Biology subjects

Herrmann, M.

Publications and source records attributed to Herrmann, M..

At least 19 recordsLinked to original sources

bioRxiv2026

Traversing the canopy: phenology-driven changes and within-canopy transport shape the phyllosphere microbiome in a temperate floodplain hardwood forest

O_LIPhyllosphere microbiomes are subject to microbial import from various sources and undergo substantial changes during phenological changes of plants. However, these processes are still poorly understood for forest canopies. We propose that phenology-driven changes in host properties, and rainwater-mediated, within-canopy transport shape the phyllosphere microbiome in temperate forests. Leaves and throughfall samples were collected from oak, ash and linden trees at top, mid, and bottom canopy positions at the Leipzig canopy crane facility (Germany) at time points representing early, mid and late phenological stages. Bacterial community composition was assessed by 16S rRNA gene amplicon sequencing. C_LIO_LIPhenological stages explained 19% of phyllosphere bacterial community variation, followed by tree species identity (12%) and canopy position (2%). Later phenological stages exhibited more homogeneous and functionally redundant phyllosphere communities along with a strong decline of plant pathogens and increasing potential for microbially mediated biocontrol mechanisms. Throughfall transported up to 1011 bacterial cells per litre with maximum bacterial fluxes at the canopy top. C_LIO_LIOur findings demonstrate that in temperate forests, phenology-driven effects on the phyllosphere microbiome are far more important than tree species specific effects. Extent and selectivity of throughfall-mediated mobilization may play a crucial role for the spatial heterogeneity of microbial communities in tree crowns. C_LI

ecology↗

bioRxiv2026

Yellow fever vaccine propagation in primary human hepatocytes triggers antiviral and cytolytic responses

Yellow fever virus (YFV) infection can cause severe-to-fatal liver damage in humans, while immunization with the attenuated 17D vaccine strain has an excellent safety record, priming protective host immunity in the absence of pathology. To investigate virus-host correlates associated with these differential clinical outcomes, we combined YFV genome-level evolutionary analyses with investigations of vaccine and virulent strain hepatotropism. Evolutionary analyses confirmed purifying selection is the dominant force driving global YFV genome divergence, with functional constraints associated with the YFV transmission cycle selecting against vaccine attenuating mutations in virulent strains. In immune deficient hepatoma cells, 17D exhibited enhanced early propagation, spreading and apoptosis induction when compared to virulent strains. Ex vivo infections performed in primary human hepatocytes (PHH) from multiple donors confirmed robust propagation of both 17D and virulent YFV strains. RNA-sequencing revealed consistent and shared induction of IFNB and IFNL1-4, modulating overlapping gene programs associated with antiviral responses, immunity, chemotaxis and inflammation, cell-death, metabolic reprogramming and protein translation. Subtle differences in virion production kinetics and the magnitude and tempo of PHH transcriptional responses were observed. Antiviral responses to 17D were activated earlier while responses to virulent YFV were delayed but enhanced, mirroring virus propagation kinetics. More broadly, cellular responses to YFV infection are likely dominated by paracrine IFN signalling, with enriched LRP1 expression coupled with impaired IFN production in PHH contributing to YFVs robust hepatotropism. In summary, we demonstrate comparable propagation kinetics and PHH transcriptional responses to vaccine and virulent YFV strains, highlighting impaired hepatotropism is not a correlate of vaccine attenuation. These data imply that unknown barriers restrict liver access and associated organ pathology upon vaccination with 17D.

microbiology↗

bioRxiv2025

Continuous theta-burst stimulation of the ventromedial prefrontal cortex reduces Pavlovian go-invigoration and enhances thalamo-striatal reward prediction error signals

