Biology Commons^™

Plasticity In Patterns Of Histone Modifications And Chromosomal Proteins In Drosophila Heterochromatin, Nicole Riddle, Aki Minoda, Peter Kharchenko, Artyom Alekseyenko, Yuri Schwartz, Michael Tolstorukov, Andrey Gorchakov, Jacob Jaffe, Cameron Kennedy, Daniela Linder-Basso, Sally Peach, Gregory Shanower, Haiyan Zheng, Mitzi Kuroda, Vincenzo Pirrotta, Peter Park, Sarah C.R. Elgin, Gary Karpen

Biology Faculty Research

Eukaryotic genomes are packaged in two basic forms, euchromatin and heterochromatin. We have examined the composition and organization of Drosophila melanogaster heterochromatin in different cell types using ChIP-array analysis of histone modifications and chromosomal proteins. As anticipated, the pericentric heterochromatin and chromosome 4 are on average enriched for the "silencing" marks H3K9me2, H3K9me3, HP1a, and SU(VAR)3-9, and are generally depleted for marks associated with active transcription. The locations of the euchromatin-heterochromatin borders identified by these marks are similar in animal tissues and most cell lines, although the amount of heterochromatin is variable in some cell lines. Combinatorial analysis of chromatin …

Ampk Directly Inhibits Ndpk Through A Phosphoserine Switch To Maintain Cellular Homeostasis, R. U. Onyenwoke, L. J. Forsberg, L. Liu, Tyisha Williams, O. Alzate, J. E. Brenman

Biology Faculty Research

AMP-activated protein kinase (AMPK) is a key energy sensor that regulates metabolism to maintain cellular energy balance. AMPK activation has also been proposed to mimic benefits of caloric restriction and exercise. Therefore, identifying downstream AMPK targets could elucidate new mechanisms for maintaining cellular energy homeostasis. We identified the phosphotransferase nucleoside diphosphate kinase (NDPK), which maintains pools of nucleotides, as a direct AMPK target through the use of two-dimensional differential in-gel electrophoresis. Furthermore, we mapped the AMPK/NDPK phosphorylation site (serine 120) as a functionally potent enzymatic “off switch” both in vivo and in vitro. Because ATP is usually the most abundant …

Amp-Activated Protein Kinase (Ampk) Activity Is Not Required For Neuronal Development But Regulates Axogenesis During Metabolic Stress, Tyisha Williams, J. Courchet, B. Viollet, J. E. Brenman, F. Polleux

Biology Faculty Research

Mammalian brain connectivity requires the coordinated production and migration of billions of neurons and the formation of axons and dendrites. The LKB1/Par4 kinase is required for axon formation during cortical development in vivo partially through its ability to activate SAD-A/B kinases. LKB1 is a master kinase phosphorylating and activating at least 11 other serine/threonine kinases including the metabolic sensor AMP-activated protein kinase (AMPK), which defines this branch of the kinome. A recent study using a gene-trap allele of the β1 regulatory subunit of AMPK suggested that AMPK catalytic activity is required for proper brain development including neurogenesis and neuronal survival. …

An Assessment Of Histone-Modification Antibody Quality, Thea Egelhofer, Aki Minoda, Sarit Klugman, Kyungjoon Lee, Paulina Kolasinska-Zwierz, Artyom Alekseyenko, Ming-Sin Cheung, Daniel Day, Sarah Gadel, Andrey Gorchakov, Tingting Gu, Peter Kharchenko, Samantha Kuan, Isabel Latorre, Daniela Linder-Basso, Ying Luu, Queminh Ngo, Marc Perry, Andreas Rechtsteiner, Nicole Riddle, Yuri Schwartz, Gregory Shanower, Anne Vielle, Julie Ahringer, Sarah C.R. Elgin, Mitzi Kuroda, Vincenzo Pirrotta, Bing Ren, Susan Strome, Peter Park, Gary Karpen, R Hawkins, Jason Lieb

Biology Faculty Research

We have tested the specificity and utility of more than 200 antibodies raised against 57 different histone modifications in Drosophila melanogaster, Caenorhabditis elegans and human cells. Although most antibodies performed well, more than 25% failed specificity tests by dot blot or western blot. Among specific antibodies, more than 20% failed in chromatin immunoprecipitation experiments. We advise rigorous testing of histone-modification antibodies before use, and we provide a website for posting new test results (http://compbio.med.harvard.edu/antibodies/).

