Biology subjects

Manuel, M.

Publications and source records attributed to Manuel, M..

16 recordsLinked to original sources

bioRxiv2026

Aberrant Pain Phenotypes Emerge Following Prenatal Hypoxic-Ischemic Injury in a Rabbit Model of Cerebral Palsy

Cerebral Palsy (CP) is the most common motor disability in childhood, and the most frequent comorbidity is pain. Rabbit kits subjected to prenatal hypoxia-ischemia (HI) exhibit allodynia and an expansion of nociceptive afferents in the lumbar spinal cord at postnatal day (P5). In this study, we examined how HI alters the development of multiple sensory modalities and its effect on psychosocial measures and C-fiber distribution in the spinal cord. To do this, we performed an HI surgery to occlude blood flow to fetal New Zealand White rabbits for 40 minutes, or a sham surgery. We performed von Frey, Hargreaves, and a cold allodynia test at P1, P5, P11, and P18. Additionally, we performed open field, a two-texture preference test, and immunofluorescence assays at P18. HI kits exhibit altered development and allodynia in von Frey and Hargreaves and decreased sensitivity to cold. HI kits spend less time on the aversive side of the two-texture preference apparatus and more time in the center of an open field but a higher ratio of that time immobile. This is accompanied by changes in the distribution of C-fibers in the dorsal horn of the cervical and lumbar spinal cord. A principal components analysis revealed prenatal HI produces coordinated alterations across sensory and behavioral domains and multivariate phenotyping captures the overall HI phenotype more comprehensively than any single measure. Overall, HI rabbits kits exhibit altered sensory development, allodynia, anxiety-like behavior, and changes to the distribution of nociceptive afferents in the dorsal horn of the spinal cord.

neuroscience↗

bioRxiv2026

A novel machine-learning classification model detects oxidative fiber type transitions in a rabbit model of cerebral palsy

The distribution of slow-and fast-twitch fiber types in a skeletal muscle heavily influences its physiology. Muscle biopsy studies indicate atypical fiber type composition and fiber size variation in children with cerebral palsy (CP), but subjects have variable treatment history and a variety of muscles affected, so uncertainties remain. In this study, we developed a novel machine-learning classification model to perform high-throughput fiber typing of complete transverse muscle sections. Our XGBoost algorithm-based prediction model yielded a balanced accuracy score of 0.89 and a macro F1-score of 0.89, reflecting its ability to robustly predict muscle fiber type from myosin heavy chain (MyHC) isoform immunofluorescence intensities and morphological descriptors. This is the first reported fiber type classifier to consider hybrid fibers, which is a major advance, considering at least 20% of myofibers are hybrid yet they are routinely overlooked due to difficulty in their detection. We used this classification model to define fiber types of more than 7 million myofibers from flexor-extensor muscle pairs in rabbits that experienced hypoxia-ischemia (HI) injury in utero (modeling CP), and typically developing sham rabbits. We observed an oxidative fiber type shift in flexor muscles (biceps brachii and tibialis anterior) of HI rabbits at postnatal day (P)14-20 and P30-32 (weaning age). This altered fiber type composition imparts reduced contractile force and is amenable to sustained muscle activity; it may reflect chronic low-frequency motor unit activation. This work supports prior clinical reports that developmental trajectories of muscle fibers are disrupted in CP.

neuroscience↗

bioRxiv2026

Chronic diazepam reveals excessive homeostatic gain in SOD1G93A mouse spinal motoneurons

Motoneurons are under strong pressure to maintain stable motor output throughout an individual life, through homeostatic regulation of their electrical properties. Dysregulated spinal motoneuron excitability has long been implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS). Recent work in SOD1G93A mice suggests that the homeostatic response of motoneurons becomes dysregulated as cellular processes are disrupted by the disease, causing fluctuations in motoneuron electrical properties. Yet, few studies directly test whether ALS motoneurons respond differently than wild type motoneurons to a common chronic perturbation. Here, we used in vivo electrophysiology to test whether motoneurons from pre-symptomatic SOD1G93A mice modulate excitability differently than wild type motoneurons in response to the same homeostatic perturbation: chronic inhibition exerted by the benzodiazepine diazepam. Using linear mixed-effects statistical models, we assessed whether diazepam treatment differentially modulated passive properties, firing behavior, spike properties, and/or synaptic inputs in SOD1G93A versus wild type motoneurons. We identified a significant genotype x treatment interaction effect selectively for properties related to passive membrane integration and spike initiation, including membrane time constant, peak input resistance, and recruitment current. In contrast, firing gain, spike waveform characteristics, and synaptic inputs were largely unaffected. These findings indicate that sustained inhibitory perturbation selectively triggered overactive intrinsic compensatory mechanisms in SOD1G93A motoneurons rather than inducing widespread changes in firing or synaptic transmission. Together, our results provide direct evidence for over-active homeostatic control of motoneuron excitability and support a view of motoneuron dysfunction in ALS as a problem of altered feedback regulation rather than simply hyper- or hypo-excitability. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=52 SRC="FIGDIR/small/725609v1_ufig1.gif" ALT="Figure 1"> View larger version (18K): org.highwire.dtl.DTLVardef@25f125org.highwire.dtl.DTLVardef@faf2c9org.highwire.dtl.DTLVardef@15993a8org.highwire.dtl.DTLVardef@1ed006a_HPS_FORMAT_FIGEXP M_FIG C_FIG

