Biology subjects

Levi, A.

Publications and source records attributed to Levi, A..

12 recordsLinked to original sources

bioRxiv2025

Population-level super-pangenome reveals genome evolution and empowers precision breeding in watermelon

Pangenomes are increasingly critical for harnessing crop genetic diversity, yet their resolution and utility are often limited by insufficient sampling of high-quality genome assemblies. Here, we report a population-level watermelon super-pangenome constructed from 138 reference-grade assemblies, including 135 newly generated near-gapless genomes representing all seven watermelon species. The super-pangenome captures approximately one million structural variants (SVs), enabling accurate variant genotyping across ~900 watermelon accessions and substantially expanding variant discovery both across and within species. Broader sampling within the pangenome provides insights into genome evolution among watermelon species and sheds light on the origin of cultivated watermelon. SV-inclusive genome-wide association studies enhance trait mapping resolution and identify a copy number variation upstream of ClFCI1 that regulates flesh color intensity in a dosage-dependent manner. Leveraging this comprehensive variation map, we developed high-accuracy genomic prediction models for 18 agronomic traits. Together, our findings and genomic resources establish a foundational framework for dissecting complex traits and accelerating precision breeding in watermelon, while offering a valuable model for SV-resolved pangenomics in crop species.

plant biology↗

bioRxiv2024

Short-term antibiotics, induced magnetic field, and magnetic sensitivity in a migratory songbird

The use of magnetoreception is widespread in the animal kingdom. Although much effort has been invested in unraveling the receptor and the mechanism behind this ability, the results remain inconclusive. The recently proposed symbiotic magnetic sensing hypothesis suggests that magnetotactic bacteria symbiotically act as magnetic sensors for the host. In this study, we examined the changes in magnetic orientation of Eurasian reed warblers (Acrocephalus scirpaceus) placed in Emlen funnels under the influence of antibiotics, in response to a manipulated magnetic field. We found that reed warblers of the control group showed no significant magnetic orientation when placed in a manipulated magnetic field. In contrast, reed warblers placed in an unplugged coil showed significant magnetic southwest orientation. Furthermore, reed warblers exposed to short-term antibiotic treatment (12 h) demonstrated significant magnetic orientation (southwest, regardless of season) and significantly lower directional variance. We hypothesize that individuals from the control group identified the electromagnetic noise induced by the artificial magnetic field. Taken together, this unexpected result may demonstrate the sensitivity of passerines to electromagnetic noise and a possible damping effect of antibiotics on this sensitivity. Assuming our interpretations are correct, we consider this result as indirect experimental support for the symbiotic magnetic sensing hypothesis.

animal behavior and cognition↗

bioRxiv2024

Dorsal CA1 silencing degrades tactile short-term memory

Previous studies in rodents showed that the hippocampus is involved in spatial short-term memory (STM), but hippocampal necessity for maintaining short-term sensory memories is unknown. Here, we develop tactile discrimination and STM tasks for freely-moving mice. Subjects learn to discriminate between textures after four shaping sessions and a single post-shaping session, and learn the STM task within a dozen sessions. Transient closed-loop silencing of dorsal hippocampal region CA1 during memory maintenance degrades task performance, compared to interleaved control blocks. Thus, uninterrupted hippocampal activity is required for acting upon tactile information maintained in STM. The findings suggest that the role of the hippocampus extends beyond spatial navigation, encoding memories, and long-term consolidation of experiences.

neuroscience↗

bioRxiv2023

Local activation of CA1 pyramidal cells induces theta phase precession

Hippocampal theta phase precession is involved in spatiotemporal coding and generating multineural spike sequences, but how precession originates remains unresolved. To determine whether precession can be generated directly in CA1 and disambiguate multiple competing mechanisms, we used optogenetic activation to impose artificial place fields in pyramidal cells of mice running on a linear track. More than a third of the CA1 artificial fields exhibited synthetic precession that persisted for a full cycle. In contrast, artificial fields in the parietal cortex did not exhibit synthetic precession. The findings are incompatible with precession models based on inheritance, spreading activation, dual-input, or inhibition-excitation summation. Thus, a precession generator resides locally within CA1.

neuroscience↗

bioRxiv2023

A Citrullus genus super-pangenome reveals extensive variations in wild and cultivated watermelons and sheds light on watermelon evolution and domestication

