Biology Commons^™

The Effect Of In Vitro Cultivation On The Transcriptome Of Adult Brugia Malayi, Cristina Ballesteros, Lucienne Tritten, Maeghan O'Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew Moorhead, Steven A. Williams, Timothy G. Geary

Biological Sciences: Faculty Publications

Filarial nematodes cause serious and debilitating infections in human populations of tropical countries, contributing to an entrenched cycle of poverty. Only one human filarial parasite, Brugia malayi, can be maintained in rodents in the laboratory setting. It has been a widely used model organism in experiments that employ culture systems, the impact of which on the worms is unknown.

The Effect Of In Vitro Cultivation On The Transcriptome Of Adult Brugia Malayi, Cristina Ballesteros, Lucienne Tritten, Maeghan O’Neill, Erica Burkman, Weam I. Zaky, Jianguo Xia, Andrew Moorhead, Steven A. Williams, Timothy G. Geary

Biological Sciences: Faculty Publications

Infections with filarial worms cause serious physical impairment and affect tens of millions of people in tropical and subtropical countries. To better understand the biology and phar- macology of these parasites, Brugia malayi is often used as a model. This parasite can be maintained in the laboratory in Mongolian jirds, enabling researchers to test drugs in vivoand in vitro, among other studies. The effects of removing worms from their hosts and cul- turing them may affect many aspects of their physiology, including response to drugs, but the extent to which the worms undergo changes during culture has remained unknown. Using …

Consequences Of Elevated Salt Concentrations Expression Profiles In The Rhizobium S. Meliloti 1021 Likely Involved In Heat And Desiccation Stress, Jan A.C. Vriezen, Caroline M. Finn

Biological Sciences: Faculty Publications

No abstract provided.

Appearance Of Membrane Compromised, Viable But Not Culturable And Culturable Rhizobial Cells As A Consequence Of Desiccation, Jan A.C. Vriezen, Frans J. De Bruijn

Biological Sciences: Faculty Publications

For agricultural purposes, drought related stresses negatively affect the Rhizobiaceae in at least three ways. Firstly, rhizobial populations are affected by desertification of agricultural soils. Secondly, the quality of dry-base inocula, also called formula, is negatively affected by a drying step, and thirdly, rhizosphere bacteria protect crop-plants against drought. Although survival of cultivatable bacteria has been studied intensively in dry-base seed inocula and in-vitro, thus far research has only marginally addressed the bacterial cell, its cellular structures and physiology. Many questions remain regarding the sensing of and physiological response of rhizobia to desiccation. This review will focus on the three …

Are Microbes Fundamentally Different Than Macroorganisms? Convergence And A Possible Case For Neutral Phenotypic Evolution In Testate Amoeba (Amoebozoa: Arcellinida), Angela M. Oliverio, Daniel J.G. Lahr, Jessica Grant, Laura A. Katz

Biological Sciences: Faculty Publications

This study reveals extensive phenotypic convergence based on the non-monophyly of genera and morphospecies of testate (shelled) amoebae. Using two independent markers, small subunit ribosomal DNA (ssu-rDNA) and mitochondrial cytochrome oxidase I (COI), we demonstrate discordance between morphology and molecules for ‘core Nebela’ species (Arcellinida; Amoebozoa). Prior work using just a single locus, ssu-rDNA, also supported the non-monophyly of the genera Hyalosphenia and Nebela as well as for several morphospecies within these genera. Here, we obtained COI gene sequences of 59 specimens from seven morphospecies and ssu-rDNA gene sequences of 50 specimens from six morphospecies of hyalosphenids. Our analyses …

An Epigenetic Toolkit Allows For Diverse Genome Architectures In Eukaryotes, Xyrus X. Maurer-Alcalá, Laura A. Katz

Biological Sciences: Faculty Publications

Genome architecture varies considerably among eukaryotes in terms of both size and structure (e.g. distribution of sequences within the genome, elimination of DNA during formation of somatic nuclei). The diversity in eukaryotic genome architectures and the dynamic processes are only possible due to the well-developed epigenetic toolkit, which probably existed in the Last Eukaryotic Common Ancestor (LECA). This toolkit may have arisen as a means of navigating the genomic conflict that arose from the expansion of transposable elements within the ancestral eukaryotic genome. This toolkit has been coopted to support the dynamic nature of genomes in lineages across the eukaryotic …

