Biology subjects

Mueller, J.

Publications and source records attributed to Mueller, J..

At least 55 records · Page 3Linked to original sources

bioRxiv2024

Neural contrast sensitivity is not affected by myopic blur

PurposeThe prevalence of myopia is increasing worldwide, accompanied by an increase of potentially under-corrected myopes. Because the neural pathways processing the retinal image are prone to adaptation in relation to the retinal image quality, we wondered to what extent neural contrast sensitivity (NCS) is altered in the presence of myopic blur. Additionally, the impact of retinal abnormalities like foveal hypoplasia with albinism on NCS was tested. MethodsNCS was psychophysically determined for 11 emmetropic, 23 myopic well-corrected and 15 myopic under-corrected otherwise healthy young (27 {+/-} 6 years) participants and 1 albinism patient. Aberration-free stimulation, independent of the eyes refractive state, was achieved by using a unique spatial light modulator-based interferometric system to bypass the eyes optics. ResultsNo significant differences in NCS were observed between the three groups (Median area-under-curve: 61.9, 62.1, and 62.9 for emmetropes, well-corrected, and under-corrected myopes, respectively; all p > 0.1) but were significantly equivalent between emmetropes and myopes (all p < 0.001). However, the NCS function of the albinism patient differed significantly from the here defined "normal" NCS function. ConclusionsNCS is unaffected by myopic blur and remains stable even for under-correction of up to 1.5 D. This means, that long-term under-corrected myopes still can achieve normal visual acuity as soon as their refractive errors are sufficiently corrected. Furthermore, NCS testing can relate visual deficits to an underlying neurological disorder.

neuroscience↗

bioRxiv2024

Experimental Infection of greater white-toothed Shrews (Crocidura russula) with Borna disease virus 1: Insights into Viral Spread and Shedding

Numbers of human encephalitis cases caused by infection with Borna disease virus 1 (BoDV1) increase continuously in endemic areas. The reservoir host of BoDV1 is the bicoloured white-toothed shrew, albeit few naturally infected individuals of other shrew species have been detected. To establish a reliable experimental reservoir model, 15 greater white-toothed shrews were infected with a shrew-derived BoDV1 isolate by different inoculation routes (intracerebral, intranasal, oral, subcutaneous, intraperitoneal) and monitored up to 41 days. Except for the oral route all other animals (12/15) were successfully infected, and the majority of them displayed temporary reduced feed intake and loss of body weight but no inflammatory lesions. Infectious virus was isolated from 11/12 infected animals. Viral RNA was demonstrated by RT-qPCR in the central nervous system (CNS) and the majority of organs. Immunohistochemistry demonstrated BoDV1 antigen in neurons and astrocytes in the CNS and peripheral nerves. High viral loads in the CNS and the spinal cord points towards spread from periphery to the CNS to enhance viral replication, and subsequent centrifugal spread to organs capable of secretion and excretions. In general, successful experimental BoDV1 infection of shrews proves their usefulness as animal model, enabling further studies on maintenance, transmission, pathogenesis, and risk assessment for human spill-over infections.

pathology↗

bioRxiv2024

An adapted typology of tree-related microhabitats including tropical forests

Tree-related microhabitats (TreMs) describe the microhabitats that a tree can provide for a multitude of other taxonomic groups and have been proposed as an important indicator for forest biodiversity (Asbeck et al., 2021). So far, the focus of TreM studies has been on temperate forests, although many trees in the tropics harbour exceptionally high numbers of TreMs. In this study, TreMs in the lowland tropical forests of the Choco (Ecuador) and in the mountain tropical forests of Mount Kilimanjaro (Tanzania) were surveyed. Our results extend the existing typology of TreMs of Larrieu et al. (2018) to include tropical forests and enabled a comparison of the relative recordings and diversity of TreMs between tropical and temperate forests. A new TreM form, Root formations, and three new TreM groups, concavities build by fruits or leaves, dendrotelms, and root formations, were established. In total, 15 new TreM types in five different TreM groups were specified. The relative recordings of most TreMs were similar between tropical and temperate forests. However, ivy and lianas, and ferns were more common in the lowland rainforest than in temperate forests, and bark microsoil, limb breakage, and foliose and fruticose lichens in tropical montane forest than in lowland rainforest. Mountain tropical forests hosted the highest diversity for common and dominant TreM types, and lowland tropical forest the highest diversity for rare TreMs. Our extended typology of tree-related microhabitats can support studies of forest-dwelling biodiversity in tropical forests. Specifically, given the ongoing threat to tropical forests, TreMs can serve as an additional tool allowing rapid assessments of biodiversity in these hyperdiverse ecosystems.

