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Sommer, A.

Publications and source records attributed to Sommer, A..

11 recordsLinked to original sources

P-DOpE probes reveal local amplification of phasic noradrenergic release in the hippocampus

Fiber photometry (FP) has become a tool of choice for in vivo monitoring of genetically encoded biosensors. The ability to record and optogenetically manipulate circuits through the same fiber stub is powerful, but limited, as biosensors typically do not sample membrane voltage, leaving the experimenter blind to the direct effects of opsin photoactivation. Here we developed the Photometry Device with Optogenetics and Electrophysiology (P-DOpE) probe, fabricated via a new convergence taper-break (CTB) method that integrates industry-standard silica optical waveguides with low-impedance metal electrodes that can be arranged in experimenter-defined configurations. We demonstrate that chronically implanted P-DOpE probes provide months-long recordings of local field potential, single unit recording, and fiber photometry, with parallel optogenetic circuit perturbation. Conducting fiber photometry with same-site optogenetic stimulation, we identified a robust fluorescence signal that scaled with network activity and survived biosensor antagonism. As this confound could not be eliminated with standard isosbestic controls, we propose a simple correction strategy. As a first application, we used the probe to test a proposed mechanism for focal modulation of noradrenergic signaling in and by cortical circuits receiving afferents from the locus coeruleus. We found that increasing spiking activity in CA1 amplifies noradrenergic signaling evoked by contextual arousal by [~]50%, but does not induce norepinephrine release in the absence of a phasic trigger - thus supporting the central prediction of the glutamate amplifies noradrenergic effects (GANE) hypothesis. The P-DOpE probe thus enables optogenetic manipulation and multimodal readout in a configurable low-cost, scalable, and robust format.

neuroscience↗

Pseudomonas simiae-induced resistance in barley is associated with compromised JA signaling and phyllosphere microbiome responses

Interactions of plant growth-promoting rhizobacteria with plant roots can trigger induced resistance (IR) protecting above-ground tissues from disease, a process that is increasingly recognized for its potential to support sustainable crop protection strategies. Although the molecular basis of IR has been extensively studied in Arabidopsis thaliana, considerably less is known about the underlying mechanisms in cereal crops. Here, we show that Pseudomonas simae WCS417r triggers IR in barley (Hordeum vulgare), reducing the propagation of Blumeria graminis f. sp. hordei, the causative agent of barley powdery mildew. Analysis of defense-associated marker genes revealed pathogen-dependent transcriptional responses during IR: HvPATHOGENESIS-RELATED1 (HvPR1) was induced by powdery mildew but not by the bacterial pathogen Xanthomonas translucens pathovar cerealis, whereas HvPR5 responded to both pathogens, with its induction by X. translucens depending on WCS417r-IR. To improve our molecular understanding of IR, transcriptomic responses to methyl jasmonate, salicylic acid and abscisic acid were characterized and used to identify hormone-responsive genes. Notably, several jasmonate-responsive genes were suppressed during powdery mildew infection, and this suppression was more pronounced in plants undergoing IR, indicative of priming. Finally, metabarcoding of the phyllosphere microbiome demonstrated that IR was not associated with major shifts in bacterial community composition. Alpha and beta diversity remained largely unchanged, while a limited number of amplicon sequence variants differed in abundance between treatments. Together, these results show that P. simiae WCS417r induces resistance against powdery mildew in barley through priming pathogen-dependent transcriptional changes while leaving the overall phyllosphere microbiome structure largely intact.

plant biology↗

The induction of systemic resistance to barley powdery mildew by rhizosphere bacterial communities does not disrupt the structure or function of native microbial communities

1.Synthetic microbial communities (SynComs) could help plants withstand biotic stress and reduce the need for pesticides. With this in mind, we created two SynComs, comprising bacterial strains isolated from the rhizospheres of barley and wheat. We then studied their potential to trigger induced systemic resistance against the barley pathogen Blumeria graminis f. sp. hordei (Bgh). To investigate the plant-microbial interactions from the perspective of both plants and microbes, we performed DAF staining to quantify Bgh propagation in plant leaves, analysed leaf transcriptomes and conducted rhizosp here 16S rRNA gene metabarcoding and rhizosphere metatranscriptome analysis. Our results demonstrate that the SynComs elicit defence responses in barley against Bgh in a manner similar to that of the positive control strain Pseudomonas simiae WCS417r. The SynComs act without triggering a strong gene response prior to inoculation with the plant pathogen or affecting plant-associated prokaryote communities; they only mildly influence bacterial gene expression in the rhizosphere. Instead, they act as priming agents, preparing the plant for further pathogen attack. These findings suggest that protective SynComs can be applied in the field without causing signficant disruption to native microbial communities.

