Biology Commons^™

Structured Growth And Genetic Drift Raise Relatedness In The Social Amoeba Dictyostelium Discoideum, Neil J. Buttery, Chandra N. Jack, Boahemaa Adu-Oppong, Kate T. Snyder, Christoper R L Thompson, David C. Queller, Joan E. Strassmann

Biology Faculty Research

One condition for the evolution of altruism is genetic relatedness between altruist and beneficiary, often achieved through active kin recognition. Here, we investigate the power of a passive process resulting from genetic drift during population growth in the social amoeba Dictyostelium discoideum. We put labelled and unlabelled cells of the same clone in the centre of a plate, and allowed them to proliferate outward. Zones formed by genetic drift owing to the small population of actively growing cells at the colony edge. We also found that single cells could form zones of high relatedness. Relatedness increased at a significantly …

Mind The Gap: A Comparative Study Of Migratory Behavior In Social Amoebae, Owen M. Gilbert, Jennie J. Kuzdzal-Fick, David C. Queller, Joan E. Strassmann

Biology Faculty Research

Social amoebae aggregate to form a multicellular slug that migrates some distance. Most species produce a stalk during migration, but some do not. We show that Dictyostelium giganteum, a species that produces stalk during migration, is able to traverse small gaps and utilize bacterial resources following gap traversal by shedding live cells. In contrast, we found that Dictyostelium discoideum, a species that does not produce stalk during migration, can traverse gaps only when in the presence of other species’ stalks or other thin filaments. These findings suggest that production of stalk during migration allows traversal of gaps that commonly occurs …

Functional Analysis Of Conserved Motifs In The Mechanosensitive Channel Homolog Mscs-Like2 From Arabidopsis Thaliana, Gregory S. Jensen, Elizabeth S. Haswell

Biology Faculty Research

The Mechanosensitive channel of Small conductance (MscS) of Escherichia coli has become an excellent model system for the structural, biophysical, and functional study of mechanosensitive ion channels. MscS, a complex channel with multiple states, contributes to protection against lysis upon osmotic downshock. MscS homologs are widely and abundantly dispersed among the bacterial and plant lineages, but are not found in animals. Investigation into the eukaryotic branch of the MscS family is in the beginning stages, and it remains unclear how much MscS homologs from eukaryotes resemble E. coli MscS with respect to structure, function, and regulation. Here we test the …

Drosophila Piwi Functions Downstream Of Pirna Production Mediating A Chromatin-Based Transposon Silencing Mechanism In Female Germ Line, Sidney Wang, Sarah C.R. Elgin

Biology Faculty Research

Transposon control is a critical process during reproduction. The PIWI family proteins can play a key role, using a piRNA-mediated slicing mechanism to suppress transposon activity posttranscriptionally. In Drosophila melanogaster, Piwi is predominantly localized in the nucleus and has been implicated in heterochromatin formation. Here, we use female germ-line-specific depletion to study Piwi function. This depletion of Piwi leads to infertility and to axis specification defects in the developing egg chambers; correspondingly, widespread loss of transposon silencing is observed. Germ-line Piwi does not appear to be required for piRNA production. Instead, Piwi requires Aubergine (and presumably secondary piRNA) for proper …

Competencies: A Cure For Pre-Med Curriculum, Winston Anderson, Richard Amasino, Manuel Ares, Utpal Banerjee, Bonnie Bartel, Victor Corces, Catherine Drennan, Sarah C.R. Elgin, Irving Epstein, Ellen Fanning, Louis Guillette, Jo Handelsman, Graham Hatfull, Ronald Hoy, Darcy Kelley, Leslie Leinwand, Richard Losick, Yi Lu, David Lynn, Claudia Neuhauser, Diane O'Dowd, Toto Olivera, Pavel Pevzner, Rebecca Richards-Kortum, Jasper Rine, Robert Sah, Scott Strobel, Graham Walker, David Walt, Isiah Warner, Sue Wessler, Huntington Willard, Richard Zare

Biology Faculty Research

No abstract provided.

