Biology subjects

Schroeder, K.

Publications and source records attributed to Schroeder, K..

8 recordsLinked to original sources

bioRxiv2026

An integrated stereotaxic injection architecture for mouse intracranial surgeries with AI-driven domain expertise

Stereotaxic intracranial microinjection in mice is a critical step in neuroscience workflows, enabled by robust hardware design, precise operation, and neuroanatomical expertise. Manual injections are prone to error and stereotax-mountable commercial automated injectors are extremely expensive. Further, the knowledge needed for performing accurate intracranial injections and surgeries is heterogeneous and disparate. Here we demonstrate the design and characterization of the UD Neuroinjector software-hardware-knowledge architecture, which serves to both reduce the cost of performing precisely controlled stereotaxic microinjections and provide a web platform for planning accurate targeting of specific mouse brain regions. We designed the UD Neuroinjector using low-cost hardware and 3D-printed parts, with a total build-cost of $300 --- less than 0.1x the cost of a commercial injector. Arduino-based firmware enables programmable flow rates, automated injection and extraction, and manual joystick control. Capillary-fluid measurements show stable, highly linear displacement (R2 > 0.93) at commonly used injection rates. In a head-to-head comparison with a commercial injector, in vivo DAPI injections into the mouse thalamus showed comparable spread and DAPI+ cell counts. For effective experimental design of intracranial injections, the web-based components of our architecture provide AI-enabled assistance and atlas-guided navigation. We used a hybrid retrieval-augmented generation (RAG) approach to ground AI-assisted protocol guidance for mouse intracranial surgeries using a corpus of 3,738 papers. Using the Common Coordinate Framework version 3 (CCFv3), we designed an interactive tool for identifying target coordinates. Together, the UD Neuroinjector architecture integrates and enables efficient knowledge discovery, experimental design, planning, and implementation of mouse intracranial surgeries.

neuroscience↗

bioRxiv2026

Verification of nanopore sequencing technology for clinical carbapenem-resistant Enterobacterales surveillance

Carbapenem-resistant Enterobacterales (CRE) pose a critical threat to global public health and often contribute to the rapid plasmid-mediated dissemination of carbapenemase genes. While established routine diagnostics can confirm the presence of the most common carbapenemases, these approaches do not resolve the genomic context of resistance and thus cannot confirm transmission events, cross-species dissemination, or atypical resistance mechanisms. Nanopore sequencing-based whole-genome sequencing (WGS) can capture this genomic context through complete de novo genome and plasmid assemblies. However, for routine clinical use of nanopore WGS for CRE surveillance, direct comparisons with established diagnostics and clear guidelines on required sequencing depths are needed. We used 100 carbapenemase-producing CRE isolates from routine diagnostics at a tertiary-care hospital to compare results from WGS against established diagnostics, and determined the sequencing depth required for species identification, strain typing, carbapenemase detection, and plasmid-level epidemiology. We additionally examined 10 carbapenem-non-susceptible CRE isolates, for which routine diagnostics identified no carbapenemase gene despite phenotypic carbapenem non-susceptibility. Across all isolates, nanopore WGS reproduced routine carbapenemase family and pathogen detections, and additionally resolved the carbapenemase subtypes and their genomic context, the bacterial species and strain, and resistance mechanisms that established diagnostics had missed. Such strain typing and plasmid-level resolution are essential for infection control responses to differentiate between clonal spread of CRE, dissemination of shared plasmid, or unrelated infection events. Our study thus strongly supports the integration of cost-efficient nanopore WGS into CRE diagnostics, surveillance, and outbreak investigation. The required sequencing depth depends on the clinical objective, with species identification being reliable at a depth of 10x, strain typing and carbapenemase detection at a depth of at least 20x, and robust plasmid-level characterisation at a depth of at least 40x. Across our CRE collection, the detected carbapenemases were mostly plasmid-borne, and predominantly encoded by relatively conserved IncN and more heterogenous IncL/M plasmids. ImportanceCarbapenem-resistant bacteria are among the most serious threats in modern medicine, leaving clinicians with few treatment options. Nanopore sequencing can be a powerful tool to rapidly and precisely track resistance and guide infection control, but limited comparisons with clinically established diagnostics and uncertainty about how much sequencing data is needed currently limit routine clinical use. We show that nanopore sequencing detects all relevant carbapenemase genes identified by routine diagnostics, resolves carbapenem resistance mechanisms that standard tests miss, and generally increases the resolution of pathogen characterizations for transmission and outbreak tracing. We provide guidance on the sequencing depth required for diagnostic tasks, from identifying species to tracking plasmid-borne resistance genes across time and pathogens. By benchmarking nanopore sequencing against established diagnostics and matching sequencing effort to the clinical question, we offer a framework that makes genomic surveillance of carbapenem-resistant bacteria accessible and cost-efficient.