microbiology↗

Nuclear mechanostability emerges from satellite DNA condensation into chromocenters

As the largest organelle, the nucleus endures significant mechanical stresses over the cellular lifespan, and mechanostability, i.e. the ability to resist deformation, is critical for genome integrity and function. Here, we reveal that nuclear mechanostability is an emergent property arising from the clustering of satellite DNA repeats into nuclear condensates known as chromocenters. Targeted chromocenter disruption in Drosophila testes subjected to natural and artificial mechanical stress compromises nuclear mechanostability, leading to deformed nuclei, DNA damage, and chromosome breaks. Conversely, enhancing chromocenter coalescence through genetic means improves mechanostability. Molecular dynamics simulations suggest that chromocenters enable physically linked chromosomes to respond collectively, rather than individually, to mechanical challenge, and dissipate external forces over a larger nuclear surface. We propose that the satellite DNA-dependent mechanostability framework described here likely extends to other cells and tissues facing mechanical stress, and offers an explanation for the evolutionary success of these non-coding repeats across eukaryotes.

cell biology↗

Ontogeny drives stage-specific effects of a Gata1 mutation

The biography of an organism, including, for instance, its genetic background and exposure to environmental influences, determines the penetrance and expressivity of monogenic diseases between individuals. This also applies at the single-cell level. Interestingly, mature blood and immune cells originate from anatomically and temporally distinct stem and progenitor populations at different stages of development. Here we show that the ontogeny or progenitor origin of megakaryocytes determines their developmental trajectory at the cellular and transcriptional level. As a result, a mutation in the key transcription factor Gata1 dysregulates megakaryopoiesis in an ontogeny-specific manner causing a stage-specific disorder. Particularly, only early extraembryonic hematopoietic progenitors drive blast-like cell development leading to a transient accumulation of megakaryocytes in the fetus but not in the adult. Therefore, pediatric blood disorders may differ functionally from adult diseases due to changing progenitor sources of mature blood and immune cells throughout development. HighlightsO_LIFetal and adult megakaryopoiesis pass through distinct immunophenotypic stages C_LIO_LIOntogeny of megakaryocytes dictates their unique transcriptional trajectory C_LIO_LIProgenitor origin rather than the differentiation pathway determines the effect of mutant Gata1 C_LIO_LIBlock in maturation at the progenitor level causes the accumulation of yolk sac-derived megakaryocytes in the presence of mutant Gata1 C_LIO_LIMutant Gata1 drives blast cell formation exclusively in yolk sac-derived lineages C_LI

developmental biology↗

ROR and RYK extracellular region structures suggest that receptor tyrosine kinases have distinct WNT-recognition modes

SUMMARYWNTs play key roles in development and disease, by binding both Frizzled (FZD) seven-pass transmembrane receptors and numerous co-receptors that include the ROR and RYK receptor tyrosine kinases (RTKs). We describe crystal structures and WNT-binding characteristics of extracellular regions from the Drosophila ROR and RYK orthologs Nrk (neurospecific receptor tyrosine kinase) and Derailed-2 (Drl-2). RORs bind WNTs though a FZD-related cysteine-rich domain (CRD), and RYKs through a WNT-inhibitory factor (WIF) domain. Our structures suggest that neither the Nrk CRD nor the Drl-2 WIF domain can accommodate the acyl chain typically attached to WNTs. The Nrk CRD contains a deeply buried bound fatty acid, unlikely to be exchangeable with a WNT acyl chain. The Drl-2 WIF domain lacks the lipid-binding site seen in WIF-1. We also show that DWnt-5, which regulates Drosophila ROR and RYK orthologs, lacks an acyl chain. Together with analysis of WNT/receptor interaction sites, these structures provide new insight into how WNTs recruit their RTK co-receptors into signaling complexes.

biochemistry↗

Interferons Reshape the 3D Conformation and Accessibility of Macrophage Chromatin

Engagement of macrophages in innate immune responses is directed and enhanced by type I and type II interferons. An essential component of IFN activity is the use of JAK-STAT signal transduction for the transcriptional control of interferon-stimulated genes (ISG). Here, we study the immediate early nuclear response to type I IFN and IFN-{gamma} in murine macrophages. Despite their distinct immunological activities, both IFN types triggered highly overlapping epigenomic and transcriptional changes. These changes included a rapid rearrangement of the 3D chromatin organization and an increase of DNA accessibility at ISG loci. ISGF3, the major transcriptional regulator of ISG, controlled homeostatic as well as induced-state DNA accessibility at a subset of ISG. Increases in DNA accessibility correlated with the appearance of activating histone marks at surrounding nucleosomes. Collectively our data emphasize changes in the three-dimensional nuclear space and epigenome as an important facet of transcriptional control by the IFN-induced JAK-STAT pathway.

