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I need to find out the name of a nineteenth century biologist who compared developmental biology to crystallography. His idea was that crystals are formed from 'cells' (defined molecular units) that bond together to form arrays. In living organisms cells are bound together but the rules that form the structures change as the organism grows, especially in animals, which is why we have different organs. In both cases you have units that coalesce undirected but according to rules to form structures. I remember finding out about this biologist from a documentary which also showed illustrations from the book he wrote on the subject. I can't find his name or that of his book using a web search because it's too obscure and that would only work with the correct terms. Does anyone know anything about this?
The idea to compare biologic cells and crystal is mostly related to a German physiologist Theodor Schwann (1810-1882):
His work "Microscopic researches on the Conformity in Structure and Growth Between Animals and Plants, 1839 relates to this idea.
He believed that new cells form principally outside pre-existing cells, and wanted to draw an analogy to crystal formation.
The cell is the unit of structure, physiology, and organization in living things. The cell retains a dual existence as a distinct entity and a building block in the construction of organisms. Cells form by free-cell formation, similar to the formation of crystals (spontaneous generation).
(other related scientists are Schleiden, Virchow, Muller).
Computational biology involves the development and application of data-analytical and theoretical methods, mathematical modelling and computational simulation techniques to the study of biological, ecological, behavioural, and social systems.  The field is broadly defined and includes foundations in biology, applied mathematics, statistics, biochemistry, chemistry, biophysics, molecular biology, genetics, genomics, computer science, and evolution. 
Computational biology is different from biological computing, which is a subfield of computer engineering using bioengineering and biology to build computers.
Looking at life with a scientific lens
Correlating developmental trajectories with transcriptome readout
Article in Nature, Vol. 531, 31 March 2016, pp. 637-641, “The mid-development transition and the evolution of animal body plans” Summary of article: Transcriptomes of developing animals were correlated with the mid-developmental transitions thereby, providing a molecular depiction of developmental transitions. Link to original article: https://www.nature.com/articles/nature16994 Category: Interesting scientific articles, developmental biology, &hellip More Correlating developmental trajectories with transcriptome readout
Understanding phytobiome effect on plant growth and productivity
Article in Scientific American, August 2017, pp. 61-67, “Building a better harvest”. Summary of article: Effect of phytobiome, the collection of microorganisms, soil, climate, and plant pathogens that interact with plant growth, on the productivity of crops was delineated. The data obtained points to the possibilities of how understanding the different facets of plant &hellip More Understanding phytobiome effect on plant growth and productivity
Phylogenetic trees track the evolutionary relatedness of genes and proteins
The tree of life is currently defined by a phylogenetic analysis of the 16S rRNA gene, which harbours deep evolutionary information on the development of various species on Earth. Specifically, it is highly conserved across species, and yet possesses sufficient variability for individual species to be identified by differential sequence at the gene level. Thus, &hellip More Phylogenetic trees track the evolutionary relatedness of genes and proteins
Role of activating mutation in potentiating cancer
Article in Nature, Vol. 539, 10 November 2016, pp. 304, “Leukaemogenic effects of Ptpn11 activating mutations in the stem cell microenvironment” Summary of article: Effect of the postulated activating mutation, Ptpn11, on leukaemia was investigated in genetically altered mice harbouring the mutation. Link to the original article: https://www.ncbi.nlm.nih.gov/pubmed/27783593 Category: cancer, biochemistry, developmental &hellip More Role of activating mutation in potentiating cancer
Single cell RNA sequencing for understanding the lineage of cancer cells
Article in Nature, Vol. 539, 10 November 2016, pp. 309, “Single-cell RNA-seq supports a developmental hierarchy in human oligodendroglioma” Summary of article: Single cell RNA sequencing of cancer cells from human oligodendroglioma reveals hierarchical development pathway in the cancer thereby, opening up the technique for use in profiling the developmental pathway and lineage traversed &hellip More Single cell RNA sequencing for understanding the lineage of cancer cells
Standardization of nomenclature in cell biology and biological sciences
The fields of cell biology and biological sciences is awashed with difficult to remember names and abbreviations that do not identify the function of the proteins or their subunits. For example, the FEAR network in the field of cell biology. Thus, I was wondering if some form of standardization could be instituted by the leading &hellip More Standardization of nomenclature in cell biology and biological sciences
Macrophages as delineators of stripe patterns in zebrafish
Perspective article in Science, Vol. 355, Issue 6331, pp. 1258-1259, “Macrophage, a long-distance middlemen” Summary of article: Macrophages are immune cells that profile for foreign viruses and cells that invade a multicellular organism, but its myriad characteristics and roles in cellular genesis and developmental biology is only beginning to be understood at both a &hellip More Macrophages as delineators of stripe patterns in zebrafish
Contemporary biology covers an enormous spectrum, from research on basic cellular processes to predictions about global climate change. But this spectrum is not always continuous: while there is abundant evidence that organisms can adapt to their natural environment, it is often not obvious what the underlying genetic, molecular and developmental processes are. Similarly, while we have an increasing appreciation for the complexities of population genetic events, the underlying ecological factors are often unclear. A major difficulty in answering these questions stems from the fact that many of these processes operate on different spatial and temporal scales. At the MPI for Developmental Biology, we aim to bridge these different scales, by studying fundamental aspects of microbial, plant and animal biology both in the laboratory and in natural settings. To this end, we make use of approaches that range from biochemistry, cell and developmental biology to evolutionary and ecological genetics, functional genomics and computational biology.
Who compared developmental biology to crystallography? - Biology
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Cell and Developmental Biology Center
The Cell and Developmental Biology Center aims to understand the molecules and the molecular interactions inside cells that build the organelle systems that support basic and specialized functions to control cell fate and behavior. This Center studies how cell behavior guides normal development, including the creation and maintenance of tissues and organs. Researchers combine biochemical, molecular, cellular, genetic, and quantitative approaches to investigate fundamental biological processes across a range of organisms, including fish, flies, mammals, microbes, and viruses. This Center also seeks to apply its basic cell and developmental biological research to the understanding and treatment of human diseases.
The process of directed cellular movement is of critical importance to human health, as is observed when immune cells seek out infected tissues or metastatic cancer cells invade new organs. The Laboratory of Cell and Tissue Morphodynamics, led by Dr. Clare Waterman, has made pioneering discoveries into the complex and dynamic mechanical interactions between organelle systems within cells that are required for directed movement. Dr. Waterman’s laboratory established that the two classes of cytoskeletal polymers—microtubules and filamentous actin (f-actin)—exhibit both direct structural interactions and regulatory interactions mediated by Rho GTPases it also developed specific technologies, including quantitative fluorescent speckle microscopy (qFSM) to systematically dissect the critical features of these interactions.
Movement of and within cells is fundamental to life, whether in development of an organism, defense against infection, repair after injury, or in pathologies such as cancer and heart disease. Myosin was first identified in skeletal muscle as a motor protein critical to muscle contraction. Two heavy and two pairs of light chains comprise this conventional myosin (now known as myosin II), which polymerizes into filaments to interact with actin and generate force through the hydrolysis of ATP. The Laboratory of Cell Biology is led by Dr. Edward Korn, who has been studying the function and regulation of the actomyosin system in its diverse forms since he discovered the first unconventional non-filamentous myosin, myosin I (containing only a single heavy chain), in the single-cell soil protozoan Acanthamoeba castellanii, approximately forty years ago. Dr. Korn’s laboratory brings the tools of biochemistry and cell biology to focus on three research areas: the role of the actin cytoskeleton in Dictyostelium fruiting body development, the molecular basis of the regulation of actin-activated ATPase activity in myosin II, and the mechanism of association of myosin I with cell membranes.
The primary research interest of the Laboratory of Cellular Physiology, led by Dr. Lois Greene, is in the formation and breakdown of normal and pathological protein complexes in the cell, with an emphasis on the role of molecular chaperones. Dr. Greene studies the role of molecular chaperones and their co-factors in the formation of vesicular compartments from clathrin-coated pits in the cellular membrane during endocytosis. She has applied her wealth of experience in the cell biology of protein folding and membrane trafficking toward deciphering the mechanisms of prion formation and propagation. However, it is becoming increasingly clear that many neurodegenerative diseases—such as Huntington's disease, amyotrophic lateral sclerosis (ALS), and others that are associated with abnormal protein aggregation initiated through genetic mutations—have a prion-like component to their transmission. Once such proteins are misfolded, they may provide a template for other proteins to misfold. Moreover, these misfolded templates could be transmitted between cells. If correct, such a cumulative model of neurodegenerative transmission could partially account for the relatively late onset of these diseases.
Selfish genetic elements distort their own transmission ratio by preferentially segregating to the egg during female meiosis. The Laboratory of Chromosome Dynamics and Evolution, led by Dr. Takashi Akera investigates this non-Mendelian transmission of selfish elements called meiotic drive. Meiotic drive has significant impacts on genetics, evolution, and reproduction, as selfish elements distort transmission ratios and allele frequencies in populations and manipulate gamete production. Dr. Akera’s lab uses the mouse oocyte model to reveal both the cell biological basis and evolutionary consequences of meiotic drive.
Research in the Developmental Neurobiology Laboratory, led by Dr. Herbert M. Geller, focuses on understanding the mechanisms that control axonal growth and pathfinding during neural development and also the mechanisms that stimulate regeneration after injury to the brain or spinal cord. The development of neurons and the neuronal response to injury are influenced by interactions between neurons and the second major cell type in the nervous system, glia. The predominant glial cells in the central nervous system, astrocytes, normally provide a favorable environment for neurons by promoting neuronal migration and the outgrowth of dendritic and axonal processes during development. However, after injury, astrocytes become reactive and form a major part of the glial scar that forms around the injury site and inhibit regeneration. Dr. Geller is identifying the molecular mechanisms at work under these different conditions. His ultimate goal is to promote neuronal regeneration after injury by preventing these changes in astrocytes, adding permissive molecules to astrocytes, or causing neurons to ignore inhibitory cues.
Viruses are experts at exploiting and manipulating the host in numerous and diverse ways throughout their lifecycle. Elucidating these viral mechanisms provides insight into the viral lifecycle and opportunities for therapeutic intervention. It also can provide insight into the host lifecycle, revealing cellular pathways that we did not know existed until viruses were found taking advantage of it. Using cutting edge imaging and spectroscopic technologies combined with novel lipidomic and proteomic approaches, investigations in the Laboratory of Host-Pathogen Dynamics, led by Dr. Nihal Altan-Bonnet, have been at the forefront of understanding the virus-host interface, revealing novel replication and transmission mechanisms shared by many different human viruses. Their investigations are broadly focused on understanding the role of membranes and specifically lipids, in the viral lifecycle.
