Yale Passamaneck

United States Bureau of Reclamation · Technical Service Center - Ecological Research Laboratory

Spiralia is a large, ancient and diverse clade of animals, with a conserved early developmental program but diverse larval and adult morphologies. One trait shared by many spiralians is the presence of ciliary bands used for locomotion and feeding. To learn more about spiralian-specific traits we have examined the expression of 20 genes with protei...

Background: Phoronids, rhynchonelliform and linguliform brachiopods show striking similarities in their embryonic fate maps, in particular in their axis specification and regionalization. However, although brachiopod development has been studied in detail and demonstrated embryonic patterning as a causal factor of the gastrulation mode (protostomy...

Background: Answering the question how conserved patterning systems are across evolutionary lineages requires a broad taxon sampling. Phoronid development has previously been studied using fate mapping and morphogenesis, yet molecular descriptions are missing. Here we report the expression patterns of the evolutionarily conserved anterior (otx, gsc...

Background: Answering the question how conserved patterning systems are across evolutionary lineages requires a broad taxon sampling. Phoronid development has previously been studied using fate mapping and morphogenesis, yet molecular descriptions are missing. Here we report the expression patterns of the evolutionarily conserved anterior (otx, gsc...

In a multitude of organisms, transcription factors of the basic helix-loop-helix (bHLH) family control the expression of genes required for organ development and tissue differentiation. The functions of different bHLH transcription factors in the specification of nervous system and paraxial mesoderm have been widely investigated in various model sy...

Temporal collinearity is often considered the main force preserving Hox gene clusters in animal genomes. Studies that combine genomic and gene expression data are scarce, however, particularly in invertebrates like the Lophotrochozoa. As a result, the temporal collinearity hypothesis is currently built on poorly supported foundations. Here we chara...

The mouth opening of bilaterian animals develops either separate from (deuterostomy) or connected to (protostomy) the embryonic blastopore, the site of endomesoderm internalization. Although this distinction preluded the classification of bilaterian animals in Deuterostomia and Protostomia, and has influenced major scenarios of bilaterian evolution...

Cordylophora caspia (Pallas, 1771) colonies have significant biofouling potential at hydropower facilities, which can increase maintenance and cause system failure. In 2015, C. caspia colonies were observed at dams along the Lower Colorado River system in Lake Powell UT, Lake Mead NV/AZ, Lake Mohave AZ/NV, and Lake Havasu AZ/CA. The hydroid was ser...

A main challenge of modern biology is to understand how specific constellations of genes are activated to differentiate cells and give rise to distinct tissues. This study focuses on elucidating how gene expression is initiated in the notochord, an axial structure that provides support and patterning signals to embryos of humans and all other chord...

Architectural constraints, sequence motifs and interspecies conservation of Ciona notochord CRMs. Related to Figs 1 and 3. a-d: Impact of the alteration of structural features on the function of Ci-CRM76 in notochord cells. (Left) schematic representations of wild-type (WT) and mutant versions of Ci-CRM76 containing the changes in enhancer architec...

Properties of genomic regions containing sequence motifs found in subsets of notochord CRMs. (DOCX)

Initial characterization of a subset of the notochord CRMs described in Fig 1. a-f: Schematic representations of wild-type notochord CRMs and site-specific mutants of selected binding sites (see Fig 1 for key). Maroon bars represent constructs capable of directing notochord expression of the LacZ reporter, while inactive configurations are depicte...

Deletion/mutation analysis of the notochord CRMs described in Fig 3 and of Ci-CRM9. a-e: (Left) Schematic representations of notochord CRMs and their mutant versions. Putative binding sites are depicted as shown in the key on the top right in a. Color-coding is as in S1 Fig. Mutagenized sites are indicated by “X” signs and the mutant sequences are...

Primers utilized for the PCR amplification of the most relevant constructs used for CRM characterization. (DOCX)

Deletion/mutation analysis of the notochord CRMs described in Fig 2. a,b,d: Schematic representations of wild-type notochord CRMs and site-directed mutants of the binding sites shown in the key (top right). The color-coding of the bars representing the DNA regions is the same as in Fig 2. “X” signs indicate mutagenized sites, and mutant sequences...

Genomic locations of minimal notochord CRMs. (DOCX)

Properties of (AC) microsatellite clusters tested for notochord activity. (DOCX)

Properties of genomic regions near notochord genes showing arrangements of sites resembling those found in selected notochord CRMs. (DOCX)

Detoxification is a fundamental cellular stress defense mechanism, which allows an organism to survive or even thrive in the presence of environmental toxins and/or pollutants. The glutathione S-transferase (GST) superfamily is a set of enzymes involved in the detoxification process. This highly diverse protein superfamily is characterized by multi...

