Biology subjects

Wagner, M.

Publications and source records attributed to Wagner, M..

At least 37 records · Page 2Linked to original sources

bioRxiv2024

Mitophagosomes induced during EV-D68 infection promote viral nonlytic release

Enterovirus-D68 (EV-D68) is a plus-strand RNA virus that primarily causes infant respiratory infections. In rare pediatric cases, infection with EV-D68 has been associated with acute flaccid myelitis, a polio-like paralytic disease. We have previously demonstrated that EV-D68 induces nonselective autophagy for its benefit. Here, we demonstrate that EV-D68 induces mitophagy, the specific autophagic degradation of mitochondria. EV-D68 infection induces mitophagosome formation and several hallmarks of mitophagy, including mitochondrial fragmentation, mitochondrial membrane potential loss, and Parkin translocation to the mitochondria were observed in EV-D68 infected cells. The 3C protease of EV-D68 cleaves the mitochondrial fusion protein, mitofusin-2, near the C-terminal HR2 domain to induce mitochondrial fragmentation, and these fragmented mitochondria colocalized with double-stranded RNA (dsRNA), which labels viral RNA replication sites after peak viral RNA replication. Depleting components of mitophagy signaling specifically reduced EV-D68 release without impacting viral intracellular titers. Our results suggest that whereas the machinery of macroautophagy supports various stages of enterovirus replication, including viral genomic RNA replication and capsid maturation, mitophagy is the specific form of autophagy that regulates the nonlytic release of enteroviruses from cells. SignificanceEV-D68 is a respiratory pathogen and a significant cause of acute respiratory illness in infants, against which no prophylactic vaccines or antivirals exist. We have previously shown that EV-D68, like other enteroviruses, triggers and benefits from nonselective autophagy. However, it was unclear whether the virus induces selective autophagy. Here, we demonstrate that EV-D68 infection induces mitophagy and uses mitophagosomes to traffic virions to the surface of cells for nonlytic release. Our findings suggest that mitophagy may constitute the specific form of autophagy that facilitates the autophagosome-mediated nonlytic release of enteroviruses from infected cells and that targeting mitophagy could be an effective strategy to impede EV-D68 nonlytic release.

microbiology↗

bioRxiv2024

Low-input soil management increases yield and decreases CO2-emissions but aggravates risk of nitrate leaching and diseases in winter wheat cropping systems under climate change

Empirical data is key to anticipate the impact of climate change on cropping systems and develop land management strategies that are sustainable while ensuring food security. Here, the combined effects of projected increases in temperature, atmospheric CO2-concentrations, solar irradiation and altered precipitation patterns on winter wheat cropping systems were investigated using an Ecotron. Experimental plant-soil systems were subjected to three different climatic conditions representing a gradient of ongoing climate change implementing the weather patterns of the years 2013, 2068, and 2085 respectively. The wheat plants were grown in two differentially manged agricultural soil types: one with long-term low organic matter (OM) inputs and the other one with long-term high OM inputs. In the low OM system, the risk for plant diseases and nitrate leaching was increased, but it outperformed the high OM system with higher yields and lower CO2-emissions. Developing high-yielding cropping systems leveraging the CO2-fertilisation effect without sacrificing environmental health will therefore require further refined of management practices to improve nutrient cycling and reduce greenhouse gas emissions. One possibility is adapting crop rotations and cover crops to the shorter wheat cycle observed in the future climates to replenish soil nutrients and break disease cycles. Further, in both here studied soil types the wheat plants developed natural coping mechanisms against environmental stressors, such as enhanced root growth and increased levels of proline and silicon. Unravelling the molecular mechanisms that trigger such inherent plant defences is a further interesting target for breeding future crops. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=177 HEIGHT=200 SRC="FIGDIR/small/626142v2_ufig1.gif" ALT="Figure 1"> View larger version (36K): org.highwire.dtl.DTLVardef@fefc32org.highwire.dtl.DTLVardef@5f6757org.highwire.dtl.DTLVardef@1799ca4org.highwire.dtl.DTLVardef@11aec5c_HPS_FORMAT_FIGEXP M_FIG C_FIG

