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Student Bio’s 2013 MBL Embryology Course Woods Hole, MA
Student Bio’s
2013 MBL Embryology Course
Woods Hole, MA
Name: Alice Accorsi
Title of my research: Soluble factors in immune-neuroendocrine system in
invertebrate models
Brief description of my research: I am attending the second year of the PhD course in Cell Biology
and Evolution. My research activity concerns Comparative Immunobiology and Development. In
broad terms, I am interested in evaluating the role and the evolution of sequences and structures
of soluble factors involved in the functioning of the immune-neuroendocirne system, (e.g.
cytokines, growth factors and antimicrobial peptides). I am focusing my interest on invertebrate
models, that at present have included insects, anellids and molluscs.
In 2007, the first putative α-helical cytokine of invertebrates, called Helical factor (Hf), has been
identified in the fruit fly Drosophila melanogaster. Experiments performed on S2 cell line (cultured
Drosophila embryonic hemocytes) suggested the involvement of Hf in the immune system of D.
melanogaster. During my internship (2010-2011) (University of Modena and Reggio Emilia, Italy) I
have analyzed the expression level of Hf and AMPs in immunologically challenged S2 cells and I
am currently investigating the molecular pathway activated by Hf during D. melanogaster immune
response. Moreover, I am interested also in studying soluble factors promoting autophagy in insect
fat body cells.
In 2011 and 2012, I have been working for 6 months as a visiting student (Laboratory LSMBFA,
University of Lille, France), on the role of the soluble factor Allograft Inflammatory Factor-1 (AIF-1)
in the regeneration process of central nervous system of the medicinal leech, Hirudo medicinalis.
AIF-1 is a well-conserved molecule and, as in vertebrate macrophages, its production is increased
in microglial cells during an immune challenge.
Since AIF-1 has already been identified in some molluscs, I am now investigating it also in
Pomacea canaliculata, a gastropod mollusc with important aspects as a model for invertebrate
immunity studies. In invertebrate immunity, as well as in vertebrates, cell-mediated and humoral
responses are connected and cooperate. Before analyzing molecular aspects of P. canaliculata
immunity I have, as a first step, characterized the hemocytes morphologically and functionally.
Then, I evidenced an AIF-1-like molecule in P. canaliculata hemocytes by immunoblot and
immunocytochemistry and works on molecular characterization are in progress.
Moreover, I have extended my analyses in P. canaliculata also to in vivo studies on the reaction
of the nervous system to an immune challenge, also from an epigenetic point of view. I am
however mostly interested in molecular aspects of hematopoietic process of P canaliculata.
My picture:
Mary Colasanto University of Utah The role of Tbx3 in limb musculoskeletal development The vertebrate musculoskeletal system is essential for structural support and locomotion. Development of a functional musculoskeleton requires that differentiating myofibers are correctly patterned into distinct muscles and are then assembled with muscle connective tissue, tendons, and bones. The close developmental association of muscle, muscle connective tissue, and tendon suggests that interactions between these tissues may be critical for their development. How muscles, tendons, and muscle connective tissue are specified, patterned, and assembled is largely unknown and defective in multiple congenital syndromes. Tbx3 is a transcription factor expressed in the anterior and posterior margins of the developing limb and has been implicated in limb patterning. Autosomal dominant mutations in Tbx3 result in Ulnar-Mammary Syndrome, in which patients have congenital malformations of the limb skeleton. Using conditional mutagenesis in mouse, I have specifically deleted Tbx3 in the lateral plate mesoderm, which recapitulates the skeletal phenotype seen in Ulnar-Mammary Syndrome patients. In addition, I have found that deletion of Tbx3 in lateral plate mesoderm, but not in myogenic cells, also results in muscle and tendon patterning defects. This suggests that Tbx3 in lateral plate mesoderm extrinsically patterns muscle. In the area where muscle defects are present, there is an increase in the number of tendon cells. My aim is to understand how Tbx3 is regulating tendon cell fate and how tendon affects muscle patterning. This research will provide insight into how muscle and tendon is patterned during normal limb musculoskeletal morphogenesis and elucidate the etiology of limb musculoskeletal defects associated with Ulnar-Mammary Syndrome.
