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Students working with biology researcher Bonnie Blazer-Yost

Research

Research & Scientific Expertise
Current research is being undertaken in the following areas: 
 

Biochemistry

Biochemistry and biochemical reactions underpin all living and cellular phenomena. Behind every nerve impulse, every calorie consumed, every cell turning malignant, every medicine having its intended effect or side effect is a biochemical process worthy of study.  Research in biochemistry strives to describe biological phenomena at their basic levels. The study of biochemical processes tells us not just whysomething happens, but importantly how something happens. A number of faculty members in the Biology Department undertake research of a biochemical nature, and some of the areas under active study include:

  • Anderson Lab: How bacterial membrane proteins influence infection by the respiratory pathogen Pseudomonas aeruginosa.
  • Atkinson Lab: Effects of metabolic signaling on cytoskeletal dynamics in kidney injury and disease; Mechanisms of RNAi therapeutics in the kidney.
  • Balakrishnan Lab: Understanding mechanisms involved in maintenance of genome stability.
  • Baucum Lab: Identification and characterization of synaptic protein complexes in a brain region called the striatum.
  • Kusmierczyk Lab:  Assembly of multi-protein complexes and cellular mechanisms of protein quality control.
  • Randall Lab: Mechanisms of plant responses to environmental stress (cold and drought).

Biochemistry-related resources in the Biology Department include: HPLC/FPLC; 1D and 2D gel electrophoresis (large scale and "mini"); gas-liquid chromatography; centrifuges and ultracentrifuge; temperature-controlled incubators and platform-shakers for growth of microorganisms; various spectrophotometers (multiwell plate; NanoDrop; standard UV-Vis, fluorescence); gel-documentation system; fluorescence microscopes; biolistic particle delivery (gene gun) for transformation of plants; bath and probe sonicator; hot and cold rooms.

Researchers:

Biology Education

Cell Biology

Cell Biology research at IUPUI includes a diverse range of science.  Cells are the basis of all life, and cellular activities control the workings of tissues and organs, which determine the health and well-being of the organism.  Cell biology combines approaches and methods from various disciplines, including biochemistry, genetics and developmental biology.  Biology faculty investigate numerous topics in cell biological research, including the cytoskeleton, cell adhesion, multiprotein complex assembly, cell physiology, intracellular signaling and cellular development mechanisms.  These research topics also have specific medical relevance for conditions like renal disease, bone repair and neural disorders.

Cell biology laboratories have extensive research resources within the Biology Department, the School of Science and across the IUPUI campus, which include state-of-the-art microscopy, molecular genetics, proteomics, cell sorting and mouse genetics.

Faculty research:

  • Atkinson laboratory examines 1) Rho GTPase signaling and cytoskeletal organization in normal and ischemic kidney epithelial cells; 2) Cellular mechanisms and therapeutic uses of RNAi in the kidney.
  • Baucum laboratory focuses on identification and characterization of synaptic protein complexes in a brain region called the striatum.
  • Belecky-Adams laboratory examines several aspects of visual system function, including 1) the dynamics of chromatin organization in retinal and optic nerve development and disease, 2) understanding the photoreceptor in health and disease, 3) the regeneration of the retina and optic nerve.  Our findings can be directly translated into new preventative and therapeutic tools for the treatment of such diseases as glaucoma, retinitis pigmentosa, and Joubert syndrome.
  • Blazer-Yost laboratory examines regulation of epithelial cell ion transport in health and disease.
  • Dai laboratory examines hepatic stellate cells as progenitor cells in liver physiology and pathology.
  • Kusmierczyk laboratory is developing cell biological tools to study the assembly of multi-protein complexes.  Specifically, the use of fluorescence microscopy to study the assembly, localization, and function of the proteasome.
  • Li laboratory research activities include understanding the molecular and cellular mechanisms of mechanotransduction, the process of conversion of mechanical signals into biological signals in bone cells, and studying cell based therapy for bone fracture repair and tissue regeneration.
  • Marrs laboratory examines cellular development mechanisms, including neural development, using the zebrafish model.
  • Meyer laboratory uses human induced pluripotent stem cells to study mechanisms of neural fate determination, with a particular focus on the retina of the eye.  Additional studies focus on the ability to use patient-specific induced pluripotent stem cells to understand mechanisms of neurological diseases.

Developmental Biology

The Department of Biology features a vibrant group of developmental biology laboratories at the forefront of investigating the molecular and cellular mechanisms that generate and maintain various cell types and organs in embryonic and adult organisms.