The Laboratory of Human Endosymbiont Medicine, led by Dr. Neal Epstein, focuses on the further analysis of a novel life form that has been identified by our laboratory to exist within a subset of most all nucleated human cells, forming isolated foci in most tissues. This is distinct from the microbiome as presently studied, which exists on the surfaces of cells, on the skin, and in the gut lumen. The endosymbiont's nucleic acid sequence, physiology, and EM defined morphology show it to be unique with no homologues in GenBank or the literature. A unique antibody shows it is present in the human egg allowing the vertical transmission from mother to progeny as is standard for many endosymbionts in Arthropoda. Facultative free living, it is motile and can be tagged with a fluorescent antibody allowing visualization of it entering human cells in primary culture. The laboratory focuses on its further characterization and its role in human health and disease.
As prototypical cellular motor proteins, most myosins convert the energy of ATP into movement. Contractile muscle myosin II proteins participate in the beating of the heart and movement of the body, while non-muscle myosin IIs play an integral role in cellular movement, shape regulation, and cell division. The Laboratory of Molecular Cardiology, led by Dr. Robert S. Adelstein, is focused on the role of non-muscle myosin II (NM II) in development and disease. Research projects include: the role of NM IIA in spermatogenesis, the function of NM IIs in cardiac development, using whole genomic sequencing to study causative genes for Pentalogy of Cantrell understanding the role of NM IIA in squamous cell carcinoma NM II and mechanotransduction and studying the functions of the Rbfox family of RNA binding proteins.
The primary research interests of the Molecular Cell Biology Laboratory, led by Dr. John A. Hammer, revolve around the roles played by motor proteins and cytoskeletal protein dynamics in driving the motility of organelles and cells. The inside of a living cell is not a still place. From the motor protein-dependent transport of organelles inside the cell, to the changes in overall cell shape driven by cytoskeletal dynamics, normal cell function is highly dependent on movement. Dr. Hammer’s lab uses cell biological, genetic, biochemical, and biophysical approaches, coupled with advanced imaging techniques, to study the molecular interactions that give rise to cellular and intracellular movements, and to define the functional significance of these movements in the context of whole organisms. Recently, Dr. Hammer has focused more efforts on understanding the role played by cytoskeletal protein dynamics in driving the proper function of certain white blood cells called T lymphocytes.
The Laboratory of Molecular Machines and Tissue Architecture, led by Dr. Nasser M. Rusan, studies the role of centrosomes during animal development. The centrosome is a non-membrane bound organelle that serves as the main microtubule (MT) organizing center of most animal cells. Centrosomes function to initiate and maintain cell polarity, guide cell migration, direct intracellular cargos, and properly distribute other organelles. In mitosis, or cell division, centrosomes are critical for accurate construction of the mitotic spindle to ensure faithful chromosome separation to the two daughter cells. Thus, it is not a surprise that defects in centrosome function lead to a wide range of failures at the cellular level, which in turn, leads to tissue defects and many human diseases. The lab aims to determine how centrosomes are properly constructed from their individual parts and how centrosomes function in a wide range of cell types to avoid human diseases such as polycystic kidney disease, microcephaly, and cancer.
Early work in the Laboratory of Molecular Physiology, led by Dr. James R. Sellers, focused on the regulation of the myosin II isoforms found in smooth muscle and non-muscle cells. Myosins are cellular motor proteins. As new myosin isoforms were discovered, his interests shifted to also include studies of these “unconventional” myosins. Dr. Sellers has focused on studying myosin diversity as a means of understanding meaningful molecular differences that give rise to disparate functions. His interdisciplinary laboratory brings together a breadth of experience in fields such as developmental biology, biochemistry, cell biology, biophysics, and engineering and encompasses studies of systems ranging from single molecules to fruit fly models (Drosophila melanogaster).
The selective recycling of lipids and proteins is critical to healthy cellular function. Many genes associated with human diseases encode components of the cellular machinery that sorts lipids and proteins for selective trafficking along endocytic pathways leading to lysosomal degradation. The Laboratory of Protein Trafficking and Organelle Biology, led by Dr. Rosa Puertollano, seeks to understand precisely how defects in intracellular trafficking—specifically, in endosomal and lysosomal pathways—contribute to human diseases.
The overarching goal of the Laboratory of Stem Cell and Neurovascular Research, led by Dr. Yoh-suke Mukouyama, is to uncover the molecular control of the morphologic processes underlying the branching morphogenesis and patterning of the vascular and nervous systems. These systems share several anatomic and functional characteristics and are often patterned similarly in peripheral tissues. These characteristics suggest that there is interdependence between these two networks during tissue development and homeostasis. Thus, Dr. Mukouyama is studying neuronal influences on vascular branching patterns and vascular influences on both neuronal guidance and neural stem cell maintenance. He has recently extended the lab’s research to the unanticipated roles of tissue macrophages and microglia in neuronal and vascular development. His laboratory approaches these problems using a combination of high-resolution whole-mount imaging, advanced genetic perturbations, and in vitro organ culture techniques.
The laboratory of Structural Cell Biology aims to understand the molecular mechanisms governing specialized cell shapes, such as those of neurons, activated immune cells or platelets and certain cancer cells. We visualize the key factors determining different cell morphologies using in situ cellular cryo-electron tomography in combination with interdisciplinary techniques such as single-particle cryo-EM, X-ray crystallography, in vitro reconstitution and light microscopy.
These advances have been the result of contributions from scientists in many different fields. Physicists have provided much of the technology, such as the advanced electron detectors that increased the speed and sensitivity of modern cryo-EM devices. Chemists have developed brighter florescent probes that illuminate targets for longer. Statisticians and computer scientists have improved image processing and analysis techniques. “The acceleration in imaging has come about through this incredible synergy,” says Jennifer Lippincott-Schwartz, a cell biologist at the Howard Hughes Medical Institute’s Janelia Research Campus in Ashburn, Virginia, who helped to lay the foundations for the development of super-resolution microscopy with work during the 1990s on the use of green fluorescent proteins to visualize cellular trafficking pathways in living cells 2 .
Many advances have been made using these microscopy tools. Lippincott-Schwartz and her colleagues, for example, used a form of light-sheet fluorescence microscopy with confocal microscopy to capture 3D colour footage of the interactions between different types of organelle. “We were able to map out the relationships between six types of organelles, how fast they were moving and the contacts they made with each other,” says Lippincott-Schwartz, whose paper 3 was published in Nature in 2017. “That’s important if you want to understand the cross-communication between organelles, which is one of the big interests among cell biologists right now.”
Jennifer Lippincott-Schwartz demonstrates a microscope capable of super-resolution imaging. Credit: Matt Staley
The growing availability of these advanced techniques presents opportunities for early-career cell biologists. Most obviously, it increases the number of processes cell biologists can probe. “These techniques open up tremendous vistas for the types of questions we can answer,” says Lippincott-Schwartz. Structural biologist David Barford at the MRC Laboratory of Molecular Biology in Cambridge, UK, has used cryo-EM to advance understanding of some of the cellular mechanisms involved in mitosis 4 , a type of cell division that results in the formation of two daughter cells with the same chromosomes as the parent cell. “For academic scientists, the ability to determine structures at atomic resolution with electron cryo-microscopy can be very important in the design of new experiments and testing of biological hypotheses,” he says.
Barford adds that the potential benefits to early-career researchers of acquiring an in-depth understanding of the latest imaging techniques could extend beyond the immediate research questions they are seeking to answer. “Drug companies are becoming very keen on electron cryo-microscopy as a means to determine the structures of proteins and drug targets, so moving into it could be a very good career choice,” he says. Barford also thinks these techniques will grow more important and overtake older techniques used by biologists. “It will probably supersede crystallography in the job market.”
It is impossible to become proficient in the use of all or even many of the latest imaging tools. Early-career cell biologists seeking to use them need to decide whether to specialize in a particular technique, or to identify collaborators who can do it for them (see ‘Meetings of minds’ for some of the conferences popular in cell biology). Ridley, who studies the role of cell migration in cancer progression, advises those doing PhDs to take up any opportunities available to them to get a flavour of the different techniques. “I would recommend that anyone doing a PhD programme with the option to do rotations in different labs and gain experience of different imaging areas to do so,” she says. “Even if you don’t become an expert in electron microscopy, for example, working in that area for a couple of months will give you an understanding of what it can and can’t do.” Barford adds that researchers who leave it to collaborators to do their imaging for them risk falling behind in other ways. “If you become just a user rather than a developer, it limits your future potential to contribute to the field through developing and advancing the technology.”
Meetings of minds
Delegates at the joint meeting of the American Society for Cell Biology and the European Molecular Biology Organization in 2018. Credit: Paul Sakuma Photography
Symposia and conferences are good for getting updates and overviews of a field.
Researchers often have to choose between going to broad or specialized meetings. For those seeking an overview of the state of the field, the joint meeting of the American Society for Cell Biology and the European Molecular Biology Organization is by far the largest annual gathering of cell biologists in the world. Around 6,000 people are expected to attend this year’s, in Washington DC on 7–11 December. Subjects to be covered will be wide-ranging, including emerging topics such as non-conventional model organisms, computational modelling and synthetic biology.
Bruce Stillman, president and chief executive of Cold Spring Harbor Laboratory in New York, will give the keynote lecture on his work on chromosome duplication in cells. There will be a variety of symposia, workshops, poster sessions and special-interest sessions. On the day before the main meeting, there will be a full day of session on careers and professional development for academics, and a one-day mini biotech course, at which attendees can learn how scientific discoveries are turned into bioscience ventures. Other sessions will cover careers in non-profit science advocacy, science policy, outreach, scientific infrastructure management and bench-based research in industry.
There are many other options for researchers wanting to dig deeper into a particular branch of the discipline. A symposium called Seeing is Believing, for example, brings together the developers of cutting-edge imaging techniques with those applying them in the lab. This meeting attracted some 400 participants when it was last held, at the European Molecular Biology Lab in Heidelberg, Germany, in October this year. It featured sessions on the latest tools and methods transforming researchers’ abilities to visualize proteins, protein complexes, organelles, cells, tissues, organs and whole organisms.
One of the draws of imaging for Lippincott-Schwartz is its purity as an empirical method for acquiring knowledge. “When you are imaging, you are first observing, then generating hypotheses and then designing approaches for testing your hypotheses. It’s the perfect avenue for fulfilling the scientific method.” She adds that the proliferation of advanced tools has made microscopy all the more attractive as a focus for cell biologists. “It can make imaging a very creative direction to take,” she says.
Nature 575, S91-S94 (2019)
This article is part of Nature Career Guide: Cell biology, an editorially independent supplement. Advertisers have no influence over the content.
