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Full-Text Articles in Biochemistry, Biophysics, and Structural Biology

Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner Jul 2018

Activities And Classroom Demonstrations In Biological Physics: A Resource Document, Philip C. Nelson, William Berner

Department of Physics Papers

We give detailed recipes for a number of classroom demonstrations relevant to biological physics instruction. We developed them mainly for use in 2nd-3rd year undergraduate Physics courses. But you can (and we do) use them for primary school, through high school, up to PhD candidates. You adapt the words for each audience, but a phenomenon is a phenomenon.

We also outline a 1-hour introduction to Python for undergraduate scientific computing.

Finally we document some outcomes from courses taught at U Pennsylvania using these resources and others cited here. This material was presented at a workshop at the AAPT meeting in ...


Time To Stop Telling Biophysics Students That Light Is Primarily A Wave, Philip C. Nelson Jan 2018

Time To Stop Telling Biophysics Students That Light Is Primarily A Wave, Philip C. Nelson

Department of Physics Papers

Standard pedagogy introduces optics as though it were a consequence of Maxwell’s equations, and only grudgingly admits, usually in a rushed aside, that light has a particulate character that can somehow be reconciled with the wave picture. Recent revolutionary advances in optical imaging, however, make this approach more and more unhelpful: How are we to describe two-photon imaging, FRET, localization microscopy, and a host of related techniques to students who think of light primarily as a wave? I was surprised to find that everything I wanted my biophysics students to know about light, including image formation, x-ray diffraction, and ...


Induction Of Antibodies To Hiv-1 Envelope Using Simian Adenovirus Vaccines, Kristel Lucie Emmer Jan 2018

Induction Of Antibodies To Hiv-1 Envelope Using Simian Adenovirus Vaccines, Kristel Lucie Emmer

Publicly Accessible Penn Dissertations

Human immunodeficiency virus type 1 (HIV-1) has infected 76 million people since the beginning of the epidemic. The first evidence that an HIV-1 vaccine could prevent infection in humans was provided in the RV144 vaccine efficacy trial. RV144 demonstrated 31.2% efficacy and immune correlate analyses indicated that antibodies targeting the variable 2 (V2) region of HIV-1 envelope (Env) correlated with decreased risk of infection. However, significant improvements are needed to develop a globally effective vaccine against HIV-1.

Several approaches can be employed to improve upon vaccination strategies: heterologous prime-boost regimens, immunogen design, and alternative adjuvants. To enhance Env-specific antibodies ...


Use Of Induced Pluripotent Stem Cell Models To Elucidate Retinal Disease Pathogenesis And To Develop Gene-Based Therapies, Thu Thi Duong Jan 2018

Use Of Induced Pluripotent Stem Cell Models To Elucidate Retinal Disease Pathogenesis And To Develop Gene-Based Therapies, Thu Thi Duong

Publicly Accessible Penn Dissertations

Choroideremia (CHM) is a rare monogenic, X-linked recessive inherited retinal degenerative disease caused by mutations in the Rab Escort Protein-1 (REP1) encoding CHM gene. CHM is characterized by childhood-onset night blindness (nyctalopia), progressive peripheral vision loss due to the degeneration of neural retina, RPE and choroid in a peripheral-to-central fashion. Most of CHM mutations are loss-of-function mutations leading to the complete lacking of REP1 protein. However, the primary retinal cell type leading to CHM and molecular mechanism remains unknown in addition to the fact of lacking proper disease models. In this study, we explored the utility of induced pluripotent stem ...