neuroscience↗

bioRxiv2026

Whole-Mount Optical Clearing of Rabbit Tenuissimus Muscle for Assessment of Muscle Spindle Morphology

Proprioception and reflexive control of muscle tone depend on the activity of muscle spindles, specialized sensory receptors embedded deep within skeletal muscle that detect changes in muscle length. Their location and complex three-dimensional architecture have historically limited morphological analysis to techniques such as silver-impregnation, muscle teasing, or serial sectioning followed by volumetric reconstruction. Here, we describe a workflow for three-dimensional, in situ visualization of muscle spindles in the rabbit tenuissimus muscle, a preparation uniquely enriched in spindles and well suited for whole-mount imaging. The protocol combines fluorescent labeling of spindle sensory and motor innervation, including intrafusal {gamma} neuromuscular junctions labeled with -bungarotoxin, with immunolabeling and solvent-based optical clearing. Optically cleared tenuissimus muscles were compatible with both whole-mount confocal and light-sheet microscopy, enabling volumetric imaging of complete spindle structures and detailed visualization of Ia annulospiral endings at the spindle equator. This approach provides access to spindle morphology and connectivity at multiple spatial scales while avoiding physical sectioning and reconstruction. By enabling reproducible three-dimensional imaging of intact muscle spindles, this workflow offers a practical platform for studying spindle structure and plasticity in health and disease.

neuroscience↗

bioRxiv2026

Determination of diagnostic cycle threshold (Ct) cut-offs for qPCR-based prevalence surveys of soil-transmitted helminth infections

WHO guidelines for control of soil-transmitted helminths (STH) rely on coproscopic methods to assess population prevalence. In low-prevalence and light-intensity STH settings, quantitative PCR (qPCR) has higher sensitivity and specificity for detection. For qPCR to accurately identify transmissible infections of public health significance, it is essential to interpret the qPCR cycle threshold (Ct) results. As part of the DeWorm3 community-based cluster randomized trial on interrupting STH transmission, we conducted population-based surveys using high-throughput qPCR and aimed to establish appropriate Ct cut-offs to detect transmissible infections. Experimental approaches including egg and genome-equivalent spiking experiments were hindered by inefficient fecal DNA extraction despite optimization efforts. The Ct results for 29,980 samples (pre-intervention, cross-sectional surveys) revealed a bimodal distribution for two of the four species tested, N. americanus and A. lumbricoides. The first peak was assumed to represent transmissible infections, and the second peak to represent indeterminate or non-transmissible infections. Using a finite mixture model, we defined true qPCR positivity as any Ct result with a [≥]5% chance of belonging to the first peak. This approach yielded Ct cut-offs of 34.4398 for N. americanus and 28.57587 for A. lumbricoides. For hookworms, sensitivity of qPCR was 96.7%, compared to 73.2% for Kato-Katz and moderate- to heavy-intensity infections (median Ct: 19.1, interquartile range [IQR]: 17.9-19.8) were differentiated from light-intensity infections and Kato-Katz negative samples (25.3, IQR: 22.5-27.9). Our findings demonstrate the feasibility and utility of evidence-based Ct cut-offs to identify transmissible STH infections in large scale surveys, and to categorize infection intensity as programmatically relevant. Author SummaryQuantitative PCR (qPCR) has been used for the detection of soil-transmitted helminths but with limited emphasis on determining cycle threshold (Ct) cut-offs to accurately identify transmissible infections which are of public health significance. When qPCR is used to assess interventions, or, in the future, to potentially make programmatic decisions, it will be crucial to validate positivity criteria to avoid underestimation (false negatives) or overestimation (false positives) of results. As part of the DeWorm3 trial, a community-based cluster randomized trial on interrupting transmission of STH, we developed and applied a validated STH qPCR to test 29,980 samples collected pre-intervention and explored experimental approaches to establish assay-specific Ct cut-offs. The Ct values from these samples showed a bimodal distribution for N. americanus and A. lumbricoides, suggesting the presence of two distinct groups. For this reason, a statistical approach with a finite mixture model was employed to determine Ct cut-offs that differentiated epidemiologically relevant, transmissible, egg-positive STH infections from those that are likely to represent detection of non-transmissible DNA or indeterminate results. While our data were applied in three different country settings, India, Benin and Malawi, it is important to note that no single Ct cut-off may be applicable across all epidemiological scenarios. Our findings demonstrate the feasibility of developing evidence-based Ct cut-offs with high sensitivity to accurately detect transmissible STH infections in large scale surveys.

