Biology Commons^™

Transformation Of Stimulus Correlations By The Retina, Kristina D. Simmons, Jason Prentice, Gašper Tkačik, Jan Homann, Heather K. Yee, Stephanie E. Palmer, Philip C. Nelson, Vijay Balasubramanian

Publications and Research

Redundancies and correlations in the responses of sensory neurons may seem to waste neural resources, but they can also carry cues about structured stimuli and may help the brain to correct for response errors. To investigate the effect of stimulus structure on redundancy in retina, we measured simultaneous responses from populations of retinal ganglion cells presented with natural and artificial stimuli that varied greatly in correlation structure; these stimuli and recordings are publicly available online. Responding to spatio-temporally structured stimuli such as natural movies, pairs of ganglion cells were modestly more correlated than in response to white noise checkerboards, but …

Microtubule Severing At Crossover Sites By Katanin Generates Ordered Cortical Microtubule Arrays In Arabidopsis, Quan Zhang, Erica Fishel, Tyler Bertroche, Ram Dixit

Biology Faculty Publications & Presentations

Highlights

• Severing primarily depolymerizes the overlying CMT at crossover sites
• Severing probability increases nonlinearly with crossover time
• Katanin localizes to crossover sites and is required for severing
• Loss of katanin activity prevents the formation of coaligned CMT arrays

Summary
The noncentrosomal cortical microtubules (CMTs) of land plants form highly ordered parallel arrays that mediate cell morphogenesis by orienting cellulose deposition [1, 2 and 3]. Since new CMTs initiate from dispersed cortical sites at random orientations [4], parallel array organization is hypothesized to require selective pruning of CMTs that are not in the dominant orientation. Severing of CMTs at crossover sites …

Novel Neuroprotective Function Of Apical-Basal Polarity Genecrumbs In Amyloid Beta 42 (Aβ42) Mediated Neurodegeneration, Andrew Steffensmeier, Meghana Tare, Oorvashi Roy Puli, Rohan Modi, Jaison Nainaparampil, Madhuri Kango-Singh, Amit Singh

Biology Faculty Publications

Alzheimer's disease (AD, OMIM: 104300), a progressive neurodegenerative disorder with no cure to date, is caused by the generation of amyloid-beta-42 (Aβ42) aggregates that trigger neuronal cell death by unknown mechanism(s). We have developed a transgenic Drosophilaeye model where misexpression of human Aβ42 results in AD-like neuropathology in the neural retina. We have identified an apical-basal polarity gene crumbs (crb) as a genetic modifier of Aβ42-mediated-neuropathology. Misexpression of Aβ42 caused upregulation of Crb expression, whereas downregulation of Crb either by RNAi or null allele approach rescued the Aβ42-mediated-neurodegeneration. Co-expression of full length Crb with Aβ42 increased severity of Aβ42-mediated-neurodegeneration, …

A Force Of Nature: Molecular Mechanisms Of Mechanoperception In Plants, Gabriele B. Monshausen, Elizabeth S. Haswell

Biology Faculty Publications & Presentations

The ability to sense and respond to a wide variety of mechanical stimuli-gravity, touch, osmotic pressure, or the resistance of the cell wall-is a critical feature of every plant cell, whether or not it is specialized for mechanotransduction. Mechanoperceptive events are an essential part of plant life, required for normal growth and development at the cell, tissue, and whole-plant level and for the proper response to an array of biotic and abiotic stresses. One current challenge for plant mechanobiologists is to link these physiological responses to specific mechanoreceptors and signal transduction pathways. Here, we describe recent progress in the identification …

Recurrent Modification Of A Conserved Cis-Regulatory Element Underlies Fruit Fly Pigmentation Diversity, William A. Rogers, Joseph R. Salomone, David J. Tacy, Eric M. Camino, Kristen A. Davis, Mark Rebeiz, Thomas M. Williams

Biology Faculty Publications

The development of morphological traits occurs through the collective action of networks of genes connected at the level of gene expression. As any node in a network may be a target of evolutionary change, the recurrent targeting of the same node would indicate that the path of evolution is biased for the relevant trait and network. Although examples of parallel evolution have implicated recurrent modification of the same gene and cis-regulatory element (CRE), little is known about the mutational and molecular paths of parallel CRE evolution. InDrosophila melanogaster fruit flies, the Bric-à-brac (Bab) transcription factors control the development …

