Biology subjects

Eckhardt, J.

Publications and source records attributed to Eckhardt, J..

6 recordsLinked to original sources

bioRxiv2026

Joint experience-dependent representations of odors and temporal context in the zebrafish homolog of piriform cortex

Intelligent behavior requires experience-dependent internal representations of relevant information. We examined representational learning in telencephalic area pDp of adult zebrafish, the homolog of piriform cortex. Activity was measured by multiphoton imaging through a prism in head-fixed fish trained in an odor discrimination task. Population dynamics could be decomposed into independent modes, each consisting of distributed activity across mixed-selectivity neurons, that encoded odor identity, novelty, and the progression of time. Training sharpened novelty detection, strengthened odor-specific response components, and geometrically untangled representational manifolds. Experience-driven plasticity generalized across chemically related stimuli. Main observations could be reproduced phenomenologically by a model assuming linear interactions between novelty-, identity- and time-encoding activity modes. We conclude that pDp jointly represents olfactory and temporal information relevant for episodic memory. Experience enhances the accessibility and generalization of information, indicating that pDp supports brain-wide learning by geometrically organizing olfactory and time-related information on neural manifolds.

neuroscience↗

bioRxiv2026

Dynamic cognitive representations in the dorsal pallium of adult zebrafish

Brains rely on internal models of the world to interpret sensory input and to simulate the future. In the mammalian hippocampal-entorhinal network, environments are represented by cognitive maps that contain spatially selective neurons such as place, grid, head direction and object-vector cells1-6. Neurons with allocentric spatial tuning have recently been discovered also in non-mammalian organisms including larval zebrafish7 but it remains unclear to what extent these neurons establish internal cognitive representations. We measured neuronal activity in telencephalic area Dc of head-fixed adult zebrafish exploring a novel, richly structured virtual reality. Neurons were sharply tuned to one or multiple locations and collectively represented environmental space. Activity fields exhibited neuron-specific associations to visual landmarks, indicating a prominent vectorial component in spatial representations. Population activity evolved and became increasingly informative as fish explored the environment. When landmarks were removed after familiarization, landmark-associated activity partially persisted and subsets of neurons reported prediction errors, implying that activity was in part driven by an internal representation. Strong functional coupling among neuronal ensembles and winner-take-all dynamics suggest that representations evolve by refinements of pre-structured networks. The teleost brain therefore generates internal models of structured environments that are optimized by experience and enable cognitive inference and prediction.

neuroscience↗

bioRxiv2024

Robotic Imaging and Machine Learning Analysis of Seed Germination: Dissecting the Influence of ABA and DOG1 on Germination Uniformity

Seed germination research has evolved over the years, increasingly incorporating technology. Recent advances in phenotyping platforms have increased the accessibility of high throughput phenotyping technologies to more labs, leading to valuable insights into germination biology. These platforms benefit researchers by limiting manual labor and increasing the temporal resolution of imaging. Each of the platforms developed presents unique benefits and challenges, from scalability to price to computing resources. Performing experiments involving thousands of seeds remains a daunting task due to the limitations of current phenotyping platforms and image analysis pipelines. To overcome these challenges, we introduce SPENCER (Seed Phenotype Evaluation and Germination Curve Estimation Robot), a high-throughput phenotyping platform. SPENCER accommodates 32 rectangular petri plates, capable of assessing up to 8000 Arabidopsis seeds per experiment. Our design allows for high quality images while maintaining optimal humidity, crucial for precise germination assessment over longer experiments. The image analysis workflow incorporates advanced image analysis using semantic segmentation models trained for Arabidopsis and lettuce, providing researchers with accessible, reproducible, and efficient tools. We applied SPENCER to investigate the relative roles of DELAY OF GERMINATION 1 (DOG1) and abscisic acid (ABA) in Arabidopsis dormancy. DOG1 mutants exhibited rapid germination, whereas ANT application had a greater impact on the slower-germinating Ler ecotype. Our findings suggest that DOG1 plays a significant role in dormancy, particularly in non-dormant accessions, while ABAs influence is more pronounced under stress conditions. Additionally, we explored germination uniformity, another agriculurally relevant trait, observing parallels with germination timing. SPENCER offers a powerful and accessible tool for dissecting complex biological traits in conjunction with chemical and genetic manipulations. Its scalability and versatility make it suitable for large-scale genetic and chemical germination screens.

plant biology↗

bioRxiv2024

The ABA Receptor Antagonist Antabactin Restores Germination of Thermoinhibited Lettuce

