1,721,005 research outputs found
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Early germ line development in the hemipteran insect Oncopeltus fasciatus
No full textThe cell lineage that forms eggs and sperm is referred to as the germ line, and the integrity of this cell lineage is critical for the successful reproduction and the survival of a species. The earliest progenitors of the germ line are known as primordial germ cells (PGCs), and PGCs form during embryonic development. In most animals, germ cells are formed in a location that is distant from the location where gonads (testes or ovaries) will develop, and therefore germ cells must migrate, often long distances, during embryonic development. I investigate the mechanisms for two major processes in early germ line development: specification and migration. To study these processes, I look to insects, the most diverse group of animals, where we can study mechanisms that govern germ line development in a comparative context and generate evolutionary hypotheses about how these mechanisms evolve. While most mechanistic studies of developmental processes have been in holometabolous insects (insects that undergo metamorphosis), hemimetabolous insects have many features that are more representative of an ancestral form of insect development. Here, I study the hemimetabolous insect, the large milkweed bug Oncopeltus fasciatus (Hemiptera), which is in a group sister to the monophyletic Holometabola. It is therefore in an ideal phylogenetic position to make comparisons to mechanisms that have been well-studied in holometabolous insects such as the fruit fly Drosophila melanogaster (Diptera). In Chapter 1, I review evidence in the literature showing the roles of the Bone Morphogenetic Protein (BMP) pathway in reproductive system development and function across animals. I propose that there is an ancient association with BMP signaling in the development of both the germ line and supporting somatic gonad tissue that may have arisen with the segregation of the germ line early in metazoan evolution. In Chapter 2, I investigate whether the BMP pathway has a role in PGC specification in O. fasciatus where the signaling factors specifying PGCs are currently unknown. I provide evidence that O. fasciatus PGCs are competent to receive BMP signal, but future work is needed to assess whether this pathway is required for PGC formation in this insect. In Chapter 3, I characterize the dynamics of PGC migration in O. fasciatus and use a candidate gene approach to find genes involved in regulating PGC migration. I provide evidence that at least one member of the JAK/STAT signaling pathway is involved in PGC migration in O. fasciatus. To my knowledge, this is the first functional genetic study into the mechanism of PGC migration in a hemimetabolous insect
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Crickets, Cross-Veins, Crumpling, Crystals, and Computers
No full textThe world around us appears unimaginably complex: creases on sheets of paper, the patterns on animals, not to mention the assembly of life itself.
In this thesis, I use computational tools to shed light on the organizing principles of a selection of systems that appear disordered at first glance.
The topics are diverse, as are the tools I used to investigate them.
Yet, in all cases, the ultimate aim has been the same: to uncover simple rules/patterns about seemingly complex systems using an evolving computational toolbox.
The first chapter looks at how nuclei arrange themselves in the dance of life.
In collaboration with the Extavour Lab (Harvard Department of Organismic and Evolutionary Biology (OEB)), we tracked live imaged 3-D datasets of nuclei from the cricket \emph{Gryllus bimaculatus}.
We found that nearly every quantifiable aspect of the motion of nuclei can be explained by the local density that the nuclei experience.
From this experimental data, we developed a computational model that we used to bolster our findings and make concrete predictions about embryonic development.
Some of these predictions we were able to experimentally validate through experimental modification of developing embryos.
In the second chapter, my collaborators and I characterize the geometric patterns formed by the veins in insect wings.
Dividing up the wing into a series of polygonal shapes, we ask geometric questions about the open spaces formed by the veins.
Looking at odonate wings (dragonflies and damselflies), we propose a simple developmental that is able to recapitulate the complex patterns observed.
Then, we extend the mathematical toolkit introduced in the first manuscript to a broader selection of insect wings.
In the third chapter, I use machine learning to ask if we can uncover geometric order in a classically disordered system: crumpled sheets.