Faculty and students in this area use a wide assortment of techniques including epigenetic analysis, genetics, molecular biology, proteomics, genomics, biochemistry, and advanced imaging using species as diverse as Xenopus laevis, zebrafish, mouse, rat and human. The collective works of these laboratories are directed toward novel strategies for the treatment of cancer, fetal alcohol syndrome, neurological disorders, Down syndrome, Bardet-Biedl syndrome, glaucoma, growth hormone deficiency, and regeneration of lost or danaged organs and tissues.

Developmental Biology Faculty:

  • Teri Belecky-Adams, PhD:  Development, disease, and regeneration of the vertebrate eye.
  • Ellen Chernoff, PhD:  Development and Regeneration of Limb and Spinal Cord.
  • Jim Marrs, PhD:  Cellular and developmental mechanisms using zebrafish.
  • Jason Meyer, PhD: Neuronal development and disease processes using induced pluripotent stem cells.
  • Simon Rhodes, PhD:  Genetic pathways that control pituitary gland organogenesis.
  • Randall Roper, PhD: Developmental abnormalities in craniofacial and skeletal precursors of Down syndrome
  • David Skalnik, PhD:  Regulators of epigenetic modifications, chromatin structure, and gene expression during mammalian development

Genetics

Current research in Genetics in the Department of Biology includes:

  • Developmental biology of the eye: The Belecky-Adams research group examines several aspects of visual system function, including 1) the dynamics of chromatin organization in retinal and optic nerve development and disease, 2) understanding the photoreceptor in health and disease, 3) the regeneration of the retina and optic nerve.  Our findings can be directly translated into new preventative and therapeutic tools for the treatment of such diseases as glaucoma, retinitis pigmentosa, and Joubert syndrome.
  • Physiology of polycystic kidney disease: The Blazer-Yost research group examines the role of kidney, intestinal and lung epithelia in salt and water homeostasis. Their research uses physiological techniques to understand and develop drugs to treat polycystic kidney disease.
  • Mechanisms of cellular proteasome assembly: By using yeast as a model organism, the Kusmierczyk lab investigates the assembly of the eukaryotic proteasome.  The long term goals of the lab are to inhibit proteasome assembly and utilize these mechanisms as drug targets for cancer treatment as well as analyze mechanisms that cells use to ensure protein quality control.  
  • Induced pluripotent stem cells for studies of neural development and disease:  The Meyer lab uses induced pluripotent stem cells to study mechanisms of neural fate determination, with a particular focus on the retina of the eye.  Additional studies focus on the ability to use patient-specific induced pluripotent stem cells to understand mechanisms of neurological diseases. 
  • Mechanisms of DNA repair and recombination: The goal of research conducted in Malkova laboratory is to unravel the mechanisms of DNA repair using baking yeast as a model.  The lab is focusing on double-strand DNA breaks, which can be very dangerous for human cells since their abnormal repair leads to genetic instability, which is believed to promote cancer in humans. The laboratory research focuses on two areas: the mechanism and genetic control of one particular pathway of DSB repair which is called Break-Induced Replication (BIR) and mechanisms that channel repair of double-strand breaks (DSBs) into gross chromosomal rearrangements (GCRs).
  • Population genetics of ephemeral resource-associated arthropods: The Picard lab looks to elucidate the population genetic structure of insects associated with ephemeral resources, specifically using the association of the blow fly (Diptera: Calliphoridae) and carrion as a model.   Our long terms goals are to characterize the population structure of several species based on distinct life history differences, and model population structure. This research has direct implication in forensics, where many of these organisms are used to estimate the minimum time since death (PMI), but dependent on a wide range of assumptions we hope to address.
  • Genetics of pituitary gland organogenesis: The Rhodes lab research program investigates the genetic pathways that control pituitary gland organogenesis. Through collaborations with pediatric endocrinologists, they have translated this work to the clinic, defining new forms of combined pediatric hormone deficiency diseases and developing new diagnostic and genetic counseling tools.
  • Genetics of craniofacial and skeletal abnormalities in Down syndrome: The Roper lab uses mouse models of Down syndrome to understand the cellular and genetic mechanisms disrupted by trisomy in neural crest and other skeletal precursors. The long term goal of their research is to use these findings to develop effective screening, therapeutic and preventative strategies for phenotypes associated with Down syndrome.
  • Epigenetic regulation of mammalian development: The Skalnik laboratory is interested in understanding the epigenetic regulation of mammalian development.  We use a variety of genetic and biochemical approaches to identify and study critical regulators of epigenetic modifications, chromatin structure, and gene expression.

