Motility in Unicellular and Filamentous Cyanobacteria 11 Bianca Brahamsha and Devaki Bhaya
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Glossary - Cellbiology
1 Glossary - Cellbiology Blotting: (Blot Analysis) Widely used biochemical technique for detecting the presence of specific macromolecules (proteins, mRNAs, or DNA sequences) in a mixture. A sample first is separated on an agarose or polyacrylamide gel usually under denaturing conditions; the separated components are transferred (blotting) to a nitrocellulose sheet, which is exposed to a radiolabeled molecule that specifically binds to the macromolecule of interest, and then subjected to autoradiography. Northern B.: mRNAs are detected with a complementary DNA; Southern B.: DNA restriction fragments are detected with complementary nucleotide sequences; Western B.: Proteins are detected by specific antibodies. Cell: The fundamental unit of living organisms. Cells are bounded by a lipid-containing plasma membrane, containing the central nucleus, and the cytoplasm. Cells are generally capable of independent reproduction. More complex cells like Eukaryotes have various compartments (organelles) where special tasks essential for the survival of the cell take place. Cytoplasm: Viscous contents of a cell that are contained within the plasma membrane but, in eukaryotic cells, outside the nucleus. The part of the cytoplasm not contained in any organelle is called the Cytosol. Cytoskeleton: (Gk. ) Three dimensional network of fibrous elements, allowing precisely regulated movements of cell parts, transport organelles, and help to maintain a cell’s shape. • Actin filament: (Microfilaments) Ubiquitous eukaryotic cytoskeletal proteins (one end is attached to the cell-cortex) of two “twisted“ actin monomers; are important in the structural support and movement of cells. Each actin filament (F-actin) consists of two strands of globular subunits (G-Actin) wrapped around each other to form a polarized unit (high ionic cytoplasm lead to the formation of AF, whereas low ion-concentration disassembles AF). -
PCR Based Molecular Characterization of Cyanobacteria with Special Emphasis on Non-Heterocystous Filamentous Cyanobacteria Gunapati Oinam, O.N.Tiwari* and G.D
ERSITY IV N S Assam University Journal of Science & Technology : ISSN 0975-2773 U I L M C H A S A Biological and Environmental Sciences R S A Vol. 7 Number I 101-113, 2011 PCR Based Molecular Characterization of Cyanobacteria with Special Emphasis on Non-Heterocystous Filamentous Cyanobacteria Gunapati Oinam, O.N.Tiwari* and G.D. Sharma** Microbial Bioprospecting Laboratory Institute of Bioresources and Sustainable Development Takyelpat, Imphal-795001, Manipur, INDIA ** Department of Life science, Assam University, Silchar, Assam *Corresponding author email : [email protected] Abstract Cyanobacteria have an ancient history dating almost 3.5 billion years and diversified extensively to become one of the most successful and ecologically significant organisms on earth, with respect to longevity of lineage and impact on earth’s early environment. Despite the availability of various monograph based on morphological and ecological variants, the identification and classification of cyanobacteria remain a difficult and confusing task leading to uncertain identifications. Therefore, molecular approaches based on PCR techniques and DNA fingerprinting have been adopted for taxonomical studies. Molecular markers such as RAPD, RFLP and AFLP are used for the PCR techniques. Keywords: Non-heterocystous, cyanobacteria, molecular characterization. Introduction Cyanobacteria are an ancient group of prokaryotic aided by the presence of exopolysaccharides such microorganisms exhibiting the general as mucilage and / or a firm sheath. The presence characteristics of gram-negative bacteria. They or absence of a heterocyst is an important feature are unique among the prokaryotes in possessing separating genera. However, gas vacuoles, the capacity of oxygenic photosynthesis. structures that aid buoyancy, are found in species Cyanobacteria are a morphologically diverse group of many different genera. -
Single-Cell Twitching Chemotaxis in Developing Biofilms