Sweet watermelon (Citrullus lanatus subsp. vulgaris) is among the most important vegetable crops in the world. Wild relatives are important resources for watermelon breeding. Here we report high-quality reference genomes of three wild watermelons, C. mucosospermus, C. amarus and C. colocynthis, and the divergence and genome evolution of different Citrullus species. Using genomic data from 547 watermelon accessions spanning four Citrullus species, we construct a super-pangenome to represent the Citrullus gene repertoire and provide a catalogue of orthologous relationships among species. Gene presence/absence variation analysis uncovers many disease resistance genes that are missing in cultivated watermelons, as well as genes with significantly different occurrence frequencies between populations that might underlie watermelon evolution and domestication. We revisit watermelon domestication using the recently identified wild progenitor, Kordofan melon, which provides insights into the domestication of fruit bitterness, sweetness and flesh coloration. The Citrullus super-pangenome provides a valuable resource for breeding and biological discovery, and our comparative genomic analyses shed additional light on watermelon evolution and domestication.

plant biology↗

bioRxiv2023

Wired together, change together: Spike timing modifies transmission in converging assemblies

Precise timing of neuronal spikes may lead to changes in synaptic connectivity and is thought to be crucial for learning and memory. However, the effect of spike timing on neuronal connectivity in the intact brain remains unknown. Using closed-loop optogenetic stimulation in CA1 of freely-moving mice, we generated new spike patterns between presynaptic pyramidal cells (PYRs) and postsynaptic parvalbumin-immunoreactive (PV) cells. This stimulation led to spike transmission changes which occurred together across all presynaptic PYRs connected to the same postsynaptic PV cell. The precise timing of all presynaptic and postsynaptic cells spikes impacted transmission changes. These findings reveal an unexpected plasticity mechanism, wherein spike timing of a whole cell assembly has a more substantial impact on effective connectivity than that of individual cell pairs.

neuroscience↗

bioRxiv2023

Learning to learn: Single session acquisition of new rules by freely-moving mice

Learning from examples and adapting to new rules are fundamental attributes of human cognition. However, it is unclear what conditions allow for fast and successful learning, especially in non-human subjects. To determine how rapidly freely-moving mice can learn a new rule, we designed a two-alternative forced-choice visual discrimination paradigm in which the rules governing the task can change between sessions. We find that experienced animals can learn a new rule after being exposed to only five training and three testing trials. The propensity for single session learning improves over time and is accurately predicted based on animal experience and rule difficulty. After establishing procedural learning of a paradigm, mice continuously improve their performance on new rules. Thus, mice learn to learn.

neuroscience↗

bioRxiv2023

Positive and biphasic extracellular waveforms correspond to return currents and axonal spikes

Multiple biophysical mechanisms may generate non-negative extracellular waveforms during action potentials, but the origin and prevalence of positive spikes and biphasic spikes in the intact brain are unknown. Using extracellular recordings from densely-connected cortical networks in freely-moving mice, we find that a tenth of the waveforms are non-negative. Positive phases of non-negative spikes occur in synchrony or just before wider same-unit negative spikes. Narrow positive spikes occur in isolation in the white matter. Isolated biphasic spikes are narrower than negative spikes, occurring right after spikes of verified inhibitory units. In CA1, units with dominant non-negative spikes exhibit place fields, phase precession, and phase-locking to ripples. Thus, near-somatic narrow positive extracellular potentials correspond to return currents, and isolated non-negative spikes correspond to axonal potentials. Identifying non-negative extracellular waveforms that correspond to non-somatic compartments during spikes can enhance the understanding of physiological and pathological neural mechanisms in intact animals.

neuroscience↗

bioRxiv2022

Graph-based pangenomics maximizes genotyping density and reveals structural impacts on fungal resistance