Allison Edgar
Duke University
“e state of the sea urchin gene regulatory network near fertilization and its relationship to axial patterning”
Traits as essential to fi tness as axial patterning make excellent case studies for how genes, and gene networks in general, are co-opted in the course of evolution for diverse functions. Such traits help to explain observed phenomena of evolution as well as reveal surprising evolutionary relationships. I am co-advised by David McClay and Gregory Wray as I investigate maternal determinants and early axial patterning in the sea urchin. My current project is an attempt to verify in Lytechinus variegatus the results obtained by Coffman et al. (2004) that mitochondria are asymmetrically distributed in the eggs of Strongylocentrotus purpuratus, and act as a maternally deposited determinant of oral-aboral axial polarity. If my results in L. variegatus are consistent with this hypothesis, I next plan to investigate whether reactive oxygen species or other factors, such as mRNAs associated with the mitochondria, are responsible for the phenomenon. I also plan to use whole-organism transcriptomic analysis of unfertilized eggs and early zygotes to better understand the state of the sea urchin’s gene regulatory network at fertilization. I am currently analyzing differences in the transcriptome of conspecific and interspecific crosses of two direct-developing urchins, S. purpuratus and S. droebachiensis.
Kazutaka Hosoda
My name is Kazutaka Hosoda.
I’m a third year graduate student of the
Laboratory for Molecular
Developmental Biology in Kyoto
University in Japan.
Title of my research: Identification of
genes involved in body patterning during
regeneration of the planarian Dugesia
japonica.
Planarians possess very high regenerative ability that enables them to regenerate
from even a tiny fragment if they are amputated anywhere on the body. This regeneration
process requires differentiation of pluripotent stem cells termed neoblasts scattered
throughout the planarian body, and the differentiation requires appropriate signaling
according to the position in the body to regenerate a complete individual. Studies in the
past few years have shown that several signaling pathways which are highly conserved
among multicellular organisms, such as the FGF signaling pathway, Wnt/β-catenin
signaling pathway and Hh signaling pathway, play crucial roles that decide the fate of a
region in a regenerant during regeneration. RNAi of nou-darake, which is a kinase-
deleted FGFR, causes the formation of ectopic brains during regeneration and RNAi of
Djβ-catenin or Djhh causes bipolar head regeneration in planarian.
I’m interested in the mechanism of reconstruction of the complete body pattern
from a fragment in planarian. What other molecules or signaling pathways are involved
in regeneration in planarian? And how do planarians integrate signaling pathways for
their orderly regeneration?
I want to find out how signaling pathways in planarian determine the position of
the body parts during regeneration.
Nathan Kenny Evolution and Development Research Group Dept of Zoology, University of Oxford Supervisor: Sebastian Shimeld Thesis title: The Evolution and Development of Left/Right Asymmetry in the Lophotrochozoa 3rd Year Doctoral Student After finishing my undergraduate studies at the University of Otago in Dunedin, New Zealand, on the functional role of neurotransmitter receptors in lophotrochozoans (and in particular in the rotifer Brachionus plicatilis), I moved over to the UK in 2010 to begin my doctoral work. Here I work primarily with a limpet species – Patella vulgata – although often with the serpulid annelid Pomatoceros lamarckii, to try and untease how the establishment of left/right asymmetry in animals in the Spiralia occurs. My work has had a wee bit of a genomics-y bent in the last few years, as we worked to build up sequence resources in our model animals of interest, but this work is paying dividends, revealing potential regulators of the processes that regulate the establishment of asymmetry, and in particular the elements of the Nodal pathway, which plays a central role in this. We are now functionally testing these processes in a range of ways in our embryos, although mainly with pharmacological inhibition. This work will allow us to understand how the developmental steps that demarcate the left and right sides of our bodies proceed, and how they have diversified between vertebrates and other species. When allowed out of the lab, I am generally to be found mooching around a museum and talking incessantly about dinosaurs, although rugby or cricket may be mixed in there too.
BRIJESH KUMAR
I am Brijesh Kumar, fourth year graduate student working in the
Department of Biological Sciences and Bioengineering at Indian
Institute of Technology Kanpur, India under the supervision of
Dr. Amitabha Bandyopadhyay (Bone Lab).
Functional vertebrate limb as a complex organ develops by the
coordinated interaction and differentiation of multiple cell
lineages. Various classes of molecules have been implicated in
limb development but molecules related to Metabolism were
largely ignored. Compelling evidences from the literature and the premise that every
organ/tissue produces their type of macromolecules during development provided the
sufficient evidences to study Metabolism related genes during development.
We have carried out the “Genome wide expression based screening of Metabolism related
genes in Chicken during early development”. Many of them express in tissue specific manner
and limb expresses majority of them. As a part of my research interest area, I am working on
the “Roles and Regulation of Metabolism related genes during limb development in Chicken”.
I am trying to elucidate their role in events leading to functional limb by individual targeting of
gene function and their coordinated function in terms of syn-expression groups.
Besides digging the development of limb, I like to dribble Basketball which pushes me for
research. Photography and Basketball game are some of my passions.