Single-cell twitching chemotaxis in developing biofilms Nuno M. Oliveiraa,b,1, Kevin R. Fostera,b,2, and William M. Durhama,2 aDepartment of Zoology, University of Oxford, Oxford OX1 3PS, United Kingdom; and bOxford Centre for Integrative Systems Biology, University of Oxford, Oxford OX1 3PS, United Kingdom Edited by Howard C. Berg, Harvard University, Cambridge, MA, and approved April 19, 2016 (received for review January 15, 2016) Bacteria form surface-attached communities, known as biofilms, this form of movement is common throughout biofilm formation which are central to bacterial biology and how they affect us. Although (10, 11), here we follow the movement of solitary bacteria in the surface-attached bacteria often experience strong chemical gradients, it early stages of biofilm development so that we can readily calculate remains unclear whether single cells can effectively perform chemo- each cell’s chemical environment and resolve how it modifies their taxis on surfaces. Here we use microfluidic chemical gradients and behavior. Importantly, the microfluidic assays used here are analo- – massively parallel automated tracking to study the behavior of the gous to those used in classical studies of biofilm development (9 11), pathogen Pseudomonas aeruginosa during early biofilm development. and the cells whose movement we analyze subsequently form 3D We show that individual cells can efficiently move toward chemoat- biofilm structures (Fig. 1 F and G and SI Appendix,Fig.S1). To tractants using pili-based “twitching” motility and the Chp chemosen- generate stable chemical gradients, we use two inlet microfluidic devices where flow balances the smoothing effect of molecular sory system. -
Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas
microorganisms Article Characteristic Microbiomes Correlate with Polyphosphate Accumulation of Marine Sponges in South China Sea Areas 1 1, 1 1 2, 1,3, Huilong Ou , Mingyu Li y, Shufei Wu , Linli Jia , Russell T. Hill * and Jing Zhao * 1 College of Ocean and Earth Science of Xiamen University, Xiamen 361005, China; [email protected] (H.O.); [email protected] (M.L.); [email protected] (S.W.); [email protected] (L.J.) 2 Institute of Marine and Environmental Technology, University of Maryland Center for Environmental Science, Baltimore, MD 21202, USA 3 Xiamen City Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen 361005, China * Correspondence: [email protected] (J.Z.); [email protected] (R.T.H.); Tel.: +86-592-288-0811 (J.Z.); Tel.: +(410)-234-8802 (R.T.H.) The author contributed equally to the work as co-first author. y Received: 24 September 2019; Accepted: 25 December 2019; Published: 30 December 2019 Abstract: Some sponges have been shown to accumulate abundant phosphorus in the form of polyphosphate (polyP) granules even in waters where phosphorus is present at low concentrations. But the polyP accumulation occurring in sponges and their symbiotic bacteria have been little studied. The amounts of polyP exhibited significant differences in twelve sponges from marine environments with high or low dissolved inorganic phosphorus (DIP) concentrations which were quantified by spectral analysis, even though in the same sponge genus, e.g., Mycale sp. or Callyspongia sp. PolyP enrichment rates of sponges in oligotrophic environments were far higher than those in eutrophic environments. -
Marine Microplankton Ecology Reading
Marine Microplankton Ecology Reading Microbes dominate our planet, especially the Earth’s oceans. The distinguishing feature of microorganisms is their small size, usually defined as less than 200 micrometers (µm); they are all invisible to the naked eye. As a group, sea microbes are extremely diverse, and extremely versatile with respect to their abilities to make and eat food. All marine microbes are too small to swim against the current and are therefore classified as plankton. First we will discuss several ways to classify marine microbes. 1. Size Planktonic marine organisms can be divided into the following size categories: Category Size femtoplankton <0.2 µm picoplankton 0.2-2 µm nanoplankton 2-20 µm microplankton 20-200 µm mesoplankton 200-2000 µm In this laboratory we are concerned with the microscopic portion of the plankton, less than 200 µm. These organisms are not visible to the naked eye (Figure 1). Figure 1. Size classes of marine plankton 2. Type A. Viruses Viruses are the smallest and simplest microplankton. They range from 0.01 to 0.3 um in diameter. Externally, viruses have a capsid, or protein coat. Viruses can also have simple or complex external morphologies with tail fibers and structures that are used to inject DNA or RNA into their host. Viruses have little internal morphology. They do not have a nucleus or organelles. They do not have chlorophyll. Inside a virus there is only nucleic acid, either DNA or RNA. Viruses do not grow and have no metabolism. Marine viruses are highly abundant. There are up to 10 billion in one liter of seawater! B. -