genomics↗

bioRxiv2026

GIRAF 1.0: A unified global framework to anticipate plant pest invasions

Plant pests threaten 10-40% of global food production, resulting in $55-220 billion in annual economic losses. Despite these escalating risks, biosecurity remains largely reactive, lacking anticipatory frameworks that integrate pest-specific drivers governing transboundary spread. We present GIRAF 1.0 (Global Invasion Risk Assessment Framework), the first quantitative, data-driven system that unifies pest-specific multi-host landscapes, abiotic suitability, and global trade networks with international phytosanitary policies. We applied GIRAF to four globally devastating pests - ranging from viral to insect taxa - to reconstruct a century of transcontinental spread and generate the first multiscale atlases of future invasion potential. GIRAF reveals that 22-37% of Earths land surface can contain host communities that largely overlap with environmentally suitable hotspots. Over 115 countries are highly vulnerable to trade-mediated pest introductions despite adopted phytosanitary policies. GIRAF provides a foundation for proactive surveillance and pandemic preparedness, offering a scalable path for transnational biosecurity agencies and global food industries.

ecology↗

bioRxiv2025

Orco regulates the circadian activity of pheromone-sensitive olfactory receptor neurons in hawkmoths

1The mating behavior of nocturnal Manduca sexta hawkmoths is under strict temporal control. It is orchestrated via circadian and ultradian oscillations in sex-pheromone stimuli as social Zeitgeber. The extremely sensitive pheromone-detecting olfactory receptor neurons (ORNs) that innervate the long trichoid sensilla on the males antennae are peripheral circadian clocks. They express the transcriptional-translational feedback loop (TTFL) circadian clockwork, best characterized in Drosophila melanogaster. In hawkmoths, it is still unknown whether or how the ORN TTFL clockwork regulates the daily rhythms in pheromone sensitivity and in temporal resolution of ultradian pheromone pulses as prerequisites to the temporal regulation of hawkmoth mating behavior. We hypothesize that, rather than the slow TTFL clock, a more rapidly adaptive post-translational feedback loop (PTFL) clockwork, assembled in a signalosome in the ORN plasma membrane, allows for temporal control of pheromone detection via generation of multiscale endogenous membrane potential oscillations. The potential oscillations of the PTFL clock could rapidly synchronize to oscillations of pheromone stimuli at different time scales, thus enabling the prediction of stimulus patterns as a mechanism for active sensing. With in vivo long-term tip recordings of long trichoid sensilla of male hawkmoths, we analyzed the spontaneous spiking activity indicative of the ORNs endogenous membrane potential oscillations. Consistent with our hypothesis of a multiscale PTFL clock in hawkmoth ORNs, spontaneous spiking was modulated on ultradian and circadian time scales, with maximum activity at night. When we blocked the evolutionarily conserved olfactory receptor coreceptor (Orco), the circadian modulation was abolished but the ultradian frequency modulation of the spontaneous activity remained. Consistent with PTFL control, Orco was not under the transcriptional control of the TTFL clock, but its modulation of spontaneous spiking activity was dependent on cAMP. We could replicate the experimental data in a conductance-based computational model of an ORN. In this model, Orco conductance changed as a function of fluctuating 2nd messenger levels. This study demonstrates that a PTFL clock is sufficient to impose a circadian pattern on ORN sensitivity. Future experiments are necessary to further challenge our novel hypothesis. 2. Significance statementIt is generally assumed that all circadian rhythms in an organism are driven by a transcriptional-translational feedback loop (TTFL) clock. In this study, we demonstrate with in vivo recordings of hawkmoth pheromone-sensitive olfactory receptor neurons (ORNs) that the olfactory receptor coreceptor (Orco) is the key pacemaker channel for controlling circadian rhythms in spontaneous spiking activity. Since Orco expression is not driven by the TTFL clock, we put forward the novel hypothesis that Orco is a core element of a post-translational feedback loop (PTFL) membrane clock assembled in a signalosome controlling interlinked oscillations in 2nd messengers and membrane potential. Accordingly, our computational model predicts that ORN sensitivity is tuned by circadian changes in the conductance of an Orco ion channel, which is mediated by cycling levels of cyclic nucleotides. Our novel hypothesis that highlights the contribution of feedback-controlled post-translational modifications to the generation of endogenous circadian rhythmicity should spark further challenges.

