Hernando M. Vergara

Hernando M. Vergara

Experimental and computational neurobiologist

Publications

MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data

Published in Nature Methods, 2023

Modern microscopy produces massive image datasets that enable detailed multi-scale analysis and can combine several modalities. Visualizing, exploring and sharing such data are challenges both during the execution of a research project and after publication to enable open access. To this end we have developed MoBIE, a Fiji1 plugin for multi-modal big image data sharing and exploration. It supports visualization of multi-scale data of heterogeneous dimensionality (that is, combined 2D, 3D or 4D data) and several-terabyte image data, as well as the exploration of image segmentations, corresponding measurements and annotations. MoBIE uses next-generation image file formats, such as OME-Zarr2, that enable access to multi-scale data on local or cloud storage, permitting the transparent sharing and publication of data without the need to run a web service. In addition, MoBIE allows users to easily configure and share fully reproducible ‘views’ of their data. MoBIE has enabled integration of multiple modalities and open access for data from different domains of the life sciences. This includes data from studies in developmental biology3 (Fig. 1a), correlative microscopy, high-throughput screening microscopy4, plant biology and spatial transcriptomics5 (all Fig. 1c). Further applications can be found in Supplementary Note 8 and Supplementary Figs. 1–4. Video tutorials for MoBIE are available at https://www.youtube.com/@MoBIE-Viewer and documentation at https://mobie.github.io/.

Recommended citation: Constantin Pape, Kimberly Meechan, Ekaterina Moreva, Martin Schorb, Nicolas Chiaruttini, Valentyna Zinchenko, Hernando Vergara, Giulia Mizzon, Josh Moore, Detlev Arendt, Anna Kreshuk, Yannick Schwab, Christian Tischer, "MoBIE: a Fiji plugin for sharing and exploration of multi-modal cloud-hosted big image data." Nature Methods, 2023.

Action prediction error: a value-free dopaminergic teaching signal that drives stable learning

Published in bioRxiv, 2022

Animals choice behavior is characterized by two main tendencies: taking actions that led to rewards and repeating past actions. Theory suggests these strategies may be reinforced by different types of dopaminergic teaching signals: reward prediction error (RPE) to reinforce value-based associations and movement-based action prediction errors to reinforce value-free repetitive associations. Here we use an auditory-discrimination task in mice to show that movement-related dopamine activity in the tail of the striatum encodes the hypothesized action prediction error signal. Causal manipulations reveal that this prediction error serves as a value-free teaching signal that supports learning by reinforcing repeated associations. Computational modeling and experiments demonstrate that action prediction errors cannot support reward-guided learning but when paired with the RPE circuity they serve to consolidate stable sound-action associations in a value-free manner. Together we show that there are two types of dopaminergic prediction errors that work in tandem to support learning.

Recommended citation: Francesca Greenstreet, Hernando Vergara, Sthitapranjya Pati, Laura Schwarz, Matthew Wisdom, Fred Marbach, Yvonne Johansson, Lars Rollik, Theodore Moskovitz, Claudia Clopath, Marcus Stephenson-Jones, "Action prediction error: a value-free dopaminergic teaching signal that drives stable learning." bioRxiv, 2022.

The conserved core of the nereid brain: Circular CNS, apical nervous system and lhx6-arx-dlx neurons

Published in Current Opinion in Neurobiology, 2021

When bilaterian animals first emerged, an enhanced perception of the Precambrian environment was key to their stunning success. This occurred through the acquisition of an anterior brain, as found in most extant bilaterians. What were the core circuits of the first brain, and how do they relate to today's diversity? With two landmark resources – the full connectome and a multimodal cellular atlas combining gene expression and ultrastructure – the young worm of the marine annelid Platynereis dumerilii takes center stage in comparative bilaterian neuroanatomy. The new data suggest a composite structure of the ancestral bilaterian brain, with the anterior end of a circular CNS fused to a sensory-neurosecretory apical system, and with lhx6-arx-dlx chemosensory circuits giving rise to associative centers in the descending bilaterian lineages.