Mathematical Modelling and Analysis of Aspects of Planktonic Bacterial Motility
Mathematical modelling and analysis of aspects of planktonic bacterial motility Gabriel Aaron Rosser St Anne's College University of Oxford A thesis submitted for the degree of Doctor of Philosophy Michaelmas 2012 Contents 1 The biology of bacterial motility and taxis 8 1.1 Bacterial motility and taxis . .8 1.2 Experimental methods used to probe bacterial motility . 14 1.3 Tracking . 20 1.4 Conclusion and outlook . 21 2 Mathematical methods and models of bacterial motility and taxis 23 2.1 Modelling bacterial motility and taxis: a multiscale problem . 24 2.2 The velocity jump process . 34 2.3 Spatial moments of the general velocity jump process . 46 2.4 Circular statistics . 49 2.5 Stochastic simulation algorithm . 52 2.6 Conclusion and outlook . 54 3 Analysis methods for inferring stopping phases in tracking data 55 3.1 Analysis methods . 58 3.2 Simulation study comparison of the analysis methods . 76 3.3 Results . 80 3.4 Discussion and conclusions . 86 4 Analysis of experimental data 92 4.1 Methods . 92 i 4.2 Results . 109 4.3 Discussion and conclusions . 124 5 The effect of sampling frequency 132 5.1 Background and methods . 133 5.2 Stationary distributions . 136 5.3 Simulation study of dynamic distributions . 140 5.4 Analytic study of dynamic distributions . 149 5.5 Discussion and conclusions . 159 6 Modelling the effect of Brownian buffeting on motile bacteria 162 6.1 Background . 163 6.2 Mathematical methods . 166 6.3 A model of rotational diffusion in bacterial motility . 173 6.4 Results . 183 6.5 Discussion and conclusion . -
Photosymbiosis for Biomedical Applications
fbioe-08-577204 October 3, 2020 Time: 17:45 # 1 REVIEW published: 06 October 2020 doi: 10.3389/fbioe.2020.577204 Photosymbiosis for Biomedical Applications Myra N. Chávez1†, Nicholas Moellhoff2†, Thilo L. Schenck2, José Tomás Egaña3* and Jörg Nickelsen1* 1 Molecular Plant Science, Department Biology I, Ludwig-Maximilians-Universität München, Munich, Germany, 2 Division of Hand, Plastic and Aesthetic Surgery, University Hospital, Ludwig Maximilian Universität München, Munich, Germany, 3 Institute for Biological and Medical Engineering, Schools of Engineering, Biological Sciences and Medicine, Pontificia Universidad Católica de Chile, Santiago, Chile Without the sustained provision of adequate levels of oxygen by the cardiovascular system, the tissues of higher animals are incapable of maintaining normal metabolic activity, and hence cannot survive. The consequence of this evolutionarily suboptimal design is that humans are dependent on cardiovascular perfusion, and therefore highly susceptible to alterations in its normal function. However, hope may be at hand. Edited by: “Photosynthetic strategies,” based on the recognition that photosynthesis is the source Bruce Alan Bunnell, University of North Texas Health of all oxygen, offer a revolutionary and promising solution to pathologies related to Science Center, United States tissue hypoxia. These approaches, which have been under development over the past Reviewed by: 20 years, seek to harness photosynthetic microorganisms as a local and controllable Matjaž Jeras, source of oxygen to circumvent the need for blood perfusion to sustain tissue survival. University of Ljubljana, Slovenia Kar Wey Yong, To date, their applications extend from the in vitro creation of artificial human tissues to University of Alberta, Canada the photosynthetic maintenance of oxygen-deprived organs both in vivo and ex vivo, *Correspondence: while their potential use in other medical approaches has just begun to be explored. -
Gastrointestinal Motility Physiology