Synthesis Of Phylogeny And Taxonomy Into A Comprehensive Tree Of Life, Cody E. Hinchliff, Stephen A. Smith, James F. Allman, J. Gordon Burleigh, Ruchi Chaudhary, Lyndon M. Coghill, Keith A. Crandall, Jiabin Deng, Bryan T. Drew, Romina Gazis, Karl Gude, David S. Hibbett, Laura A. Katz, H. Dail Laughinghouse Iv, Emily Jane Mctavish, Peter E. Midford, Christopher L. Owen, Richard H. Ree, Jonathan A. Rees, Douglas E. Soltis, Tiffani Williams, Karen A. Cranston

Biological Sciences: Faculty Publications

Reconstructing the phylogenetic relationships that unite all line- ages (the tree of life) is a grand challenge. The paucity of homologous character data across disparately related lineages currently renders direct phylogenetic inference untenable. To reconstruct a comprehensive tree of life, we therefore synthesized published phylogenies, together with taxonomic classifications for taxa never incorporated into a phylogeny. We present a draft tree containing 2.3 million tips— the Open Tree of Life. Realization of this tree required the assembly of two additional community resources: (i) a comprehensive global reference taxonomy and (ii) a database of published phylogenetic trees mapped to this taxonomy. …

Recent Events Dominate Interdomain Lateral Gene Transfers Between Prokaryotes And Eukaryotes And, With The Exception Of Endosymbiotic Gene Transfers, Few Ancient Transfer Events Persist, Laura A. Katz

Biological Sciences: Faculty Publications

While there is compelling evidence for the impact of endosymbiotic gene transfer (EGT; transfer from either mitochondrion or chloroplast to the nucleus) on genome evolution in eukaryotes, the role of interdomain transfer from bacteria and/or archaea (i.e. prokaryotes) is less clear. Lateral gene transfers (LGTs) have been argued to be potential sources of phylogenetic information, particularly for reconstructing deep nodes that are difficult to recover with traditional phylogenetic methods. We sought to identify interdomain LGTs by using a phylogenomic pipeline that generated 13 465 single gene trees and included up to 487 eukaryotes, 303 bacteria and 118 archaea. Our goals …

Gene Expression Associated With White Syndromes In A Reef Building Coral, Acropora Hyacinthus, Rachel M. Wright, Galina V. Aglyamova, Eli Meyer, Mikhail V. Matz

Biological Sciences: Faculty Publications

Background: Corals are capable of launching diverse immune defenses at the site of direct contact with pathogens, but the molecular mechanisms of this activity and the colony-wide effects of such stressors remain poorly understood. Here we compared gene expression profiles in eight healthy Acropora hyacinthus colonies against eight colonies exhibiting tissue loss commonly associated with white syndromes, all collected from a natural reef environment near Palau. Two types of tissues were sampled from diseased corals: visibly affected and apparently healthy. Results: Tag-based RNA-Seq followed by weighted gene co-expression network analysis identified groups of co-regulated differentially expressed genes between all health …

Analyses Of Alternatively Processed Genes In Ciliates Provide Insights Into The Origins Of Scrambled Genomes And May Provide A Mechanism For Speciation, Feng Gao, Scott W. Roy, Laura A. Katz

Biological Sciences: Faculty Publications

Chromosome rearrangements occur in a variety of eukaryotic life cycles, including during the development of the somatic macronuclear genome in ciliates. Previous work on the phyllopharyngean ciliate Chilodonella uncinata revealed that macronuclear β-tubulin and protein kinase gene families share alternatively processed germ line segments nested within divergent regions. To study genome evolution in this ciliate further, we characterized two additional alternatively processed gene families from two cryptic species of the ciliate morphospecies C. uncinata: those encoding histidine acid phosphatase protein (Hap) and leishmanolysin family protein (Lei). Analyses of the macronuclear Hap and Lei sequences reveal that each gene family consists …

Sapocribrum Chincoteaguense N. Gen. N. Sp.: A Small, Scale-Bearing Amoebozoan With Flabellinid Affinities, Daniel J.G. Lahr, Jessica Grant, Robert Molestina, Laura A. Katz, O. Roger Anderson