ecology↗

bioRxiv2024

Contribution of ammonia oxidizers to inorganic carbon fixation in the dark ocean

Ammonia-oxidizing archaea are the most abundant chemolithoautotrophs in the ocean, comprising up to 40% of microbial cells in deep waters, and are assumed to dominate dissolved inorganic carbon (DIC) fixation below the sunlit surface layer. Yet, the supply of reduced nitrogen from particulate organic matter flux from the surface is insufficient to support the amount of nitrification required to sustain measured DIC fixation rates in the dark ocean. The aim of this study was to quantify the contribution of ammonia oxidizers to DIC fixation in the dark ocean. We used phenylacetylene - a specific inhibitor of the ammonia monooxygenase enzyme - to selectively inhibit ammonia oxidizers during two oceanographic expeditions in the eastern tropical and subtropical Pacific Ocean spanning 35{o} N to 10{o} S. We show that ammonia oxidizers contribute only a small fraction to dark DIC fixation, accounting for 2 to 22% of the depth-integrated rates in the eastern tropical Pacific. The highest contributions were observed at the depth of the nitrification maximum, where ammonia oxidation could account for up to 50% of dark DIC fixation. Our results help to reconcile the observed discrepancies between nitrogen supply and DIC fixation at depth, and provide a new perspective on global ocean chemolithoautotrophy, revealing that the majority of DIC fixation within the lower euphotic zone and below 200 m depth is not fueled by ammonia oxidation. SignificanceMicrobes in the ocean play important roles in the global carbon cycle and the oceans capacity to sequester carbon. Despite this importance, deciphering the contributions of different microbial metabolic processes to the oceanic carbon budget remains challenging. Particularly in the dark ocean, large discrepancies between organic matter fluxes and measured microbial metabolic rates are observed. We show that abundant chemoautotrophs - ammonia-oxidizing microbes - contribute only a small fraction to dark carbon fixation in the Pacific Ocean, challenging the current view that carbon fixation in the dark ocean is primarily sustained by nitrification. This work advances our understanding of microbial carbon processing, and offers new insights into the long-standing question of the main energy sources fueling carbon fixation in the dark ocean.

microbiology↗

bioRxiv2024

Acidotolerant soil nitrite oxidiser 'Candidatus Nitrobacter laanbroekii' NHB1 alleviates constraints on growth of acidophilic soil ammonia oxidisers

Nitrobacter strain NHB1 is a nitrite-oxidising bacterium previously co-enriched with the neutrophilic ammonia-oxidising bacterium Nitrosospira AHB1, a consortium that nitrifies under acidic conditions. Here we characterise the growth of isolated Nitrobacter strain NHB1 as a function of pH and nitrite (NO2-) concentration, and its influence on the activity of acidophilic soil ammonia-oxidising archaea (AOA) in co-culture. NHB1 is acidotolerant and grows optimally at pH 6.0 (range 5.0 - 7.5) at initial NO2- concentrations of 500 {micro}M. However, the optimum decreases to pH 5.0 at lower initial NO2- concentrations closer to those found in soil, with detectable growth down to pH 3.5. NHB1 has a comparatively high affinity for NO2- with an apparent-half-saturation constant (54 {micro}M) one order of magnitude lower than its closest relative, the neutrophilic strain Nitrobacter hamburgensis X14. In co-culture, NHB1 enhances the growth of acidophilic AOA. Specifically, Nitrosotalea devaniterrae Nd1 and Nitrosotalea sinensis Nd2 are sensitive to NO2--derived compounds and only oxidise [~]200-300 {micro}M ammonia (NH3) in batch cultures. However, in co-culture with NHB1, pH ranges were lowered by [~]0.5 pH units and both strains could oxidise up to 2.7-2.9 mM NH3, only limited by buffering capacity. NHB1 possesses a cyanase facilitating reciprocal cross-feeding via generating cyanate-derived NH3 and utilising AOA-derived NO2-. Removal of NO2- is likely crucial for nitrifier growth in acidic soils and this study highlights the importance of considering substrate and metabolic product concentrations when characterising physiology. Genome analysis reveals that NHB1 is distinct from validated species and the name Nitrobacter laanbroekii is proposed.