GASTROINTESTINAL MOTILITY PHYSIOLOGY JAYA PUNATI, MD DIRECTOR, PEDIATRIC GASTROINTESTINAL, NEUROMUSCULAR AND MOTILITY DISORDERS PROGRAM DIVISION OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION, CHILDREN’S HOSPITAL LOS ANGELES VRINDA BHARDWAJ, MD DIVISION OF PEDIATRIC GASTROENTEROLOGY AND NUTRITION CHILDREN’S HOSPITAL LOS ANGELES EDITED BY: CHRISTINE WAASDORP HURTADO, MD REVIEWED BY: JOSEPH CROFFIE, MD, MPH NASPGHAN PHYSIOLOGY EDUCATION SERIES SERIES EDITORS: CHRISTINE WAASDORP HURTADO, MD, MSCS, FAAP [email protected] DANIEL KAMIN, MD [email protected] CASE STUDY 1 • 14 year old female • With no significant past medical history • Presents with persistent vomiting and 20 lbs weight loss x 3 months • Initially emesis was intermittent, occurred before bedtime or soon there after, 2-3 hrs after a meal • Now occurring immediately or up to 30 minutes after a meal • Emesis consists of undigested food and is nonbloody and nonbilious • Associated with heartburn and chest discomfort 3 CASE STUDY 1 • Initial screening blood work was unremarkable • A trial of acid blockade was started with improvement in heartburn only • Antiemetic therapy with ondansetron showed no improvement • Upper endoscopy on acid blockade was normal 4 CASE STUDY 1 Differential for functional/motility disorders: • Esophageal disorders: – Achalasia – Gastroesophageal Reflux – Other esophageal dysmotility disorders • Gastric disorders: – Gastroparesis – Rumination syndrome – Gastric outlet obstruction : pyloric stricture, pyloric stenosis • -
Force Generation by Groups of Migrating Bacteria
Force generation by groups of migrating bacteria Benedikt Sabassa,b,1, Matthias D. Kochc, Guannan Liuc,d, Howard A. Stonea, and Joshua W. Shaevitzc,d,1 aDepartment of Mechanical and Aerospace Engineering, Princeton University, NJ 08544; bInstitute of Complex Systems 2, Forschungszentrum Julich,¨ D-52425 Juelich, Germany; cLewis-Sigler Institute for Integrative Genomics, Princeton University, NJ 08544; and dJoseph Henry Laboratories of Physics, Princeton University, NJ 08544 Edited by Ulrich S. Schwarz, Heidelberg University, Heidelberg, Germany, and accepted by Editorial Board Member Herbert Levine May 23, 2017 (received for review December 30, 2016) From colony formation in bacteria to wound healing and embry- at a typical Myxococcus migration speed of 1 µm=min is on the onic development in multicellular organisms, groups of living cells order of 10−2 pN. Large traction forces will only occur if cells must often move collectively. Although considerable study has need to overcome friction with the surface or if the translation probed the biophysical mechanisms of how eukaryotic cells gener- machinery itself has internal friction, similar to the situation for ate forces during migration, little such study has been devoted to eukaryotic cells (18). Collective migration of bacteria within a bacteria, in particular with regard to the question of how bacte- contiguous group is even less understood. Could forces arise ria generate and coordinate forces during collective motion. This from a balance between cell–substrate and cell–cell interactions? question is addressed here using traction force microscopy. We Would this balance be local, or span larger distances within the study two distinct motility mechanisms of Myxococcus xanthus, group? Might one have “leader” cells at the advancing front of namely, twitching and gliding. -
JMY: Actin up in Cell Motility Migrate Faster in a Wound Healing Assay That Assesses Cell Motility
RESEARCH HIGHLIGHTS Nature Reviews Molecular Cell Biology | AOP, published online 2 April 2009; doi:10.1038/nrm2678 — the area closest to the direction CYTOSKELETON of movement — in motile cells. This suggests a role for JMY in cell motility. Indeed, cells that overexpress JMY JMY: actin up in cell motility migrate faster in a wound healing assay that assesses cell motility. By contrast, Actin nucleation — the initial step in filaments. A study now identifies the knockdown of JMY decreases the rate the formation of new actin filaments p53 cofactor JMY as a novel actin of wound healing as a result of reduced — can be induced by the actin-related nucleation factor that combines the ...JMY actin nucleation. Significantly, JMY was protein 2/3 (Arp2/3) complex, which nucleating activities of these proteins specifically induced to the cell leading creates branched actin filaments, to promote cell motility. contributes to edge in response to wounding. Thus, and spire, which creates unbranched The authors observed a potential the assembly the activity of JMY as a transcriptional Arp2/3-activating sequence, WWWCA, of the actin cofactor and actin nucleation factor in JMY. WWWCA contains three repeats seems to be regulated by its cellular of the actin monomer-binding domain cytoskeleton localization. WH2, in addition to a domain that can and cell In short, the authors propose that bind actin and Arp2/3. Intriguingly, in motility... JMY contributes to the assembly of the vitro, JMY can both activate Arp2/3 and, actin cytoskeleton and cell motility by in the absence of Arp2/3, induce rapid first nucleating new filaments, using actin polymerization. -
