Biology subjects

Meyer, T.

Publications and source records attributed to Meyer, T..

32 records · Page 2Linked to original sources

bioRxiv2021

Cdt1 inhibits CMG helicase in early S phase to separate origin licensing from DNA synthesis

A fundamental concept in eukaryotic DNA replication is the temporal separation of G1 origin licensing from S phase origin firing. Re-replication and genome instability ensue if licensing occurs after DNA synthesis has started. In humans and other vertebrates, the E3 ubiquitin ligase CRL4Cdt2 starts to degrade the licensing factor Cdt1 after origins fire, raising the question of how cells prevent re-replication in early S phase. Here, using quantitative microscopy, we show that Cdt1 inhibits DNA synthesis during an overlap period when cells fire origins while Cdt1 is still present. Cdt1 inhibits DNA synthesis by suppressing CMG helicase progression at replication forks through the MCM-binding domain of Cdt1, and DNA synthesis commences once Cdt1 is degraded. Thus, instead of separating licensing from firing to prevent re-replication in early S phase, cells separate licensing from DNA synthesis through Cdt1-mediated inhibition of CMG helicase after firing. Highlights- Cdt1 is present together with fired origins of replication at the start of S phase - Cdt1 delays DNA synthesis by inhibiting CMG helicase progression after origins fire - Cdt1 inhibits CMG helicase progression through the MCM-binding domain of Cdt1

cell biology↗

bioRxiv2021

Chelator sensing and lipopeptide interplay mediates molecular interspecies interactions between soil bacilli and pseudomonads

AbstractSome bacterial species are important members of the rhizosphere microbiome and confer protection to the host plant against pathogens. However, our knowledge of the multitrophic interactions determining the ecological fitness of these biocontrol bacteria in their highly competitive natural niche is still limited. In this work, we investigated the molecular mechanisms underlying interactions between B. velezensis, considered as model plant-associated and beneficial species in the Bacillus genus, and Pseudomonas as a rhizosphere-dwelling competitor. Our data show that B. velezensis boosts its arsenal of specialized antibacterials upon the perception of the secondary siderophore enantio-pyochelin produced by phylogenetically distinct pseudomonads and some other genera. We postulate that B. velezensis has developed some chelator sensing systems to learn about the identity of its surrounding competitors. Illustrating the multifaceted molecular response of Bacillus, surfactin is another crucial component of the secondary metabolome mobilized in interbacteria competition. Its accumulation not only enhances motility but, unexpectedly, the lipopeptide also acts as a chemical trap that reduces the toxicity of other lipopeptides released by Pseudomonas challengers. This in turn favors the persistence of Bacillus populations upon competitive root colonization. Our work thus highlights new ecological roles for bacterial secondary metabolites acting as key drivers of social interactions.

microbiology↗

bioRxiv2021

Surfactin stimulated by pectin molecular patterns and root exudates acts as a key driver of Bacillus-plant mutualistic interaction

Bacillus velezensis is considered as model species belonging to the so-called B. subtilis complex that typically evolved to dwell in the soil rhizosphere niche and establish intimate association with plant roots. This bacterium provides protection to its natural host against diseases and represents one of the most promising biocontrol agents. However, the molecular basis of the cross-talk that this bacterium establishes with its natural host has been poorly investigated. We show here that these plant-associated bacteria have evolved some polymer-sensing system to perceive their host and that in response, they increase the production of the surfactin-type lipopeptide. Furthermore, we demonstrate that surfactin synthesis is favoured upon growth on root exudates and that this lipopeptide is a key component used by the bacterium to optimize biofilm formation, motility and early root colonization. In this specific nutritional context, the bacterium also modulates qualitatively the pattern of surfactin homologues co-produced in planta and mainly forms variants that are the most active at triggering plant immunity. Surfactin represents a shared good as it reinforces the defensive capacity of the host. ImportanceWithin the plant-associated microbiome, some bacterial species are of particular interest due to the disease protective effect they provide via direct pathogen suppression and/or stimulation of host immunity. While these biocontrol mechanisms are quite well characterized, we still poorly understand the molecular basis of the cross talk these beneficial bacteria initiate with their host. Here we show that the model species Bacillus velezensis stimulates production of the surfactin lipopeptide upon sensing pectin as cell surface molecular pattern and upon feeding on root exudates. Surfactin favors bacterial rhizosphere fitness on one hand and primes the plant immune system on the other hand. Our data therefore illustrate how both partners use this multifunctional compound as unique shared good to sustain mutualistic interaction.