The Society of Craniofacial Genetics and Developmental Biology 34th Annual Meeting
This article is an introduction to active areas of research in craniofacial genetics and developmental biology as highlighted by Dr. Brian Hall's accompanying article in this issue of AJMG (Hall BK 2012. AJMG XX) and the publication in this issue of the abstracts which were presented as either talks or posters at the 34th annual meeting of the Society of Craniofacial Genetics and Developmental Biology (SCGDB). The meeting hosted by the faculty of Dentistry at McGill University convened in October 2011, in Montreal, Quebec, Canada. The Society met in conjunction with the International Congress of Human Genetics-American Society of Human Genetics meeting. Clinical Craniofacial Dysmorphology was the theme of the scientific sessions given by invited speakers.
The SCGDB is an international organization established in 1975 as the Society of Craniofacial Genetics. In 2011, the name of the society was expanded to include developmental biology to reflect the tight yet hierarchical integration between genetics and development/embryogenesis. The objectives of the Society are to promote understanding, research, and interdisciplinary communication concerning craniofacial genetics and developmental biology, and to apply the results of basic and clinical research to the care and management of individuals with craniofacial problems. (http://craniofacialgenetics.org/index.php?section=ABOUT+US for detailed objectives).
The society is enormously active in pursuit of its objectives. To bring to attention the work of those who have and are contributing to the advancement of the Society two awards were established in 2011 for graduate students demonstrating research excellence. The first was to recognize the significant contributions to craniofacial genetics, developmental biology and the Society by Dr. Geoffrey Sperber. As befits Geoff's status in the field and role in the Society, the “Geoffrey Sperber Award for Excellence in Craniofacial Research” was presented at the Montreal meeting. Zohreh Khavandgar of the Faculty of Dentistry at McGill University received this award for her research on mechanisms of bone mineralization. A second award, the genesis Award for Excellence in Craniofacial Research, generously funded by the journal genesis was won by Christopher Percival for his research on bone mineral density in a mouse model for Beare–Stevenson Cutis Gyrata Syndrome.
The 2012 annual meeting of the SCFDB is scheduled to convene on November 5th in San Francisco in conjunction with the annual meeting of the American Society of Human Genetics (ASHG) to be held November 6–10 (http://www.ashg.org). Mark your calendar and monitor the SCGDB and ASHG web sites for details.
Abstracts of the 34th Annual Meeting of the Society of Craniofacial Genetics and Developmental Biology (SCGDB) in Montreal, Quebec on 11 October 2011
Inherited Retinal Disorders: Hope for Treatment
1 Lady Davis Institute, Jewish General Hospital, Department of Human Genetics, McGill University, Montreal, Quebec, Canada
Inherited retinal diseases can be broadly classified into developmental defects and retinal degenerations. I will give a brief overview of these conditions, and focus in particular on our current understanding of the mechanisms that underlie photoreceptor death in the inherited degenerations. In our work on these diseases, we are addressing two fundamental questions: First, why do the neurons die? And second, how is it that they can function perfectly normally for decades, yet still be at risk of death? Are they sick? What are the biochemical changes that result from the mutation, and that eventually kill the cells? Some insight into these difficult questions has been obtained by many groups over the past decade (reviewed in Bramall et al. ). I will also review exciting progress in the treatment of inherited retinal disease, both cell replacement therapy and gene therapy. In Phase 1 clinical trials, gene therapy appears to have been effective in partially correcting the blindness of at least one retinal degeneration, and cell replacement therapy in mouse models of retinal degeneration is very promising. Finally, I will report new findings on the role of one transcription factor gene, Prdm8, in retinal development. Loss of function of this gene leads to a virtual absence of bipolar cells, the major interneurons in the retina, and also to fascinating neuromuscular abnormalities [Ross et al., 2011].
Supported in part by grants from the Canadian Institutes of Health Research and the Macula Vision Research Foundation.
Bramall AN, Wright AF, Jacobson SG, McInnes RR. 2010. The genomic, biochemical, and cellular responses of the retina in inherited photoreceptor degenerations and prospects for the treatment of these disorders. Annu Rev Neurosci 33:441–472.
Ross SE, McCord AE, Jung C, Atan D, Mok SI, Hemberg M, Kim TK, Salogiannis J, Hu L, Cohen S, Lin Y, Harrar D, McInnes RR, Greenberg ME. 2012. Bhlhb5 and prdm8 form a repressor complex involved in neuronal circuit assembly. Neuron. Jan 2673(2):292–303.
What Can One Learn From Fetal Facies: Is it a Clue to Diagnosis?
1 Department of Orthopaedic Surgery, Human Genetics and Obstetrics and Gynecology, David Geffen School of Medicine, UCLA, Los Angeles, California
Improvements in prenatal fetal ultrasound based on technological advancements have yielded superior images of many organ systems throughout gestational ages. This is especially true of the fetal facies. Ultrasound can evaluate both the bony structures as well as the soft tissue contours. Absolute measurements of the orbital diameters, philtrum, and mandible can give definite evidence for hypo- and hypertelorism, abnormal philtrums, and micrognathia. The recognition of well-described craniofacial disorders can be translated into the fetal period, as soon as the early second trimester. Abnormal craniofacial finding can be readily appreciated in the skeletal dysplasia group of disorders, craniosynostosis group of disorders, and cleft/lip palate syndromes. Determining the constellation of abnormal facial findings can help direct the prenatal geneticists toward differential diagnoses, including recognition of novel disorders. These diagnoses can then be refined based on abnormalities in other organ systems and well as using molecular diagnostics to help identify the causative mechanisms.
Clinical Approach to the Child With Cleft or Craniofacial Anomalies
1 Division of Genetics, Department of Pediatrics, University of California, San Diego and Rady Children's Hospital, San Diego, California
Facial clefts and other craniofacial anomalies (CFA) constitute a group of birth defects that are both pathogenically and etiologically heterogeneous. With respect to pathogenesis, CFA's can be classified as malformations, deformations, disruptions, or dysplasias. Malformations do not change over time. Most are due to multifactorial inheritance and the treatment is typically surgical. Deformations have the potential to improve with time and postural intervention. Disruptions do not recur, but the treatment is surgical. The altered growth potential in dysplasias raises concerns about progression and the development of neoplasia over time.
With respect to etiology, CFAs are the result of genomic changes (dosage imbalance with gain or loss of groups of genes), genetic changes (at the level of the DNA itself), environmental factors, or the interaction of environmental factors with a specific genetic background that renders an individual at risk for a specific CFA. The clinical approach starts with defining the pathogenesis of the specific craniofacial anomaly (such as failure of formation of the frontonasal process leading to a midline cleft lip) and using the history and physical examination to elucidate etiology (such as parent with a single central incisor might suggest a mutation in SHH where as a history of poorly controlled diabetes and the presence of sacral agenesis might suggest diabetic embryopathy).
Genetic Regulation of Bone Extracellular Matrix Mineralization
1 Department of Medicine and Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
Mineralization of vertebrate bone extracellular matrix (ECM) is a physiologic process. In contrast, soft tissue mineralization is a pathologic condition. Initiation of ECM mineralization requires a scaffold of fibrillar proteins such as collagen or elastin within which critically sized nuclei of salts of calcium and inorganic phosphate precipitate and become stable. These precipitates later grow and mature into hydroxyapatite crystals. Interestingly, although suitable scaffolding proteins are present in many soft tissues, normally, ECMs in these tissues do not mineralize. There are two possibilities that may explain this phenomenon. Firstly, it is possible that an activator of mineralization is missing in these soft tissues, and secondly, that soft tissue mineralization is actively prevented by the presence of mineralization inhibitors. Several key studies now identify the latter as the most likely explanation. In fact, absence or removal of mineralization inhibitors is a prerequisite for the initiation of mineralization in the bone microenvironment. We provided genetic evidence suggesting that bone mineralization can be explained, at least in part, by the matrix composition and by the enzymatic removal of pyrophosphate, a ubiquitously present small-molecule mineralization inhibitor, from the bone ECM. More recently, we demonstrated a local role for Sphingomyelin phosphodiesterase 3 (SMPD3), a lipid metabolizing enzyme, in bone mineralization. A deletion mutation in Smpd3 leads to severe skeletal dysplasia in mice. Our in vivo genetic experiments suggest that SMPD3 enzymatic activity is necessary for normal bone mineralization and skeletal development.
Mammalian Mandibular Modules: 20 Years Since the “Atchley–Hall” Model
1 Department of Biology, Dalhousie University, Halifax, Nova Scotia, Canada
It is 20 years since Atchley and Hall  published a model for the development and evolution of complex morphological structures using the mammalian mandible (dentary) as the exemplar anatomical structure. Included in the model was the development of the concept of modularity of morphology, modules consisting of aggregations (condensations) of cells that are the primary resource for the development of individual bones or cartilages. In this first of a series of presentations/papers to review the model, I examine our current understanding of cellular modules of the murine dentary. The 1991 model postulated that the dentary arose from six cell condensations of neural-crest-derived cells. Four were skeletogenic forming the ramus and the three processes of the dentary. Two were odontogenic, forming the incisor and molar teeth and associated alveolar bone. Subsequent studies reveal that a single skeletogenic unit forms the bone of the ramus and the angular, condylar, and coronoid processes. In mice the distal cartilages on these processes are secondary, arising from the periosteum. In rats and humans, these cartilages are sesamoids arising in separate condensations outside the dentary. Thus, the single osteo-chondrogenic condensation in mice is represented in rats and humans by four cell populations one osteogenic and three sesamoid (chondrogenic) condensations. The significance of these differences for our understanding of the cellular and molecular mechanism underlying mandibular development and for the application of studies from other mammalian species to human craniofacial development will be documented and discussed.
Supported by NSERC of Canada (A5056).
Atchley WR, Hall BK. 1991. A model for development and evolution of complex morphological structures. Biol Rev Camb Philos Soc 66:101–157.
