Motility, Mixing, and Multicellularity
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Pulse Generation in the Quorum Machinery of Pseudomonas Aeruginosa
This is a repository copy of Pulse generation in the quorum machinery of Pseudomonas aeruginosa. White Rose Research Online URL for this paper: https://eprints.whiterose.ac.uk/116745/ Version: Published Version Article: Alfiniyah, Cicik Alfiniyah, Bees, Martin Alan and Wood, Andrew James orcid.org/0000- 0002-6119-852X (2017) Pulse generation in the quorum machinery of Pseudomonas aeruginosa. Bulletin of Mathematical Biology. pp. 1360-1389. ISSN 1522-9602 https://doi.org/10.1007/s11538-017-0288-z Reuse This article is distributed under the terms of the Creative Commons Attribution (CC BY) licence. This licence allows you to distribute, remix, tweak, and build upon the work, even commercially, as long as you credit the authors for the original work. More information and the full terms of the licence here: https://creativecommons.org/licenses/ Takedown If you consider content in White Rose Research Online to be in breach of UK law, please notify us by emailing [email protected] including the URL of the record and the reason for the withdrawal request. [email protected] https://eprints.whiterose.ac.uk/ Bull Math Biol (2017) 79:1360–1389 DOI 10.1007/s11538-017-0288-z ORIGINAL ARTICLE Pulse Generation in the Quorum Machinery of Pseudomonas aeruginosa Cicik Alfiniyah1,2 · Martin A. Bees1 · A. Jamie Wood1,3 Received: 28 September 2016 / Accepted: 3 May 2017 / Published online: 19 May 2017 © The Author(s) 2017. This article is an open access publication Abstract Pseudomonas aeruginosa is a Gram-negative bacterium that is responsible for a wide range of infections in humans. -
Zygote Germination in Pleodorina Starrii (Volvocaceae, Chlorophyta)*
Biologia 63/6: 778—780, 2008 Section Botany DOI: 10.2478/s11756-008-0098-8 Zygote germination in Pleodorina starrii (Volvocaceae, Chlorophyta)* Hisayoshi Nozaki Department of Biological Sciences, Graduate School of Science, University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033, Japan; e-mail: [email protected] Abstract: Zygote germination of the anisogamous/oogamous colonial green flagellate Pleodorina starrii was observed. After the zygotes were transferred to the usual, illuminated conditions from the dark treatment on the agar plate, they began to germinate. The germinating zygotes gave rise to one or two viable biflagellate gone cells. This type of zygote germination is rare in the colonial Volvocales and may characterize a certain lineage within the anisogamous/oogamous members of the colonial Volvocales. Key words: Chlorophyta; Volvocales; Volvocaceae; Pleodorina starrii; morphology; zygote germination Introduction packet formation, conjugation between male and female ga- metes and zygote maturation occurred. Mature zygotes were transferred to 1% agar plates (AF-6 medium, Kasai et al. During our research of the male specific “OTOKOGI” ◦ (PlestMID) gene in the anisogamous/oogamous colo- 2004), and put into darkness for 1–3 months at 20–25 C. nial volvocalean Pleodorina starrii (Nozaki et al. After the dark treatment, the zygotes were transferred to the liquid AF-6 medium under 14:10 h LD and 20–25 ◦C. 2006a, Nozaki 2008) two heterothallic strains (2000- Light microscopy was carried out using an OLYMPUS BX60 602-P14female and 2000-602-P15male) of P. starrii microscope (KS OLYMPUS, Tokyo, Japan), equipped with were used. These two strains were established in June Nomarski interference optics. -
Subtilase Sprp Exerts Pleiotropic Effects in Pseudomonas Aeruginosa
ORIGINAL RESEARCH Subtilase SprP exerts pleiotropic effects in Pseudomonas aeruginosa Alexander Pelzer1, Tino Polen2, Horst Funken1, Frank Rosenau3, Susanne Wilhelm1, Michael Bott2 & Karl-Erich Jaeger1 1Institute of Molecular Enzyme Technology, Research Centre Juelich, Heinrich-Heine-University Duesseldorf, D-52426 Juelich, Germany 2Institut of Bio- und Geosciences IBG-1: Biotechnology, Research Centre Juelich, D-52426 Juelich, Germany 3Institute of Pharmaceutical Biotechnology, Ulm-University, Albert-Einstein-Allee 11, D-89069 Ulm, Germany Keywords Abstract Biofilm, microarray, motility, orf PA1242, protease, Pseudomonas aeruginosa, The open reading frame PA1242 in the genome of Pseudomonas aeruginosa Pyoverdine. PAO1 encodes a putative protease belonging to the peptidase S8 family of