ecology↗

bioRxiv2024

Phaeocystis blooms caused carbon drawdown during the Antarctic Cold Reversal from sedimentary ancient DNA

The Southern Ocean plays a crucial role in the global carbon budget. Modeling studies propose that the atmospheric CO2 plateau during the Antarctic Cold Reversal (ACR; 14,700 to 12,700 calibrated years before present (cal yr BP)) is related to increased marine productivity. However, proxy evidence relating environmental conditions as well as primary community composition and productivity to carbon drawdown is missing. Our ancient DNA shotgun metagenomic analysis of marine sediments revealed Phaeocystis antarctica (haptophyte) as a key element of the primary producer community. Independent proxy evidence (blooming-related bacteria, Ba/Fe ratio) from the same sediment record point to high productivity in response to enhanced sea-ice seasonality caused by ACR cooling. Post ACR, abrupt Phaeocystis community loss shows how sensitive this ecosystem is to warming, potentially representing a key tipping element that may be further enhanced by the Phaeocystis-related sulfur cycle-climate feedback. As an analogy for present warming, it highlights the importance of regions with high seasonal sea-ice variability and Phaeocystis-dominance, such as the Ross Sea, for stabilizing atmospheric CO2 content. Additionally, our shotgun metagenomic data portray complex Holocene ecosystem establishment including key Antarctic taxa such as penguins, whales, and Antarctic fishes with implications for ongoing conservation efforts.

ecology↗

bioRxiv2024

Dynamic land-plant carbon sources in marine sediments inferred from ancient DNA

Terrigenous organic matter in marine sediments is considered a significant long-term carbon sink, yet our knowledge regarding its source taxa is severely limited. Here, we leverage land-plant ancient DNA from six globally distributed marine sediment cores covering the Last Glacial-Holocene transition as a proxy for the share, accumulation rate, preservation, and composition of terrigenous organic matter. We show that the spatial and temporal plant composition as revealed by sedaDNA records reflects mainly the vegetation dynamics of nearby continents as revealed by comparison with pollen from land archives. However, we also find indications of a global north-to-south translocation of sedaDNA. The plant composition shows that upland vegetation is strongly underrepresented in the record compared to riverine and coastal sources. We also find that plant sedaDNA has a higher accumulation rate in samples from the Late Glacial, which is characterized by high runoff and mineral load. Thus plant DNA in marine sediments allows for new perspectives on the global linkages between the terrestrial and marine carbon cycle which would benefit from a more quantitative understanding of DNA preservation and dispersal. This represents the basis of how climate change and land-use change translate into carbon-sink dynamics and also informs about natural carbon-capture solutions.

ecology↗

bioRxiv2024

Biophysics of microRNA-34a targeting and its influence on down-regulation

microRNAs (miRNAs) regulate target mRNA expression post-transcriptionally through their association with Argonaute 2 (AGO2) proteins. Predicting the efficiency of mRNA repression by miRNA has been limited by our comprehension of the structure-function relationship within miRNA binding sites. Using a combination of EMSA, luciferase reporter assays, and structural probing, we investigated the interaction between the human tumour suppressor miR-34a and 12 mRNA targets. Comparison of direct RNA:RNA interactions and those within the functional AGO2 protein revealed that the isolated mRNA:miRNA duplex serves as a strong predictor for duplex affinity and structure within AGO2. Our findings reveal that AGO2 has a bidirectional capacity to modulate affinity; weakening tight RNA:RNA binders while strengthening weak ones. We identified three distinct structural groups that form upon miR-34a binding and reveal a novel structural group that exhibits a guide strand bulge. MD simulations indicate a conceivable fit of this miRNA-bulge structure within AGO2. Our results demonstrate that the structural characteristics of mRNA:miRNA duplexes could serve as contributing determinants of repression efficacy.

biophysics↗

bioRxiv2024

Liquid footprinting: A novel approach for DNA footprinting using short double-stranded cell-free DNA from plasma