Mechanosensing By The Nuclear Lamina: From Embryonic Development To Aging, Sangkyun Cho Jan 2018

Mechanosensing By The Nuclear Lamina: From Embryonic Development To Aging, Sangkyun Cho

Publicly Accessible Penn Dissertations

‘Nuclear mechanosensing’ encompasses a wide range of biophysical pathways that are emerging as key processes in the regulation of cell function and fate. Many of these mechanisms involve the main structural protein of the nucleus, lamin-A, which is abundant in stiff and mechanically stressed tissues such as striated muscle, but is comparatively low in soft tissues such as the brain. Lamin-A’s increase with tissue stiffness correlates strongly with elevated levels of collagen-I fibers in the extracellular matrix (ECM), but mechanisms and functional consequences of any matrix-nucleus interplay remain unclear. Here, in the first set of studies, we show that ...


A Tale Of Two Sirtuins: The Impact Of Sirt1 And Sirt3 On The Pathophysiology Of Shock, Carrie Adelia Sims Jan 2018

A Tale Of Two Sirtuins: The Impact Of Sirt1 And Sirt3 On The Pathophysiology Of Shock, Carrie Adelia Sims

Publicly Accessible Penn Dissertations

Both acute blood loss and severe infection activate common cellular pathways leading to shock – a pathologic condition characterized by systemic inflammation, oxidative stress, and mitochondrial dysfunction. Sirtuins, a highly conserved group of NAD-dependent enzymes, play a critical role in cellular survival and many of the benefits associated with sirtuin activation are thought to be secondary to decreased inflammation, reduced oxidative stress, and improved mitochondrial physiology. As such, we hypothesized that sirtuin pathways play a crucial role in shock and could be could be targeted to improve outcomes following acute blood loss and severe infection. In a series of in vivo ...


Reprogramming The Retina: Next Generation Strategies Of Retinal Neuroprotection And Gene Therapy Vector Potency Assessment, Devin Scott Mcdougald Jan 2018

Reprogramming The Retina: Next Generation Strategies Of Retinal Neuroprotection And Gene Therapy Vector Potency Assessment, Devin Scott Mcdougald

Publicly Accessible Penn Dissertations

Mutations within over 250 known genes are associated with inherited retinal degeneration. Clinical success following gene replacement therapy for Leber’s congenital amaurosis type 2 establishes a platform for the development of downstream treatments targeting other forms of inherited and acquired ocular disease. Unfortunately, several challenges relevant to complex disease pathology and limitations of current gene transfer technologies impede the development of gene replacement for each specific form of retinal degeneration. Here we describe gene augmentation strategies mediated by recombinant AAV vectors that impede retinal degeneration in pre-clinical models of acquired and inherited vision loss. We demonstrate distinct neuroprotective effects ...


Chromatin Remodeling Dynamics During Brown Adipogenesis, Suzanne Natalie Shapira Jan 2018

Chromatin Remodeling Dynamics During Brown Adipogenesis, Suzanne Natalie Shapira

Publicly Accessible Penn Dissertations

Brown adipose tissue (BAT) is specialized to expend energy through the action of the mitochondrial uncoupling protein UCP1. Increasing brown fat mass or activity through genetic or chemical manipulation in mice suppresses obesity and its comorbidities; as such, there is great interest in developing approaches to increase the amount and/or function of brown fat to combat metabolic disorders. My thesis work aimed to dissect the molecular mechanisms by which the helix- loop-helix transcription factor Early B-Cell Factor 2 (EBF2) regulates brown adipocyte commitment and terminal differentiation. Through analysis of tissue-specific knockout mouse models, we found that EBF2 is required ...


Reverse Micelle Encapsulation And Its Use In Examining The Interplay Between Hydration And Protein Dynamics, Bryan Stephen Marques Jan 2018

Reverse Micelle Encapsulation And Its Use In Examining The Interplay Between Hydration And Protein Dynamics, Bryan Stephen Marques

Publicly Accessible Penn Dissertations

As the universal solvent, water is unquestionably essential to most aspects of protein biophysics from protein folding to enzymatic activity. Much has been learned about the relationship between proteins and surrounding solvent waters; however, it is often difficult to experimentally examine these interactions in a site-specific manner without perturbing molecular structure. Furthermore, the effect of nearby hydration dynamics on protein dynamics (and, in effect, protein conformational entropy) is poorly understood at atomic resolution. With the use of a combination of Nuclear Magnetic Resonance (NMR) spectroscopy and protein reverse micelle (RM) encapsulation, it is possible to examine both the dynamic behavior ...