microbiology↗

bioRxiv2024

Microflora Danica: the atlas of Danish environmental microbiomes

The last 20 years have witnessed unprecedented advances in revealing the microbiomes underpinning important processes in natural and human associated environments. Recent large-scale metagenome surveys record the variety of microbial life in the oceans1, wastewater2, human gut3,4, and earth5,6, with compilations encompassing thousands of public datasets7-13. So far, large-scale microbiome studies either miss functional information or consistency in sample processing, and although they may cover thousands of locations, these are missing resolution, sparsely located, or lacking metadata. Here, we present Microflora Danica, an atlas of Danish environmental microbiomes, encompassing 10,686 shotgun metagenomes and 449 full-length 16S and 18S rRNA datasets linked to a detailed 5 level habitat classification scheme. We determine that while human-disturbed habitats have high alpha diversity, the same species reoccur, revealing hidden homogeneity and underlining the importance of natural systems for total species (gamma) diversity. In-depth studies of nitrifiers, a functional group closely linked to climate change, challenge existing perceptions regarding habitat preference and discover several novel nitrifiers as more abundant than canonical nitrifiers. Together, the Microflora Danica dataset provides an unprecedented resource and the foundation for answering fundamental questions underlying microbial ecology: what drives microbial diversity, distribution and function.

microbiology↗

bioRxiv2024

Development, validation and application of an LC-MS/MS method quantifying free forms of the micronutrients queuine and queuosine in human plasma using a surrogate matrix approach

Queuosine (Q) is a hypermodified 7-deaza-guanosine nucleoside exclusively synthesized by bacteria. This micronutrient and its respective nucleobase form queuine (q) are salvaged by humans either from gut microflora, or digested food. Depletion of Q-tRNA in human or mouse cells causes protein misfolding that triggers endoplasmic reticular stress and activation of the unfolded protein responses. In vivo, this reduces neuronal architecture of the mouse brain affecting learning and memory. Herein, a sensitive method for quantifying free q and Q in human blood was developed, optimised and validated. After evaluating q/Q extraction efficiency in several different solid-phase sorbents, Bond Elut PBA (phenylboronic acid) cartridges were found to have the highest extraction recovery for q (82%) and Q (71%) from pooled human plasma. PBS with 4% BSA was used as surrogate matrix for method development and validation. An LC-MS/MS method was validated across the concentration range of 0.0003 - 1 {micro}M for both q and Q, showing excellent: linearity (r2 = 0.997 (q) and r2 = 0.998 (Q)), limit of quantification (0.0003 {micro}M), accuracy (100.39% - 125.71%) and precision (CV% < 15.68%). In a sampling of healthy volunteers (n = 44) there was no significant difference in q levels between male (n = 14; mean = 0.0068 {micro}M) and female (n = 30; mean = 0.0080 {micro}M) participants (p = 0.50). Q was not detected in human plasma. This validated method can now be used to further our understanding of the role of q/Q in nutrition, physiology and pathology.

biochemistry↗

bioRxiv2024

Neuronal downregulation of PLCG2 impairs synaptic function and elicits Alzheimer disease hallmarks

We developed a high content screening to investigate how Alzheimer disease (AD) genetic risk factors may affect synaptic mechanisms in rat primary neuronal cultures. Out of the target genes identified, we found that Plcg2 downregulation in mouse dentate gyrus neurons consistently disrupted dendritic morphology and synaptic function. In human neuronal cultures (hNCs), PLCG2 downregulation also impaired synaptic function and increased A{beta} levels and Tau phosphorylation. Very rare PLCG2 loss-of-function (LoF) variants were associated with a 10-fold increased AD risk. PLCG2 LoF carriers exhibit low mRNA/protein PLCG2/PLC{gamma}2 levels and the R953* LoF mutation compromised synaptic function and increased AD hallmarks in hNCs. Single nuclei RNAseq analyses confirmed that the downregulation of PLCG2 impacted pathways related to synaptic and neuronal functions, potentially through neurexin in neurons. In conclusion, PLC{gamma}2 downregulation could increase AD risk by impairing synaptic functions and increasing the A{beta} levels and Tau phosphorylation in neurons.