Expanding The Diversity Of Mycobacteriophages: Insights Into Genome Architecture And Evolution., Welkin Pope, Deborah Jacobs-Sera, Daniel Russell, Craig Peebles, Zein Al-Atrache, Turi Alcoser, Lisa Alexander, Matthew Alfano, Samantha Alford, Nichols Amy, Marie Anderson, Alexander Anderson, Andrew Ang, Manuel Ares Jr, Amanda Barber, Lucia Barker, Jonathan Barrett, William Barshop, Cynthia Bauerle, Ian Bayles, Katherine Belfield, Aaron Best, Agustin Borjon Jr, Charles Bowman, Christine Boyer, Kevin Bradley, Victoria Bradley, Lauren Broadway, Keshav Budwal, Kayla Busby, Ian Campbell, Anne Campbell, Alyssa Carey, Steven Caruso, Rebekah Chew, Chelsea Cockburn, Lianne Cohen, Jeffrey Corajod, Steven Cresawn, Kimberly Davis, Lisa Deng, Dee Denver, Breyon Dixon, Sahrish Ekram, Sarah C.R. Elgin, Angela Engelsen, Belle English, Marcella Erb, Crystal Estrada, Laura Filliger, Ann Findley, Lauren Forbes, Mark Forsyth, Tyler Fox, Melissa Fritz, Roberto Garcia, Zindzi George, Anne Georges, Christopher Gissendanner, Shannon Goff, Rebecca Goldstein, Kobie Gordon, Russell Green, Stephanie Guerra, Krysta Guiney-Olsen, Bridget Guiza, Leila Haghighat, Garrett Hagopian, Catherine Harmon, Jeremy Harmson, Grant Hartzog, Samuel Harvey, Siping He, Kevin He, Kaitlin Healy, Ellen Higinbotham, Erin Hildebrandt, Jason Ho, Gina Hogan, Victoria Hohenstein, Nathan Holz, Vincent Huang, Ericka Hufford, Peter Hynes, Arrykka Jackson, Erica Jansen, Jonathan Jarvik, Paul Jasinto, Tuajuanda Jordan, Tomas Kasza, Murray Katelyn, Jessica Kelsey, Larisa Kerrigan, Daryl Khaw, Junghee Kim, Justin Knutter, Ching-Chung Ko, Gail Larkin, Jennifer Laroche, Asma Latif, Kohana Leuba, Sequoia Leuba, Lynn Lewis, Kathryn Loesser-Case, Courtney Long, A Javier Lopez, Nicholas Lowery, Tina Lu, Victor Mac, Isaac Masters, Jazmyn Mccloud, Molly Mcdonough, Andrew Medenbach, Anjali Menon, Rachel Miller, Brandon Morgan, Patrick Ng, Elvis Nguyen, Katrina Nguyen, Emilie Nguyen, Kaylee Nicholson, Lindsay Parnell, Caitlin Peirce, Allison Perz, Luke Peterson, Rachel Pferdehirt, Seegren Philip, Kit Pogliano, Joe Pogliano, Tamsen Polley, Erica Puopolo, Lauren Rodriguez, Hannah Rabinowitz, Michael Resiss, Corwin Rhyan, Yetta Robinson, Andrew Rose, Jeffrey Rubin, Jessica Ruby, Margaret Saha, James Sandoz, Judith Savitskaya, Dale Schipper, Christine Schnitzler, Amanda Schott, J Bradley Segal, Christopher Shaffer, Kathryn Sheldon, Erica Shepard, Jonathan Shepardson, Madav Shroff, Jessica Simmons, Erika Simms, Brandy Simpson, Kathryn Sinclair, Robert Sjoholm, Ingrid Slette, Blaire Spaulding, Clark Straub, Joseph Stukey, Trevor Sughrue, Tin-Yun Tang, Lyons Tatyana, Stephen Taylor, Barbara Taylor, Louise Temple, Jasper Thompson, Michael Tokarz, Stephanie Trapani, Alexander Troum, Jonathan Tsay, Anthony Thomas Tubbs, Jillian Walton, Danielle Wang, Hannah Wang, John Warner, Emilie Weisser, Samantha Wendler, Kathleen Weston-Hafer, Hilary Whelan, Kurt Williamson, Angelica Willis, Hannah Wirtshafter, Theresa Wong, Phillip Wu, Yun Jeong Yang, Brandon Yee, David Zaidins, Bo Zhang, Melina Zúniga, Roger Hendrix, Graham Hatfull

