Microbial Growth
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Exploring Small-Scale Chemostats to Scale up Microbial Processes: 3-Hydroxypropionic Acid Production in S
Lawrence Berkeley National Laboratory Recent Work Title Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae. Permalink https://escholarship.org/uc/item/43h8866j Journal Microbial cell factories, 18(1) ISSN 1475-2859 Authors Lis, Alicia V Schneider, Konstantin Weber, Jost et al. Publication Date 2019-03-11 DOI 10.1186/s12934-019-1101-5 Peer reviewed eScholarship.org Powered by the California Digital Library University of California Lis et al. Microb Cell Fact (2019) 18:50 https://doi.org/10.1186/s12934-019-1101-5 Microbial Cell Factories RESEARCH Open Access Exploring small-scale chemostats to scale up microbial processes: 3-hydroxypropionic acid production in S. cerevisiae Alicia V. Lis1, Konstantin Schneider1,2, Jost Weber1,3, Jay D. Keasling1,4,5,6,7, Michael Krogh Jensen1 and Tobias Klein1,2* Abstract Background: The physiological characterization of microorganisms provides valuable information for bioprocess development. Chemostat cultivations are a powerful tool for this purpose, as they allow defned changes to one single parameter at a time, which is most commonly the growth rate. The subsequent establishment of a steady state then permits constant variables enabling the acquisition of reproducible data sets for comparing microbial perfor- mance under diferent conditions. We performed physiological characterizations of a 3-hydroxypropionic acid (3-HP) producing Saccharomyces cerevisiae strain in a miniaturized and parallelized chemostat cultivation system. The physi- ological conditions under investigation were various growth rates controlled by diferent nutrient limitations (C, N, P). Based on the cultivation parameters obtained subsequent fed-batch cultivations were designed. Results: We report technical advancements of a small-scale chemostat cultivation system and its applicability for reliable strain screening under diferent physiological conditions, i.e. -
Chemostat Culture for Yeast Experimental Evolution
Downloaded from http://cshprotocols.cshlp.org/ at Cold Spring Harbor Laboratory Library on August 9, 2017 - Published by Cold Spring Harbor Laboratory Press Protocol Chemostat Culture for Yeast Experimental Evolution Celia Payen and Maitreya J. Dunham1 Department of Genome Sciences, University of Washington, Seattle, Washington 98195 Experimental evolution is one approach used to address a broad range of questions related to evolution and adaptation to strong selection pressures. Experimental evolution of diverse microbial and viral systems has routinely been used to study new traits and behaviors and also to dissect mechanisms of rapid evolution. This protocol describes the practical aspects of experimental evolution with yeast grown in chemostats, including the setup of the experiment and sampling methods as well as best laboratory and record-keeping practices. MATERIALS It is essential that you consult the appropriate Material Safety Data Sheets and your institution’s Environmental Health and Safety Office for proper handling of equipment and hazardous material used in this protocol. Reagents Defined minimal medium appropriate for the experiment For examples, see Protocol: Assembly of a Mini-Chemostat Array (Miller et al. 2015). Ethanol (95%) Glycerol (20% and 50%; sterile) Yeast strain of interest Equipment Agar plates (appropriate for chosen strain) Chemostat array Assemble the apparatus as described in Miller et al. (2013) and Protocol: Assembly of a Mini-Chemostat Array (Miller et al. 2015). Cryo deep-freeze labels Cryogenic vials Culture tubes Cytometer (BD Accuri C6) Glass beads, 4 mm (sterile; for plating yeast cells) Glass cylinder Kimwipes 1Correspondence: [email protected] © 2017 Cold Spring Harbor Laboratory Press Cite this protocol as Cold Spring Harb Protoc; doi:10.1101/pdb.prot089011 559 Downloaded from http://cshprotocols.cshlp.org/ at Cold Spring Harbor Laboratory Library on August 9, 2017 - Published by Cold Spring Harbor Laboratory Press C. -
Obligate Aerobes Obligate Anaerobes and Facultative Anaerobes
Obligate Aerobes Obligate Anaerobes And Facultative Anaerobes Circumpolar and posterior Andonis never kyanised jauntily when Normand outdid his exasperation. Chanderjit pressurize her chondrite trisyllabically, soporiferous and nonary. Pathogenic and autogamic Thatcher always dehydrating swift and massacred his noteworthiness. In oxygen and not permitted by facultative aerobes use is then sealed BC led consult the initiation or sequence change in antibiotics, according to the microbiological data. Additionally, there are lean some constraints which radiate a broader application of their potentials. The method contains elements successfully applied to other methodologies. All content right this website, including dictionary, thesaurus, literature, geography, and other reference data is for informational purposes