Biology Commons^™

Enrichment Of Hp1a On Drosophila Chromosome 4 Genes Creates An Alternate Chromatin Structure Critical For Regulation In This Heterochromatic Domain, Nicole Riddle, Youngsook Jung, Tingting Gu, Artyom Alekseyenko, Dalal Asker, Hongxing Gui, Peter Kharchenko, Aki Minoda, Annette Plachetka, Yuri Schwartz, Michael Tolstorukov, Mitzi Kuroda, Vincenzo Pirrotta, Gary Karpen, Peter Park, Sarah C.R. Elgin

Biology Faculty Research

Chromatin environments differ greatly within a eukaryotic genome, depending on expression state, chromosomal location, and nuclear position. In genomic regions characterized by high repeat content and high gene density, chromatin structure must silence transposable elements but permit expression of embedded genes. We have investigated one such region, chromosome 4 of Drosophila melanogaster. Using chromatin-immunoprecipitation followed by microarray (ChIP-chip) analysis, we examined enrichment patterns of 20 histone modifications and 25 chromosomal proteins in S2 and BG3 cells, as well as the changes in several marks resulting from mutations in key proteins. Active genes on chromosome 4 are distinct from those in …

Ectopic Assembly Of Heterochromatin In Drosophila Melanogaster Triggered By Transposable Elements, Monica Sentmanat, Sarah C.R. Elgin

Biology Faculty Research

A persistent question in biology is how cis-acting sequence elements influence trans-acting factors and the local chromatin environment to modulate gene expression. We reported previously that the DNA transposon 1360 can enhance silencing of a reporter in a heterochromatic domain of Drosophila melanogaster. We have now generated a collection of variegating phiC31 landing-pad insertion lines containing 1360 and a heat-shock protein 70 (hsp70)-driven white reporter to explore the mechanism of 1360-sensitive silencing. Many 1360-sensitive sites were identified, some in apparently euchromatic domains, although all are close to heterochromatic masses. One such site (line 1198; insertion near the base of chromosome …

Condition And Brightness Of Structural Blue-Green: Motmot Tail-Racket Brightness Is Related To Speed Of Feather Growth In Males, But Not In Females, Troy G. Murphy, Tiffany T. Pham

Biology Faculty Research

Coloration plays an important role in sexual and social communication, and in many avian species both males and females maintain elaborate colours. Recent research has provided strong support for the hypothesis that elaborate female traits can be maintained by sexual or social selection; however, most research on female ornamentation has focused on pigment-based colours, and less is known about how structural colours are maintained. Both sexes of the turquoise-browed motmot (Eumomota superciliosa) have a blue-green racket-tipped tail, and it remains unknown if tail coloration serves as a sexual or social signal in one or both sexes. Here, we …

Sequence-Specific Targeting Of Dosage Compensation In Drosophila Favors An Active Chromatin Context, Artyom Alekseyenko, Joshua Ho, Shouyong Peng, Marnie Gelbart, Michael Tolstorukov, Annette Plachetka, Peter Kharchenko, Youngsook Jung, Andrey Gorchakov, Erica Larschan, Tingting Gu, Aki Minoda, Nicole Riddle, Yuri Schwartz, Sarah C.R. Elgin, Gary Karpen, Vincenzo Pirrotta, Mitzi Kuroda, Peter Park

Biology Faculty Research

The Drosophila MSL complex mediates dosage compensation by increasing transcription of the single X chromosome in males approximately two-fold. This is accomplished through recognition of the X chromosome and subsequent acetylation of histone H4K16 on X-linked genes. Initial binding to the X is thought to occur at "entry sites" that contain a consensus sequence motif ("MSL recognition element" or MRE). However, this motif is only ∼2 fold enriched on X, and only a fraction of the motifs on X are initially targeted. Here we ask whether chromatin context could distinguish between utilized and non-utilized copies of the motif, by comparing …

Amino Acid Function And Docking Site Prediction Through Combining Disease Variants, Structure Alignments, Sequence Alignments, And Molecular Dynamics: A Study Of The Hmg Domain, Jeremy W. Prokop, Thomas C. Leeper, Zhong-Hui Duan, Amy Milsted

Biology Faculty Research

Background: The DNA binding domain of HMG proteins is known to be important in many diseases, with the Sox sub-family of HMG proteins of particular significance. Numerous natural variants in HMG proteins are associated with disease phenotypes. Integrating these natural variants, molecular dynamic simulations of DNA interaction and sequence and structure alignments give detailed molecular knowledge of potential amino acid function such as DNA or protein interaction. Results: A total of 33 amino acids in HMG proteins are known to have natural variants in diseases. Eight of these amino acids are normally conserved in human HMG proteins and 27 are …

Computer Simulation And Mathematical Models Of The Noncentrosomal Plant Cortical Microtubule Cytoskeleton, Ezgi Can Eren, Natarajan Gautam, Ram Dixit