BRIJESH KUMAR
GRADUATE STUDENT
INDIAN INSTITUTE OF TECHNOLOGY
KANPUR, INDIA (208016)
http://www.facebook.com/brijesh.risky?ref=tn_tnmn
Ezgi Kunttas Tatli- 4th year PhD Student from Carnegie Mellon University
Over the course of my graduate studies, I have had a chance to work on a variety
of projects that bridged different areas of biology including, cell and molecular biology, development, biochemistry, bioinformatics, computational biology, and genetics. I consider myself very lucky to be able to work with Drosophila as a model system in many of these projects, but also used bakerʼs yeast and Drosophila cell culture to complement these studies. My research took me from studying the function of the kinase CK2 during Drosophila neurogenesis, to investigating the role of the tumor suppressor APC2
in Wnt signaling and regulation of the actin cytoskeleton. Currently, one aspect of my work in the McCartney lab is to understand
the role of the APC proteins in Wnt signaling and how the phosphorylation and dimerization of APC proteins may play a role in the assembly/function of the destruction complex.
Another aspect of my work in the McCartney lab is to understand the role of the APC proteins as regulators of the actin cytoskeleton. In order to study the role of APC in actin organization, I am using the Drosophila syncytial embryo as an in vivo model system. I am testing the role of APC proteins in the early embryo actin assembly by performing live and fix imaging.
Lastly, I am also interested in understanding the evolution of APC gene/protein family across many species from early invertebrates to humans. Itʼs quite interesting to see how the protein sequence of various regions of the protein is highly conserved but other regions are quite diverse. Iʼm hoping to discriminate the functional evolution of this multifunction protein family.
Lara Linden Elucidating the Mechanism and Function of Stem Cell Enwrapment by the Germline Niche in C. elegans
Currently, I am a second year graduate student in Dave Sherwood’s lab in the Developmental and Stem Cell Biology Program at Duke University. My thesis project investigates the stem cell-niche interactions in the C. elegans gonad. The niche cell, called the distal tip cell, enwraps adjacent germ stem cells and extends long cytonemes. Somatic gonad enwrapping of germ cells has been observed in Drosophila as well, yet the regulation, mechanism, and function of enwrapping are not understood. Strikingly, my research suggests that germ cells can induce enwrapment. Next, by performing a mutagenesis screen, I will obtain mutants defective in enwrapping. This will enable me to elucidate the mechanism of enwrapping and potentially reveal the inductive cue from the germline. Finally, I anticipate that examining enwrapping mutants for phenotypes including germline proliferation defects or failure to preserve germ stem cells during starvation will reveal functions of enwrapping. Through my work, I will develop new understanding of this intriguing stem cell-niche interaction.
Lisandro Maya-Ramos Establishment of the cardiogenic mesoderm and its underlying endoderm. I am currently a third year MD Ph.D. and first year graduate student in the laboratory of Dr. Takashi Mikawa at the University of California, San Francisco. My thesis project focuses on gastrulation in amniotes. Gastrulation is an imperative and dynamic developmental process through which the germ layers are established. In amniotes, this process is initiated by the formation of the primitive streak (PS). Once the PS is formed, epiblast cells ingress giving rise to endoderm and mesoderm. How ingression and migration of mesoderm and endoderm are regulated to form the three-layer embryo is virtually unknown. My thesis studies will address this issue. I am very interested in how mesoderm and endoderm layers are established. My particular focus is on the cardiogenic mesoderm and its underlying endoderm (CMEn) since these are established first during germ layer formation. Furthermore, reciprocal interactions between CMEn play key roles for the proper development of each tissue. Damage to endoderm shortly after gastrulation results in cardia bifida in several species leading to lethality. Similarly, lack of cardiogenic mesoderm leads to liver formation failure. This points to an indispensable presence of both layers for proper development and suggests the existence of tightly controlled mechanisms ensuring their proper establishment to the cardiac crescent. Therefore, my project seeks to uncover the mechanisms by which the CMEn are established to the cardiac crescent in the chick embryo.
KathrynMcClellandCharacterisingthesteroidogeniccelllineageofthetestes:UncoveringnewcandidategenesforinvolvementinDisordersofSexualDevelopmentIamcurrently in the thirdyearofmyPhD in the labofProf. Peter Koopman at the Institute for MolecularBioscience,Brisbane,Australia.Iamworkinginthefieldofsexdeterminationanddifferentiation.InmyPhDIamcharacterising the steroidogenic lineage of the fetalmurine testis inorder toexamine thedifferentiationofthispopulation.My current PhD projects are heavily focused on translation of developmentalmechanisms frommouse to human. I am undertaking a deep sequencing project tocompare different cell populations in the gonad.We know relatively little about thesteroidogenicpopulationof testis andwehypothesis that failureof steroidogenic celldifferentiationordysfunctionisanunrecognisedsourceofpathophysiology.Duringmy PhD, in addition to developing amethodology to sort cell lineages of thegonad,Ihavedevelopedanexvivoknockdownsystemingonadculturetobeusedasapre‐screeningtoolpriortothedecisiontoembarkonknockoutmousegeneration.Thishighthroughputscreeningmethodologyutilisesatooltraditionallyusedinthezebrafishbutrarelyappliedinmice.OverthelastpartofmyPhDIwillanalysetheoutputsfromthedeepsequencingscreenand functionally validate potential DSD target genes. In addition, I will look atmechanismsofsteroidogeniccelldifferentiationinthetestis.My research has been focused on murine developmental biology but exposure toconcepts of evolution and development during my undergraduate studies was animportantfactorinmydecisiontopursueacareerindevelopmentalbiology.Therefore,Iamenthusiasticabouttheprospectofbroadeningmyunderstandingofdevelopmentalparadigmsandexpandingmythinkingtolearnmoreaboutalternatemodelsystems.
