570 Biowissenschaften; Biologie
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Cytoskeletal-based mechanisms differently regulate in vivo and in vitro proplatelet formation
(2021)
Platelets are produced by bone marrow megakaryocytes through cytoplasmic protrusions, named native proplatelets (nPPT), into blood vessels. Proplatelets also refer to protrusions observed in megakaryocyte culture (cPPT) that are morphologically different. Contrary to cPPT, the mechanisms of nPPT formation are poorly understood. We show here in living mice that nPPT elongation is in equilibrium between protrusive and retraction forces mediated by myosin-IIA. We also found, using WT and β1-tubulin-deficient mice, that microtubule behavior differs between cPPT and nPPT, being absolutely required in vitro, while less critical in vivo. Remarkably, microtubule depolymerization in myosin-deficient mice did not affect nPPT elongation. We then calculated that blood Stokes'forces may be sufficient to promote nPPT extension, independently of myosin and microtubules. Together, we propose a new mechanism for nPPT extension that might explain contradictions between severely affected cPPT production and moderate platelet count defects in some patients and animal models.
Leaf-cutting ant colonies largely differ in size, yet all consume O2 and produce CO2 in large amounts because of their underground fungus gardens. We have shown that in the Acromyrmex genus, three basic nest morphologies occur, and investigated the effects of architectural innovations on nest ventilation. We recognized (i) serial nests, similar to the ancestral type of the sister genus Trachymyrmex, with chambers excavated along a vertical tunnel connecting to the outside via a single opening, (ii) shallow nests, with one/few chambers extending shallowly with multiple connections to the outside, and (iii) thatched nests, with an above-ground fungus garden covered with plant material. Ventilation in shallow and thatched nests, but not in serial nests, occurred via wind-induced flows and thermal convection. CO2 concentrations were below the values known to affect the respiration of the symbiotic fungus, indicating that shallow and thatched nests are not constrained by harmful CO2 levels. Serial nests may be constrained depending on the soil CO2 levels. We suggest that in Acromyrmex, selective pressures acting on temperature and humidity control led to nesting habits closer to or above the soil surface and to the evolution of architectural innovations that improved gas exchanges.
Survival rate and changes in foraging performances of solitary bees exposed to a novel insecticide
(2021)
Solitary bees are among the most important pollinators worldwide however population declines especially in croplands has been noticed. The novel pesticide sulfoxaflor is a competitive modulator of nicotinic acetylcholine receptors (nAChR) in insects. While there is evidence of a negative impact of neonicotinoids on bees of several social organization levels, our overall knowledge on the impact of sulfoxaflor on bees is poor. Here we present for the first time a study showing effects of field realistic doses of sulfoxaflor on solitary bees. Bees submitted to long term exposure of field realistic doses of sulfoxaflor (5 µg dm-3, 10 µg dm-3, 50 µg dm-3) and control were observed regarding their survival rate. Moreover, we recorded metrics related to flower visitation and flight performance. We discover that the highest field realistic dose is lethal to Osmia bicornis along five days of exposure. The effect of sulfoxaflor reduces the outcome of foraging, important features for fruit and seed production of cross-pollinated plant species. Bees exposed to pesticide visited flowers mostly walking rather than flying. Flight performance was also impaired by the pesticide.
Wild bee populations are threatened by current agricultural practices in many parts of the world, which may put pollination services and crop yields at risk. Loss of pollination services can potentially be predicted by models that link bee abundances with landscape-scale land-use, but there is little knowledge on the degree to which these statistical models are transferable across time and space. This study assesses the transferability of models for wild bee abundance in a mass-flowering crop across space (from one region to another) and across time (from one year to another). The models used existing data on bumblebee and solitary bee abundance in winter oilseed rape fields, together with high-resolution land-use crop-cover and semi-natural habitats data, from studies conducted in five different regions located in four countries (Sweden, Germany, Netherlands and the UK), in three different years (2011, 2012, 2013). We developed a hierarchical model combining all studies and evaluated the transferability using cross-validation. We found that both the landscape-scale cover of mass-flowering crops and permanent semi-natural habitats, including grasslands and forests, are important drivers of wild bee abundance in all regions. However, while the negative effect of increasing mass-flowering crops on the density of the pollinators is consistent between studies, the direction of the effect of semi-natural habitat is variable between studies. The transferability of these statistical models is limited, especially across regions, but also across time. Our study demonstrates the limits of using statistical models in conjunction with widely available land-use crop-cover classes for extrapolating pollinator density across years and regions, likely in part because input variables such as cover of semi-natural habitats poorly capture variability in pollinator resources between regions and years.
