(2024) Development "The people behind the papers - Nadia Manzi and Daniel Dickinson."

[Development, 2024]

The mitotic kinase Aurora A has been shown to regulate the anterior-posterior polarity in developing Caenorhabditis elegans embryos. In a new study, Daniel Dickinson and colleagues find that Aurora A has temporally distinct roles in coordinating the localization of Partitioning defective (PAR) proteins to establish cell polarity during development. To find out more about the story behind the paper, we caught up with first author Nadia Manzi and corresponding author Daniel Dickinson, Assistant Professor at the University of Texas at Austin.

(2019) Development "The people behind the papers - Daniel Osorio, Elaine Chan, Joana Saramago and Ana Carvalho."

[Development, 2019]

Animal cytokinesis is driven by an actomyosin ring that assembles at the cell equator and constricts to physically separate the two daughters. Although myosin is known to be essential for cytokinesis in multiple systems, whether this requirement reflects its motor or actin crosslinking activities has recently been a matter of contention. A new paper in Development now addresses this problem using the first divisions of the <i>Caenorhabditis elegans</i> embryo as a model. We caught up with the paper's three first authors Daniel Osorio, Elaine Chan and Joana Saramago, and their supervisor Ana Carvalho, Principal Investigator at the University of Porto's i3S consortium, to find out more about the story.

Zhao H et al. (2022) Entropy (Basel) "Modeling the Evolution of Biological Neural Networks Based on Caenorhabditis elegans Connectomes across Development."

Shi Z, He S, Gong Z, Zhao H

[Entropy (Basel), 2022]

Knowledge of the structural properties of biological neural networks can help in understanding how particular responses and actions are generated. Recently, Witvliet et al. published the connectomes of eight isogenic Caenorhabditis elegans hermaphrodites at different postembryonic ages, from birth to adulthood. We analyzed the basic structural properties of these biological neural networks. From birth to adulthood, the asymmetry between in-degrees and out-degrees over the C. elegans neuronal network increased with age, in addition to an increase in the number of nodes and edges. The degree distributions were neither Poisson distributions nor pure power-law distributions. We have proposed a model of network evolution with different initial attractiveness for in-degrees and out-degrees of nodes and preferential attachment, which reproduces the asymmetry between in-degrees and out-degrees and similar degree distributions via the tuning of the initial attractiveness values. In this study, we present the well-preserved structural properties of C. elegans neuronal networks across development, and provide some insight into understanding the evolutionary processes of biological neural networks through a simple network model.

Meng, Jun et al. (2017) International Worm Meeting "Myrf ER-bound transcription factors drive C. elegans synaptic plasticity via cleavage-dependent nuclear translocation."

Jin, Xia, Tao, Huaping, Dong, Meng-Qiu, Qi, Yingchuan, Witvliet, Daniel, Ma, Xiaoxia, Michell, James, Jin, Yishi, Zhu, Ming, Meng, Jun, Zhen, Mei

[International Worm Meeting, 2017]

One of the enigmatic characteristics of the developing nervous system is its ability to remodel and refine neuronal connections during its transition into a functional, mature nervous system. A striking and informative example of synaptic refinement occurs during the development of the C. elegans nervous system, in which the GABAergic dorsal D (DD) neuron reverses its axonal and dendritic domains without overt changes in morphology. The synaptic rewiring allows DD neurons to acquire new connectivity and be integrated into a more mature motor circuit. This dramatic process offers a powerful model in which we can identify genes that are essential for the developmental plasticity of neurons. We have identified myrf-1, a homologue of Myrf (Myelin regulatory factor) family transcription factors, as a key regulator of synaptic rewiring in C. elegans. MYRF-1 and its paralog MYRF-2 are functionally redundant specifically in synaptic rewiring. They co-exist in the same protein complex, and act cooperatively to regulate synaptic rewiring. We find that the MYRF proteins localize to the endoplasmic reticulum membrane, and that they are cleaved into active N-terminal fragments, which then translocate into the nucleus to drive synaptic rewiring. Over-expression of active forms of MYRF is sufficient to accelerate synaptic rewiring. MYRF-1 and MYRF-2 are the first genes identified to be indispensable for promoting synaptic rewiring in C. elegans. These findings reveal a novel molecular mechanism underlying synaptic rewiring and developmental circuit plasticity.