GWAS Follow-Up Mutation Screen and Expression Analysis Implicate ARHGAP29 as a Novel Candidate Gene for Nonsyndromic Cleft Lip/Palate
Elizabeth J. Leslie 1 , M. Adela Mansilla 1 , Leah C. Biggs 1 , Kristi Schuette 1 , Steve Bullard 2 , Tian-Xiao Zhang 3 , Margaret Cooper 4 , Martine Dunnwald 1 , Andrew C. Lidral 2 , Mary L. Marazita 4 , Terri H. Beaty 3 , Jeffrey C. Murray 1
1 Department of Pediatrics, University of Iowa, Iowa City, Iowa
2 Department of Orthodontics, University of Iowa, Iowa City, Iowa
3 Department of Epidemiology, School of Public Health, Johns Hopkins University, Baltimore, Maryland
4 Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
Nonsyndromic cleft lip and/or palate (NSCL/P) is a common birth defect with complex etiology. Genome-wide association studies have successfully identified novel loci associated with NSCL/P including one near the ABCA4 gene, mutations in which cause several retinal disorders. Neither expression analysis nor mutation screening support a role for ABCA4 in the etiology of NSCL/P, so we investigated the adjacent gene, ARHGAP29, encoding Rho GTPase activating protein 29. ARHGAP29 has preferential activity toward RhoA, which has many functions related to cellular shape, movement, and proliferation, all critical for craniofacial development. Expression analysis using a mouse demonstrated that Arhgap29 is present in the epithelium and mesenchyme of the medial and lateral nasal processes and the mandibular processes at E10.5, and the oral and medial edge epithelia and palatal mesenchyme at E14.5. Sequencing of ARHGAP29 in 962 individuals with NSCL/P and 972 unrelated controls from the Philippines and the US revealed one nonsense, one frameshift, and 14 missense variants, which are overrepresented in cases (P = 0.03). We tested the most associated SNP (rs560426) near ABCA4 and ARHGAP29 for genetic interaction with other candidate genes, identifying a possible interaction with IRF6 (rs2235371 P = 0.04). This interaction is supported by reduced expression of Arhgap29 in the oral epithelium of an Irf6-null mouse, suggesting a novel pathway for clefting involving the transcription factor IRF6 interacting with the Rho pathway via ARHGAP29. The combination of genome-wide association, rare coding sequence variants, craniofacial expression, and interactions with a known clefting gene support a role for ARHGAP29 in NSCL/P.
Supported by NIH DE08559 and DE020057.
Autosomal Dominant Multiple Natal Teeth With Selective Tooth Agenesis
John M. Graham Jr 1 , Nancy Kramer 1 , Vincent Funari 1 , Ophir Klein 2 , Kerstin Seidel 2 , Piranit Kantaputra 3 , Kent D. Taylor 1
1 Medical Genetics Institute, Cedars Sinai Medical Center, Los Angeles, California
2 Department Orofacial Sciences, University of California, San Francisco, California
3 Faculty of Dentistry, Chiang Mai University, Chiang Mai, Thailand
We report a 5-generation family with autosomal dominant multiple natal teeth followed by selective tooth agenesis, which is not associated with any nondental features. Natal teeth are usually a sporadic isolated finding in an otherwise normal infant. Familial occurrence is rare but has been reported to be autosomal dominant. Autosomal dominant agenesis of teeth can be caused by mutations in the homeobox gene MSX1. Other families with autosomal dominant oligodontia have mutations in PAX9, and selective agenesis of only the permanent teeth has been linked to 10q11.2-q21. A family with isolated X-linked selective tooth agenesis resulted from mutations EDA. Mutations in WNT10A have been associated with isolated hypodontia. The genetic basis for isolated natal teeth is unknown. DNA from 28 family members was analyzed on the Illumina OMNI-express chip using 733,120 SNPs and mapped to an approximately 2 Mb segment on chromosome 1q36.11 with LOD score 2.97 at 23.8–25.8 Mb (GRCh37/hg19 MERLIN). By dividing the pedigree into three 3-generation families, a region of association was found located between LOC284632 and GRHL3 (parenTDT, P = 0.005 for rs11249039, rs11249045, or rs7526505). GRHL3 is a gene expressed exclusively in surface ectoderm in drosophila, where it plays an essential role in cuticle formation. Expression of the murine Grhl3 gene is found in ectodermally derived tissues including the oral epithelium. Sequencing of the region of association is underway, and experimental models are being developed to test the hypothesis that variation in the regulation of this gene might play a role in this phenotype.
Is the Craniofacial Phenotype Sufficient to Characterize FGFR-Related Craniosynostosis Syndromes?
Yann Heuzé 1 , Neus Martínez-Abadías 1 , Jennifer M. Stella 1 , Federico Di Rocco 2 , Corinne Collet 3 , Gemma García Fructuoso 4 , Mariana Alamar 4 , Lun-Jou Lo 5 , Simeon A. Boyadjiev 6 , Joan T. Richtsmeier 1
1 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
2 Craniofacial Surgery Unit, Department of Pediatric Neurosurgery, Hôpital Necker–Enfants Malades,University Paris V, Paris, France
3 Laboratoire de Biochimie et de Biologie Moléculaire, INSERM U606, Paris, France
4 Servei de Neurocirurgia, Hospital Sant Joan de Déu, Barcelona, Spain
5 Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
6 Section of Genetics, Department of Pediatrics, University of California Davis, Sacramento, California
More than 180 craniosynostosis syndromes (CS) have been described, the more common CS being associated with mutations in fibroblast growth factor receptors (FGFRs). These “FGFR-related CS” show the characteristic premature fusion of one or several cranial sutures along with additional craniofacial, neural, limb, heart, lung, and/or skin anomalies. Despite the potentially high number of causative mutations for some of these FGFR-related CS, clinical diagnoses are quite reliable. However, our morphometric analysis based on landmarks collected from skull CT images of patients with Apert (n = 19), Crouzon (n = 9), Pfeiffer (n = 5), and Muenke (n = 4) syndromes along with those of unaffected children (n = 20) shows that these diagnostic categories are more difficult to establish when skull shape is the only trait considered. Indeed, we observe substantial overlap between craniofacial phenotypes, particularly of Apert, Pfeiffer and Muenke syndromes. The craniofacial phenotype as characterized by CT data is not sufficient to characterize FGFR-related CS. The cases that are most different from the unaffected individuals are the syndromic cases with bicoronal craniosynostosis. When syndromic cases displaying bicoronal craniosynostosis (n = 17) are compared with unaffected individuals (n = 20) and with children presenting with nonsyndromic bicoronal craniosynostosis (n = 14), our data provide a clear separation between craniofacial phenotypes of syndromic and nonsyndromic cases. The syndromic cases with bicoronal craniosynostosis display frontal bossing and severe midfacial hypoplasia. These last results indicate that in the case of bicoronal craniosynostosis the FGFR-related causative mutation and/or the molecular pathway affected by this mutation generates additional cranial dysmorphologies.
Supported in part by NIH/NIDCR R01DE018500, 3R01 DE018500-02S1, R01DE016886, and CDC 5R01 DD000350.
Understanding Phenotypic Variability in Neurodevelopmental Disorders
Santhosh Girirajan 1 , Jill A. Rosenfeld 2 , Blake C. Ballif 2 , Lisa G. Shaffer 2 , Evan E. Eichler 1
1 Department of Genome Sciences, University of Washington, Seattle, Washington
2 Signature Genomics Laboratory, Spokane, Washington
We recently proposed a two-hit model to explain the phenotypic variability associated with a 520-kbp microdeletion on chromosome 16p12.1, wherein, the microdeletion both predisposes to neuropsychiatric phenotypes as a single event and exacerbates neurodevelopmental phenotypes in association with other large (>500 kbp) copy number variants (CNVs). We extended our model to include 72 genomic disorders and examined CNV data from 32,587 cases with intellectual disability and congenital malformation for the presence of two large CNVs compared to 8,635 controls. Of the 2,312 cases with a known genomic disorder, 233 (10.2%) cases carried another CNV >500 kbp and 373 carried another CNV >150 kbp elsewhere in the genome. For 45/233 (19%) of these two-hit carriers, the second CNV was also associated with a genomic disorder. While the frequency of second hits was higher in CNVs associated with variable expressivity such as del15q13.3, del16p11.2, dup16p13.11, del16p12.1, and del and dup1q21.1, we found a positive correlation (Spearman correlation, r = 0.64, P < 0.001) between the proportion of inherited cases and the prevalence of the second hit. Analysis of parental DNA shows a combination of inherited and de novo events contributing to the occurrence of two hits in the probands. Pathway analysis of genes within the second hit CNVs shows disruption of genes involved in cellular signaling, neurological, and developmental functions. Our data provide strong support for the two-hit model to explain variable expressivity in genomic disorders and, overall, presents an oligogenic basis for the study of complex diseases.
Supported by NIH HD065285 to EEE.
Sphingomyelin Phosphodiesterase 3, a Novel Regulator of Skeletal Development and Mineralization
Zohreh Khavandgar 1 , Robert Scott Kiss 2 , Jingjing Li 3 , Monzur Murshed 1,3
1 Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
2 Division of Cardiology, McGill University Health Center, Montreal, Quebec, Canada
3 Department of Medicine, McGill University, Montreal, Quebec, Canada
Mineralization of vertebrate bone and tooth extracellular matrix is a genetically regulated process. One of the latest additions to the growing list of mineralization regulators is Sphingomyelin phosphodiesterase 3 (Smpd3). Smpd3 encodes a neutral sphingomyelinase that cleaves sphingomyelin to generate bioactive lipid metabolites. A deletion mutation called fragilitas ossium (fro) in the murine Smpd3 gene leads to severe skeletal dysplasia and perinatal death. In a recent study, it has been suggested that SMPD3 activity in the brain regulates skeletal development through endocrine factors. To further understand the role of SMPD3 in skeletal development, we examined endochondral ossification during early skeletogenesis in fro/fro mice. We observed an impaired apoptosis of the hypertrophic chondrocytes and severely under-mineralized cortical bones in E15.5 fro/fro embryos. To investigate whether SMPD3 plays a cell-autonomous role in these tissues, we generated fro/froCol1a1-Smpd3 mice, in which osteoblast-specific expression of Smpd3 corrected the fro/fro skeletal abnormalities and prevented perinatal deaths. Although the bone mineralization defects were fully corrected in fro/froCol1a1-Smpd3 embryos, their cartilage phenotype was largely unaffected. In the current study, we demonstrate a critical role for SMPD3 metabolites during in vitro mineral deposition by MC3T3-E1 pre-osteoblasts. Our data identify SMPD3 as a novel regulator of skeletal development and mineralization.
Supported by Canadian Institute of Health Research and Osteogenesis Imperfecta Foundation, USA.
