinal parasites by using Telemann concentration for worm eggs, Kinyoun staining for coccidia, and Heidenhain staining for other protozoa. Adult helminths were additionally stained with carmine acid for species determination. Eleven different helminth species, five coccidians, and three other protozoa species were detected. Simultaneous infection of one host by different helminths was common. Hymenolepis spp. (20.7%) were the most common zoonotic helminths in the investigated hosts. Coccidia, including Eimeria spp. (30.6%), Cryptosporidium spp. (17.1%), and Sarcocystis spp. (17.1%), were present in 40.5% of the feces samples of small mammals. Protozoa, such as Giardia spp. and amoebae, were rarely detected, most likely because of the repeated freeze-thawing of the samples during preparation. The zoonotic pathogens detected in this pilot study may be potentially transmitted to humans by drinking water, smear infection, and airborne transmission.
Plants located adjacent to agricultural fields are important for maintaining biodiversity in semi-natural landscapes. To avoid undesired impacts on these plants due to herbicide application on the arable fields, regulatory risk assessments are conducted prior to registration to ensure proposed uses of plant protection products do not present an unacceptable risk. The current risk assessment approach for these non-target terrestrial plants (NTTPs) examines impacts at the individual-level as a surrogate approach for protecting the plant community due to the inherent difficulties of directly assessing population or community level impacts. However, modelling approaches are suitable higher tier tools to upscale individual-level effects to community level. IBC-grass is a sophisticated plant community model, which has already been applied in several studies. However, as it is a console application software, it was not deemed sufficiently user-friendly for risk managers and assessors to be conveniently operated without prior expertise in ecological models. Here, we present a user-friendly and open source graphical user interface (GUI) for the application of IBC-grass in regulatory herbicide risk assessment. It facilitates the use of the plant community model for predicting long-term impacts of herbicide applications on NTTP communities. The GUI offers two options to integrate herbicide impacts: (1) dose responses based on current standard experiments (acc. to testing guidelines) and (2) based on specific effect intensities. Both options represent suitable higher tier options for future risk assessments of NTTPs as well as for research on the ecological relevance of effects.
Plants located adjacent to agricultural fields are important for maintaining biodiversity in semi-natural landscapes. To avoid undesired impacts on these plants due to herbicide application on the arable fields, regulatory risk assessments are conducted prior to registration to ensure proposed uses of plant protection products do not present an unacceptable risk. The current risk assessment approach for these non-target terrestrial plants (NTTPs) examines impacts at the individual-level as a surrogate approach for protecting the plant community due to the inherent difficulties of directly assessing population or community level impacts. However, modelling approaches are suitable higher tier tools to upscale individual-level effects to community level. IBC-grass is a sophisticated plant community model, which has already been applied in several studies. However, as it is a console application software, it was not deemed sufficiently user-friendly for risk managers and assessors to be conveniently operated without prior expertise in ecological models. Here, we present a user-friendly and open source graphical user interface (GUI) for the application of IBC-grass in regulatory herbicide risk assessment. It facilitates the use of the plant community model for predicting long-term impacts of herbicide applications on NTTP communities. The GUI offers two options to integrate herbicide impacts: (1) dose responses based on current standard experiments (acc. to testing guidelines) and (2) based on specific effect intensities. Both options represent suitable higher tier options for future risk assessments of NTTPs as well as for research on the ecological relevance of effects.
Characterisation of gene-regulatory network (GRN) interactions provides a stepping stone to understanding how genes affect cellular phenotypes. Yet, despite advances in profiling technologies, GRN reconstruction from gene expression data remains a pressing problem in systems biology. Here, we devise a supervised learning approach, GRADIS, which utilises support vector machine to reconstruct GRNs based on distance profiles obtained from a graph representation of transcriptomics data. By employing the data fromEscherichia coliandSaccharomyces cerevisiaeas well as synthetic networks from the DREAM4 and five network inference challenges, we demonstrate that our GRADIS approach outperforms the state-of-the-art supervised and unsupervided approaches. This holds when predictions about target genes for individual transcription factors as well as for the entire network are considered. We employ experimentally verified GRNs fromE. coliandS. cerevisiaeto validate the predictions and obtain further insights in the performance of the proposed approach. Our GRADIS approach offers the possibility for usage of other network-based representations of large-scale data, and can be readily extended to help the characterisation of other cellular networks, including protein-protein and protein-metabolite interactions.