The diagnostic potential of short double-stranded cell-free DNA (cfDNA) in blood plasma has not been recognized, yet. Here, we present a method for enrichment of double-stranded cfDNA with an average length of about 40 base pairs from cfDNA for high-throughput DNA sequencing. This class of cfDNA is enriched at gene promoters and binding sites of transcription factors or structural DNA-binding proteins, so that a genome-wide DNA footprint is directly captured from liquid biopsies. In short double-stranded cfDNA from healthy individuals, we found significant enrichment of 203 transcription factor motifs. Additionally, short double-stranded cfDNA signals at specific genomic regions correlate negatively with DNA-methylation, positively with H3K4me3 histone modifications and gene transcription. When comparing short double-stranded cfDNA from patient samples of pancreatic ductal adenocarcinoma with colorectal carcinoma or septic with post-operative controls, we identified 731 and 1,107 differentially enriched loci, respectively. Using these differentially enriched loci, the disease types can be clearly distinguished by principal component analysis demonstrating the diagnostic potential of short double-stranded cfDNA signals as a new class of biomarkers for liquid biopsies.

genomics↗

bioRxiv2024

Targeting glioblastoma tumor hyaluronan to enhance therapeutic interventions that regulate metabolic cell properties

Despite extensive advances in cancer research, glioblastoma (GBM) still remains a very locally invasive and thus challenging tumor to treat, with a poor median survival. Tumor cells remodel their microenvironment and utilize extracellular matrix to promote invasion and therapeutic resistance. We aim here to determine how GBM cells exploit hyaluronan (HA) to maintain proliferation using ligand-receptor dependent and ligand-receptor independent signaling. We use tissue engineering approaches to recreate the three-dimensional tumor microenvironment in vitro, then analyze shifts in metabolism, hyaluronan secretion, HA molecular weight distribution, as well as hyaluronan synthetic enzymes (HAS) and hyaluronidases (HYAL) activity in an array of patient derived xenograft GBM cells. We reveal that endogenous HA plays a role in mitochondrial respiration and cell proliferation in a tumor subtype dependent manner. We propose a tumor specific combination treatment of HYAL and HAS inhibitors to disrupt the HA stabilizing role in GBM cells. Taken together, these data shed light on the dual metabolic and ligand - dependent signaling roles of hyaluronan in glioblastoma. SignificanceThe control of aberrant hyaluronan metabolism in the tumor microenvironment can improve the efficacy of current treatments. Bioengineered preclinical models demonstrate potential to predict, stratify and accelerate the development of cancer treatments.

bioengineering↗

bioRxiv2023

Plant infection by the necrotrophic fungus Botrytis requires actin-dependent generation of high invasive turgor pressure

The devastating pathogen Botrytis cinerea infects a broad spectrum of host plants, causing great socio-economic losses. The necrotrophic fungus rapidly kills plant cells, nourishing their walls and cellular contents. To this end, necrotrophs secretes a cocktail of cell wall degrading enzymes, phytotoxic proteins and metabolites. Additionally, many fungi produce specialized invasion organs that generate high invasive pressures to force their way into the plant cell. However, for most necrotrophs, including Botrytis, the biomechanics of penetration and its contribution to virulence are poorly understood. Here we use a combination of quantitative micromechanical imaging and CRISPR-Cas guided mutagenesis to show that Botrytis uses substantial invasive pressure, in combination with strong surface adherence, for penetration. We found that the fungus establishes a unique mechanical geometry of penetration that develops over time during penetration events, and which is actin cytoskeleton dependent. Furthermore, interference of force generation by blocking actin polymerization was found to decrease Botrytis virulence, indicating that also for necrotrophs, mechanical pressure is important in host colonization. Our results demonstrate for the first time mechanistically how a necrotrophic fungus such as Botrytis employs this "brute force" approach, in addition to the secretion of lytic proteins and phytotoxic metabolites, to overcome plant host resistance.

biophysics↗

bioRxiv2023

Isolation and quantification of bacterial membrane vesicles for quantitative metabolic studies using mammalian cell cultures