Brachiopods undergo radial cleavage, which is distinct from the stereotyped development of closely related spiralian taxa. The mesoderm has been inferred to derive from the archenteron walls following gastrulation, and the primary mesoderm derivative in the larva is a complex musculature. To investigate the specification and differentiation of the...

Background The primary hormone of the vertebrate pineal gland, melatonin, has been identified broadly throughout the eukaryotes. While the role for melatonin in cyclic behavior via interactions with the circadian clock has only been reported in vertebrates, comparative research has shown that the transcription-translation loops of the animal circad...

The aryl hydrocarbon receptor (AHR) is a member of the basic helix-loop-helix/Per-ARNT-Sim (bHLH-PAS) family of transcription factors and has diverse roles in development, physiology, and environmental sensing in bilaterian animals. Studying the expression of conserved genes and function of proteins in outgroups to protostomes and deuterostomes ass...

Author Summary Transcription factors control where and when gene expression is switched on by binding to specific stretches of DNA known as cis-regulatory modules (CRMs). In this study, we investigated the architecture and composition of CRMs that direct gene expression in the notochord—a transient rod-like structure found in all embryos that belon...

Bilaterian photoreceptor cells are characterized by the expression of opsins, signal transduction genes, and ion channels, which together facilitate behavioral responses to light. We have previously identified a ciliary opsin gene from the brachiopod Terebratalia transversa, whose expression in gastrula stage embryos coincides with a photoresponse...

Background The contribution of cell proliferation to regeneration varies greatly between different metazoan models. Planarians rely on pluripotent neoblasts and amphibian limb regeneration depends upon formation of a proliferative blastema, while regeneration in Hydra can occur in the absence of cell proliferation. Recently, the cnidarian Nematoste...

Larval features such as the apical organ, apical ciliary tuft, and ciliated bands often complicate the evaluation of hypotheses regarding the origin of the adult bilaterian nervous system. Understanding how neurogenic domains form within the bilaterian head and larval apical organ requires expression data from animals that exhibit aspects of both c...

Phylogenetic analysis of Tt-synaptotagmin 1. Phylogram of Tt-synaptotagmin 1 and related synaptotagmin proteins, supporting the orthology assignment of Tt-synaptotagmin 1. Posterior probability for the synaptotagmin 1 clade, including Tt-synaptotagmin 1, is 100 percent (inclusive of the presumptive paralogs Mus Syt2, Mus Syt5 and Mus Syt8). The phy...

Presumed light-perceptive cilium of the pigment cell in a larval eye of Terebratalia. (A-I) Series of aligned sections to illustrate the ciliary membrane forming the stack of membranes (m) in the optical cavity enclosed by the lens (ls) and the pigment granules (pg). (J) Close-up of the membrane stack (m) showing the invagination of the ciliary mem...

Alignment of deduced amino acid sequences for C-terminus of Terebratalia c-opsin and representative c-opsins from other taxa. Alignment of the of Terebratalia c-opsin C-terminus to the C-termini of other c-opsins. The conserved C-terminus domain is required for localization of c-opsin proteins to the ciliary compartment, through binding to the ligh...

Middle gastrula swimming with directional illumination. Time lapse imaging of middle gastrula stage embryos swimming in the phototaxis chamber 20 minutes after the initiation of directional illumination. Embryos are clustered on the left side of the chamber, closest to the source of directional illumination. Frame rate is 5× faster than real-time.

Middle gastrula swimming prior to directional illumination. Time lapse imaging of middle gastrula stage embryos swimming in the phototaxis chamber prior to the initiation of directional illumination. Embryos are evenly distributed throughout the chamber. Frame rate is 5× faster than real-time.

Middle gastrula swimming after directional illumination. Time lapse imaging of middle gastrula stage embryos swimming in the phototaxis chamber 10 minutes after the cessation of directional illumination. Embryos have returned to an even distribution throughout the chamber. Frame rate is 5× faster than real-time.

Eyes in bilaterian metazoans have been described as being composed of either ciliary or rhabdomeric photoreceptors. Phylogenetic distribution, as well as distinct morphologies and characteristic deployment of different photopigments (ciliary vs. rhabdomeric opsins) and transduction pathways argue for the co-existence of both of these two photorecep...

For over a century, muscle formation in the ascidian embryo has been representative of 'mosaic' development. The molecular basis of muscle-fate predetermination has been partly elucidated with the discovery of Macho1, a maternal zinc-finger transcription factor necessary and sufficient for primary muscle development, and of its transcriptional inte...

The notochord is a defining feature of the chordate body plan. Experiments in ascidian, frog and mouse embryos have shown that co-expression of Brachyury and FoxA class transcription factors is required for notochord development. However, studies on the cis-regulatory sequences mediating the synergistic effects of these transcription factors are co...