Lysophosphatidic Acid Stimulates Lymphangiogenesis In Human Lymphatic Endothelial Cells, John Macbeth, Donna Nofziger-Plank

Featured Research

Lymphangiogenesis is the process by which new lymphatic vessels sprout and grow from existing vessels whether under developmental, immunological, or cancerous conditions. Proper lymphatic vessel formation is important in working alongside normal angiogenesis in order to help regulate the body’s tissue fluid as well as aid in immunosurveillance. Various factors regulate lymphangiogenesis such as members of the vascular endothelial growth factor family (VEGF). Another factor that has recently been identified to play a role in lymphangiogenesis is the bio-active phospholipid lysophosphatidic acid (LPA) however the molecular mechanism by which LPA regulates lymphangiogenesis has not been well characterized. In this study, …

The Survivin And Ciap1 Anti-Apoptotic Proteins Are Differentially Downregulated In Response To Endoplasmic Reticulum Stress, Vicki Mercado, Jay L. Brewster

Featured Research

The endoplasmic reticulum (ER) is an organelle tasked with synthesis and transport of 50% of new cellular proteins. Dysfunction within this organelle creates signals for repair, adaptation, and in severe cases, cellular apoptosis. Multiple human diseases have been associated with ER dysfunction, and the activation of apoptosis in important populations of cells. Inhibitor of Apoptosis (IAP) proteins are cytosolic proteins that play an anti-apoptotic role in the cytosol. The relationship between endoplasmic reticulum (ER) stress and the expression/stability of IAPs is not well characterized. The objective of this study was to characterize the affect of ER stress on the expression/stability …

Evaluating Itpr-Dependence Of Apoptotic Signaling From The Endoplasmic Reticulum, Agustin Vargas, Jay L. Brewster

Featured Research

Stress within the endoplasmic reticulum (ER) can be induced by misfolded proteins accumulating in the lumen of this organelle. Signaling of ER stress to other parts of the cell results in altered gene expression, physiological adaptation, and with sustained stress, apoptosis (cell suicide). ER stress is often studied with highly toxic compounds that create severe ER stress rapidly, and a condition that is likely not physiologically relevant within an organism. In this study, we examine the apoptotic signaling induced by moderate ER stress, and in particular the inositol 1,4,5-trisphosphate receptor (ITPR). The ITPR regulates Ca2+ release from the ER lumen, …

Carbon Black And Titanium Dioxide Nanoparticles Differentially Activate Oxidative Stress And Apoptosis In A549 Human Alveolar Epithelial Cells, Sarah Alvarado, Brianna Manes, Jay L. Brewster

Featured Research

Recent studies have demonstrated that variation between particulate matter compositions have universally adverse effects on cells and living tissues. Carbon black and titanium dioxide are two such particulates that we are continuously exposed to, yet there is limited research to examine the potential deleterious effects on living tissue. The objective of this study is to characterize the effect of carbon black (CB) and titanium dioxide (TiO2) particulates on A549 human alveolar epithelial lung cells. CB and TiO2 powders were dispersed throughout a solution of water and bovine serum albumin by high-powered sonication. The effects of these particulates on A549 cells …

The Regulatory Effect Of Semaphorin 7a On Proliferation And Migration In Human Umbilical Vein Endothelial Cells, Steven R. Flemming, Donna Nofziger-Plank

Featured Research

Semaphorin 7A (SEMA 7A), a factor originally identified as regulating axon growth, has recently been implicated as a pro-angiogenic factor. The molecular mechanisms for this ability to stimulate angiogenesis have not been identified. This study examines if SEMA 7A can have a direct effect on vascular endothelial cells or whether it indirectly induces angiogenesis through stimulation and recruitment of macrophages as has been suggested. Using a human umbilical vein endothelial cells (HUVECs), the ability of SEMA 7A to affect proliferation and migration was examined. HUVECs were exposed to SEMA 7A directly or to conditioned media collected from macrophages exposed to …

Germline Transgenic Methods For Tracking Cells And Testing Gene Function During Regeneration In The Axolotl, Shahryar Khattak, Maritta Schuez, Tobias Richter, Dunja Knapp, Saori L. Haigo, Tatiana Sandoval-Guzmán, Kristyna Hradlikova, Annett Duemmler, Ryan R. Kerney, Elly M. Tanaka