Immunology

Overall mission
The immune system of the human body is exquisitely structured in a way that protects it against pathogens by building innate and adaptive immune responses as guardian for health; and yet it may aggravate the viability and function of bystander cells by excessive activity and become an active element in disease pathogenesis.  Our overall research is to understand the fundamental nature of immune physiology with ultimate goals of manipulating immunity effectors in various disease manifestations.  We aim to translate bench-based findings into the clinic via establishing a multifaceted research project by collaborating with colleagues and making use of state-of-the-art technological tools.  In addition, the research curriculum in our section will provide a means for academic instruction for undergraduate/graduate students and fellows to bridge basic sciences and translational research.

One aspect in our section is to study the immune responses elicited by Pseudomonas aeruginosa and other pathogenic bacteria in infectious diseases.  Studies by plant molecular biologists in our department reveal the fundamental regulation for seed development, which is translated to nutritional immunology.  Work is underway to investigate the effects of dietary soypeptide on the immune cells, particularly natural killer (NK) cells, and the potential application to enhancing anti-tumor and anti-viral immunity as well as modulating allergic inflammation.  Studies on extracellular matrix are defining the role of type VI collagen (COL6) on macrophage-mediated inflammation particularly in the lung.

Specific Projects:
Nutritional immunology
Using the natural dietary soypeptide for harnessing the activity of NK cells, the projects are as follows:

Tumor immunology:

  • Enhancement of immunosurveillance for preemptive strategies
  • Harnessing immunotherapy for potential therapeutic regimens
  • Manipulating NK cells for potential cellular therapy following adoptive transfer

Anti-viral immunity: 
Enhancement of NK-mediated defense mechanism against viral infection using vaccinia model system

Anti-allergic inflammation:
Thwart Th2-mediated allergic inflammation by IFNg-producing NK cells to mitigate allergen-induced allergic diseases

NK cell biology:
Define the epigenetic regulation in NK cells by this soybean peptide

Type VI collagen (COL6) in Inflammation
Alterations in homeostasis of extracellular matrix (ECM) would affect the function of cells in the tissues.  The goal is to understand the interplay between increased amounts of COL6 and subsequent immune responses in lung diseases.  The projects are as follows:

  • Define the effects of COL6 on macrophages
  • Define the signaling pathway mediated by COL6 in macrophages
  • Role of COL6 from chronic inflammation to cancer in the lung

Microbiology

Microbiological research in the Biology Department encompasses all three domains of life: Prokaryotes, Eukaryotes, and Archaea. Using a combination of genetics and biochemical analyses, our faculty members, students, and staff investigate microbial pathogenesis as well as cell maintenance functions of microbes. Dr. Gregory Anderson studies the molecular basis of bacterial biofilm formation and chronic lung infection by Pseudomonas aeruginosa and other pathogenic bacteria. Also using yeast as a model organism, Dr. Anna Malkova investigates the molecular mechanisms and genetic control of double-strand DNA break repair. Dr. Andrew Kusmierczyk studies protein quality control and assembly of multi-protein complexes using yeast and archaeal systems. The research performed in these laboratories is uncovering the basic biology of some of the most fundamental organisms on Earth.

Molecular Biology

Molecular Biology research in the Department of Biology is conducted by a number of laboratories studying a range of molecular mechanisms. Thus:

  • Dr. Anderson investigates the mechanisms responsible for biofilm formation and chronic lung infection by Pseudomonas aeruginosa and other pathogenic bacteria.
  • Dr. Baucum's laboratory focuses on the identification and characterization of synaptic protein complexes in a brain region called the striatum.
  • Dr. Atkinson's laboratory is investigating mechanisms and effects of RNAi-based therapeutics in the kidney.
  • The research of Dr. Belecky-Adams is focused on mechanisms of development and injury repair in the vertebrate eye.
  • Dr. Chernoff studies genes associated with activation of neural stem cells in spinal cord and limb regeneration.
  • Dr. Dai investigates the molecular mechanisms regulating hepatocyte proliferation and liver growth.
  • Dr. Kusmierczyk investigates the mechanisms of cellular proteosome assembly.
  • Dr. Malkova's research is aimed to understand the molecular mechanisms responsible for repair of DNA breaks.
  • Dr. Meyer investigates induced pluripotent stem cells for studies of neural development and disease.
  • The goal of Dr. Stephen Randall is to characterize mechanisms by which plants respond and adapt to environmental stresses such as cold and drought conditions.
  • Dr. Watson's goal is to understand directional root growth and light-regulated development in plant seedlings at the molecular, cellular, and genetic levels. 