neuroscience↗

bioRxiv2024

Migration of endocrine and metabolism disrupting chemicals from plastic food packaging

Plastics constitute a vast array of substances, with over 16 000 known plastic chemicals, including intentionally and non-intentionally added substances. Toxicity and thousands of chemicals are extractable from plastics; however, the extent to which toxicity and chemicals migrate from everyday plastic products remains poorly understood. This study aims to characterize the endocrine and metabolism disrupting activity, as well as chemical composition of migrates from plastic food contact articles (FCAs) from four countries as significant sources of human exposure. Additionally, strategies for prioritization of chemicals were explored. Fourteen plastic FCAs covering seven polymer types with high global market shares were migrated into water and a water-ethanol mixture as food simulants according to European regulations. The migrates were analyzed using reporter gene assays for nuclear receptors relevant to human health and non-target chemical analysis to characterize the chemical composition of the migrates. All FCA migrates interfered with at least two nuclear receptors, predominantly targeting pregnane X receptor. Moreover, peroxisome proliferator receptor gamma was broadly activated by the migrates, though mostly with lower potencies, while estrogenic and antiandrogenic activities were more selectively induced by specific FCAs. Fewer chemicals and less toxicity migrated into water compared to the water-ethanol mixture. The latter exhibited similar toxicity and number of chemicals as methanol extracts of the same FCAs. Novel strategies were employed to address the chemical complexity of FCAs and narrow down the list of potential active chemicals. By comparing the composition of multiple leachates of one sample and using stepwise partial least squares regressions, we successfully reduced the chemical complexity, pinpointed potential endocrine disruptors such as triphenyl phosphate and prioritized chemicals for further identification efforts. This study demonstrates the migration of endocrine and metabolism disrupting chemicals from plastic FCAs into food simulants, rendering a migration of these compounds into food and beverages probable. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=113 SRC="FIGDIR/small/588263v4_ufig1.gif" ALT="Figure 1"> View larger version (42K): org.highwire.dtl.DTLVardef@32490dorg.highwire.dtl.DTLVardef@15a1047org.highwire.dtl.DTLVardef@1e2b565org.highwire.dtl.DTLVardef@f323e2_HPS_FORMAT_FIGEXP M_FIG C_FIG

pharmacology and toxicology↗

bioRxiv2024

The predicted secreted proteome of activated sludge microorganisms indicate distinct nutrient niches

In wastewater treatment plants (WWTPs) complex microbial communities process diverse chemical compounds from sewage. Secreted proteins are critical because many are the first to interact with or degrade external (macro)molecules. To better understand microbial functions in WWTPs, we predicted secreted proteomes of WWTP microbiota from more than 1000 high-quality metagenome-assembled genomes (MAGs) from 23 Danish WWTPs with biological nutrient removal. Focus was placed on examining secreted catabolic exoenzymes that target major classes of macromolecules. We demonstrate that Bacteroidota have high potential to digest complex polysaccharides, but also proteins and nucleic acids. Poorly understood activated sludge members of Acidobacteriota and Gemmatimonadota also have high capacities for extracellular polysaccharide digestion. Secreted nucleases are encoded by 61% of MAGs indicating an importance for extracellular DNA and/or RNA digestion in WWTPs. Secreted lipases were the least-common macromolecule-targeting enzymes predicted, encoded mainly by Gammaproteobacteria and Myxococcota. In contrast, diverse taxa encode extracellular peptidases, indicating that proteins are widely used nutrients. Diverse secreted multi-heme cytochromes suggest capabilities for extracellular electron-transfer by various taxa, including some Bacteroidota that encode undescribed cytochromes with >100 heme-binding motifs. Myxococcota have exceptionally large secreted protein complements, probably related to predatory lifestyles and/or complex cell cycles. Many Gammaproteobacteria MAGs (mostly former Betaproteobacteria) encode few or no secreted hydrolases, but many periplasmic substrate-binding proteins and ABC- and TRAP-transporters, suggesting they are mostly sustained by small molecules. Together, this study provides a comprehensive overview of how WWTPs microorganisms interact with the environment, providing new insights into their functioning and niche partitioning. ImportanceWastewater treatment plants are critical biotechnological systems that clean wastewater, allowing the water to reenter the environment and limit eutrophication and pollution. They are also increasingly important for recovery of resources. They function primarily by the activity of microorganisms, which act as a living sponge, taking-up and transforming nutrients, organic material and pollutants. Despite much research, many microorganisms in WWTPs are uncultivated and poorly characterized, limiting our understanding of their functioning. Here, we analyzed a large collection of high-quality metagenome-assembled genomes from WWTPs for encoded secreted enzymes and proteins, with special emphasis on those used to degrade organic material. This analysis showed highly distinct secreted proteome profiles among different major phylogenetic groups of microorganisms, thereby providing new insights into how different groups function and co-exist in activated sludge. This knowledge will contribute to a better understanding of how to efficiently manage and exploit WWTP microbiomes.

