Biology subjects

Koehler, F.

Publications and source records attributed to Koehler, F..

8 recordsLinked to original sources

bioRxiv2025

Nutrient stress activates Rab5b-mediated autophagy to remodel the synaptic proteome

Synaptic proteostasis is crucial for maintaining neuronal function and plasticity, yet how synapses adapt to metabolic stress remains poorly understood. Here, we show that nutrient deprivation, particularly serum withdrawal, induces robust autophagy-dependent remodeling of the synaptic proteome, while mTORC1 inhibition has more limited effects. Nutrient stress rapidly activates autophagy both globally and at synapses, with synaptic autophagy peaking within 1-2 hours of serum withdrawal. Mechanistically, we uncover that the LC3 lipidation complex (ATG5-ATG12-ATG16L1) is recruited to synapses via Rab5b-positive endosomes in a dynein-dependent manner. Live imaging reveals enhanced Rab5b-ATG16L1 co-trafficking and increased ATG5 mobility upon serum withdrawal, supporting a model of spatiotemporally controlled autophagy precursor delivery to synaptic compartments. Functionally, nutrient deprivation acutely dampens neuronal excitability in vitro, while a two-week fasting-mimicking diet in vivo triggers synaptic proteome remodeling that overlaps with starvation-induced autophagy cargo. In contrast, restriction of mTORC1-activating amino acids fails to induce comparable synaptic changes, suggesting that synaptic autophagy is regulated by nutrient signals beyond mTORC1. Our findings define a Rab5b-mediated trafficking mechanism that couples nutrient sensing to localized synaptic degradation, providing new insight into how neurons preserve proteostasis under metabolic challenge.

neuroscience↗

bioRxiv2025

When discrete characters are wanting: Continuous character integration under the phylospecies concept informs the revision of the Australian land snail Thersites (Eupulmonata, Camaenidae)

Species that are predominantly characterized by continuous instead of discrete morphological characters pose a challenge to species delimitation. Under the phylospecies concept, species are delimited by apomorphies, which are difficult to establish when characters are not discrete. In the present study, we address these challenges in the Australian land snail genus Thersites (family Camaenidae), where accepted species exhibit a scarcity of discrete distinguishing characters and differ in a limited range of continuous characters according to prior taxonomic studies. We integrate analyses of genome-scale molecular data with evaluations of several continuous, qualitative, and discrete morphological characters derived from landmarks to delineate species by identifying apomorphies. We found that dimensions of shell and genitals overlapped considerably among the currently accepted species. These overlaps may indicate morphospace saturation, which may affect species delineation through the gen-morph species concept. Statistical methods, such as Dunns test, failed to consistently delineate monophyletic taxa. Additionally, we could not derive apomorphies from discretized landmarks for the prevalence of outlier specimens. However, applying the Kruskal-Wallis test at certain nodes of the tree revealed significant differences in some continuous characters. We propose that these inferred differences represent apomorphies of taxonomic lineages. Ultimately, we suggest based on our findings that of the four currently accepted species, two should be synonymized. To maintain monophyly of taxa, we synonymize Thersites mitchellae with T. novaehollandiae and T. darlingtoni with T. richmondiana. Distinct character states of the umbilicus support the existence of two independent lineages: One with an open (T. sp1 + T. sp2) and one with a closed umbilicus (T. novaehollandiae + T. richmondiana). Overall, the Kruskal-Wallis tests support four distinct species, T. novaehollandiae and T. richmondiana plus two newly described species. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=122 SRC="FIGDIR/small/649343v2_ufig1.gif" ALT="Figure 1"> View larger version (58K): org.highwire.dtl.DTLVardef@1d9dc53org.highwire.dtl.DTLVardef@ff619org.highwire.dtl.DTLVardef@1e618aeorg.highwire.dtl.DTLVardef@15e80e6_HPS_FORMAT_FIGEXP M_FIG C_FIG

evolutionary biology↗

bioRxiv2025

Adeno-associated viruses escort nanomaterials to specific cells and tissues

The delivery of nanotherapeutics to specific tissues relies on bespoke targeting strategies or invasive surgeries. Conversely, adeno-associated viruses (AAVs) can target specific tissues following intravenous injections. Here we show that cell-targeting properties of AAVs could be broadly conferred to nanomaterials. We develop a strategy to couple AAV capsids to nanoparticles that is invariant of viral serotype or nanomaterial chemistry and permits control over stoichiometry of the AAV-nanoparticle chimeras. The chimeras selectively escort nanoparticles into cell classes governed by AAV serotypes. When applied to magnetic nanoparticles, the AAV-nanoparticle chimeras enable magnetically localized gene delivery. In vivo, we show that leveraging the brain-targeting AAV serotype CAP-B10 achieves nanoparticle delivery to the parenchyma with [~]10% efficiency (% injected dose/g[brain]) while avoiding accumulation in the liver. The enhanced delivery efficiency and tissue specificity highlight the potential of AAV-chimeras as a versatile strategy to escort broad classes of nanotherapeutics to the brain and beyond.

bioengineering↗

bioRxiv2025

On the impact of reference selection on variant calling in phylogenomics: How to avoid systematic error in target-enrichment studies of non-model organisms