microbiology↗

bioRxiv2020

Intravital imaging reveals cell cycle-dependent satellite cell migration during muscle regeneration.

During muscle regeneration, extracellular signal-regulated kinase (ERK) promotes both proliferation and migration. However, the relationship between proliferation and migration is poorly understood in this context. To elucidate this complex relationship on a physiological level, we established an intravital imaging system for measuring ERK activity, migration speed, and cell-cycle phases in mouse muscle satellite cells. We found that in vivo, ERK was maximally activated in satellite cells two days after injury, and this is then followed by increases in cell number and motility. With limited effects of immediate ERK activity on migration, we hypothesized that ERK increases migration speed in the later phase by promoting cell-cycle progression. Our cell-cycle analysis further revealed that in satellite cells, ERK activity is critical for the G1/S transition, and cells migrate more rapidly in the S/G2 phase three days after injury. Finally, migration speed of satellite cells was suppressed after CDK1/2, but not CDK1, inhibitor treatment, demonstrating a critical role of CDK2 in satellite cell migration. Overall, our study demonstrates that in satellite cells, the ERK-CDK2 axis not only promotes the G1/S transition, but also migration speed, which may provide a novel mechanism for efficient muscle regeneration.

cell biology↗

bioRxiv2019

Evidence for dual targeting of Arabidopsis plastidial glucose-6-phosphate transporter GPT1 to peroxisomes via the ER

Former studies on Arabidopsis glucose-6-phosphate/phosphate translocator isoforms GPT1 and GPT2 reported viability of gpt2 mutants, however an essential function for GPT1, manifesting as a variety of gpt1 defects in the heterozygous state during fertilization/seed set. Among other functions, GPT1 is important for pollen and embryo-sac development. Since previous work on enzymes of the oxidative pentose phosphate pathway (OPPP) revealed comparable effects, we investigated whether GPT1 might dually localize to plastids and peroxisomes. In reporter fusions, GPT2 was found at plastids, but GPT1 also at the endoplasmic reticulum (ER) and around peroxisomes. GPT1 contacted oxidoreductases and also peroxins that mediate import of peroxisomal membrane proteins from the ER, hinting at dual localization. Reconstitution in yeast proteoliposomes revealed that GPT1 preferentially exchanges glucose-6-phosphate for ribulose-5-phosphate. Complementation analyses of heterozygous gpt1 plants demonstrated that GPT2 is unable to compensate for GPT1 in plastids, whereas genomic GPT1 without transit peptide (enforcing ER/peroxisomal localization) increased gpt1 transmission significantly. Since OPPP activity in peroxisomes is essential during fertilization, and immuno-blot analyses hinted at unprocessed GPT1-specific bands, our findings suggest that GPT1 is indispensable at both plastids and peroxisomes. Together with the G6P-Ru5P exchange preference, dual targeting explains why GPT1 exerts functions distinct from GPT2 in Arabidopsis. One sentence summaryIn contrast to plastidial GPT2, GPT1 exhibits slightly different exchange preferences and alternatively targets the ER, from where the protein can be relocated to peroxisomes on demand.

plant biology↗

bioRxiv2019

Measuring stepwise binding of a thermally fluctuating particle to a cell membrane without labeling