The ventromedial prefrontal cortex (vmPFC) represents value, i.e. whether environmental cues are good or bad. Rewarding cue value is aligned with a tendency to act or to inhibit in case of potential punishment, a so-called Pavlovian Bias. Value-related vmPFC activation may therefore impact Pavlovian bias. However, it remains unknown how the activity in the vmPFC modulates the Pavlovian bias. Thus, we applied continuous theta-burst stimulation (cTBS), a non-invasive protocol that transiently reduces cortical excitability, over the vmPFC in a single-blinded, between-subject study. 90 healthy adults performed a motivational Go/NoGo learning task during fMRI after receiving cTBS (n=45) or sham (n=45) stimulation. Behaviourally, cTBS reduced overall Go response rates and slowed reaction times. Computational modelling showed a decrease in the learning rate, selectively for rewarding outcomes. Computational fMRI analysis showed stronger reward prediction error (RPE) signals in the vmPFC, mediodorsal thalamus, and left dorsal striatum after cTBS, without changes in neural signals at cue onset. These findings provide causal evidence that the vmPFC drives the action-invigoration component of the Pavlovian bias. Significance statementWe causally link ventromedial prefrontal cortex (vmPFC) function to motivated action in humans. In a single-blind cTBS-fMRI study (n=90), transient vmPFC inhibition reduced Go responding, slowed reaction times, and selectively lowered the positive learning rate early in learning. At the same time, reward-prediction-error signals increased in mediodorsal thalamus, dorsal striatum, and vmPFC, while cue-onset value/choice signals were unchanged. Together, the results indicate that vmPFC normally speeds value updating and invigorates actions; when inhibited, control shifts toward slower, subcortically supported learning under higher uncertainty.

neuroscience↗

bioRxiv2025

Quantitative phase deformability cytometry (QP-DC) for precise and clinically relevant multiparametric immune cell profiling

Imaging flow cytometry enables the detailed analysis of cell morphology and internal structures through high-throughput cell imaging, and quantitative phase imaging (QPI)-based microfluidic approaches have extended this by providing label-free measures such as dry mass and refractive index (RI). Building on these developments, we present quantitative phase deformability cytometry (QP-DC), which integrates QPI with deformability cytometry to simultaneously measure morphology, mechanics, and intrinsic biophysical parameters such as mass density and dry mass. Numerical refocusing ensures in-focus images independent of axial position, improving precision in contour detection and feature extraction. Using microspheres and whole blood, we validated QP-DC and then applied it to neutrophils under lipopolysaccharide (LPS) stimulation and from patients with systemic lupus erythematosus (SLE). QP-DC revealed LPS-induced reductions in neutrophil mass density and identified heterogeneous subpopulations in SLE. These results demonstrate the capability of QP-DC for precise biophysical and mechanical characterization, offering significant potential for research and clinical diagnostics.

biophysics↗

bioRxiv2025

Rainwater-driven transport of matter and microbes from phyllosphere to soil in a temperate beech forest

In forest ecosystems, the transport of organic matter including microbial cells by throughfall and stemflow represents a central linkage between the phyllosphere and soil. However, the extent and taxon-specificity of rainwater-mediated vertical transfer of microorganisms, and its relevance for matter fluxes is sparsely understood. We investigated the rainwater-driven transport of bacteria and its contribution to matter transport in bulk rainfall, throughfall, stemflow and seepage in a temperate deciduous forest and compared the transported communities to those in phyllosphere and soil. Throughfall-mediated cell fluxes equaled those in seepage below the litter layer, pointing to a substantial above-ground translocation of bacteria. Bacterial cells contributed up to 11 % and 33 % to the exported total organic carbon and total nitrogen, respectively. Bacteria affiliated with Pseudomonadaceae, Oxalobacteraceae, Hymenobacteraceae, and Sphingomonadaceae were differentially transmitted from the canopy with increased abundances in throughfall and stemflow compared to bulk rain. A small fraction of shared taxa pointed to the import, proliferation and mobilization of selected bacterial taxa between neighboring ecohydrological compartments. The genetic potential of the transported bacterial communities was strongly linked to organic matter degradation particularly of carbohydrates and proteins. Our findings extend our understanding of rainwater-mediated vertical matter transport in forest ecosystems and highlight the contribution of microbial cells to this transport especially in above-ground compartments. Strong shifts in community composition and abundance of the transported taxa between throughfall, stemflow and soil seepage are linked to differences in source communities but may also point to different mechanisms of cell detachment across compartments. HighlightsO_LIRainwater flow paths are important carriers for organic matter and microorganisms. C_LIO_LIThroughfall and stemflow contained high abundances of microbial cells. C_LIO_LIBacteria contributed up to 11 % and 33 % to exported carbon and nitrogen. C_LIO_LIBacterial taxa were selectively mobilized by throughfall, stemflow and seepage. C_LI

microbiology↗

bioRxiv2025

Balancing Act: Groundwater microbiome''s resilience and vulnerability to hydroclimatic extremes