Biological Sciences: Faculty Publications

The isolate American Type Culture Collection (ATCC)^® 50979^™ is a small amoebozoan whose actin gene was previously characterized, but did not allow a stable phylogenetic placement. This isolate was originally mis-identified upon deposition, and subsequently mis-illustrated in a recent publication. Here, we provide both a detailed morphological description as well as additional molecular analyses in order to clarify the isolate's phylogenetic relationships. The amoeba is minute (less than 5 μm), and presents the behavior of staying in a fixed location, while emitting one or two thin pseudopods. Transmission electron microscopy reveals that the cell is covered in a …

Osr1 Is Required For Podocyte Development Downstream Of Wt1a, Ritu Tomar, Sudha P. Mudumana, Narendra Pathak, Neil A. Hukriede, Iain A. Drummond

Neuroscience: Faculty Publications

Odd-skipped related 1 (Osr1) encodes a zinc finger transcription factor required for kidney development. Osr1 deficiency in mice results in metanephric kidney agenesis, whereas knockdown or mutation studies in zebrafish revealed that pronephric nephrons require osr1 for proximal tubule and podocyte development. osr1-deficient pronephric podocyte progenitors express the Wilms' tumor suppressor wt1a but do not undergo glomerular morphogenesis or express the foot process junctional markers nephrin and podocin. The function of osr1 in podocyte differentiation remains unclear, however. Here, we found by double fluorescence in situ hybridization that podocyte progenitors coexpress osr1 and wt1a. Knockdown of wt1a disrupted podocyte differentiation …

How Discordant Morphological And Molecular Evolution Among Microorganisms Can Revise Our Notions Of Biodiversity On Earth, Daniel J.G. Lahr, Haywood Dail Laughinghouse, Angela M. Oliverio, Feng Gao, Laura A. Katz

Biological Sciences: Faculty Publications

Microscopy has revealed tremendous diversity of bacterial and eukaryotic forms. Recent molecular analyses show discordance in estimates of biodiversity between morphological and molecular analyses. Moreover, phylogenetic analyses of the diversity of microbial forms reveal evidence of convergence at scales as deep as interdomain: morphologies shared between bacteria and eukaryotes. Here, we highlight examples of such discordance, focusing on exemplary lineages such as testate amoebae, ciliates, and cyanobacteria. These have long histories of morphological study, enabling deeper analyses on both the molecular and morphological sides. We discuss examples in two main categories: (i) morphologically identical (or highly similar) individuals that are …

Phylogenomic Study Indicates Widespread Lateral Gene Transfer In Entamoeba And Suggests A Past Intimate Relationship With Parabasalids, Jessica R. Grant, Laura A. Katz

Biological Sciences: Faculty Publications

Lateral gene transfer (LGT) has impacted the evolutionary history of eukaryotes, though to a lesser extent than in bacteria and archaea. Detecting LGT and distinguishing it from single gene tree artifacts is difficult, particularly when considering very ancient events (i.e., over hundreds of millions of years). Here, we use two independent lines of evidence - A taxon-rich phylogenetic approach and an assessment of the patterns of gene presence/absence- to evaluate the extent of LGT in the parasitic amoebozoan genus Entamoeba. Previous work has suggested that a number of genes in the genome of Entamoeba spp. were acquired by LGT. Our …

Molecular Xenomonitoring Using Mosquitoes To Map Lymphatic Filariasis After Mass Drug Administration In American Samoa, Mark A. Schmaedick, Amanda L. Koppel, Nils Pilotte, Melissa Torres, Steven A. Williams, Stephen L. Dobson, Patrick J. Lammie, Kimberly Y. Won

Biological Sciences: Faculty Publications

Background: Mass drug administration (MDA) programs have dramatically reduced lymphatic filariasis (LF) incidence in many areas around the globe, including American Samoa. As infection rates decline and MDA programs end, efficient and sensitive methods for detecting infections are needed to monitor for recrudescence. Molecular methods, collectively termed ‘molecular xenomonitoring,’ can identify parasite DNA or RNA in human blood-feeding mosquitoes. We tested mosquitoes trapped throughout the inhabited islands of American Samoa to identify areas of possible continuing LF transmission after completion of MDA.