Sophie Rachel Miller The Development of Olfactory Ensheathing Cells
Olfactory Ensheathing Cells (OECs) are a unique
population of glia which envelop bundles of olfactory receptor neuron axons and support their outgrowth from the olfactory epithelium in the periphery to the olfactory bulb in the forebrain. These glia are thought to be critical for axonal growth and synaptic targeting both during development and adult life. Patient-derived OECs are promising candidates for cell-mediated repair of neural injuries as they are accessible within the nasal lamina, and both axonal regeneration and remyelination have been reported after transplantation into the damaged central nervous system (CNS) of animal models. The major difficulty in translating this to the clinic is producing OECs in large enough numbers, and avoiding contamination with Schwann cells, the glial cells of all
other peripheral nerves, which are less effective at promoting repair. Our lab has shown that OECs, like Schwann cells, are derived from the embryonic neural crest. Since neural crest stem cells persist in adult skin and hair follicles, it might one day be feasible to produce large numbers of patient-specific OECs by culturing these stem cells. However, very little is known about the normal process of OEC development and the extent to which this differs from Schwann cell development.
I have started the characterisation of Schwann cell markers and other candidate molecular markers in developing OECs and Schwann cells during relevant stages of chick embryo development, using in situ hybridisation (ISH) on sections. The data so far suggest that OECs are very similar to Schwann cell precursors, which fits well with the fact that these cells (unlike more mature Schwann cells) behave similarly to OECs when transplanted into CNS lesions.
More recently, I have begun characterising the expression of Notch pathway members throughout OEC development, as this pathway is known to play a critical role in gliogenesis. Currently, I am attempting in ovo electroporation of constructs which either block or constitutively activate Notch signalling in the neural crest precursors of OECs. This precise spatial and temporal control is afforded by the Tet-on/Tol2 system in which the target gene and GFP can be targeted specifically into neural crest cells, and expression activated at any desired stage of development by injecting doxycycline into the egg. Using such techniques, I can investigate the role of multiple signalling pathways in OEC development, and bypass any earlier requirements for these pathways in the developing neural crest. This will give us insight into the normal control of neural crest cell differentiation into OECs, rather than Schwann cells, informing future strategies for generating these cells in culture and advancing our basic understanding of how different glial phenotypes arise during development. A thorough understanding of the mechanisms underlying OEC development should greatly aid future production of these cells in sufficiently large numbers to exploit their potential for transplant-mediated neural repair.
Role of Rho-GTPase RhoA in segregation ofzebrafish germ plasm mRNAs
Jerónimo Roberto Miranda Rodríguez
Germ plasm is a collection of mRNAs and proteins that associate in a dis-tinct region of the cytoplasm inside oocytes and embryos of various animals,including model organisms Xenopus laevis (frog), Danio rerio (zebrafish)and Drosophila melanogaster (fruit fly). When an oocyte is fertilized and celldivisions commence, germ plasm segregates only to certain cells which willbecome the gametes of the forming embryo.
We are studying germ plasm aggregation in zebrafish because its mRNAcomponents migrate through different pathways to converge on a peculiarpattern of germ plasm mRNA localization: four clumps symmetrically loca-lized in the distal portions of cell cleavages by the four cell stage, as shownon the next figure.
This stereotypical localization is dependent on microtubules, f-actin andmyosin [Theusch et al., 2006; Urven et al., 2006].
RhoA is a RhoGTPase that is localized in the cleavage furrow of earlyzebrafish embryos. This, together with the known regulatory capabilities ofRhoA over the cytoskeleton led us to believe that RhoA might have a role inzebrafish germ plasm localization. We have seen, in preliminary experiments,that inhibition of RhoA activity in early zebrafish embryos interferes withthe correct localization of zebrafish germ plasm.
My research currently centers on confirming the effect of RhoA inhibitionon germ plasm localization and finding out which RhoA effector is involvedin this process.