GeneReg
(2020)
Motivation
Large-scale metabolic models are widely used to design metabolic engineering strategies for diverse biotechnological applications. However, the existing computational approaches focus on alteration of reaction fluxes and often neglect the manipulations of gene expression to implement these strategies.
Results
Here, we find that the association of genes with multiple reactions leads to infeasibility of engineering strategies at the flux level, since they require contradicting manipulations of gene expression. Moreover, we identify that all of the existing approaches to design gene knockout strategies do not ensure that the resulting design may also require other gene alterations, such as up- or downregulations, to match the desired flux distribution. To address these issues, we propose a constraint-based approach, termed GeneReg, that facilitates the design of feasible metabolic engineering strategies at the gene level and that is readily applicable to large-scale metabolic networks. We show that GeneReg can identify feasible strategies to overproduce ethanol in Escherichia coli and lactate in Saccharomyces cerevisiae, but overproduction of the TCA cycle intermediates is not feasible in five organisms used as cell factories under default growth conditions. Therefore, GeneReg points at the need to couple gene regulation and metabolism to design rational metabolic engineering strategies.
Identifying the entirety of gene regulatory interactions in a biological system offers the possibility to determine the key molecular factors that affect important traits on the level of cells, tissues, and whole organisms. Despite the development of experimental approaches and technologies for identification of direct binding of transcription factors (TFs) to promoter regions of downstream target genes, computational approaches that utilize large compendia of transcriptomics data are still the predominant methods used to predict direct downstream targets of TFs, and thus reconstruct genome-wide gene-regulatory networks (GRNs). These approaches can broadly be categorized into unsupervised and supervised, based on whether data about known, experimentally verified gene-regulatory interactions are used in the process of reconstructing the underlying GRN. Here, we first describe the generic steps of supervised approaches for GRN reconstruction, since they have been recently shown to result in improved accuracy of the resulting networks? We also illustrate how they can be used with data from model organisms to obtain more accurate prediction of gene regulatory interactions.
Background:
Many felid species are of high conservation concern, and with increasing human disturbance the situation is worsening. Small isolated populations are at risk of genetic impoverishment decreasing within-species biodiversity. Movement is known to be a key behavioural trait that shapes both demographic and genetic dynamics and affects population survival. However, we have limited knowledge on how different manifestations of movement behaviour translate to population processes. In this study, we aimed to 1) understand the potential effects of movement behaviour on the genetic diversity of small felid populations in heterogeneous landscapes, while 2) presenting a simulation tool that can help inform conservation practitioners following, or considering, population management actions targeting the risk of genetic impoverishment.
Methods:
We developed a spatially explicit individual-based population model including neutral genetic markers for felids and applied this to the example of Eurasian lynx. Using a neutral landscape approach, we simulated reintroductions into a three-patch system, comprising two breeding patches separated by a larger patch of differing landscape heterogeneity, and tested for the effects of various behavioural movement syndromes and founder population sizes. We explored a range of movement syndromes by simulating populations with various movement model parametrisations that range from 'shy' to 'bold' movement behaviour.
Results:
We find that movement syndromes can lead to a higher loss of genetic diversity and an increase in between population genetic structure for both "bold" and "shy" movement behaviours, depending on landscape conditions, with larger decreases in genetic diversity and larger increases in genetic differentiation associated with bold movement syndromes, where the first colonisers quickly reproduce and subsequently dominate the gene pool. In addition, we underline the fact that a larger founder population can offset the genetic losses associated with subpopulation isolation and gene pool dominance. Conclusions We identified a movement syndrome trade-off for population genetic variation, whereby bold-explorers could be saviours - by connecting populations and promoting panmixia, or sinks - by increasing genetic losses via a 'founder takes all' effect, whereas shy-stayers maintain a more gradual genetic drift due to their more cautious behaviour. Simulations should incorporate movement behaviour to provide better projections of long-term population viability and within-species biodiversity, which includes genetic diversity. Simulations incorporating demographics and genetics have great potential for informing conservation management actions, such as population reintroductions or reinforcements. Here, we present such a simulation tool for solitary felids.