Yu, Xinwei et al. (2021) International Worm Meeting "Fast deep learning correspondence for neuron tracking and identification in C. elegans using semi-synthetic training"

Sharma, Anuj K., Linderman, Scott W., Randi, Francesco, Yu, Xinwei, Leifer, Andrew M., Creamer, Matthew S.

[International Worm Meeting, 2021]

The nervous system of the nematode C.elegans is well characterized, such that each of the 302 neurons is named and has stereotyped locations across animals(Witvliet et al., 2020). The capability to find corresponding neurons across animals is essential to investigate neural coding and neural dynamics across animals. Despite the worm's overall stereotypy, the variability in neurons' spatial arrangement is sufficient to make predicting neural correspondence a challenge. We present an automated method to track and identify neurons in C. elegans, called "fast Deep Learning Correspondence" or fDLC, based on the transformer network architecture(Vaswani et al., 2017). The transformer has shown great success in natural language processing tasks by modeling the dependencies between words in a sentence. We reasoned this same architecture would be well-suited to extract spatial relationships between neurons in order to build a representation that facilitates finding correspondence to neurons in a template worm. The model is trained once on empirically derived semi-synthetic data and then predicts neural correspondence across held-out real animals via transfer learning. The same pre-trained model both tracks neurons across time and identifies corresponding neurons across individuals. Performance is evaluated against hand-annotated datasets, including NeuroPAL(Yemini et al., 2020). Using only position information, the method achieves 80.0% accuracy at tracking neurons within an individual and 65.8% accuracy at identifying neurons across individuals. Accuracy is even higher on a published dataset(Chaudhary et al., 2021). Accuracy reaches 76.5% when using color information from NeuroPAL. Unlike previous methods, fDLC does not require straightening or transforming the animal into a canonical coordinate system. The method is fast and predicts correspondence in 10 ms making it suitable for future real-time applications. Witvliet D, Mulcahy B, Mitchell JK, Meirovitch Y, Berger DR, Wu Y, et al.Connectomes across development reveal principles of brain maturation in C.elegans. bioRxiv. 2020;doi:10.1101/2020.04.30.066209. Vaswani A, Shazeer N, Parmar N, Uszkoreit J, Jones L, Gomez AN, et al.Attention is All You Need; 2017.Available from:https://arxiv.org/pdf/1706.03762.pdf. Yemini E, Lin A, Nejatbakhsh A, Varol E, Sun R, Mena GE, et al. NeuroPAL: A multicolor atlas for whole-brain neuronal identification in C. Elegans. Cell.2020;doi:10.1016/j.cell.2020.12.012. Chaudhary S, Lee SA, Li Y, Patel DS, Lu H. Graphical-model framework for automated annotation of cell identities in dense cellular images. eLife.2021;10:e60321. doi:10.7554/eLife.60321.

Vo, An A. et al. (2021) MicroPubl Biol

Ward, Jordan D., Ragle, James Matthew, Levenson, Max T., Vo, An A.

[MicroPubl Biol, 2021]

