Notes

Adjusting your Cloud-Point and Flocculation Temperature regarding Poly(2-(diethylamino)ethyl methacrylate)-Based Nanoparticles using a Postpolymerization Betainization Approach.
Choanoflagellates, the closest living relatives of animals, have the potential to reveal the genetic and cell biological foundations of complex multicellular development in animals. Here we describe the history of research on the choanoflagellate Salpingoeca rosetta. From its original isolation in 2000 to the establishment of CRISPR-mediated genome editing in 2020, S. rosetta provides an instructive case study in the establishment of a new model organism.Although certain organisms are chosen and employed to better understand a specific problem in biology (so-called model organisms), sometimes an animal model reveals its' biomedical importance by happenstance. In many ways, the advent of spiny mice (Acomys) as an emerging model to study regeneration and menstruation stands as a case study in scientific pseudoserendipity (Diaz de Chumaceiro, 1995). As we recount in this chapter, the discovery of these phenotypes, while not entirely accidental, was nonetheless unexpected. In addition to recounting how we uncovered these unusual mammalian traits, we outline recent work by our groups and others that has begun to outline the cellular and genetic mechanisms underlying bonafide mammalian tissue regeneration and a human-like mode of reproduction in spiny mice.The salamander Ambystoma mexicanum, commonly called "the axolotl" has a long, illustrious history as a model organism, perhaps with one of the longest track records as a laboratory-bred vertebrate, yet it also holds a prominent place among the emerging model organisms. Or rather it is by now an "emerged" model organism, boasting a full cohort molecular genetic tools that allows an expanding community of researchers in the field to explore the remarkable traits of this animal including regeneration, at cellular and molecular precision-which had been a dream for researchers over the years. This chapter describes the journey to this status, that could be helpful for those developing their respective animal or plant models.The vast majority of extant vertebrate diversity lies within the bony and cartilaginous fish lineages of jawed vertebrates. There is a long history of elegant experimental investigation of development in bony vertebrate model systems (e.g., mouse, chick, frog and zebrafish). However, studies on the development of cartilaginous fishes (sharks, skates and rays) have, until recently, been largely descriptive, owing to the challenges of embryonic manipulation and culture in this group. This, in turn, has hindered understanding of the evolution of developmental mechanisms within cartilaginous fishes and, more broadly, within jawed vertebrates. The little skate (Leucoraja erinacea) is an oviparous cartilaginous fish and has emerged as a powerful and experimentally tractable developmental model system. Here, we discuss the collection, husbandry and management of little skate brood stock and eggs, and we present an overview of key stages of skate embryonic development. We also discuss methods for the manipulation and culture of skate embryos and illustrate the range of tools and approaches available for studying this system. Finally, we summarize a selection of recent studies on skate development that highlight the utility of this system for inferring ancestral anatomical and developmental conditions for jawed vertebrates, as well as unique aspects of cartilaginous fish biology.Amphioxus (cepholochordates) have long been used to infer how the vertebrates evolved from their invertebrate ancestors. However, some of the body part homologies between amphioxus and vertebrates have been controversial. This is not surprising as the amphioxus and vertebrate lineages separated half a billion years ago-plenty of time for independent loss and independent gain of features. The development of new techniques in the late 20th and early 21st centuries including transmission electron microscopy and serial blockface scanning electron microscopy in combination with in situ hybridization and immunocytochemistry to reveal spatio-temporal patterns of gene expression and gene products have greatly strengthened inference of some homologies (like those between regions of the central nervous system), although others (like nephridia) still need further support. These major advances in establishing homologies between amphioxus and vertebrates, together with strong support from comparative genomics, have firmly established amphioxus as a stand-in or model for the ancestral vertebrate.Hemichordates have long been recognized as a critical group for addressing hypotheses of chordate origins. Historically this was due to anatomical traits that resembled those of chordates, most strikingly the dorsolateral gill slits. As molecular data and phylogenetic analyses were found to support a close phylogenetic relationship between hemichordates and chordates within the deuterostomes, interest was revived in hemichordates. In particular, Saccoglossus kowalevskii has been developed as a molecular model to represent hemichordate developmental biology. Herein, we highlight the considerations when choosing a particular species to study and the challenges we encountered when developing S. kowalevskii. We discuss our findings and how method and tool development enabled them, and how we envision expanding our repertoire of molecular tools in the future. Establishing a new model organism comes with many obstacles-from identifying a reliable season to collect animals, to developing modern molecular techniques. The Saccoglossus research community has benefited greatly from the collaborations and teamwork established over the years. As a result, Saccoglossus is well positioned to contribute to a new century of evolutionary developmental (evo-devo) research.Many species of echinoderms have long been considered model research organisms in biology. Historically, much of this research has focused on the embryology of sea