We find that by augmenting experimental datasets of crumpled mylar with simulated examples from a sister system---rigid flat folding---we are able to achieve non-trivial predictions on the geometric arrangement of ridges and valleys in the experimental data.
In the fourth chapter, I use a variational autoencoder (VAE) to encode and decode 3-D crystal structures.
This project is a first step in a larger goal of using modern deep learning methods as a way to search the unimaginably large space of potential structures for possibly (environmentally) useful molecules.
The approaches presented in this chapter could easily be extended to many other types of 3-D structure, a topic that is still largely unexplored in the field of generative models.
In the fifth chapter, I discuss a few other projects that I worked on in the course of my PhD.
In the first project, I discuss a collaboration where we develop a novel machine learning architecture with a physically informed inductive bias.
We assume the world is composed of sparsely interacting mechanisms that infrequently interact.
We create a neural network architecture based on this idea and show that it achieves impressive prediction results on physical systems and also generalizes better than current methods.
In the latter part of the chapter, I discuss two new computational methods relating to Graph Neural Networks that my collaborators and I developed.
These disparate topics can all be characterized by using data-driven methods and developing data-driven techniques to cast a simplifying light on seemingly complex systems.Engineering and Applied Sciences - Applied Mat
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Evolution of embryonic germ line development in insects
No full textDuring development, animals must specify and maintain the germ line, a dedicated lineage of cells uniquely capable of giving rise to the next generation of animals. Mechanisms of germ line development vary widely even within closely related animal taxa such as insects (Extavour and Akam, 2003). For instance, in insect embryos, germ cells may be specified as early as the syncytial blastoderm stage, as in the fruit fly Drosophila melanogaster (Huettner, 1923), or much later during the germ band stage, as in the cricket Gryllus bimaculatus (Ewen-Campen et al., 2013a). In this dissertation, I explore the evolution of diverse mechanisms of germ line development across insects. First, in Chapter 1, I review the literature on germ cell specification in panarthropods and discuss how the timing and mechanism of this process has shifted in evolution. Next, I take advantage of functional genetic tools in emerging model insects to study two different aspects of germ line development. In Chapter 2, I investigate the role of germ cell-less in germ line development in two hemimetabolous insects, finding that the germ line function of this gene has changed through evolution. In Chapter 3, I examine somatic gonad development in the milkweed bug Oncopeltus fasciatus and determine that its invariant gamete tube number arises from segmental specification of somatic gonad precursors. Overall, this work highlights the potential of developmental genetics in emerging model insects to address questions of insect development.Biology, Molecular and Cellula
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The evolution and development of the insect egg and ovary
No full textLife comes in many shapes and sizes, and efforts to describe, categorize, and understand this diversity have been a driving force behind biological discovery. Evolutionary developmental biology, or evo-devo, seeks to understand the origins of diversity by investigating evolutionary changes to the developmental process, that in turn lead to novel and complex traits. But the field of evo-devo is at an inflection point. In recent decades, rich and complex datasets have become much more accessible and inexpensive to generate from a wide variety of organisms. The outcome is that we have unprecedented opportunities to investigate the developmental basis of diversity. However, our ability to make robust inferences about developmental evolution will require us to compare data across taxa using statistical methods based in evolutionary theory. In this thesis I investigate the origins of shape and size diversity through the application of evolutionary inference methods to large datasets of morphological and developmental traits. In Chapter 1, I describe the state of the field of evo-devo, and advocate for a shift in the framework often used in analyses, toward one rooted in evolutionary tree-based thinking. Chapter 2 presents a dataset of 10,000 descriptions of insect egg size and shape, assembled using custom software tools to extract descriptions from the published literature. Chapter 3 analyzes this dataset on a phylogenetic tree of insects to test hypotheses about size and shape evolution in relation to ecological and developmental features. Chapter 4 combines egg size data with a dataset of more than 3,000 ovary descriptions to test a longstanding hypothesis about the size and number of offspring. Chapter 5 investigates the evolutionary relationships of a specific lineage of Hawaiian flies in the family Drosophilidae, identifying specific evolutionary shifts in egg and ovary diversification
