Biology subjects

Keller, N.

Publications and source records attributed to Keller, N..

13 recordsLinked to original sources

bioRxiv2026

The Aspergillus fumigatus C2-Domain Protein SppA is required for septal integrity and alters susceptibility to echinocandins and neutrophil killing during infection

Aspergillus fumigatus is a major opportunistic fungal pathogen whose ability to maintain hyphal integrity and withstand host defenses is critical for virulence. Septal pores, which connect hyphal compartments, are dynamically regulated to preserve cellular integrity under stress, yet the molecular components governing this process remain incompletely defined. Here, we identify and characterize a septal pore-associated protein, SppA, and demonstrate its essential role in maintaining septal integrity in A. fumigatus. We show that expression of SppA is positively regulated by the transcription factor ZfpA and is induced in response to the cell wall-targeting antifungal caspofungin. Deletion of sppA resulted in defective septal organization and increased susceptibility to hyphal damage. The mutant exhibited heightened sensitivity to cell wall-targeting antifungal agents, indicating a role in cell wall stress tolerance. In a zebrafish model of invasive aspergillosis, loss of SppA significantly attenuated virulence which was abrogated in neutrophil-deficient zebrafish. Further, the mutant strain displayed increased susceptibility to killing by primary human neutrophils, suggesting that proper septal pore formation contributes to fungal survival during host immune attack. Together, our findings establish SppA as a critical determinant of septal integrity, antifungal tolerance, and pathogenicity in A. fumigatus, and position it as part of a ZfpA-regulated, caspofungin-responsive pathway that supports fungal survival during stress and infection. Author SummaryAspergillus fumigatus is a common environmental mold that can cause life-threatening infections in people with weakened immune systems. For successful invasion of host tissue, the fungus requires the ability to protection sections of its hyphae from cell wall targeting antifungals and host immune cell attack by closing septal (cross wall) pores distributed throughout hyphal strands. We have identified an A. fumigatus protein, SppA, required for proper septal pore closure. Loss of SppA reduces the ability of hyphae to withstand treatment with antifungals and the ability of A. fumigatus to cause disease in a zebrafish infection model. The SppA mutant was particularly susceptible to killing by neutrophils, key immune cells that help control fungal infections. Our findings reveal an important mechanism that helps A. fumigatus survive environmental and host-imposed stresses and highlight septal pore regulation as a potential target for future antifungal strategies.

microbiology↗

bioRxiv2024

Integrative cardiovascular dose-response to graded lower body negative pressure

BackgroundLower body negative pressure (LBNP) has been posited as a potential spaceflight countermeasure to counteract the physiological deconditioning related to fluid shifts in micro-gravity. However, open questions remain as to the magnitude of LBNP that should be applied. We systematically characterized the cardiovascular effects of LBNP and quantified the effect size of varied LBNP doses across different parts of the cardiovascular system. MethodsTwenty-four subjects (12M, 12F) were exposed to graded LBNP from 0 mmHg to -50 mmHg in 10 mmHg increments, both in supine (0{degrees}) and 15{degrees} head-down tilt postures. We measured the steady-state response in a large range of variables, including those related to the systemic circulation, cardiovascular control, and hemodynamics of the eyes and neck. ResultsBuilding on the experimental data, dose-response curves were constructed using a Bayesian multivariate hierarchical modeling framework to quantify the effect size of every variable considered when subjected to LBNP. The methodology allows direct comparison of the variables and the underlying structural relationships between them. Further, we demonstrated the potential for LBNP to reduce jugular venous flow stagnation, which is considered one of the major health risks during human spaceflight. ConclusionsThe Dose-response curves and effect sizes generated from this research effort establish the most comprehensive framework available to date that characterizes physiological responses to LBNP. These results directly inform the development of countermeasures to mitigate the negative effects of spaceflight, including cardiovascular deconditioning, spaceflight-associated neuro-ocular syndrome, and venous thromboembolism events. Key Points SummaryO_LILower body negative pressure (LBNP) has been posited as a potential countermeasure for multiple risks associated with spaceflight, including cardiovascular deconditioning, spaceflight-associated neuro-ocular syndrome, and venous thromboembolism events. However, the specific LBNP dose needed to mitigate these risks is still unknown. C_LIO_LIWe constructed the LBNP dose-response curves in supine and 15{degrees} head-down-tilt positions to quantify the acute response of a large variety of hemodynamics, autonomic, ocular, and neck variables across a range of LBNP levels. C_LIO_LIWe also used a Bayesian multivariate modeling framework to identify significant relationships between variables and to compare their effect sizes under different levels of LBNP. C_LIO_LIIn addition, results indicate that LBNP is a promising countermeasure to reduce jugular venous flow stagnation occurring during microgravity exposure. C_LIO_LIThis study constitutes the most comprehensive analysis of cardiovascular hemodynamics, autonomic, and cephalad response to LBNP to date. This framework informs the development of countermeasures to mitigate the detrimental effects of spaceflight. C_LI

