Search bioRxiv⌕ Search

Biology subjects

Cohen, Y.

Publications and source records attributed to Cohen, Y..

At least 19 recordsLinked to original sources

Taxon-in-context reveals ecological individuality in the human gut microbiome

Ecological theory holds that a microbe's role depends on its surrounding community. Yet abundance profiles and fixed ecological groupings leave its individual context implicit. We introduce taxon-in-context, a reproducible representation of each microbe's context within an individual's microbiome. Across 7,700 metagenomes, we show that common gut species occupy different contexts in different people. This flexibility peaked in early life and declined through adulthood, a pattern reproduced in a larger genus-level compendium. For selected species, context within each person's microbiome revealed age associations beyond species abundance and the person's context mixture. In an independent longitudinal urinary tract infection cohort, microbes switched contexts within individuals. Taxon-in-context enabled recurrence prediction where an abundance-based model performed near chance. Taxon-in-context and these findings expose a measurable, dynamic and individualized layer of microbiome organization, providing a basis for investigating why the same microbe or intervention may have different biological consequences across people.

systems biology↗

The enigmatic bone reduction pattern of thalidomide embryopathy is set by sequential exit from the sensitive window

Thalidomide reduces the limb bones in a puzzling order, starting with the thumb, the radius and the humerus and then returning to the ulna and the ulnar digits. To understand that order we analysed 435 thalidomide-affected limbs from the published record (1962-2025), of which 269 were upper limbs - 142 human and 127 non-human primate. Reconstructed by forward-chain assembly the reduction order runs: Digit 1 [->] Radius [->] Humerus [->] Digit 2 [->] Ulna [->] Digit 3 [->] Digit 4 [->] Digit 5. The co-reductions resolved into two rules. Within a segment (autopod, zeugopod), no bone is reduced before every bone anterior to it. Among the most posterior bones of the three segments (digit 5, ulna, humerus): no bone is reduced before every bone proximal to it. Behind these antero-posterior (A-P) and proximo-distal (P-D) reduction rules stands a maturation wave advancing postero-anteriorly and disto-proximally. In developmental terms the bone precursors exit their sensitive windows after the autopod is built, in a biaxial order: from digit 5 towards digit 1, from the ulna to radius, and across segments from the autopod towards the stylopod (Digit 5 [->] Digit 4 [->] Digit 3 [->] Ulna [->] Digit 2 [->] Humerus [->] Radius [->] Digit 1). A co-reduction is therefore a snapshot of the prospective bones still sharing a sensitive window before their sequential biaxial maturation: exposure during elongation truncates the limb proximal to the progress zone, while later exposure reduces only the bones still immature at the time of exposure.

developmental biology↗

Genome sequencing reveals novel pathogenic deep-intronic PCDH15 variants, amenable to antisense oligonucleotide-based splice correction

Despite substantial advances in diagnostic testing, 10-15% of Usher syndrome patients remain without a genetic diagnosis, having significant implications for genetic counseling and potential future therapeutic interventions. In this study, genome sequencing data from probands clinically presenting with Usher syndrome were analyzed. Two novel deep-intronic variants were identified in PCDH15, c.3983+3635A>G and c.3123-1728A>G, in two independent patients. Both deep-intronic variants were classified as likely pathogenic and predicted to alter PCDH15 pre-mRNA splicing. Using a minigene splice assay and iPSC-derived photoreceptor precursor cells from patients, we confirmed that both variants lead to the inclusion of a pseudoexon in the PCDH15 transcript introducing a stop codon and subsequent premature termination of protein translation. We designed and evaluated antisense oligonucleotides (ASOs) with the purpose of redirecting aberrant pre-mRNA splicing caused by both deep-intronic variants. For both variants, designed ASOs were successful in restoring normal splicing patterns, highlighting their potential as a future therapeutic intervention strategy to halt the progression of retinitis pigmentosa caused by these novel variants. Overall, these findings contribute to the understanding of Usher syndrome caused by deep-intronic pathogenic variants in PCDH15 and describe for the first time the use of an ASO-mediated splice correction strategy for individuals diagnosed with these variants.

genetics↗

Different Sources of Expectations Differentially Modulate Communication Between Auditory and Prefrontal Cortices During Auditory Decision-Making