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The evolution of Oskar function in insects
No full textThe emergence of genetic novelty underlies major shifts in the evolution of development. In this thesis, I investigate evolution in primordial germ cell specification in insects, with a particular focus on the gene oskar. As a lineage-restricted, rapidly evolving gene with essential roles not only in the germ line, but also in the developing nervous system of some species, oskar presents a compelling case study of how genetic innovation drives phenotypic evolution. First, I synthesize observational and experimental data on the origin of primordial germ cells to describe how germ cell specification has evolved in insects, and more broadly across panarthropods. I also speculate on how evolution in germ line gene expression and function may drive shifts in the mechanisms of germ cell formation. Next, I specifically investigate evolution in oskar, which has undergone functionally significant sequence divergence over a short evolutionary timescale. I determine how protein-coding sequence differences between oskar orthologs from Drosophila melanogaster and D. virilis prevent the D. virilis ortholog from rescuing D. melanogaster oskar loss-of-function. I identify domains of the D. virilis Oskar protein that differentially impact localization of germ line and patterning determinants and dramatically influence downstream cell fate decisions. By leveraging this natural sequence variation as an evolution-guided mutagenesis strategy, I uncover new insights into the in vivo mechanisms of Oskar function. These experiments also reveal how oskar gene dosage affects germ plasm assembly and germ cell specification, shedding light on how embryos respond to changes not only in gene sequence but also quantity. Finally, I explore the potential co-option of oskar to different tissue contexts. I present preliminary data testing the hypothesis that oskar is expressed in the central nervous system of D. melanogaster, and I describe ongoing efforts to characterize oskar expression and function in other insect species. This broader comparative approach will eventually allow us to reconstruct the trajectory of oskar’s functional evolution across insects. I conclude by outlining promising directions for future research into the evolution of development, particularly through the lens of the genes that both influence and are influenced by these processes.Biology, Molecular and Cellula
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Isolated branches in the phylogeny of Platyhelminthes
No full textThis dissertation examines the early phylogenetic divergences of the phylum Platyhelminthes using molecular sequence data, with an emphasis on the placement and evolutionary significance of several enigmatic and largely overlooked lineages. Firstly, I assess platyhelminth interrelationships using a representational sampling of all free-living orders for the “standard” 18S and 28S rRNA loci (plus two mtDNA markers). These analyses place numerous problematic taxa, most notably Gnosonesimida, which is recovered in a position consistent with the classical hypothesis in which this order retains a primitive form of ectolecithality. I also investigate the status of the crustacean-parasitic genus Genostoma, classified presently within Fecampiida, which has however been proposed on the basis of ultrastructural data to lie outside this order. These efforts robustly position Genostoma as the sister-taxon to the free-living order Prolecithophora, suggesting the recognition of a new higher taxon to accommodate this morphologically distinct, but poorly diverse lineage.
To overcome the inherent limits of rRNA phylogenetics, I used massively parallel sequencing to survey transcriptomes from representatives of all “turbellarian” orders. From concatenation and consensus analyses of 512 orthologs, a robust signal of platyhelminth phylogeny emerges, congruent with previous results but also presenting several unanticipated relationships. Most notable among these, the monospecific order Bothrioplanida is recovered as the sister-group of Neodermata, the major vertebrate-parasitic clade within Platyhelminthes. These analyses prompt consideration of novel hypotheses on the origins and consequences of parasitism within Platyhelminthes, and motivate many previously unexplored comparisons among free-living taxa.