microbiology↗

bioRxiv2024

Distinguishable topological properties of functional genome networks in HIV-1 reservoirs

HIV-1 reservoirs display heterogeneous nature, lodging both intact and defective proviruses. Recent evidence has shed light on their difference, particularly in the context of immune-mediated selection. To deepen our understanding of such heterogeneous HIV-1 reservoirs and their functional implications, we pioneered the integration of basic concepts of graph theory to characterize the composition of HIV-1 reservoirs. Our analysis revealed noticeable topological properties in networks, featuring immunologic signatures enriched by genes harboring intact and defective proviruses, when comparing antiretroviral therapy (ART)-treated HIV-1-infected individuals and elite controllers. The key variable, the rich factor, played a pivotal role in classifying distinct topological properties in networks. The host gene expression strengthened the accuracy of classification between elite controllers and ART-treated patients. Overall, our work provides a prime example of leveraging genomic approaches alongside mathematical tools to unravel the complexities of HIV-1 reservoirs.

genomics↗

bioRxiv2024

Nitrous oxide respiration in acidophilic methanotrophs

Methanotrophic bacteria mitigate methane (CH4) emissions from natural environments. Although aerobic methanotrophs are considered strict aerobes, they are often highly abundant in extremely hypoxic and even anoxic environments. Despite the presence of denitrification genes, it remains to be verified whether denitrification contributes to their growth. Here, we revealed that two acidophilic methanotrophs encoding N2O reductase (clade I and type II nosZ, respectively): Methylocella tundrae T4 and Methylacidiphilum caldifontis IT6, respired N2O and grew anaerobically on diverse non-methane substrates, including methanol, C-C substrates, and hydrogen. However, NO3 - and NO2 - could be reduced during methanol oxidation in Methylocella tundrae T4 and Methylocella silvestris BL2 without significantly increasing cell biomass. The lack of growth on methanol + NO3- or NO2- was likely due to the production of toxic reactive nitrogen species and C1 metabolites. However, the oxidation of pyruvate, a C3 electron donor, combined with NO3- or NO2- reduction resulted in anaerobic growth of Methylocella tundrae T4 and Methylocella silvestris BL2. In the extreme acidophile, Methylacidiphilum caldifontis IT6, N2O respiration supported cell growth at an extremely acidic pH of 2.0. In Methylocella tundrae T4, simultaneous consumption of N2O and CH4 was observed in suboxic conditions, both in microrespirometry and growth experiments, indicating the robustness of its N2O reductase activity in the presence of O2. Furthermore, CH4 oxidation per O2 reduced in O2-limiting conditions increased when N2O was added, indicating that cells of T4 can direct more O2 towards methane monooxygenase when respiring N2O as a terminal electron acceptor. Upregulation of nosZ and distinct repertories of methanol dehydrogenase-encoding genes (XoxF- and MxaFI-type) in Methylocella tundrae T4 cells grown anaerobically on methanol with N2O as the sole electron acceptor indicated adaptation mechanisms to anoxia. Our findings demonstrate that some methanotrophs can respire N2O independently or in tandem with O2, significantly expanding their potential ecological niche and paving the way for enhanced growth and survival in dynamic environments. This metabolic capability has application potential for simultaneously mitigating the emissions of the key greenhouse gases, CO2, CH4, and N2O, from natural and engineered environments.