sub- tilases. The respective enzyme termed SprP consists of an N-terminal signal Correspondence peptide and a so-called S8 domain linked by a domain of unknown function Karl-Erich Jaeger, Institute of Molecular (DUF). Presumably, this DUF domain defines a discrete class of Pseudomonas Enzyme Technology, Heinrich-Heine- proteins as homologous domains can be identified almost exclusively in pro- University Duesseldorf, Research Centre Juelich, D-52426 Juelich, Germany. teins of the genus Pseudomonas. The sprP gene was expressed in Escherichia coli Δ Tel: (+49)-2461-61-3716; Fax: (+49)-2461-61- and proteolytic activity was demonstrated. A P. aeruginosa sprP mutant was 2490; E-mail: [email protected] constructed and its gene expression pattern compared to the wild-type strain by genome microarray analysis revealing altered expression levels of 218 genes. Funding Information Apparently, SprP is involved in regulation of a variety of different cellular pro- 2021 As a member of the CLIB -Graduate cesses in P. -
JUDD W.S. Et. Al. (2002) Plant Systematics: a Phylogenetic Approach. Chapter 7. an Overview of Green
UNCORRECTED PAGE PROOFS An Overview of Green Plant Phylogeny he word plant is commonly used to refer to any auto- trophic eukaryotic organism capable of converting light energy into chemical energy via the process of photosynthe- sis. More specifically, these organisms produce carbohydrates from carbon dioxide and water in the presence of chlorophyll inside of organelles called chloroplasts. Sometimes the term plant is extended to include autotrophic prokaryotic forms, especially the (eu)bacterial lineage known as the cyanobacteria (or blue- green algae). Many traditional botany textbooks even include the fungi, which differ dramatically in being heterotrophic eukaryotic organisms that enzymatically break down living or dead organic material and then absorb the simpler products. Fungi appear to be more closely related to animals, another lineage of heterotrophs characterized by eating other organisms and digesting them inter- nally. In this chapter we first briefly discuss the origin and evolution of several separately evolved plant lineages, both to acquaint you with these important branches of the tree of life and to help put the green plant lineage in broad phylogenetic perspective. We then focus attention on the evolution of green plants, emphasizing sev- eral critical transitions. Specifically, we concentrate on the origins of land plants (embryophytes), of vascular plants (tracheophytes), of 1 UNCORRECTED PAGE PROOFS 2 CHAPTER SEVEN seed plants (spermatophytes), and of flowering plants dons.” In some cases it is possible to abandon such (angiosperms). names entirely, but in others it is tempting to retain Although knowledge of fossil plants is critical to a them, either as common names for certain forms of orga- deep understanding of each of these shifts and some key nization (e.g., the “bryophytic” life cycle), or to refer to a fossils are mentioned, much of our discussion focuses on clade (e.g., applying “gymnosperms” to a hypothesized extant groups. -
Lateral Gene Transfer of Anion-Conducting Channelrhodopsins Between Green Algae and Giant Viruses
bioRxiv preprint doi: https://doi.org/10.1101/2020.04.15.042127; this version posted April 23, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 5 Lateral gene transfer of anion-conducting channelrhodopsins between green algae and giant viruses Andrey Rozenberg 1,5, Johannes Oppermann 2,5, Jonas Wietek 2,3, Rodrigo Gaston Fernandez Lahore 2, Ruth-Anne Sandaa 4, Gunnar Bratbak 4, Peter Hegemann 2,6, and Oded 10 Béjà 1,6 1Faculty of Biology, Technion - Israel Institute of Technology, Haifa 32000, Israel. 2Institute for Biology, Experimental Biophysics, Humboldt-Universität zu Berlin, Invalidenstraße 42, Berlin 10115, Germany. 3Present address: Department of Neurobiology, Weizmann 15 Institute of Science, Rehovot 7610001, Israel. 4Department of Biological Sciences, University of Bergen, N-5020 Bergen, Norway. 5These authors contributed equally: Andrey Rozenberg, Johannes Oppermann. 6These authors jointly supervised this work: Peter Hegemann, Oded Béjà. e-mail: [email protected] ; [email protected] 20 ABSTRACT Channelrhodopsins (ChRs) are algal light-gated ion channels widely used as optogenetic tools for manipulating neuronal activity 1,2. Four ChR families are currently known. Green algal 3–5 and cryptophyte 6 cation-conducting ChRs (CCRs), cryptophyte anion-conducting ChRs (ACRs) 7, and the MerMAID ChRs 8. Here we 25 report the discovery of a new family of phylogenetically distinct ChRs encoded by marine giant viruses and acquired from their unicellular green algal prasinophyte hosts. -