Cluster K Mycobacteriophages: Insights Into The Evolutionary Origins Of Mycobacteriophage Tm4, Welkin Pope, Christina Ferreira, Deborah Jacobs-Sera, Robert Benjamin, Ariangela Davis, Randall Dejong, Sarah C.R. Elgin, Forrest Guilfoile, Mark Forsyth, Alexander Harris, Samuel Harvey, Lee Hughes, Peter Hynes, Arrykka Jackson, Marilyn Jalal, Elizabeth Macmurray, Coreen Manley, Molly Mcdonough, Jordan Mosier, Larissa Osterbann, Hannah Rabinowitz, Corwin Rhyan, Daniel Russell, Margaret Saha, Christopher Shaffer, Stephanie Simon, Erika Sims, Isabel Tovar, Emilie Weisser, John Wertz, Kathleen Weston-Hafer, Kurt Williamson, Bo Zhang, Steven Cresawn, Paras Jain, Mariana Piuri, William Jacobs, Roger Hendrix, Graham Hatfull

Biology Faculty Research

Five newly isolated mycobacteriophages--Angelica, CrimD, Adephagia, Anaya, and Pixie--have similar genomic architectures to mycobacteriophage TM4, a previously characterized phage that is widely used in mycobacterial genetics. The nucleotide sequence similarities warrant grouping these into Cluster K, with subdivision into three subclusters: K1, K2, and K3. Although the overall genome architectures of these phages are similar, TM4 appears to have lost at least two segments of its genome, a central region containing the integration apparatus, and a segment at the right end. This suggests that TM4 is a recent derivative of a temperate parent, resolving a long-standing conundrum about its biology, …

Single Molecule Analysis Of The Arabidopsis Fra1 Kinesin Shows That It Is A Functional Motor Protein With Unusually High Processivity, Chuanmei Zhu, Ram Dixit

Biology Faculty Research

The Arabidopsis FRA1 kinesin contributes to the organization of cellulose microfibrils through an unknown mechanism. The cortical localization of this kinesin during interphase raises the possibility that it transports cell wall-related cargoes along cortical microtubules that either directly or indirectly influence cellulose microfibril patterning. To determine whether FRA1 is an authentic motor protein, we combined bulk biochemical assays and single molecule fluorescence imaging to analyze the motor properties of recombinant, GFP-tagged FRA1 containing the motor and coiled-coil domains (designated as FRA1(707)–GFP). We found that FRA1(707)–GFP binds to microtubules in an ATP-dependent manner and that its ATPase activity is dramatically stimulated …

Dynamic Characterization Of The Ikk:Κbα:Nfκb Negative Feedback Loop Using Real-Time Bioluminescence Imaging, Britney Moss

All Theses and Dissertations (ETDs)

The transcription factor NF-κB is a pivotal regulator of mammalian cell function, modulating genes implicated in cellular stress responses, proliferation, differentiation, cell survival and apoptosis, as well as immune and inflammatory responses. Improper regulation of NF-κB signaling has been implicated in a myriad of human pathological disorders, including cardiovascular and neurodegenerative diseases, chronic inflammation, and various cancers. A key regulatory node within canonical NF-κB signaling is the IKK:NF-κB: IκBα negative feedback loop that plays a major role in regulating the strength and duration of NF-κB transcriptional activity. We have developed and characterized an unique bioluminescent reporter (κB_5àIκBα-FLuc) …

Sunday Driver/Jip3 Binds Kinesin Heavy Chain Directly And Enhances Its Motility, Faneng Sun, Chuanmei Zhu, Ram Dixit, Valeria Cavalli

Biology Faculty Research

Neuronal development, function and repair critically depend on axonal transport of vesicles and protein complexes, which is mediated in part by the molecular motor kinesin‐1. Adaptor proteins recruit kinesin‐1 to vesicles via direct association with kinesin heavy chain (KHC), the force‐generating component, or via the accessory light chain (KLC). Binding of adaptors to the motor is believed to engage the motor for microtubule‐based transport. We report that the adaptor protein Sunday Driver (syd, also known as JIP3 or JSAP1) interacts directly with KHC, in addition to and independently of its known interaction with KLC. Using an in vitro motility assay, …