physiology↗

bioRxiv2024

Hawkmoth pheromone transduction involves G protein-dependent phospholipase Cβ signaling

1Evolutionary pressures adapted insect chemosensation to the respective insects physiological needs and tasks in their ecological niches. Solitary nocturnal moths rely on their acute olfactory sense to find mates at night. Pheromones are detected with maximized sensitivity and high temporal resolution through mechanisms that are mostly unknown. While the inverse topology of insect olfactory receptors and heteromerization with the coreceptor Orco suggest ionotropic transduction via odorant-gated receptor-ion channel complexes, contradictory data propose amplifying G protein-coupled transduction. Here, we used in vivo tip-recordings of pheromone-sensitive sensilla of male Manduca sexta hawkmoths at specific times of day (rest vs. activity). Since the olfactory receptor neurons distinguish signal parameters in three consecutive temporal windows of their pheromone response (phasic; tonic; late, long-lasting), respective response parameters were analyzed separately. Disruption of G protein-coupled transduction and block of phospholipase C decreased and slowed the phasic response component during the activity phase of hawkmoths without affecting any other component of the response during activity and rest. A more targeted disruption of G subunits by blocking Go or sustained activation of Gs using bacterial toxins affected the phasic pheromone response, while toxins targeting Gq and G12/13 were ineffective. Consistent with these data, the expression of phospholipase C{beta}4 depended on zeitgeber time, which indicates circadian clock-modulated metabotropic pheromone transduction cascades that maximize sensitivity and temporal resolution of pheromone transduction during the hawkmoths activity phase. Thus, discrepancies in the literature on insect olfaction may be resolved by considering circadian timing and the distinct odor response components. 2 Significance statementInsect chemosensory transduction is typically thought to be ionotropic, but data from different insect species suggests that metabotropic olfactory signaling may occur, either alongside or instead of ionotropic mechanisms. Nocturnal moths, known for their extraordinarily sensitive pheromone-detecting olfactory receptor neurons, likely use metabotropic signal amplification. To overcome limitations of previous in vitro studies, we conducted tip-recordings of pheromone-sensitive sensilla in healthy hawkmoths at specific zeitgeber times. Disrupting G protein signaling and phospholipase C{beta} reduced sensitivity and altered response kinetics, revealing strict temporal control of transduction. Thus, contradictory findings in insect olfaction may be reconciled by considering diverse evolutionary pressures for distinct chemosensory signals in different species, zeitgeber time, and disparate odor response parameters.

physiology↗

bioRxiv2020

The chaperonin GroESL facilitates Caulobacter crescentus cell division by supporting the function of the actin homologue FtsA