Social Behaviour in Microorganisms 13
13 Social behaviour in microorganisms Kevin R. Foster OVERVIEW Sociobiology has come a long way. We now have Many species do all of this in surface-attached a solid base of evolutionary theory supported communities, known as biofilms, in which the by a myriad of empirical tests. It is perhaps less diversity of species and interactions reaches appreciated, however, that first discussions of bewildering heights. Grouping can even involve social behaviour and evolution in Darwin’s day differentiation and development, as in the spec- drew upon single-celled organisms. Since then, tacular multicellular escape responses of slime microbes have received short shrift, and their moulds and myxobacteria. Like any society, how- full spectrum of sociality has only recently come ever, microbes face conflict, and most groups to light. Almost everything that a microorgan- will involve instances of both cooperation and ism does has social consequences; simply divid- competition among their members. And, as in ing can consume another’s resources. Microbes any society, microbial conflicts are mediated by also secrete a wide range of products that affect three key processes: constraints on rebellion, others, including digestive enzymes, toxins, mol- coercion that enforces compliance, and kinship ecules for communication and DNA that allows whereby cells direct altruistic aid towards clone- genes to mix both within and among species. mates. 13.1 Introduction indeed sociology, microbes have featured in descrip- tions of social life. Prominent among these are the We must be prepared to learn some day, from the students writings of Herbert Spencer, the social philosopher of microscopical pond-life, facts of unconscious mutual sup- who coined the term survival of the fi ttest in the wake port, even from the life of micro-organisms. -
The Genome of Prasinoderma Coloniale Unveils the Existence of a Third Phylum Within Green Plants
Downloaded from orbit.dtu.dk on: Oct 10, 2021 The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants Li, Linzhou; Wang, Sibo; Wang, Hongli; Sahu, Sunil Kumar; Marin, Birger; Li, Haoyuan; Xu, Yan; Liang, Hongping; Li, Zhen; Cheng, Shifeng Total number of authors: 24 Published in: Nature Ecology & Evolution Link to article, DOI: 10.1038/s41559-020-1221-7 Publication date: 2020 Document Version Publisher's PDF, also known as Version of record Link back to DTU Orbit Citation (APA): Li, L., Wang, S., Wang, H., Sahu, S. K., Marin, B., Li, H., Xu, Y., Liang, H., Li, Z., Cheng, S., Reder, T., Çebi, Z., Wittek, S., Petersen, M., Melkonian, B., Du, H., Yang, H., Wang, J., Wong, G. K. S., ... Liu, H. (2020). The genome of Prasinoderma coloniale unveils the existence of a third phylum within green plants. Nature Ecology & Evolution, 4, 1220-1231. https://doi.org/10.1038/s41559-020-1221-7 General rights Copyright and moral rights for the publications made accessible in the public portal are retained by the authors and/or other copyright owners and it is a condition of accessing publications that users recognise and abide by the legal requirements associated with these rights. Users may download and print one copy of any publication from the public portal for the purpose of private study or research. You may not further distribute the material or use it for any profit-making activity or commercial gain You may freely distribute the URL identifying the publication in the public portal If you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediately and investigate your claim. -
Phylogenetic Analysis of ''Volvocacae'