Emily Mis
In Scott Weatherbee’s lab at Yale University, we study a number of mouse
mutants with a variety of embryonic phenotypes. Though all of our projects fall under the broad category of limb development, they range from the regulation of epidermal stem cell quiescence to the role of ciliary protein composition in Shh signaling. My PhD research project, however, focuses on the role of the extra cellular matrix in regulating chondrocyte maturation and skeletal element length. The diversity of phenotypes that we study in our lab introduces me to different perspectives, and encourages me to ask questions about the many aspects of development that continue to fascinate me.
Forward genetics reveals Xylt1 as a key regulator of bone development Chondrogenesis is the process of aggregation and differentiation of mesenchymal
cells into chondrocytes, followed by the subsequent, step-wise maturation of chondrocytes in order to lay down mature bone. Defects in this process can lead to dwarfism, excessive bone growth, and limb deformities. My project focuses on characterizing a mutant mouse pug with dwarfism that was identified in a forward genetics screen. pug animals display a reduction in skeletal element length early in embryonic development, which increases in severity after birth and resolves into disproportional shortening of proximal elements within the skeleton. The gene affected in pug was determined to be Xylt1, which has not been previously studied in mouse models of dwarfism, nor has it been implicated in human dwarfism. Xylt1 modifies the proteoglycans that make up the extra cellular matrix surrounding the chondrocytes in cartilage, and the pug allele of Xylt1 affects both normal protein localization and enzymatic activity. My goal currently is to understand how the proteoglycan network regulates early steps in chondrocyte maturation, and how the extra cellular matrix can perturb chondrocyte maturation as it progresses to result in an increased severity of the dwarfism phenotype.
Tetsuto Miyashita Department of Biological Sciences, University of Alberta Fishing for Jaws in Early Vertebrate Evolution Unless you have vested interest in evolution, no two things seem farther apart than embryos and fossils. But as evo-devo continues to unfold, these are the days when developmental biologists use fossils to fill in their evolutionary stories, and when paleontologists need to learn a bit about pattern formation, gene regulation, and modularity. I am a trained paleontologist (in a typical summer, I still go out with a team to excavate dinosaur fossils), but now have particular interest in the origin and early evolution of vertebrates from both developmental and paleontological points of view. Vertebrates without jaws are very rare today — only hagfish and lampreys survive as a minor component of marine and freshwater systems respectively. But looking into the fossil record, the morphological diversity of jawless vertebrates probably exceeded the current morphological diversity of fishes. I study these important transitional stages from jawless to jawed, as one of the definitive key events in vertebrate evolution, using hagfish, lampreys, and many jawless vertebrate fossils. I look into the development of hagfish and lampreys for a clue to understand fossil phenotypes. For example, hagfish have a weird type of cartilage in the feeding apparatus that is histologically almost identical to and little less elastic than tendons. Does this strange cartilage represent an intermediate stage between cartilage and tendons? If so, did the vertebrate tendon evolve from cartilages, and did hagfish retain that primitive tissue or independently derive a special type of cartilage? An inference can also be made backward. Jawed vertebrates have hard mineralized skeletons, which necessarily require a mobile joint, particularly a synovial joint for a jaw. Jawless vertebrates, on the other hand, have no need of such joints but rely on elasticity of cartilaginous endoskeletons, regardless of whether or not they have hard exoskeletons. So jawless vertebrates did not always have the functional requirement to develop such a complex system as a synovial joint. How did a synovial joint evolve? Do we find a precursor state to synovial joints in jawless vertebrates, a precursor that could have been co-opted to a mobile joint at the origin of jawed vertebrates? At least hagfish have a blood sinus morphologically similar to a synovial joint near the ventilation structures. I am looking for its counterpart in lampreys and also looking at fossil evidence. These are just a sample of questions I am working on currently. Half of my time is still devoted to projects on dinosaurs, my love since childhood.
Hi! My name is B. Duygu Özpolat (pronounce as do-ee-gou, and it will be close enough). I studied joint tissue regeneration in the chick embryo for my Ph.D. dissertation at Ken Muneoka’s lab at Tulane University. As I was finishing the graduate school, it was very clear to me that I wanted to study evolution of regeneration in metazoa, by using different animal groups and conducting comparative analyses. Consequently now, I am a post-doctoral researcher at Alexa Bely’s lab, where we study the evolution of post-embryonic developmental processes such as regeneration and asexual reproduction in the segmented worms (Annelids), focusing mainly on the species Pristina leidyi (it is a lovely little aquatic earth worm!). After I joined Dr. Bely’s lab, I got interested in germline/gonad maintenance and regeneration in P. leidyi, which reproduces mainly asexually, but it retains sexual reproduction ability. P. leidyi is also very good at regeneration, which enabled me to investigate how are several ways the species regenerates its gonads and maintains the germline. A cool aspect of regeneration we are starting to discover through the recent non-model invertebrate studies is that, the multipotent cells and/or stem cells that take part in regeneration in these organisms express the “germline genes”. Traditionally, these genes such as piwi, nanos and vasa were thought to be specific for the germline, but it is becoming clear that they have a more general role for maintaining stemness or multipotency in a wider range of cell types. Hence, I could title my project as piwi expression during different strategies of germline maintenance and regeneration in the annelid Pristina leidyi, although I have been working on a bunch of other aspects of regeneration and germline in the segmented worms.