In acute ischemic stroke due to large vessel occlusion (LVO) infarcts rapidly grow into the penumbra, which represents dysfunctional, but still viable brain tissue amenable to rescue by vessel recanalization. However, infarct progression and/or delayed patient presentation are serious and frequent limitations of this so far only acute therapy. Thus, a major goal of translational research is to “freeze” the penumbra already during LVO (before opening the vessel) and thereby extend individual time windows for non-futile recanalization. We used the filament occlusion model of the middle cerebral artery (MCAO) in mice and assessed progressive infarction under occlusion at 2, 3, and 4 h after onset. We show that blocking the activatory platelet receptor glycoprotein (GP)VI substantially delayed progressive neocortical infarction compared to isotype control antibody treated mice. Moreover, the local vascular recruitment of infiltrating neutrophils and T-cells was mitigated. In conclusion, our experimental data support ongoing clinical trials blocking platelet GPVI in acute ischemic stroke.
Progress in biological imaging is intrinsically linked to advances in labeling methods. The explosion in the development of high-resolution and super-resolution imaging calls for new approaches to label targets with small probes. These should allow to faithfully report the localization of the target within the imaging resolution – typically nowadays a few nanometers - and allow access to any epitope of the target, in the native cellular and tissue environment. We report here the development of a complete labeling and imaging pipeline using genetic code expansion and non-canonical amino acids in neurons that allows to fluorescently label masked epitopes in target transmembrane proteins in live neurons, both in dissociated culture and organotypic brain slices. This allows us to image the differential localization of two AMPA receptor (AMPAR) auxiliary subunits of the transmembrane AMPAR regulatory protein family in complex with their partner with a variety of methods including widefield, confocal, and dSTORM super-resolution microscopy.
Paternal obesity is known to have a negative impact on the male’s reproductive health as well as the health of his offspring. Although epigenetic mechanisms have been implicated in the non-genetic transmission of acquired traits, the effect of paternal obesity on gene expression in the preimplantation embryo has not been fully studied. To this end, we investigated whether paternal obesity is associated with gene expression changes in eight-cell stage embryos fathered by males on a high-fat diet. We used single embryo RNA-seq to compare the gene expression profile of embryos generated by males on a high fat (HFD) versus control (CD) diet. This analysis revealed significant upregulation of the Samd4b and Gata6 gene in embryos in response to a paternal HFD. Furthermore, we could show a significant increase in expression of both Gata6 and Samd4b during differentiation of stromal vascular cells into mature adipocytes. These findings suggest that paternal obesity may induce changes in the male germ cells which are associated with the gene expression changes in the resulting preimplantation embryos.
It is generally recognized that phages are a mortality factor for their bacterial hosts. This could be particularly true in spring phytoplankton blooms, which are known to be closely followed by a highly specialized bacterial community. We hypothesized that phages modulate these dense heterotrophic bacteria successions following phytoplankton blooms. In this study, we focused on Flavobacteriia, because they are main responders during these blooms and have an important role in the degradation of polysaccharides. A cultivation-based approach was used, obtaining 44 lytic flavobacterial phages (flavophages), representing twelve new species from two viral realms. Taxonomic analysis allowed us to delineate ten new phage genera and ten new families, from which nine and four, respectively, had no previously cultivated representatives. Genomic analysis predicted various life styles and genomic replication strategies. A likely eukaryote-associated host habitat was reflected in the gene content of some of the flavophages. Detection in cellular metagenomes and by direct-plating showed that part of these phages were actively replicating in the environment during the 2018 spring bloom. Furthermore, CRISPR/Cas spacers and re-isolation during two consecutive years suggested that, at least part of the new flavophages are stable components of the microbial community in the North Sea. Together, our results indicate that these diverse flavophages have the potential to modulate their respective host populations.