The AID system has emerged as a powerful tool to conditionally deplete proteins in a wide-range of organisms and cell types (Nishimura et al. 2009; Holland et al. 2012; Zhang et al. 2015; Natsume et al. 2016; Trost et al. 2016; Brown et al. 2017; Daniel et al. 2018; Chen et al. 2018; Camlin and Evans 2019). The system is comprised of two components. A plant F-box protein Transport Inhibitor Response 1 (TIR1) is expressed and forms a complex with endogenous Skp1 and Cul1 proteins to form a functional SCF ubiquitin ligase (Nishimura et al. 2009; Natsume and Kanemaki 2017). TIR1 can either be expressed constitutively or in a tissue-specific manner depending on promoter choice. A degron sequence from the IAA17 protein is fused to the protein of interest (Nishimura et al. 2009; Natsume and Kanemaki 2017). Commonly used auxin-inducible degrons include 44 amino acid (AID*) and 68 amino acid (mAID) fragments of IAA17 (Morawska and Ulrich 2013; Li et al. 2019). Addition of the plant hormone auxin bridges an interaction between TIR1 and the degron and the SCF ligase ubiquitylates the degron-fused protein leading to proteasomal degradation.

Chen, Sway et al. (2015) International Worm Meeting "Functional and anatomical analysis of the L1 motor circuit."

Schalek, Richard, Laskova, Valeriya, Chen, Sway, Cook, Steven, Suriyalaksh, Manusnan, Lichtman, Jeff, Guan, Asuka, Mitchell, James, Neubauer, Marianna, Witvliet, Daniel, Wen, Quan, Zhen, Mei, Samuel, Aravinthan, Lu, Yangning, Mulcahy, Ben

[International Worm Meeting, 2015]

At all developmental stages, C. elegans navigates its environment by generating and propagating bending waves along its body. The neuronal circuit controlling locomotory behavior, however, changes significantly at the end of the L1 larval stage. During the L1 stage, B- and A-type cholinergic motor neurons innervate dorsal body wall muscles but not ventral muscles. D-type GABAergic motor neurons innervate ventral muscles but not dorsal muscles. Calcium imaging and optogenetic stimulation suggest that D-type neurons are inhibitory at the L1 stage, causing ventral muscles to relax. At the L2 stage and beyond, both ventral and dorsal muscles are symmetrically innervated by cholinergic and GABAergic motor neurons, and phasic excitation coupled to contralateral inhibition is thought to be responsible for the propagation of undulatory waves. So how does the worm produce undulatory behavior at the L1 stage given the profound ventral/dorsal asymmetry in excitatory cholinergic and inhibitory GABAergic inputs? To answer this question, we have reconstructed the L1 motor circuit using serial section electron microscopy. We are now using targeted cellular ablation, calcium imaging, and optogenetics to pinpoint the mechanism for ventral muscle contraction, and understand how alternating waves of excitation and relaxation drive undulation during the L1 stage. Our goal is a detailed mechanistic model of L1 locomotion. Comparing the circuit basis of L1 with adult worm locomotion should shed light on conserved principles of rhythmic locomotion and development of motor circuits.

Mulcahy, Ben et al. (2017) International Worm Meeting "The Dynamics of Synaptic Remodeling: insights from the C. elegans Motor Circuit."

Holmyard, Douglas, Christensen, Ryan, Lichtman, Jeff, Koh, WanXian, Witvliet, Daniel, Schroff, Hari, Mitchell, James, Qu, Yixin, Chisholm, Andrew, Samuel, Aravi, Bermant, Peter, Schalek, Richard, Zhen, Mei, Mulcahy, Ben, Chang, Maggie, Fetter, Rick

[International Worm Meeting, 2017]

During development, neural circuits undergo constant changes: they incorporate new neurons, and maintain, prune or remodel existing synapses. The small and rapidly developing nervous system of C. elegans allows us to address the developmental dynamics of synapses and neurons in the context of an intact neural ensemble. The vast majority of C. elegans postembryonic neurons are motor neurons. Previous studies suggest that at least one group of motor neurons, DD, reverse their neurite polarity entirely: they innervate ventral body wall muscles in the first larval stage, whereas they innervate dorsal muscles in adults. Their role of innervating ventral muscle is taken over by a group of post-embryonically born motor neurons, VD. Precisely how and when such processes occur, without disrupting motility as the motor circuit transitions into the adult form, is poorly described. We used serial section electron microscopy to reconstruct DD and VD motor neurons across development to define the beginning and ending of remodeling. We identified a series of elegantly coordinated synaptogenesis and remodeling events where synaptogenesis events follow different sequential orders for embryonic (DD) and post-embryonic (VD) neurons. Developing VD neurons have some interaction with DD neurons that may help to guide neurite extension and synaptogenesis. These events implicate an elegant mechanism that allows a gradual and seamless transition of the motor circuit to take place without disrupting its functional output.