During the two years I have spent at Dr. Bely’s lab, I have transformed into a researcher who is absolutely in love with the invertebrates. It is such exciting times for evo-devo and non-model organism-based research, with the sequencing technologies becoming more accesible and cheap. However, besides looking at worm pictures and thinking how adorable they are, I also spend a lot of time doing public science education activism, nowadays mainly by playing the editor-in-chief for a not-for-profit organization, which translates UC Berkeley’s Understanding Evolution website into Turkish, called Hard workers for Evolution. You can find more information about the organization in this interview.
I am incredibly excited to have been accepted to the MBL course and looking forward to meeting and getting to know everyone, and speding a great, productive, inspiring 6 weeks together.
Jong Hwee Park DNA repair and programmed genome rearrangement in the sea lamprey, Petromyzon marinus During early embryogenesis, the sea lamprey (Petromyzon marinus) undergoes programmed genome rearrangement resulting in the 20% loss of genomic information within all somatic cells. It is suggested that during this time, not only does DNA loss occur but certain genes may be reorganized in a manner analogous to the VDJ recombination which is present in jawed vertebrates. Currently only one group of genes known as the Variable Lymphocyte Receptors (VLR) is believed to utilize the programmed genome rearrangement in order to generate diversity within its receptor domains. The VLR system is analogous to the VDJ recombination system as the gene loci under genetic rearrangement in order to produce a functional loci producing functional immune receptors capable of mounting an adaptive immune response. While the mechanism underlying VDJ recombination is well known, very little is known about how VLR rearrangement mechanisms and its relationship to programmed genome rearrangement in the lamprey.
I am interested in both the mechanism driving programmed genome rearrangement and its genomic consequences. Previous experiments and sequence analysis have been unable to identify homologous genes in lamprey known to be involved in recombination in jawed vertebrates. Work in the Amemiya lab utilizing BAC library sequences, germline DNA analysis, and other methods have quantified the loss of genomic material throughout embryogenesis and identified several sites where sequence deletions have occurred. TUNEL assays have also shown that during this time many cells stained positive which usually implicates possible apoptotic cells by detecting dsDNA breaks. Caspase 3 assay was used to determine the amount of apoptotic cells; however, nearly all cells were negative for Caspase 3 activity which confirms that these dsDNA breaks are not resulting in cell death and shows that these DNA breaks may be the result of programmed genome rearrangement.
Currently I am looking at the mechanism underwhich these dsDNA breaks are repaired. Using embryonic RNA transcriptome, I identified several genes known to be involved in DNA repair. Morpholinos were used to knockdown the gene ataxia telangiectasia mutated (ATM) in lamprey embryos. This gene codes for a serine-threonine protein kinase and is known to be involved in the dsDNA damage detection and repair by activating various pathways resulting in DNA repair, cell cycle arrest, and apoptosis. ATM knockdown resulted in embryos with noticeable retardation of development resulting in gross morphological differences between the knockdown embryos and the wildtype embryos. Along with these developmental changes, apoptotic cells were detected via the Caspase 3 assay. It is likely that the knockdown of ATM resulted in cells being unable to properly repair the dsDNA breaks which ultimately forced the cell to undergo apoptosis.
I hope to uncover the extent of ATM's role in DNA repair during programmed genome rearrangement and what other repair mechanisms are involved in this process. I will also be looking to uncover whether or not there is a specific pattern to DNA loss during early embryogenesis in relation to cell cycle, amount of DNA fragments generated and lost. This research along with further sequence analysis will hopefully help me to discover how DNA loss is occurring and the evolutionary pressures which led to this adaptation in the sea lamprey.
Poulomi Ray
Integration of mechanical forces and molecular signaling during skeletal
condensation
I am interested in how complex shapes and
patterns arise during development from chaotic
cell dynamics. I recently graduated from Dr.
Susan Chapman’s laboratory at Clemson
University. In my Ph.D. thesis work, I
investigated the interplay between mechanical
forces and molecular signaling during skeletal
condensation. The classical model defines
condensation as an aggregation of cells with
increased cell density. Based on my results, I
proposed a revised model for condensation,
dependent on differential cell shape changes and independent of increased cell density.