Perceptual decisions can be influenced by expectations that arise from different sources. However, relatively little is known about how and where in the brain these different sources affect decision formation, particularly in the auditory system. To begin to address this question, we recorded local field potentials (LFPs) simultaneously from the auditory cortex (AC) and ventrolateral prefrontal cortex (vlPFC) while monkeys performed an auditory frequency-discrimination task. We manipulated their expectations by presenting either informative cues (LEDs that predicted the target frequency) or uninformative cues (tone sequences that did not predict the target frequency) prior to target onset. Both cues had similar effects on the monkeys accuracy and response times but induced distinct neurophysiological signatures. Coherence, a measure of undirected coupling, between AC and vlPFC increased from cue to target presentation on informative trials but decreased from cue to target presentation on uninformative trials. Phase-slope index (PSI), a measure of directed coupling, between AC and vlPFC was strongest when the target tone contradicted expectations, particularly for ambiguous stimulus conditions when expectations were most valuable. These expectation-dependent changes in the magnitude of functional connectivity also included changes in its spatial organization. Together, these findings provide new insights into how different expectations can dynamically reconfigure functional connectivity between cortical brain areas to support different task demands and behavioral outcomes.

neuroscience↗

Neural Responses to Unexpected Stimulus Repetitions and Omissions in Auditory Cortex Provide Mixed Evidence for Predictive Coding

Humans and other animals process sensory uncertainty by integrating stimulus information with prior knowledge and expectations. Predictive coding conceptualizes perception as a form of Bayesian inference wherein hierarchical brain circuits update internal models to reconcile bottom-up sensory input with top-down predictions. Whereas predictive coding is a leading theory, the extent to which it is implemented in primary sensory cortices remains a matter of debate. To further investigate this issue, we examined single-neuron spiking activity in macaque primary auditory cortex (A1) to expected versus unexpected stimulus repetitions and to expected versus unexpected omissions. On average, we found that A1 neurons did not show enhanced responses to unexpected stimulus repetitions, contrary to predictive-coding theory. However, they did show enhanced responses to unexpected stimulus omissions. Taken together, these mixed results place empirical restraints on how PC is implemented in A1. Significance StatementPerception depends on the brains ability to infer the causes of sensory inputs by integrating new information with prior knowledge under uncertainty. Our results reveal nuanced evidence for predictive coding within the primary auditory cortex (A1). Specifically, spiking activity during unexpected stimuli and unexpected stimulus omissions provide conflicting and supporting, respectively, data for this Bayesian framework. These findings refine our understanding of neural mechanisms underlying perception and provide empirical constraints on the neurobiological implementation of predictive processing.

neuroscience↗

Development of a differential panel to identify Peronospora belbahrii races in sweet basil (Ocimum basilicum)

First reported in the United States in 2007, downy mildew of sweet basil (Ocimum basilicum), caused by the oomycete pathogen Peronospora belbahrii, has become a major challenge in global basil production. Downy mildew-resistant cultivars have been developed and commercially available since 2018, but observations of isolates overcoming resistance were reported after each new introduction. The rapid development of pathogens overcoming genetic resistance suggests the evolution of new races under selective pressure. In this study, we report on the development of a differential panel of distinct basil cultivars with varying and differential sources of genetic resistance tested against P. belbahrii strains obtained from geographically diverse multi-year collections from basil-producing locations in the US, Israel, and Italy. Screening multiple P. belbahrii isolates revealed three distinct virulence profiles that distinguished race 0, race 1, and race 2. Races 1 and 2 were defined by virulence in cultivars with single gene resistance loci Pb1 and Pb2, respectively. Evaluation of cultivars with quantitative resistance revealed more variation in susceptibility or partial resistance, suggesting "broad spectrum" (or race-nonspecific) resistance. With continued isolate collection and screening efforts, the denomination of P. belbahrii races may be further expanded, and newly developed resistant cultivars can be added to the proposed panel to definitively evaluate novel P. belbahrii strains. This study lays the groundwork to further explore dynamics of race evolution and mechanisms of resistance breakdown, which will be essential for discovering new sources of resistance for controlling basil downy mildew.

plant biology↗

Extracellular Vesicles Mediate Glucose Regulation by GLUT4-Overexpressing Engineered Muscle Tissue in T2D Mice