immunology↗

Induced systemic resistance impacts the phyllosphere microbiome through plant-microbe-microbe interactions

Both above- and below-ground parts of plants are constantly confronted with microbes, which are main drivers for the development of plant-microbe interactions. Plant growth-promoting rhizobacteria enhance the immunity of above-ground tissues, which is known as induced systemic resistance (ISR). We show here that ISR also influences the leaf microbiome. We compared ISR triggered by the model strain Pseudomonas simiae WCS417r (WCS417) to that triggered by Bacillus thuringiensis israelensis (Bti) in Arabidopsis thaliana. In contrast to earlier findings, immunity elicited by both strains depended on salicylic acid. Both strains further relied on MYC2 for signal transduction in the plant, while WCS417-elicited ISR additionally depended on SAR-associated metabolites, including pipecolic acid. A metabarcoding approach applied to the leaf microbiome revealed a significant ISR-associated enrichment of amplicon sequence variants with predicted plant growth-promoting properties. WCS417 caused a particularly dramatic shift in the leaf microbiota with more than 50% of amplicon reads representing two bacterial species: WCS417 and Flavobacterium sp.. Co-inoculation experiments using WCS417 and At-LSPHERE Flavobacterium sp. Leaf82, suggest that the proliferation of these bacteria is influenced by both microbial and plant-derived factors. Together, our data connect systemic immunity with leaf microbiome dynamics and highlight the importance of plant- microbe-microbe interactions for plant health.

plant biology↗

A mathematical model-based approach to optimize loading schemes of isometric resistance training sessions

Individualized resistance training (RT) is necessary to optimize training results. A model-based optimization of loading schemes could provide valuable impulses for practitioners and complement the predominant manual program design by customizing the loading schemes to the trainee and the training goals. We compile a literature overview of model-based approaches used to simulate or optimize the response to single RT sessions or to longterm RT plans in terms of strength, power, muscle mass, or local muscular endurance by varying the loading scheme. To the best of our knowledge, contributions employing a predictive model to algorithmically optimize loading schemes for different training goals are nonexistent in the literature. Thus, we propose to set up optimal control problems as follows. For the underlying dynamics, we use a phenomenological model of the time course of maximum voluntary isometric contraction force. Then, we provide mathematical formulations of key performance indicators for loading schemes identified in sport science and use those as objective functionals or constraints. We then solve those optimal control problems using previously obtained parameter estimates for the elbow flexors. We discuss our choice of training goals, analyze the structure of the computed solutions, and give evidence of their real-life feasibility. The proposed optimization methodology is independent from the underlying model and can be transferred to more elaborate physiological models once suitable ones become available.

physiology↗

Neural signatures of performance feedback in the paced auditory serial addition task (PASAT): an ERP study

Due to its importance for successful human behavior, research into cognitive control functioning has gained increasing interest. The paced auditory serial addition task (PASAT) has been used to test and train this fundamental function. It is a challenging task, requiring a high cognitive load in a stressful and frustrating environment. Its underlying neural mechanisms, however, are still unclear. To explore the neural signatures of the PASAT and their link to ongoing cognitive processing, feedback locked event-related potentials were derived from healthy participants during an adaptive 2-back version of the PASAT. Larger neural activation after negative feedback was found for feedback related negativity (FRN), P300 and late positive potential (LPP). In early stages of feedback processing (FRN), a larger difference between positive and negative feedback responses was associated with poorer overall performance, whereas this association was inverted for the later stages (P300 and LPP). This indicates stage-dependent associations of neural activation after negative information and cognitive functioning. Conceivably, increased early responses to negative feedback signify distraction whereas higher activity at later stages reflect cognitive control processes to preserve ongoing performance.

neuroscience↗

Need for high-resolution Genetic Analysis in iPSC: Results and Lessons from the ForIPS Consortium

Genetic integrity of induced pluripotent stem cells (iPSCs) is essential for their validity as disease models and for potential therapeutic use. We describe the comprehensive analysis in the ForIPS consortium: an iPSC collection from donors with neurological diseases and healthy controls. Characterization included pluripotency confirmation, fingerprinting, conventional and molecular karyotyping in all lines. In the majority, somatic copy number variants (CNVs) were identified. A subset with available matched donor DNA was selected for comparative exome sequencing. We identified single nucleotide variants (SNVs) at different allelic frequencies in each clone with high variability in mutational load. Low frequencies of variants in parental fibroblasts highlight the importance of germline samples. Somatic variant number was independent from reprogramming, cell type and passage. Comparison with disease genes and prediction scores suggest biological relevance for some variants. We show that high-throughput sequencing has value beyond SNV detection and the requirement to individually evaluate each clone.

genomics↗