Thermal motions enable a particle to probe the optimal interaction state when binding to a cell membrane. However, especially on the scale of microseconds and nanometers, position and orientation fluctuations are difficult to observe with common measurement technologies. Here we show that it is possible to detect single binding events of IgG-coated polystyrene beads, which are held in an optical trap nearby the cell membrane of a macrophage. Changes in the spatial and temporal thermal fluctuations of the particle were measured interferometrically and no fluorophore labelling was required. We demonstrate both by Brownian dynamic simulations and by experiments that sequential step-wise increases in the force constant of the bond between a bead and a cell of typically 20 pN / {micro}m are clearly detectable. In addition, this technique provides estimates about binding rates and diffusion constants of membrane receptors. The simple approach of thermal noise tracking points out new strategies in understanding interactions between cells and particles, which are relevant for a large variety of processes including phagocytosis, drug delivery or the effects of small microplastics and particulates on cells.\n\nSIGNIFICANCEInteractions of cells with nearby particles, e.g. bacteria, viruses or synthetic material, is a very fundamental and complex process, often deciding about the cellular fate. The investigation of binding processes between particle and cell is typically investigated by fluorescence techniques, where fluorophores often hinder the molecular interaction of specific binding partners. Therefore, label-free detection or imaging techniques are essential, which are hardly available especially for live cell investigations. Molecular binding is based on thermal position and orientation fluctuations of the binding partners to find the best interaction state. Here, we present a label-free measurement technique that allows us to detect multiple stepwise binding events of molecules on an optically trapped particle close to the cell membrane.

biophysics↗

bioRxiv2019

Systematic assessment of blood-borne microRNAs highlights molecular profiles of endurance sport and carbohydrate uptake

Multiple studies endorsed the positive effect of regular exercising on mental and physical health. However, the molecular mechanisms underlying training-induced fitness in combination with personal life-style remain largely unexplored. Circulating biomarkers such as microRNAs (miRNAs) offer themselves for studying systemic and cellular changes since they can be collected from the bloodstream in a low-invasive manner. In Homo sapiens miRNAs are known to regulate a substantial number of protein-coding genes in a post-transcriptional manner and hence are of great interest to understand differential gene expression profiles, offering a cost-effective mechanism to study molecular training adaption, and connecting the dots from genomics to observed phenotypes.\n\nHere, we investigated molecular expression patterns of 2, 549 miRNAs in whole-blood samples from 23 healthy and untrained adult participants of a cross-over study, consisting of 8 weeks of endurance training, with several sessions per week, followed by 8 weeks of washout and another 8 weeks of running, using microarrays. Participants were randomly assigned to one of the two study groups, one of which administered carbohydrates before each session in the first training period, switching the treatment group for the second training period. During running sessions clinical parameters as heartbeat frequency were recorded. This information was extended with four measurements of maximum oxygen uptake (VO2 max) for each participant.\n\nWe observed that multiple circulating miRNAs show expression changes after endurance training, leveraging the capability to separate the blood samples by training status. To this end, we demon-strate that most of the variance in miRNA expression can be explained by both common and known biological and technical factors. Our findings highlight six distinct clusters of miRNAs, each exhibiting an oscillating expression profile across the four study timepoints, that can effectively be utilized to predict phenotypic VO2 max levels. In addition, we identified miR-532-5p as a candidate marker to determine personal alterations in physical training performance on a case-by-case analysis taking the influence of a carbohydrate-rich nutrition into account. In literature, miR-532-5p is known as a common down-regulated miRNA in diabetes and obesity, possibly providing a molecular link between cellular homeostasis, personal fitness levels, and health in aging.\n\nWe conclude that circulating miRNAs expression can be altered due to regular endurance training, independent of the carbohydrate availability in the timeframe around training. Further validation studies are required to confirm the role of exercise-affected miRNAs and the extraordinary function of miR-532-5p in modulating the metabolic response to a high availability of glucose.

systems biology↗

bioRxiv2019

Membrane proximal F-actin restricts local membrane protrusions and directs cell migration