Biology Faculty Research

There is rising interest in modeling the noncentrosomal cortical microtubule cytoskeleton of plant cells, particularly its organization into ordered arrays and the mechanisms that facilitate this organization. In this review, we discuss quantitative models of this highly complex and dynamic structure both at a cellular and molecular level. We report differences in methodologies and assumptions of different models as well as their controversial results. Our review provides insights for future studies to resolve these controversies, in addition to underlining the common results between various models. We also highlight the need to compare the results from simulation and mathematical models with …

Putting A Bifunctional Motor To Work: Insights Into The Role Of Plant Kch Kinesins, Ram Dixit

Biology Faculty Research

Comment on: A novel actin-microtubule cross-linking kinesin, NtKCH, functions in cell expansion and division. [New Phytol. 2012 Feb;193(3):576-89. doi: 10.1111/j.1469-8137.2011.03944.x. ]

Single-Molecule Analysis Of The Microtubule Cross-Linking Protein Map65-1 Reveals A Molecular Mechanism For Contact-Angle-Dependent Microtubule Bundling, Amanda Tulin, Sheri Mcclerklin, Yue Huang, Ram Dixit

Biology Faculty Research

Bundling of microtubules (MTs) is critical for the formation of complex MT arrays. In land plants, the interphase cortical MTs form bundles specifically following shallow-angle encounters between them. To investigate how cells select particular MT contact angles for bundling, we used an in vitro reconstitution approach consisting of dynamic MTs and the MT-cross-linking protein MAP65-1. We found that MAP65-1 binds to MTs as monomers and inherently targets antiparallel MTs for bundling. Dwell-time analysis showed that the affinity of MAP65-1 for antiparallel overlapping MTs is about three times higher than its affinity for single MTs and parallel overlapping MTs. We also …

It Isn't Always Sexy When Both Are Bright And Shiny: Considering Alternatives To Sexual Selection In Elaborate Monomorphic Species, K. A. Tarvin, Troy G. Murphy

Biology Faculty Research

Since the dawn of abstract thinking, humans have wondered about the seemingly unnecessary elaborate ornamentations of birds. Gaudy colours, cumbersome tails, complex vocalizations and bizarre displays are found in bird species from all corners of the globe. Darwin (1871) provided an elegant explanation for the existence of these non-utilitarian traits: they increase mating success, and although they may impair survival, the costs of producing and bearing elaborate ornaments can be repaid in the currency of additional offspring. Darwin’s model still serves as the foundation for our concept of sexual selection but great strides have been made in our understanding of …

Carotenoid-Based Ornaments Of Female And Male American Goldfinches (Spinus Tristis) Show Sex-Specific Correlations With Immune Function And Metabolic Rate, R. J. Kelly, Troy G. Murphy, K. A. Tarvin, G. Burness

Biology Faculty Research

Conspicuous ornamentation has been linked to immunological and physiological condition in males of many species. In species where both sexes are ornamented, it is unclear whether the signal content of ornaments differs between males and females. We examined the immunological and physiological correlates of carotenoid-based bill and plumage ornamentation in American goldfinches Spinus tristis, a species in which bright orange bills are sexually monomorphic but yellow plumage is sexually dimorphic during the breeding season. Because bill color is dynamic over short periods while plumage color is static over longer time frames, we tested whether these signals have the potential to …

Why Wasp Foundresses Change Nests: Relatedness, Dominance, And Nest Quality, Perttu Seppä, David C. Queller, Joan E. Strassmann

Biology Faculty Research

The costs and benefits of different social options are best understood when individuals can be followed as they make different choices, something that can be difficult in social insects. In this detailed study, we follow overwintered females of the social wasp Polistes carolina through different nesting strategies in a stratified habitat where nest site quality varies with proximity to a foraging area, and genetic relatedness among females is known. Females may initiate nests, join nests temporarily or permanently, or abandon nests. Females can become helpers or egglayers, effectively workers or queens. What they actually do can be predicted by a …

Plastids And Pathogens: Mechanosensitive Channels And Survival In A Hypoosmotic World, Kira M. Veley, Elizabeth S. Haswell

Biology Faculty Research

In bacteria, MscS-type mechanosensitive channels serve to protect cells from lysis as they swell during extreme osmotic stress. We recently showed that two MscS homologs from Arabidopsis thaliana serve a similar purpose in the epidermal plastids of the leaf, indicating that the plant cell cytoplasm can present a dynamic osmotic challenge to the plastid. MscS homologs are predicted to be targeted to both plastids and mitochondrial envelopes and have been found in the genomes of intracellular pathogens. Here we discuss the implications of these observations, and propose that MS channels provide an essential mechanism for osmotic adaptation to both intracellular …

Amino Acid Repeats Cause Extraordinary Coding Sequence Variation In The Social Amoeba Dictyostelium Discoideum, Clea Scala, Xiangjun Tian, Natasha J. Mehdiabadi, Margaret H. Smith, Gerda Saxer, Katie Stephens, Prince Buzombo, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Protein sequences are normally the most conserved elements of genomes owing to purifying selection to maintain their functions. We document an extraordinary amount of within-species protein sequence variation in the model eukaryote Dictyostelium discoideum stemming from triplet DNA repeats coding for long strings of single amino acids. D. discoideum has a very large number of such strings, many of which are polyglutamine repeats, the same sequence that causes various human neurological disorders in humans, like Huntington’s disease. We show here that D. discoideum coding repeat loci are highly variable among individuals, making D. discoideum a candidate for the most variable …

