Biology Commons^™

Recent Characterizations Of Mscs And Its Homologs Provide Insight Into The Basis Of Ion Selectivity In Mechanosensitive Channels, Grigory Maksaev, Elizabeth S. Haswell

Biology Faculty Research

The bacterial mechanosensitive channel MscS provides an excellent model system for the study of mechanosensitivity and for investigations into the cellular response to hypoosmotic shock. Numerous studies have elucidated the structure, function and gating mechanism of Escherichia coli MscS, providing a wealth of information for the comparative analysis of MscS family members in bacteria, archaea, fungi and plants. We recently reported the electrophysiological characterization of MscS-Like (MSL)10, a MscS homolog from the model flowering plant Arabidopsis thaliana. Here we summarize our results and briefly compare MSL10 to previously described members of the MscS family. Finally, we comment on how …

Characterization Of The Placenta-Specific 8.1 Gene Function During Zebrafish Embryogenesis, Haiting Ma

All Theses and Dissertations (ETDs)

The PLAC8 gene encodes for a small, cysteine-rich protein conserved in vertebrates that is a member of a large family of PLAC8-motif containing proteins with diverse functions in animals, plants, and algae. Recently, high levels of PLAC8 expression have been detected in aggressive colorectal cancer and invasive breast cancer, and potentially contributing to the cancer pathogenesis. However, the molecular and cellular functions of PLAC8 in vertebrate development, homeostasis, and disease remain unclear. To determine the function of PLAC8 under disease and normal conditions, in this thesis work, I identified plac8.1 as a PLAC8 homolog in zebrafish, a vertebrate model system …

Metagenomic Analyses Of The Human Gut Virome, Alejandro Reyes

All Theses and Dissertations (ETDs)

The human gut harbors tens of trillions of microbes belonging to all three domains of life, Bacteria, Archaea, and Eukarya; most are members of Bacteria. These organisms collaborate and compete for functional niches and physical space: habitats), together forming a continuously functioning metabolic organ that influences many aspects of host biology. The factors that drive the assembly, determine the stability, and shape the adaptive responses of the gut microbiota to a variety of perturbations are the subject of intense study as greater appreciation is gained of the importance of this microbial community for human health. My thesis focused on the …

The Physiological And Morphological Responses Of The Bladder Urothelium To Differential Injury, Kristina Marie Stemler

All Theses and Dissertations (ETDs)

The bladder is the site of various diseases such as urinary tract infections: UTI), bladder pain syndrome/interstitial cystitis: BPS/IC), and bladder cancer. UTIs and BPS/IC primarily afflict women and treatment costs over $5 billion and almost $200 million respectively in 2006. Quality of life in BPS/IC patients is low; comparable to individuals with end stage renal disease. Recent research has identified a role for the epithelial lining of the bladder, which is usually targeted by these afflictions, in potentially contributing to enhancing pain. The bladder epithelium also showcases a rapid ability to regenerate after injury.

Knowledge of the contribution of …

Plant-Pollinator Interactions Over 120 Years: Loss Of Species, Co-Occurrence, And Function, Laura A. Burkle, John C. Marlin, Tiffany M. Knight

Biology Faculty Research

Using historic data sets, we quantified the degree to which global change over 120 years disrupted plant-pollinator interactions in a temperate forest understory community in Illinois, USA. We found degradation of interaction network structure and function and extirpation of 50% of bee species. Network changes can be attributed to shifts in forb and bee phenologies resulting in temporal mismatches, nonrandom species extinctions, and loss of spatial co-occurrences between extant species in modified landscapes. Quantity and quality of pollination services have declined through time. The historic network showed flexibility in response to disturbance; however, our data suggest that networks will be …

Hematopoietic Stem Cells And Progenitors In Murine Autoimmune Arthritis, Kwadwo Asare Oduro Jr.

All Theses and Dissertations (ETDs)

Although the physiological role of stem cells in generating and maintaining a functional biological system is widely appreciated, very little is known about the behavior of these cells in pathological conditions. If and how these primitive cells are affected by a disease process or may contribute to the disease process has not been adequately explored. We have studied the Hematopoietic System, with particular emphasis on Hematopoietic Stem Cells: HSCs) and Progenitors, in a spontaneous murine autoimmune arthritis model. We found that these mice have a systemic increase in myeloid cells, which correlated with an increased frequency of granulocyte-monocyte progenitors relative …

Dictyostelium Development Shows A Novel Pattern Of Evolutionary Conservation, Xiangjun Tian, Joan E. Strassmann, David C. Queller

Biology Faculty Research

von Baer's law states that early stages of animal development are the most conserved. More recent evidence supports a modified "hourglass" pattern in which an early but somewhat later stage is most conserved. Both patterns have been explained by the relative complexity of either temporal or spatial interactions; the greatest conservation and lowest evolvability occur at the time of the most complex interactions, because these cause larger effects that are harder for selection to alter. This general kind of explanation might apply universally across independent multicellular systems, as supported by the recent finding of the hourglass pattern in plants. We …