A Rare DNA Variant in a cis-Overlapping Motif (COM) in an IRF6 Enhancer Element is Associated With Van der Woude Syndrome
Walid D. Fakhouri 1 , Fedik Rahimov 2 , Huiqing Zhou 3 , Tianli Du 1 , Evelyn N. Kouwenhoven 3 , Hans van Bokhoven 3,4 , Jeffrey C. Murray 2 , Brian C. Schutte 1,5
1 Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan
2 Department of Pediatrics, The University of Iowa, Iowa City, Iowa
3 Department of Human Genetics, Nijmegen Centre for Molecular Life Sciences, Nijmegen, The Netherlands
4 Department of Cognitive Neuroscience, Donders Institute for Brain, Cognition, and Behavior, Radboud University Nijmegen Medical Centre, Nijmegen, The Netherlands
5 Department of Pediatrics and Human Development, Michigan State University, East Lansing, Michigan
Cleft lip and palate (CLP) is one of the most common birth defects in humans. Mutations in interferon regulatory factor 6 (IRF6) cause Van der Woude syndrome (VWS), an autosomal dominant form of CLP, and contribute risk for isolated CLP, including a common DNA variant rs642961. Rs642961 is located in MCS9.7, a multi-species conserved sequence that is near IRF6. MCS9.7 element was shown to possess enhancer activity that mimicked the expression of endogenous Irf6. In order to identify possible etiologic DNA variants, we sequenced MCS9.7 in DNA samples obtained from individuals with VWS. We screened 48 DNA samples for which no disease-causing mutation was detected in IRF6 exons. We observed one new DNA variant that is an A insertion and is predicted to disrupt the DNA binding for both p63 and for bHLH transcription factors. We focused on four members of bHLH family whose expression pattern appeared to overlap with Irf6. Using a DNA binding assay, we observed that this DNA variant abrogated binding by p63 and reduced the binding affinity for the bHLH trans factors. In a transient transactivation assay, we observed strong enhancer activity by the MCS9.7 element. This activation was highly dependent on p63, and the activation was abrogated by the A insertion mutation. In conclusion, these data are consistent with the hypothesis that the rare DNA variant at the cis-overlapping motif in MCS9.7 is etiologic for VWS, and supports the rationale for additional mutation screening of the MCS9.7 enhancer element in patients with CLP.
Supported in part by NIH-DE13513.
A Systems Biology Approach to Cleft Lip and Palate
1 Department of Anthropology, Ball State University, Muncie, Indiana
The etiology of clefts may follow a multifactorial-threshold model. That model, however, fits poorly. Some clefts are teratogenic others, genetic, occasionally following a Mendelian pattern. Although human sibships are usually too small for testing, the recurrence frequency may approximate what would be expected for a double recessive in a two factor cross, 1/16 or 6.25%. About 25% of CLP is attributable to known genetic pathways. It appears that CLPs result from alleles or teratogens which slow neural crest cell migration as the known pathways may. My group (Bowers) have found that CLPs are systematic disorders, not alterations of the head and face alone. Affected children sometimes have reduced heights and delayed maturation, and frequently have reduced elbow breadths, with normal triceps skinfolds and arm circumferences. We found significantly negative standard deviation scores (Zs) for elbow breadth in a sample of 209 children, ages 2–18:11, divided by sex, age group, and whether the cleft was unilateral or bilateral. Average Zs ranged from −0.40 (P < 0.05) to −1.27 (P < 0.001). Only boys above age 7:7 with bilateral CLP had non-significant average Zs, and these too were negative. This suggests that one of the molecules contributing to the formation of both membranous and endochondral bone, such as the transcription factor RUNX2, may be involved. Here, I start to trace the regulatory circuitry which may link Runx2 to the pathways with known involvement.
Bowers EJ, Mayro RF, Whitaker LA, Pasquariello PS, LaRossa D, Randall P. 1987. General body growth in children with clefts of the lip, palate and craniofacial structure. Scand J Plastic Reconstr Surg 21:7–14.
Bowers EJ, Mayro RF, Whitaker LA, Pasquariello PS, LaRossa D, Randall P. 1988. General body growth in children with cleft palate and related disorders: Age differences. Am J Phys Anth 75:503–515.
Bowers EJ. 2011. Growth in children with clefts: Serial hand-wrist X-ray evidence. Cleft Palate Craniofacial J 48(6):762–772.
Alterations in Postnatal Craniofacial Bone Mineral Density and Volume in the Fgfr2 Y394C/+ Beare–Stevenson Cutis Gyrata Syndrome Mouse Model
Christopher Percival 1 , Yingli Wang 2 , Xueyan Zhou 2 , Ethylin Jabs 2 , Joan Richtsmeier 1
1 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
2 Department of Genetics and Genomic Sciences, Mt. Sinai School of Medicine, New York, New York
A novel technique is used to quantify individual cranial bone volume and relative bone mineral density across the murine skull from micro-computed tomography images and, in doing so, highlights the association between low bone density, low bone volume, and craniosynostosis in the Fgfr2 Y394C/+ mouse model of Beare–Stevenson cutis gyrata syndrome at P0 and at P8. While landmark based morphometric analysis indicates that the severity of dysmorphology in craniofacial form varies across the skull, the influence of the Fgfr2 Y394C mutation on rates of bone volume increase appear standard for all bones measured. These results suggest that this mutation influences bone cell activity across the skull, even at sites quite distant from the prematurely fused sutures that define craniosynostosis syndromes. The net volume reduction of high-density material in some mutant bones suggests that osteoclast activity, in addition to that of osteoblast, is affected during this early postnatal period. This novel study provides important information on the effect of the Fgfr2 Y394C mutation on endochondral and intramembranous bone development across the skull, complementing the results of morphometric analyses, and providing the basis for hypotheses that can be tested with more in depth histological, molecular, and cellular studies.
Supported in part by NIH/NIDCR R01-DE018500 (JTR), 3R01 DE018500-02S1 (JTR and EWJ), and NSF BCS-0725227.
Assessing the Oral Microbiota of Healthy and Alcohol-Treated Rats Using Whole-Genome DNA Probes From Human Bacteria
Zaher Jabbour 1 , Cássio do Nascimento 2 , Michel El-Hakim 3 , Janet E. Henderson 4 , Rubens Albuquerque 1
1 Faculty of Dentistry, Division of Restorative Dentistry, McGill University, Montreal, Quebec, Canada
2 Faculty of Dentistry of Ribeirao Preto, Department of Dental Materials and Prosthodontics, University of Sao Paulo, Sao Paulo, Brazil
3 Division of Oral and Maxillofacial Surgery, Faculty of Dentistry, McGill University, Montreal, Quebec, Canada
4 Division of Orthopedic Surgery, Faculty of Medicine, McGill University, Montreal, Quebec, Canada
Molecular methods for bacterial identification and quantification have been considered faster and more reliable than conventional methods. This study aimed to evaluate the capacity of whole-genome DNA probes prepared from human oral bacteria to detect and quantify oral bacterial species of rats, and to assess the influence of alcohol ingestion on the oral biofilm. Twenty-four mature Wistar rats were equally divided in two groups. One group (control) was fed balanced diet of rat pellets and water. The alcohol-treated group (AT) received the same diet and 20% ethanol solution. Upon euthanasia after 30 days, bacterial samples from the oral biofilm covering the animals' teeth were collected using microbrushes. Bacteria identification and quantification were based on the intensity of chemiluminescent signals released by DNA–DNA checkerboard hybridization with 33 probes prepared from human oral bacteria. Bacteria levels were compared using a Mann–Whitney U-test with a significance level < 0.05. All targeted strains, except Streptococcus mutans and Streptococcus mitis, were detected in the control group. Escherichia coli, Psuedomonas aeruginosa, Porphyromonas endodontalis, and Veillonella parvula were the only species detected in the AT group. Significantly higher bacteria levels were found in the control group compared to the AT group (P = 0.001). The percentage of E. coli was highest in both groups. Whole-genome DNA probes prepared from human oral bacteria can cross-react with rats' oral bacterial strains. Alcohol consumption is associated with lower bacterial diversity and numbers in the oral cavity of rats.
Supported by Fundação de Amparo a Pesquisa do Estado de São Paulo (FAPESP).
Nonsyndromic Sagittal Craniosynostosis Associated With Novel Variants in FGFR1, TWIST1, and RAB23 Genes
Xiaoqian Ye 1,2 , Audrey Guilmatre 1 , Ethylin Wang Jabs 1 , Yann Heuzé 3 , Joan Richtsmeier 3 , Deborah J. Fox 4,5 , Charlotte M. Druschel 4,5 , Rhinda J. Goedken 6 , Paul A. Romitti 6
1 Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, New York, New York
2 The State Key Laboratory Breeding Base of Basic Science of Stomatology (Hubei-MOST), Key Laboratory of Oral Biomedicine Ministry of Education, School & Hospital of Stomatology, Wuhan University, Wuhan, China
3 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
4 Department of Epidemiology and Biostatistics, School of Public Health, University at Albany State University of New York, Albany, New York
5 Congenital Malformations Registry, New York State Department of Health, Troy, New York, New York
6 Department of Epidemiology, The University of Iowa College of Public Health, Iowa City, Iowa
Craniosynostosis, the premature fusion of one or more cranial sutures, occurs in approximately one in 2,500 live births. Among various forms, midline sagittal nonsyndromic craniosynostosis represents the most prevalent type. In syndromic craniosynostosis, causative mutations are known on fibroblast growth factor receptors (FGFRs), TWIST1, RAB23, and other genes. However, the etiology of nonsyndromic craniosynostosis is largely unknown. We used data from an ongoing, population-based case-control study in Iowa and New York State to identify novel candidate genes for nonsyndromic sagittal craniosynostosis. In this study, we evaluated 96 nonsyndromic sagittal craniosynostosis cases and performed extensive candidate genes analysis by direct sequencing. Two isoforms (intron 7 of isoform 1, exon 6 of isoform 5-6) of FGFR1, intron 9 of FGFR2, TWIST1, and RAB23 were selected based on previous publications, their expression patterns, animal models, and/or roles in known human craniosynostosis syndromes. Novel nucleotide variants were found in FGFR1 (isoform 5 and 6, n = 2), TWIST1 (n = 1), and RAB23 (n = 1). These variants detected in our study were unique and did not occur in 316 alleles from healthy controls or in the NCBI dbSNP, Human Gene Mutation Database and CHIP Bioinformatics databases. Our aggregate data suggest that mutations in these candidate genes are likely to contribute to nonsyndromic sagittal craniosynostosis, although they would account for only a small proportion of the total cases. These findings add to the perception of nonsyndromic sagittal craniosynostosis as a complex developmental anomaly under potential polygenic control.
Supported in part by grant from CDC 5R01 DD000350.
Differential Gene Expression in the Face of CL/Fr Mouse Embryos at E11.5 Based on Microarray Analysis
Brennan Takagi 1 , T.J. Hynd 1 , S. Jack Somponpun 1 , Kazuaki Nonaka 2 , Scott Lozanoff 1
1 Department of Anatomy, Biochemistry and Physiology, University of Hawaii School of Medicine, Honolulu, Hawaii
2 Faculty of Dentistry, Section of Pediatric Dentistry, Kyushu University, Fukuoka, Japan
The CL/Fr mouse demonstrates heritable bilateral and unilateral cleft lip and palate (CLP) at a rate of approximately 35%, generally above the background “A” strain mouse. Using classical mouse breeding strategies, it has been suggested that at least two disease loci, clf1 and clf2, are involved in the defect and candidate genes have been identified. Additionally, gene-targeting analyses strongly suggest that Wnt9b contributes to CLP in the “A” strain mice. The aim of this study was to test the expression of clf1 and clf2 candidate genes in the facial prominences of CL/Fr embryos, utilizing microarray analysis. Medial nasal, lateral nasal, and maxillary prominences of phenotypically normal as well as cleft E11.5 CL/Fr mice were dissected and RNA was extracted using standard techniques for Agilent-microarray protocol. Results indicate that expression of the clf1 candidate genes, Wnt9b and Wnt3, and the clf2 candidate genes, Adcy2 and Ube2ql1, are significantly reduced (−3.11, −1.50, −2.22, and −1.83-fold, respectively) in the CL/Fr cleft tissues, suggesting that all four genes may be involved in the CLP mutation in CL/Fr mice. Future gene expression studies through quantitative RT-PCR and regional expression analyses through immunohistochemistry will be performed to further test the expression of these clf1 and clf2 candidate genes.