The position of Platyhelminthes within Spiralia, and the related question of whether the phylum is “primitive” in morphology, remains controversial. I therefore also used transcriptomic data to resolve the phylogeny of Spiralia, with emphasis on the status of the “platyzoan” phyla, and on positioning several problematic interstitial lineages. These data robustly position Lobatocerebrum and Diurodrilus as members of Annelida. I also recover strong support for the non-monophyly of the platyzoan phyla, with Gnathifera as the earliest-splitting branch and a clade of Platyhelminthes and Gastrotricha as the nearest relative of Trochozoa. This phylogeny hence simultaneously highlights the importance of “reductive” processes in the evolution of interstitial organisms, as well as the possibility of the primitive nature of at least some of the “simple” features that have classically inspired zoological interest in Platyhelminthes.
Finally, I present a focused inquiry on the internal phylogeny of one “isolated” flatworm clade, the continental order Prorhynchida. The recovered topology is broadly congruent with traditional classification, with most prorhynchid species falling into two genera. Remarkably, however, two rare taxa that share morphologically similar copulatory apparatus are recovered as unrelated basal branches, indicating the probable plesiomorphic nature of this morphology. Also, a little-known groundwater species, Geocentrophora boui, is supported as the sister taxon of the self-fertilizing genus Xenoprorhynchus, illuminating the functional specialization of the “copulatory” apparatus as a venom delivery system in this lineage. Field collections from this study uncovered over 31 new species, many of these unexpectedly terrestrial, more than doubling the known diversity of the order, and highlighting the need for continued systematic research on these remarkable but understudied animals.Platyhelminthes; phylogen
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The Effect of Development and Ecology on the Evolution of Ovary Size in Drosophila
No full textHow the size of an organ is established and altered during evolution is poorly understood. The ovary of fruit flies of the genus Drosophila serves as an interesting model for understanding organ size evolution, as the number of egg-producing structures called ovarioles determines the ovary’s functional ‘size’. Species with more ovarioles can lay more eggs, and ovariole number can evolve rapidly between closely related species. However, the developmental and genetic mechanisms that determine and alter ovariole number were poorly characterized at the beginning of this thesis. I first analyzed the developmental basis of plasticity and species-specific ovariole number changes in D. melanogaster and closely related species. This analysis revealed distinct developmental mechanisms that alter ovariole number via changes in one cell type (terminal filament cells) in the developing ovary. To characterize the genetic mechanisms underlying proliferation patterns and potential cell-type interactions within the ovary, I then studied the role of the Hippo pathway in the somatic and germ cells of D. melanogaster. I uncovered a complex interaction between somatic cells and germ line cells, where proportional growth of these cell types is maintained by the Hippo pathway via interactions with the EGFR and JAK/STAT pathways. Finally, I expanded this work to investigate the physical, ecological, and developmental parameters that influence ovariole number evolution in Hawaiian Drosophila, where previous studies suggested that ovariole number correlated with larval food substrate. I describe my ongoing efforts to test correlations of ecology and ovariole number in a phylogenetic context in Hawaiian Drosophila. Primary differences in ovariole number between species occur through changes in cell number.Biology, Organismic and EvolutionaryEvolution; Development; Evo-devo; Evolutionary Developmental Biology; Biology; Genetics; Reproduction; Drosophila; Ecology;
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Developmental and Genetic Mechanisms of Ovariole Number Evolution in Drosophila
Get PDFThe goal of the "Quantitative Trait Gene" (QTG) program is to identify genes and mutations that underlie natural phenotypic variation. My goal with this work was to contribute an additional model to the program: ovariole number evolution in Drosophila. In this thesis I describe the progress I have made towards identifying a specific genetic change that contributed to the divergence of ovariole number between two Drosophila lineages. I identify specific developmental mechanisms relevant to establishing ovariole number in different Drosophila lineages by detailing ovarian cell-type specific specification, proliferation, and differentiation. I test specific candidates of genetic regulators of these developmental mechanisms with mutational analysis in D. melanogaster. I show that independent evolution of ovariole number has resulted from changes in distinct