microbiology↗

bioRxiv2024

Candidatus Nitrosocosmicus members are the dominant archaea associated with pepper (Capsicum annuum L.) and ginseng (Panax ginseng C.A. Mey.) plants rhizospheres

BackgroundAlthough archaea are widespread in terrestrial environments, little is known about the selection forces that shape their composition, functions, survival, and proliferation strategies in the rhizosphere. The ammonia-oxidizing archaea (AOA), which are abundant in soil environments, catalyze the first step of nitrification and have the potential to influence plant growth and development significantly. ResultsBased on archaeal 16S rRNA and amoA gene (encoding the ammonia monooxygenase subunit A) amplicon sequencing analysis, distinct archaeal communities dominated by AOA were found to be associated with the root systems of pepper (Capsicum annuum L.) and ginseng (Panax ginseng C.A. Mey.) plants compared to bulk soil not penetrated by roots. AOA related to "Candidatus Nitrosocosmicus", which, unlike most other AOA, harbor genes encoding manganese catalase (MnKat), dominated rhizosphere soils, and thus contributed to the development of distinct archaeal communities in rhizospheres. Accordingly, for both plant species, the copy number ratios of AOA MnKat genes to amoA genes were significantly higher in rhizosphere soils than in bulk soils. In contrast to MnKat-negative strains from other AOA clades, the catalase activity of a representative isolate of "Ca. Nitrosocosmicus" was demonstrated. Members of this clade were enriched in H2O2-amended bulk soils, and constitutive expression of their MnKat gene was observed in both bulk and rhizosphere soils. ConclusionsDue to their abundance, "Ca. Nitrosocosmicus" members can be considered key players mediating the nitrification process in rhizospheres. The selection of this MnKat-containing AOA in rhizospheres of several agriculturally important plants hints at a previously overlooked AOA-plant interaction. For additional mechanistic analyses of the interaction, this key clade of AOA with cultured representatives can be employed.

microbiology↗

bioRxiv2023

Novel nitrifying symbiont lineages are vertically inherited and widespread in marine sponges

Ammonia-oxidising archaea and nitrite-oxidising bacteria are common members of marine sponge microbiomes. They derive energy for carbon fixation and growth from nitrification - the oxidation of ammonia to nitrite and further to nitrate - and are proposed to play essential roles in the carbon and nitrogen cycling of sponge holobionts. In this study, we characterise two novel nitrifying symbiont lineages, Ca. Nitrosokoinonia and Ca. Nitrosymbion in the marine sponge Coscinoderma matthewsi using a combination of molecular tools, single-cell imaging techniques, and physiological rate measurements. Both represent a new genus in the ammonia-oxidising archaeal class Nitrososphaeria and the nitrite-oxidising bacterial order Nitrospirales, respectively. Furthermore, we show that larvae of this viviparous sponge are densely colonised by representatives of Ca. Nitrosokoinonia and Ca. Nitrosymbion indicating vertical transmission. In adults, the representatives of both symbiont genera are located extracellularly in the mesohyl. Comparative metagenome analyses and physiological data suggest that ammonia-oxidising archaeal symbionts of the genus Ca. Nitrosokoinonia strongly rely on endogenously produced nitrogenous compounds (i.e., ammonium, urea, nitriles/cyanides, and creatinine) rather than on exogenous ammonium sources taken up by the sponge. Additionally, the nitrite-oxidising bacterial symbionts Ca. Nitrosymbion may reciprocally support the ammonia-oxidisers with ammonia via the utilisation of sponge-derived urea and cyanate. Interestingly, comparative analyses of published environmental 16S rRNA amplicon data revealed that Ca. Nitrosokoinonia and Ca. Nitrosymbion are widely distributed and predominantly associated with marine sponges and corals, suggesting a broad relevance of our findings.