Recommended citation: Detlev Arendt, Idoia Urzainqui, Hernando Vergara, "The conserved core of the nereid brain: Circular CNS, apical nervous system and lhx6-arx-dlx neurons." Current Opinion in Neurobiology, 2021.

The Nereid on the rise: Platynereis as a model system

Published in EvoDevo, 2021

The Nereid Platynereis dumerilii (Audouin and Milne Edwards (Annales des Sciences Naturelles 1:195-269, 1833) is a marine annelid that belongs to the Nereididae, a family of errant polychaete worms. The Nereid shows a pelago-benthic life cycle: as a general characteristic for the superphylum of Lophotrochozoa/Spiralia, it has spirally cleaving embryos developing into swimming trochophore larvae. The larvae then metamorphose into benthic worms living in self-spun tubes on macroalgae. Platynereis is used as a model for genetics, regeneration, reproduction biology, development, evolution, chronobiology, neurobiology, ecology, ecotoxicology, and most recently also for connectomics and single-cell genomics. Research on the Nereid started with studies on eye development and spiralian embryogenesis in the nineteenth and early twentieth centuries. Transitioning into the molecular era, Platynereis research focused on posterior growth and regeneration, neuroendocrinology, circadian and lunar cycles, fertilization, and oocyte maturation. Other work covered segmentation, photoreceptors and other sensory cells, nephridia, and population dynamics. Most recently, the unique advantages of the Nereid young worm for whole-body volume electron microscopy and single-cell sequencing became apparent, enabling the tracing of all neurons in its rope-ladder-like central nervous system, and the construction of multimodal cellular atlases. Here, we provide an overview of current topics and methodologies for P. dumerilii, with the aim of stimulating further interest into our unique model and expanding the active and vibrant Platynereis community.

Recommended citation: B. Özpolat, Nadine Randel, Elizabeth Williams, Luis Bezares-Calderon, Gabriele Andreatta, Guillaume Balavoine, Paola Bertucci, David Ferrier, Maria Gambi, Eve Gazave, Mette Handberg-Thorsager, Jörg Hardege, Cameron Hird, Yu-Wen Hsieh, Jerome Hui, Kevin Mutemi, Stephan Schneider, Oleg Simakov, Hernando Vergara, Michel Vervoort, Gaspar Jekely, Kristin Tessmar-Raible, Florian Raible, Detlev Arendt, "The Nereid on the rise: Platynereis as a model system." EvoDevo, 2021.

Standardized and reproducible measurement of decision-making in mice

Published in eLife, 2021

Progress in science requires standardized assays whose results can be readily shared, compared, and reproduced across laboratories. Reproducibility, however, has been a concern in neuroscience, particularly for measurements of mouse behavior. Here, we show that a standardized task to probe decision-making in mice produces reproducible results across multiple laboratories. We adopted a task for head-fixed mice that assays perceptual and value-based decision making, and we standardized training protocol and experimental hardware, software, and procedures. We trained 140 mice across seven laboratories in three countries, and we collected 5 million mouse choices into a publicly available database. Learning speed was variable across mice and laboratories, but once training was complete there were no significant differences in behavior across laboratories. Mice in different laboratories adopted similar reliance on visual stimuli, on past successes and failures, and on estimates of stimulus prior probability to guide their choices. These results reveal that a complex mouse behavior can be reproduced across multiple laboratories. They establish a standard for reproducible rodent behavior, and provide an unprecedented dataset and open-access tools to study decision-making in mice. More generally, they indicate a path toward achieving reproducibility in neuroscience through collaborative open-science approaches.