The key finding from my study is that tension dependent dynamic cell shape changes
drive skeletal condensation. The cell shapes regulate the activation of FGF and BMP
signaling in the condensing mesenchyme. Actomyosin contractions and differential cell
cortex tension drive cytoskeletal reorganization and temporally downregulates TGF-β
signaling to form a condensation. Furthermore, dorsal and ventral condensations have
distinct cellular morphology and BMP signaling drives dorsal specific cytoskeletal
reorganization. My study elucidates the fundamental principles of interplay between
mechanical forces and molecular signaling, in a self-organizing system, generating shape
and form.
Misty R. Riddle In vivo forced reprogramming and remodeling of
differentiated somatic cells and organs by brief
expression of a single transcription factor
Early embryonic cells in the nematode C. elegans are pluripotent and can be
forced to adopt alternative fates by ectopic expression of key regulators of
endoderm, mesoderm, or ectoderm development. Postmitotic differentiated somatic
cells in larvae and adults are generally considered locked in fate. We found that
brief ectopic expression of ELT-‐7, a GATA transcription factor that regulates
endoderm differentiation, reprograms fully differentiated somatic cells into
intestine-‐like cells without the removal of inhibitory factors. Cells that form the
pharynx and somatic gonad appear specifically competent to reprogramming by
ELT-‐7. The reprogrammed cells express intestine-‐specific genes, paralleling loss of
expression of the original cell-‐fate specific genes. Reprogrammed cells undergo
dramatic remodeling at the ultrastructural level to resemble intestinal cells. Cells
that form the somatic gonad become reorganized after ectopic ELT-‐7 expression to
form a second intestinal lumen with remarkable similarity to the endogenous
intestine. Thus, we may have observed forced “trans-‐organogenesis” of one organ
into another. PHA-‐4, a transcription factor required for specification and
differentiation of pharyngeal cells is required for postmitotic reprogramming in the
pharynx, suggesting that pharyngeal cell identity is required for transdifferentiation
to an intestine-‐like fate. Our results show that terminally differentiated postmitotic
cells can be remodeled to cells of another germ layer in the absence of cell division
or prior removal of the original cell fate, and suggest that susceptibility to
reprogramming is determined by a combination of cellular context and the factors
used to induce cell fate change.
Betsy Schock
Characterizing primary cilia function in the developing craniofacial complex using the Talpid2 avian mutant
I am a first year graduate student in Samantha Brugmann’s lab at Cincinnati Children's Hospital Medical Center. Our lab is interested in understanding the etiology of craniofacial defects by using both avian and murine model systems.
Primary cilia are dynamic, microtubule-based organelles that protrude from the cell into the extracellular matrix. They are important for coordinating signal transduction of multiple signaling pathways. The Sonic Hedgehog (Shh) pathway, a pathway required for proper craniofacial development, is transduced through the primary cilium. Improper propagation of Shh leads to midline defects e i t h e r c h a r a c t e r i z e d b y a w i d e n i n g (hypertelorism) or collapse (hypotelorism) of the midline. My lab is interested in how defects in primary cilia cause craniofacial defects. To study this phenomena, our lab uses both avian and murine model systems. My work is currently focused on the avian mutant, Talpid2, which has both limb and craniofacial defects. We have recently identified C2cd3, a ciliary protein, as the causative gene for this mutation. Little is known about what function C2cd3 serves in the primary cilia. We have shown that Shh signaling is disrupted in the facial prominence of these animals. In my future work, I will begin to dissect the mechanism of C2cd3 action in the developing face.
Amy Shyer The Role of Mechanical Forces in Patterning and Morphogenesis of the Vertebrate Gut In order to efficiently pack the lengthy small intestine into the body cavity, the developing vertebrate gut tube forms a reproducible looped pattern as it grows. We previously determined that gut looping morphogenesis is driven by the forces that arise from the differential growth between the gut tube and the anchoring dorsal mesenteric sheet. I am currently exploring the formation of intestinal villi, finger-like projections that drastically increase the absorptive surface of the intestine. We find that, in chick, intestinal villi form in a stepwise process as a result of physical forces generated as proliferating endodermal and mesenchymal tissues are constrained by sequentially differentiating layers of smooth muscle. We built a computational model incorporating measured parameters from developing chick gut which recapitulates chick villi formation, and can be applied more broadly to explain intestinal surface patterns in other species. I am also studying the process by which proliferating progenitors in the intestinal endoderm, the presumptive precursors of adult stem cells, are localized to the base of each villus where the crypt will ultimately form.