Phylogenetic analysis of ‘‘Volvocacae’’ for comparative genetic studies Annette W. Coleman† Division of Biology and Medicine, Brown University, Providence, RI 02912 Edited by Elisabeth Gantt, University of Maryland, College Park, MD, and approved September 28, 1999 (received for review June 30, 1999) Sequence analysis based on multiple isolates representing essen- most of those obtained previously with data for other DNA tially all genera and species of the classic family Volvocaeae has regions in identifying major clades and their relationships. clarified their phylogenetic relationships. Cloned internal tran- However, the expanded taxonomic coverage revealed additional scribed spacer sequences (ITS-1 and ITS-2, flanking the 5.8S gene of and unexpected relationships. the nuclear ribosomal gene cistrons) were aligned, guided by ITS transcript secondary structural features, and subjected to parsi- Materials and Methods mony and neighbor joining distance analysis. Results confirm the The algal isolates that form the basis of this study are listed below notion of a single common ancestor, and Chlamydomonas rein- and Volvocacean taxonomy is summarized in Table 1. The taxon harditii alone among all sequenced green unicells is most similar. names are those found in the culture collection listings. Included Interbreeding isolates were nearest neighbors on the evolutionary is the Culture Collection designation [University of Texas, tree in all cases. Some taxa, at whatever level, prove to be clades National Institute for Environmental Studies (Japan), A.W.C. or by sequence comparisons, but others provide striking exceptions. R. C. Starr collection], an abbreviated name, and the GenBank The morphological species Pandorina morum, known to be wide- accession number. -
Ecological and Evolutionary Implications of Shape During Population Expansion
ECOLOGICAL AND EVOLUTIONARY IMPLICATIONS OF SHAPE DURING POPULATION EXPANSION Submitted by Christopher Lee Coles to the University of Exeter as a thesis for the degree of Doctor of Philosophy in Biological Sciences January 2015 This thesis is available for library use on the understanding that it is copyright material and that no quotation from the thesis may be published without proper acknowledgement. I certify that all material in this thesis which is not my own work has been identified and that no material has previously been submitted and approved for the award of a degree by this or any other University. Signature: ................................... ~ 1 ~ In loving memory of Laura Joan Coles ~ 2 ~ Abstract The spatial spread of populations is one of the most visible and fundamental processes in population and community ecology. Due to the potential negative impacts of spatial spread of invasive populations, there has been intensive research into understanding the drivers of ecological spread, predicting spatial dynamics, and finding management strategies that best constrain or control population expansion. However, understanding the spread of populations has proved to be a formidable task and our ability to accurately predict the spread of these populations has to date been limited. Microbial populations, during their spread across agar plate environments, can exhibit a wide array of spatial patterns, ranging from relatively circular patterns to highly irregular, fractal-like patterns. Work analysing these patterns of spread has mainly focused on the underlying mechanistic processes responsible for these patterns, with relatively little investigation into the ecological and evolutionary drivers of these patterns. With the increased recognition of the links between microbial and macrobial species, it is possible that many of the ecological/evolutionary mechanisms responsible for these patterns of spread at a microbial level extrapolate to the spatial spread of populations in general. -
Using New Strains of “Volvox Africanus”
RESEARCH ARTICLE Delineating a New Heterothallic Species of Volvox (Volvocaceae, Chlorophyceae) Using New Strains of “Volvox africanus” Hisayoshi Nozaki1*, Ryo Matsuzaki1, Kayoko Yamamoto1, Masanobu Kawachi2, Fumio Takahashi3 1 Department of Biological Sciences, Graduate school of Science, University of Tokyo, Tokyo, Japan, 2 Center for Environmental Biology and Ecosystem Studies, National Institute for Environmental Studies, Tsukuba, Ibaraki, Japan, 3 Ritsumeikan University, College of Life Sciences, Kusatsu, Shiga, Japan * [email protected] Abstract The volvocine algae represent an excellent model lineage in which to study evolution of female and male genders based on comparative analyses of related species. Among these OPEN ACCESS species, Volvox carteri has been extensively studied as a model of an oogamous and com- plex organism. However, it may have unique derived features that are not present in other Citation: Nozaki H, Matsuzaki R, Yamamoto K, Kawachi M, Takahashi F (2015) Delineating