All The Right Noises: Causes And Consequences Of Stochastic Trimethylamine Oxide Reductase Expression In Escherichia Coli, Jeffrey Carey Jan 2018

All The Right Noises: Causes And Consequences Of Stochastic Trimethylamine Oxide Reductase Expression In Escherichia Coli, Jeffrey Carey

Publicly Accessible Penn Dissertations

Microbial populations can maximize fitness in dynamic environments through bet hedging, a process wherein a subpopulation assumes a phenotype not optimally adapted to the present environment but well adapted to an environment likely to be encountered. Here we show that oxygen induces fluctuating expression of the trimethylamine oxide (TMAO) respiratory system of Escherichia coli, diversifying the cell population and enabling a bet-hedging strategy that permits growth following oxygen loss. This regulation by oxygen affects the variance in gene expression but leaves the mean unchanged. We show that the oxygen-sensitive transcription factor IscR is the key regulator of variability. Oxygen causes ...


Wnt5a Signaling Induced Phosphorylation Increases Acyl Protein Thioesterase Activity And Promotes Melanoma Metastatic Behavior, Rochelle Shirin Sadeghi Jan 2018

Wnt5a Signaling Induced Phosphorylation Increases Acyl Protein Thioesterase Activity And Promotes Melanoma Metastatic Behavior, Rochelle Shirin Sadeghi

Publicly Accessible Penn Dissertations

Wnt5a has been implicated in melanoma progression and metastasis, although the exact downstream signaling events that contribute to melanoma metastasis are poorly understood. Wnt5a signaling results in acyl protein thioesterase 1 (APT1) mediated depalmitoylation of pro-metastatic cell adhesion molecules CD44 and MCAM, resulting in increased melanoma invasion. The mechanistic details that underlie Wnt5a-mediated regulation of APT1 activity and cellular function remains unknown. Here, we show Wnt5a signaling regulates APT1 activity through induction of APT1 phosphorylation and we further investigate the functional role of APT1 phosphorylation on its depalmitoylating activity. We found phosphorylation increased APT1 depalmitoylating activity and reduced APT1 dimerization ...


Exploring The Role Of Tet1 In Genomic Imprinting, Jennifer Myers Sanmiguel Jan 2018

Exploring The Role Of Tet1 In Genomic Imprinting, Jennifer Myers Sanmiguel

Publicly Accessible Penn Dissertations

DNA methylation is an essential epigenetic mark crucial for normal mammalian development. This modification controls the expression of a unique class of genes, designated as imprinted, which are expressed monoallelically and in a parent-of-origin-specific manner. Proper parental allele-specific DNA methylation at imprinting control regions (ICRs) is necessary for appropriate imprinting. Processes that deregulate DNA methylation of imprinted loci cause disease in humans. DNA methylation patterns dramatically change during mammalian development: first, the majority of the genome, with the exception of ICRs, is demethylated after fertilization, and subsequently undergoes genome-wide de novo DNA methylation. Secondly, after primordial germ cells are specified ...


Gene Therapy Approaches To Immune Tolerance Induction In Canine Hemophilia, Robert French Jan 2018

Gene Therapy Approaches To Immune Tolerance Induction In Canine Hemophilia, Robert French

Publicly Accessible Penn Dissertations

A key issue in gene therapy is the immune response to the therapeutic transgene. This is especially important in applications where current treatments often elicit an antibody response, like hemophilia, where protein replacement therapy results in neutralizing

antibodies (“inhibitors”) in ~25% of severe hemophilia A and 1-3% of severe hemophilia B patients. To test the ability of skeletal muscle-directed gene therapy to prevent an immune response, we used an inhibitor-prone dog model of severe hemophilia B to express a hyperactive factor IX (FIX) variant from skeletal muscle via adeno-associated viral (AAV) vector and observed curative levels of expression that lasted ...


Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins, Mara Olenick Jan 2018

Cargo Specific Regulation Of Cytoplasmic Dynein By Effector Proteins, Mara Olenick

Publicly Accessible Penn Dissertations

Axonal transport is vital for the development and survival of neurons. The transport of cargo and organelles from the axon to the cell body is driven almost completely by the molecular motor, cytoplasmic dynein. Yet, it remains unclear how dynein is spatially and temporally regulated given the variety of cargo that must be properly localized to maintain cellular function. Previous work has suggested that adaptor proteins provide a mechanism for cargo-specific regulation of motors. During my thesis work, I have investigated the role of mammalian Hook proteins, Hook1 and Hook3, as potential motor adaptors. Using optogenetic and single molecule assays ...


Structure, Function & Dynamics At The Membrane, Evan O'Brien Jan 2018

Structure, Function & Dynamics At The Membrane, Evan O'Brien

Publicly Accessible Penn Dissertations

The biological membrane is necessary for maintaining cellular identity, yet must also allow for interaction with the extracellular environment in order to respond to stimuli. Proteins that are directly embedded in the membrane or that interact more peripherally are responsible for these extracellular signaling events, which lie at the heart of cell communication. The first major goal of this work was to interrogate the peripheral interaction of cytochrome c and the mitochondrial lipid cardiolipin at atomic resolution using solution nuclear magnetic resonance (NMR) techniques; this interaction is key to promoting apoptosis. After demonstrating that the protein was correctly folded in ...


Β Cell Replacement Therapy: A Novel Application For Targeted Epigenetic Editing, Kristy Ou Jan 2018

Β Cell Replacement Therapy: A Novel Application For Targeted Epigenetic Editing, Kristy Ou

Publicly Accessible Penn Dissertations

Pancreatic β cells are the exclusive source of insulin, which normalizes blood glucose levels under hyperglycemic conditions. In 2015, over 252,000 deaths in the United States were contributed by diabetes, a family of disorders directly linked to defects in the pancreatic β cells. β cell deficiency or dysfunction leads to insufficient insulin secretion, resulting in chronic hyperglycemia and increased risk for severe health complications. Although severely diabetic patients can clinically manage their glucose levels with mealtime delivery of insulin analogues, many still experience potentially life-threatening hypoglycemic episodes due to erroneous insulin administration. Only β cell replacement therapy, through the ...


The Role Of Molecular Motors In Peripheral Nerve Regeneration, Melissa D. Priest Jan 2018

The Role Of Molecular Motors In Peripheral Nerve Regeneration, Melissa D. Priest

Publicly Accessible Penn Dissertations

Following injury, axons of the peripheral nervous system have retained the capacity for regeneration. While it is well established that injury signals require molecular motors for their transport from the injury site to the nucleus, whether kinesin and dynein motors play additional roles in peripheral nerve regeneration is not well understood. Here we use genetic mutants of motor proteins in a zebrafish peripheral nerve regeneration model to visualize and define in vivo roles for kinesin and dynein. We find that both kinesin-1 and dynein are required for zebrafish peripheral nerve regeneration. While loss of kinesin-1 reduced the overall robustness of ...