Recommended citation: The Laboratory, Valeria Aguillon-Rodriguez, Dora Angelaki, Hannah Bayer, Niccolo Bonacchi, Matteo Carandini, Fanny Cazettes, Gaelle Chapuis, Anne Churchland, Yang Dan, Eric Dewitt, Mayo Faulkner, Hamish Forrest, Laura Haetzel, Michael Häusser, Sonja Hofer, Fei Hu, Anup Khanal, Christopher Krasniak, Ines Laranjeira, Zachary Mainen, Guido Meijer, Nathaniel Miska, Thomas Mrsic-Flogel, Masayoshi Murakami, Jean-Paul Noel, Alejandro Pan-Vazquez, Cyrille Rossant, Joshua Sanders, Karolina Socha, Rebecca Terry, Anne Urai, Hernando Vergara, Miles Wells, Christian Wilson, Ilana Witten, Lauren Wool, Anthony Zador, "Standardized and reproducible measurement of decision-making in mice." eLife, 2021.

Whole-body integration of gene expression and single-cell morphology

Published in Cell, 2021

Animal bodies are composed of cell types with unique expression programs that implement their distinct locations, shapes, structures, and functions. Based on these properties, cell types assemble into specific tissues and organs. To systematically explore the link between cell-type-specific gene expression and morphology, we registered an expression atlas to a whole-body electron microscopy volume of the nereid Platynereis dumerilii. Automated segmentation of cells and nuclei identifies major cell classes and establishes a link between gene activation, chromatin topography, and nuclear size. Clustering of segmented cells according to gene expression reveals spatially coherent tissues. In the brain, genetically defined groups of neurons match ganglionic nuclei with coherent projections. Besides interneurons, we uncover sensory-neurosecretory cells in the nereid mushroom bodies, which thus qualify as sensory organs. They furthermore resemble the vertebrate telencephalon by molecular anatomy. We provide an integrated browser as a Fiji plugin for remote exploration of all available multimodal datasets.

Recommended citation: Hernando Vergara, Constantin Pape, Kimberly Meechan, Valentyna Zinchenko, Christel Genoud, Adrian Wanner, Kevin Mutemi, Benjamin Titze, Rachel Templin, Paola Bertucci, Oleg Simakov, Wiebke Dürichen, Pedro Machado, Emily Savage, Lothar Schermelleh, Yannick Schwab, Rainer Friedrich, Anna Kreshuk, Christian Tischer, Detlev Arendt, "Whole-body integration of gene expression and single-cell morphology." Cell, 2021.

miR-206 is required for changes in cell adhesion that drive muscle cell morphogenesis in Xenopus laevis

Published in Developmental Biology, 2018

MicroRNAs (miRNAs) are highly conserved small non-coding RNA molecules that post-transcriptionally regulate gene expression in multicellular organisms. Within the set of muscle-specific miRNAs, miR-206 expression is largely restricted to skeletal muscle and is found exclusively within the bony fish lineage. Although many studies have implicated miR-206 in muscle maintenance and disease, its role in skeletal muscle development remains largely unknown. Here, we examine the role of miR-206 during Xenopus laevis somitogenesis. In Xenopus laevis, miR-206 expression coincides with the onset of somitogenesis. We show that both knockdown and over-expression of miR-206 result in abnormal somite formation affecting muscle cell rotation, attachment, and elongation. In particular, our data suggests that miR-206 regulates changes in cell adhesion that affect the ability of newly formed somites to adhere to the notochord as well as to the intersomitic boundaries. Additionally, we show that β-dystroglycan and F-actin expression levels are significantly reduced, suggesting that knockdown of miR-206 levels affects cellular mechanics necessary for cell shape changes and attachments that are required for proper muscle formation.

Recommended citation: Hernando Vergara, Julio Ramirez, Trista Rosing, Ceazar Nave, Rebecca Blandino, Daniel Saw, Parag Saraf, Gabriel Piexoto, Coohleen Coombes, Melissa Adams, Carmen Domingo, "miR-206 is required for changes in cell adhesion that drive muscle cell morphogenesis in Xenopus laevis." Developmental Biology, 2018.

Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body

Published in Molecular Biology and Evolution, 2018

{Animal bodies comprise diverse arrays of cells. To characterize cellular identities across an entire body, we have compared the transcriptomes of single cells randomly picked from dissociated whole larvae of the marine annelid Platynereis dumerilii. We identify five transcriptionally distinct groups of differentiated cells, each expressing a unique set of transcription factors and effector genes that implement cellular phenotypes. Spatial mapping of cells into a cellular expression atlas, and wholemount in situ hybridization of group-specific genes reveals spatially coherent transcriptional domains in the larval body, comprising, for example, apical sensory-neurosecretory cells versus neural/epidermal surface cells. These domains represent new, basic subdivisions of the annelid body based entirely on differential gene expression, and are composed of multiple, transcriptionally similar cell types. They do not represent clonal domains, as revealed by developmental lineage analysis. We propose that the transcriptional domains that subdivide the annelid larval body represent families of related cell types that have arisen by evolutionary diversification. Their possible evolutionary conservation makes them a promising tool for evo–devo research.}

Recommended citation: Kaia Achim, Nils Eling, Hernando Vergara, Paola Bertucci, Jacob Musser, Pavel Vopalensky, Thibaut Brunet, Paul Collier, Vladimir Benes, John Marioni, Detlev Arendt, "Whole-Body Single-Cell Sequencing Reveals Transcriptional Domains in the Annelid Larval Body." Molecular Biology and Evolution, 2018.

Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas

Published in RNA Detection: Methods and Protocols, 2018

The method described here aims at the construction of a single-cell resolution gene expression atlas for an animal or tissue, combining in situ hybridization (ISH) and single-cell mRNA-sequencing (scRNAseq).

Recommended citation: Kaia Achim, Hernando Vergara, Jean-Baptiste Pettit, "Spatial Transcriptomics: Constructing a Single-Cell Resolution Transcriptome-Wide Expression Atlas." RNA Detection: Methods and Protocols, 2018.

Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii

Published in Proceedings of the National Academy of Sciences of the United States of America, 2017

The comparative study of cell types is a powerful approach toward deciphering animal evolution. To avoid selection biases, however, comparisons ideally involve all cell types present in a multicellular organism. Here, we use image registration and a newly developed “Profiling by Signal Probability Mapping” algorithm to generate a cellular resolution 3D expression atlas for an entire animal. We investigate three-segmented young worms of the marine annelid Platynereis dumerilii, with a rich diversity of differentiated cells present in relatively low number. Starting from whole-mount expression images for close to 100 neural specification and differentiation genes, our atlas identifies and molecularly characterizes 605 bilateral pairs of neurons at specific locations in the ventral nerve cord. Among these pairs, we identify sets of neurons expressing similar combinations of transcription factors, located at spatially coherent anterior-posterior, dorsal-ventral, and medial-lateral coordinates that we interpret as cell types. Comparison with motor and interneuron types in the vertebrate neural tube indicates conserved combinations, for example, of cell types cospecified by Gata1/2/3 and Tal transcription factors. These include V2b interneurons and the central spinal fluid-contacting Kolmer-Agduhr cells in the vertebrates, and several neuron types in the intermediate ventral ganglionic mass in the annelid. We propose that Kolmer-Agduhr cell-like mechanosensory neurons formed part of the mucociliary sole in protostome-deuterostome ancestors and diversified independently into several neuron types in annelid and vertebrate descendants.

Recommended citation: Hernando Vergara, Paola Bertucci, Peter Hantz, Maria Tosches, Kaia Achim, Pavel Vopalensky, Detlev Arendt, "Whole-organism cellular gene-expression atlas reveals conserved cell types in the ventral nerve cord of Platynereis dumerilii." Proceedings of the National Academy of Sciences of the United States of America, 2017.