physiology↗

bioRxiv2024

The impact of Agri-Environment Schemes (AES) and red fox (Vulpes vulpes) on the density of European brown hare (Lepus europaeus) populations in Hungary

Most Lepus species can easily adapt to new or changing environments. Until the 1960s, the brown hare estimated stock in Hungary went above 1,200,000 specimens. But also in Hungary and across Europe, hare densities have decreased in the past few decades. The primary cause of declining hare populations is habitat alteration in agricultural landscapes caused by the intensification of agricultural practices. Because the well-being and herd size of small game species, such as the hare, are strongly influenced by the ecological environment, following in their population characteristics can be used as an indicator of habitat quality, with the results being used not only in wildlife management, but also in nature conservation and agricultural greening programs. Our goal is to compare the size of the hare game management to the efficiency of the agricultural support system, vegetation types, and the quantity of red fox, all of which can have an impact on the hares density. In a large-scale survey we found that the estimated hare density index decreased year after year. There were no more animals discovered in the "better areas" overall. According to the model, if the game management units contained a large proportion of AKG arable land, the expected hare density would rise. Similarly, if the region had a high proportion of AKG fields but a low or average fox harvest rate, the hare population would be unable to grow. Animal density decreased slightly, albeit in a trend, as the number of AKG lawns increased. Hare distribution has shrunk over time, especially in areas with a high percentage of suitable habitat. The hare harvest density remained constant year after year in VGEs with a higher proportion of AKG grassland. The foxs declining rate had no effect on the increase in harvest density. Overall, it appears from a national spatial scale study that even in less good areas, the support could not improve the habitat because its effect did not depend on the proportion of good areas, i.e. even in the case of VGEs with a small proportion of good areas, it could not add much to the hare population density a lot of AKG. Cattle pasture comprised a significant portion of the AKG grasslands. Because the effect of intensively grazed regions on hares is clearly negative due to excessively short grass, the high standard deviation values observed in high proportion AKG grasslands may be explained by this.

ecology↗

bioRxiv2023

It All Rolls Downstream: Upstream Control of Physical Activity Regulation

Physical activity is regulated by a variety of genetic molecules. However, the pathways through which those molecules work to regulate activity is largely unknown. The purpose of this study was to gather the known genetic molecules that are associated with activity regulation and define overall upstream regulator pathways through which these molecules work. We conducted a systematic review to gather all available published datasets related to physical activity regulation, standardized the data for genomic location and species, and used this data, in an unbiased manner to create a dataset that was used: (1) to physically map and visualize all identified molecules to homologous chromosome locations and (2) as the dataset for which an Upstream Regulator Analysis (URA) was conducted using Qiagen Ingenuity Pathway Analysis (IPA) software. Our search resulted in 469 genetic molecules (e.g. genomic variant, transcript, protein, micro-RNA) that were split into brain (n=366) and muscle (n=345) sub-groups, which was our attempt to separate differences in central vs peripheral pathways. The brain and muscle data sets had several potential upstream regulators, the top-rated being {beta}-estradiol as a regulator for 19.5% and 21% of the brain and muscle datasets respectively. To our knowledge, {beta}-estradiols identification as a potential regulator, is the first evidence to link the well-known effects of sex hormones on physical activity with genetic regulation of physical activity. There were a variety of potential upstream regulators for the molecules collected in this review, but interestingly, three of the top five for both brain and muscle are nuclear receptor binding ligands; estradiol (estrogen receptor), dexamethasone (glucocorticoid receptor), and tretinoin (retinoic acid receptor), indicating a potential role of nuclear receptors in the regulation of physical activity. Selective nuclear receptor modulation may be an area of interest in future mechanistic studies of the genetic regulation of physical activity.