1Type 2 diabetes (T2D) is characterized by impaired glucose uptake in skeletal muscle and adipose tissues, which contributes to systemic hyperglycemia. GLUT4 is a crucial component in insulin-stimulated glucose uptake and its expression as well as translocation are impaired in T2D onset. This study explored the role of extracellular vesicles (EVs) derived from GLUT4-overexpressing engineered muscle constructs (G4OE-EMC) in glucose metabolism. G4OE-EMC-derived EVs enhanced glucose uptake and insulin sensitivity both in vitro, when tested on wild-type (WT) engineered muscle constructs, and in vivo using the diet-induced obesity (DIO) mouse model. Proteomic and transcriptomic analyses revealed that the EVs were enriched in IGF1 and contained reduced levels of miRNAs, such as miR-122-5p, miR-16-5p, and miR-486-5p, which target IGF1R. The multi-omic approach used here suggests a mechanism whereby G4OE-EMC-derived EVs enhance glucose metabolism via IGF1 signaling and miRNA-mediated regulation of IGF1R expression, offering a potential therapeutic strategy for T2D.

bioengineering↗

Measurements and simulations of transmembrane water exchange by diffusion NMR methods: From yeast cells to optic nerve ex vivo

Non-invasive measurement of exchange is paramount in different fields, ranging from material to biological sciences. Unaccounted exchange may even blur micro-structural or other characteristics of multi compartmental systems studied by MR methods. Despite the growing interest in diffusion-exchange studies of complex systems, comparative studies remain scarce. Most existing investigations have applied different diffusion MR methods to different biological samples under varying experimental conditions, making direct comparisons difficult. Moreover, the lack of a gold standard for exchange rate measurements further complicates efforts to validate and interpret results. To address these challenges, we employed two diffusion NMR-based methods--the constant-gradient pulsed field gradient (CG-PFG) and the recently introduced filter-exchange NMR spectroscopy (FEXSY)--to investigate apparent water exchange in yeast cells and optic nerves, both before and after fixation. We first evaluated the effect of the q-values on the extracted indices and then evaluated the repeatability and reproducibility of the measurements. The CG-PFG and FEXSY experiments were collected on the same sample to allow comparison of the results. The intracellular mean residence times (MRTs) ({tau}i) extracted from the log-linear fit of the CG-PFG NMR experiments were found to be 554 {+/-} 6 ms and 337 {+/-} 10 ms for yeast cells before and after fixation, respectively. The respective{tau} i values extracted from the FEXSY experiments before and after fixation were found to be 368 {+/-} 14 ms and 146 {+/-} 24 ms, respectively. Despite the difference in absolute values of MRTs, the same qualitative behavior is observed in the two methodologies, and both could be analyzed using the bi-compartmental Karger model. The same methodologies were then used to study exchange in the more complex porcine optic nerves. There, the bi-compartmental Karger model analysis is shown to be inadequate. Extensive Monte Carlo simulations are used to narrow down on the most possible explanation, suggesting that optic nerves are multi-compartmental systems where not all spins are free to undergo exchange. Supporting theoretical calculations point to the existence of at least one additional non-exchanging restricted compartment. Thus, a tri-compartmental model is derived and used to analyze the data. The new model fits the data significantly better and results in dramatically different exchange rates when used on white matter (WM) data: CG-PFG experiments were found to be 730 {+/-} 40 ms and 803 {+/-} 16 ms for optic nerves before and after fixation, respectively. The respective{tau} i values extracted from the FEXSY experiments before and after fixation were found to be 530 {+/-} 125 ms and 387 {+/-} 104 ms, respectively. These values are considerably lower than the values previously reported. Finally, we use simulations to show that the quantitative discrepancy between CG-PFG and FEXSY can be attributed, at least partially, to the difference in T2 values between the intra- and extracellular compartments. We thus encourage the pairing of exchange and spin-spin relaxation measurements in future studies. We end with a discussion on the current state of the diffusion-exchange, and in an attempt to put a spotlight on essential corner stones that are still missing despite the great advance of recent years: experimental standardization, method comparison, and adequate modeling.

neuroscience↗

Distinct cortical populations drive multisensory modulation of segregated auditory sources

Auditory perception can be modulated by other sensory stimuli. However, we do not fully understand the neural mechanisms that support multisensory behavior. Here, we recorded spiking activity from the primary auditory cortex (A1) in non-human primates, while they detected a target vocalization that was embedded in a background chorus of vocalizations. We found that a congruent video of a monkey eliciting a vocalization improved the monkeys behavior, relative to their performance when we only presented a static image of the monkey. As a proxy for the functional organization of A1, we compared the contribution of neurons with significant spectrotemporal response fields (STRFs) with those that had non-significant STRFs (nSTRFs). Based on spike-waveform shape and functional connectivity, STRF and nSTRF neurons appeared to belong to distinct neural populations. Consistent with this, we found that although STRF neurons encoded stimulus information through synchronized activity, the population of nSTRF neurons encoded task-related information in the primate A1 more as a structured dynamic process. Together, these findings demonstrate a functional distinction between the behavioral contributions of nSTRF and STRF neurons.