microbiology↗

bioRxiv2025

Machine-Learning Classification of Motor Unit Types in the Adult Mouse

The diversity of motor units arises from differences in the contractile properties of muscle fibers and the intrinsic electrical properties of their motoneurons. In mice, however, this relationship has not been quantitatively defined, and conventional classification often relies on subjective thresholds. Here, we combined in vivo intracellular recordings with supervised and unsupervised machine-learning methods to test whether motoneuron electrophysiology can predict the physiological identity of mouse motor units. Unbiased clustering identified four groups corresponding to slow (S), fast fatigue-resistant (FR), intermediate (FI), and fast fatigable (FF) types. A multinomial logistic regression model performed well, with most errors occurring between FI and FF types, which showed substantial overlap. Reducing the task to three classes improved accuracy. Feature selection revealed that four electrophysiological properties (input conductance, rheobase, AHP duration, maximal frequency) were sufficient for high predictive performance. Overall, this study provides a quantitative description of mouse motor-unit properties and a framework for incorporating motor-unit diversity into future investigations of neuromuscular physiology and disease.

neuroscience↗

bioRxiv2024

Global diversity of soil-transmitted helminths reveals population-biased genetic variation that impacts diagnostic targets

Soil-transmitted helminths (STHs) are intestinal pathogens affecting over a billion people worldwide. STH control relies on microsopy-based diagnostics to monitor parasite prevalence and enable post-treatment surveillance, however, molecular diagnostics are rapidly being developed due to increased sensitivity, particularly in low-STH-prevalence settings. The genetic diversity of helminths and its potential impact on molecular diagnostics remains unclear. Using low-coverage genome sequencing, we assessed the presence of STHs in worm, faecal and purified egg samples from 27 countries, identifying differences in the genetic connectivity and diversity of STH-positive samples across regions and cryptic diversity between closely related human- and pig-infective species. We defined substancial copy number and sequence variants in current diagnostic targets and validated the impact of genetic variants on qPCR diagnostics using in vitro assays. Our study provides insights into the diversity and genomic epidemiology of STHs, highlighting challenges and opportunities for developing molecular diagnostics needed to support STH control efforts.

genomics↗

bioRxiv2024

Environmental surveillance of soil-transmitted helminths and other enteric pathogens in settings without networked wastewater infrastructure

Soil-transmitted helminths (STH) are one of the most prevalent enteric infections world-wide. To control STH-related morbidity, the World Health Organization recommends targeted deworming and improvements in water, sanitation and hygiene. Current surveillance strategies for STH focus on identifying and quantifying eggs in stool samples via microscopy, which exhibits poor specificity and sensitivity, especially in settings with low-intensity infections. Wastewater-based epidemiology is a surveillance tool used to monitor pathogen circulation and could replace stool- based approaches for STH detection. However, sampling strategies for settings lacking networked sanitation outside large urban settlements are not well developed. Here, we report evaluation of sampling strategies for soil and wastewater STH surveillance in rural and peri-urban settings without networked sanitation. We used multi-parallel qPCR assays to detect STH DNA in soil collected from high foot-traffic locations and three types of wastewater samples (passive Moore swabs, grab samples, and sediment from drainage ditches) in Come, Benin and Timiri and Jawadhu Hills in Tamil Nadu, India. We detected STH in soil (India = 32/95, Benin = 39/121) and wastewater (India = 24/60, Benin = 8/64) with a detection frequency across all sample types of 36% in India and 25% in Benin. We evaluated which sample locations and types allowed for more sensitive detection of STH DNA and determined that STH prevalence varied by sample site but did not vary significantly within a given sample site location (e.g., samples collected from multiple locations within one market). Further, we determined that wastewater sediment samples outperformed grab and Moore swab sample types for STH detection. Finally, we expanded our methods to include detection of other enteric pathogens using multiplexed qPCR for wastewater samples. Our results establish sampling strategies for environmental and wastewater surveillance of a wide range of enteric pathogens in settings without networked sanitation.