Biology Faculty Publications

The salamander is the only tetrapod that regenerates complex body structures throughout life. Deciphering the underlying molecular processes of regeneration is fundamental for regenerative medicine and developmental biology, but the model organism had limited tools for molecular analysis. We describe a comprehensive set of germline transgenic strains in the laboratory-bred salamander Ambystoma mexicanum(axolotl) that open up the cellular and molecular genetic dissection of regeneration. We demonstrate tissue-dependent control of gene expression in nerve, Schwann cells, oligodendrocytes, muscle, epidermis, and cartilage. Furthermore, we demonstrate the use of tamoxifen-induced Cre/loxP-mediated recombination to indelibly mark different cell types. Finally, we inducibly …

Use Of Image Cytometry For Quantification Of Pathogenic Fungi In Association With Host Cells, Charlotte A. Berkes, Leo Li-Ying Chan, Alisha Wilkinson, Benjamin Paradis

Biology Faculty Publications

Studies of the cellular pathogenesis mechanisms of pathogenic yeasts such as Candida albicans, Histoplasma capsulatum, and Cryptococcus neoformans commonly employ infection of mammalian hosts or host cells (i.e. macrophages) followed by yeast quantification using colony forming unit analysis or flow cytometry. While colony forming unit enumeration has been the most commonly used method in the field, this technique has disadvantages and limitations, including slow growth of some fungal species on solid media and low and/or variable plating efficiencies, which is of particular concern when comparing growth of wild-type and mutant strains. Flow cytometry can provide rapid quantitative information regarding yeast …

Plant Cytoskeleton: Della Connects Gibberellins To Microtubules, Ram Dixit

Biology Faculty Publications & Presentations

A new study reveals that DELLA proteins directly interact with the prefoldin complex, thus regulating tubulin subunit availability in a gibberellin-dependent manner. This finding provides a mechanistic link between the growth-promoting plant hormone gibberellin and cortical microtubule organization.

Effects Of Arsenic Responsive P21 On Innate Immunity And Apoptosis In Zebrafish, Gabriel O. Vachon

Honors College

Arsenic is a heavy metal that is frequently found in drinking water, especially well-water in the Northeastern United States. Arsenic is thought to be involved with numerous negative health conditions. This project examined the impact of this environmental toxicant, on the zebrafish innate immune system. Specifically, this project characterized the gene encoding for the protein p21. The particular gene is cdkn1a (will be referred to here by its product "p21" both for the protein and gene itself which will be italicized) and had increased expression as a result of arsenic exposure from a previously complete microarray analysis. In attempt to …

Evolutionary And Molecular Analysis Of Conserved Vertebrate Immunity To Fungi, Erin Carter

Honors College

The innate immune system is highly conserved amongst all multicellular organisms. Yet a constant battle exists between host cells and pathogens due to the rapid evolution of immune system components. Functional genomics and in silico methods can be employed to elucidate the evolutionary patterns of vertebrate immunity to pathogenic fungi such as Candida albicans, an opportunistic fungal pathogen that can cause lethal candidiasis in the immunocompromised. Mammals such as humans and mice possess conserved C-type lectin receptors that recognize the C. albicans cell wall. However, these receptors have not been identified in fish. Here I describe how we identified potential …

The Use Of Genomic “Knock-In” Strategy To Examine The Role Of The Protein Acyl Transferase (Dhhc) Family Of Enzymes Using Dictyostelium Discoideum, Joshua Little

Honors College

Palmitoylation is a reversible, post translational, lipid modification performed by proteinacyltransferases (PAT). PATs are membrane-bound enzymes which contain a conserved region that is rich in cysteine residues and contains a DHHC (Asp-His-His-Cys) conserved domain. This region is involved in the transfer of a 16-carbon palmitate from palmitoyl-CoA to a target protein. Palmitoylation plays many important functions such as targeting the protein to a lipid raft, shuttling the target protein or anchoring it to the cell membranes as well as aiding in the three dimensional folding of the protein. This process plays an important role in signal transduction, anchoring and cellular …

Immobile Myosin-Ii Plays A Scaffolding Role During Cytokinesis In Budding Yeast, C. Wloka, Elizabeth Ann Vallen, Lydia Thé , '08, X. Fang, Y. Oh, E. Bi

Biology Faculty Works

Core components of cytokinesis are conserved from yeast to human, but how these components are assembled into a robust machine that drives cytokinesis remains poorly understood. In this paper, we show by fluorescence recovery after photobleaching analysis that Myo1, the sole myosin-II in budding yeast, was mobile at the division site before anaphase and became immobilized shortly before cytokinesis. This immobility was independent of actin filaments or the motor domain of Myo1 but required a small region in the Myo1 tail that is thought to be involved in higher-order assembly. As expected, proteins involved in actin ring assembly (tropomyosin and …

Long-Term Data For Endemic Frog Genera Reveal Potential Conservation Crisis In The Bale Mountains, Ethiopia, David J. Gower, Roman K. Aberra, Silvia Schwaller, Malcolm J. Largen, Ben Collen, Stephen Spawls, Michele Menegon, Breda M. Zimkus, Rafael O. De Sá, Et Al.