neuroscience↗

Canary Mating Season Songs Move Between Order and Disorder

Many complex behaviors involve sequences of basic motor or vocal elements governed by syntactic rules, which facilitate flexible and adaptive actions. Songbirds that crystallize their repertoire of vocal syllables and transitions allow researchers to build probabilistic models of syntax rules, providing insight into underlying neural mechanisms. However, in many complex behaviors, syntax rules change over time, such as during learning or in response to new environmental and social contexts. In this study, we investigated the songs of canaries, a seasonal songbird species. Canaries learn a repertoire of 30-50 syllable types, produce syllables in repeat phrases, and organize these phrases into sequences with long-range syntactic dependencies. Since canaries are known to adapt their repertoire annually, we recorded their songs during the spring mating season and examined the syntactic properties that determine syllable sequencing. Over days and weeks, we observed changes in syllable usage rates, syllable numbers within phrases, phrase positions in songs, and in the long-range dependencies of phrase transitions. Acoustic features of syllables were also found to shift alongside these syntactic changes. Quantifying the variability of these properties revealed that the observed changes were not random. Most birds exhibited a clear trend of moving between order and disorder in their songs syntactic and acoustic features. Interestingly, this trend varied across individuals; some birds increased their stereotypy and decreased variability across days, while others adopted more disordered and variable song structures. These findings establish canaries as a valuable animal model for studying the neural mechanisms underlying syntax rules in complex motor sequences, their plasticity in social and environmental adaptation, and in implementing individual-specific strategies.

neuroscience↗

Automated, Stress-Free, and Precise Measurement of Songbird Weight in Neuroscience Experiments

Monitoring the health and well-being of research animals is essential for both ethical and scientific purposes. In songbirds, body weight is one of the main indicators for their overall condition, yet traditional weighing methods can be intrusive and stress-inducing, which could decrease their song rate. We developed a novel, automated system designed to continuously monitor the weight of untethered and tethered birds without disrupting their natural behavior in neuroscience experiments. We used the system to track weight fluctuations in six canaries over several weeks, revealing physiological patterns such as overnight weight loss, with one bird losing approximately 5.17% of its body weight during a 9.5-hour period of inactivity. Our systems high sensitivity detected weight changes below 1% of body mass, validating its reliability for long-term studies. Control experiments confirmed that weight fluctuations observed were physiological rather than due to equipment deviations. By eliminating the need for manual handling, this system offers a non-invasive, hands-free approach that reduces stress and improves the accuracy of health assessments. This study demonstrates the systems potential for expanding research on how environmental factors, diet, and other variables influence bird physiology and behavior. Future applications could integrate additional health metrics, providing a more comprehensive understanding of animal welfare in neuroscience and behavioral studies.

neuroscience↗

A spiking neural network model for proprioception of limb kinematics in insect locomotion

Proprioception plays a key role in all behaviours that involve the control of force, posture or movement. Computationally, many proprioceptive afferents share three common features: First, their strictly local encoding of stimulus magnitudes leads to range fractionation in sensory arrays. As a result, encoding of large joint angle ranges requires integration of convergent afferent information by first-order interneurons. Second, their phasic-tonic response properties lead to fractional encoding of the fundamental sensory magnitude and its derivatives (e.g., joint angle and angular velocity). Third, the distribution of disjunct sensory arrays across the body accounts for distributed encoding of complex movements, e.g., at multiple joints or by multiple limbs. The present study models the distributed encoding of limb kinematics, proposing a multi-layer spiking neural network for distributed computation of whole-body posture and movement. Spiking neuron models are biologically plausible because they link the sub-threshold state of neurons to the timing of spike events. The encoding properties of each network layer are evaluated with experimental data on whole-body kinematics of unrestrained walking and climbing stick insects, comprising concurrent joint angle time courses of 6 x 3 leg joints. The first part of the study models strictly local, phasic-tonic encoding of joint angle by proprioceptive hair field afferents by use of Adaptive Exponential Integrate-and-Fire neurons. Convergent afferent information is then integrated by two types of first-order interneurons, modelled as Leaky Integrate-and-Fire neurons, tuned to encode either joint position or velocity across the entire working range with high accuracy. As in known velocity-encoding antennal mechanosensory interneurons, spike rate increases linearly with angular velocity. Building on distributed position/velocity encoding, the second part of the study introduces second- and third-order interneurons. We demonstrate that simple combinations of two or three position/velocity inputs from disjunct arrays can encode high-order movement information about step cycle phases and converge to encode overall body posture. Author summaryWhen stick insects climb through a bramble bush at night, they successfully navigate through highly complex terrain with little more sensory information than touch and proprioception of their own body posture and movement. To achieve this, their central nervous system needs to monitor the position and motion of all limbs, and infer information about whole-body movement from integration in a multi-layer neural network. Although the encoding properties of some proprioceptive inputs to this network are known, the integration and processing of distributed proprioceptive information is poorly understood. Here, we use a computational model of a spiking neural network to simulate peripheral encoding of 6 x 3 joint angles and angular velocities. The second part of the study explores how higher-order information can be integrated across multiple joints and limbs. For evaluation, we use experimental data from unrestrained walking and climbing stick insects. Spiking neurons model the key response properties known from their real biological counterparts. In particular, we show that the first integration layer of the model is able to encode joint angle and velocity both linearly and accurately from an array of phasic-tonic input elements. The model is simple, accurate and based, where possible, on biological evidence.