Dissecting The Molecular Basis Of The Scaffold Protein Jade In Hbo1 Histone Acetyltransferase (Hat) Activity, Joseph Han Jan 2018

Dissecting The Molecular Basis Of The Scaffold Protein Jade In Hbo1 Histone Acetyltransferase (Hat) Activity, Joseph Han

Publicly Accessible Penn Dissertations

HBO1 is a member of the human MYST family of acetyltransferases that is evolutionarily conserved from yeast to human. HBO1 functions in the context of a multi-protein histone acetyltransferase (HAT) complex containing JADE1/2/3, HBO1, ING4/5 and Eaf6 to regulate DNA replication, transcription, and other important cellular processes. HBO1 is shown to be responsible for the majority of H4 acetylation throughout the human genome. HBO1 functions in many important biological processes such as interaction with the origin recognition complex (ORC) and loading of the minichromosome maintenance protein complex (MCM), highlighting its importance in DNA replication. In addition, HBO1 ...


A Genetically Encoded Fluorescent Amino Acid Reveals Protein Dynamics Regulating The Bacterial Dna Damage Response, Zachary Michael Hostetler Jan 2018

A Genetically Encoded Fluorescent Amino Acid Reveals Protein Dynamics Regulating The Bacterial Dna Damage Response, Zachary Michael Hostetler

Publicly Accessible Penn Dissertations

Diversification of the genetic code in response to selective pressures can render organisms more fit to particular stresses. In many bacteria, the inducible prokaryotic DNA damage (SOS) response facilitates survival and adaptation to genotoxic stresses by upregulating genes involved in both high-fidelity and pro-mutagenic DNA damage repair. Within pathogenic bacteria, treatment with genotoxic antibiotics can induce the SOS response and lead to the acquisition of antibiotic resistance. Interest in disarming the SOS-dependent ability of bacteria to evade antibiotics has prompted investigation into the mechanisms underlying SOS pathway activation. Two proteins, the repressor LexA and the DNA recombinase RecA, operate together ...


Optimization Of Nuclear Magnetic Resonance Spectroscopy Methods For Measuring Protein Hydration In Reverse Micelles, Christine Jorge Jan 2018

Optimization Of Nuclear Magnetic Resonance Spectroscopy Methods For Measuring Protein Hydration In Reverse Micelles, Christine Jorge

Publicly Accessible Penn Dissertations

Water is fundamental to all aspects of protein function including folding, stability, catalysis, and dynamics. The unique characteristics of water make it the ideal solvent for supporting life but also make it incredibly difficult to study. While much has been learned about the role of water in protein function, a site resolved understanding of these interactions has remained elusive thereby leaving a large hole in the biophysical puzzle. Experimental techniques that provide a site-resolved view of protein hydration without mutation of the protein are necessary to understand the thermodynamic role of water on protein function. It has been shown that ...


Defining And Exploiting The Cytosine Deaminase Activity Of Apobec3a On The Extended Epigenome, Emily Katharine Schutsky Jan 2018

Defining And Exploiting The Cytosine Deaminase Activity Of Apobec3a On The Extended Epigenome, Emily Katharine Schutsky

Publicly Accessible Penn Dissertations

AID/APOBEC family cytosine deaminases canonically play crucial roles in immunity by converting cytosine to uracil in single-stranded DNA (ssDNA). Outside of this established physiological role, AID/APOBEC enzymes have also been implicated in the poorly-understood process of DNA demethylation through their proposed deamination of epigenetically-modified cytosine bases like 5-methylcytosine (mC) and 5-hydroxymethylcytosine (hmC). However, there has been no thorough biochemical characterization of AID/APOBEC activity on these substrates, or on the recently-discovered 5-formylcytosine (fC) and 5-carboxylcytosine (caC) to inform this proposed role. Here, we provide the first steady-state kinetic measurements of the most active family member–APOBEC3A(A3A)–against ...


Synthesis And Characterization Of Photolabile Ruthenium Polypyridyl Crosslinkers With Applications In Soft Materials And Biology, Teresa Rapp Jan 2018

Synthesis And Characterization Of Photolabile Ruthenium Polypyridyl Crosslinkers With Applications In Soft Materials And Biology, Teresa Rapp

Publicly Accessible Penn Dissertations

Since its discovery in 1844, ruthenium has solidified its position as the most widely used transition metal in catalysis and excited state chemistry. Its lower toxicity and relatively low price (compared to other platinum group metals) have enabled many applications of ruthenium coordination compounds. In this dissertation I discuss ruthenium polypyridyl complexes that undergo photoinduced ligand exchange, and how this unique property can be harnessed to develop next-generation smart materials and responsive chemical biology tools.