microbiology↗

bioRxiv2023

Diagnostic images for mild cognitive impairment reveal biomarker status and abnormal scene processing

Research on the impairment of episodic memory in Alzheimers disease often focuses on the processes of memory rather than the content of the specific images being remembered. We recently showed that patients with mild cognitive impairment (MCI), Stage 3 of Alzheimers disease, can memorize certain images quite well, suggesting that episodic memory is not uniformly impaired. Certain images, on the other hand, could not be memorized by MCI patients and were instead diagnostic for distinguishing MCI from healthy older adults. In this study, we investigate whether poor memory for diagnostic images is related to impaired neural processing in specific brain regions due to Alzheimers biomarker pathology. 64 healthy controls and 48 MCI participants in the DELCODE dataset performed a visual scene memory task during fMRI, with CSF Alzheimers disease biomarker data collected (i.e., amyloid and tau biomarkers). We found that diagnostic images have larger behavior-biomarker correlations for total tau, phospho-tau, A{beta}42/A{beta}40, A{beta}42/phospho-tau compared to non-diagnostic images, suggesting that memory for these specific images are more affected by Alzheimers disease pathology. The fMRI data revealed an interaction effect between group membership (healthy control / MCI) and image diagnosticity (diagnostic / non-diagnostic scene images), with MCI participants having higher activation in scene processing regions (parahippocampal place area, retrosplenial cortex and occipital place area) for diagnostic images than non-diagnostic images. In contrast, healthy controls showed no differences in processing between diagnostic and non-diagnostic images. These results suggest that MCI individuals may engage in inefficiently heightened encoding activation for these diagnostic images. Our results show that special "diagnostic" images exist that can reveal amyloid and tau pathology and differences in neural activity in scene regions.

neuroscience↗

bioRxiv2023

The Parkinson's drug entacapone disrupts gut microbiome homeostasis via iron sequestration

Increasing evidence shows that many human-targeted drugs alter the gut microbiome, leading to implications for host health. However, much less is known about the mechanisms by which drugs target the microbiome and how drugs affect microbial function. Here we combined quantitative microbiome profiling, long-read metagenomics, stable isotope probing and single cell chemical imaging to investigate the impact of two widely prescribed nervous system targeted drugs on the gut microbiome. Ex vivo supplementation of physiologically relevant concentrations of entacapone or loxapine succinate to faecal samples significantly impacted the abundance of up to one third of the microbial species present. Importantly, we demonstrate that the impact of these drugs on microbial metabolism is much more pronounced than their impact on abundances, with low concentrations of drugs reducing the activity, but not the abundance of key microbiome members like Bacteroides, Ruminococcus or Clostridium species. We further demonstrate that entacapone impacts the microbiome due to its ability to complex and deplete available iron, and that microbial growth can be rescued by replenishing levels of microbiota-accessible iron. Remarkably, entacapone-induced iron starvation selected for iron-scavenging organisms carrying antimicrobial resistance and virulence genes. Collectively, our study unveils the impact of two under-investigated drugs on whole microbiomes and identifies metal sequestration as a mechanism of drug-induced microbiome disturbance.

microbiology↗

bioRxiv2023

Global abundance patterns, diversity, and ecology of Patescibacteria in wastewater treatment plants