Aaron Gillette , Eugenics And The Nature Nurture Debate In The Twentieth Century, Garland E. Allen

Biology Faculty Research

Aaron Gillette, Eugenics and the Nature–Nurture Debate in the Twentieth Century, Palgrave Studies in the History of Science and Technology [2007], digital reprint (New York, NY: Palgrave Macmillan, 2010), pp. ix, 239, index, £18.99, paperback, ISBN: 9780230108455. This book treats an important subject – the history of the nature–nurture debate (focused on the US but with references to European players and movements) – and its implications for current theories of evolutionary psychology.

A New Social Gene In Dictyostelium Discoideum, Chtb, Lorenzo A. Santorelli, Adam Kuspa, Gad Shaulsky, David C. Queller, Joan E. Strassmann

Biology Faculty Research

BACKGROUND:

Competitive social interactions are ubiquitous in nature, but their genetic basis is difficult to determine. Much can be learned from single gene knockouts in a eukaryote microbe. The mutants can be competed with the parent to discern the social impact of that specific gene. Dictyostelium discoideum is a social amoeba that exhibits cooperative behavior in the construction of a multicellular fruiting body. It is a good model organism to study the genetic basis of cooperation since it has a sequenced genome and it is amenable to genetic manipulation. When two strains of D. discoideum are mixed, a cheater strain …

“Culling The Herd”: Eugenics And The Conservation Movement In The United States, 1900–1940, Garland E. Allen

Biology Faculty Research

While from a late twentieth- and early twenty-first century perspective, the ideologies of eugenics (controlled reproduction to eliminate the genetically unfit and promote the reproduction of the genetically fit) and environmental conservation and preservation, may seem incompatible, they were promoted simultaneously by a number of figures in the progressive era in the decades between 1900 and 1950. Common to the two movements were the desire to preserve the ‘‘best’’ in both the germ plasm of the human population and natural environments (including not only natural resources, but also undisturbed nature preserves such as state and national parks and forests). In …

Greater Sexual Reproduction Contributes To Differences In Demography Of Invasive Plants And Their Noninvasive Relatives, Jean H. Burns, Eleanor A. Pardini, Michele R. Schutzenhofer, Y Anny Chung, Katie J. Seidler, Tiffany M. Knight

Biology Faculty Research

An understanding of the demographic processes contributing to invasions would improve our mechanistic understanding of the invasion process and improve the efficiency of prevention and control efforts. However, field comparisons of the demography of invasive and noninvasive species have not previously been conducted. We compared the in situ demography of 17 introduced plant species in St. Louis, Missouri, USA, to contrast the demographic patterns of invasive species with their less invasive relatives across a broad sample of angiosperms. Using herbarium records to estimate spread rates, we found higher maximum spread rates in the landscape for species classified a priori as …

Maternal Depletion Of Piwi, A Component Of The Rnai System, Impacts Heterochromatin Formation In Drosophila, Tingting Gu, Sarah C.R. Elgin

Biology Faculty Research

A persistent question in epigenetics is how heterochromatin is targeted for assembly at specific domains, and how that chromatin state is faithfully transmitted. Stable heterochromatin is necessary to silence transposable elements (TEs) and maintain genome integrity. Both the RNAi system and heterochromatin components HP1 (Swi6) and H3K9me2/3 are required for initial establishment of heterochromatin structures in S. pombe. Here we utilize both loss of function alleles and the newly developed Drosophila melanogaster transgenic shRNA lines to deplete proteins of interest at specific development stages to dissect their roles in heterochromatin assembly in early zygotes and in maintenance of the silencing …

A Bacterial Symbiont Is Converted From An Inedible Producer Of Beneficial Molecules Into Food By A Single Mutation In The Gaca Gene, Pierre Stallforth, Debra A. Brock, Alexandra M. Cantley, Xiangjun Tian, David C. Queller, Joan E. Strassmann, Jon Clardy

Biology Faculty Research

Stable multipartite mutualistic associations require that all partners benefit. We show that a single mutational step is sufficient to turn a symbiotic bacterium from an inedible but host-beneficial secondary metabolite producer into a host food source. The bacteria's host is a "farmer" clone of the social amoeba Dictyostelium discoideum that carries and disperses bacteria during its spore stage. Associated with the farmer are two strains of Pseudomonas fluorescens, only one of which serves as a food source. The other strain produces diffusible small molecules: pyrrolnitrin, a known antifungal agent, and a chromene that potently enhances the farmer's spore production and …

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 Research

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

Biology Faculty Research

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

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 …

A Ranksum Statistics Based Framework To Decipher Transcription Regulation, Iuan-Bor Chen

Arts & Sciences Graduate Student 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

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 …

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 …

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 …

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 …