urchins and the use of their extensive gene regulatory networks as a tool to understand how the genome controls cell state specification and patterning. The establishment of Patiria miniata, the bat sea star, as a research organism has allowed us to expand on the concepts explored with sea urchins, viewing these genetic networks through a comparative lens, gaining great insight into the evolutionary mechanisms that shape developmental diversity. Extensive molecular tools have been developed in P. miniata, designed to explore gene expression dynamics and build gene regulatory networks. Echinoderms also have a robust set of bioinformatic and computational resources, centered around echinobase.org, an extensive database containing multiomic, developmental, and experimental resources for researchers. In addition to comparative evolutionary development, P. miniata is a promising system in its own right for studying whole body regeneration, metamorphosis and body plan development, as well as marine disease.Investigating developmental evolution usually requires comparing differences across related species to infer how phenotypic change results from embryological modifications. However, when comparing organisms from different environments, ecologies, and evolutionary histories there can be many confounding factors to finding a genetic basis for developmental differences. In the marine annelid Streblospio benedicti, there are two distinct types of offspring with independent developmental pathways that converge on the same adult phenotype. To my knowledge, S. benedicti is the only known species that has heritable (additive) genetic variation in developmental traits that results in alternative life-history strategies. Females produce either hundreds of small, swimming and feeding larvae, or dozens of large, nonfeeding larvae. The larvae differ in their morphology, ecology, and dispersal potential. This developmental dimorphism makes S. benedicti a unique and useful model for understanding how genetic changes result in developmental modifications that ultimately lead to overall life-history differences. Because the offspring phenotypes of S. benedicti are heritable, we can use forward genetics within a single evolutionary lineage to disentangle how development evolves, and which genes and regulatory mechanisms are involved.Regeneration, asexual agametic reproduction, and other forms of postembryonic development are ecologically important and widely variable across animals, yet our understanding of this important aspect of animal diversity remains limited. A significant limitation has been the dearth of adequate study systems for exploring the mechanisms and evolution of these processes. Here I describe key parts of our journey in developing naid annelids as a study system for investigating the evolution and development of regeneration and fission. Naids are small freshwater annelids that provide numerous advantages for studying postembryonic development they are small and reproduce readily by fission, they include species with diverse regenerative abilities, and many species are easy to culture. Among the naids, Pristina leidyi is a particularly useful study species, being largely transparent and quite robust to a variety of experimental manipulations. Building on a sparse but long history of past research on these animals, we have developed this system by establishing methods and generating resources for working with them. Naids are yielding novel insights into the evolution of regeneration and fission, providing one of many examples of the value of developing new study species to enable the exploration of fundamental and understudied questions in biology. Establishing new study systems comes with challenges but is exciting and rewarding, and I provide perspectives from my own experiences with the hope of encouraging the further expansion of study systems in biology.My goals in this chapter are to share my enthusiasm for studying the biology of leeches, to place this work in context by presenting my rationale for studying non-traditional biological models in general, and to sample just three of the questions that intrigue me in leech biology, namely segmentation, genome evolution and neuronal fate specification. I first became excited about the idea of using leeches as a subject of investigation as an undergraduate in 1970 and have been engaged in this work since I arrived at Berkeley as a postdoc in 1976, intending to study leech neurobiology. Both my research interests and the rationale for the work have expanded greatly since then. What follows is a fragmentary personal and historical account-the interested reader may find more comprehensive treatments elsewhere (Kuo et al., 2020; Shankland & Savage, 1997; Shain, 2009; Weisblat & Huang, 2001; Weisblat & Kuo, 2009, 2014; Weisblat & Winchell, 2020).Over the last few decades, the annelid Capitella teleta has been used increasingly as a study system for investigations of development and regeneration. Its favorable properties include an ability to continuously maintain a laboratory culture, availability of a sequenced genome, a stereotypic cleavage program of early development, substantial regeneration abilities, and established experimental and functional genomics techniques. With this review I tell of my adventure of establishing the Capitella teleta as an emerging model and share examples of a few of the contributions our work has made to the fields of evo-devo and developmental biology. I highlight examples of conservation in developmental programs as well as surprising deviations from existing paradigms that highlight the importance of leveraging biological diversity to shift thinking in the field. The story for each study system is unique, and every animal has its own advantages and disadvantages as an experimental system. Just like most progress in science, it takes strategy, hard work and determination to develop tools and resources for a less studied animal, but luck and serendipity also play a role.
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