microbiology↗

bioRxiv2024

Spinal microcircuits go through multiphasic homeostatic compensations in a mouse model of motoneuron degeneration

In many neurological conditions, early-stage neural circuit adaption can preserve relatively normal behaviour. In some diseases, spinal motoneurons progressively degenerate yet movement is initially preserved. We therefore investigated whether these neurons and associated microcircuits adapt in a mouse model of progressive motoneuron degeneration. Using a combination of in vitro and in vivo electrophysiology and super-resolution microscopy, we found that, early in the disease, neurotransmission in a key pre-motor circuit, the recurrent inhibition mediated by Renshaw cells, is reduced by half due to impaired quantal size associated with decreased glycine receptor density. This impairment is specific, and not a widespread feature of spinal inhibitory circuits. Furthermore, it recovers at later stages of disease. Additionally, an increased probability of release from proprioceptive afferents leads to increased monosynaptic excitation of motoneurons. We reveal that in motoneuron degenerative conditions, spinal microcircuits undergo specific multiphasic homeostatic compensations that may contribute to preservation of force output.

neuroscience↗

bioRxiv2023

Spinal motoneurons respond aberrantly to serotonin in a rabbit model of cerebral palsy

Cerebral palsy (CP) is caused by a variety of factors that damage the developing central nervous system. Impaired motor control, including muscle stiffness and spasticity, is the hallmark of spastic CP. Rabbits that experience hypoxic-ischemic (HI) injury in utero (at 70-80% gestation) are born with muscle stiffness, hyperreflexia, and, as recently discovered, increased serotonin (5-HT) in the spinal cord. To determine whether serotonergic modulation of spinal motoneurons (MNs) contributes to motor deficits, we performed ex vivo whole cell patch clamp in neonatal rabbit spinal cord slices at postnatal day (P) 0-5. HI MNs responded to application of -methyl 5-HT (a 5-HT1/5-HT2 receptor agonist) and citalopram (a selective 5-HT reuptake inhibitor) with hyperpolarization of persistent inward currents and threshold voltage for action potentials, reduced maximum firing rate, and an altered pattern of spike frequency adaptation while control MNs did not exhibit any of these responses. To further explore the differential sensitivity of MNs to 5-HT, we performed immunohistochemistry for inhibitory 5-HT1A receptors in lumbar spinal MNs at P5. Fewer HI MNs expressed the 5-HT1A receptor compared to age-matched controls. This suggests many HI MNs lack a normal mechanism of central fatigue mediated by 5-HT1A receptors. Other 5-HT receptors (including 5-HT2) are likely responsible for the robust increase in HI MN excitability. In summary, by directly exciting MNs, the increased concentration of spinal 5-HT in HI rabbits can cause MN hyperexcitability, muscle stiffness, and spasticity characteristic of CP. Therapeutic strategies that target serotonergic neuromodulation may be beneficial to individuals with CP. Key pointsO_LIAfter prenatal hypoxia-ischemia (HI), neonatal rabbits that show hypertonia are known to have higher levels of spinal serotonin C_LIO_LIWe tested responsivity of spinal motoneurons (MNs) in neonatal control and HI rabbits to serotonin using whole cell patch clamp C_LIO_LIMNs from HI rabbits showed a more robust excitatory response to serotonin than control MNs, including hyperpolarization of the persistent inward current and threshold for action potentials, larger post-inhibitory rebound, and less spike frequency adaptation C_LIO_LIBased on immunohistochemistry of lumbar MNs, fewer HI MNs express inhibitory 5HT1A receptors than control MNs, which could account for the more robust excitatory response of HI MNs. C_LIO_LIThese results suggest that after HI injury, the increased serotonin could trigger a cascade of events leading to muscle stiffness and altered motor unit development C_LI

