Selected papers (see entire list here)

Neurogenin regulates effectors of migratory neuron cell behaviors in Ciona [Preprint]

Susanne Gibboney, Kwantae Kim, Florian Razy-Krajka, Wei Wang, and Alberto Stolfi (2019)

RNAseq was used to identify potential effectors of Bipolar Tain Neuron cell behaviors like delamination, migration, and polarization. We identified various such candidate genes downstream of the transcription factor Neurogenin, including a potential small G alpha protein subunit that might act as a molecular “switch” for BTN delamination. LINK

Neuron subtype-specific effector gene expression in the Motor Ganglion of Ciona [Preprint]

Susanne Gibboney, Kwantae Kim, Christopher J. Johnson, Jameson Orvis, Paula Martinez-Feduchi, Elijah K. Lowe, Sarthak Sharma, and Alberto Stolfi (2019)

Transcriptional profiles of two distinct Motor Ganglion neuron subtype (ddN vs. MGIN2) were compared, resulting in candidate effectors of MG neuron subtype-specific functional and morphological traits. Among these are intriguing intracellular and extracellular proteins that might be controlling the dynamic repolarization of ddNs as they extend their axons across the midline. LINK

A cis-regulatory change underlying the motor neuron-specific loss of terminal selector gene expression in immotile tunicate larvae [Preprint]

Elijah K. Lowe, Claudia Racioppi, Nadine Peyriéras, Filomena Ristoratore, Lionel Christiaen, Billie J. Swalla, and Alberto Stolfi (2019)

We identified a cis-regulatory change underlying the reduced expression of a key neuronal regulator, Collier/Olf/Ebf (COE) in the Motor Ganglion of tail-less, non-swimming larvae of Molgula occulta. The MG-specific reduction of Ebf expression in turn might underlie a loss of motor neuron differentiation, as a result of relaxed purifying selection. LINK

Regulation and evolution of muscle development in tunicates

Florian Razy-Krajka and Alberto Stolfi (2019)

In this review article, we summarize the current literature on muscle specification and differentiation in tunicates, covering all major tunicate classes and orders, including thaliaceans (salps, pyrosomes, and doliolids) and appendicularians. We discuss these findings in the context of tunicate and animal evolution in general. LINK

Single-cell transcriptome profiling of the Ciona larval brain

Sarthak Sharma, Wei Wang, and Alberto Stolfi (2019)

Single-cell RNAseq was used to identify specific subsets of cells isolated and selected from the brains of Ciona larvae, and to determine the unique gene expression profiles of each cell type. PDF

Developmental system drift in motor ganglion patterning between distantly related tunicates

Elijah K. Lowe and Alberto Stolfi (2018)

Here we demonstrate that the specification and final arrangement of the distinct neuronal subtypes of the tunicate spinal cord homolog, the Motor Ganglion, is deeply conserved between distantly related solitary tunicates, suggesting that this structure represents an ancient and highly adapted minimal central pattern generator for larval swimming. PDF

Evolutionary loss of melanogenesis in the tunicate Molgula occulta

Claudia Racioppi, Maria Carmen Valoroso, Ugo Coppola, Elijah K. Lowe, C. Titus Brown, Billie J. Swalla, Lionel Christiaen, Alberto Stolfi, and Filomena Ristoratore (2017)

We found that the tunicate Molgula occulta has lost the genes encoding crucial enzymes for melanin synthesis, perhaps because its tail-less larvae do not swim and have no need for pigmented light- and gravity-sensing organs. PDF

Evaluation and rational design of guide RNAs for efficient CRISPR/Cas9-mediated mutagenesis in Ciona

Shashank Gandhi, Maximilian Haeussler, Florian Razy-Krajka, Lionel Christiaen, and Alberto Stolfi (2017)

We developed a novel pipeline for rapid yet accurate design, synthesis, and evaluation of efficient sgRNAs for high-throughput, tissue-specific CRISPR/Cas9 knockouts in Ciona embryos. PDF