Eugenics And Modern Biology: Critiques Of Eugenics, 1910-1945, Garland E. Allen

Biology Faculty Research

Eugenics in most western countries in the first four decades of the twentieth century was based on the idea that genes control most human phenotypic traits, everything from physical features such as polydactyly and eye color to physiological conditions such as the A-B-O blood groups to mental and personality traits such as “feeblemindedness”, alcoholism and pauperism. It assessing the development of the eugenics movement – its rise and decline between 1900 and 1950 – it is important to recognize that its naïve assumptions and often flawed methodologies were openly criticized at the time by scientists and non-scientists alike. This paper …

Comprehensive Analysis Of The Chromatin Landscape In Drosophila Melanogaster, Peter Kharchenko, Artyom Alekseyenko, Yuri Schwartz, Aki Minoda, Nicole Riddle, Jason Ernst, Peter Sabo, Erica Larschan, Andrey Gorchakov, Tingting Gu, Daniela Linder-Basso, Annette Plachetka, Gregory Shanower, Michael Tolstorukov, Lovelace Luquette, Ruibin Xi, Youngsook Jung, Richard Park, Eric Bishop, Theresa Canfield, Richard Sandstrom, Robert Thurman, David Macalpine, John Stamatoyannopoulos, Manolis Kellis, Sarah C.R. Elgin, Mitzi Kuroda, Vincenzo Pirrotta, Gary Karpen, Peter Park

Biology Faculty Research

Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory …

A Synthesis Of Plant Invasion Effects On Biodiversity Across Spatial Scales, Kristin I. Powell, Jonathan M. Chase, Tiffany M. Knight

Biology Faculty Research

PREMISE OF THE STUDY:

Invasive plant species are typically thought to pose a large threat to native biodiversity, and local-scale studies typically confirm this view. However, plant invaders rarely cause regional extirpations or global extinctions, causing some to suggest that invasive species' influence on native biodiversity may not be so dire. We aim to synthesize the seemingly conflicting literature in plant invasion biology by evaluating the effects of invasive plant species across spatial scales.

METHODS:

We first conducted a meta-analysis on the effects of invasive plants on the species richness of invaded communities across a range of spatial extents. We …

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 …

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 …

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 …

Cell Culture Models Of Genetic Variation, Joshua T. Witten

Arts & Sciences Graduate Student Theses and Dissertations

Studying genetic variation presents a dilemma. While the genetic variation of greatest interest is that causing variation in traits and disease risk in natural populations, natural populations have characteristics that make them challenging to study. In this work, I have assessed the use of cell culture methods as a solution to some of these challenges. In particular, I studied genetic variation in the budding yeast Saccharomyces cerevisiae that was generated by selection in the lab as a model for natural genetic variation. I have found that even simplistic selection programs in the laboratory, including the use of chemical mutagenesis to …

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 …

A Search For Genetic Modifiers Responsible For Congenital Heart Disease Variability In The Presence Of Nkx2-5 Haploinsufficiency, Julia Brandeis Winston Honold

All Theses and Dissertations (ETDs)

While a clear heritable risk has been observed for congenital heart disease, there is considerable variation in penetrance and presentation likely due to multiple genetic and environmental risk factors. To identify causative factors and interactions responsible for variability in heart development, greater than 4,200 hearts from Nkx2-5 heterozygous knockout mice have been collected and examined. Nkx2-5+/- mice in the inbred strain background C57Bl/6 frequently have atrial and ventricular septal defects. The incidences are substantially reduced in the Nkx2-5+/- progeny of first-generation: F1) outcrosses to the strains FVB/N or A/J. Defects recur in the second generation: F2) of the F1xF1 intercross …

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 …

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 …