Mscs-Like10 Is A Stretch-Activated Ion Channel From Arabidopsis Thaliana With A Preference For Anions, Grigory Maksaev, Elizabeth S. Haswell

Biology Faculty Research

Like many other organisms, plants are capable of sensing and responding to mechanical stimuli such as touch, osmotic pressure, and gravity. One mechanism for the perception of force is the activation of mechanosensitive (or stretch-activated) ion channels, and a number of mechanosensitive channel activities have been described in plant membranes. Based on their homology to the bacterial mechanosensitive channel MscS, the 10 MscS-Like (MSL) proteins of Arabidopsis thaliana have been hypothesized to form mechanosensitive channels in plant cell and organelle membranes. However, definitive proof that MSLs form mechanosensitive channels has been lacking. Here we used single-channel patch clamp electrophysiology to …

Mechanosensitive Channels Protect Plastids From Hypoosmotic Stress During Normal Plant Growth, Kira M. Veley, Sarah Marshburn, Cara E. Clure, Elizabeth S. Haswell

Biology Faculty Research

Cellular response to osmotic stress is critical for survival and involves volume control through the regulated transport of osmolytes [1-3]. Organelles may respond similarly to abrupt changes in cytoplasmic osmolarity [4-6]. The plastids of the Arabidopsis thaliana leaf epidermis provide a model system for the study of organellar response to osmotic stress within the context of the cell. An Arabidopsis mutant lacking two plastid-localized homologs of the bacteria mechanosensitive channel MscS (MscS-like [MSL] 2 and 3) exhibits large round epidermal plastids that lack dynamic extensions known as stromules [7]. This phenotype is present under normal growth conditions and does not …

A Role For Mechanosensitive Channels In Chloroplast And Bacterial Fission., Margaret E. Wilson, Elizabeth S. Haswell

Biology Faculty Research

The division site in both chloroplasts and bacteria is established by the medial placement of the FtsZ ring, a process that is in part regulated by the evolutionarily conserved components of the Min system. We recently showed that mechanosensitive ion channels influence FtsZ ring assembly in both Arabidopsis thaliana chloroplasts and in Escherichia coli; in chloroplasts they do so through the same genetic pathway as the Min system. Here we describe the effect of heterologous expression of the Arabidopsis MS channel homolog MSL2 on FtsZ ring placement in E. coli. We also discuss possible molecular mechanisms by which MS channels …

A Pre-Embedding Immunogold Approach Reveals Localization Of Myosin Vi At The Ultrastructural Level In The Actin Cones That Mediate Drosophila Spermatid Individualization, Marta Lenartowska, Mamiko Isaji, Kathryn G. Miller

Biology Faculty Research

Stable actin structures play important roles in the development and specialization of differentiated cells. How these structures form, are organized, and are used to mediate physiological processes is not well understood in most cases. In Drosophila testis, stable actin structures, called actin cones, mediate spermatid individualization, a large-scale cellular remodeling process. These actin cones are composed of two structural domains, a front meshwork and a rear region of parallel bundles. Myosin VI is an important player in proper actin cone organization and function. Myosin VI localizes to the cones' fronts and its specific localization is required for proper actin cone …

Whole Genome Sequencing Of Mutation Accumulation Lines Reveals A Low Mutation Rate In The Social Amoeba Dictyostelium Discoideum, Gerda Saxer, Paul Havlak, Sara A. Fox, Michael A. Quance, Sharu Gupta, Yuriy Fofanov, Joan E. Strassmann, David C. Queller

Biology Faculty Research

Spontaneous mutations play a central role in evolution. Despite their importance, mutation rates are some of the most elusive parameters to measure in evolutionary biology. The combination of mutation accumulation (MA) experiments and whole-genome sequencing now makes it possible to estimate mutation rates by directly observing new mutations at the molecular level across the whole genome. We performed an MA experiment with the social amoeba Dictyostelium discoideum and sequenced the genomes of three randomly chosen lines using high-throughput sequencing to estimate the spontaneous mutation rate in this model organism. The mitochondrial mutation rate of 6.76×10(-9), with a Poisson confidence interval …

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, …

Relationships Among Reproductive Morphology, Behavior, And Testosterone In A Natural Population Of Green Anole Lizards, Michele A. Johnson, R. E. Cohen, J. R. Vandecar, J. Wade

Biology Faculty Research

Laboratory studies of reproductive systems have long supported the idea that neural and/or muscular structures used frequently are often enhanced in size. However, field studies integrating behavioral, morphological, and hormonal data are needed to better understand relationships in natural environments. We examined a natural population of green anole lizards (Anolis carolinensis) to determine whether variation in reproductive morphology both within and between the sexes paralleled differences in courtship and copulatory behaviors and circulating testosterone levels. Display rate in males was positively correlated with the sizes of the cartilage supporting the dewlap (a throat fan used in courtship and …

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 …

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 …