Supported in part by NIH/NCRR 5P20RR024206 (SJS) and R01-DK-064752 (SL).
Differential Gene Expression in Mice With Misexpression of six2 Associated With Frontonasal Dysplasia
Thomas Hynd 1 , Ben Fogelgren 1 , S. Jack Somponpun 1 , Sheri F.T. Fong 1 , Scott Lozanoff 1
1 Department of Anatomy, Biochemistry, and Physiology, University of Hawaii School of Medicine, Honolulu, Hawaii
We have previously described the Br mutant mouse displaying heritable frontonasal dysplasia. Linkage analysis mapped the mutation near the homeobox transcription factor six2, normally expressed in the facial mesenchyme during embryonic development. The purpose of this study is to determine expression patterns of six2, as well as possible upstream and downstream targets of six2, in the developing midface. The three sets of paired facial prominences (medial, lateral, and maxillary) of E11.5 embryos were dissected and RNA extracted for qPCR assays and Agilent microarray analysis. Medial nasal prominences (MNP) were also taken for cell culture. qPCR results indicated six2 expression is highest in the MNP and demonstrated haploinsufficient down-regulation in each of the three facial prominence sets in the Br mouse. Microarray results suggested the misregulation of several genes involved in a wide variety of genetic pathways, including the transcription factor six3. Further validation will be required to corroborate these microarray results, including qPCR, immunohistochemistry and RNA interference. Preliminary results using an in vitro knockdown of six2, performed on an MNP cell culture system utilizing siRNA, demonstrated a 65–70% knockdown of six2. These results may enable further in vitro work in order to elucidate a pathway in the developing midface involving six2.
This work was supported, in part, by NIH/NCRR R01DK064752 (SL) & 5P20RR024206 (SJS).
Genome-Wide Meta-Analysis of Nonsyndromic Cleft Lip With or Without Cleft Palate (NSCL/P) Identifies Multiple New Loci
Kerstin U. Ludwig 1,2 , Stefan Herms 1,2 , Michael Knapp 3 , Markus M. Nöthen 1,2 , Elisabeth Mangold 1
1 Institute of Human Genetics, University of Bonn, Bonn, Germany
2 Department of Genomics, Life and Brain Center, Institute of Human Genetics, University of Bonn, Bonn, Germany
3 Institute of Medical Biometry, Informatics, and Epidemiology, University of Bonn, Bonn, Germany
Nonsyndromic cleft lip with or without cleft palate (NSCL/P) is amongst the most common birth defects. The etiology of this malformation, which involves environmental and genetic factors, has recently been enlightened by the discovery of six genetic susceptibility loci in genome-wide association studies (GWAS). To identify additional loci we conducted a meta-analysis of the two largest GWAS on NSCL/P, that is, a case–control study of Central Europeans [Mangold et al., 2010] and a family-based study involving European and Asian trios [Beaty et al., 2010, data retrieved from dbGaP]. Our analysis confirms all previously identified loci and identifies six new susceptibility regions for the European population (1p36, 2p21, 3p11.1, 8q21.3 13q31.1, and 15q22). Population-specific analysis revealed that five of them also play a role in the Asian population, suggesting that we have identified common genetic risk factors for NSCL/P. Candidate genes within these regions include SPRY2, THADA, PAX7, and EPHA3, opening new starting points for subsequent in-depth genetic and functional studies.
Supported by DFG grants (MA 2546/3-1, KR 1912/7-1, NO 246/6-1, WI 1555/5-1), dbGaP-data were obtained at http://www.ncbi.nlm.nih.gov/gap through dbGaP accession number phs000094.v1.p1.
Mangold E, Ludwig KU, Birnbaum S, Baluardo C, Ferrian M, Herms S, Reutter H, de Assis NA, Chawa TA, Mattheisen M, Steffens M, Barth S, Kluck N, Paul A, Becker J, Lauster C, Schmidt G, Braumann B, Scheer M, Reich RH, Hemprich A, Pötzsch S, Blaumeiser B, Moebus S, Krawczak M, Schreiber S, Meitinger T, Wichmann HE, Steegers-Theunissen RP, Kramer FJ, Cichon S, Propping P, Wienker TF, Knapp M, Rubini M, Mossey PA, Hoffmann P, Nöthen MM. 2010. Genome-wide association study identifies two susceptibility loci for nonsyndromic cleft lip with or without cleft palate. Nat Genet 42:24–26.
Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Liang KY, Wu T, Murray T, Fallin MD, Redett RA, Raymond G, Schwender H, Jin SC, Cooper ME, Dunnwald M, Mansilla MA, Leslie E, Bullard S, Lidral AC, Moreno LM, Menezes R, Vieira AR, Petrin A, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Huang S, Yeow V, Chong SS, Jee SH, Shi B, Christensen K, Melbye M, Doheny KF, Pugh EW, Ling H, Castilla EE, Czeizel AE, Ma L, Field LL, Brody L, Pangilinan F, Mills JL, Molloy AM, Kirke PN, Scott JM, Arcos-Burgos M, Scott AF. 2010. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4. Nat Genet 42:525–529.
Growth of the Skull and Brain in a Mouse Model for Apert Syndrome
Cheryl A. Hill 1 , Jordan R. Austin 1 , Joan T. Richtsmeier 2 , Susan Motch 2 , Neus Martínez-Abadías 2 , Yingli Wang 3 , Ethylin Wang Jabs 3 , Kristina Aldridge 1
1 Department of Pathology and Anatomical Sciences, University of Missouri-Columbia, Columbia, Missouri
2 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
3 Department of Genetics and Genomic Sciences, Mt. Sinai School of Medicine, New York, New York
Craniofacial and neural tissues develop in concert throughout pre- and postnatal growth. Craniosynostosis syndromes, such as Apert syndrome (AS), are associated with specific phenotypes involving both the skull and the brain. Analysis of a mouse model for AS, the Fgfr2 +/P253R mouse, allows for study of the effects of this specific mutation on these two tissues simultaneously over the course of development. Previous work on this mouse model has demonstrated specific and localized differences in the brain and skull. The purpose of this study is to compare theFgfr2 +/P253R mouse and their wild-type littermates at two developmental time points, to determine whether growth patterns differ in brain and skull. Both three-dimensional micro-magnetic resonance images and computed tomography scans were acquired from mice with the Fgfr2 +/P253R mutation and their wild-type littermates. The sample consisted of newborn (P0) mice (N = 28) and 2-day-old (P2) mice (N = 23). Coordinate data for 15 brain and 24 skull landmarks were collected using Amira© and Analyze 10.0© software and statistically compared using Euclidean Distance Matrix Analysis. Results demonstrate that the Fgfr2 +/P253R mice show reduced growth in the cerebrum and the face, while the height and width of the neurocranium and posterior regions of the brain show increased growth as compared to wild-type mice. This localized correspondence of differential growth patterns in skull and brain point to their continued interaction through development, while also demonstrating that both tissues display divergent postnatal growth patterns as compared to their wild-type littermates.
Supported in part by NIH/NIDCR R01 DE018500 (JTR), R01DE18500-02S1 (JTR and EWJ).
Phenotypic Continuum in FGFR Syndromic Craniosynostosis? Evidence From Human Patients and Mouse Models
Neus Martínez-Abadías 1 , Yann Heuzé 1 , Yingli Wang 2 , Susan Motch 1 , Talia Pankratz 1 , Jennifer M. Stella 1 , Gemma García Fructuoso 3 , Mariana Alamar 3 , Federico Di Rocco 4 , Corinne Collet 5 , Lun-Jou Lo 6 , Simeon A. Boyadjiev 7 , Ethylin Wang Jabs 2 , Joan T. Richtsmeier 1
1 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
2 Department of Genetics and Genomic Sciences, Mount Sinai School of Medicine, One Gustave L. Levy Place, New York, New York
3 Servei de Neurocirurgia, Hospital Sant Joan de Déu, Barcelona, Spain
4 Craniofacial Surgery Unit, Department of Pediatric Neurosurgery, Hôpital Necker–Enfants Malades, University Paris V, Paris, France
5 Laboratoire de Biochimie et de Biologie Moléculaire, INSERM U606, Paris, France
6 Department of Plastic and Reconstructive Surgery, Chang Gung Memorial Hospital, Chang Gung University, Taoyuan, Taiwan
7 Section of Genetics, Department of Pediatrics, University of California Davis, Sacramento, California
Of the more than 180 craniosynostosis syndromes (CS) with a prevalence of 1/10,000 live births, many are caused by mutations in fibroblast growth factor receptors (FGFRs). The FGFR-related CS involve premature fusion of cranial sutures associated with craniofacial, neural, limb, and visceral malformations. The precise definition and classification of FGFR-related CS can be difficult due to phenotypic variation within diagnostic categories, such that genetic testing is often required. However, there is no one-to-one correspondence between genetic mutations and phenotypes: a single mutation can result in different phenotypes, and mutations in different genes may produce similar phenotypes. We focus on a subset of CS caused by mutations in FGFR1, 2, and 3 (Apert, Crouzon, Pfeiffer and Muenke syndromes) to precisely quantify the phenotypic spectrum of these disorders based on geometric morphometric analysis of 3D landmark coordinates collected from CT reconstructions of the skull of human patients (N = 37), unaffected individuals (N = 20) and mouse models for CS (N = 96 mutant 109 non-mutant littermates). Our analyses suggest that there is correspondence between human and mouse data and that within both organisms the cranial morphologies associated with CS are distributed over a phenotypic continuum that ranges from no dysmorphology to various degrees of mild and severe dysmorphology. Individuals with Apert syndrome are the most severely affected, whereas individuals with Crouzon, Pfeiffer, and Muenke syndromes display mild to severe dysmorphologies. Along this phenotypic spectrum fairly well-defined diagnostic groups overlap due to high degrees of within-group variation, suggesting that common genetic and phenotypic variation underlie FGFR-related CS.
