Biology subjects

Hummel, K.

Publications and source records attributed to Hummel, K..

6 recordsLinked to original sources

bioRxiv2025

Varied monoamine reuptake inhibitors reduce parvalbumin expression; implications for pyramidal cell disinhibition and enhanced neuroplasticity

First-line antidepressants are effective in a significant percent of individuals but a full understanding of how these therapeutics target specific endpoints is lacking. Prior work has shown that depression is associated with hippocampal atrophy and that antidepressants can increase neurotrophin levels to increase hippocampal neurogenesis as well as hippocampal pyramidal cell (PC) spine density and arbor. These effects likely contribute to amelioration of symptoms. A less well-explored possibility is that antidepressants concomitantly disinhibit hippocampal PC activity, which could also facilitate increased PC arbor, spinogenesis and/or activity. In accordance, previous studies have shown antidepressants can attenuate stress-induced upregulation of perineuronal nets (PNNs). PNNs are predominantly localized to parvalbumin (PV) expressing GABAergic interneurons and increase PV expression and neuronal activity. Though specific antidepressants have been explored for effects on regional PNN expression, the question of whether hippocampal PNN/ECM remodeling is a shared feature of varied antidepressant drugs and more importantly, of whether it is associated with significant hippocampal PV inhibition, has not been well-addressed. Herein we examine three monoamine reuptake inhibitors, fluoxetine, venlafaxine and viloxazine, in animal models for effects on PNN remodeling and PV expression, a proxy for PV activity. We observe shared effects of these therapeutics including the ability to increase PNN degrading effectors that can downregulate PV activity. Consistent with this, we observe shared effects of these drugs in terms of their ability to significantly reduce PV levels. These findings highlight the possibility that ECM remodeling and associated hippocampal PC disinhibition represent a shared feature of varied antidepressant medications.

neuroscience↗

bioRxiv2025

CCL5/CCR5 signaling modulates depression-relevant behavior, neuronal oscillations, and long-term depression of synaptic activity.

Major depressive disorder (MDD) is a debilitating disorder, often associated with perseverative thinking and anxiety. Localized reductions in pyramidal cell activity may contribute to associated symptoms, and effective antidepressant treatments typically enhance overall neuronal excitation. CCL5 is a chemokine that has been shown to reduce excitatory-neuronal activity, and is also increased with MDD and conditions that increase MDD risk. Here, we investigate the CCL5/CCR5 axis for its ability to modulate depression-relevant endpoints that are diminished in MDD, including neuronal oscillations, as well as biochemical and behavioral correlates of the disorder. In comparison to wildtype mice, CCR5 knockouts had increased gamma and theta power, and stronger theta/high-gamma phase amplitude coupling during dark-cycle EEG recordings. Compared to strain-matched wildtype mice, CCR5 knockouts also demonstrated reduced anxiety, increased sucrose preference, and improved associative memory. Proteomic analysis of the hippocampus showed that CCR5 knockouts had reduced levels of the GABA receptor alpha-4 subunit, which mediates tonic inhibition and restricts pyramidal cell plasticity. In complementary primary neuronal culture studies, CCL5 diminished GSK-3{beta} activity and impaired NMDA-dependent long-term depression (LTD), a form of plasticity that promotes cognitive flexibility. In addition, CCL5 signaling increased parvalbumin expression in GABAergic neurons through a CCR5-dependent manner. In combination with the ability of CCR5 to restrain gamma oscillation power and LTD, our data raise the possibility that CCL5/CCR5 signaling inhibits neuronal excitation through increased PV+ interneuron activity. Moreover, data are consistent with the possibility that CCR5 antagonists might share the ability of established antidepressants to both increase PC excitation and reduce PC inhibition. Significance StatementMajor depressive disorder (MDD) is a global leading cause of disability, and is associated with increased chemokine activation and inflammation. In this study, we investigate how the CCR5/CCL5 chemokine axis regulates behavioral and cognitive endpoints associated with MDD. This study aims to provide insight to how chemokine signaling underlies mood and behavioral symptoms of neuropsychiatric disorders. We hope this research supports further investigation of CCR5 antagonists for MDD and related mood and anxiety disorders.

neuroscience↗

bioRxiv2025

Pioneer bark beetle attacks induce multifaceted localized defense responses in Norway spruce

Conifer forests worldwide are increasingly threatened by environmental stressors, especially bark beetle infestations. In a novel experimental field setup with controlled attacks on clonal trees, we investigated the molecular defense responses of 35-year-old Norway spruce trees to colonization attempts by the spruce bark beetle, Ips typographus. A multi-omics approach was used to study tree responses to bark beetle pioneers under natural conditions. At the site of the attacks, increased levels in jasmonic acid, together with changes in other phytohormones, induced differential gene expression of up to 1,900 genes from multiple defense-related pathways. These transcriptomic alternations were corroborated by proteomic and metabolomic shifts, which ultimately showed increased levels of compounds involved in deterring bark beetle attacks, such as phenolic aglycones, diterpene resin acids, mono- and sesquiterpenes, and lignin. Our study highlights the intricate yet rapid and effective local defense response of Norway spruce against pioneer bark beetle attacks and lays a foundation for in-depth studies of this and other conifers resistance to phloem-feeding insects.

plant biology↗

bioRxiv2025

The inner dynamics of positive human-animal interactions: investigating the roles of oxytocin, opioids, dopamine, serotonin and the proteome