a New species of Volvox. Therefore, information regarding the characteristics of sexual reproduc- Heterothallic Species of Volvox (Volvocaceae, tion of other species of Volvox is also important. In 1971, Starr studied four types of sexuality “Volvox Chlorophyceae) Using New Strains of in several global strains identified as Volvox africanus; however, further taxonomic studies africanus”. PLoS ONE 10(11): e0142632. doi:10.1371/journal.pone.0142632 of these strains have been lacking, and strains of three of the four sexual types are not avail- able. Here, we studied the morphology, sexual reproduction, and taxonomy of two V. africa- Editor: James G. Umen, Donald Danforth Plant Science Center, UNITED STATES nus-like species isolated recently from Lake Biwa, Japan. -
A Preliminary Study of Chemical Profiles of Honey, Cerumen
foods Article A Preliminary Study of Chemical Profiles of Honey, Cerumen, and Propolis of the African Stingless Bee Meliponula ferruginea Milena Popova 1 , Dessislava Gerginova 1 , Boryana Trusheva 1 , Svetlana Simova 1, Alfred Ngenge Tamfu 2 , Ozgur Ceylan 3, Kerry Clark 4 and Vassya Bankova 1,* 1 Institute of Organic Chemistry with Centre of Phytochemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria; [email protected] (M.P.); [email protected] (D.G.); [email protected] (B.T.); [email protected] (S.S.) 2 Department of Chemical Engineering, School of Chemical Engineering and Mineral Industries, University of Ngaoundere, 454 Ngaoundere, Cameroon; [email protected] 3 Food Quality Control and Analysis Program, Ula Ali Kocman Vocational School, Mugla Sitki Kocman University, 48147 Ula Mugla, Turkey; [email protected] 4 Volunteer Advisor in Beekeeping and Bee Products with Canadian Executive Services Organization, P.O. Box 2090, Dawson Creek, BC V1G 4K8, Canada; [email protected] * Correspondence: [email protected]; Tel.: +359-2-9606-149 Abstract: Recently, the honey and propolis of stingless bees have been attracting growing atten- tion because of their health-promoting properties. However, studies on these products of African Meliponini are still very scarce. In this preliminary study, we analyzed the chemical composition of honey, two cerumen, and two resin deposits (propolis) samples of Meliponula ferruginea from Tanzania. The honey of M. ferruginea was profiled by NMR and indicated different long-term stability Citation: Popova, M.; Gerginova, D.; from Apis mellifera European (Bulgarian) honey. It differed significantly in sugar and organic acids Trusheva, B.; Simova, S.; Tamfu, A.N.; content and had a very high amount of the disaccharide trehalulose, known for its bioactivities. -
Cell Density and Mobility Protect Swarming Bacteria Against Antibiotics
Cell density and mobility protect swarming bacteria against antibiotics Mitchell T. Butler, Qingfeng Wang, and Rasika M. Harshey1 Section of Molecular Genetics and Microbiology, and Institute of Cellular and Molecular Biology, University of Texas, Austin, TX 78712 Edited by Raghavendra Gadagkar, Indian Institute of Science, Bangalore, India, and approved December 9, 2009 (received for review September 23, 2009) Swarming bacteria move in multicellular groups and exhibit Bacillus and Serratia—and show that cell density and mobility are adaptive resistance to multiple antibiotics. Analysis of this phe- common protective features for survival against antimicrobials. nomenon has revealed the protective power of high cell densities to withstand exposure to otherwise lethal antibiotic concentra- Results and Discussion tions. We find that high densities promote bacterial survival, even Antibiotic Resistance Is a Property of High Cell Density and Is Favored in a nonswarming state, but that the ability to move, as well as the by Mobility. In soft agar (0.3%), cells swim individually inside the speed of movement, confers an added advantage, making swarm- agar and are referred to as swimmers. In medium agar (0.6%), ing an effective strategy for prevailing against antimicrobials. We cells move as a group on the surface and are referred to as find no evidence of induced resistance pathways or quorum- swarmers. The original E-test strip assay showing differential sensing mechanisms controlling this group resistance, which occurs antibiotic resistance of swimmer and swarmer cells of Salmonella at a cost to cells directly exposed to the antibiotic. This work has (13, 14) is shown in Fig. 1A.