Biology subjects

Siemens, J.

Publications and source records attributed to Siemens, J..

12 recordsLinked to original sources

bioRxiv2026

A mobile optical coherence microscope for studying aquatic organisms in- and outside the laboratory

High-resolution, three-dimensional imaging of live organisms has largely depended on laboratory-bound microscopes, limiting quantitative analysis of morphology and dynamics to species that survive transport and thrive under lab-controlled conditions. Here we present a mobile optical coherence microscopy (OCM) platform that overcomes this constraint, delivering [~]2.5 {micro}m axial resolution, label-free, volumetric imaging of live aquatic organisms in both laboratory and remote field environments. We demonstrate the platform across a broad range of aquatic organisms from the lab and field, spanning multiple phyla - including cnidarians, poriferans, annelids, arthropods and echinoderms - resolving internal anatomy, tissue boundaries and organismal morphology at micrometer scale without fixation, fluorescent labeling, or specialized sample preparation. High-speed acquisition, with up to 250 kHz A-line rate and 7.7 Hz volume rate, further enabled morphodynamic imaging of live biological processes, including cellular aggregate motility, embryonic cell division, and organ-level peristaltic dynamics in intact, living animals. To demonstrate field deployability, the platform was operated during the EMBL TREC pan-European expedition, enabling on-site, label-free imaging of marine organisms and plankton immediately upon collection. By decoupling high-resolution volumetric imaging from fixed laboratory settings, mobile OCM opens a path toward field-ready quantitative morphological and dynamic phenotyping of aquatic life.

bioengineering↗

bioRxiv2026

Quaternary ammonium compounds (QACs), QAC resistance genes, and QAC tolerant bacteria in livestock and human waste streams

Quaternary ammonium compounds (QACs) are high production volume biocidal compounds increasingly scrutinized for their potential to promote antimicrobial resistance spread. This study compared the release of QACs, QAC resistance indicator genes (qacE/qacE{Delta}1), and QAC tolerant bacteria from livestock and human waste streams into the environment. Five livestock farms with on-farm biogas plants (BGPs), a rural and an urban municipal wastewater treatment plant (WWTP) were studied in parallel. In WWTPs, <1% of incoming QACs were discharged with treated wastewater but 10-20% were transferred to sewage sludge. QAC concentrations in sewage sludge far exceeded those in raw and digested manure. The qacE/qacE{Delta}1 genes were detected in all samples with a higher relative abundance in solid than liquid samples. Relative abundances of QAC tolerant fast growing heterotrophic bacteria cultivated under high nutrient conditions at 37{degrees}C were higher in human than livestock waste streams. Providencia and Pseudomonas dominated the cultivated QAC tolerant bacteria in both systems but showed higher QAC tolerance when originating from human waste streams. Additionally, Enterobacteriaceae with higher QAC tolerance were cultivated from human waste streams. Most QAC tolerant strains carried antibiotic resistances without strong system differences. Only few strains carried the qacE/qacE{Delta}1 gene indicating that other mechanisms must be responsible for the increased QAC tolerance. In conclusion, QACs, qacE/qacE{Delta}1, and viable QAC tolerant bacteria including potential pathogenic bacteria were released from livestock and human waste streams into the environment with highest abundances in a post-pandemic sewage sludge sample. Highlights- QACs most abundant in human waste streams, especially biosolids - Higher relative abundance of QAC tolerant bacteria in human waste streams - Pseudomonas and Providencia dominated QAC tolerant bacteria in both waste streams - Enterobacteriaceae with higher QAC tolerance abundant in human waste streams - Most QAC tolerant strains carried additional antibiotic resistances Environmental implicationMunicipal wastewater treatment plants (WWTPs) and livestock farms are hotspots for antimicrobial resistance (AMR) propagation. We compared the simultaneous occurrence of quaternary ammonium compounds (QACs), resistance genes (RGs), QAC-tolerant bacteria, and their multidrug-resistance status in livestock and human waste streams. QACs, indicators of QAC tolerance and AMR occurred in both systems but were higher in WWTPs, especially sewage sludge. Our findings highlight the need for prudent disinfectant use and enhanced waste treatments to reduce the risks of spreading micropollutants, pathogens, and AMR via organic fertilizers or treated wastewater recycled in circular agricultural practice.

microbiology↗

bioRxiv2026

Antimicrobial resistant bacteria in wastewater-irrigated Mexican soils and transfer of resistant bacteria from irrigated soils to cilantro plants