Descriptive and functional approaches for a system-level understanding of Platynereis dumerilii and the evolution of locomotor circuits in Bilateria

Published in Heidelberg University Library, 2016

The nervous system, built by the powerful capability of neurons to intercommunicate, is the most fascinating biological achievement, which through evolution has given rise to highly complex structures responsible for remarkable animal behaviours. It is therefore surprising, and at the same time highly motivating for a scientist, to realise how little we know about this evolutionary process. Traditional approaches like palaeontology and phylogenomics lack the resolution to confidently solve the history of neuronal circuits. Nevertheless, thanks to modern comprehensive techniques and integrative approaches, it is possible to molecularly, morphologically and functionally describe entire nervous systems by their constituent components, the cell types. The comparison of cell types and circuits across animals will help elucidate the different evolutionary steps that led to extant nervous systems. Within this thesis, the reader will find a description of the research I have conducted on the implementation of system-level approaches to characterize cell types, with the goal of achieving an integrative understanding of the nervous system of Platynereis dumerilii, an animal suited for these system-level evolutionary studies. A special emphasis has been given to the generation of a new automatic pipeline to build gene expression atlases for complex body plans, the design of image analysis routines to monitor and quantify animal behaviour, and the implementation of the Crispr/Cas9 technique in this organism. I also describe pioneer work to reconstruct the full connectome of the larvae at six days post fertilization, the combination of light-sheet microscopy and calcium indicators to monitor neuronal activity in thousands of neurons, and the proof-of-principle of using optogenetics to manipulate neuronal activity in Platynereis. Because of the relevance of the control of muscle contraction for the evolution of nervous systems, and the vast amount of information collected for various animals with regards to locomotion (Goulding, 2009), I focus my analysis on the post-mitotic Platynereis ventral nerve cord. I show that this structure contains the circuits responsible for the crawling behaviour, and describe in detail the kinematics of these movements, which suggest a similar organization of circuits than vertebrates and segmental protostomes. Using the expression atlas, I unbiasedly unravel the molecular substructure of the ventral nerve cord, which consists of cell types grouped into general medio-lateral domains, remarkably similar to those in vertebrates, as well as different territories unique to protostomes. I further characterize in detail a commissural cell population, showing strong similarities with both vertebrates and Drosophila in terms of position, molecular profile, morphology and function. These findings support the idea of an ancestral cell type, specified by a newly acquired gene, which controlled the coordination between the two sides of the body during locomotion in the bilaterian ancestor.

Recommended citation: Hernando Martinez, "Descriptive and functional approaches for a system-level understanding of Platynereis dumerilii and the evolution of locomotor circuits in Bilateria." Heidelberg University Library, 2016.

The Role of Sdf-1α signaling in Xenopus laevis somite morphogenesis

Published in Developmental Dynamics, 2014

Background: Stromal derived factor-1α (sdf-1α), a chemoattractant chemokine, plays a major role in tumor growth, angiogenesis, metastasis, and in embryogenesis. The sdf-1α signaling pathway has also been shown to be important for somite rotation in zebrafish (Hollway et al., 2007). Given the known similarities and differences between zebrafish and Xenopus laevis somitogenesis, we sought to determine whether the role of sdf-1α is conserved in Xenopus laevis. Results: Using a morpholino approach, we demonstrate that knockdown of sdf-1α or its receptor, cxcr4, leads to a significant disruption in somite rotation and myotome alignment. We further show that depletion of sdf-1α or cxcr4 leads to the near absence of β-dystroglycan and laminin expression at the intersomitic boundaries. Finally, knockdown of sdf-1α decreases the level of activated RhoA, a small GTPase known to regulate cell shape and movement. Conclusion: Our results show that sdf-1α signaling regulates somite cell migration, rotation, and myotome alignment by directly or indirectly regulating dystroglycan expression and RhoA activation. These findings support the conservation of sdf-1α signaling in vertebrate somite morphogenesis; however, the precise mechanism by which this signaling pathway influences somite morphogenesis is different between the fish and the frog.

Recommended citation: Marisa Leal, Sarah Fickel, Armbien Sabillo, Julio Ramirez, Hernando Vergara, Ceazar Nave, Daniel Saw, Carmen Domingo, "The Role of Sdf-1α signaling in Xenopus laevis somite morphogenesis." Developmental Dynamics, 2014.