genetics↗

bioRxiv2023

Role of DNA-DNA sliding friction and non-equilibrium dynamics in viral genome ejection and packaging

Many viruses eject their DNA via a nanochannel in the viral shell, driven by internal forces arising from the high-density genome packing. The speed of DNA exit is controlled by friction forces that limit the molecular mobility, but the nature of this friction is unknown. We introduce a method to probe the mobility of the tightly confined DNA by measuring DNA exit from phage phi29 capsids with optical tweezers. We measure extremely low initial exit velocity, a regime of exponentially increasing velocity, stochastic pausing that dominates the kinetics, and large dynamic heterogeneity. Measurements with variable applied force provide evidence that the initial velocity is controlled by DNA-DNA sliding friction, consistent with a Frenkel-Kontorova model for nanoscale friction. We confirm several aspects of the ejection dynamics predicted by theoretical models. Features of the pausing suggest it is connected to the phenomenon of "clogging" in soft-matter systems. Our results provide evidence that DNA-DNA friction and clogging control the DNA exit dynamics, but that this friction does not significantly affect DNA packaging.

biophysics↗

bioRxiv2022

Enterobacteriaceae isolated from patients share antibiotic resistance conferring plasmids recently acquired from those isolated from sinks in the same treatment room

Identifying how and where pathogens acquire antibiotic resistance is crucial to developing effective strategies to limit its spread. Many bacterial species carry and share plasmids harboring antibiotic resistant genes. Plasmids are mobile genetic elements whose horizontal transmission is difficult to assess through genomic comparison due to assembly issues when using short-read sequencing alone. In this study, we use hybrid assembly to fully assemble plasmids that are shared between different Enterobacteriaceae isolated from patients and sinks in the same hospital rooms. We isolated and sequenced pairs of carbapenem resistant Enterobacter hormaechei subsp. xiangfangensis and Klebsiella pneumoniae from patients and sinks within the same hospital room. The isolate pairs share plasmids that putatively confer antibiotic resistance, including carbapenem resistance. These plasmids differ by few mutations and structural changes, while the isolates carry unique plasmids. Together, this suggests that plasmids can act as vectors of antibiotic resistance spread from sink reservoirs to patients.

microbiology↗

bioRxiv2022

Group A Streptococcus antibiotic tolerance in necrotizing fasciitis

ObjectivesGroup A Streptococcus (GAS) necrotizing fasciitis (NF) is a difficult-to-treat bacterial infection associated with high morbidity and mortality despite extensive surgery and targeted antibiotic treatment. Bacteria surviving prolonged antibiotic exposure without displaying genetic resistance, so-called persisters, are associated with difficult-to-treat infections, such as GAS-NF. In the present study, we investigated the presence of persistent GAS in tissue freshly debrided from three NF patients and examined more in depth the persisters phenomenon in GAS-NF clinical isolates. MethodsTime-lapse imaging of freshly isolated GAS-NF clinical isolates, the image analysis software ColTapp and antibiotic challenge-based persisters assays were used to assess the presence of persisters. ResultsWe show for the first time that GAS recovered directly from freshly debrided NF patients tissue are characterized by increased colony appearance time heterogeneity, indicating the presence of persisters. Acidic pH or nutrient stress exposure, mimicking the NF-like environment in vitro, similarly leads to phenotypic heterogeneity resulting in enhanced antibiotic survival and confirming the presence of GAS persisters. ConclusionsGAS persisters are present in the tissue freshly debrided from GAS-NF patients and might be one explanation for antibiotic treatment failure and surgery requirement in GAS-NF. Tailored treatment options, including the use of persisters-targeting drugs, need to be developed to increase GAS-NF therapy success.

microbiology↗

bioRxiv2022

Does forest heterogeneity affect mean throughfall for regenerating secondary forests on Borneo?