Gene Content and Organization
Photosynth Res DOI 10.1007/s11120-006-9122-4 REGULAR PAPER Complete nucleotide sequence of the freshwater unicellular cyanobacterium Synechococcus elongatus PCC 6301 chromosome: gene content and organization Chieko Sugita Æ Koretsugu Ogata Æ Masamitsu Shikata Æ Hiroyuki Jikuya Æ Jun Takano Æ Miho Furumichi Æ Minoru Kanehisa Æ Tatsuo Omata Æ Masahiro Sugiura Æ Mamoru Sugita Received: 30 August 2006 / Accepted: 6 December 2006 Ó Springer Science+Business Media B.V. 2006 Abstract The entire genome of the unicellular of the potential protein-coding genes showed cyanobacterium Synechococcus elongatus PCC 6301 sequence similarities to experimentally identified and (formerly Anacystis nidulans Berkeley strain 6301) predicted proteins of known function, and the prod- was sequenced. The genome consisted of a circular ucts of 35% of the genes showed sequence similarities chromosome 2,696,255 bp long. A total of 2,525 to the translated products of hypothetical genes. The potential protein-coding genes, two sets of rRNA remaining 9% of genes lacked significant similarities genes, 45 tRNA genes representing 42 tRNA species, to genes for predicted proteins in the public DNA and several genes for small stable RNAs were databases. Some 139 genes coding for photosynthesis- assigned to the chromosome by similarity searches and related components were identified. Thirty-seven computer predictions. The translated products of 56% genes for two-component signal transduction systems were also identified. This is the smallest number of such genes identified in cyanobacteria, except for marine cyanobacteria, suggesting that only simple signal transduction systems are found in this strain. The gene arrangement and nucleotide sequence of Synechococcus elongatus PCC 6301 were nearly & C. -
Phototactic Purple Bacteria Extinction Or Miscalculation?
SCIENTIFIC CORRESPONDENCE the light source through the gradient of Phototactic purple decreasing light intensity; on the other Extinction or hand, if their movement is scotophobic, bacteria the colony should move in the opposite miscalculation? direction. R. centenum swarm colonies SIR - In 1883 T. Engelmann! discovered irradiated laterally with infrared light in SIR - Heywood et al. I have discussed that purple photosynthetic bacteria re fact moved rapidly towards the light uncertainties in modelling rates. One way verse their swimming direction when the source, as for positive phototaxis. to check a predictive model's validity is to light intensity is suddenly reduced. He Anoxygenic photosynthetic bacteria see how well it predicts past events. In this described this photosensory effect as and the oxygenic cyanobacteria and algae case, the species-area relation model does "Schreckbewegung" ('movement of share several similar physiological re fairly well in predicting the number of fright'), but it is more properly designated quirements, so it is not surprising that bird and mammal extinctions during the as a scotophobic response, past 500 years in the United States and that is, a fear of darkness. a Canada .. Scotophobic behaviour is Time (min) Infrared Here I consider species extirpated fol typical of motile purple bac lowing habitat destruction initiated by 2 teria, is independent of the o Europeans in North America , combined direction of illumination, with currently endangered or threatened 3 and does not occur if the 30 species , to check if species loss is con light intensity is reduced ..'Q" gruent with habitat loss. Although exact only gradually. By contrast, 60 figures are difficult to come by, I take as oxygenic cyanobacteria and 20% the amount of land removed from algae exhibit phototactic re- 120 native North American mammal and bird 4 sponses, that is, oriented habitats .