Biology Faculty Research

Mycobacteriophages are viruses that infect mycobacterial hosts such as Mycobacterium smegmatis and Mycobacterium tuberculosis. All mycobacteriophages characterized to date are dsDNA tailed phages, and have either siphoviral or myoviral morphotypes. However, their genetic diversity is considerable, and although sixty-two genomes have been sequenced and comparatively analyzed, these likely represent only a small portion of the diversity of the mycobacteriophage population at large. Here we report the isolation, sequencing and comparative genomic analysis of 18 new mycobacteriophages isolated from geographically distinct locations within the United States. Although no clear correlation between location and genome type can be discerned, these genomes expand …

Expression And Characterization Of The Bacterial Mechanosensitive Channel Mscs In Xenopus Laevis Oocytes., Elizabeth S. Haswell, Grigory Maksaev

Biology Faculty Research

We have successfully expressed and characterized mechanosensitive channel of small conductance (MscS) from Escherichia coli in oocytes of the African clawed frog, Xenopus laevis. MscS expressed in oocytes has the same single-channel conductance and voltage dependence as the channel in its native environment. Two hallmarks of MscS activity, the presence of conducting substates at high potentials and reversible adaptation to a sustained stimulus, are also exhibited by oocyte-expressed MscS. In addition to its ease of use, the oocyte system allows the user to work with relatively large patches, which could be an advantage for the visualization of membrane deformation. …

Myosin Vi Regulates Actin Structure Specialization Through Conserved Cargo-Binding Domain Sites, Mamiko Isaji, Marta Lenartowska, Tatsuhiko Noguchi, Deborah J. Frank, Kathryn G. Miller

Biology Faculty Research

Actin structures are often stable, remaining unchanged in organization for the lifetime of a differentiated cell. Little is known about stable actin structure formation, organization, or maintenance. During Drosophila spermatid individualization, long-lived actin cones mediate cellular remodeling. Myosin VI is necessary for building the dense meshwork at the cones' fronts. We test several ideas for myosin VI's mechanism of action using domain deletions or site-specific mutations of myosin VI. The head (motor) and globular tail (cargo-binding) domains were both needed for localization at the cone front and dense meshwork formation. Several conserved partner-binding sites in the globular tail previously identified …

On The Utility Of Population Models For Invasive Plant Management: Response To Evans And Davis, Eleanor A. Pardini, John M. Drake, Tiffany M. Knight

Biology Faculty Research

No abstract provided.

Will The Use Of Less Fecund Cultivars Reduce The Invasiveness Of Perennial Plants?, Tiffany M. Knight, Kayri Havens, Pati Vitt

Biology Faculty Research

Many invasive species were originally introduced for horticultural purposes, and several continue to be profitable for the green (nursery, horticulture, and landscape) industry. Recently, some plant suppliers have marketed less fecund cultivars of several invasive species, including glossy buckthorn (Frangula alnus), burning bush (Euonymus alatus), and Japanese barberry (Berberis thunbergii), as “safe” alternatives to invasive relatives. We use published matrix population models to simulate the effect of reducing fecundity on the population growth rates of invasive species. We show that large changes in fecundity result in relatively small changes to the population growth rates of long-lived species, which suggests that …

Mechanosensitive Channels: What Can They Do And How Do They Do It?, Elizabeth S. Haswell, Rob Phillips, Douglas C. Rees

Biology Faculty Research

While mechanobiological processes employ diverse mechanisms, at their heart are force-induced perturbations in the structure and dynamics of molecules capable of triggering subsequent events. Among the best characterized force-sensing systems are bacterial mechanosensitive channels. These channels reflect an intimate coupling of protein conformation with the mechanics of the surrounding membrane; the membrane serves as an adaptable sensor that responds to an input of applied force and converts it into an output signal, interpreted for the cell by mechanosensitive channels. The cell can exploit this information in a number of ways: ensuring cellular viability in the presence of osmotic stress and …

Changing The Culture Of Science Education At Research Universities, W. Anderson, U Banerjee, C Drennan, Sarah C.R. Elgin, I Epstein, J Handelsman, G Hatfull, R Losick, D O'Dowd, B Olivera, S Strobel, G Walker, I Warner

Biology Faculty Research

No abstract provided.