Biology Faculty Publications

Populations of many frogs have declined alarmingly in recent years, placing nearly one third of the > 6,000 species under threat of extinction. Declines have been attributed largely to habitat loss, environmental degradation and/or infectious diseases such as chytridiomycosis. Many frogs undergo dramatic natural population fluctuations such that long-term data are required to determine population trends without undue influence of stochastic factors. We present long-term quantitative data (individuals encountered per person hour of searching) for four monotypic frog genera endemic to an Afromontane region of exceptional importance but growing conservation concern: one endemic to the Ethiopian highlands (Spinophrynoides osgoodi) and three …

Stiffness And Modulus And Independent Controllers Of Breast Cancer Metastasis, Dannielle Ryman

Masters Theses 1911 - February 2014

One out of eight women in the United States will develop breast cancer during their lifetime. Ninety percent of cancer related deaths are due to metastasis. Metastasis is the biological process where individual or aggregate cancerous cells break away from the primary tumor site and colonize distant, non-adjacent locations throughout the body. It is my objectives to study how mechanical, topographical and biochemical cues affect metastatic breast cancer metastasis at an early developmental stage. ECM components have previously been shown to affect cell motility via ligand-receptor interactions, and physical cues, such as matrix stiffness and protein density. The primary tumor …

Examining The Functional Role Of Dprl-1 In Drosophila Melanogaster, John Valenzuela

Summer Research

The Phosphatase of Regenerating Liver (PRL) family of proteins control cell growth, motility and proliferation. They have been shown to elevate the levels of these functions, leading to an increase in cancer metastasis (“malignancy”), when they are overexpressed. The goal of this experiment is to knockout PRL gene expression to examine the general function of PRL proteins. Drosophila melanogaster have only one copy of the PRL gene (dPRL-1), as opposed to humans and other mammals, which have 3. Thus, using P-element imprecise excision to create mutant strains either fully lacking or with decreased function of the dPRL-1 protein, …

Comparison Of Th1 Cytokines And T Cell Markers Gene Expressions Between Virulent And An Attenuated Eiav Vaccine Strain, Talia R. Henkle

Lewis Honors College Capstone Collection

The equine infectious anemia virus (EIAV) is closely related to HIV and has been used as a model to identify protective mechanisms against lentivirus infection. In horses, EIA infection progresses for about a year before infected horses manage to control virus replication. This naturally-gained protection is absolutely dependent on active immune responses as evidenced by the fact that immunosuppressive drugs can induce the recurrence of disease. As the resolution of initial viremia correlates with the appearance of virus specific cytotoxic T lymphocytes (CTL), we believe that cellular immune responses play a key role in controlling EIAV in the horse. In …

Detection Of Viable Microorganisms Using Propidium Monoazide, Erik J. Mcfarland, Adrian Ponce Dr.

STAR Program Research Presentations

Propidium monoazide (PMA) is a molecular tool used to assess viability of microorganisms. Currently, PMA is thought to discern viability through membrane permeability; PMA enters only membrane compromised cells, irreversibly crosslinks to theirDNAand precipitates theDNAout of solution, preventing it from being amplified during polymerase chain reaction (PCR). Using PMA on a sample of live and dead microorganisms results in only theDNAof living organisms being amplified and identified. Therefore, a comparison ofPCRresults with and without PMA allows one to determine the live fraction and total population, respectively.

Current literature provides conflicting evidence as to the effectiveness of the technique. Our research …

Hydraphiles: A Rigorously Studied Class Of Synthetic Channel Compounds With In Vivo Activity, Saeedeh Negin, Bryan Smith, Alexandra Unger, W. Leevy, George Gokel

Chemistry & Biochemistry Faculty Works

No abstract provided.

Evaluation Of Antibiotic Resistance Emerging From Use Of Antibiotics In Cafos, J. R. Robbins, D. Hellman, N. Pease, M. Costello

Faculty Scholarship

No abstract provided.