The highly conserved chaperonin GroESL performs a crucial role in protein folding, however the essential cellular pathways that rely on this chaperone are underexplored. Loss of GroESL leads to severe septation defects in diverse bacteria, suggesting the folding function of GroESL may be integrated with the bacterial cell cycle at the point of cell division. Here, we describe new connections between GroESL and the bacterial cell cycle, using the model organism Caulobacter crescentus. Using a proteomics approach, we identify candidate GroESL client proteins that become insoluble or are degraded specifically when GroESL folding is insufficient, revealing several essential proteins that participate in cell division and peptidoglycan biosynthesis. We demonstrate that other cell cycle events such as DNA replication and chromosome segregation are able to continue when GroESL folding is insufficient, and find that deficiency of the bacterial actin homologue FtsA function mediates the GroESL-dependent block in cell division. Our data suggest that a GroESL-FtsA interaction is required to maintain normal dynamics of the FtsZ scaffold and divisome functionality in C. crescentus. In addition to supporting FtsA function, we show that GroESL is required to maintain the flow of peptidoglycan precursors into the growing cell wall. Linking a chaperone to cell division may be a conserved way to coordinate environmental and internal cues that signal when it is safe to divide. ImportanceAll organisms depend on mechanisms that protect proteins from misfolding and aggregation. GroESL is a highly conserved molecular chaperone that functions to prevent protein aggregation in organisms ranging from bacteria to humans. Despite detailed biochemical understanding of GroESL function, the in vivo pathways that strictly depend on this chaperone remain poorly defined in most species. This study provides new insights into how GroESL is linked to the bacterial cell division machinery, a crucial target of current and future antimicrobial agents. We identify a functional interaction between GroESL and FtsA, a conserved bacterial actin homologue, suggesting that as in eukaryotes, some bacteria exhibit a connection between cytoskeletal actin proteins and chaperonins. Our work further defines how GroESL is integrated with cell wall synthesis, and illustrates how highly conserved folding machines ensure the functioning of fundamental cellular processes during stress.

microbiology↗

bioRxiv2020

Bio-upcycling of polyethylene terephthalate

Over 359 million tons of plastics were produced worldwide in 2018, with significant growth expected in the near future, resulting in the global challenge of end-of-life management. The recent identification of enzymes that degrade plastics previously considered non-biodegradable opens up opportunities to steer the plastic recycling industry into the realm of biotechnology. Here, we present the sequential conversion of polyethylene terephthalate (PET) into two types of bioplastics: a medium chain-length polyhydroxyalkanoate (PHA) and a novel bio-based poly(amide urethane) (bio-PU). PET films were hydrolyzed by a thermostable polyester hydrolase yielding 100% terephthalate and ethylene glycol. A terephthalate-degrading Pseudomonas was evolved to also metabolize ethylene glycol and subsequently produced PHA. The strain was further modified to secrete hydroxyalkanoyloxy-alkanoates (HAAs), which were used as monomers for the chemo-catalytic synthesis of bio-PU. In short, we present a novel value-chain for PET upcycling, adding technological flexibility to the global challenge of end-of-life management of plastics. Graphical abstract O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=130 SRC="FIGDIR/small/993592v1_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@1433e0dorg.highwire.dtl.DTLVardef@19efc71org.highwire.dtl.DTLVardef@cf97f7org.highwire.dtl.DTLVardef@101f123_HPS_FORMAT_FIGEXP M_FIG C_FIG

bioengineering↗

bioRxiv2018

Growth-driven displacement of protein aggregates along the cell length ensures partitioning to both daughter cells in Caulobacter crescentus

All living cells must deal with protein aggregation, which can occur as a result of experiencing stress. In the bacteria Escherichia coli and Mycobacterium smegmatis, aggregates collect at the cell poles and are retained over consecutive cell divisions only in the daughter cell that inherits the old pole, resulting in aggregation-free progeny within a few generations. Here we have studied the in vivo kinetics of aggregate formation and clearance following heat and antibiotic stress in Caulobacter crescentus, which divides by a pre-programmed asymmetric cell cycle. Unexpectedly, we find that aggregates do not preferentially collect at the cell poles, but form as multiple distributed foci throughout the cell volume. Time-lapse microscopy revealed that under moderate stress, the majority of protein aggregates are short-lived and rapidly dissolved by the major chaperone DnaK and the disaggregase ClpB. Severe stress or genetic perturbation of the protein quality machinery results in long-lived protein aggregates, which individual cells can only clear by passing on to their progeny. Importantly, these persistent aggregates are neither collected at the old pole over multiple generations nor inherited exclusively by the old pole-inheriting stalked cell, but instead are partitioned between both daughter cells during successive division events in the same ratio. Our data indicate that this symmetric mode of aggregate inheritance is driven by the elongation and division of the growing mother cell. In conclusion, our study revealed a new pattern of aggregate inheritance in bacteria.

microbiology↗