Migratory neuronal progenitors arise from the neural plate borders in tunicates

Alberto Stolfi, Kerrianne Ryan, Ian A. Meinertzhagen, and Lionel Christiaen (2015)

We show that a neuronal cell type in the  larva of the tunicate Ciona, the bipolar tail neuron, shares a set of features with neural-crest-derived spinal ganglia neurons in vertebrates, hinting at the pre-vertebrate origins of the neural crest. PDF

Tissue-specific genome editing in Ciona embryos by CRISPR/Cas9

Alberto Stolfi, Shashank Gandhi, Farhana Salek, and Lionel Christiaen (2014)

We report the first use of CRISPR/Cas9 for tissue-specific genome editing in the tunicate Ciona. Using this technique to disrupt the Ebf gene in different cell lineages, we revealed that its function is required for specification motor ganglion neurons and atrial siphon muscles. PDF

Divergent mechanisms regulate conserved cardiopharyngeal development and gene expression in distantly related ascidians

Alberto Stolfi*, Elijah Lowe*, Claudia Racioppi, Filomena Ristoratore, C. Titus Brown, Billie J. Swalla, and Lionel Christiaen (2014) *equal contributions

Comparisons between the distantly related tunicates Molgula and Ciona reveal cryptic turnover
of regulatory mechanisms that underlie identical gene expression patterns. PDF

Coordinated regulation of cholinergic motor neuron traits through a conserved terminal selector gene

Paschalis Kratsios, Alberto Stolfi, Michael Levine, and Oliver Hobert (2012)

We show that UNC-3/Ebf is a terminal selector for cholinergic motor neuron differentiation whose function is conserved across phylogeny, from C. elegans to Ciona. PDF

Genetic and genomic toolbox of the chordate Ciona intestinalis

Alberto Stolfi and Lionel Christiaen (2012)

A review on the tools, techniques, and resources available to the Ciona geneticist, citing examples of studies that employed such strategies in the elucidation of gene function in Ciona: electroporation, transgenesis, genetic screens, and a preview of the emergence of genetic engineering platforms like CRISPR/Cas9. PDF

Neural tube patterning by Ephrin, FGF, and Notch signaling relays

Alberto Stolfi, Eileen Wagner, J. Matthew Taliaferro, Seemay Chou, and Michael Levine (2011)

We show that the Ciona Motor Ganglion is patterned by sequential Ephrin/FGF/MAPK and Delta/Notch signaling events that lead to localized expression of conserved homeodomain codes for the specification of distinct neuronal subtypes. PDF

Neuronal subtype specification in the spinal cord of a protovertebrate

Alberto Stolfi and Michael Levine (2011)

We used fluorescent reporter constructs to label and identify invariant but morphologically distinct moto- and interneuron subtypes in the Motor Ganglion of the Ciona larva. We also perturbed neuronal subtype specification in predictable ways by targeting specific transcription factors and signaling molecules. PDF

Early chordate origins of the vertebrate second heart field

Alberto Stolfi, T. Blair Gainous, John J. Young, Alessandro Mori, Michael Levine, and Lionel Christiaen (2010)

We found that heart progenitor cells of the simple chordate Ciona also generate precursors of the pharyngeal muscles. These precursors express Islet and Tbx1/10, evocative of the splanchnic mesoderm that produces the lower jaw muscles and Second Heart Field of vertebrates. We propose that the last common ancestor of tunicates and vertebrates possessed multipotent cardiopharyngeal muscle precursors, and that their reallocation might have contributed to the emergence of the SHF. PDF

Gene regulatory networks underlying the compartmentalization of the Ciona central nervous system

Kaoru S. Imai, Alberto Stolfi, Michael Levine, and Yutaka Satou (2009)

Here we document provisional gene regulatory networks operating in the developing central nervous system of Ciona, at single-cell resolution. This revealed a striking conservation in neural gene expression and patterning relative to vertebrates. More careful analysis revealed a role for FGF8 in patterning the Ciona hindbrain in a manner reminiscent of the midbrain/hindbrain boundary organizer in vertebrates. PDF