Germination is critical to agricultural productivity because low germination rates and/or asynchronous germination negatively affect stand establishment and subsequent yields. Exposure to high temperatures during seed imbibition can decrease both germination synchrony and rates through an ABA-mediated process called thermoinhibition. Methods to reduce thermoinhibition would be agriculturally valuable, particularly with increasing global mean temperatures. Lettuce seed germination is particularly sensitive to high temperatures and is a classic system for studying thermoinhibition. Extensive evidence using mutants and carotenoid biosynthetic inhibitors (e.g. fluridone) has demonstrated that endogenous abscisic acid (ABA) biosynthesis is required for thermoinhibition in lettuce and Arabidopsis. In principle, ABA biosynthetic inhibitors could be used to block thermoinhibition, but carotenoid biosynthetic inhibitors are not well-suited for this application due to their herbicidal effects and current hydroxamate ABA biosynthetic inhibitors lack potency. Here we explore the potential of ABA receptor antagonism to disrupt thermoinhibition using Antabactin (ANT), a broad spectrum high-affinity receptor antagonist. We show low {micro}M ANT treatments (10{micro}M) during seed imbibition reduce thermoinhibition at temperatures of up to 40{degrees}C, demonstrating that ABA signaling is required for thermoinhibition. We further explored interactions between ANT and seed priming, which is used commercially to improve seed germination and reduce thermoinhibition and is achieved by partial hydration and subsequent desiccation of seeds. We show that primed lettuce seeds have improved germination rates at high temperatures, consistent with previous observations; moreover, seeds primed in the presence of ANT show further increases in germination at elevated temperatures, showing that the two treatments can be combined to improve lettuce seed germination. Our data demonstrate that ABA antagonists are candidate agrochemicals for mitigating the effects of high temperature on seed germination and stand establishment that may be of increasing importance due to climate change.

plant biology↗

bioRxiv2022

Quantitative proteomic analysis of skeletal muscles from wild type and transgenic mice carrying recessive Ryr1 mutations linked to congenital myopathies

Skeletal muscle is a highly structured and differentiated tissue responsible for voluntary movement and metabolic regulation. Muscles however, are heterogeneous and depending on their location, speed of contraction, fatiguability and function, can be broadly subdivided into fast and slow twitch as well as subspecialized muscles, with each group expressing common as well as specific proteins. Congenital myopathies are a group of non-inflammatory non-dystrophic muscle diseases caused by mutations in a number of genes, leading to a weak muscle phenotype. In most cases specific muscles types are affected, with preferential involvement of fast twitch muscles as well as extraocular and facial muscles. Here we performed relative and absolute quantitative proteomic analysis of EDL, soleus and extraocular muscles from wild type and transgenic mice carrying compound heterozygous mutations in Ryr1 identified in a patient with a severe congenital myopathy. Our quantitative proteomic study shows that recessive Ryr1 mutations not only decrease the content of RyR1 protein in muscle, but also impact the content of many other proteins; in addition, we provide important insight into the pathological mechanism of congenital myopathies linked to mutations in other genes encoding components of the excitation contraction coupling molecular complex.

physiology↗

bioRxiv2022

High-throughput Identification of Novel Heat Tolerance Genes via Genome-wide Pooled Mutant Screens in the Model Green Alga Chlamydomonas reinhardtii

Different high temperatures adversely affect crop and algal yields with various responses in photosynthetic cells. The list of genes required for thermotolerance remains elusive. Additionally, it is unclear how carbon source availability affects heat responses in plants and algae. We utilized the insertional, indexed, genome-saturating mutant library of the unicellular, eukaryotic green alga Chlamydomonas reinhardtii to perform genome-wide, quantitative, pooled screens under moderate (35{degrees}C) or acute (40{degrees}C) high temperatures with or without organic carbon sources. We identified heat-sensitive mutants based on quantitative growth rates and identified putative heat tolerance genes (HTGs). By triangulating HTGs with heat-induced transcripts or proteins in wildtype cultures and MapMan functional annotations, we present a high/medium-confidence list of 933 Chlamydomonas genes with putative roles in heat tolerance. Triangulated HTGs include those with known thermotolerance roles and novel genes with little or no functional annotation. About 50% of these high-confidence HTGs in Chlamydomonas have orthologs in green lineage organisms, including crop species. Arabidopsis thaliana mutants deficient in the ortholog of a high-confidence Chlamydomonas HTG were also heat sensitive. This work expands our knowledge of heat responses in photosynthetic cells and provides engineering targets to improve thermotolerance in algae and crops.

plant biology↗