Groundwater health is increasingly threatened by climate change, which alters precipitation patterns, leading to groundwater recharge shifts. These shifts impact subsurface microbial communities, crucial for maintaining ecosystem functions. In this decade-long study of carbonate aquifers, we analyzed 815 bacterial 16S rRNA gene datasets, 226 dissolved organic matter (DOM) profiles, 387 metabolomic datasets, and 174 seepage microbiome sequences. Our findings reveal distinct short- and long-term temporal patterns of groundwater microbiomes driven by environmental fluctuations. Microbiomes of hydrologically connected aquifers exhibit lower temporal stability due to stochastic processes and greater susceptibility to surface disturbances, yet they demonstrate remarkable resilience. Conversely, isolated aquifer microbiomes show resistance to short-term changes, governed by deterministic processes, but exhibit reduced stability under prolonged stress. Variability in seepage-associated microorganisms, DOM, and metabolic diversity further drive microbiome dynamics. These findings highlight the dual vulnerability of groundwater systems to acute and chronic pressures, emphasizing the critical need for sustainable management strategies to mitigate the impacts of hydroclimatic extremes.

microbiology↗

bioRxiv2024

IgA displays site- and subclass-specific glycoform differences despite equal glycoenzyme expression

BackgroundGlycosylation is an important posttranslational modification of proteins and in most cases indispensable for proper protein function. Like most soluble proteins, IgA, the second most prevalent antibody in human serum, contains several N- and O-glycosylation sites. While for IgG the impact of Fc glycosylation on effector functions and inflammatory potential has been intensively studied, only little is known for IgA. In addition, only glimpses exist regarding the regulation of IgA glycosylation. We have previously shown that IgA1 and IgA2 differ functionally and also show differences in their glycosylation pattern. The more pro-inflammatory IgA2 which is linked to autoimmune diseases displays decreased sialylation, galactosylation, fucosylation and bisection as compared to IgA1. In the present study, we aimed to investigate these differences in glycosylation in detail and to explore the mechanisms underlying them. MethodsIgA1 and IgA2 was isolated from serum of 12 healthy donors. Site specific glycosylation was analyzed by mass spectrometry. In addition, human bone marrow plasma cells were investigated using single cell mRNA sequencing, flow cytometry and ELISpot. ResultsWe found that certain glycoforms greatly differ in their abundance between IgA1 and IgA2 while others are equally abundant. Overall, the IgA2 glycans displayed a more immature phenotype with a higher prevalence of oligomannose and fewer fully processed glycans. Of note, these differences cant be explained by differences in the glycosylation enzyme machinery as mRNA sequencing and flow cytometry analysis showed equal enzyme expression in IgA1 and IgA2 producing plasma cells. ELISpot analysis suggested a slightly increased antibody production rate in IgA2 producing plasma cells which might contribute to its lower glycan processing rates. But this difference was only minor, suggesting that further factors such as steric accessibility determine glycan processing. This is supported by the fact that glycans at different positions on the same IgA chain differ dramatically in fucosylation, sialylation and bisection. ConclusionIn summary, our detailed overview of IgA1 and IgA2 glycosylation shows a class, subclass, and site-specific glycosylation fingerprint, most likely due to structural differences of the protein backbones.

immunology↗

bioRxiv2024

TSniffer: Unbiased de novo identification of RNA editing sites and quantification of editing activity in RNA-seq data

RNA editing by adenosine deaminases acting on RNA (ADARs) is an evolutionarily conserved posttranscriptional modification essential for organismal development and normal cell function. Three catalytically active ADARs are conserved in mammals: two isoforms of ADAR1 referred to as ADAR1-p150 and ADAR1-p110, as well as ADAR2. All recognize and edit double-stranded RNA (dsRNA) structures but demonstrate target specificity and selectivity that dictate the unique essential biological functions of the three enzymes. The editing activity of ADAR1-p150 suppresses autoimmune responses against self-RNA structures, whereas ADAR1-p110 and ADAR2 have other primary functions. To better understand the mechanism of target selection by ADARs, we developed TSniffer, which allows accurate de novo identification of edited transcripts and quantification of the extent of editing within each transcript. We found that 17-40% of protein coding transcripts in mice, ferrets, and humans are edited by ADARs. Individual transcripts can harbor hundreds and thousands of editing sites, mostly within inverted retrotransposable elements. For human transcripts, we found differential editing by ADAR1 and ADAR2, aligning with a supportive role for ADAR2, while some targets were dominantly edited by ADAR1. Relying only on RNA-seq data and reference genome, TSniffer represents a novel tool to decipher the role of ADAR editing in different physiological states including disease models. Its unbiased approach is suitable for any organism.