The notochord is a defining character of the chordates, and the T-box transcription factor Brachyury has been shown to be required for notochord development in all chordates examined. In the ascidian Ciona intestinalis, at least 44 notochord genes have been identified as bona fide transcriptional targets of Brachyury. We examined the embryonic expr...

To reconstruct a minimum complement of notochord genes evolutionarily conserved across chordates, we scanned the Ciona intestinalis genome using the sequences of 182 genes reported to be expressed in the notochord of different vertebrates and identified 139 candidate notochord genes. For 66 of these Ciona genes expression data were already availabl...

Acid-sensing ion channels (ASICs) constitute a family of neuron-specific voltage-insensitive sodium channels gated by extracellular protons. Functions of ASICs in mammals include nociception, mechanosensation, and modulation of synaptic transmission. However, the role protons play in mediating the effects of ASICs remains elusive. We have examined...

Synchronous development of imaged and control embryos. (A) Embryo imaged by laser scanning for 2 hours during tail extension. The embryo was maintained at ambient room temperature of 21°C and the photomicrograph was captured at 10 hours post fertilization. (B, C) Wild type embryos from the same fertilization as the embryo in (A). Wild type embryos...

Muscle cells are correctly specified in embryos electroporated with sna>Bix. Expression of marker genes of muscle differentiation in wild type and sna>Bix embryos. (A, B) Expression of muscle actin in wild type and sna>Bix embryos. (C, D) Expression of myosin regulatory light chain (MRLC) in wild type and sna>Bix embryos. (E, F) Expression of tropo...

Phenotypes and movement of wild type and sna>Bix larvae. A time series is shown with sna>Bix larvae (left) and wild type larvae (right). Images were taken at two second intervals. Arrows indicate the movement of the two wild type larvae due to muscle contractions during the time series. Note that neither of the sna>Bix larvae has changed position....

Organization of myofibrils in wild type and sna>Bix larvae, as visualized by rhodamine phalloidin labeling. (A) Myofibrils in a wild type larva. (B) Myofibrils in a larva electroporated with sna>Bix. Myofibrils in the sna>Bix larvae are less numerous and less organized than those in wild type larvae. (2.39 MB TIF)

Changes in muscle cell geometry during tail extension visualized with the vital dye FM4-64. (A) Embryo electroporated with Tbx6b>H2B-GFP to mark muscle cells and incubated with FM4-64 to label cell membranes. (B) Graph of average muscle cell shape (ratio of length to height; n = 5) from the Tbx6b>H2B-GFP+FM4-64 embryo plotted against tail length, w...

Changes in muscle cell shape in a wild type embryo during tail extension. (0.83 MB MOV)

Organization of myofibrils in wild type and sna>Bix muscle cells, as visualized by transmission electron microscopy (TEM). (A) Low magnification TEM image of a semi-longitudinal section of the tail of a Ciona larva. Muscle cells are distinguishable based on their shape and on the high number of mitochondria. (B) Higher magnification of the area out...

Changes in muscle cell shape in a sna>Bix embryo during tail extension. (0.94 MB MOV)

High speed imaging of an embryo coelectroporated with sna>Bix and Tbx6b>PH-YFP. (1.00 MB MOV)

Time lapse imaging of an embryo electroporated with sna>Venus. (5.69 MB MOV)

Tail extension is perturbed in embryos electroporated with sna>Bix. (A) Brightfield images of wild type and sna>Bix embryos at mid tailbud and late tailbud stages. Time stamps are shown in each image. (B) Change in tail length in wild type and sna>Bix embryos for the period of development represented in panel (A). (2.92 MB TIF)

Time lapse imaging of tail extension is shown in a wild type embryo coelectroporated with sna>GPI-GFP and sna>H2B-RFP. (1.94 MB MOV)

Movement of muscle cell nuclei in a wild type embryo during tail extension. Tracked cells are false-colored. (0.27 MB MOV)

Wide field time-lapse of late tailbud or larval stage sna>Bix embryos. (3.29 MB MOV)

Movement of muscle cell nuclei in a sna>Bix embryo during tail extension. Tracked cells are false-colored. (0.34 MB MOV)

High speed imaging of a wild type embryo electroporated with sna>GPI-GFP. Note protrusive activity of the muscle cell surfaces during the neurula and early tailbud stages. (8.95 MB MOV)

High speed imaging of a wild type embryo electroporated with Tbx6b>PH-YFP. (10.34 MB MOV)

Axial elongation is a key morphogenetic process that serves to shape developing organisms. Tail extension in the ascidian larva represents a striking example of this process, wherein paraxially positioned muscle cells undergo elongation and differentiation independent of the segmentation process that characterizes the formation of paraxial mesoderm...