Georgina Stooke-Vaughan PhD research title: The role of hair cells and cilia in otolith formation and inner ear development in the zebrafish embryo. My research focuses on the role of cilia in the zebrafish otic vesicle. In particular, their role in tethering the forming otoliths (ear stones: structures required for the sensation of gravity), and in patterning the inner ear and sensory patches before five days post fertilization. I have found that hair cells play a major role in tethering the forming otolith by producing otolith precursor binding factors. The otolith precursor binding factors are normally localized to the tips of the hair cell kinocilia, where they interact with components of the forming otolith. Motile cilia within the otic vesicle, combined with embryonic movement, play a role in preventing formation of fused and untethered otoliths. My findings have helped to resolve controversies in the literature and have implications for the understanding of human ciliopathies and vestibular disease.
SOPHIE TINTORI
Second-Year Graduate Student in the labs of Bob Goldstein and Jason Lieb at the University of North Carolina Chapel Hill
GENETIC CUES FOR THE INITIATION OF MORPHOGENESIS
A fundamental feature of nearly all complex multicellular organisms is the coordination of cells to form functional structures larger than any single cell could make alone. Many of the mechanical changes that occur during these morphogenetic events, such as gastrulation, have been relatively well characterized. It has been historically difficult, though, to determine how the genetic patterning of an embryo leads to these mechanical changes. Morphogenetic events are thought to be quite robust, and so traditional forward genetic screens that attempt to identify single genes at a time have likely missed morphogenesis cues because such screens would leave other contributing pathways intact. In the context of modern high-throughput sequencing, though, we can utilize whole transcriptome profiles of cells initiating morphogenesis to identify the full cast of transcriptional players present at such an event, regardless of how well the system is buffered. We can use these profiles to identify genes with expression patterns that suggest a functional role, and then test such a hypothesis.
I am in the early stages of a project in which I will be comparing the transcriptional changes in a few discrete groups of C. elegans cells that are each independently moving to the inside of the embryo, collectively comprising gastrulation. By comparing several cell types that each internalize separately and will each realize different fates, I hope to enrich for the genes contributing to the common cell behavior, which is the entry into gastrulation. In this way I will generate a list of candidate genes to follow up on with functional studies.
One of the aspects of this project that excites me most is the versatility of the dataset I will be generating: I will generate a separate transcriptome profile for each individual cell of the entire C. elegans embryo from multiple time points in early development, which will open the door to study a number of developmental phenomena, including initiation of morphogenesis, the transition from extraordinarily fast and synchronized cell cycling to the slower cycles characteristic of each cell type, potential regulators of the cell fates broadly conserved in Metazoa, and to the cues leading to apoptosis as a cell fate in contrast to apoptosis as a quality control measure.
Wei Wang
Department of Biological Sciences,
The University of Alabama, Tuscaloosa, AL, USA, 35487
Abdominal segment number in Diptera as a genetic model
for the evolution of novel morphology
The diverse abdominal morphologies found throughout insects constitute an attractive model
for investigating developmental and evolutionary mechanisms underlying morphological
novelty. Cyclorrhapha, a monophyletic clade of diptera including Phoridae, Muscidae and
Drosophiliidae, generates sexually dimorphic adult abdominal segment numbers: males have
fewer segments than females. Non‐Cyclorrhaphan flies, such as the mosquito Anopheles
gambiae, retain the ancestral condition of sexually monomorphic segment number. In
D.melanogaster, and likely conserved throughout the Cyclorrhapha, sexually dimorphic
segment number is coordinately controlled by the posterior Hox protein Abdominal‐B (Abd‐B)
and the sex specific transcription factor doublesex (dsx). I have shown this reduction is
principally controlled through male‐specific transcriptional repression of the morphogen
Wingless (Wg) in the posterior‐most abdominal segment A7. To investigate whether Abd‐B and
dsx directly regulate wg expression, I have performed a systematic molecular screen to identify
cis‐regulatory elements (CREs) governing wg expression in pupal abdomen. Interestingly, I have
identified two distinct CREs each capable of driving expression of a reporter gene in patterns
reflecting endogenous abdominal Wg protein. I am currently characterizing the direct
regulation of wg abdominal expression by Abd‐B and Dsx. Furthermore, I am also performing
comparative wg expression studies in different fly species to investigate if differential
regulation of wg in posterior abdominal segments contributes to the variation of adult
abdominal segment number in Diptera.
Wiebke (Veebka) Wessels
Genetic and molecular bases of early development in hard and soft corals
My PhD project involves the investigation of candidate genes in the early development of corals, with a focus on soft corals. The principal
aim is to establish the first morphological and molecular basis of development in Alcyoniidea using a comparative transcriptomics approach. However, I am
also interested in the post-gastrula development in scleractinian (reef-building) corals, including the role of developmental genes in swimming planulae and
during the critical processes of settlement and metamorphosis. Together with other members of my working group, I plan to investigate and compare the expression
of developmental genes among several species of corals with differing morphologies, life history attributes and reproductive modes (broadcast spawning and brooding).
Coral spawning, December 2012