Society For The Advancement Of Biology Education Research (Saber), Erika G. Offerdahl, Teri Balser, Clarissa Dirks, Kathryn Miller, Jennifer L. Momsen, Lisa Montplaisir, Marcy Osgood, Karen Sirum, Mary Pat Wenderoth, Brian White, William B. Wood, Michelle Withers, Robin Wright

Biology Faculty Research

No abstract provided.

Two Mechanosensitive Channel Homologs Influence Division Ring Placement In Arabidopsis Chloroplasts, Margaret E. Wilson, Gregory S. Jensen, Elizabeth S. Haswell

Biology Faculty Research

Chloroplasts must divide repeatedly to maintain their population during plant growth and development. A number of proteins required for chloroplast division have been identified, and the functional relationships between them are beginning to be elucidated. In both chloroplasts and bacteria, the future site of division is specified by placement of the Filamentous temperature sensitive Z (FtsZ) ring, and the Min system serves to restrict FtsZ ring formation to mid-chloroplast or mid-cell. How the Min system is regulated in response to environmental and developmental factors is largely unstudied. Here, we investigated the role in chloroplast division played by two Arabidopsis thaliana …

The Burden Of Motherhood: The Effect Of Reproductive Load On Female Lizard Locomotor, Foraging, And Social Behavior, Michele A. Johnson, J. L. Caton, R. E. Cohen, J. R. Vandecar, J. Wade

Biology Faculty Research

The costs of reproduction, involving demands associated with both current and future reproductive efforts, may place a substantial burden on females. However, animals may minimize these costs by modifying their behavior across the reproductive cycle. We examined the effects of reproductive load on three types of behavior (locomotion, foraging, and social displays) in green anole lizards (Anolis carolinensis) by comparing egg, follicle, and oviduct mass and volume with field observational data. We found that female locomotor and social display behaviors decreased as reproductive load increased, suggesting behavioral modification in these traits, but we detected no relationship between foraging and …

Identification Of Functional Elements And Regulatory Circuits By Drosophila Modencode, Sushmita Roy, Jason Ernst, Peter Kharchenko, Pouya Kheradpour, Nicolas Negre, Matthew Eaton, Jane Landolin, Christopher Bristow, Lijia Ma, Michael Lin, Stefan Washietl, Bradley Arshinoff, Ferhat Ay, Patrick Meyer, Nicolas Robine, Nicole Washington, Luisa Di Stefano, Eugene Berezikov, Christopher Brown, Rogerio Candeias, Joseph Carlson, Adrian Carr, Irwin Jungreis, Daniel Marbach, Rachel Sealfon, Michael Tolstorukov, Sebastian Will, Artyom Alekseyenko, Carlo Artieri, Benjamin Booth, Angela Brooks, Qi Dai, Carrie Davis, Michael Duff, Xin Feng, Andrey Gorchakov, Tingting Gu, Jorja Henikoff, Philipp Kapranov, Renhua Li, Heather Macalpine, John Malone, Aki Minoda, Jared Nordman, Katsutomo Okamura, Marc Perry, Sara Powell, Nicole Riddle, Akiko Sakai, Anastasia Samsonova, Jeremy Sandler, Yuri Schwartz, Noa Sher, Rebecca Spokony, David Sturgill, Marijke Van Baren, Kenneth Wan, Li Yang, Charles Yu, Elise Feingold, Peter Good, Mark Guyer, Rebecca Lowdon, Kami Ahmad, Justen Andrews, Bonnie Berger, Steven Brenner, Michael R. Brent, Lucy Cherbas, Sarah C.R. Elgin, Thomas Gingeras, Robert Grossman, Roger Hoskins, Thomas Kaufman, William Kent, Mitzi Kuroda, Terry Orr-Weaver, Norbert Perrimon, Vincenzo Pirrotta, James Posakony, Bing Ren, Steven Russell, Peter Cherbas, Brenton Graveley, Suzanna Lewis, Gos Micklem, Brian Oliver, Peter Park, Susan Celniker, Steven Henikoff, Gary Karpen, Eric Lai, David Macalpine, Lincoln Stein, Kevin White, Manolis Kellis

Biology Faculty Research

To gain insight into how genomic information is translated into cellular and developmental programs, the Drosophila model organism Encyclopedia of DNA Elements (modENCODE) project is comprehensively mapping transcripts, histone modifications, chromosomal proteins, transcription factors, replication proteins and intermediates, and nucleosome properties across a developmental time course and in multiple cell lines. We have generated more than 700 data sets and discovered protein-coding, noncoding, RNA regulatory, replication, and chromatin elements, more than tripling the annotated portion of the Drosophila genome. Correlated activity patterns of these elements reveal a functional regulatory network, which predicts putative new functions for genes, reveals stage- and …