Microscopical and genetic analysis to identify peptide release sites and their molecular composition
(2024)
The neuropeptide pigment-dispersing factor (PDF) is a key player to orchestrate the central clock of Drosophila melanogaster. In the fly brain PDF is expressed by the ventral lateral neurons which are the central pacemakers of the Drosophila circadian system and therefore align different clock neurons and modulate downstream circuits. The terminals of the small ventral lateral neurons (s-LNv) undergo daily circadian morphological changes which also affects the synaptic organization of these neurons. However, PDF function and release seems to be unaffected by the circadian plasticity. In Drosophila presynaptic sites are organized by the active zone protein Bruchpilot (BRP), a homolog of the mammalian ELKS protein. BRP and other active zone scaffold proteins are crucial for the recruiting and membrane fusion of small synaptic vesicles that contain amino-acid or monoamide transmitters. Neuropeptides, like PDF, are produced from larger preproproteins within the regulated secretory pathway. The preproproteins are directed to the lumen of the rough endoplasmic reticulum where, after removal of the signal peptide, the resulting proprotein can be modified and is then exported to the trans-Golgi network. Finally, the proproteins are packaged within dense-core vesicles (DCV) and transported to release sites. Within the trans-Golgi and the dense-core vesicles, the bioactive peptides are processed from the proprotein by a set of specific enzymes. Neuropeptide release sites seem to be non-correlated to active zones (AZ), indicating an independence of PDF release from synaptic scaffold proteins. This study aims to elucidate the relevance of AZ for the release of neuropeptides, especially for PDF, by taking both anatomical and functional aspects into consideration. I employed endogenous BRP labeling to examine the spatial correlation between immunolabeled PDF-containing DCV and BRP-labeled AZs in the s-LNv. The number of BRP-labeled puncta in the s-LNv terminals remained stable between morning (Zeitgeber time 2) and night (Zeitgeber time 14) but the puncta-density changed during circadian plasticity. This is an indicator for recycling of BRP in the s-LNv terminals. The relative distance between BRP- and PDF-labeled puncta was higher in the morning, around the reported time of PDF release. This is also the time of day when the terminal arborization complexity is most prominent. Investigation of the publically available ssTEM dataset (FAFB) suggests that spontaneous DCV release profiles in the s-LNv lacked spatial correlation to BRP-organized AZs (T-bars). Functional impairment of PDF signaling via RNAi expression in the sLNvs leads to a shift of circadian locomotor activity and a weaker rhythmicity under constant darkness. Both were not affected by downregulation of brp in the s-LNvs. However, the knockdown of the peptide release factor cadps or proteins involved in the SNARE complex significantly impaired rhythmic strength. To further investigate the impact of brp knockdown in DCV release, I employed another RNAi screen in the Inka cells, which produce the ecdysis triggering hormone (ETH). Knockdown of eth, cadps and SNARE proteins led to severely impaired behaviour, while knockdown of brp and other AZ scaffold proteins did not phenocopy the impairment of ETH signaling. Taken together, the data collected in this study suggest that DCV release of PDF and ETH is independent of BRP-organized AZs, supporting the hypothesis of different release processes for neuropeptides and classical neurotransmitters. Further investigations are necessary to elucidate the recruitment and targeting of DCV release. Anatomical investigation of CNS in the Drosophila brain proves challenging for structures that are as tiny as ACs since their size lies beyond the diffraction limit of light. Many studies employ electron microscopy (EM) to visualize structures in the scale of nanometers. However, fixation methods for EM reduce the toolset for immunostaining methods because epitopes, neccessary to identify the regions of interests (ROIs) in histology samples are blocked or denaturated. Correlative light and electron microscopy (CLEM) offer a solution to this dilemma by combining the best of both worlds. In this study I adjusted a protocol, which was originally published for C. elegans to Drosophila brain-tissue samples. I was able to label PDF immunostained on serial plastic sections and reconstruct a ROI with a z-resolution of 100nm.