Mathematical analysis of partial differential equations (PDEs) has led to many insights regarding the effect of organism movements on spatial population dynamics. However, their use has mainly been confined to the community of mathematical biologists, with less attention from statistical and empirical ecologists. We conjecture that this is principally due to the inherent difficulties in fitting PDEs to data. To help remedy this situation, in the context of movement ecology, we show how the popular technique of step selection analysis (SSA) can be used to parametrize a class of PDEs, calleddiffusion-taxismodels, from an animal's trajectory. We examine the accuracy of our technique on simulated data, then demonstrate the utility of diffusion-taxis models in two ways. First, for non-interacting animals, we derive the steady-state utilization distribution in a closed analytic form. Second, we give a recipe for deriving spatial pattern formation properties that emerge from interacting animals: specifically, do those interactions cause heterogeneous spatial distributions to emerge and if so, do these distributions oscillate at short times or emerge without oscillations? The second question is applied to data on concurrently tracked bank volesMyodes glareolus. Our results show that SSA can accurately parametrize diffusion-taxis equations from location data, providing the frequency of the data is not too low. We show that the steady-state distribution of our diffusion-taxis model, where it is derived, has an identical functional form to the utilization distribution given by resource selection analysis (RSA), thus formally linking (fine scale) SSA with (broad scale) RSA. For the bank vole data, we show how our SSA-PDE approach can give predictions regarding the spatial aggregation and segregation of different individuals, which are difficult to predict purely by examining results of SSA. Our methods provide a user-friendly way into the world of PDEs, via a well-used statistical technique, which should lead to tighter links between the findings of mathematical ecology and observations from empirical ecology. By providing a non-speculative link between observed movement behaviours and space use patterns on larger spatio-temporal scales, our findings will also aid integration of movement ecology into understanding spatial species distributions.
Protein-protein interactions (PPIs) are of fundamental importance in several cellular processes. While "classical" biochemical methods are commonly used to monitor protein multimerization in biological samples, fluorescence microscopy offers the possibility to investigate PPIs directly in living cells, even distinguishing among different cellular compartments. In this chapter, we shortly describe the most common procedures used to label proteins with fluorescent probes. Furthermore, we discuss a variety of fluorescence microscopy techniques that can be used to obtain quantitative information about protein multimerization. Special emphasis is given to fluorescence fluctuation techniques and their applications in the context of, e.g., receptor multimerization and virus assembly.
Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that certain thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate.
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Thermal stress response is an essential physiological trait that determines occurrence and temporal succession in nature, including response to climate change. We compared temperature-related demography in closely related heat-tolerant and heat-sensitive Brachionus rotifer species. We found significant differences in heat response, with the heat-sensitive species adopting a strategy of long survival and low population growth, while the heat-tolerant followed the opposite strategy. In both species, we examined the genetic basis of physiological variation by comparing gene expression across increasing temperatures. Comparative transcriptomic analyses identified shared and opposing responses to heat. Interestingly, expression of heat shock proteins (hsps) was strikingly different in the two species and mirrored differences in population growth rates, showing that hsp genes are likely a key component of a species’ adaptation to different temperatures. Temperature induction caused opposing patterns of expression in further functional categories including energy, carbohydrate and lipid metabolism, and in genes related to ribosomal proteins. In the heat-sensitive species, elevated temperatures caused up-regulation of genes related to meiosis induction and post-translational histone modifications. This work demonstrates the sweeping reorganizations of biological functions that accompany temperature adaptation in these two species and reveals potential molecular mechanisms that might be activated for adaptation to global warming.
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.