Using Student-Generated Uv-Induced Escherichia Coli Mutants In A Directed Inquiry Undergraduate Genetics Laboratory, Frank G. Healy, Kevin D. Livingstone

Biology Faculty Research

We report a thematic sequence of directed inquiry-based labs taking students from bacterial mutagenesis and phenotypic identification of their own self-created mutant, through identification of mutated genes by biochemical testing, to verification of mutant alleles by complementation, and finally to mutant allele characterization by DNA sequence analysis. The lab utilizes UV mutagenesis with wild-type Escherichia coli and a UV-sensitive isogenic derivative optimized for undergraduate use. The labs take advantage of the simplicity of E. coli in a realistic genetic investigation using safe UV irradiation methods for creation and characterization of novel mutants. Assessment data collected over three offerings of the …

Behavioural Display Systems Across Nine Anolis Lizard Species: Sexual Dimorphisms In Structure And Function, Michele A. Johnson, J. Wade

Biology Faculty Research

Relationships between structure and function are a primary focus in biology, yet they are most often considered within individual species. Sexually dimorphic communication behaviours and the morphology of associated structures can vary widely, even among closely related species, and these traits provide an ideal opportunity to investigate the evolution of structure-function patterns. Using nine Anolis lizard species, we addressed a series of questions regarding sex differences in and the evolution of relationships between extension of the throat fan (dewlap) and morphology of the muscles and cartilage controlling it. The main results indicated that within species, males displayed the dewlap more …

The Genomics Education Partnership: Successful Integration Of Research Into Laboratory Classes At A Diverse Group Of Undergraduate Institutions, Christopher Shaffer, Wilson Leung, Jeremy Buhler, Elaine Mardis, Sarah C.R. Elgin, David Lopatto, Consuelo Alvarez, Cheryl Bailey, Daron Barnard, Satish Bhalla, Chitra Chandrasekaran, Vidya Chandrasekaran, Hui-Min Chung, Douglas Dorer, Chunguang Du, Todd Eckdahl, Jeff Poet, Donald Frohlich, Anya Goodman, Yuying Gosser, Charles Hauser, Laura Hoopes, Diana Johnson, Christopher Jones, Marian Kaehler, Nighat Kokan, Olga Kopp, Gary Kuleck, Gerard Mcneil, Robert Moss, Jennifer Myka, Alexis Nagengast, Robert Morris, Paul Overvoorde, Elizabeth Shoop, Susan Parrish, Kelynne Reed, Gloria Regisford, Dennis Revie, Anne Rosenwald, Kenneth Saville, Stephanie Schroeder, Mary Shaw, Gary Skuse, Christopher Smith, Mary Smith, Eric Spana, Mary Spratt, Joyce Stamm, Jeff Thompson, Matthew Wawersik, Barbara Wilson, James Youngblom

Biology Faculty Research

Genomics is not only essential for students to understand biology but also provides unprecedented opportunities for undergraduate research. The goal of the Genomics Education Partnership (GEP), a collaboration between a growing number of colleges and universities around the country and the Department of Biology and Genome Center of Washington University in St. Louis, is to provide such research opportunities. Using a versatile curriculum that has been adapted to many different class settings, GEP undergraduates undertake projects to bring draft-quality genomic sequence up to high quality and/or participate in the annotation of these sequences. GEP undergraduates have improved more than 2 …

Breeding Biology And Longevity Of Russet-Crowned Motmots In Central Mexico, Troy G. Murphy, V. G. Rohwer, E. Scholes

Biology Faculty Research

Motmots, with their distinctive racketed-tails, represent one of the most easily recognized tropical birds, yet little is known about the basic natural history of most species in the family Momotidae. We report basic breeding biology and longevity of Russet-crowned Motmots (Momotus mexicanus), a medium-sized Neotropical bird that ranges from northwest Mexico to central Guatemala. We monitored nest success of eight pairs from 1 May to 17 July 1998 in tropical deciduous forests in central Mexico. Motmots laid an average of 4.1 eggs and incubated for approximately 20 d. Four of eight nests fledged young. Of these four nests, …