Ru(LL)2X22+ complexes, where LL is a bidentate aromatic heterocycle such as 2,2’-bipyridine, 1,10-phenanthroline, or 2,2’-biquinoline, and X is ...


Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function, Alex Martin Rohacek Jan 2018

Discovering Novel Hearing Loss Genes: Roles For Esrp1 And Gas2 In Inner Ear Development And Auditory Function, Alex Martin Rohacek

Publicly Accessible Penn Dissertations

Hearing loss is the most common form of congenital birth defect, affecting an estimated

35 million children worldwide. To date, nearly 100 genes have been identified which

contribute to a deafness phenotype in humans, however, many cases remain in which a

causative mutation has yet to be found. In addition, the exact mechanism by which

hearing loss occurs in the presence of many of these mutations is still not understood.

This is due, in part, to the complex nature of the development and function of the

cochlear duct, the organ of hearing. The cochlea undergoes an intricate morphogenetic

development and ...


Elucidation Of Histone Modifications And Nucleosomal Structure Using Novel Mass Spectrometry Approaches, Kelly Karch Jan 2018

Elucidation Of Histone Modifications And Nucleosomal Structure Using Novel Mass Spectrometry Approaches, Kelly Karch

Publicly Accessible Penn Dissertations

The fundamental repeating unit of chromatin is the nucleosome, composed of 147 base pairs of DNA wrapped around a histone protein octamer containing two copies of H2A, H2B, H3, and H4. Histone proteins are involved in many critical nuclear processes including transcription and maintenance of chromatin structure. Histone function is mediated by a dynamic and extensive array of post-translational modifications (PTMs). Mass spectrometry (MS) has emerged as a leading tool to study these complex histone PTM profiles. Generally, MS experiments utilize data dependent acquisition (DDA) methods on high-resolution MS instruments because they can more readily distinguish PTMs with small mass ...


Structural Remodeling Of Alpha-Synuclein By Small Molecules: A Novel Path To Neuroprotective Therapeutics, Malcolm James Daniels Jan 2018

Structural Remodeling Of Alpha-Synuclein By Small Molecules: A Novel Path To Neuroprotective Therapeutics, Malcolm James Daniels

Publicly Accessible Penn Dissertations

Neurodegenerative diseases share the unifying features of insoluble protein aggregates and irreversible neuron loss. Parkinson’s disease (PD) is defined by proteinaceous Lewy bodies—which contain α-synuclein—and loss of dopamine neurons leading to motor dysfunction. Growing evidence implicates α-synuclein aggregation as a causal driver of neurodegeneration in certain forms of PD. However, the precise mechanism(s) by which the process or products of α-synuclein aggregation drive neuron death remains unknown. Better understanding of this key question might further development of neuroprotective therapies for PD and related disorders. To address this gap, we reviewed how the native conformation of α-synuclein ...


Nonclassical Sex Hormone Signaling In Melanocytes And Melanoma, Christopher Anthony Natale Jan 2018

Nonclassical Sex Hormone Signaling In Melanocytes And Melanoma, Christopher Anthony Natale

Publicly Accessible Penn Dissertations

The primary pigment in mammalian skin and hair is melanin, which is synthesized locally by differentiated melanocytes and transferred into surrounding epidermal keratinocytes and hair shafts. Because pigmentation differences are often readily visible clinically, melanocyte function is known to correlate with changes in environment, as well as physiologic and pathologic changes in other organ systems. We utilized these clinical associations to inspire the hypothesis that sex hormones influence melanocyte biology. For over 2,000 years, it has been appreciated that pregnancy is associated with changes in skin pigmentation, but the specific processes, hormones, receptors, and downstream signaling cascades responsible have ...


