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Articles 1 - 21 of 21
Full-Text Articles in Life Sciences
Nature And Function Of Insulator Protein Binding Sites In The Drosophila Genome, Yuri Schwartz, Daniela Linder-Basso, Peter Kharchenko, Michael Tolstorukov, Maria Kim, Hua-Bing Li, Andrey Gorchakov, Aki Minoda, Gregory Shanower, Artyom Alekseyenko, Nicole Riddle, Youngsook Jung, Tingting Gu, Annette Plachetka, Sarah C.R. Elgin, Mitzi Kuroda, Peter Park, Mikhail Savitsky, Gary Karpen, Vincenzo Pirrotta
Nature And Function Of Insulator Protein Binding Sites In The Drosophila Genome, Yuri Schwartz, Daniela Linder-Basso, Peter Kharchenko, Michael Tolstorukov, Maria Kim, Hua-Bing Li, Andrey Gorchakov, Aki Minoda, Gregory Shanower, Artyom Alekseyenko, Nicole Riddle, Youngsook Jung, Tingting Gu, Annette Plachetka, Sarah C.R. Elgin, Mitzi Kuroda, Peter Park, Mikhail Savitsky, Gary Karpen, Vincenzo Pirrotta
Biology Faculty Publications & Presentations
Chromatin insulator elements and associated proteins have been proposed to partition eukaryotic genomes into sets of independently regulated domains. Here we test this hypothesis by quantitative genome-wide analysis of insulator protein binding to Drosophila chromatin. We find distinct combinatorial binding of insulator proteins to different classes of sites and uncover a novel type of insulator element that binds CP190 but not any other known insulator proteins. Functional characterization of different classes of binding sites indicates that only a small fraction act as robust insulators in standard enhancer-blocking assays. We show that insulators restrict the spreading of the H3K27me3 mark but …
Functions Of The Arabidopsis Kinesin Superfamily Of Microtubule-Based Motor Proteins, Chuanmei Zhu, Ram Dixit
Functions Of The Arabidopsis Kinesin Superfamily Of Microtubule-Based Motor Proteins, Chuanmei Zhu, Ram Dixit
Biology Faculty Publications & Presentations
Plants possess a large number of microtubule-based kinesin motor proteins. While the kinesin-2, 3, 9, and 11 families are absent from land plants, the kinesin-7 and 14 families are greatly expanded. In addition, some kinesins are specifically present only in land plants. The distinctive inventory of plant kinesins suggests that kinesins have evolved to perform specialized functions in plants. Plants assemble unique microtubule arrays during their cell cycle, including the interphase cortical microtubule array, preprophase band, anastral spindle and phragmoplast. In this review, we explore the functions of plant kinesins from a microtubule array viewpoint, focusing mainly on Arabidopsis kinesins. …
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
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 Publications & Presentations
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 …
A Ranksum Statistics Based Framework To Decipher Transcription Regulation, Iuan-Bor Chen
A Ranksum Statistics Based Framework To Decipher Transcription Regulation, Iuan-Bor Chen
Arts & Sciences Electronic Theses and Dissertations
The unbiased generation of specific and meaningful hypotheses from the deluge of data generated by modern genomic methods remains a challenge. These datasets require increasing level of expertise to analyze fully, and are often underutilized even in the originating lab. It would be desirable to have a computational strategy that is easy to implement, robust against outliers and missing data, and broadly applicable to diverse experimental designs. In this dissertation, I present a set of ranksum statistics-based analytical methods as a framework to extract testable hypotheses from large and complex datasets. To illustrate its utility, this framework was applied to …
Ectopic Assembly Of Heterochromatin In Drosophila Melanogaster Triggered By Transposable Elements, Monica Sentmanat, Sarah C.R. Elgin
Ectopic Assembly Of Heterochromatin In Drosophila Melanogaster Triggered By Transposable Elements, Monica Sentmanat, Sarah C.R. Elgin
Biology Faculty Publications & Presentations
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 …
Delicious-Ology: The Science Of Delicious Food, Sasha Yan
Delicious-Ology: The Science Of Delicious Food, Sasha Yan
Undergraduate Theses—Unrestricted
You can read this book two ways. If you want to “just cook,” flip to the recipe index, pick a recipe, and skip straight to that page. The surrounding text will explain some aspects of the science behind the recipe. While the recipes in this book are chosen to complement and provide examples of the science, they’re also recipes that are fantastic in and of themselves.
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
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 Publications & Presentations
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 …
Computer Simulation And Mathematical Models Of The Noncentrosomal Plant Cortical Microtubule Cytoskeleton, Ezgi Can Eren, Natarajan Gautam, Ram Dixit
Computer Simulation And Mathematical Models Of The Noncentrosomal Plant Cortical Microtubule Cytoskeleton, Ezgi Can Eren, Natarajan Gautam, Ram Dixit
Biology Faculty Publications & Presentations
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
Putting A Bifunctional Motor To Work: Insights Into The Role Of Plant Kch Kinesins, Ram Dixit
Biology Faculty Publications & Presentations
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
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 Publications & Presentations
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 …
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
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 Publications & Presentations
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 …
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
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 Publications & Presentations
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 …
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
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 Publications & Presentations
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 …
Why Wasp Foundresses Change Nests: Relatedness, Dominance, And Nest Quality, Perttu Seppä, David C. Queller, Joan E. Strassmann
Why Wasp Foundresses Change Nests: Relatedness, Dominance, And Nest Quality, Perttu Seppä, David C. Queller, Joan E. Strassmann
Biology Faculty Publications & Presentations
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 …
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
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 Publications & Presentations
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 …
Mscs-Like10 Is A Stretch-Activated Ion Channel From Arabidopsis Thaliana With A Preference For Anions, Grigory Maksaev, Elizabeth S. Haswell
Mscs-Like10 Is A Stretch-Activated Ion Channel From Arabidopsis Thaliana With A Preference For Anions, Grigory Maksaev, Elizabeth S. Haswell
Biology Faculty Publications & Presentations
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 …
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
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 Publications & Presentations
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 …
A Role For Mechanosensitive Channels In Chloroplast And Bacterial Fission., Margaret E. Wilson, Elizabeth S. Haswell
A Role For Mechanosensitive Channels In Chloroplast And Bacterial Fission., Margaret E. Wilson, Elizabeth S. Haswell
Biology Faculty Publications & Presentations
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 …
Plastids And Pathogens: Mechanosensitive Channels And Survival In A Hypoosmotic World, Kira M. Veley, Elizabeth S. Haswell
Plastids And Pathogens: Mechanosensitive Channels And Survival In A Hypoosmotic World, Kira M. Veley, Elizabeth S. Haswell
Biology Faculty Publications & Presentations
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 …
Mechanosensitive Channels Protect Plastids From Hypoosmotic Stress During Normal Plant Growth, Kira M. Veley, Sarah Marshburn, Cara E. Clure, Elizabeth S. Haswell
Mechanosensitive Channels Protect Plastids From Hypoosmotic Stress During Normal Plant Growth, Kira M. Veley, Sarah Marshburn, Cara E. Clure, Elizabeth S. Haswell
Biology Faculty Publications & Presentations
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 …
Functional Analysis Of Conserved Motifs In The Mechanosensitive Channel Homolog Mscs-Like2 From Arabidopsis Thaliana, Gregory S. Jensen, Elizabeth S. Haswell
Functional Analysis Of Conserved Motifs In The Mechanosensitive Channel Homolog Mscs-Like2 From Arabidopsis Thaliana, Gregory S. Jensen, Elizabeth S. Haswell
Biology Faculty Publications & Presentations
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 …