developmental mechanisms, each of which may have a different underlying genetic basis in Drosophila. I use the interspecies comparison of D. melanogaster versus D. sechellia to test for functional differences in insulin/insulin-like growth factor (IIS) signaling between the two species. I show that IIS activity levels and sensitivity have diverged between species, leading to both species-specific ovariole number and species-specific nutritional plasticity in ovariole number. Moreover, plastic range of ovariole number correlates with ecological niche, suggesting that the degree of nutritional plasticity may be an adaptive trait. My work and quantitative genetic analyses strongly support the hypothesis that evolution of the Drosophila insulin-like receptor (InR) gene, specifically, is at least partially responsible for the divergence in ovariole number and nutritional plasticity of ovariole number between D. melanogaster and D. sechellia. I detail ongoing experiments to test this hypothesis explicitly via cross-species transgenesis
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Computational Approaches to Developmental Biology
No full textThe origin and evolution of new genes is an active topic of research, relying on the taxonomical diversity now present in sequence databases. Using those databases, we described how \textit{oskar}, a key determinant of germ cell determination, likely arose from a horizontal gene transfer and then described its evolution and conservation in insects. The number of ovarioles, the egg-producing unit of the insect ovary, is hypothesized to inform the individual’s reproductive capacity. Using network biology approaches, we analyzed the effect of signaling pathway genes on the number of ovarioles and eggs laid by Drosophila melanogaster. We found putative gene modules regulating both traits and predicted novel genes affecting both phenotypes. The specification of germ layers is a central mechanism of the embryogenesis of animals, but the underlying molecular mechanisms have only been extensively studied in model organisms. Using Parhyale hawaiensis, a crustacean amphipod, I generated preliminary methods for the generation of single cell RNA sequencing of early embryogenesis, as well as recorded with light sheet microscopy the first three days of embryogenesis. The preliminary analyses of the sequencing datasets were inconclusive, but, analyzing one of the microscopy datasets, I described new preliminary cellular dynamic results. Finally, to observe and annotate 4D microscopy datasets, I developed a tool that allows the visualization of large volumetric datasets in Virtual Reality
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An evolutionary perspective on germ cell specification genes in insects
Get PDFThis dissertation investigates the embryonic specification of a specific group of cells: the germ cells. Germ cells, which give rise to sperm and egg, are the only cells in sexually-reproducing animals that directly contribute hereditary information to the next generation. Germ cells are therefore a universal cell type across animals, and represent a profound novelty that likely arose near the base of the animal phylogeny. Yet despite their conserved, essential function in all animals, there is surprising diversity in the mechanisms that specify these cells during embryonic development. In this dissertation, I address the diversity of germ cell specification mechanisms in insects. I focus on two species, the milkweed bug Oncopeltus fasciatus (Hemiptera) and the cricket Gryllus bimaculatus (Orthoptera), which both branch basally to the Holometabola (those insects which undergo metamorphosis, including the well-studied fruit fly Drosophila melanogaster), and thus provide important phylogenetic breadth to our understanding of germ cell specification across insects. Using functional genetic approaches, I show that germ cell specification in both Oncopeltus and Gryllus differs fundamentally from germ cell specification in Drosophila. Specifically, I provide evidence that germ cells arise via inductive cell signaling during mid-embryogenesis, rather than via maternally-supplied cytoplasmic determinants localized in the oocyte, as is the case for Drosophila. These data suggest that Drosophila employs an evolutionarily derived mode of germ cell specification. In further support of this hypothesis, I show that several of the genes required for Drosophila germ cell specification perform other functions in both Oncopeltus and Gryllus. I demonstrate that one of these genes, oskar, which is the only gene both necessary and sufficient for germ cell specification in Drosophila, instead functions in nervous system of the cricket, both during embryonic development and in the adult brain. I suggest that the evolution of the derived mode of germ cell specification seen in Drosophila may have involved co-opting oskar into the germ cell specification pathway from an ancestral role in the nervous system
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