Agricultural fields in the Mezquital Valley, Mexico, were irrigated with untreated wastewater over several decades. Following the construction of a wastewater treatment plant (WWTP) in Atotonilco de Tula, WWTP effluent is used for irrigation. To evaluate the effects of changed irrigation, a soil incubation experiment was performed. Soils of the Mezquital Valley long-term irrigated with untreated wastewater were irrigated with WWTP influent or effluent, both unspiked and spiked with antibiotics and biocidal compounds and incubated four weeks. We investigated the effects of shifted irrigation on the abundance of cultivable total heterotrophic and resistant bacteria (RB). Additionally, RB were cultivated from Coriandrum sativum (cilantro) sown in soil of the incubation experiment. While wastewater treatment significantly reduced the bacterial abundance in effluent, spiking increased RB abundance in both wastewater types including ciprofloxacin (CIP) RB. Before wastewater addition, all soils contained cultivable RB. Irrigation increased the relative abundance of RB cultivated on Mueller Hinton (MH) agar in Leptosols and Phaeozems, compared to soils prior to wastewater addition irrespective of the water type, but not in Vertisols, suggesting the soil type rather than water qualities influenced the RB abundance. Diverse CIP RB were cultivated including strains of 14 genera of three phyla. Among those, Achromobacter spp. strains related to potentially pathogenic A. spanius originating from soil were abundant in both leaves and roots of cilantro. Our results showed that the implementation of wastewater treatment does not reduce the abundance of cultivable RB in Mezquital Valley soils and cilantro plants. Health risk associated monitoring should include long-term persistent RB colonizing plants cultivated in wastewater irrigated soils.

microbiology↗

bioRxiv2026

Reduced antibiotic effect of ciprofloxacin on bacteria in the presence of montmorillonite

Antibiotic residues exceeding selective concentrations for antibiotic-resistant bacteria have been detected in various environments, including manure, wastewater, and effluents from wastewater treatment plants. When these residues come into contact with soils, for instance, due to wastewater irrigation or fertilization with manure, they interact with soil constituents. Soil colloids (1-1000 nm), such as montmorillonite, have been observed to adsorb pharmaceuticals, including antibiotics. We investigated the effect of colloids on the bioavailability of ciprofloxacin and found, that added to bacterial growth medium, montmorillonite reduces, but does not completely prevent, the growth-inhibitory effect of the antibiotic. The bacteria were able to grow at up to roughly double the concentration of ciprofloxacin in the presence of montmorillonite. We show that the incomplete deactivation of ciprofloxacin was most probably caused by medium components that decreased the adsorption of ciprofloxacin to montmorillonite. We conclude that a selective potential of this highly active antibiotic in contaminated soils, which also contain nutrients enabling bacterial growth, cannot be ruled out. Environmental implicationAntibiotics such as ciprofloxacin are frequently detected in water bodies and soils due to wastewater irrigation or manure application. These residues raise concerns about environmental toxicity and antibiotic resistance. This study demonstrates that montmorillonite, a common clay mineral in soils, significantly reduces the antimicrobial efficacy of environmental ciprofloxacin concentrations by sorption. The findings reveal a natural attenuation mechanism that may influence the environmental fate and bioavailability of antibiotics. Understanding such interactions is critical for predicting antibiotic behavior in terrestrial systems and for designing more accurate environmental risk assessments.

microbiology↗

bioRxiv2026

Wastewater and colloidal extracts of wastewater-irrigated soils select for resistant Acinetobacter baylyi beyond what measured antibiotic concentrations predict

Numerous studies have shown that the abundance of antibiotic-resistant bacteria (ARBs) or antibiotic-resistance genes (ARGs) in soil increases after irrigation with wastewater. However, it is unclear whether this increase is due to the selection effects of pharmaceutical residues in the irrigation water or the continuous introduction of ARBs and ARGs with the wastewater. Further, it is unclear how the binding of antibiotics to natural colloids (1-1000 nm) affects their biological effects compared to truly dissolved substances (< 1 nm). We conducted competition experiments with resistant and susceptible Acinetobacter baylyi BD413 strains in wastewater, as well as in colloidal and truly dissolved extracts of soils irrigated with wastewater. Although the concentrations of our six target antibiotics were far below the measured minimum selective concentrations of the tested strains, we demonstrate that the resistant strain was favored in the wastewater and the colloidal extracts. In contrast, the truly dissolved fractions exhibited weaker and more variable selective effects. A non-targeted analysis revealed the presence of 82 additional substances in our extracts, including further antibiotics, pesticides, and different non-antibiotic drugs that may influence the selection of our resistant A. baylyi BD413 strain. Our findings suggest that antibiotic resistance is selected for in wastewater and wastewater-irrigated soils. This cannot be explained by antibiotic concentrations alone, but may also arise from the effects of complex mixtures of co-occurring contaminants, particularly those associated with colloidal particles.