The discovery of UBA6 in 2007 has challenged the ubiquitin field, as for a long time, the ubiquitin-activating enzyme 1 (UBA1) was thought to be the sole E1 responsible for the activation of ubiquitin. UBA6 shares 40% sequence identity with UBA1 in humans. However, UBA6 is present only in mammals, zebrafish, and sea urchins. UBA6 and UBA1 use a different spectrum of E2 enzymes and direct ubiquitin to different subsets of E3 enzymes and consequently substrates. Since UBA1 initiates 99% of the ubiquitylation events, UBA6 is presumably responsible for a subset of substrates. Moreover, UBA6 is an unusual E1 enzyme as it activates both ubiquitin and FAT10. FAT10 is a ubiquitin-like modifier and consists of two ubiquitin-like domains arranged in tandem. FAT10 is present in vertebrates only, and its expression is synergistically induced by the pro-inflammatory cytokines interferon γ (INFγ) and tumor necrosis factor α (TNFα). Furthermore, FAT10 is the only ubiquitin-like modifier besides ubiquitin, which can directly target proteins for proteasomal degradation.
The involvement of UBA6-mediated ubiquitylation and FATylation in a broad spectrum of cellular pathways and diseases, along with the ongoing preclinical development of E1 inhibitors such as MNL4924 (Pevonedistat) and MLN7243 (TAK-243), has spurred increased research efforts to develop additional E1 inhibitors. UBA6, with its more limited role in catalyzing ubiquitin activation and being the sole E1 for FAT10, is considered to be a possible drug target. However, to reach this goal, the dual specificity of UBA6 needs to be understood first. Inhibition of UBA6-mediated FATylation while not affecting ubiquitylation or vice versa will not only provide a possibility to further investigate the roles that UBA6 plays in downstream pathways, but also open a window for targeting either the ubiquitylation or FATylation of UBA6 with specific inhibitors.
In this thesis, the crystal structure of UBA6 in complex with FAT10 will be described. In the UBA6-FAT10 complex, the C-terminal domain of FAT10 interacts with UBA6 in a similar manner as ubiquitin with UBA1, while its N-terminal domain binds to the 3-helix bundle inserted into the inactive adenylation domain of UBA6. The structure was corroborated by functional studies, which, surprisingly, identified UBA6 residues specifically abrogating the activation of either ubiquitin or FAT10. These results provide the foundation to study the individual roles that UBA6 is playing in the activation of either ubiquitin or FAT10 in downstream cellular pathways.
In addition, a high-throughput screening (HTS) assay for the identification of compounds inhibiting UBA6 was established, which provides the starting point to identify small molecules exclusively inhibiting the UBA6-activated ubiquitylation or FATylation.
Lastly, FATylation shares a common UBA6-USE1 cascade with UBA6-activated ubiquitylation, and several studies demonstrated that the cooperation between UBA6 and USE1 is functionally crucial in different pathways. Given that USE1 is currently one of the main dedicated E2 enzymes for UBA6, the underlying mechanism regarding the transfer is unclear yet. To visualize the transthioesterification between UBA6 and USE1, a cross-linking strategy was applied to form the binary UBA6-USE1 complex. Besides, to improve the yield and homogeneity of the complex samples, a non-catalytical cysteine variant of USE1 (3M_USE1) was generated, thus representing promising starting point samples that can be used for cryo-EM screening and x-ray crystallography. Ultimately, visualizing the catalytic transfer of ubiquitin/FAT10 from UBA6 to USE1 would provide insights into the molecular basis of UBA6-USE1 pathway mediated ubiquitylation and FATylation.