Utilising a reconstructed ancestral mitochondrial genome of a clade to design hybridisation capture baits can provide the opportunity for recovering mitochondrial sequences from all its descendent and even sister lineages. This approach is useful for taxa with no extant close relatives, as is often the case for rare or extinct species, and is a viable approach for the analysis of historical museum specimens. Asiatic linsangs (genus Prionodon) exemplify this situation, being rare Southeast Asian carnivores for which little molecular data is available. Using ancestral capture we recover partial mitochondrial genome sequences for seven banded linsangs (P. linsang) from historical specimens, representing the first intraspecific genetic dataset for this species. We additionally assemble a high quality mitogenome for the banded linsang using shotgun sequencing for time-calibrated phylogenetic analysis. This reveals a deep divergence between the two Asiatic linsang species (P. linsang, P. pardicolor), with an estimated divergence of ~12 million years (Ma). Although our sample size precludes any robust interpretation of the population structure of the banded linsang, we recover two distinct matrilines with an estimated tMRCA of ~1 Ma. Our results can be used as a basis for further investigation of the Asiatic linsangs, and further demonstrate the utility of ancestral capture for studying divergent taxa without close relatives.
In this work, a novel electrochemical molecularly imprinted polymer (MIP) sensor for the detection of the lipopeptide antibiotic Daptomycin (DAP) is presented which integrates gold decorated platinum nanoparticles (Au-Pt NPs) into the nanocomposite film. The sensor was prepared by electropolymerization of o-phenylenediamine (o-PD) in the presence of DAP using cyclic voltammetry. Cyclic voltammetry and differential pulse voltammetry were applied to follow the changes in the MIP-layer related to rebinding and removal of the target DAP by using the redox marker [Fe(CN)(6)](3-/4-). Under optimized operational conditions, the MIP/Au-Pt NPs/ GCE nanosensor exhibits a linear response in the range of 1-20 pM towards DAP. The limit of detection and limit of quantification were determined to be 0.161pM +/- 0.012 and 0.489pM +/- 0.012, respectively. The sensitivity towards the antibiotics Vancomycin and Erythromycin and the amino acids glycine and tryptophan was below 7 percent as compared with DAP. Moreover, the nanosensor was also successfully used for the detection of DAP in deproteinated human serum samples.
A biosensor for phenolic compounds based on a chemically modified laccase from Coriolus hirsula immobilized on functionalized screen-printed carbon electrodes (SPCEs) was achieved. Different enzyme modifications and immobilization strategies were analyzed. The electrochemical response of the immobilized laccase on SPCEs modified with carboxyl functionalized multi-walled carbon nanotubes (COOH-MWCNT) was the highest when laccase was aminated prior to the adsorption onto the working electrode. The developed lactase biosensor sensitivity toward different phenolic compounds was assessed to determine the biosensor response with several phenolic compounds. The highest response was obtained for ABTS with a saturation value of I-max = 27.94 mu A. The electrocatalytic efficiency (I-max/K-m(app)) was the highest for ABTS (5588 mu A mu M-1) followed by syringaldazine (3014 mu A.mu M-1). The sensors were considerably stable, whereby 99.5, 82 and 77% of the catalytic response using catechol as substrate was retained after 4, 8 and 10 successive cycles of reuse respectively, with response time average of 5 s for 12 cycles. No loss of activity was observed after 20 days of storage.
All roads lead to growth
(2020)
Plant growth is a highly complex biological process that involves innumerable interconnected biochemical and signalling pathways. Many different techniques have been developed to measure growth, unravel the various processes that contribute to plant growth, and understand how a complex interaction between genotype and environment determines the growth phenotype. Despite this complexity, the term 'growth' is often simplified by researchers; depending on the method used for quantification, growth is viewed as an increase in plant or organ size, a change in cell architecture, or an increase in structural biomass. In this review, we summarise the cellular and molecular mechanisms underlying plant growth, highlight state-of-the-art imaging and non-imaging-based techniques to quantitatively measure growth, including a discussion of their advantages and drawbacks, and suggest a terminology for growth rates depending on the type of technique used.