BackgroundMicroorganisms are responsible for nutrient removal and resource recovery in wastewater treatment plants (WWTPs), and their diversity is often studied by 16S rRNA gene amplicon sequencing. However, this approach underestimates the abundance and diversity of Patescibacteria due to the low coverage of commonly used PCR primers for this highly divergent bacterial phylum. Therefore, our current understanding of the global diversity, distribution, and ecological role of Patescibacteria in WWTPs is very incomplete. This is particularly relevant as Patescibacteria are considered to be associated with microbial host cells and can therefore influence the abundance and temporal variability of other microbial groups that are important for WWTP functioning. ResultsHere, we evaluated the in silico coverage of widely used 16S rRNA gene-targeted primer pairs and redesigned a primer pair targeting the V4 region of bacterial and archaeal 16S rRNA genes to expand its coverage for Patescibacteria. We then experimentally evaluated and compared the performance of the original and modified V4-targeted primers on 565 WWTP samples from the MiDAS global sample collection. Using the modified primer pair, the percentage of ASVs classified as Patescibacteria increased from 5.9% to 23.8%, and the number of detected patescibacterial genera increased from 560 to 1,576, while the detected diversity of the remaining microbial community remained similar. Due to this significantly improved coverage of Patescibacteria, we identified 23 core genera of Patescibacteria in WWTPs and described the global distribution pattern of these unusual microbes in these systems. Finally, correlation network analysis revealed potential host organisms that might be associated with Patescibacteria in WWTPs. Interestingly, strong indications were found for an association between Patescibacteria of the Saccharimonadia and globally abundant polyphosphate-accumulating organisms of the genus Ca. Phosporibacter. ConclusionsOur study (i) provides an improved 16S rRNA gene V4 region-targeted amplicon primer pair inclusive of Patescibacteria with little impact on the detection of other taxa, (ii) reveals the diversity and distribution patterns of Patescibacteria in WWTPs on a global scale, and (iii) provides new insights into the ecological role and potential hosts of Patescibacteria in WWTPs.

ecology↗

bioRxiv2023

Cognitive Reserve Against Alzheimer's Pathology Is Linked to Brain Activity During Memory Formation

The cognitive reserve (CR) hypothesis posits that individuals can differ in how their brain function is disrupted by pathology associated with aging and neurodegeneration. Here, we tested this hypothesis in the Alzheimers disease continuum using longitudinal data from 490 participants of the DELCODE multicentric observational study. Brain function was measured using task fMRI of visual memory encoding. Using a multivariate moderation analysis we identified a CR-related activity pattern underlying successful memory encoding that moderated the detrimental effect of AD pathological load on cognitive performance. CR was mainly represented by a more pronounced expression of the task-active network encompassing the default mode network (DMN), anterior cingulate cortex (ACC) and inferior temporal regions including the fusiform gyrus. We devised personalized fMRI-based CR scores that moderated the impact of AD pathology on cognitive performance and were positively associated with years of education. Furthermore, higher CR scores were associated with slower cognitive decline over time. Our findings suggest maintenance of core cognitive circuits including the DMN and ACC as the primary mechanism of CR. Individual brain activity levels of these areas during memory encoding have prognostic value for future cognitive decline.

neuroscience↗

bioRxiv2023

Beyond the nucleus: Plastic chemicals activate G protein-coupled receptors

O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=84 SRC="FIGDIR/small/560665v1_ufig1.gif" ALT="Figure 1"> View larger version (23K): org.highwire.dtl.DTLVardef@e3b5edorg.highwire.dtl.DTLVardef@1bcf3aeorg.highwire.dtl.DTLVardef@224012org.highwire.dtl.DTLVardef@9c61ea_HPS_FORMAT_FIGEXP M_FIG C_FIG G protein-coupled receptors (GPCRs) are central mediators of cell signaling and physiological function. Despite their biological significance, GPCRs have not been widely studied in the field of toxicology. Herein, we investigated these receptors are novel targets of plastic chemicals using a high-throughput drug screening assay with 126 human non-olfactory GPCRs. In a first-pass screen, we tested the activity of triphenol phosphate, bisphenol A, and diethyl phthalate as well as three real-world mixtures of chemicals extracted from plastic food packaging covering all major polymer types. We found 11 GPCR-chemical interactions, of which the chemical mixtures exhibited the most robust activity at Adenosine receptor 1 (ADORA1) and Melatonin receptor 1 (MTNR1A) in a confirmatory secondary screen. We further confirmed that polyvinyl chloride and polyurethane products contain ADORA1 or MTNRA1 agonists using pharmacological knockdown experiments. Finally, an analysis of the associated gene ontology terms suggests that ADORA1 and MTNR1A activation may be linked to downstream effects on circadian and metabolic processes. Our findings exemplify the diversity of endpoints plastic chemicals can target and demonstrate the relevance of non-genomic pathways which have thus far remained unexplored.

pharmacology and toxicology↗