A major component of cell migration is F-actin polymerization driven membrane protrusion in the front. However, F-actin proximal to the plasma membrane also has a scaffolding role to support and attach the membrane. Here we developed a fluorescent reporter to monitor changes in the density of membrane proximal F-actin during membrane protrusion and cell migration. Strikingly, unlike total F-actin concentration, which is high in the front of migrating cells, the density of membrane proximal F-actin is low in the front and high in the back. Furthermore, local membrane protrusions only form following local decreases in membrane proximal F-actin density. Our study suggests that low density of membrane proximal F-actin is a fundamental structural parameter that locally directs membrane protrusions and globally stabilizes cell polarization during cell migration.\n\nOne Sentence SummaryMembrane protrusion and cell migration are directed by local decreases in the density of membrane proximal F-actin

cell biology↗

bioRxiv2019

A parallel cell-cycle entry pathway with inverted G1 signaling and alternate point of no return

Cell-cycle entry relies on an orderly progression of signaling events. To start, cells first activate the kinase cyclin D-CDK4/6, which leads to eventual inactivation of the retinoblastoma protein Rb. Hours later, cells inactivate APC/CCDH1 and cross the final commitment point. However, many cells with genetically deleted cyclin Ds, which activate and confer specificity to CDK4/6, can compensate and proliferate. Despite its importance in cancer, how this alternate pathway operates and whether wild-type cells use this pathway remain unknown. Here, using single-cell microscopy, we demonstrate that cells with acutely inhibited CDK4/6 enter the cell cycle with slowed and fluctuating cyclin E-CDK2 activity. Surprisingly, in this alternate pathway, the order of APC/CCDH1 and Rb inactivation is inverted in both cell lines and wild-type mice. Finally, we show that as a consequence of the signaling inversion, Rb inactivation replaces APC/CCDH1 inactivation as the point of no return. Together, we provide molecular characterization of a parallel cell-cycle entry pathway, and reveal temporal plasticity that underlies the G1 regulatory circuit.

cell biology↗

bioRxiv2019

Solid state anaerobic digestion of mixed organic waste: the synergistic effect of food waste addition on the destruction of paper and cardboard

Full-scale anaerobic digestion processes for organic solid waste are common in Europe, but generally unaffordable in Canada and the United States because of inadequate regulations to restrict cheaper forms of disposal, particularly landfill. We investigated the viability of solid-state anaerobic digestion (SS-AD) as an alternative that reduces the costs of waste pretreatment and subsequent wastewater treatment. A laboratory SS-AD digester, comprising six 10L leach beds and an upflow anaerobic sludge blanket reactor treating the leachate, was operated continuously for 88 weeks, with a mass balance of 101{+/-}2%. The feed was a mixture of cardboard, boxboard, newsprint, and fine paper, and varying amounts of food waste (from 0% to 29% on a COD basis). No process upset or instability was observed. The addition of food waste showed a synergistic effect, raising CH4 production from the fibre mixture from 52.7 L.kg-1COD fibreadded to 152 L.kg-1COD fibreadded, an increase of 190%. Substrate COD destruction efficiency reached 65% and a methane yield of 225 L.kg-1 CODadded was achieved at 29% food waste on a COD basis, and a solids retention time of 42 days. This performance was similar to that of a completely stirred tank reactor digesting similar wastes, but with much lower energy input. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=152 SRC="FIGDIR/small/564203v1_ufig1.gif" ALT="Figure 1"> View larger version (122K): org.highwire.dtl.DTLVardef@15c0e8aorg.highwire.dtl.DTLVardef@beadb3org.highwire.dtl.DTLVardef@7def43org.highwire.dtl.DTLVardef@1e717f5_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2019

Papillomavirus can be transmitted through the blood and produce infections in blood recipients: Evidence from two animal models