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
Metagenomic sequencing has revolutionised our knowledge of virus diversity, with new virus sequences being reported faster than ever before. However, virus discovery from metagenomic sequencing usually depends on detectable homology: without a sufficiently close relative, so-called ‘dark’ virus sequences remain unrecognisable. An alternative approach is to use virus-identification methods that do not depend on detecting homology, such as virus recognition by host antiviral immunity. For example, virus-derived small RNAs have previously been used to propose ‘dark’ virus sequences associated with the Drosophilidae (Diptera). Here, we combine published Drosophila data with a comprehensive search of transcriptomic sequences and selected meta-transcriptomic datasets to identify a completely new lineage of segmented positive-sense single-stranded RNA viruses that we provisionally refer to as the Quenyaviruses. Each of the five segments contains a single open reading frame, with most encoding proteins showing no detectable similarity to characterised viruses, and one sharing a small number of residues with the RNA-dependent RNA polymerases of single- and double-stranded RNA viruses. Using these sequences, we identify close relatives in approximately 20 arthropods, including insects, crustaceans, spiders, and a myriapod. Using a more conserved sequence from the putative polymerase, we further identify relatives in meta-transcriptomic datasets from gut, gill, and lung tissues of vertebrates, reflecting infections of vertebrates or of their associated parasites. Our data illustrate the utility of small RNAs to detect viruses with limited sequence conservation, and provide robust evidence for a new deeply divergent and phylogenetically distinct RNA virus lineage.
CytoSeg 2.0
(2020)
Motivation:
Actin filaments (AFs) are dynamic structures that substantially change their organization over time. The dynamic behavior and the relatively low signal-to-noise ratio during live-cell imaging have rendered the quantification of the actin organization a difficult task.
Results:
We developed an automated image-based framework that extracts AFs from fluorescence microscopy images and represents them as networks, which are automatically analyzed to identify and compare biologically relevant features. Although the source code is freely available, we have now implemented the framework into a graphical user interface that can be installed as a Fiji plugin, thus enabling easy access by the research community.
Recent advances in microscopy have led to an improved visualization of different cell processes. Yet, this also leads to a higher demand of tools which can process images in an automated and quantitative fashion. Here, we present two applications that were developed to quantify different processes in eukaryotic cells which rely on the organization and dynamics of the cytoskeleton.. In plant cells, microtubules and actin filaments form the backbone of the cytoskeleton. These structures support cytoplasmic streaming, cell wall organization and tracking of cellular material to and from the plasma membrane. To better understand the underlying mechanisms of cytoskeletal organization, dynamics and coordination, frameworks for the quantification are needed. While this is fairly well established for the microtubules, the actin cytoskeleton has remained difficult to study due to its highly dynamic behaviour. One aim of this thesis was therefore to provide an automated framework to quantify and describe actin organization and dynamics. We used the framework to represent actin structures as networks and examined the transport efficiency in Arabidopsis thaliana hypocotyl cells. Furthermore, we applied the framework to determine the growth mode of cotton fibers and compared the actin organization in wild-type and mutant cells of rice. Finally, we developed a graphical user interface for easy usage. Microtubules and the actin cytoskeleton also play a major role in the morphogenesis of epidermal leaf pavement cells. These cells have highly complex and interdigitated shapes which are hard to describe in a quantitative way. While the relationship between microtubules, the actin cytoskeleton and shape formation is the object of many studies, it is still not clear how and if the cytoskeletal components predefine indentations and protrusions in pavement cell shapes. To understand the underlying cell processes which coordinate cell morphogenesis, a quantitative shape descriptor is needed. Therefore, the second aim of this thesis was the development of a network-based shape descriptor which captures global and local shape features, facilitates shape comparison and can be used to evaluate shape complexity. We demonstrated that our framework can be used to describe and compare shapes from various domains. In addition, we showed that the framework accurately detects local shape features of pavement cells and outperform contending approaches. In the third part of the thesis, we extended the shape description framework to describe pavement cell shape features on tissue-level by proposing different network representations of the underlying imaging data.
Objective:
The Indonesia Basic Health Research 2018 indicates that Indonesian children are still among the shortest in the world. When referred to World Health Organization Child Growth Standards (WHOCGS), the prevalence of stunting reaches up to 43% in several Indonesian districts. Indonesian National Growth Reference Charts (INGRC) were established in order to better distinguish between healthy short children and children with growth disorders. We analyzed height and weight measurements of healthy Indonesian children using INGRC and WHOCGS.
Methods:
6972 boys and 5800 girls (n = 12,772), aged 0-59 months old, from Bandung District were measured. Z-scores of length/height and body mass index were calculated based on INGRC and WHOCGS.