microbiology↗

bioRxiv2026

A sensory - preoptic circuit drives capsaicin-induced hypothermia

Capsaicin, the principal agonist of the heat-sensitive transient receptor potential vanilloid 1 (TRPV1) channel, triggers profound hypothermia by suppressing thermogenesis and promoting heat loss. While TRPV1 has been extensively characterized as a molecular sensor of heat and inflammatory mediators, the neural circuits through which capsaicin drives body cooling remain poorly defined. Emerging work suggests that peripheral TRPV1 activation modulates afferent input to central thermoregulatory networks, yet how --and where-- these signals are integrated within the central nervous system to induce hypothermia has remained unresolved. Intriguingly, optogenetic or chemogenetic activation of specific neuronal populations in the preoptic area (POA) of the hypothalamus has been shown to evoke deep hypothermia, raising the possibility that capsaicin engages overlapping thermoregulatory circuits. However, whether capsaicin-driven hypothermia depends on these POA neuron populations has not been directly tested. Here, we address this question by selectively and permanently silencing defined POA neuronal subtypes and assessing their contribution to capsaicin-evoked hypothermia. Silencing VMPOLepR or POAVgat neurons attenuated the hypothermic response but did not abolish it, whereas silencing POAVglut2 neurons nearly eliminated capsaicin-induced hypothermia. These findings identify POAVglut2 neurons as a critical central node through which peripheral TRPV1 activation drives body cooling. Together, our results demonstrate that capsaicin induces hypothermia via afferent sensory pathways that converge onto hypothalamic preoptic thermoregulatory neurons, revealing a direct circuit-level link between peripheral TRPV1 signalling and central control of body temperature.

neuroscience↗

bioRxiv2024

Thermally-induced neuronal plasticity that mediates heat tolerance

Heat acclimation is an adaptive process that improves physiological performance and supports survival in the face of increasing environmental temperatures. Understanding the underlying mechanisms holds potential to mitigate health risks and reduces the steadily increasing number of heat-related casualties associated with global warming. Here we report the identification of a discrete group of hypothalamic preoptic neurons that transform to rheostatically increase their activity over the course of heat acclimation, a property required for mice to become heat tolerant. Peripheral thermo-afferent pathways via the parabrachial nucleus activate preoptic neurons and mediate acute heat-defense mechanisms in non-acclimated animals. However, long-term heat exposure promotes the preoptic neurons to gain intrinsically warm-sensitive activity, independent of thermo-afferent parabrachial input. Our data shows that their newly gained cell-autonomous warm-sensitivity is required to recruit peripheral heat tolerance mechanisms in acclimated animals. Mechanistically, we find a combination of increased sodium leak current and enhanced utilization of the Nav1.3 ion channel to drive their pacemaker-like, warm-sensitive activity. We propose a salient neuronal plasticity mechanism, adaptively driving acclimation to promote heat tolerance. HighlightsO_LIHeat acclimation induces tonic, warm-sensitive firing in hypothalamic VMPO neurons C_LIO_LITonic activity in VMPO neurons primes peripheral organs to gain heat tolerance capacity C_LIO_LIWarm-sensitive tonic firing recruits heat tolerance mechanisms in acclimated animals C_LIO_LINaV1.3 persistent sodium currents drive tonic, warm-sensitive firing in VMPO neurons C_LI

neuroscience↗

bioRxiv2024

An Intra-Hypothalamic Pathway Modulating Body Temperature and Feeding

The intricate interplay between energy metabolism and body temperature regulation underscores the necessity of finely tuned mechanisms to maintain thermo-energetic homeostasis. Hot environments are known to suppress food intake and to reduce energy expenditure. However, the interplay between thermoregulatory and caloric-regulatory hypothalamic areas remains largely unexplored. In this study, we unveil two unconventional pathways originating from a subpopulation of genetically defined excitatory, leptin receptor-expressing POA neurons (VMPOLepR) that connect to the paraventricular nucleus of the hypothalamus (PVH) and the dorsomedial hypothalamic nucleus (DMH). Both, VMPOLepR[->]PVH and VMPOLepR[->]DMH connections, inhibit brown adipose tissue (BAT) thermogenesis and reduce body temperature; surprisingly, the VMPOLepR[->]PVH connection additionally exhibits the unique ability to suppress food intake and also promotes tail vasodilation. Our findings suggest that the excitatory VMPOLepR[->]PVH loop integrates temperature and caloric information to complement the canonical inhibitory arcuate nucleus (ARC)[->]PVH pathway. We propose that this novel pathway contributes to energy and temperature homeostasis in hot environments, offering new insights into previously unrecognized neuronal circuits orchestrating thermo-metabolic balance in response to environmental challenges.