Yohann Duverger et al. (2006) European Worm Meeting "A French Functional Genomics Platform"

Yohann Duverger, Jonathan Ewbank, Jerome Reboul, Daniel Wong

[European Worm Meeting, 2006]

Yohann Duverger1, Jrme Reboul2, Daniel Wong1 and Jonathan Ewbank1 For the last three years, we have offered a service of worm sorting based around the Union Biometrica COPAS platform. The COPAS machine is equipped with a Zymark twister robot, allowing automated analysis of multiple 96 well plates. We recently upgraded the machine to include the Profiler II that generates >1000 individual measurements per worm simultaneously for up to 4 channels (including 2 fluorescent). This equipment has been applied to a wide range of biological questions. They include quantifying the level of fluorescent reporter gene expression, large-scale RNAi and genetic screens and combinatorial library drug screening. Examples of each will be presented.. This platform is part of a fully integrated functional genomics facility open to the academic community (see http://www.ciml.univ-mrs.fr/EWBANK_jonathan /RIO.html). Other resources include the ORFeome (developed in Marc Vidals laboratory), and Julie Ahringers RNAi library, together with whole-genome microarrays. For the latter, through a collaboration with the Genome Sequencing Center at Washington, and the transcriptome platform at Nice, we have spotted the Illumina long oligo set onto glass slides and provide microarrays free of charge to the French C.elegans community and at cost price to academic researchers in Europe.. This French functional genomics platform has been made possible through funding from the National Genopole network, Marseille-Nice genopole, the CNRS and support from Union Biometrica.

Berger, Daniel et al. (2015) International Worm Meeting "The mind of an L1 worm - how do neuronal circuits function and remodel throughout development?."

Samuel, Aravinthan, Emmons, Scott, Neubauer, Marianna, Lichtman, Jeff, Witvliet, Daniel, Chisholm, Andrew, Laskova, Valeriya, Mitchell, James, Mulcahy, Ben, Cook, Steven, Zhen, Mei, Schalek, Richard, Berger, Daniel, Hall, David, Holmyard, Douglas, Kersen, David, Qu, Angie

[International Worm Meeting, 2015]

When humans and worms are born, they have neuronal circuits in place to integrate sensory cues and effect appropriate behavioural or homeostatic responses. During the course of development, a substantial amount of remodelling occurs in the nervous system. New neurons are born and integrated into existing circuits, and existing neurons and circuits are remodelled. The rules of this remodelling are poorly characterised, because in order to investigate neuronal circuit development one needs a connectome-level analysis of the circuit across multiple time points, in multiple animals. This strategy requires serial-section electron microscopy, which has been very low-throughput and labour-intensive.C. elegans represents an ideal organism to perform these studies on, because of their small size and stereotypical development - some of the reasons they were chosen for the original adult serial-section EM reconstruction that culminated in the acquisition of the adult connectome, dubbed 'The mind of a worm'. Since the publication of this landmark paper, new technologies have been developed that improve the fidelity and throughput of the connectome reconstruction, including better fixation methods, increased computational power and more advanced microscopes.We are reconstructing the entire nervous system of multiple L1 worms using serial-section transmission and scanning electron microscopy. The L1 worm is of special interest because of the major remodelling that occurs at the end of L1, including the birth of new major classes of motor neurons. We are finding both conserved and unreported structure and connectivity from the published adult wiring diagram. This dataset will be used as a framework to functionally interrogate the interplay between developing circuits and sensorimotor behaviours, and the mechanisms that allow this dialogue to take place.