neuroscience↗

Individual-specific strategies inform category learning

Categorization is an essential task for sensory perception. Individuals learn category labels using a variety of strategies to ensure that sensory signals, such as sounds or images, can be assigned to proper categories. Categories are often learned on the basis of extreme examples, and the boundary between categories can differ among individuals. The trajectories for learning also differ among individuals, as different individuals rely on different strategies, such as repeating or alternating choices. However, little is understood about the relationship between individual learning trajectories and learned categorization. To study this relationship, we trained mice to categorize auditory stimuli into two categories using a two-alternative forced choice task. Because the mice took several weeks to learn the task, we were able to quantify the time course of individual strategies and how they relate to how mice categorize stimuli around the categorization boundary. Different mice exhibited different trajectories while learning the task. Mice displayed preferences for a specific category, manifested by a choice bias in their responses, but this bias drifted with learning. We found that this drift in choice bias correlated with variability in the category boundary for sounds with ambiguous category membership. Next, we asked how stimulus-independent, individual-specific strategies informed learning. We found that the tendency to repeat choices, which is a form of perseveration, contributed to long-term learning. These results indicate that long-term trends in individual strategies during category learning affect learned category boundaries.

neuroscience↗

predicTTE: An accessible and optimal tool for time-to-event prediction in neurological diseases

Time-to-event prediction is a key task for biological discovery, experimental medicine, and clinical care. This is particularly true for neurological diseases where development of reliable biomarkers is often limited by difficulty visualising and sampling relevant cell and molecular pathobiology. To date, much work has relied on Cox regression because of ease-of-use, despite evidence that this model includes incorrect assumptions. We have implemented a set of deep learning and spline models for time-to-event modelling within a fully customizable app and accompanying online portal, both of which can be used for any time-to-event analysis in any disease by a non-expert user. Our online portal includes capacity for end-users including patients, Neurology clinicians, and researchers, to access and perform predictions using a trained model, and to contribute new data for model improvement, all within a data-secure environment. We demonstrate a pipeline for use of our app with three use-cases including imputation of missing data, hyperparameter tuning, model training and independent validation. We show that predictions are optimal for use in downstream applications such as genetic discovery, biomarker interpretation, and personalised choice of medication. We demonstrate the efficiency of an ensemble configuration, including focused training of a deep learning model. We have optimised a pipeline for imputation of missing data in combination with time-to-event prediction models. Overall, we provide a powerful and accessible tool to develop, access and share time-to-event prediction models; all software and tutorials are available at www.predictte.org.

neuroscience↗

Organellomics: AI-driven deep organellar phenotyping of human neurons

Systematic assessment of organelle architectures, termed the organellome, offers valuable insights into cellular states and pathomechanisms, but remains largely uncharted. Here, we present a deep phenotypic learning based on vision transformers, resulting in the Neuronal Organellomics Vision Atlas (NOVA) model that studies confocal images of more than 30 markers of distinct membrane-bound and membraneless organelles in 11.5 million images of human neurons. Organellomics analysis quantifies perturbation-induced changes in organelle localization and morphology using a rigorous mixed-effects meta-analytic framework that accounts for sampling variance and experimental heterogeneity. Applying this approach, we delineate phenotypic alterations in neurons carrying ALS-associated mutations and uncover a physical and functional crosstalk between cytoplasmic mislocalized TDP-43, a hallmark of ALS, and processing bodies (P-bodies), membraneless organelles regulating mRNA stability. These findings are validated in patient-derived neurons and human neuropathology. NOVA establishes a scalable framework for quantitative mapping of subcellular phenotypes and provides a new avenue for investigating the neurocellular basis of disease.