neuroscience↗

bioRxiv2022

PAX6 LIMITS THE COMPETENCE OF DEVELOPING CEREBRAL CORTICAL CELLS

The development of stable specialized cell types in multicellular organisms relies on mechanisms controlling inductive intercellular signals and the competence of cells to respond to such signals. In developing cerebral cortex, progenitors generate only glutamatergic excitatory neurons despite being exposed to signals with the potential to initiate the production of other neuronal types, suggesting that their competence is limited. Here we tested the hypothesis that this limitation is due to their expression of transcription factor Pax6. We used bulk and single cell RNAseq to show that conditional cortex-specific Pax6 deletion from the onset of cortical neurogenesis allowed some progenitors to generate abnormal lineages resembling those normally found outside the cortex. Analysis of selected gene expression showed that the changes occurred in specific spatiotemporal patterns. We then compared the responses of control and Pax6-deleted cortical cells to in vivo and in vitro manipulations of extracellular signals. We found that Pax6 loss increased cortical progenitors competence to generate inappropriate lineages in response to extracellular factors normally present in developing cortex, including the morphogens Shh and Bmp4. Regional variation in the levels of these factors could explain spatiotemporal patterns of fate change following Pax6 deletion in vivo. We propose that Pax6s main role in developing cortical cells is to minimize the risk of their development being derailed by the potential side-effects of morphogens engaged contemporaneously in other essential functions.

neuroscience↗

bioRxiv2021

Conservation of locomotion-induced oculomotor activity through evolution in higher tetrapods

Efference copies are neural replicas of motor outputs used to anticipate the sensory consequences of a self-generated motor action or to coordinate neural networks involved in distinct motor behaviors1. An established example of this motor-to-motor coupling is the efference copy of the propulsive motor command that supplements classical visuo-vestibular reflexes to ensure gaze stabilization during amphibian larval locomotion2. Such feedforward replica from spinal pattern-generating circuits produces a spino-extraocular motor coupled activity that evokes eye movements, spatio-temporally coordinated to tail undulation independently of any sensory signal3,4. Exploiting the evolutionary-development characteristic of the frog1, studies in metamorphing Xenopus demonstrated the persistence of this spino-extraocular motor command in adults, and its developmental adaptation to tetrapodal locomotion5,6. Here, we demonstrate for the first time the existence of a comparable locomotor-to-ocular motor coupling in the mouse. In neonates, ex vivo nerve recordings from brainstem-spinal cord preparation reveals a spino-extraocular motor coupled activity similar to the one described in Xenopus. In adult mice, trans-synaptic rabies injection in lateral rectus eye muscle labels cervical spinal cord neurons projecting directly to abducens motor neurons. Finally, treadmill-elicited locomotion in decerebrated preparations7 evokes rhythmic eye movements in synchrony with the limb gait pattern. Overall, our data are evidence for the conservation of locomotor-induced eye movements in higher tetrapods. Thus, in mammals as in amphibians, during locomotion CPG-efference copy feedforward signals might interact with sensory feedback to ensure efficient gaze control. HighlightsO_LISpino-extraocular motor coupling is evidenced from newborn mice ex vivo preparations C_LIO_LIAdult decerebrated mice exhibit conjugated rhythmic eye movements during treadmill locomotion C_LIO_LILocomotor-induced oculomotor activity occurs in absence of visuo-vestibular inputs C_LIO_LIConserved CPG-based efference copy signal in vertebrates with common features. C_LI eTOC blurbWe report a functional coupling between spinal locomotor and oculomotor networks in the mouse, similar to the one previously described in Amphibians. This is the first evidence for the direct contribution of locomotor networks to gaze control in mammals, suggesting a conservation of the spino-extraocular coupling in higher tetrapods during sustained locomotion.

neuroscience↗

bioRxiv2020

Sub-optimal Discontinuous Current-Clamp switching rates lead to deceptive mouse neuronal firing