Investigating Molecular Mechanisms Underlying Mild Phenotype In Friedreich Ataxia Patients With G130v Missense Mutation, Elisia Clark Jan 2018

Investigating Molecular Mechanisms Underlying Mild Phenotype In Friedreich Ataxia Patients With G130v Missense Mutation, Elisia Clark

Publicly Accessible Penn Dissertations

Friedreich’s Ataxia (FRDA) is an incurable neurodegenerative disease caused by mutations in the frataxin (FXN) gene, resulting in decreased expression of the mitochondrial protein FXN. 2-3% of FRDA patients carry a GAA expansion on one FXN allele, and a missense mutation on the other. The mechanism behind the disease‐causing features remains elusive. The phenotype associated with patients carrying point mutations cannot be predicted with certainty; these patients can have a mild or severe clinical outcome, creating a unique platform to understand clinical heterogeneity. FXN is important for proper mitochondrial function, and is involved in Fe-S cluster biogenesis, metabolism ...


Development And Characterization Of Novel Raf Dimer Inhibitors To Target Brafv600e Inhibitor Resistance, Michael Joseph Grasso Jan 2018

Development And Characterization Of Novel Raf Dimer Inhibitors To Target Brafv600e Inhibitor Resistance, Michael Joseph Grasso

Publicly Accessible Penn Dissertations

ABSTRACT

BRAF is a notable oncoprotein within the MAPK signaling pathway, which is a pathway that sends a signal from the surface of a cell to the nucleus of a cell via phosphorylation cascades. This pathway regulates cell growth, differentiation, and survival. BRAF is known to be mutated in about 50% of melanomas, and less frequently in a wide variety of other cancers, making BRAF a bona-fide target for therapy. In melanoma, a single V600E activation segment mutation (BRAFV600E) accounts for ~90% of BRAF mutant malignant tumors. BRAFV600E selective inhibitors, such as vemurafenib, extend the survival of patients in the ...


Epigenetic Mechanisms Governing Behavioral Reprogramming In The Ant Camponotus Floridanus, Riley John Graham Jan 2018

Epigenetic Mechanisms Governing Behavioral Reprogramming In The Ant Camponotus Floridanus, Riley John Graham

Publicly Accessible Penn Dissertations

Eusocial insect colonies divide behaviors among specialist groups called castes. In some species, caste identity is determined by the interaction of endogenous (e.g. genomic) and exogenous (e.g. juvenile hormone from nurses) signals during larval development, suggesting epigenetic mechanisms underlie plastic traits tied to caste identity. Previous work demonstrated a link between patterns of histone H3 lysine 27 acetylation (H3K27ac) and caste-specific gene expression in Major and Minor workers of the ant Camponotus floridanus, and we hypothesized caste-specific behaviors such as foraging may be similarly regulated by histone acetylation. To test this hypothesis, we fed mature (~30d old) Majors ...


Decoding Calcium Encoding Through Bi-Directional Optogenetic Control Over Gq-Protein Signaling, Pimkhuan Hannanta-Anan Jan 2018

Decoding Calcium Encoding Through Bi-Directional Optogenetic Control Over Gq-Protein Signaling, Pimkhuan Hannanta-Anan

Publicly Accessible Penn Dissertations

Calcium is a fundamental secondary messenger responsible for relaying information from the extracellular space to the cell interior. Extracellular cues are temporally encoded through calcium signals, which often arise in the form of oscillations. These oscillations are then decoded to inform cellular decisions and regulate cellular functions. Despite its crucial role in cell signaling, the encoding and decoding of calcium oscillations is poorly understood. The current biological tools and methods used to study calcium signaling lack the temporal precision and specificity necessary to precisely manipulate, perturb, and dissect calcium signaling circuits. To address this need, we developed a new set ...