systems biology↗

Compensatory adaptation does not fully alleviate the costs associated with rifampicin resistance and occurs predominantly through off-target mutations

The manner in which costs associated with antibiotic resistance mutations are alleviated through the acquisition of compensatory mutations has bearing on the dynamics of resistance accumulation and spread as well as on our more general understanding of the persistence of adaptive genotypes. Here, we combine evolutionary experiments, fitness analyses, and whole genome sequencing to examine the way compensation to alleviate costs associated with rifampicin resistance is achieved, both when resistance is fixed and when initial majorities of resistant cells are grown alongside susceptible cells. We found compensatory mutations to occur across all examined populations. However, compensation never fully alleviates the initial costs of resistance. In contrast to prevalent assumptions, compensatory mutations mostly occurred outside of the RNA polymerase core enzyme, which serves as the target of rifampicin. The target size for compensatory mutations appears to be high, as great variation exists in compensatory mutations, even within a single population. At the same time, the pathways of compensation are quite convergent, meaning that, across independent populations, we often observe compensatory mutations in the same loci and sometimes even observe the precise same compensatory mutations across populations.

evolutionary biology↗

The interplay of uncertainty, relevance and learning influences auditory categorization

Auditory perception requires categorizing sound sequences, such as speech or music, into classes, such as syllables or notes. Auditory categorization depends not only on the acoustic waveform, but also on variability and uncertainty in how the listener perceives the sound - including sensory and stimulus uncertainty, the listeners estimated relevance of the particular sound to the task, and their ability to learn the past statistics of the acoustic environment. Whereas these factors have been studied in isolation, whether and how these factors interact to shape categorization remains unknown. Here, we measured human participants performance on a multi-tone categorization task and modeled each participants behavior using a Bayesian framework. Task-relevant tones contributed more to category choice than task-irrelevant tones, confirming that participants combined information about sensory features with task relevance. Conversely, participants poor estimates of task-relevant tones or high-sensory uncertainty adversely impacted category choice. Learning the statistics of sound category over both short and long timescales also affected decisions, biasing the decisions toward the overrepresented category. The magnitude of this effect correlated inversely with participants relevance estimates. Our results demonstrate that individual participants idiosyncratically weigh sensory uncertainty, task relevance, and statistics over both short and long timescales, providing a novel understanding of and a computational framework for how sensory decisions are made under several simultaneous behavioral demands.

neuroscience↗

Early detection of late blight in potato by whole-plant redox imaging

Late blight caused by the oomycete Phytophthora infestans is a most devastating disease of potatoes (Solanum tuberosum). Its early detection is crucial for suppressing disease spread. Necrotic lesions are normally seen in leaves at 4 dpi (days post inoculation) when colonized cells are dead, but early detection of the initial biotrophic growth stage, when the pathogen feeds on living cells, is challenging. Here, the biotrophic growth phase of P. infestans was detected by whole-plant redox imaging of potato plants expressing chloroplast-targeted reduction-oxidation sensitive green fluorescent protein (chl-roGFP2). Clear spots on potato leaves with a lower chl-roGFP2 oxidation state were detected as early as 2 dpi, before any visual symptoms were recorded. These spots were particularly evident during light-to-dark transitions and reflected mislocalization of chl-roGFP2 outside the chloroplasts, demonstrating perturbation of the chloroplast import system by the pathogen. Image analysis based on machine learning enabled systematic identification and quantification of spots and unbiased classification of infected and uninfected leaves in inoculated plants. Comparing redox to chlorophyll fluorescence imaging showed that infected leaf areas which exhibit mislocalized chl-roGFP2 also showed reduced non-photochemical quenching (NPQ) and enhanced quantum PSII yield ({Phi}PSII) compared to the surrounding leaf areas. The data suggest that mislocalization of chloroplast-targeted proteins is an efficient marker of late blight infection and demonstrate how it can be utilized for nondestructive monitoring of the disease biotrophic stage using whole-plant redox imaging.

plant biology↗