AO_SCPLOWBSTRACTC_SCPLOWIntracellular recordings using sharp microelectrodes often rely on a technique called Discontinuous Current-Clamp to accurately record the membrane potential while injecting current through the same microelectrode. It is well known that a poor choice of DCC switching rate can lead to under-or over-estimation of the cell potential, however, its effect on the cell firing is rarely discussed. Here, we show that sub-optimal switching rates lead to an overestimation of cell excitability. We performed intracellular recordings of mouse spinal motoneurons and recorded their firing in response to pulses and ramps of current in Bridge and DCC mode at various switching rates. We demonstrate that using an incorrect (too low) DCC frequency leads not only to an underestimation of the input resistance, but also, paradoxically, to an artificial overestimation of the firing of these cells: neurons fire at lower current, and at higher frequencies than at higher DCC rates, or than the same neuron recorded in Bridge mode. These effects are dependent on the membrane time constant of the recorded cell, and special care needs to be taken in large cells with very short time constants. Our work highlights the importance of choosing an appropriate DCC switching rate to obtain not only accurate membrane potential readings but also an accurate representation of the firing of the cell. SO_SCPLOWIGNIFICANCEC_SCPLOW SO_SCPLOWTATEMENTC_SCPLOWDiscontinuous Current-Clamp is a technique often used during intracellular recordings in vivo. However, incorrect usage of this technique can lead to incorrect interpretations. Poor choice of the DCC switching rate can lead to under- or over-estimation of the cell potential. In addition, we show here that sub-optimal switching rates lead to an overestimation of the cell excitability.

neuroscience↗

bioRxiv2020

Time course of alterations in adult spinal motoneuron properties in the SOD1(G93A) mouse model of ALS

Although ALS is an adult-onset neurodegenerative disease, motoneuron electrical properties are already altered during embryonic development. Motoneurons must therefore exhibit a remarkable capacity for homeostatic regulation to maintain a normal motor output for most of the life of the patient. In the present paper, we demonstrate how maintaining homeostasis could come at a very high cost. We studied the excitability of spinal motoneurons from young adult SOD1(G93A) mice to end-stage. Initially homeostasis is highly successful in maintaining their overall excitability. This initial success, however, is achieved by pushing some cells far above the normal range of passive and active conductances. As the disease progresses, both passive and active conductances shrink below normal values in the surviving cells. This shrinkage may thus promote survival, implying the previously large values contribute to degeneration. These results support the hypothesis that motoneuronal homeostasis may be "hyper-vigilant" in ALS and a source of accumulating stress. Significance StatementDuring ALS, motoneurons exhibit a remarkable ability to maintain a normal motor output despite continuous alterations of their electrophysiological properties, up to the point when overt symptoms become apparent. We show that this homeostatic process can sometimes push motoneurons beyond the normal range, which may be causing long-lasting harm.

neuroscience↗

bioRxiv2018

Tissue-specific actions of Pax6 on proliferation-differentiation balance in the developing forebrain are Foxg1-dependent

Differences in the growth and maturation of diverse forebrain tissues depends on region-specific transcriptional regulation. Individual transcription factors act simultaneously in multiple regions that develop very differently, raising questions about the extent to which their actions vary regionally. We found that the transcription factor Pax6 affects the transcriptomes and the balance between proliferation and differentiation in opposite directions in murine diencephalon versus cortex. We tested several possible mechanisms to explain Pax6s tissue-specific actions and found that the presence of the transcription factor Foxg1 in cortex but not diencephalon was most influential. We found that Foxg1 is responsible for many of the differences in cell cycle gene expression between diencephalon and cortex. In cortex lacking Foxg1, Pax6s action on the balance of proliferation versus differentiation became diencephalon-like. Our findings reveal a mechanism for generating regional forebrain diversity in which the actions of one transcription factor completely reverse the actions of another.

developmental biology↗

bioRxiv2018

The genome of the jellyfish Clytia hemisphaerica and the evolution of the cnidarian life-cycle

Jellyfish (medusae) are a distinctive life-cycle stage of medusozoan cnidarians. They are major marine predators, with integrated neurosensory, muscular and organ systems. The genetic foundations of this complex form are largely unknown. We report the draft genome of the hydrozoan jellyfish Clytia hemisphaerica and use multiple transcriptomes to determine gene use across life-cycle stages. Medusa, planula larva and polyp are each characterised by distinct transcriptome signatures reflecting abrupt life cycle transitions, and all deploy a mixture of phylogenetically old and new genes. Medusa specific transcription factors, including many with bilaterian orthologs, associate with diverse neurosensory structures. Compared to Clytia, the polyp-only hydrozoan Hydra has lost many of the medusa-expressed transcription factors, despite similar overall rates of gene content and sequence evolution. Absence of expression and gene loss among Clytia orthologs of genes patterning the anthozoan aboral pole, secondary axis and endomesoderm support simplification of planulae and polyps in Hydrozoa, including loss of bilateral symmetry. Consequently, although the polyp and planula are generally considered the ancestral cnidarian forms, in Clytia the medusa maximally deploys ancestral cnidarian-bilaterian transcription factor gene complexity.

evolutionary biology↗