Supported in part by NIH/NIDCR (R01 DE018500, 3R01 DE018500-02S1, R01 DE016886), CDC (5R01DD000350), and Beca Postdoctoral Beatriu de Pinós, AGAUR, Generalitat de Catalunya.
Proteins Regulation of Enamel Crystallographic Ultrastructure
Hazem Eimar 1 , Benedetto Marelli 1 , Showan Nazhat 1 , Samer Abinader 1 , Wala Amin 2 , Jesus Torres 3 , Rubens Albuquerque 1 , Faleh Tamimi 1
1 Faculty of Dentistry McGill University, Montreal, Quebec, Canada
2 Faculty of Dentistry, Jordan University, Amman, Jordan
3 Department of Health Science III, Universidad Rey Juan Carlos, Alcorcon, Madrid, Spain
Enamel is a composite material that comprises an inorganic matrix composed of hierarchically organized carbonated-hydroxyapatite (HA) crystals, and an organic matrix mainly composed of the protein amelogenin. Understanding the relation between tooth enamel chemical components is of special interest for the interpretation of the variations in tooth development among humans. Accordingly, this study was designed to investigate how variations in the enamel proteins may affect its ultrastructure. One-hundred extracted sound teeth were collected from adult patients attending McGill-Undergraduate Dental Clinic. FTIR and XRD were used to assess enamel chemical composition (protein content and degree of HA carbonization) and crystallography (crystal size, lattice parameters: a-axis and c-axis). The data obtained were analyzed for correlation, and statistical significance was set at P < 0.05. Tooth enamel protein content and crystallographic structure varied dramatically within the studied population. Enamel protein content was inversely correlated with its HA crystal size (R = −0.352, B = −19.4). Further analysis revealed that this correlation was not purely linear. Instead, it followed a curve in which at specific enamel protein content, tooth enamel samples had the maximum HA crystal size. However, below or above that specific enamel protein content, teeth expressed smaller HA crystals [(R = 0.32, B = 271.4) and (R = −0.36, B = −15.1), respectively]. Moreover, the amount of tooth enamel protein was positively correlated with the carbonization degree of HA crystals (R = 0.474, B = 0.410). From the present study, we conclude that tooth enamel proteins exhibited a dual behavioral effect on the size of HA crystals. Moreover, the degree of HA carbonization was also regulated by enamel proteins.
Supported in part by Fondation de l'Ordre des dentistes du Québec (FODQ).
Reading Between the Lines: The Development of Negative Spaces in a Crouzon/Pfeiffer Syndrome Mouse Model at Birth
Susan M. Motch 1 , Neus Martínez-Abadías 1 , Talia L. Pankratz 1 , Yingli Wang 2 , Kristina Aldridge 3 , Ethylin W. Jabs 2 , Thomas Neuberger 4 , Timothy M. Ryan 1,5 , Joan T. Richtsmeier 1
1 Department of Anthropology, Pennsylvania State University, University Park, Pennsylvania
2 Department of Genetics and Genomic Sciences, Mt. Sinai School of Medicine, New York, New York
3 Department of Pathology and Anatomical Sciences, University of Missouri-School of Medicine, Columbia, Missouri
4 High Field MRI Facility, Pennsylvania State University, University Park, Pennsylvania
5 Center for Quantitative Imaging, Pennsylvania State University, University Park, Pennsylvania
Crouzon syndrome is associated with nearly 50 known FGFR2 mutations, one of which, the FGFR2 C342Y mutation, is causative for Crouzon and Pfeiffer craniosynostosis syndromes. Individuals with Crouzon and Pfeiffer syndromes show marked phenotypic variation but usually display premature closure of cranial suture(s), additional craniofacial malformations, as well as defects involving other systems including respiratory disorders and auditory impairments. We used µCT and µMR images of newborn littermates of the Fgfr2c C342Y/+ mouse model for Crouzon/Pfeiffer syndromes, to investigate the global and regional impact of this mutation on the developing skull and negative spaces of the head at P0. Negative spaces were defined as the air-filled space of the nasopharynx that develop within the intramembranous facial skeleton and fluid filled structures of the cochlea and vestibular canals that develop within the otic skeleton, which is still cartilaginous at birth. Global and regional differences in skull morphology were observed using configurations of 3D landmark coordinates measured on µCT isosurfaces in Fgfr2c C342Y/+ mice (n = 28) relative to non-mutant littermates (n = 31). Results revealed dysmorphology of the facial skeleton, cranial base and cranial vault in Fgfr2c C342Y/+ mice. Volumetric measurement using µMR images indicated restriction of the nasopharynx of Fgfr2c C342Y/+ mice (n = 8) compared to non-mutant littermates (n = 11), but no difference in cochlear and semicircular canal volume. Future work aims to determine whether differences in the effect of the FGFR2 C342Y mutation on these negative spaces are due to differential effects of the mutation on endochondral and intramembranous forming bone.
Supported in part by NIH/NIDCR R01 DE018500 (JTR) 3R01 DE018500-02S1 (JTR and EWJ).
Reduced Bone Mass in Mice Lacking the Men1 Gene in Osteoblasts
Ippei Kanazawa 1 , Geetanjali Nayak 1 , Lucie Canaff 1 , Monzur Murshed 1 , Geoffrey N. Hendy 1
1 Department of Medicine, McGill University Health Centre, Montreal, Quebec, Canada
Homozygous inactivation of the multiple endocrine neoplasia type 1 (Men1) gene encoding menin in mice is embryonic lethal and fetuses exhibit clear defects in cranial and facial development. We have shown previously that menin has an important role in osteoblastogenesis and osteoblast differentiation by in vitro studies. To further understand the physiological role of menin in bone development in vivo we are generating mouse models in which the expression of the Men1 gene is altered only in osteoblasts. Mice lacking Men1 exons 3–8 in osteoblasts driven by Osteocalcin-Cre (Men1 KO mice) displayed no differences in growth rate compared to wild-type (WT) littermates. In 9-month-old female mice, micro-CT revealed that trabecular bone volume and cortical bone thickness were significantly reduced in the Men1 KO mice. Histomorphometric analysis showed that bone volume/total volume, numbers of osteoblasts and osteoclasts, as well as mineral apposition rate were all significantly reduced in the Men1 KO mice. In mice overexpressing human menin in osteoblasts from a human menin cDNA driven by a Col1a1 promoter (Men1 TG mice), at 6 months of age, the Men1 TG mice were not different from WT littermates in growth rate and bone mineral density by DXA. Taken together, depletion of menin in the osteoblast leads to decreased osteoblast and osteoclast numbers as well as impaired bone remodeling, resulting in a reduction in trabecular and cortical bone whereas overexpression has no effect at least in younger mice. Therefore, maintenance of menin expression and function in bone is important to avoid decreased bone mass.
Supported in part by grants from the Canadian Institutes of Health Research (CIHR).
Replication of GWAS Candidate Genes in Four Independent Populations Confirm the Role of Common Variants and Identifies Rare Variants in PAX7 and VAX1 Contributing to the Etiology of Non-Syndromic CL(P)
A. Butali 1 , S. Suzuki 1,2 , M.A. Mansilla 1 , A.L. Petrin 1 , E. Leslie, J. L'Heureux 1 , M.E. Cooper 4 , N. Natsume 2 , T.H. Beaty 3 , M.L. Marazita 4 , J.C. Murray 1
1 Department of Pediatrics, University of Iowa, Iowa City, Iowa
2 School of Dentistry, Aichi-Gakuin University, Japan
3 Johns Hopkins University, School of Public Health, Baltimore, Maryland
4 Center for Craniofacial and Dental Genetics, Department of Oral Biology, School of Dental Medicine, University of Pittsburgh, Pittsburgh, Pennsylvania
GWAS of CL(P) have identified several significant and near-significant genetic associations for non-syndromic CL(P) [Beaty et al., 2010]. To replicate two of the near-significant GWAS signals, the present study investigated the role of both common and rare variants in the PAX7 and VAX1 genes. Direct sequencing in and around the PAX7 and VAX1 genes in individuals of European and Asian ancestry was done. TaqMan genotyping was carried out for SNPs in VAX1 and PAX7 and Transmission Disequilibrium Test (TDT) was performed to investigate family based association in each population. Nineteen variants were found in PAX7. Eleven unreported variants were found in VAX1. TDT analysis showed strong associations with markers in VAX1 (rs7078160, P = 2.7E-06 and rs475202, P = 0.0002) in a combined Mongolian and Japanese CL (P) case–parent triads. Further analysis of parent-of-origin effects showed a significant maternal to child transmission (P = 6.7E-05, OR = 2.02) and paternal to child transmission (P = 0.009, OR = 1.62) for VAX1 marker rs7078160 in Mongolian and Japanese combined CL(P). CL(P) males were mostly responsible for the parental effects in the combined Japanese and Mongolian populations (rs7078160, P = 1.5E-05, OR = 2.95 for maternal transmission, and P = 0.05, OR = 1.65 for paternal transmission). The rs6659735 trinucleotide marker in PAX7 was significantly associated with all the Iowan cleft groups combined [P = 0.007 in all clefts and P = 0.01 in CL(P)]. Our study replicated previous GWAS findings for markers in VAX1 across three independent Asian populations, and identified rare variants in PAX7 that may contribute to the etiology of CL(P). Elucidating the role of these rare variants warrants further investigation.
Supported by NIH DE-08559, DE016148, KAKENHI, Grant-in-Aid for Young Scientist (B) No. 20791560 (Aichi-Gakuin), U01 DE-20057 and U01-DE-018993.
Beaty TH, Murray JC, Marazita ML, Munger RG, Ruczinski I, Hetmanski JB, Liang KY, Wu T, Murray T, Fallin MD, Redett RA, Raymond G, Schwender H, Jin SC, Cooper ME, Dunnwald M, Mansilla MA, Leslie E, Bullard S, Lidral AC, Moreno LM, Menezes R, Vieira AR, Petrin A, Wilcox AJ, Lie RT, Jabs EW, Wu-Chou YH, Chen PK, Wang H, Ye X, Huang S, Yeow V, Chong SS, Jee SH, Shi B, Christensen K, Melbye M, Doheny KF, Pugh EW, Ling H, Castilla EE, Czeizel AE, Ma L, Field LL, Brody L, Pangilinan F, Mills JL, Molloy AM, Kirke PN, Scott JM, Arcos-Burgos M, Scott AF. 2010. A genome-wide association study of cleft lip with and without cleft palate identifies risk variants near MAFB and ABCA4 Nat Genet 42:525–529.