Target-enrichment methods are widely used in phylogenomic studies aiming to reconstruct the relationships among diverse groups of organisms. When building phylogenomic datasets from short sequencer reads, software pipelines need to accurately align short sequencer reads to the target and identify the genetic variation in homologous DNA sequences. Variant calling, a crucial step in this process, is known to be error-prone in a phylogenetic analysis framework as it requires a conspecific reference as a template. To avoid problems relating to reference choice, existing target-enrichment pipelines often skip variant calling entirely using work-arounds. This study investigates the effect of reference genome selection on the reliability of variant calling and assesses the consequences of reference genome choice on phylogenomic analyses downstream. Employing an empirical exon capture sequence dataset, we examine how variant detection is influenced by reference genome choice. We reconstructed and analysed phylogenomic sequence datasets from short sequencer reads, which includes steps of quality control, read mapping, variant calling, multiple sequence alignment and phylogenetic analysis. We assembled the same exon capture dataset by using four different references for variant calling. These references were (1) a distantly related species, (2) a single ingroup sample, (3) a composite of all ingroup samples, and (4) a self-derived reference for each sample. We found that reference choice significantly impacted the variant detection and that these differences in variant detection influenced the phylogenetic reconstructions downstream. Comparing multiple sequence alignments and phylogenetic trees produced using different references revealed that employing a sample-specific self-reference for variant calling maximizes the accuracy of the variant detection process. Based on this finding, we recommend incorporating self-referenced variant calling in the assembly of phylogenomic datasets to ensure robustness and reproducibility, especially for datasets characterized by low read coverage.

evolutionary biology↗

bioRxiv2023

Magnetoelectric Nanodiscs Enable Wireless Transgene-Free Neuromodulation

Deep-brain stimulation (DBS) with implanted electrodes revolutionized treatment of movement disorders and empowered neuroscience studies. Identifying less invasive alternatives to DBS may further extend its clinical and research applications. Nanomaterial-mediated transduction of magnetic fields into electric potentials offers an alternative to invasive DBS. Here, we synthesize magnetoelectric nanodiscs (MENDs) with a core-double shell Fe3O4-CoFe2O4-BaTiO3 architecture with efficient magnetoelectric coupling. We find robust responses to magnetic field stimulation in neurons decorated with MENDs at a density of 1 {micro}g/mm2 despite individual-particle potentials below the neuronal excitation threshold. We propose a model for repetitive subthreshold depolarization, which combined with cable theory, corroborates our findings in vitro and informs magnetoelectric stimulation in vivo. MENDs injected into the ventral tegmental area of genetically intact mice at concentrations of 1 mg/mL enable remote control of reward behavior, setting the stage for mechanistic optimization of magnetoelectric neuromodulation and inspiring its future applications in fundamental and translational neuroscience.

bioengineering↗

bioRxiv2021

Probing Neuro-Endocrine Interactions Through Wireless Magnetothermal Stimulation of Peripheral Organs

Exposure to stress alters hypothalamic-pituitary-adrenal (HPA) axis reactivity; however, it is unclear exactly how or where within the HPA pathway these changes occur. Dissecting these mechanisms requires tools to reliably probe HPA function, particularly the adrenal component, with temporal precision. We previously demonstrated magnetic nanoparticle (MNP) technology to remotely trigger adrenal hormone release by activating thermally sensitive ion channels. Here, we applied adrenal magnetothermal stimulation to probe stress-induced HPA axis changes. MNP and control nanoparticles were injected into the adrenal glands of outbred rats subjected to a tone-shock conditioning/extinction/recall paradigm. We measured MNP-triggered adrenal release before and after conditioning through physiologic (heart rate) and serum (epinephrine, corticosterone) markers. Aversive conditioning altered adrenal function, reducing corticosterone and blunting heart rate increases post-conditioning. MNP-based organ stimulation provides a novel approach to probing the function of HPA and other neuro-endocrine axes and could help elucidate changes across stress and disease models.

bioengineering↗

bioRxiv2020

In vivo photopharmacology enabled by multifunctional fibers

To reversibly manipulate neural circuits with increased spatial and temporal control, photoswitchable ligands can add an optical switch to a target receptor or signaling cascade. This approach, termed photopharmacology, has been enabling to molecular neuroscience, however, its application to behavioral experiments has been impeded by a lack of integrated hardware capable of delivering both light and compounds to deep brain regions in moving subjects. Here, we devise a hybrid photochemical genetic approach to target neurons using a photoswitchable agonist of capsaicin receptor (TRPV1), red-AzCA-4. Using the thermal drawing process we created multifunctional fibers that can deliver viruses, photoswitchable ligands, and light to deep brain regions in awake, freely moving mice. We implanted our fibers into the ventral tegmental area (VTA), a midbrain hub of the mesolimbic pathway, and used them to deliver a transgene coding for TRPV1. This sensitized excitatory VTA neurons to red-AzCA-4, and allowed us to optically control conditioned place preference using a mammalian ion-channel, thus extending applications of photopharmacology to behavioral experiments. Applied to endogenous receptors, our approach may accelerate studies of molecular mechanisms underlying animal behavior.

neuroscience↗

bioRxiv2019

Epigenetic deregulation of lamina-associated domains in Hutchinson-Gilford Progeria Syndrome

Hutchinson-Gilford Progeria Syndrome (HGPS) is a progeroid disease characterized by the early onset of some classically age-related phenotypes including arthritis, loss of body fat and hair and atherosclerosis. Cells from affected individuals express a mutant version of the nuclear envelope protein Lamin A (termed Progerin) and have previously been shown to exhibit prominent chromatin changes. Here, we identify epigenetic deregulation of lamina-associated domains (LADs) as a central feature in the molecular pathology of HGPS. Using ATAC-see/-seq and Infinium MethylationEPIC BeadChip-mediated DNA methylation profiling, we demonstrate that dermal fibroblasts from HGPS patients exhibit both chromatin accessibility and DNA methylation changes that are enriched in LADs. Importantly, we further show that these epigenetic alterations are associated with HGPS-specific gene expression changes. Together, our results establish a central involvement of LADs in the epigenetic deregulation of HGPS and provide novel insight into the molecular changes associated with the disease.

cell biology↗