neuroscience↗

bioRxiv2023

Diverging roles of TRPV1 and TRPM2 in warm-temperature detection

The accurate perception of innocuous temperatures, particularly those experienced as pleasantly warm, is essential for achieving thermal comfort and maintaining thermoregulatory balance. Warm-sensitive neurons (WSN) innervating the skin play a central role in non-painful warmth detection. The TRP ion channels TRPV1 and TRPM2 have been suggested as sensors of warm temperature in WSNs. However, the precise contribution of these channels to the process of warmth detection is not fully understood. A significant challenge in analysing WSNs lies in their scarcity: fewer than 10 % of sensory neurons in the rodent dorsal root ganglion (DRG) respond to innocuous warm temperatures. In this study, we examined >20,000 cultured mouse DRG neurons using calcium imaging and discovered distinct contributions of TRPV1 and TRPM2 to warm-temperature sensitivity. TRPV1, and to a lesser extent TRPM2, affect the abundance of WSNs, with TRPV1 mediating the rapid, dynamic response to warmth and TRPM2 subtly affecting the population response of WSNs. By carefully tracking animal movement in a whole-body thermal preference paradigm, we observe that these cellular differences correlate with nuanced thermal behaviours. Utilizing a drift-diffusion model to quantitatively analyse the decision-making process of animals exposed to different environmental temperatures, we found that: TRPV1 deletion primarily impairs the precision of evidence accumulation, whereas TRPM2 deletion significantly increases the total duration of exposure to warmer environments that are avoided by wildtype mice. Our findings provide valuable insights into the distinct molecular responses to warmth stimuli, and underpin the subtle aspects of thermal decision-making when encountering minor temperature variations.

neuroscience↗

bioRxiv2022

Neuron-astrocyte metabolic coupling facilitates spinal plasticity and maintenance of persistent pain

Long-lasting pain stimuli can trigger maladaptive changes in the spinal cord, reminiscent of plasticity associated with memory formation. Metabolic coupling between astrocytes and neurons has been implicated in neuronal plasticity and memory formation in the CNS, but neither its involvement in pathological pain nor in spinal plasticity has been tested. Here, we report a novel form of neuroglia signaling involving spinal astrocytic glycogen dynamics triggered by persistent noxious stimulation via upregulation of the metabolic signaling molecule PTG exclusively in spinal astrocytes. PTG drove glycogen build-up in astrocytes, and blunting glycogen accumulation and turnover by Ptg gene deletion reduced pain-related behaviors and promoted faster recovery by shortening pain maintenance. Furthermore, mechanistic analyses revealed that glycogen dynamics is a critically required process for maintenance of pain by facilitating neuronal plasticity in spinal lamina 1 neurons. Finally, metabolic analysis indicated that glycolysis and lactate transfer between astrocytes and neurons fuels spinal neuron hyperexcitability. Spinal glycogen-metabolic cascades therefore hold therapeutic potential to alleviate pathological pain.

neuroscience↗

bioRxiv2020

Oxytocin Acts on Astrocytes in the Central Amygdala to Promote a Positive Emotional State

Oxytocin orchestrates social and emotional behaviors through modulation of neural circuits in brain structures such as the central amygdala (CeA). The long-standing dogma is that oxytocin signaling in the central nervous system occurs exclusively via direct actions on neurons. However, several findings over the last decades showed that astrocytes actively participate in the modulation of neuronal circuits. Here, we investigate the degree of astrocytes involvement in oxytocin functions. Using astrocyte specific gain and loss of function approaches, we demonstrate that CeA astrocytes not only directly respond to oxytocin, but are actually necessary for its effects on neuronal circuits and ultimately behavior. Our work identifies astrocytes as a crucial cellular substrate underlying the promotion of a positive emotional state by oxytocin. These results further corroborate that astrocytes are key regulators of neuronal circuits activity by responding to specific neuropeptidergic inputs, and opens up new perspectives to understand how neuromodulators gate brain functions.

neuroscience↗

bioRxiv2019

HESC-derived sensory neurons reveal an unexpected role for PIEZO2 in nociceptor mechanotransduction

Somatosensation, the detection and transduction of external and internal stimuli, has fascinated scientists for centuries. But still, some of the mechanisms how distinct stimuli are detected and transduced are not entirely understood. Over the past decade major progress has increased our understanding in areas such as mechanotransduction or sensory neuron classification. Additionally, the accessibility to human pluripotent stem cells and the possibility to generate and study human sensory neurons has enriched the somatosensory research field.\n\nBased on our previous work, the generation of functional human mechanoreceptors, we describe here the generation of hESC-derived nociceptor-like cells. We show that by varying the differentiation strategy, we can produce different nociceptive subpopulations. One protocol in particular allowed the generation of a sensory neuron population, homogeneously expressing TRPV1, a prototypical marker for nociceptors. Accordingly, we find the cells to homogenously respond to capsaicin, to become sensitized upon inflammatory stimuli, and to respond to temperature stimulation.\n\nSurprisingly, all of the generated subtypes show mechano-nociceptive characteristics and, quite unexpectedly, loss of mechanotransduction in the absence of PIEZO2.

neuroscience↗