Biology Commons^™

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 …

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 …

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 …

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.

Identification And Characterization Of A Nacl Responsive Genetic Locus Involved In 2 Survival During Desiccation In Sinorhizobium Meliloti, Jan A.C. Vriezen, Frans J. De Bruijn, Klaus R. Nüsslein

Biological Sciences: Faculty Publications

The Rhizobiaceae are a bacterial family of enormous agricultural importance due to the ability of its members to fix atmospheric nitrogen in an intimate relationship with plants. Their survival as naturally occurring soil bacteria in agricultural soils as well as popular seed inocula is affected directly by drought and salinity. Survival after desiccation in the presence of NaCl is enabled by underlying genetic mechanisms in the model organism Sinorhizobium meliloti 1021. Since salt stress parallels a loss in water activity, the identification of NaCl-responsive loci may identify loci involved in survival during desiccation. This approach enabled identification of the loci …

Lost Branches On The Tree Of Life, Bryan T. Drew, Romina Gazis, Patricia Cabezas, Kristen S. Swithers, Jiabin Deng, Roseana Rodriguez, Laura A. Katz, Keith A. Crandall, David S. Hibbett, Douglas E. Soltis

Biological Sciences: Faculty Publications

No abstract provided.

Failed Species, Innominate Forms, And The Vain Search For Species Limits: Cryptic Diversity In Dusky Salamanders (Desmognathus) Of Eastern Tennessee, Stephen G. Tilley, Joseph Bernardo, Laura A. Katz, Lizmarie López, J. Devon Roll, Renáe L. Eriksen, Justin Kratovil, Noëlle K.J. Bittner, Keith A. Crandall

Biological Sciences: Faculty Publications

Cytochrome B sequences and allozymes reveal complex patterns of molecular variation in dusky salamander (Desmognathus) populations in eastern Tennessee. One group of allozymically distinctive populations, which we refer to as the Sinking Creek form (SCF), combines morphological attributes of Desmognathus fuscus with cytB sequences characteristic of Desmognathus carolinensis. This form is abruptly replaced by D. fuscus just north of Johnson City, TN with no evidence of either sympatry or gene exchange. To the south, allozymic markers indicate a broad zone of admixture with populations characterized by distinct cytB sequences and that may or may not be ultimately referable to Desmognathus …

Rethinking The Composition Of A Rational Antibiotic Arsenal For The 21st Century, Margaret A. Riley, Sandra M. Robinson, Christopher M. Roy, Robert L. Dorit

Biological Sciences: Faculty Publications

The importance of the human microbiome in health may be the single most valuable development in our conception of the microbial world since Pasteur's germ theory of the 1860s. Its implications for our understanding of health and pathogenesis are profound. Coupled with the revolution in diagnostics that we are now witnessing - a revolution that changes medicine from a science of symptoms to a science of causes - we cannot continue to develop antibiotics as we have for the past 80 years. Instead, we need to usher in a new conception of the role of antibiotics in treatment: away from …

The Evolutionary Histories Of Clinical And Environmental Shv Β-Lactamases Are Intertwined, Robert L. Dorit, Christopher M. Roy, Sandra M. Robinson, Margaret A. Riley

Biological Sciences: Faculty Publications

The rise of antibiotic-resistant pathogens focuses our attention on the source of antibiotic resistance genes, on the existence of these genes in environments exposed to little or no antibiotics, and on the relationship between resistance genes found in the clinic and those encountered in non-clinical settings. Here, we address the evolutionary history of a class of resistance genes, the SHV β-lactamases. We focus on bla SHV genes isolated both from clinical and non-clinical sources and show that clinically important resistance determinants arise repeatedly from within a diverse pool of bla SHV genes present in the environment. While our results argue …

Pheromone Exposure Influences Preoptic Arginine Vasotocin Gene Expression And Inhibits Social Approach Behavior In Response To Rivals But Not Potential Mates, Lisa A. Mangiamele, Alex D.T. Keeney, Erin N. D'Agostino, Richmond R. Thompson

Biological Sciences: Faculty Publications

The nonapeptides arginine vasotocin (AVT) and vasopressin mediate a variety of social behaviors in vertebrates. However, the effects of these peptides on behavior can vary considerably both between and within species. AVT, in particular, stimulates aggressive and courtship responses typical of dominant males in several species, although it can also inhibit social interactions in some cases. Such differential effects may depend upon AVT influences within brain circuits that differ among species or between males that adopt alternative reproductive phenotypes and/or upon the differential activation of those circuits in different social contexts. However, to date, very little is known about how …

No Control Genes Required: Bayesian Analysis Of Qrt-Pcr Data., Mikhail V. Matz, Rachel M. Wright, James G. Scott

Biological Sciences: Faculty Publications

Model-based analysis of data from quantitative reverse-transcription PCR (qRT-PCR) is potentially more powerful and versatile than traditional methods. Yet existing model-based approaches cannot properly deal with the higher sampling variances associated with low-abundant targets, nor do they provide a natural way to incorporate assumptions about the stability of control genes directly into the model-fitting process. In our method, raw qPCR data are represented as molecule counts, and described using generalized linear mixed models under Poisson-lognormal error. A Markov Chain Monte Carlo (MCMC) algorithm is used to sample from the joint posterior distribution over all model parameters, thereby estimating the effects …