bioinformatics↗

bioRxiv2024

The genome assembly of Rhabditoides inermis from a complex microbial community reveals further evidence for parallel gene family expansions across multiple nematodes

BackgroundFree-living nematodes such as Caenorhabditis elegans and Pristionchus pacificus are powerful model systems for linking specific traits to their underlying genetic basis. To trace the evolutionary history of a candidate gene, a robust phylogenomic framework is indispensable. ResultsIn this work, we generated a near chromosome-scale genome assembly of the nematode Rhabditoides inermis which had previously been proposed as the sister group of the family Diplogastridae to which P. pacificus belongs. The genome was assembled from a complex microbial community that consists of multiple bacteria and a fungus of the genus Vanrija. The R. inermis genome has five chromosomes that likely arose from recent fusions of different Nigon elements. Phylogenomic analysis grouped R. inermis within a clade including C. elegans, Mesorhabditis belari and other rhabditids and thus, did not support a sister group relationship between R. inermis and the family Diplogastridae. Comparative genomic analyses identified abundant lineage-specific orthogroups which reveal evidence for parallel expansions of environmentally responsive gene families. ConclusionsOur work demonstrates the value of the R. inermis genome as a resource for future phylogenomic analysis and for studying gene family evolution.

genomics↗

bioRxiv2024

Magnesium hydroxide nanoneedles derived from Anthocleista schweinfurthii Gilg (Loganiaceae) support mesenchymal stromal cell proliferation and wound healing

Multiple metallic nanoparticles are able to promote cellular and tissue health, but these nanoparticles can be difficult to synthesize and can also cause unintended side-effects. Here, we study the effects on wounds healing and bone reparation of Mg(OH)2 from Anthocleista schweinfurthii Gilg (Loganiaceae) leaves (AS), which are local to the Africa region and have been used in traditional medicine to treat injuries. Mg(OH)2 nanoneedles were synthesized from aqueous extracts of Anthocleista schweinfurthii Gilg (Loganiaceae) leaves (AS) and magnesium nitrate. The quick polydispersing and crystallized Mg(OH)2-metal interface was found to be covered in plant secondary metabolites. We call this compound Mg(OH)2-AS. Using an acute dermal toxicity experiment on animal model, we determined that Mg(OH)2-AS is safe for topical application. In vitro experiments suggest that Mg(OH)2-AS has anti-inflammatory potential, and in vivo wound healing assays in Wistar rats indicate that Mg(OH)2-AS can enhance wound healing. To investigate Mg(OH)2-AS effects on the cellular level, we used bone marrow mesenchymal stromal cells (BM-MSCs). In contrast to pure Mg(OH)2 or AS, cell viability and proliferation were not impaired by Mg(OH)2-AS. Cell morphology remained unchanged upon media supplementation with Mg(OH)2-AS. Preliminary results further indicate enhanced osteogenic differentiation of BM-MSCs in media supplied with ascorbic acid, {beta}-glycerophosphate and dexamethasone and addition of Mg(OH)2-AS. These findings motivate further research towards the inclusion of the material in implants for bone fracture healing.