Bacterial membrane vesicles (BMVs) are produced by most bacteria and participate in various cellular processes, such as intercellular communication, nutrient exchange, and pathogenesis. Notably, these vesicles can contain virulence factors, including toxic proteins, DNA, and RNA. Such factors can contribute to the harmful effects of bacterial pathogens on host cells and tissues. Although the general effects of BMVs on host cellular physiology are well known, the underlying molecular mechanisms are less understood. In this study, we introduce a vesicle quantification method, leveraging the membrane dye FM4-64. We utilize a linear regression model to analyze the fluorescence emitted by stained vesicle membranes to ensure consistent and reproducible vesicle-host interaction studies using cultured cells. This method is particularly valuable for identifying host cellular processes impacted by vesicles and their specific cargo. Moreover, it outcompetes clearly unreliable protein concentration-based methods. We (1) show a linear correlation between the quantity of vesicles and the fluorescence signal emitted from the FM4-64 dye, (2) introduce the "vesicle load" as a new semi-quantitative unit, facilitating more reproducible vesicle-cell culture interaction experiments (3) show that a stable vesicle load yields consistent host responses when studying vesicles from Pseudomonas aeruginosa mutants (4) demonstrate that typical vesicle isolation contaminants, such as flagella, do not significantly skew the metabolic response of lung epithelial cells to P. aeruginosa vesicles, and (5) identify inositol-1-monophosphatase (SuhB) as a pivotal regulator in the vesicle-mediated pathogenesis of P. aeruginosa.

cell biology↗

bioRxiv2023

Frequent horizontal chromosome transfer between asexual fungal insect pathogens

Entire chromosomes are typically only transmitted vertically from one generation to the next. The horizontal transfer of such chromosomes has long been considered improbable, yet gained recent support in several pathogenic fungi where it may affect the fitness or host specificity. To date, it is unknown how these transfers occur, how common they are and whether they can occur between different species. In this study, we show multiple independent instances of horizontal transfers of the same accessory chromosome between two distinct strains of the asexual entomopathogenic fungus Metarhizium robertsii during experimental co-infection of its insect host, the Argentine ant. Notably, only the one chromosome - but no other - was transferred from the donor to the recipient strain. The recipient strain, now harboring the accessory chromosome, exhibited a competitive advantage under certain host conditions. By phylogenetic analysis we further demonstrate that the same accessory chromosome was horizontally transferred in a natural environment between M. robertsii and another congeneric insect pathogen, M. guizhouense. Hence horizontal chromosome transfer is not limited to the observed frequent events within species during experimental infections but also occurs naturally across species. The transferred accessory chromosome contains genes that might be involved in its preferential horizontal transfer, encoding putative histones and histone-modifying enzymes, but also putative virulence factors that may support its establishment. Our study reveals that both intra- and interspecies horizontal transfer of entire chromosomes is more frequent than previously assumed, likely representing a not uncommon mechanism for gene exchange. Significance StatementThe enormous success of bacterial pathogens has been attributed to their ability to exchange genetic material between one another. Similarly, in eukaryotes, horizontal transfer of genetic material allowed the spread of virulence factors across species. The horizontal transfer of whole chromosomes could be an important pathway for such exchange of genetic material, but little is known about the origin of transferable chromosomes and how frequently they are exchanged. Here, we show that the transfer of accessory chromosomes - chromosomes that are non-essential but may provide fitness benefits - is common during fungal co-infections and is even possible between distant pathogenic species, highlighting the importance of horizontal gene transfer via chromosome transfer also for the evolution and function of eukaryotic pathogens.

genomics↗

bioRxiv2023

PTMNavigator: Interactive Visualization of Differentially Regulated Post-Translational Modifications in Cellular Signaling Pathways

Post-translational modifications (PTMs) play pivotal roles in regulating cellular signaling, fine-tuning protein function, and orchestrating complex biological processes. Despite their importance, the lack of comprehensive tools for studying PTMs from a pathway-centric perspective has limited our ability to understand how PTMs modulate cellular pathways on a molecular level. Here, we present PTMNavigator, a tool integrated into the ProteomicsDB platform, which offers an interactive interface for researchers to overlay experimental PTM data with pathway diagrams. PTMNavigator provides [~]3000 canonical pathways from manually curated databases and further enables users to modify and create custom diagrams, tailored to their data. Additionally, PTMNavigator automatically runs multiple kinase and pathway enrichment algorithms whose results are directly integrated into the visualization. This offers a comprehensive view of the intricate relationship between PTMs and signaling pathways. To demonstrate the utility of PTMNavigator, we applied it to two phosphoproteomics perturbation datasets. First, PTMNavigator enhanced pathway enrichment analysis by showing how the regulated peptides and proteins are distributed in the pathways with high enrichment scores. Second, it visualized how drug treatments result in a discernable flow of PTM-driven signaling within pathways. Third, PTMNavigator aided in proposing extensions to an existing pathway by suggesting putative new links between both PTMs and pathway components. By enhancing our understanding of cellular signaling dynamics and facilitating the discovery of novel PTM-pathway interactions, PTMNavigator advances our knowledge of PTM biology and its implications in health and disease.