Tropical landscape regeneration affects hydrological ecosystem functioning by regulating the amount of water that reaches the soil surface and changing soil infiltration rates. This affects the recharge and storage of water in the soil and streamflow responses. Therefore, it is important to assess how the fraction of rainfall that reaches the forest floor changes as secondary forests mature, and how forest structure affects throughfall via changes in storage capacity and evapotranspiration. Therefore, we monitored throughfall for twelve regenerating, logged-over forest plots in Sabah, Malaysian Borneo over a 7-month period and tested if inclusion of measures of forest heterogeneity improved the prediction of throughfall as a fraction of precipitation. On average across all plots, throughfall was 84% of precipitation, but was lower (as low as 74%) in plots with a longer recovery time since logging. There was a significant relationship between throughfall and tree density and basal area, as well as the Shannon Diversity Index and the coefficient of variation of the diameter at breast height, although species and structural diversity measures (Shannon Index and the coefficient of variation) did not improve model performance substantially. The overall best performing model was a linear regression with tree density. There was no relation between LiDAR-derived Top of Canopy (TCH) and mean throughfall, suggesting that this remotely sensed proxy of canopy height is not needed to estimate throughfall and more in-depth analysis of other LiDAR-products such as point clouds may be required. Our results imply that estimating throughfall in this forest type can be reliably achieved using tree density, and that this is not substantially affected by species diversity or structural heterogeneity variables, at least in the context of logged and regenerating forests in Sabah. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=137 SRC="FIGDIR/small/500051v1_ufig1.gif" ALT="Figure 1"> View larger version (38K): org.highwire.dtl.DTLVardef@e7b11borg.highwire.dtl.DTLVardef@11c923dorg.highwire.dtl.DTLVardef@c4f3c6org.highwire.dtl.DTLVardef@607ab8_HPS_FORMAT_FIGEXP M_FIG Forest of a similar size or height can have a different structure. In this study we investigate if diversity also affects the amount of throughfall for plots across a disturbance gradient. C_FIG

ecology↗

bioRxiv2022

Heightened NLRP3 inflammasome activation is associated with aging and CMML diseases severity

Aging causes chronic low-grade inflammation known as inflamm-aging. It is a risk factor for chronic myelomonocytic leukemia (CMML), a hematological malignancy that is most prevalent in older people. Recent studies suggest a critical role for the NLRP3 inflammasome in inflamm-aging. However, the mechanisms involved in NLRP3 activation in aging and its involvement in CMML progression are not fully understood. Here, we report that aging increases interleukin-1{beta} production upon NLRP3 activation in human CD14+ monocytes. Interestingly, we found that Toll-like receptor (TLR) 1/2 agonist Pam3Cysk4 directly activates NLRP3 inflammasome without the requirement of second activation signal in monocytes from older but not from younger healthy donors. Further, we observed a dichotomous response to NLRP3 inflammasome activation in monocytes from CMML patients. Intriguingly, CMML patients with heightened NLRP3 activation showed increased treatment dependency and disease severity. Collectively, our results suggest that aging causes increased sensitivity to NLRP3 inflammasome activation at cellular level, which may explain increased inflammation and immune dysregulation in older individuals. Furthermore, NLRP3 inflammasome activation was dysregulated in CMML and positively correlated with disease severity.

immunology↗

bioRxiv2020

Dual-purpose isocyanides produced by Aspergillus fumigatus contribute to cellular copper sufficiency and exhibit antimicrobial activity