Physiology

Physiological research in the Department of Biology is multifaceted with particular strengths in hormonal signaling, eye research, renal research, neural and skeletal development. There is a strong translational component to the research that is enhanced by our proximity to collaborators in the Indiana University School of Medicine on the same campus.  In addition, the Physiology faculty are fortunate to have colleagues in other departments in the School of Science notably Chemistry, Physics and Mathematics who have partnered in research that crosses traditional boundaries and broadens the scope of the possible techniques and approaches that can be used to address important research and medical questions.  With this collective expertise the physiologists in the Department of Biology have been able to conduct studies with direct applicability to understanding and treating diseases such as glaucoma, retinitis pigmentosa, acute kidney injury, polycystic kidney disease, hypertension, metabolic syndrome,  Down Syndrome,  and liver injury.

Faculty:

  • Simon Atkinson, Ph.D.
    Effects of metabolic signaling on cytoskeletal dynamics in kidney injury and disease
  • AJ Baucum
    Identification and characterization of synaptic protein complexes in a brain region called the striatum.
  • Teri Belecky-Adams, Ph.D.
    Aspects of visual system function in health and disease.
  • Bonnie Blazer-Yost, Ph.D.
    Role of kidney, intestinal and lung epithelia in salt and water homeostasis.
  • Gouli Dai, Ph.D.
    Placental hormone-induced maternal hepatic growth response to pregnancy.
  • Jiliang Li, Ph.D.
    Molecular and cellular mechanisms of mechanotransduction, the process of conversion of mechanical signals into biological signals in bone cells, and cell based therapy for bone fracture repair and tissue regeneration.
  • Jason Meyer, Ph.D.
    Induced pluripotent stem cells for studies of neural development and disease.
  • Randall Roper, Ph.D.
    Mechanisms disrupted by trisomy in neural crest and other skeletal precursors in Down Syndrome.

Plant Biology

Faculty in the Plant Biology Section are dedicated to advancing knowledge of plant biology through research, public service, and teaching. Faculty research interests encompass the light regulation of growth and development, control of root morphology, plant genetics, adaptation of plants to extreme environments (drought and cold stress), and the impact of global environmental change (i.e., increase in atmospheric CO2 level) on plant physiology and productivity. Approaches to address these interests include plant molecular biology, plant biochemistry, plant cell biology, and plant physiology. Faculty work with both model and agronomically important plants, including invasive species, using facilities such as a greenhouse and a controlled environment bay (with nine individually controlled growth chambers).

Regenerative Biology

Regenerative Biology is the study of the mechanisms by which organisms maintain their tissue structure and regenerate this structure after tissue loss due to injury or disease. Such studies have application to the development of clinical therapies to regenerate tissues that do not normally regenerate or regenerate poorly, and also to design and build bioartificial organs that can replace dysfunctional organs. The field is highly multidisciplinary, drawing on expertise from developmental, cell and molecular biology, chemistry, informatics, mathematics and computer science, and engineering. The application of such studies constitutes the emerging field of regenerative medicine.

The department of Biology currently has seven faculty involved in research on regenerative biology. Teri Belecky-AdamsEllen ChernoffRandall RoperSimon Rhodes and Jason Meyer work on neural regeneration using a range of animal models, including chick, mouse, and amphibian. James Marrs studies auditory development and regeneration in the mouse and Guoli Dai's research is on mammalian liver regeneration. Jiliang Li works on mammalian bone regeneration and amphibian limb regeneration, respectively. These faculty members have multiple collaborations with investigators in Dentistry, Medicine and Informatics through the Center for Developmental and Regenerative Biology, and with colleagues at other universities. Their funding is derived from multiple government agencies and private foundations. Because of this collaborative network, regenerative biology faculty members have access to a wide variety of technologies, equipment, and laboratory space.

The Department of Biology offers MS and PhD degrees with concentrations in Regenerative Biology and Medicine. We encourage students with good undergraduate preparation to apply to this program through the Department of Biology. For more information see faculty profiles and the website for the Center for Regenerative Biology and Medicine.

Research experience helps guide career choices for undergrad

Tomas Meijome Biology, Undergraduate