systems biology↗

bioRxiv2023

The Plasmodium falciparum CCCH zinc finger protein MD3 regulates male gametocytogenesis through its interaction with RNA-binding proteins

Malaria transmission to mosquitoes is dependent on the formation of gametocytes. When fully matured, gametocytes are able to transform into gametes in the mosquitos midgut, a process accompanied with their egress from the enveloping erythrocyte. Gametocyte maturation and gametogenesis require a well-coordinated gene expression programme that involves a wide spectrum of regulatory proteins, ranging from histone modifiers to transcription factors to RNA-binding proteins. Here, we investigated the role of the CCCH-zinc finger protein MD3 in P. falciparum gametocytogenesis. MD3 was originally identified by us as an epigenetically regulated protein of immature gametocytes and recently shown to be involved in male development in a barcode-based screen in P. berghei. We here show that MD3 is mainly present in the cytoplasm of immature male P. falciparum gametocytes. Parasites deficient of MD3 are impaired in gametocyte maturation and male gametocyte exflagellation. BioID analysis in combination with co-immunoprecipitation assays unveiled an interaction network of MD3 with RNA-binding proteins like PABP1 and ALBA3, with translational initiators, regulators and repressors like elF4G, PUF1, NOT1 and CITH, and with other regulators of gametocytogenesis, including ZNF4, MD1 and GD1. We conclude that MD3 is part of a regulator complex crucial for post-transcriptional fine-tuning of male gametocytogenesis.

microbiology↗

bioRxiv2023

A fast-slow trait continuum at the level of entire communities

Across the tree of life, organismal functional strategies form a continuum from slow-to fast-growing organisms, in response to common drivers such as resource availability and disturbance. However, the synchronization of these strategies at the entire community level is untested. We combine trait data for >2800 above-and belowground taxa from 14 trophic guilds spanning a disturbance and resource availability gradient in German grasslands. Most guilds consistently respond to these drivers through both direct and trophically-mediated effects, resulting in a slow-fast axis at the level of the entire community. Fast trait communities were also associated with faster rates of whole ecosystem functioning. These findings demonstrate that slow and fast strategies can be manifested at the level of whole ecosystems, opening new avenues of ecosystem-level functional classification.

ecology↗

bioRxiv2023

A High-Throughput Sampling Method for Detection of Meloidogyne enterolobii and Other Root-Knot Nematodes in Sweetpotato Storage Roots

Meloidogyne enterolobii is an aggressive root-knot nematode (RKN) species that has emerged as a significant pathogen of sweetpotato in the Southeastern United States. M. enterolobii is spread primarily through the movement of infected seed sweetpotatoes used for propagation. The RKN resistance in commercially grown sweetpotato cultivars has proven ineffective against this nematode. Detecting RKN in sweetpotato by eye is unreliable, and further distinguishing M. enterolobii from other RKN species that infect sweetpotato is labor intensive; relying on molecular tests conducted on individual nematodes dissected out of host roots by trained technicians. Here, we have developed a high-throughput survey method to collect skin samples and extract total DNA from batches of sweetpotato storage roots. Combining this method with species-specific PCR assays allowed for quick and sensitive detection of M. enterolobii and other RKN species infecting sweetpotatoes. We tested this method using batches of infected storage roots at varying levels of M. enterolobii infection. We also inoculated skin samples with varying numbers of individual M. enterolobii eggs to determine the methods detection threshold and used this method to conduct surveys for RKN on fresh market sweetpotatoes. Our results show that this method can consistently and reliably detect M. enterolobii in sweetpotato batches at levels as low as 2 eggs per 10 mL skin sample. This method will be a useful tool to help screen for the presence of M. enterolobii in seed sweetpotatoes before they are replanted, thereby helping to slow the spread of this nematode to M. enterolobii-free sweetpotato growing operations.