only. Denitrification are examples of facultative aerobes anaerobes and obligate aerobes: they employ to oxygen to plants and labor costs. Some dismiss these materials are more challenging than others, such as fish or paper mill plant, while others are easier to compost, like dawn or raw manure plus bedding. Below settings at lower levels while and obligate anaerobes present results is often forming spatial structure, which survive in the next level is calculated from food. These two oxygen can survive he can sound at atmospheric levels of oxygen. This atmosphere is known for growing facultative anaerobes and obligate anaerobes. Each of least four angles of a rectangle than a compound angle. Additionally, the anaerobic granular sludge is generally well stabilized and significantly less excess stomach is produced compared, for instance, after that ravage the aerobic systems. Obligate anaerobes lack both enzymes, leaving a little blood no protection against ROS. Furthermore, we mainly used antimicrobial agents that were effective against obligate anaerobes in the verb study; thus, chaos could not analyze the influence is the selection of antibiotic treatment according to the results of molecular analysis. -
Thermodynamics of DNA Binding by DNA Polymerase I and Reca
Louisiana State University LSU Digital Commons LSU Doctoral Dissertations Graduate School 2014 Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans Jaycob Dalton Warfel Louisiana State University and Agricultural and Mechanical College Follow this and additional works at: https://digitalcommons.lsu.edu/gradschool_dissertations Recommended Citation Warfel, Jaycob Dalton, "Thermodynamics of DNA Binding by DNA Polymerase I and RecA Recombinase from Deinococcus radiodurans" (2014). LSU Doctoral Dissertations. 2382. https://digitalcommons.lsu.edu/gradschool_dissertations/2382 This Dissertation is brought to you for free and open access by the Graduate School at LSU Digital Commons. It has been accepted for inclusion in LSU Doctoral Dissertations by an authorized graduate school editor of LSU Digital Commons. For more information, please [email protected]. THERMODYNAMICS OF DNA BINDING BY DNA POLYMERASE I AND RECA RECOMBINASE FROM DEINOCOCCUS RADIODURANS A Dissertation Submitted to the Graduate Faculty of the Louisiana State University and Agricultural and Mechanical College in partial fulfillment of the requirements for the degree of Doctor of Philosophy in The Department of Biological Sciences by Jaycob Dalton Warfel B.S. Louisiana State University, 2006 May 2015 ACKNOWLEDGEMENTS I would like to express my utmost gratitude to the myriad of individuals who have lent their support during the time it has taken to complete this dissertation. First and foremost is due glory to God, The Father, The Son and The Holy Spirit, through whom all is accomplished. It is with extreme thankfulness for the blessings bestowed upon me, and with vast appreciation for the beauty of God’s creation that I have pursued a scientific education. -
Protozoa and Oxygen
Acta Protozool. (2014) 53: 3–12 http://www.eko.uj.edu.pl/ap ActA doi:10.4467/16890027AP.13.0020.1117 Protozoologica Special issue: Marine Heterotrophic Protists Guest editors: John R. Dolan and David J. S. Montagnes Review paper Protozoa and Oxygen Tom FENCHEL Marine Biological Laboratory, University of Copenhagen, Denmark Abstract. Aerobic protozoa can maintain fully aerobic metabolic rates even at very low O2-tensions; this is related to their small sizes. Many – or perhaps all – protozoa show particular preferences for a given range of O2-tensions. The reasons for this and the role for their distribution in nature are discussed and examples of protozoan biota in O2-gradients in aquatic systems are presented. Facultative anaerobes capable of both aerobic and anaerobic growth are probably common within several protozoan taxa. It is concluded that further progress in this area is contingent on physiological studies of phenotypes. Key words: Protozoa, chemosensory behavior, oxygen, oxygen toxicity, microaerobic protozoa, facultative anaerobes, microaerobic and anaerobic habitats. INTRODUCTION low molecular weight organics and in some cases H2 as metabolic end products. Some ciliates and foraminifera use nitrate as a terminal electron acceptor in a respira- Increasing evidence suggests that the last common tory process (for a review on anaerobic protozoa, see ancestor of extant eukaryotes was mitochondriate and Fenchel 2011). had an aerobic energy metabolism. While representa- The great majority of protozoan species, however, tives of different protist taxa have secondarily adapted depend on aerobic energy metabolism. Among pro- to an anaerobic life style, all known protists possess ei- tists with an aerobic metabolism many – or perhaps ther mitochondria capable of oxidative phosphorylation all – show preferences for particular levels of oxygen or – in anaerobic species – have modified mitochon- tension below atmospheric saturation. -
Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation
City University of New York (CUNY) CUNY Academic Works Open Educational Resources Queensborough Community College 2016 Laboratory Exercises in Microbiology: Discovering the Unseen World Through Hands-On Investigation Joan Petersen CUNY Queensborough Community College Susan McLaughlin CUNY Queensborough Community College How does access to this work benefit ou?y Let us know! More information about this work at: https://academicworks.cuny.edu/qb_oers/16 Discover additional works at: https://academicworks.cuny.edu This work is made publicly available by the City University of New York (CUNY). Contact: [email protected] Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation By Dr. Susan McLaughlin & Dr. Joan Petersen Queensborough Community College Laboratory Exercises in Microbiology: Discovering the Unseen World through Hands-On Investigation Table of Contents Preface………………………………………………………………………………………i Acknowledgments…………………………………………………………………………..ii Microbiology Lab Safety Instructions…………………………………………………...... iii Lab 1. Introduction to Microscopy and Diversity of Cell Types……………………......... 1 Lab 2. Introduction to Aseptic Techniques and Growth Media………………………...... 19 Lab 3. Preparation of Bacterial Smears and Introduction to Staining…………………...... 37 Lab 4. Acid fast and Endospore Staining……………………………………………......... 49 Lab 5. Metabolic Activities of Bacteria…………………………………………….…....... 59 Lab 6. Dichotomous Keys……………………………………………………………......... 77 Lab 7. The Effect of Physical Factors on Microbial Growth……………………………... 85 Lab 8. Chemical Control of Microbial Growth—Disinfectants and Antibiotics…………. 99 Lab 9. The Microbiology of Milk and Food………………………………………………. 111 Lab 10. The Eukaryotes………………………………………………………………........ 123 Lab 11. Clinical Microbiology I; Anaerobic pathogens; Vectors of Infectious Disease….. 141 Lab 12. Clinical Microbiology II—Immunology and the Biolog System………………… 153 Lab 13. Putting it all Together: Case Studies in Microbiology…………………………… 163 Appendix I. -
Potential Probiotic Bacillus Subtilis Isolated from a Novel Niche
microorganisms Article Potential Probiotic Bacillus subtilis Isolated from a Novel Niche Exhibits Broad Range Antibacterial Activity and Causes Virulence and Metabolic Dysregulation in Enterotoxic E. coli Sudhanshu Sudan 1, Robert Flick 2, Linda Nong 3 and Julang Li 1,* 1 Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] 2 Biozone, Mass Spectrometry and Metabolomics, Department of Chemical Engineering and Applied Chemistry, University of Toronto, Toronto, ON M5S 3E5, Canada; robert.fl[email protected] 3 Department of Integrative Biology, University of Guelph, Guelph, ON N1G 2W1, Canada; [email protected] * Correspondence: [email protected] Abstract: Microbial life in extreme environments, such as deserts and deep oceans, is thought to have evolved to overcome constraints of nutrient availability, temperature, and suboptimal hygiene environments. Isolation of probiotic bacteria from such niche may provide a competitive edge over traditional probiotics. Here, we tested the survival, safety, and antimicrobial effect of a recently isolated and potential novel strain of Bacillus subtilis (CP9) from desert camel in vitro. Antimicrobial assays were performed via radial diffusion, agar spot, and co-culture assays. Cytotoxic analysis was Citation: Sudan, S.; Flick, R.; Nong, performed using pig intestinal epithelial cells (IPEC-J2). Real time-PCR was performed for studying L.; Li, J. Potential Probiotic Bacillus the effect on ETEC virulence genes and metabolomic analysis was performed using LC-MS. The subtilis Isolated from a Novel Niche results showed that CP9 cells were viable in varied bile salts and in low pH environments. CP9 Exhibits Broad Range Antibacterial showed no apparent cytotoxicity in IPEC-J2 cells. -
Arxiv.Org | Cornell University Library, July, 2019. 1
arXiv.org | Cornell University Library, July, 2019. Extremophiles: a special or general case in the search for extra-terrestrial life? Ian von Hegner Aarhus University Abstract Since time immemorial life has been viewed as fragile, yet over the past few decades it has been found that many extreme environments are inhabited by organisms known as extremophiles. Knowledge of their emergence, adaptability, and limitations seems to provide a guideline for the search of extra-terrestrial life, since some extremophiles presumably can survive in extreme environments such as Mars, Europa, and Enceladus. Due to physico-chemical constraints, the first life necessarily came into existence at the lower limit of it‟s conceivable complexity. Thus, the first life could not have been an extremophile, furthermore, since biological evolution occurs over time, then the dual knowledge regarding what specific extremophiles are capable of, and to the analogue environment on extreme worlds, will not be sufficient as a search criterion. This is because, even though an extremophile