pharmacology and toxicology↗

bioRxiv2024

Impact of high fat diet and exercise on bone and bile acid metabolism in rats

BackgroundBile acids help facilitate the intestinal lipids absorption, and have endocrine activity in glucose, lipid and bone metabolism. Obesity and exercise influence bile acid metabolism and have opposite effects in bone. This given study investigates if regular exercise helps mitigate the adverse effects of obesity on bone, potentially by reversing alterations in bile acid metabolism. MethodsFour-month-old female Sprague Dawley rats either received high fat diet (HFD) or chow-based standard diet (lean controls). During the 10-month study period, half of the animals performed 30 min of running at moderate speed on five consecutive days followed by two days of rest. The other half was kept inactive (inactive controls). At study end, bone quality was assessed by micro computed tomography and biomechanical testing. Bile acids were measured in serum and stool. ResultsHFD feeding was related to reduced trabecular (-33%, p=1.14x10-7) and cortical (-21%, p=2.9x10-8) bone mass, and lowered femoral stiffness (12-41%, p=0.005). Furthermore, HFD decreased total bile acids in serum (-37%, p=1.0x10-6), but increased bile acids in stool (+2-fold, p=7.3x10-9). These quantitative effects were accompanied by changes in the relative abundance of individual bile acids. The concentration of serum bile acids correlated positively with all cortical bone parameters (r=0.593 - 0.708), whilst stool levels showed inverse correlations at cortical (r=-0.651 - -0.805) and trabecular level (r=-0.656 - -0.750). Exercise improved some trabecular and cortical bone quality parameters (+11-31%, p=0.043 to 0.001) in lean controls, but failed to revert the bone loss related to HFD. Similarly, changes in bile acid metabolism were not mitigated by exercise. ConclusionProlonged HFD consumption induced quantitative and qualitative alterations in bile acid metabolism, accompanied by bone loss. Tight correlations between bile acids and structural indices of bone quality support further functional analyses on the potential role of bile acids in bone metabolism. Regular moderate exercise improved trabecular and cortical bone quality in lean controls but failed mitigating the effects related to HFD in bone and bile acid metabolism.

molecular biology↗

bioRxiv2023

Hepatitis C virus cell culture adaptive mutations enhance cell culture propagation by multiple mechanisms but boost antiviral responses in primary human hepatocytes

Hepatitis C virus (HCV) infection progresses to chronicity in the majority of infected individuals. Its high intra-host genetic variability enables HCV to evade the continuous selection pressure exerted by the host, contributing to persistent infection. Utilizing a cell culture adapted HCV population (p100pop) which exhibits increased replicative capacity in various liver cell lines, this study investigated virus and host determinants which underlie enhanced viral fitness. Characterization of a panel of molecular p100 clones revealed that cell culture adaptive mutations optimize a range of virus-host interactions, resulting in expanded cell tropism, altered dependence on the cellular co-factor micro-RNA 122 and increased rates of virus spread. On the host side, comparative transcriptional profiling of hepatoma cells infected either with p100pop or its progenitor virus revealed that enhanced replicative fitness correlated with activation of endoplasmic reticulum stress signaling and the unfolded protein response. In contrast, infection of primary human hepatocytes with p100pop led to a mild attenuation of virion production which correlated with a greater induction of cell-intrinsic antiviral defense responses. In summary, long-term passage experiments in cells where selective pressure from innate immunity is lacking improves multiple virus-host interactions, enhancing HCV replicative fitness. However, this study further indicates that HCV has evolved to replicate at low levels in primary human hepatocytes to minimize innate immune activation, highlighting that an optimal balance between replicative fitness and innate immune induction is key to establishing persistence. Author SummaryHCV infection remains a global health burden with 58 million people currently chronically infected. However, the detailed molecular mechanisms which underly persistence are incompletely defined. We utilized a long-term cell culture adapted HCV, exhibiting enhanced replicative fitness in different human liver cell lines, in order to identify molecular principles by which HCV optimizes its replication fitness. Our experimental data revealed that cell culture adaptive mutations confer changes in the host response and usage of various host factors. The latter allows functional flexibility at different stages of the viral replication cycle. However, increased replicative fitness resulted in an increased activation of the innate immune system, which likely poses boundary for functional variation in authentic hepatocytes, explaining the observed attenuation of the adapted virus population in primary hepatocytes.

molecular biology↗

bioRxiv2023

Differential contribution of nitrifying prokaryotes to nitrification in groundwater