Morphological Description Of Telaepolella Tubasferens N. G. N. Sp., Isolate Atcc©50593™, A Filose Amoeba In The Gracilipodida, Amoebozoa, Daniel J.G. Lahr, Gabriela M. Kubik, Anastasia L. Gant, Jessica Grant, O. Roger Anderson, Laura A. Katz

Biological Sciences: Faculty Publications

We describe the amoeboid isolate ATCC©50593™ as a new taxon, Telaepolella tubasferens n. g. n. sp. This multinucleated amoeba has filose pseudopods and is superficially similar to members of the vampyrellids (Rhizaria) such as Arachnula impatiens Cienkowski, 1876, which was the original identification upon deposition. However, previous multigene analyses place this taxon within the Gracilipodida Lahr and Katz 2011 in the Amoebozoa. Here, we document the morphology of this organism at multiple life history stages and provide data underlying the description as a new taxon. We demonstrate that T. tubasferens is distinct from Arachnula and other rhizarians (Theratromyxa, Leptophrys) in …

Resistance Is Futile: The Bacteriocin Model For Addressing The Antibiotic Resistance Challenge, Margaret A. Riley, Sandra M. Robinson, Christopher M. Roy, Morgan Dennis, Vivian Liu, Robert Dorit

Biological Sciences: Faculty Publications

Pathogenic bacteria resistant to many or all antibiotics already exist. With the decline in microbiological research at pharmaceutical companies, the high rate at which resistance has evolved and spread has demanded a novel approach to addressing this critical human health issue. In the present paper, we propose a new paradigm in antibiotic discovery and development, one that applies ecological and evolutionary theory to design antimicrobial drugs that are more difficult and/or more costly to resist. In essence, we propose to simply adopt the strategies invented and applied by bacteria for hundreds of millions of years. Our research focuses on bacteriocins, …

Engineered, Harnessed, And Hijacked: Synthetic Uses For Cytoskeletal Systems, Brian S. Goodman, Nathan D. Derr, Samara L. Reck-Peterson

Biological Sciences: Faculty Publications

Synthetic biology re-imagines existing biological systems by designing and constructing new biological parts, devices, and systems. In the arena of cytoskeleton-based transport, synthetic approaches are currently used in two broad ways. First, molecular motors are harnessed for non-physiological functions in cells. Second, transport systems are engineered in vitro to determine the biophysical rules that govern motility. These rules are then applied to synthetic nanotechnological systems. We review recent advances in both of these areas and conclude by discussing future directions in engineering the cytoskeleton and its motors for transport.

Tug-Of-War In Motor Protein Ensembles Revealed With A Programmable Dna Origami Scaffold, N. D. Derr, B. S. Goodman, R. Jungmann, A. E. Leschziner, W. M. Shih, S. L. Reck-Peterson

Biological Sciences: Faculty Publications

Cytoplasmic dynein and kinesin-1 are microtubule-based motors with opposite polarity that transport a wide variety of cargo in eukaryotic cells. Many cellular cargos demonstrate bidirectional movement due to the presence of ensembles of dynein and kinesin, but are ultimately sorted with spatial and temporal precision. To investigate the mechanisms that coordinate motor ensemble behavior, we built a programmable synthetic cargo using three-dimensional DNA origami to which varying numbers of DNA oligonucleotide-linked motors could be attached, allowing for control of motor type, number, spacing, and orientation in vitro. In ensembles of one to seven identical-polarity motors, motor number had minimal affect …

Congruence And Indifference Between Two Molecular Markers For Understanding Oral Evolution In The Marynidae Sensu Lato (Ciliophora, Colpodea), Micah Dunthorn, Laura A. Katz, Thorsten Stoeck, Wilhelm Foissner

Biological Sciences: Faculty Publications

Our understanding of the evolution of oral structures within the Colpodida is confounded by the low number of morphological characters that can be used in constructing hypotheses, and by the low taxon and character sampling in molecular phylogenetic analyses designed to assess these hypotheses. Here we increase character sampling by sequencing the mitochondrial SSU-rDNA locus for three isolates of the Marynidae sensu lato. We show that the inferred mitochondrial and nuclear SSU-rDNA trees, as well as concatenated and constrained analyses, are congruent in not recovering a monophyletic Marynidae. However, due to low node support, the trees are indifferent to whether …

Analyses Of Chromosome Copy Number And Expression Level Of Four Genes In The Ciliate Chilodonella Uncinata Reveal A Complex Pattern That Suggests Epigenetic Regulation, Laure Bellec, Laura A. Katz

Biological Sciences: Faculty Publications

Chilodonella uncinata, like all ciliates, contains two distinct nuclei in every cell: a germline micronucleus and a somatic macronucleus. The macronucleus develops from the zygotic nucleus through a series of chromosomal rearrangements. Macronuclear development in C. uncinata yields a nucleus with highly amplified gene-sized chromosomes. The macronucleus is transcriptionally active during vegetative growth while there is no expression in the micronucleus except during a brief period following conjugation. Gene family evolution in ciliates occurs through complex processes including gene duplication and an alternative processing of scrambled genes. Here we use quantitative PCR to compare relative expression levels of eight genes …