Methodology/Principle Findings: Mosquitoes were collected using BG Sentinel traps from most of the villages on American Samoa’s largest …

The Geomagnetic Environment In Which Sea Turtle Eggs Incubate Affects Subsequent Magnetic Navigation Behaviour Of Hatchlings, Matthew J. Fuxjager, Kyla R. Davidoff, Lisa A. Mangiamele, Kenneth J. Lohmann

Biological Sciences: Faculty Publications

Loggerhead sea turtle hatchlings (Caretta caretta) use regional magnetic fields as open-ocean navigational markers during trans-oceanic migrations. Little is known, however, about the ontogeny of this behaviour. As a first step towards investigating whether the magnetic environment in which hatchlings develop affects subsequent magnetic orientation behaviour, eggs deposited by nesting female loggerheads were permitted to develop in situ either in the natural ambient magnetic field or in a magnetic field distorted by magnets placed around the nest. In orientation experiments, hatchlings that developed in the normal ambient field oriented approximately south when exposed to a field that exists near the …

Cytoplasmic Carboxypeptidase 5 Regulates Tubulin Glutamylation And Zebrafish Cilia Formation And Function, Narendra Pathak, Christina A. Austin-Tse, Yan Liu, Aleksandr Vasilyev, Iain A. Drummond

Neuroscience: Faculty Publications

Glutamylation is a functionally important tubulin posttranslational modification enriched on stable microtubules of neuronal axons, mitotic spindles, centrioles, and cilia. In vertebrates, balanced activities of tubulin glutamyl ligase and cytoplasmic carboxypeptidase deglutamylase enzymes maintain organelle- and cell type-specific tubulin glutamylation pat terns. Tubulin glutamylation in cilia is regulated via restricted subcellular localization or ex pression of tubulin glutamyl ligases (ttlls) and nonenzymatic proteins, including the zebrafish TPR repeat protein Fleer/Ift70. Here we analyze the expression patterns of ccp deglutamy lase genes during zebrafish development and the effects of ccp gene knockdown on cilia formation, morphology, and tubulin glutamylation. The deglutamylases …

Climate Change And Forest Herbs Of Temperate Deciduous Forests, Jesse Bellemare, David A. Moeller

Biological Sciences: Faculty Publications

This chapter reviews what is known about the long-term, large-scale range dynamics of forest herbs in response to past climate change. It presents a new biogeographic analysis investigating how contemporary distribution and diversity patterns among a subset of rare forest herbs may relate to these past climate dynamics. It also discusses how forest herb species may be affected by contemporary climate change and considers options for species conservation.

Shelter-Building Behavior And Natural History Of Two Pyralid Caterpillars Feeding On Piper Stipulaceum, Mariana Abarca, Karina Boege, Alejandro Zaldívar-Riverón

Biological Sciences: Faculty Publications

Shelter-building behavior by caterpillars provides a mechanism of defense against predators, microenvironment enhancement, and in some cases nutritional benefits. This study provides a detailed description of the life cycle and shelter-building process of caterpillars, and identifies constraints and factors influencing this adaptive behavior in Lepidomys n. sp. near proclea Druce (Pyralidae: Chrysauginae), a tropical dry forest pyralid. Five macroscopic larval instars were detected during the life cycle, and activities performed during shelter-building were categorized and timed. Caterpillar predators were identified, and 20% of all collected larvae died due to attack by parasitoid wasps. Shelter-building behavior was found to be constrained …

Kif11 Dependent Cell Cycle Progression In Radial Glial Cells Is Required For Proper Neurogenesis In The Zebrafish Neural Tube, Kimberly Johnson, Chelsea Moriarty, Nessy Tania, Alissa Ortman, Kristina Dipietrantonio, Brittany Edens, Jean Eisenman, Deborah Ok, Sarah Krikorian, Jessica Barragan, Christophe Golé, Michael J.F. Barresi

Mathematics Sciences: Faculty Publications

Radial glia serve as the resident neural stem cells in the embryonic vertebrate nervous system, and their proliferation must be tightly regulated to generate the correct number of neuronal and glial cell progeny in the neural tube. During a forward genetic screen, we recently identified a zebrafish mutant in the kif11 loci that displayed a significant increase in radial glial cell bodies at the ventricular zone of the spinal cord. Kif11, also known as Eg5, is a kinesin-related, plus-end directed motor protein responsible for stabilizing and separating the bipolar mitotic spindle. We show here that Gfap+ radial glial cells express …