The ecophysiology of complete ammonia-oxidizing bacteria (CMX) of the genus Nitrospira and their widespread occurrence in groundwater suggests that CMX bacteria have a competitive advantage over ammonia-oxidizing bacteria (AOB) and archaea (AOA) in these environments. However, the specific contribution of their activity to nitrification processes has remained unclear. We aimed to disentangle the contribution of CMX, AOA and AOB to nitrification and to identify the environmental drivers of their niche differentiation at different levels of ammonium and oxygen in oligotrophic carbonate rock aquifers. CMX amoA genes accounted on average for 16 to 75% of the total groundwater amoA genes detected. Nitrification rates were positively correlated to CMX clade A associated phylotypes and AOB affiliated with Nitrosomonas ureae. Short-term incubations amended with the nitrification inhibitors allylthiourea and chlorate suggested that AOB contributed a large fraction to overall ammonia oxidation, while metaproteomics analysis confirmed an active role of CMX in both ammonia and nitrite oxidation. Ecophysiological niche differentiation of CMX clades A and B, AOB and AOA was linked to their requirements for ammonium, oxygen tolerance, and metabolic versatility. Our results demonstrate that despite numerical predominance of CMX, the first step of nitrification in oligotrophic groundwater appears to be primarily governed by AOB. Higher growth yields at lower ammonia turnover rates and energy derived from nitrite oxidation most likely enable CMX to maintain consistently high populations.

microbiology↗

bioRxiv2022

Multi-omics profiling of collagen-induced arthritis mouse model reveals early metabolic dysregulation via SIRT1 axis

Rheumatoid arthritis (RA) is characterized by joint infiltration of immune cells and synovial inflammation which leads to progressive disability. Current treatments improve the disease outcome, but the unmet medical need is still high. New discoveries over the last decade have revealed the major impact of cellular metabolism on immune cell functions. So far, a comprehensive understanding of metabolic changes during disease development, especially in the diseased microenvironment, is still limited. Therefore, we studied the longitudinal metabolic changes during the development of murine arthritis integrating metabolomics and bulk RNA-seq data. We identified an early change in macrophage pathways which was accompanied by oxidative stress, a drop in NAD+ level and induction of glucose transporters. We discovered inhibition of SIRT1, a NAD-dependent histone deacetylase and confirmed its dysregulation in human macrophages and synovial tissue of RA patients. Mining this database should enable the discovery of novel metabolic targets and therapy opportunities in RA.

cell biology↗

bioRxiv2021

Rates of primary production in groundwater rival those in oligotrophic marine systems

The terrestrial subsurface contains nearly all of Earths freshwater reserves1 and harbors upwards of 60% of our planets total prokaryotic biomass2,3. While genetic surveys suggest these organisms rely on in situ carbon fixation, rather than the translocation of photosynthetically derived organic carbon4-6, corroborating measurements of carbon fixation in the subsurface are absent. Using a novel ultra-low level 14C-labeling technique, we show that in situ carbon fixation rates in a carbonate aquifer reached 10% of the median rates measured in oligotrophic marine surface waters, and were up to six-fold greater than those observed in lower euphotic zone waters where deep chlorophyll levels peak. Empirical carbon fixation rates were substantiated by both nitrification and anammox rate data. Metagenomic analyses revealed a remarkable abundance of putative chemolithoautotrophic members of an uncharacterized order of Nitrospiria - the first representatives of this class expected to fix carbon via the Wood-Ljungdahl pathway. Based on these fixation rates, we extrapolate global primary production in carbonate groundwaters to be 0.11 Pg of carbon per year.

microbiology↗

bioRxiv2021

Groundwater bacterial communities evolve over time, exhibiting oscillating similarity patterns in response to recharge

Time series analyses are a crucial tool for uncovering the patterns and processes shaping microbial communities and their functions, especially in aquatic ecosystems. Subsurface aquatic environments are perceived to be more stable than oceans and lakes, due to the lack of sunlight, the absence of photosysnthetically-driven primary production, low temperature variations, and oligotrophic conditions. However, periodic groundwater recharge should affect the structure and succession of groundwater microbiomes. To disentangle the long-term temporal changes in groundwater bacterial communities of shallow fractured bedrock community, and identify the drivers of the observed patterns, we analysed bacterial 16S rRNA gene sequencing data for samples collected monthly from three groundwater wells over a six-year period (n=230) along a hillslope recharge area. We show that the bacterial communities in the groundwater of limestone-mudstone alternations were not stable over time and showed oscillating dissimilarity patterns which corresponded to periods of groundwater recharge. Further, we observed an increase in dissimilarity over time (generalized additive model P < 0.001) indicating that the successive recharge events result in communities that are increasingly more dissimilar to the initial reference time point. The sampling period was able to explain up to 29.5% of the variability in bacterial community composition and the impact of recharge events on the groundwater microbiome was linked to the strength of the recharge and local environmental selection. Many groundwater bacteria originated from the recharge-related sources (mean = 66.5%, SD = 15.1%) and specific bacterial taxa were identified as being either enriched or repressed during recharge events. Overall, similar to surface aquatic environments, groundwater microbiomes vary through time, though we revealed groundwater recharges as unique driving factors for these patterns. The high temporal resolution employed here highlights the complex dynamics of bacterial communities in groundwater and demonstrated that successive shocks disturb the bacterial communities, leading to decreased similarity to the initial state over time.