The genomic sequences segregating in experimental populations are often highly divergent from the community reference and from one another. Such divergence is problematic under various short-read-based genotyping strategies. In addition, large structural differences are often invisible despite being strong candidates for causal variation. These issues are exacerbated in specialty crop breeding programs with fewer, lower-quality sequence resources. We examined the benefits of complete genomic information, based on long-read assemblies, in a biparental mapping experiment segregating at numerous disease resistance loci in the non-model crop, melon (Cucumis melo). We find that a graph-based approach, which uses both parental genomes, results in 19% more variants callable across the population and raw allele calls with a 2 to 3-fold error-rate reduction, even relative to single reference approaches using a parent genome. We show that structural variation has played a substantial role in shaping two Fusarium wilt resistance loci with known causal genes. We also report on the genetics of powdery mildew resistance, where copy number variation and local recombination suppression are directly interpretable via parental genome alignments. Benefits observed, even in this low-resolution biparental experiment, will inevitably be amplified in more complex populations.

genetics↗

bioRxiv2022

Hybrid offspring of C57BL/6J mice exhibit improved properties for neurobehavioral research

C57BL/6 is the most commonly used mouse strain in neurobehavioral research, serving as a background for multiple transgenic lines. However, C57BL/6 exhibit behavioral and sensorimotor disadvantages that worsen with age. We bred FVB/NJ females and C57BL/6J males to generate first-generation hybrid offspring, (FVB/NJ x C57BL/6J)F1. The hybrid mice exhibit reduced anxiety-like behavior, improved learning, and enhanced long-term spatial memory. In contrast to both progenitors, older hybrids maintain sensorimotor performance and exhibit improved long-term memory. The hybrids are larger than C57BL/6J, exhibiting enhanced running behavior on a linear track during freely-moving electrophysiological recordings. Hybrids exhibit typical rate and phase coding of space by CA1 pyramidal cells. Hybrids generated by crossing FVB/NJ females with transgenic males of a C57BL/6 background support optogenetic neuronal control in neocortex and hippocampus. The hybrid mice provide an improved model for neurobehavioral studies combining complex behavior, electrophysiology, and genetic tools readily available in C57BL/6 mice.

neuroscience↗

bioRxiv2020

Immunosuppressive role of PGE2 during human tuberculosis

Prostaglandin E2 (PGE2), an active lipid compound derived from arachidonic acid, regulates different stages of the immune response of the host during several pathologies such as chronic infections or cancer. Manipulation of PGE2 levels was proposed as an approach for countering the Type I IFN signature of tuberculosis (TB), but very limited information exists about this pathway in patients with active TB. Here, we demonstrated that PGE2 exerts a potent immunosuppressive action during the immune response of the human host against M. tuberculosis. Thus, we showed that PGE2 inhibited both lymphoproliferation and cytokine production of proinflammatory cytokines, together with a significant reduction of the surface expression of several immunological receptors in human cells. However, PGE2 promoted the autophagic flux of antigen-stimulated monocytes, even in the presence of IFN. In this way, the attenuation of inflammation and immunopathology caused by an excessive immune response emerges as an attractive therapeutic target. Together, our findings contribute to the knowledge of Mtb-resistance mediated by PGE2 and highlight the potential of this lipid mediator as a tool to improve anti-TB treatment.

immunology↗

bioRxiv2019

Multi-allelic APRR2 Gene is Associated with Fruit Pigment Accumulation in Melon and Watermelon

Color and pigment content are important aspects of fruit quality and consumer acceptance of cucurbit crops. Here, we describe the independent mapping and cloning of a common causative APRR2 gene regulating pigment accumulation in melon and watermelon. We initially show that the APRR2 transcription factor is causative for the qualitative difference between dark and light green rind in both crops. Further analyses establish the link between sequence or expression level variations in the CmAPRR2 gene and pigments content in the rind and flesh of mature melon fruits. GWAS of young fruit rind color in a panel composed of 177 diverse melon accessions did not result in any significant association, leading to an earlier assumption that multiple genes are involved in shaping the overall phenotypic variation at this trait. Through resequencing of 25 representative accessions and allelism tests between light rind accessions, we show that multiple independent SNPs in the CmAPRR2 gene are causative for the light rind phenotype. The multi-haplotypic nature of this gene explain the lack of detection power obtained through GBS-based GWAS and confirm the pivotal role of this gene in shaping fruit color variation in melon. This study demonstrates the power of combining bi- and multi-allelic designs with deep sequencing, to resolve lack of power due to high haplotypic diversity and low allele frequencies. Due to its central role and broad effect on pigment accumulation in fruits, the APRR2 gene is an attractive target for carotenoids bio-fortification of cucurbit crops.

plant biology↗