Complete Genome Sequence Of Burkholderia Phymatum Stm815t , A Broad Host Range And Efficient Nitrogen-Fixing Symbiont Of Mimosa Species, Lionel Moulin, Agnieszka Klonowska, Bournaud Caroline, Kristina Booth, Jan A.C. Vriezen, Rémy Melkonian, Euan K. James, Peter W. Young, Gilles Bena, Loren Hauser, Miriam Land, Nikos Kyrpides, David Bruce, Patrick Chain, Alex Copeland, Sam Pitluck, Tanja Woyke, Michelle Lizotte-Waniewski, Jim Bristow, Margaret Riley

Biological Sciences: Faculty Publications

Burkholderia phymatum is a soil bacterium able to develop a nitrogen-fixing symbiosis with species of the legume genus Mimosa, and is frequently found associated specifically with Mimosa pudica. The type strain of the species, STM 815T , was isolated from a root nodule in French Guiana in 2000. The strain is an aerobic, motile, non-spore forming, Gram-negative rod, and is a highly competitive strain for nodulation compared to other Mimosa symbionts, as it also nodulates a broad range of other legume genera and species. The 8,676,562 bp genome is composed of two chromosomes (3,479,187 and 2,697,374 bp), a …

Nanochromosome Copy Number Does Not Correlate With Rna Levels Though Patterns Are Conserved Between Strains Of The Ciliate Morphospecies Chilodonella Uncinata, Jie Huang, Laura A. Katz

Biological Sciences: Faculty Publications

In some ciliates, extensive genome fragmentation leads to a macronucleus (i.e. somatic nucleus) containing gene-sized chromosomes that vary in copy number. Yet the relationship between copy number and expression level is not well understood as previous work has shown a variety of patterns. For example, nanochromosome copy numbers are positively correlated to mRNA levels in spirotrichous ciliates, while one study of Chilodonella uncinata suggested that they were inversely correlated. To study further copy number and expression levels in C. uncinata, we analyzed 11 members in five gene families (SSU-rDNA, actin, alpha-tubulin, histidine acid phosphatase family protein and a protein kinase …

The Marine Microbial Eukaryote Transcriptome Sequencing Project (Mmetsp): Illuminating The Functional Diversity Of Eukaryotic Life In The Oceans Through Transcriptome Sequencing, Patrick J. Keeling, Fabien Burki, Heather M. Wilcox, Bassem Allam, Eric E. Allen, Linda A. Amaral-Zettler, E. Virginia Armbrust, John M. Archibald, Arvind K. Bharti, Callum J. Bell, Bank Beszteri, Kay D. Bidle, Connor T. Cameron, Lisa Campbell, David A. Caron, Rose Ann Cattolico, Jackie L. Collier, Kathryn Coyne, Simon K. Davy, Phillipe Deschamps, Sonya T. Dyhrman, Bente Edvardsen, Ruth D. Gates, Christopher J. Gobler, Spencer J. Greenwood, Stephanie M. Guida, Jennifer L. Jacobi, Kjetill S. Jakobsen, Erick R. James, Bethany Jenkins, Uwe John, Matthew D. Johnson, Andrew R. Juhl, Anja Kamp, Laura A. Katz

Biological Sciences: Faculty Publications

No abstract provided.

Phylogenomic Analyses Support The Bifurcation Of Ciliates Into Two Major Clades That Differ In Properties Of Nuclear Division, Feng Gao, Laura A. Katz

Biological Sciences: Faculty Publications

Ciliates are a diverse assemblage of eukaryotes that have been the source of many discoveries including self-splicing RNAs, telomeres and trans-splicing. While analyses of ciliate morphology have given rise to robust hypotheses on relatively shallow level relationships, the deeper evolutionary history of ciliates is largely unknown. This is in part because studies to date have focused on only a single locus, small subunit ribosomal DNA (SSU-rDNA). In the present study, we use a taxon-rich strategy based on multiple loci from GenBank and recently completed transcriptomes to assess deep phylogenetic relationships among ciliates. Our phylogenomic data set includes up to 537 …