Research on the neuroendocrine basis of positive interactions has predominantly focused on oxytocin (OT), although dopamine (DA) and opioids also play crucial roles. Furthermore, these neurotransmitters are known to interact with each other but have seldom been studied concurrently. In this study, we quantified longitudinal changes in these neurotransmitters using a within-subject, 2 x 2 factorial design by varying human familiarity (familiar versus unfamiliar) and contact type (positive contacts versus ignoring) for 10 min human-pig interaction sessions. We repeatedly sampled cerebrospinal fluid from 10 pigs through a spinal catheter 65 and 5 min before the test and at 10, 30, 60, 120 and 240 min after the start of the test. Samples at various timepoints were analysed for OT, DA metabolites 3,4-dihydroxyphenylacetic acid (DOPAC) and homovanillic acid (HVA), serotonin metabolite 5-hydroxyindoleacetic acid (5-HIAA), {beta}-endorphin opioids concentrations, and using proteomics to explore novel protein candidates. The test condition (human familiarity x contact type) had a significant effect on the concentration of {beta}-endorphin (F1,118.59 = 4.45; P = 0.04) and 5-HIAA (F1,73.47 = 5.02; P = 0.03), and tended to affect the concentration of oxytocin (F1, 119.8 = 3.19; P = 0.08) and DOPAC (F1,70.57 = 3.31; P = 0.07), but pair-wise comparisons were not significant. There was only a minor effect on the pigs behaviour, which suggests that the test conditions may have had limited effect. Nevertheless, this approach provides a valuable method to study neurotransmitter changes over time and simultaneously. Highlights- Oxytocin was higher when pigs were ignored than when they had positive contacts - Oxytocin was highest in the novel condition of an unfamiliar human ignoring the pig - Human familiarity and contact type affected {beta}-endorphin and 5-HIAA concentrations - Dopamine metabolites and the proteome were not affected by the test conditions

animal behavior and cognition↗

bioRxiv2024

Locus-specific chromatin proteomics using dCas-guided proximity labelling in Aspergillus nidulans.

Proximity labelling that uses promiscuous biotin ligases (BirA) fused to a bait protein is a powerful tool to identify protein interaction partners in vivo under different metabolic or developmental conditions. BirA can also be used to determine protein composition and interaction partners at specific chromatin locations when it is fused with enzymatically-disabled Cas9 (dCas9) and then guided to the location of interest by sgRNAs. We adapted this method (called CasID) for fungal cells using the nitrate assimilation gene cluster of A. nidulans as a model locus and estrogen-inducible expression of the dCas9-BirA fusion to improve condition-specific labelling. For method establishment, we first verified the presence of dCas-BirA and a known transcription factor at the nitrate locus by chromatin immunoprecipitation (ChIP). Results show that both dCas-BirA and the AreA transcription factor are present at the locus of interest under the conditions used for biotinylation. We then optimized the CasID procedure for efficient labelling and background reduction using the CasID-sgRNA strain and two control strains, one lacking the sgRNA and another one lacking the whole CasID system. Here we provide proof-of-concept for the suitability of the method by showing that biotinylated proteins are enriched in the CasID strains in comparison to the controls. After background reduction, 32 proteins remained in two independent experiments exclusively enriched in the Cas-ID-sgRNA strain. Among these proteins was NmrA, an AreA-interacting regulator, and we also found several chromatin-associated proteins. Overall, our results demonstrate that Cas-ID is suitable for locus-specific labelling and identification of chromatin-associated proteins and transcription factors in A. nidulans. However, the high background of proteins that are biotinylated out of chromatin context or unspecifically attach to the affinity purification matrix needs to be addressed by implementing a set of rigorous controls. In summary, we herewith provide a detailed protocol for application of the method that proved to be useful for the identification of novel chromatin-associated proteins and their interaction partners at a specific genomic locus in divers metabolic and developmental conditions. Author summaryThis study demonstrates that locus-specific proteomics can be carried out by dCas-BirA guided proximity labelling in Aspergillus nidulans. For establishment, we targeted the well-described bidirectional promoter region between niaD, a nitrate reductase, and niiA, a nitrite reductase. At this locus we could test by chromatin immunoprecipitation (ChIP) in combination with qPCR if both, the dCas9-BirA fusion as well as a central transcription factor are at the locus under the conditions of our Cas-ID experiment. After this first control step, we considered that unspecific labelling by dCas-BirA during the time from translation to landing at the targeted chromatin locus may be one of the most relevant drawbacks of the method. Therefore, we developed a number of control strains that would allow us to clearly discriminate between background and sgRNA-dependent specific labelling at the locus. Our protein MS results validated these estimates and only considering the results of these controls enabled us to distinguish the set of locus-specific proteins from a very high general background. Finally, enrichment of biotinylated proteins through affinity purification with streptavidin resin and subsequent LC-MS/MS analysis showed that more than 800 proteins were detected in each sample, emphasizing the high background of the purification method. After background reduction of the control samples, we were able to identify 32 proteins which were exclusively detected in the test strain in two independent measurements, including several chromatin-associated proteins and NmrA, a negative regulator of the nitrate locus transcription factor AreA.

molecular biology↗

bioRxiv2017

How Well Do You Know Your Mutation? Complex Effects Of Genetic Background On Expressivity, Complementation, And Ordering Of Allelic Effects

For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and variation across alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both the scalloped and vestigial genes, which influence wing development in Drosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development) of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis.

genetics↗