Results:
Under 5-year-old Indonesian children raised in Bandung are short and slim. Mean height z-scores of boys is -2.03 [standard deviation (SD) 1.31], mean height z-scores of girls is -2.03 (SD 1.31) when referred to WHOCGS indicating that over 50 % of these children are stunted. Bandung children are heterogeneous, with substantial subpopulations of tall children. Depending on the growth reference used, between 9% and 15% of them are wasted. Wasted children are on average half a SD taller than their peers.
Conclusion:
WHOCGS seriously overestimates the true prevalence of undernutrition in Indonesian children. The present investigation fails to support evidence of undernutrition at a prevalence similar to the over 50% prevalence of stunting (WHOCGS) versus 13.3% (INGRC). We suggest refraining from using WHOCGS, and instead applying INGRC that closely mirror height and weight increments in Bandung children. INGRC appear superior for practical and clinical purposes, such as detecting growth and developmental disorders.
Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.
Accurately quantifying species' area requirements is a prerequisite for effective area-based conservation. This typically involves collecting tracking data on species of interest and then conducting home-range analyses. Problematically, autocorrelation in tracking data can result in space needs being severely underestimated. Based on the previous work, we hypothesized the magnitude of underestimation varies with body mass, a relationship that could have serious conservation implications. To evaluate this hypothesis for terrestrial mammals, we estimated home-range areas with global positioning system (GPS) locations from 757 individuals across 61 globally distributed mammalian species with body masses ranging from 0.4 to 4000 kg. We then applied block cross-validation to quantify bias in empirical home-range estimates. Area requirements of mammals <10 kg were underestimated by a mean approximately15%, and species weighing approximately100 kg were underestimated by approximately50% on average. Thus, we found area estimation was subject to autocorrelation-induced bias that was worse for large species. Combined with the fact that extinction risk increases as body mass increases, the allometric scaling of bias we observed suggests the most threatened species are also likely to be those with the least accurate home-range estimates. As a correction, we tested whether data thinning or autocorrelation-informed home-range estimation minimized the scaling effect of autocorrelation on area estimates. Data thinning required an approximately93% data loss to achieve statistical independence with 95% confidence and was, therefore, not a viable solution. In contrast, autocorrelation-informed home-range estimation resulted in consistently accurate estimates irrespective of mass. When relating body mass to home range size, we detected that correcting for autocorrelation resulted in a scaling exponent significantly >1, meaning the scaling of the relationship changed substantially at the upper end of the mass spectrum.
Plasticity of human growth
(2020)
Background:
This systematic review aimed at collecting, analyzing and summarizing scientific studies focusing on psychosocial factors that influence linear growth among humans.
Methods:
The online database "PubMed" was used in order to acquire suitable scientific studies. These studies were evaluated based on clearly defined criteria that determine whether a study was to be excluded or included in the literature review. In the end, a total sum of 36 studies remained, which were carefully analyzed and used to generate an overview of the association between psychosocial factors and linear growth.
Results:
In the 36 reviewed studies, different social and psychological factors, such as socioeconomic status, parental education or emotional deprivation were set in relation to physical growth among humans. The studies were listed and summarized, depending on the investigated psychosocial factor. A clear association between psychosocial factors and growth could be observed in most of the reviewed studies. Discussion: Based on the results of the reviewed studies it could be concluded that the regulation of linear growth is also subject to different psychosocial factors. The way in which the developing human and the specific social environment interact seemed to have a major impact on linear growth. Statusspecific stress was discussed as one possible explanation for the regulating mechanism of human linear growth.
The aim of this study was a longitudinal description of the ontogeny of the adult electric organ of Campylomormyrus rhynchophorus which produces as adult an electric organ discharge of very long duration (ca. 25 ms). We could indeed show (for the first time in a mormyrid fish) that the electric organ discharge which is first produced early during ontogeny in 33-mm-long juveniles is much shorter in duration and has a different shape than the electric organ discharge in 15-cm-long adults. The change from this juvenile electric organ discharges into the adult electric organ discharge takes at least a year. The increase in electric organ discharge duration could be causally linked to the development of surface evaginations, papillae, at the rostral face of the electrocyte which are recognizable for the first time in 65-mm-long juveniles and are most prominent at the periphery of the electrocyte.