molecular biology↗

bioRxiv2023

German-wide Malaise trap metabarcoding estimates over 33,000 insect species

Mitigating ongoing losses of insects and their key functions (e.g., pollination) requires accurately tracking large-scale and long-term community changes. However, doing so has been notoriously hindered by uniquely high insect species diversity that requires prohibitively high investments of time, funding, and taxonomic expertise. Here, we show that these concerns can be addressed through a comprehensive, scalable and cost-efficient DNA metabarcoding workflow. We use 1,815 samples from 75 Malaise traps across Germany from 2019 and 2020 to demonstrate how metabarcoding can be incorporated into large-scale insect monitoring networks for less than 50 {euro} per sample, including supplies, labor and maintenance. With on average 1.4M sequence reads per sample we uncovered 10,803 validated insect species, of which 83.9% were represented by a single OTU. We estimated another 21,403 plausible species, which likely either lack a reference barcode or are undescribed. The total of 31,846 species is similar to the number of insect species known for Germany ([~]35,500). Because Malaise traps capture only a subset of insects, our approach identified many species likely unknown from Germany or new to science. Our reproducible workflow ([~]80% OTU-similarity among years) provides a blueprint for large-scale biodiversity monitoring of insects and other biodiversity components in near real time.

ecology↗

bioRxiv2023

Transient septin sumoylation steers a Fir1-Skt5 protein complex between the split septin ring

Ubiquitylation and phosphorylation control composition and architecture of the cell separation machinery in yeast and other eukaryotes. The significance of septin sumoylation on cell separation remained an enigma. Septins form an hourglass structure at the bud neck of yeast cells that transforms into a split septin double ring during mitosis. We discovered that sumoylated septins recruit the cytokinesis checkpoint protein Fir1 to the peripheral side of the septin hourglass. Subsequent de-sumoylation and synchronized binding to the scaffold Spa2 relocate Fir1 in a seamless transition between the split septin rings. Fir1 binds and carries Skt5 on its route to the division plane where the Fir1-Skt5 complex serves as receptor for chitin synthase III. We propose that the opposite positioning of the sumoylated septins and Spa2 creates a tension across the ring that upon de-sumoylation tunnels the membrane-bound Fir1-Skt5 complex through a transiently permeable septin diffusion barrier.

cell biology↗

bioRxiv2022

Endoplasmic reticulum calnexins participate in the primary root growth response to phosphate deficiency

Accumulation of incompletely folded proteins in the endoplasmic reticulum (ER) leads to ER stress, activates ER protein degradation pathways, and upregulates genes involved in protein folding (Unfolded Protein Response; UPR). ER stress has been associated with abiotic stress conditions that affect protein folding, including salt stress. However, the role of ER protein folding in plant responses to nutrient deficiencies is unclear. We analyzed several Arabidopsis thaliana mutants affected in ER protein quality control and established that both CALNEXIN (CNX) genes function in the primary roots response to phosphate (Pi) deficiency. CNX and calreticulin (CRT) are homologous ER lectins that bind to N-glycosylated proteins to promote their folding. Growth of cnx1-1 and cnx2-2 single mutants was similar to that of the wild type under high and low Pi conditions, but the cnx1-1 cnx2-2 double mutant showed decreased primary root growth under low Pi conditions due to reduced meristematic cell division. This phenotype was specific to Pi deficiency; the double mutant responded normally to osmotic and salt stress. The root growth phenotype was Fe dependent and was associated with Fe accumulation in the root. Two genes involved in Fe-dependent inhibition of root growth under Pi deficiency, the ferroxidase gene LPR1 and P5-type ATPase PDR2, are epistatic to CNX1/CNX2. Overexpressing PDR2 failed to complement the cnx1-1 cnx2-2 root phenotype. cnx1-1 cnx2-2 showed no evidence of UPR activation, indicating a limited effect on ER protein folding. CNX might process a set of N-glycosylated proteins specifically involved in the response to Pi deficiency. One sentence summaryCalnexin, a lectin chaperone engaged in the folding of N-glycosylated proteins in the ER, participates in primary root adaptation to low phosphate conditions.

plant biology↗