Fernando Bolio ’22
Since I was little, I have always been enamored by science and attempting to understand how the body functions, one cell at a time. Our bodies are comprised of so many complex systems and interactions it would take centuries or millennia of research and experiments to understand every facet of ourselves. Personally, I’ve always been interested in examining the minute, focusing on the way that human behavior can be impacted through small changes in protein or molecule expression and how widespread that small change can be. Entering Pomona, I knew that I would major in either molecular biology or neuroscience. Unable to double major, I spoke with professors from both departments who guided me into choosing molecular biology as my major with a focus in neuroscience. This path allowed me to choose the best of both worlds, allowing me to focus on the minute systems underlying the brain while also providing a solid academic foundation to enter graduate school and explore to my heart’s desire. I believe that every mental illness has a basis in biological behavior, and with the knowledge and tools provided with the molecular biology major, I hope to contribute to our understanding of the brain’s mechanisms of action.
I love how this major provides a solid pathway to learn about molecular biology in the area of your choosing. Once you pass the introductory courses, the field opens and you’ll see boundless possibilities and opportunities for you to explore. No matter your focus, there are a variety of courses and electives that will satisfy your curiosity. I also extremely appreciate the relationships that I’ve established with professors of the department. They are incredibly supportive and love having conversations with students, even if it’s not about their classes or research. The best moments I’ve had with my professors are the ones in which we sat down for lunch or during office hours and talked about how things were going in our lives, with no focus on anything academically related.
Entering Pomona, I was extremely interested in working in a laboratory doing research as I’ve never had the opportunity before. Luckily, I found a position in Professor Lenny Seligman’s lab the second semester of my first year that I continued through the summer in a SURP. The project involved creating a novel system to engineer homing endonucleases to cut DNA sequences of our choosing, allowing us to target genes in a similar fashion to CRISPR. To accomplish this, we modified an established system known as PACE to work with I-CREI, a homing endonuclease, to allow it to go through several hundred rounds of evolution. Creating this system would be invaluable in the future of gene editing as it could provide an alternative to CRISPR and help provide solutions to genetic diseases such as sickle cell anemia. This research was extremely fascinating to learn about and develop, and through my time in the lab, I gained valuable techniques and the experience to troubleshoot and figure out solutions to problems in the lab.
I hope to come back to Pomona one day as a professor and guide future students on their path. I want to leave a positive impact on the lives of students and offer the same support, generosity and kindness that my professors have given me.
- Developmental Biology Section
Michael W. Krause, Ph.D.
- Genetic Mechanisms Section
Kiyoshi Mizuuchi, Ph.D., NIH Distinguished Investigator
- Molecular Genetics Section
Martin Gellert, Ph.D., NIH Distinguished Investigator
- Molecular Virology Section
Robert Craigie, Ph.D.
- Physical Chemistry Section
Gary Felsenfeld, Ph.D., NIH Distinguished Investigator
- Protein Stability and Quality Control Section
Yihong Ye, Ph.D.
- Structural Biochemistry Section
Frederick Dyda, Ph.D.
- Structural Biology of Membrane Proteins Section
Susan K. Buchanan, Ph.D.
- Structural Biology of Noncoding RNAs and Ribonucleoproteins Section
Jinwei Zhang, Ph.D., Stadtman Tenure-Track Investigator
- Mechanism of DNA Repair, Replication, and Recombination Section
Wei Yang, Ph.D., NIH Distinguished Investigator
Developmental Biology Section
The Developmental Biology Section investigates the transcriptional regulation of cell fate determination during metazoan development. Using the C. elegans system, we exploit forward and reverse genetic approaches to identify and characterize transcription factor function required for proper development of specific cell types, at single-cell resolution. Historically, our interest has primarily been directed at understanding muscle cell specification and differentiation as a model for both embryonic and postembryonic development. Our goal is to fully describe the transcriptional cascade that orchestrates the formation of this tissue from just after fertilization, throughout embryogenesis, and into adulthood.
Genetic Mechanisms Section
The Genetic Mechanisms Section investigates the mechanics of cellular processes that impact the genomic structure and the heritance of the genomic material. We study mechanisms of reactions that impact the stability of the linear organization of the genome, as well as the 3-dimensional dynamics involved in the heritance of bacterial chromosomes.
Molecular Genetics Section
The Molecular Genetics Section studies the rearrangement of immunoglobulin and T-cell receptor genes (known as V(D)J recombination). This process is essential for the development of lymphoid cells and is unique in sharing some properties with site-specific recombination and with the repair of radiation damage to DNA. Our aim is to understand V(D)J recombination in detail and to apply this knowledge to the immune system. Our research has shown that recombination begins with site-specific DNA breaks, which can be made by the isolated RAG1 and RAG2 proteins, and that a DNA hairpin is produced on one side of each break. This reaction shares many properties with mobile genetic elements (transposons), and we are interested in the potential role of transposition in causing chromosomal translocations of the types found in leukemias and lymphomas. Researchers in this section are also investigating the separate ubiquitin ligase activity of RAG1 and its covalent modification by auto-ubiquitylation.
Molecular Virology Section
The Molecular Virology Section focuses on mechanistic aspects of retroviral DNA integration. After entering the host cell, a DNA copy of the viral genome is made by reverse transcription. Integration of this viral DNA into a chromosome of the host cell is an essential step in the retroviral replication cycle. The key player in the retroviral DNA integration process is the virally encoded integrase protein. Integrase processes the ends of the viral DNA and covalently inserts these processed ends into host DNA. We study the molecular mechanism of these reactions using biochemical, biophysical, and structural techniques. Researchers in this section collaborate closely with NIDDK colleagues who use X-ray crystallography and NMR. Our work also investigates cellular proteins that play important accessory roles in the integration process. Of particular interest is the mechanism that prevents integrase using the viral DNA as a target for integration. Such autointegration would result in destruction of the viral DNA. We have identified a cellular protein, which we called barrier-to-autointegration factor (BAF) that prevents integration of the viral DNA into itself. Our studies suggest that compaction of the viral DNA by BAF makes it inaccessible as a target for integration.
Physical Chemistry Section
The Physical Chemistry Section studies the structure and function of several types of proteins. Specific projects investigate the relationship between chromatin structure and gene expression in eukaryotes. Researchers focus on the epigenetic mechanisms and the structure of both the individual nucleosomes (the fundamental chromatin subunits) and the folded polynucleosome fiber. Recent investigations on the role of histone variants in regulation of chromatin structure and gene expression suggest that unstable nucleosome core particles (NCPs) play a role in making active promoters more accessible for binding by regulatory factors. Other work examines long-range chromatin organization and the boundaries between independently regulated domains, which play a role in regulation of gene expression. We have focused on the properties of insulator elements that help to establish such boundaries. Our research has identified proteins that bind to the insulator sites, as well as the co-factors that those proteins recruit, and the results suggest how the enhancer blocking or barrier activity arises. Present work is examining these mechanisms in detail and includes biochemical and functional analysis of the complexes. Other studies examine the effects of protein knockdown on the local and long-range chromatin structure and histone modification patterns. In particular, we are studying long-range interactions within the nucleus in human pancreatic beta cells and between the insulin gene and other genes that may be co-regulated. This is part of a larger effort to study chromatin structure of the insulin locus and its relationship to insulin gene expression and secretion.
Protein Stability and Quality Control Section
The Protein Stability and Quality Control Section (1) performs research using in vitro reconstitution and cell-based assays to elucidate the cellular mechanisms underlying protein quality control at the endoplasmic reticulum (ER) (2) develops reagents and tools to disrupt ER protein homeostasis and evaluates their activities in anti-cancer therapy (3) studies the catalysis mechanisms for various enzymes in the ubiquitin proteasome system (4) extends our studies to address fundamental questions in other protein quality control systems and (5) supports the career development of research trainees in scientific or biomedical pursuits.
Structural Biochemistry Section
The Structural Biochemistry Section studies the molecular mechanisms underlying protein activity modulation. To function properly, cells must coordinate and choreograph a large number of simultaneous events and processes. Proteins carry out these essential processes. We primarily use X-ray crystallography to study how cells regulate the activity and function of protein-protein and protein-DNA complexes. X-ray crystallography produces high-resolution "snapshots" to visualize subtle changes in protein structure that often accompany functional regulation. With these snapshots in hand, we use a variety of biochemical, biophysical and simulation approaches to relate their structures and biological functions. Specific projects investigate how proteins control the movement of mobile genetic elements, such as transposons or viruses. One of our current areas of emphasis is the Rep protein of adeno-associated virus (AAV). This protein catalyzes the integration of the AAV genome into a specific locus in human chromosome 19, making it an extremely useful tool for gene therapy studies. In addition, we are studying how a ubiquitous group of chaperone proteins known as 14-3-3s are able to direct when and where in a cell to deliver proteins that regulate gene expression.
Structural Biology of Membrane Proteins Section
The Structural Biology of Membrane Biology Section focuses on the structure determination of integral membrane proteins by x-ray crystallography and functional analysis of these proteins using biophysical, biochemical, and cell biological techniques. We study transporters embedded in the outer membranes of Gram-negative bacteria, which are surface accessible and therefore have the potential to be good vaccine and/or drug targets against infectious diseases. We also study the membrane-associated, or soluble protein, partners that interact with outer membrane transporters to better understand how these systems function in vivo. Current topics in the lab include (1) small molecule and protein import across the bacterial outer membrane, (2) protein secretion by pathogenic bacteria, and (3) protein import across mitochondrial outer membranes. Our lab currently studies several distinct proteins. Some are common to many different kinds of bacteria and are required for their survival, while others are uniquely involved in the development of E. coli or Yersinia pestis (the bacteria that causes the plague) infections. Recently, we have also started to study mammalian proteins, which may play a role in the progression of neurodegenerative states like Alzheimer’s and Parkinson’s diseases.
Structural Biology of Noncoding RNAs and Ribonucleoproteins Section
The Structural Biochemistry of Noncoding RNAs and Ribonucleoproteins Section performs research to gain a detailed structural and mechanistic understanding of cellular and viral noncoding RNAs and their associated ribonucleoprotein complexes involved in gene regulation and human diseases. We are working to uncover general motifs and principles that govern RNA tertiary structure formation, RNA recognition by another RNA or protein, and how dynamic RNA structures contribute to the regulation of gene expression and human pathophysiology. Current research topics include:  Structure, mechanism, targeting, and engineering of gene-regulatory riboswitches.  tRNA-mediated stress sensing and response pathways in eukaryotes.  HIV and other viral RNA structures and their protein complexes.
Mechanism of DNA Repair, Replication, and Recombination Section
The Mechanism of DNA Repair, Replication, and Recombination Section is interested in studying DNA recombination, repair, and replication. In particular, we are interested in V(D)J recombination, mismatch repair, nucleotide excision repair, and translesion DNA synthesis. We use X-ray crystallography, molecular biology, and various biochemical and biophysical approaches to find out the molecular mechanisms in these biological processes.