Estrogen Receptor-Alpha In The Bed Nucleus Of The Stria Terminalis Regulates Social Affiliation In Male Prairie Voles (Microtus Ochrogaster), Kelly Lei, Bruce S. Cushing, Sergei Musatov, Sonoko Ogawa, Kristin M. Kramer

Biology Faculty Research

Estrogen receptor alpha (ER alpha) typically masculinizes male behavior, while low levels of ER alpha in the medial amygdala (MeA) and the bed nucleus of the stria terminalis (BST) are associated with high levels of male prosocial behavior. In the males of the highly social prairie vole (Microtus ochrogaster), increasing ER alpha in the MeA inhibited the expression of spontaneous alloparental behavior and produced a preference for novel females. To test for the effects of increased ER alpha in the BST, a viral vector was used to enhance ER alpha expression in the BST of adult male prairie voles. Following …

Distribution And Ecotypic Variation Of The Invasive Annual Barb Goatgrass (Aegiolops Triuncialis) On Serpentine Soil, Kelly G. Lyons, A M. Shapiro, M. W. Schwartz

Biology Faculty Research

Successful colonization of newly introduced species is driven by a multitude of factors and is highly dependent on the species. It has long been hypothesized that preadaptation and postestablishment natural selection of introduced species can facilitate their invasion; however, to date, limited research has been dedicated to these theories. In addition, although the correlation between establishment of invasive species and disturbance has been noted and widely studied, the susceptibility of undisturbed habitats to invasion remains unclear. In California, serpentine habitats are severe edaphic environments that have been relatively free of anthropogenic disturbance and nonindigenous species invasions. In this study, we …

Differences In Ultrasonic Vocalizations Between Wild And Laboratory California Mice (Peromyscus Californicus), M. C. Kalcounis-Rueppell, R. Petric, J. R. Briggs, C. Carney, M. M. Marshall, J. T. Willse, David O. Ribble, J. P. Crossland

Biology Faculty Research

Background: Ultrasonic vocalizations (USVs) emitted by muroid rodents, including laboratory mice and rats, are used as phenotypic markers in behavioral assays and biomedical research. Interpretation of these USVs depends on understanding the significance of USV production by rodents in the wild. However, there has never been a study of muroid rodent ultrasound function in the wild and comparisons of USVs produced by wild and laboratory rodents are lacking to date. Here, we report the first comparison of wild and captive rodent USVs recorded from the same species, Peromyscus californicus.

Methodology and Principal Findings: We used standard ultrasound recording techniques …

Identification Of A Nuclear Export Signal In The Catalytic Subunit Of Amp-Activated Protein Kinase, N. Kazgan, Tyisha Williams, L. J. Forsberg, J. E. Brenman

Biology Faculty Research

The metabolic regulator AMP-activated protein kinase (AMPK) maintains cellular homeostasis through regulation of proteins involved in energy-producing and -consuming pathways. Although AMPK phosphorylation targets include cytoplasmic and nuclear proteins, the precise mechanisms that regulate AMPK localization, and thus its access to these substrates, are unclear. We identify highly conserved carboxy-terminal hydrophobic amino acids that function as a leptomycin B–sensitive, CRM1-dependent nuclear export sequence (NES) in the AMPK catalytic subunit (AMPKα). When this sequence is modified AMPKα shows increased nuclear localization via a Ran-dependent import pathway. Cytoplasmic localization can be restored by substituting well-defined snurportin-1 or protein kinase A inhibitor (PKIA) …

Apparent Competition With An Invasive Plant Hastens The Extinction Of An Endangered Lupine, Emily M. Dangremond, Eleanor A. Pardini, Tiffany M. Knight

Biology Faculty Research

Invasive plants may compete with native plants by increasing the pressure of native consumers, a mechanism known as "apparent competition." Apparent competition can be as strong as or stronger than direct competition, but the role of apparent competition has rarely been examined in biological invasions. We used four years of demographic data and seed-removal experiments to determine if introduced grasses caused elevated levels of seed consumption on native plant species in a coastal dune system in California, USA. We show that the endangered, coastal dune plant Lupinus tidestromii experiences high levels of pre-dispersal seed consumption by the native rodent Peromyscus …

Webs In Vitro And In Vivo: Spiders Alter Their Orb-Web Spinning Behavior In The Laboratory, Andrew Sensenig, Ingi Agnarsson, Taylor M. Gondek, Todd A. Blackledge