The maintenance of sufficient but non-toxic pools of metal micronutrients is accomplished through diverse homeostasis mechanisms in fungi. Siderophores play a well-established role for iron homeostasis; however, no copper-binding analogs have been found in fungi. Here we demonstrate that in Aspergillus fumigatus isocyanides derived from the xan biosynthetic gene cluster (BGC) bind copper, impact cellular copper content, and have significant metal-dependent antimicrobial properties. xan BGC-derived isocyanides are secreted and bind copper as visualized by a chrome azurol S (CAS) assay and inductively coupled plasma-mass spectrometry (ICP-MS) analysis of A. fumigatus intracellular copper pools demonstrated a role for xan cluster metabolites in the accumulation of copper. A. fumigatus coculture with A. nidulans, Candida albicans and a variety of pathogenic bacteria establish copper-dependent antimicrobial properties of xan BGC metabolites including inhibition of laccase activity. Similarly, inhibition of Pseudomonas aeruginosa by low concentrations of the xan isocyanide xanthocillin was copper-dependent. Other metals also reduced xanthocillins antimicrobial properties, but less efficiently than copper. As variations of the xan BGC exist in other filamentous fungi, we suggest that xanthocillin-like natural products represent a first example for fungal small molecules that serve to maintain copper sufficiency and mediate interactions with competing microbes. SignificanceMetal homeostasis is an integral part of metabolism for any organism. A vast array of small molecules are already known to mediate metal homeostasis in fungi and bacteria; however, unlike their bacterial counterparts, to-date there are no known fungal small molecules that function to maintain copper homeostasis. Discovery of copper binding small molecules produced by A. fumigatus gives insight into mechanisms other than the extensively studied copper transporters or metalloproteins for how fungi can regulate copper. This has important ecological implications as securing scarce nutrients is central for fitness and survival. Additionally, studying this mechanism in A. fumigatus provides a basis for investigation of copper regulation pathways in other fungi.

microbiology↗

bioRxiv2020

Personalized in-silico drug response prediction based on the genetic landscape of muscle-invasive bladder cancer

In bladder cancer (BLCA) there are, to date, no reliable diagnostics available to predict the potential benefit of a therapeutic approach. The extraordinarily high molecular heterogeneity of BLCA might explain its wide range of therapy responses to empiric treatments. To better stratify patients for treatment response, we present a highly automated workflow for in-silico drug response prediction based on a tumors individual multi-omic profile. Within the TCGA-BLCA cohort, the algorithm identified a panel of 21 genes and 72 drugs, that suggested personalized treatment for 94,7% of patients - including five genes not yet reported as biomarkers for clinical testing in BLCA. The automated predictions were complemented by manually curated data, thus allowing for accurate sensitivity- or resistance-directed drug response predictions. Manual curation revealed pitfalls of current, and potential of future drug-gene interaction databases. Functional testing in patient derived models and/or clinical trials are next steps to validate our in-silico drug predictions.

bioinformatics↗

bioRxiv2018

A large-scale, standardized physiological survey reveals higher order coding throughout the mouse visual cortex

To understand how the brain processes sensory information to guide behavior, we must know how stimulus representations are transformed throughout the visual cortex. Here we report an open, large-scale physiological survey of neural activity in the awake mouse visual cortex: the Allen Brain Observatory Visual Coding dataset. This publicly available dataset includes cortical activity from nearly 60,000 neurons collected from 6 visual areas, 4 layers, and 12 transgenic mouse lines from 221 adult mice, in response to a systematic set of visual stimuli. Using this dataset, we reveal functional differences across these dimensions and show that visual cortical responses are sparse but correlated. Surprisingly, responses to different stimuli are largely independent, e.g. whether a neuron responds to natural scenes provides no information about whether it responds to natural movies or to gratings. We show that these phenomena cannot be explained by standard local filter-based models, but are consistent with multi-layer hierarchical computation, as found in deeper layers of standard convolutional neural networks.

neuroscience↗

bioRxiv2017

A LaeA- and BrlA-dependent cellular network governs tissue-specific secondary metabolism in the human pathogen Aspergillus fumigatus

Biosynthesis of many ecologically important secondary metabolites (SMs) in filamentous fungi is controlled by several global transcriptional regulators, like the chromatin modifier LaeA, and tied to both development and vegetative growth. In Aspergillus molds, asexual development is regulated by the BrlA>AbaA>WetA transcriptional cascade. To elucidate BrlA pathway involvement in SM regulation, we examined the transcriptional and metabolic profiles of {Delta}brlA, {Delta}abaA, {Delta}wetA and wild-type strains of the human pathogen Aspergillus fumigatus. We find that BrlA, in addition to regulating production of developmental SMs, regulates vegetative SMs and the SrbA-regulated hypoxia stress response in a concordant fashion to LaeA. We further show that the transcriptional and metabolic equivalence of {Delta}brlA and {Delta}laeA is mediated by a LaeA requirement preventing heterochromatic marks in the brlA promoter. These results provide a framework for the cellular network regulating not only fungal SMs but diverse cellular processes linked to virulence of this pathogen.

microbiology↗