Human papillomavirus (HPV) infections are commonly thought to be strictly sexually transmitted. However, studies have demonstrated the presence of HPV in cancers of many non-sexual internal organs, raising the question as to how the viruses gain access to these sites. A possible connection between blood transfusion and HPV-associated disease has not received much attention. We show, in two animal models, that blood infected with papillomavirus yields infections at permissive sites. Furthermore, we demonstrate that blood from actively infected mice can transmit the infection to naive animals. Finally, we report papillomavirus infections in the stomach tissues of animals infected via the blood. Stomach tissues are not known to be permissive for papillomavirus infection, although the literature suggests that HPVs may be associated with a subset of gastric cancers. These results indicate that the human blood supply, which is not screened for papillomaviruses, could be a potential source of HPV infection and subsequent cancers. SUMMARYHuman papillomaviruses cause 5% of human cancers. Currently, blood banks do not screen for these viruses. We demonstrate that blood transfused from papillomavirus-infected animals produces infections in recipients. Public health implications are significant if the same is true for humans. DefinitionsLocal papillomavirus infection: An infection initiated by the direct application of virus or viral DNA to the site of infection Intravenous (IV) papillomavirus infection: An infection resulting from blood-borne delivery of virus or viral DNA to the site of infection.

microbiology↗

bioRxiv2019

A neural correlate of image memorability

Some images are easy to remember while others are easily forgotten. While variation in image memorability is consistent across individuals, we lack a full account of its neural correlates. By analyzing data collected from inferotemporal cortex (IT) as monkeys performed a visual memory task, we demonstrate that a simple property of the visual encoding of an image, its population response magnitude, is strongly correlated with its memorability. These results establish a novel behavioral role for the magnitude of the IT response, which lies largely orthogonal to the coding scheme that IT uses to represent object identity. To investigate the origin of IT memorability modulation, we also probed convolutional neural network models trained to categorize objects. We found brain-analogous correlates of memorability that grew in strength across the hierarchy of these networks, suggesting that this memorability correlate is likely to arise from the optimizations required for visual as opposed to mnemonic processing.

neuroscience↗

bioRxiv2017

Reducing Pollen Dispersal using Forest Windbreaks.

The adoption of genetically engineered (GE) crops has created a demand for practical methods to mitigate pollen dispersal and gene flow. The goal of this project was to measure the ability of a narrow forest windbreak to reduce downwind pollen fluxes from switchgrass (Panicum virgatum L.), a North American grass and model biofuels feedstock. Switchgrass fields were established in two identical plots where one had a forest windbreak and the other was in an open (control) site. Switchgrass reproduction, pollen dispersal, wind speed, and wind direction were measured over two years. Daily release of switchgrass pollen peaked at 11:00-13:30 during a flowering period that lasted about 44 days. The best estimate for switchgrass pollen source strength (PSS) was 141 x 109 pollen/season/hectare for fields planted at commercial densities. The forest windbreak consistently decreased downwind switchgrass pollen concentrations by 333-20,000 fold compared to the control plot which had a 58-77 fold decrease due to downwind distance alone. These results suggest that forest windbreaks could be used as a barrier to reduce pollen dispersal and gene flow from switchgrass and other crops.\n\nResearch HighlightA narrow forest windbreak greatly decreased downwind pollen concentrations from a switchgrass field suggesting that trees can reduce crop gene flow, enhance coexistence between farming systems, and provide ecosystem services.

plant biology↗

bioRxiv2017

Single-exposure visual memory judgments are reflected in IT cortex

Our visual memory percepts of whether we have encountered specific objects or scenes before are hypothesized to manifest as decrements in neural responses in inferotemporal cortex (IT) with stimulus repetition. To evaluate this proposal, we recorded IT neural responses as two monkeys performed a single-exposure visual memory task designed to measure the rates of forgetting with time. We found that a weighted linear read-out of IT was a better predictor of the monkeys forgetting rates and reaction time patterns than a strict instantiation of the repetition suppression hypothesis, expressed as a total spike count scheme. Behavioral predictions could be attributed to visual memory signals that were reflected as repetition suppression and were intermingled with visual selectivity, but only when combined across the most sensitive neurons.

neuroscience↗