microbiology↗

bioRxiv2021

Initial HCV infection of adult hepatocytes triggers a temporally structured transcriptional program containing diverse pro- and anti-viral elements

Transcriptional profiling provides global snapshots of virus-mediated cellular reprogramming, which can simultaneously encompass pro- and antiviral components. To determine early transcriptional signatures associated with HCV infection of authentic target cells, we performed ex vivo infections of adult primary human hepatocytes (PHHs) from seven donors. Longitudinal sampling identified minimal gene dysregulation at six hours post infection (hpi). In contrast, at 72 hpi, massive increases in the breadth and magnitude of HCV-induced gene dysregulation were apparent, affecting gene classes associated with diverse biological processes. Comparison with HCV-induced transcriptional dysregulation in Huh-7.5 cells identified limited overlap between the two systems. Of note, in PHHs, HCV infection initiated broad upregulation of canonical interferon (IFN)-mediated defense programs, limiting viral RNA replication and abrogating virion release. We further find that constitutive expression of IRF1 in PHHs maintains a steady-state antiviral program in the absence of infection, which can additionally reduce HCV RNA translation and replication. We also detected infection-induced downregulation of [~]90 genes encoding components of the EIF2 translation initiation complex and ribosomal subunits in PHHs, consistent with a signature of translational shutoff. As HCV polyprotein translation occurs independently of the EIF2 complex, this process is likely pro-viral: only translation initiation of host transcripts is arrested. The combination of antiviral intrinsic and inducible immunity, balanced against pro-viral programs, including translational arrest, maintains HCV replication at a low-level in PHHs. This may ultimately keep HCV under the radar of extra-hepatocyte immune surveillance while initial infection is established, promoting tolerance, preventing clearance and facilitating progression to chronicity. IMPORTANCEAcute HCV infections are often asymptomatic and therefore frequently undiagnosed. We endeavored to recreate this understudied phase of HCV infection using explanted PHHs and monitored host responses to initial infection. We detected temporally distinct virus-induced perturbations in the transcriptional landscape, which were initially narrow but massively amplified in breadth and magnitude over time. At 72 hpi, we detected dysregulation of diverse gene programs, concurrently promoting both virus clearance and virus persistence. On the one hand, baseline expression of IRF1 combined with infection-induced upregulation of IFN-mediated effector genes suppresses virus propagation. On the other, we detect transcriptional signatures of host translational inhibition, which likely reduces processing of IFN-regulated gene transcripts and facilitates virus survival. Together, our data provide important insights into constitutive and virus-induced transcriptional programs in PHHs, and identifies simultaneous antagonistic dysregulation of pro-and anti-viral programs which may facilitate host tolerance and promote viral persistence.

immunology↗

bioRxiv2021

Linking Labs: Interconnecting Experimental Environments

We introduce the concept of LabLinking: a technology-based interconnection of experimental laboratories across institutions, disciplines, cultures, languages, and time zones - in other words experiments without borders. In particular, we introduce LabLinking levels (LLL), which define the degree of tightness of empirical interconnection between labs. We describe the technological infrastructure in terms of hard- and software required for the respective LLLs and present examples of linked laboratories along with insights about the challenges and benefits. In sum, we argue that linked labs provide a unique platform for a continuous exchange between scientists and experimenters, thereby enabling a time synchronous execution of experiments performed with and by decentralized user and researchers, improving outreach and ease of subject recruitment, allowing to establish new experimental designs and to incorporate a panoply of complementary biosensors, devices, hard- and software solutions.

neuroscience↗