Biology Faculty Research

Many studies of the elegant architectures of orb webs are conducted in controlled laboratory environments that remove environmental variability. The degree to which spider behavior in these circumstances resembles that of spiders in the wild is largely unknown. We compared web architecture and silk investment of furrowed orb weavers Larinioides corium's (Clerck 1757) building webs in laboratory cages and spinning webs on fences in the field and found significant differences. The volume of major ampullate silk in radii was 53% lower in cage webs, primarily because the silk was 50% thinner, but also because spiders tended to spin 14% fewer …

Seed Dispersal By Pulp Consumers, Not ‘‘Legitimate’’ Seed Dispersers, Increases Guettarda Viburnoides Population Growth, Andrea P. Loayza, Tiffany M. Knight

Biology Faculty Research

We examined the effect of seed dispersal by Purplish Jays (Cyanocorax cyanomelas; pulp consumers) and the Chestnut-eared Araçari (Pteroglossus castanotis; "legitimate" seed dispersers) on population growth of the small tree Guettarda viburnoides (Rubiaceae) in northeastern Bolivian savannas. Because each bird species differs with respect to feeding and post-feeding behavior, we hypothesized that seed dispersal by each species will contribute differently to the rate of increase of G. viburnoides, but that seed dispersal by either species will increase population growth when compared to a scenario with no seed dispersal. To examine the effects of individual dispersers on the future population size …

Chapter 27 – Studying Plus-End Tracking At Single Molecule Resolution Using Tirf Microscopy, Ram Dixit, Jennifer L. Ross

Biology Faculty Research

The highly dynamic microtubule plus-ends are key sites of regulation that impact the organization and function of the microtubule cytoskeleton. Much of this regulation is performed by the microtubule plus-end tracking (+TIP) family of proteins. +TIPs are a structurally diverse group of proteins that bind to and track with growing microtubule plus-ends in cells. +TIPs regulate microtubule dynamics as well as mediate interactions between microtubule tips and other cellular structures. Most +TIPs can directly bind to microtubules in vitro; however, the mechanisms for their plus-end specificity are not fully understood. Cellular studies of +TIP activity are complicated by the fact …

Chapter 26 – Multiple Color Single Molecule Tirf Imaging And Tracking Of Maps And Motors, Jennifer L. Ross, Ram Dixit

Biology Faculty Research

Microtubules are part of a complex mechano-chemical network inside cells. In order to understand how the components of these systems work together, careful in vitro experiments must be performed with added complexity. These experiments can ideally image all the interacting species. In order to image these molecules, multiple-color fluorescence imaging can be performed. In this chapter, we describe some methods for performing multiple-color single molecule fluorescence imaging using total internal reflection fluorescence microscopy. We give several specific examples of species of microtubule-associate proteins and motors that can be examined with detailed protocols for labeling, purification, and imaging.

A Three-Dimensional Computer Simulation Model Reveals The Mechanisms For Self-Organization Of Plant Cortical Microtubules Into Oblique Arrays, Ezgi Can Eren, Ram Dixit, Natarajan Gautam

Biology Faculty Research

The noncentrosomal cortical microtubules (CMTs) of plant cells self-organize into a parallel three-dimensional (3D) array that is oriented transverse to the cell elongation axis in wild-type plants and is oblique in some of the mutants that show twisted growth. To study the mechanisms of CMT array organization, we developed a 3D computer simulation model based on experimentally observed properties of CMTs. Our computer model accurately mimics transverse array organization and other fundamental properties of CMTs observed in rapidly elongating wild-type cells as well as the defective CMT phenotypes observed in the Arabidopsis mor1-1 and fra2 mutants. We found that CMT …

Remodeling Of The Tight Junction During Recovery From Exposure To Hydrogen Peroxide In Kidney Epithelial Cells, Jeannette E. Gonzalez, R. J. Digeronimo, D'Ann E. Arthur, Jonathan M. King

Biology Faculty Research

Renal ischemia-reperfusion injury results in oxidative stress-induced alterations in barrier function. Activation of the mitogen-activated protein (MAP) kinase pathway during recovery from oxidative stress may be an effector of oxidant-induced tight junction reorganization. We hypothesized that tight junction composition and barrier function would be perturbed during recovery from oxidative stress. We developed a model of short-term H₂O₂ exposure followed by recovery using Madin Darby canine kidney (MDCK II) cells. H₂O₂ perturbs barrier function without a significant cytotoxic effect except in significant doses. ERK-1/2 and p38, both enzymes of the MAP kinase pathway, were activated …