Genome Structure Drives Patterns Of Gene Family Evolution In Ciliates, A Case Study Using Chilodonella Uncinata (Protista, Ciliophora, Phyllopharyngea), Feng Gao, Weibo Song, Laura A. Katz

Biological Sciences: Faculty Publications

In most lineages, diversity among gene family members results from gene duplication followed by sequence divergence. Because of the genome rearrangements during the development of somatic nuclei, gene family evolution in ciliates involves more complex processes. Previous work on the ciliate Chilodonella uncinata revealed that macronuclear β-tubulin gene family members are generated by alternative processing, in which germline regions are alternatively used in multiple macronuclear chromosomes. To further study genome evolution in this ciliate, we analyzed its transcriptome and found that (1) alternative processing is extensive among gene families; and (2) such gene families are likely to be C. uncinata …

The Dynamic Nature Of Genomes Across The Tree Of Life, Angela M. Oliverio, Laura A. Katz

Biological Sciences: Faculty Publications

Genomes are dynamic in lineages across the tree of life. Among bacteria and archaea, for example, DNA content varies through out life cycles, and nonbinary cell division in diverse lineages indicates the need for coordination of the inheritance of genomes. These observations contrast with the textbook view that bacterial and archaeal genomes are monoploid (i.e., single copied) and fixed both within species and throughout an individual's lifetime. Here, we synthesize information on three aspects of dynamic genomes from exemplars representing a diverse array of bacterial and archaeal lineages: 1) ploidy level variation, 2) epigenetic mechanisms, and 3) life cycle variation. …

Characterization Of The Life Cycle And Heteromeric Nature Of The Macronucleus Of The Ciliate Chilodonella Uncinata Using Fuorescence Microscopy, Laure Bellec, Xyrus X. Maurer-Alcala, Laura A. Katz

Biological Sciences: Faculty Publications

Only a limited number of studies exist on the life cycles of nonmodel ciliates such as Chilodonella uncinata (Cl: Phyllopharyngea). The handful of papers on this taxon indicate the presence of a heteromeric macronucleus, marked by separate DNA-rich and DNA-poor regions. Here, we study the life cycle of C. uncinata using confocal laser scanning microscopy with 4′,6-diamidino-2- phenylindole staining, which allows us to differentiate nuclear dynamics of the micronucleus and the macronucleus during life-cycle stages. We photo-documented various stages and confirmed aspects of the development of the new macronucleus previously characterized by electron microscopy. We further reveal the heteromeric structure …

Time For T? Immunoinformatics Addresses Vaccine Design For Neglected Tropical And Emerging Infectious Diseases, Frances E. Terry, Leonard Moise, Rebecca F. Martin, Melissa Torres, Nils Pilotte, Steven A. Williams, Anne S. De Groot

Biological Sciences: Faculty Publications

Vaccines have been invaluable for global health, saving lives and reducing healthcare costs, while also raising the quality of human life. However, newly emerging infectious diseases (EID) and more well-established tropical disease pathogens present complex challenges to vaccine developers; in particular, neglected tropical diseases, which are most prevalent among the world's poorest, include many pathogens with large sizes, multistage life cycles and a variety of nonhuman vectors. EID such as MERS-CoV and H7N9 are highly pathogenic for humans. For many of these pathogens, while their genomes are available, immune correlates of protection are currently unknown. These complexities make developing vaccines …

Cabassous Unicinctus (Cingulata: Dasypodidae), Virginia Hayssen

Biological Sciences: Faculty Publications

Cabassous unicinctus (southern naked-tailed armadillo) is a nocturnal, solitary, fossorial myrmecophage that ranges east of the Andes across the central lowlands of South America. It occupies a wide range of habitats including grassland, rain forest, cultivated pastures, flooded grasslands, forest patches, disturbed habitats, and gallery forests. C. unicinctus is listed as "Least Concern" by the International Union for Conservation of Nature and Natural Resources.

Cabassous Chacoensis (Cingulata: Dasypodidae), Virginia Hayssen

Biological Sciences: Faculty Publications

Cabassous chacoensis (Chacoan naked-tailed armadillo) is a little-studied, primarily fossorial armadillo endemic to xeric parts of the Gran Chaco in western Paraguay and northern Argentina. C. chacoensis is listed as "Near Threatened" by the International Union for Conservation of Nature and Natural Resources.