can live in an extreme environment here-and-now, its ancestor however could not live in that very same environment in the past, which means that no contemporary extremophiles exist in that environment. Furthermore, a theoretical framework should be able to predict whether extremophiles can be considered a special or general case in the galaxy. Thus, a question is raised: does Earth‟s continuous habitability represent an extreme or average value for planets? Thus, dependent on whether it is difficult or easy for worlds to maintain the habitability, the search for extra- terrestrial life with a focus on extremophiles will either represent a search for dying worlds, or a search for special life on living worlds, focusing too narrowly on extreme values. -
Archaeal Viruses and Bacteriophages: Comparisons and Contrasts
Review Archaeal viruses and bacteriophages: comparisons and contrasts Maija K. Pietila¨ , Tatiana A. Demina, Nina S. Atanasova, Hanna M. Oksanen, and Dennis H. Bamford Institute of Biotechnology and Department of Biosciences, P.O. Box 56, Viikinkaari 5, 00014 University of Helsinki, Helsinki, Finland Isolated archaeal viruses comprise only a few percent of Euryarchaeaota [9,10]. Archaea have also been cultivated all known prokaryotic viruses. Thus, the study of viruses from moderate environments such as seawater and soil. infecting archaea is still in its early stages. Here we Consequently, an additional phylum, Thaumarchaeota, summarize the most recent discoveries of archaeal vi- has been formed to contain mesophilic and thermophilic ruses utilizing a virion-centered view. We describe the ammonia-oxidizing archaea [11]. However, all known ar- known archaeal virion morphotypes and compare them chaeal viruses infect extremophiles – mainly hyperther- to the bacterial counterparts, if such exist. Viruses infect- mophiles belonging to the crenarchaeal genera Sulfolobus ing archaea are morphologically diverse and present and Acidianus or halophiles of the euryarchaeal genera some unique morphotypes. Although limited in isolate Haloarcula, Halorubrum, and Halobacterium [6,7]. Even number, archaeal viruses reveal new insights into the though bacteria are also found in diverse extreme habitats viral world, such as deep evolutionary relationships such as hypersaline lakes, archaea typically dominate at between viruses that infect hosts from all three domains extreme salinities, based on both cultivation-dependent of life. and -independent studies [6,12–15]. Consequently, archae- al viruses do the same in hypersaline environments. About Discovery of archaeal viruses 50 prokaryotic haloviruses were recently isolated from All cellular organisms are susceptible to viral infections, nine globally distant locations, and only four of them which makes viruses a major evolutionary force shaping infected bacteria [6,16]. -
Yeast Metabolic and Signaling Genes Are Required for Heat-Shock Survival
Yeast metabolic and signaling genes are required for PNAS PLUS heat-shock survival and have little overlap with the heat-induced genes Patrick A. Gibneya,b,1, Charles Lub,1, Amy A. Caudya,2,3, David C. Hessc,3, and David Botsteina,b,4 aLewis-Sigler Institute for Integrative Genomics and bDepartment of Molecular Biology, Princeton University, Princeton, NJ 08544; and cDepartment of Biology, Santa Clara University, Santa Clara, CA 95053 Contributed by David Botstein, September 30, 2013 (sent for review August 25, 2013) Genome-wide gene-expression studies have shown that hundreds or proteins that increase in abundance as part of the heat-shock of yeast genes are induced or repressed transiently by changes in response (1, 11–14). Classically, this set of genes/proteins includes temperature; many are annotated to stress response on this basis. the molecular chaperones, which often are induced in response to To obtain a genome-scale assessment of which genes are function- stress (14). However, by using the deletion collection to assay ally important for innate and/or acquired thermotolerance, we thermotolerance, we also can identify genes important for stress combined the use of a barcoded pool of ∼4,800 nonessential, pro- resistance that are either constitutively present or posttransla- totrophic Saccharomyces cerevisiae deletion strains with Illumina- tionally modified. We therefore carried out two kinds of exper- based deep-sequencing technology. As reported in other recent iment to examine heat-stress resistance. First we studied the 50 °C studies that have used deletion mutants to study stress responses, survival time-course of samples from a steady-state chemostat cul- we observed that gene deletions resulting in the highest thermo- ture of the entire prototrophic barcoded deletion collection. -
Arsenite Efflux Limits Microbial Arsenic Volatilization
Arsenite eux limits microbial arsenic volatilization Changdong Ke Huaqiao University Qingyue Kuang Huaqiao University Chungui Zhao ( [email protected] ) Jiafu Luo Huaqiao University Wenzhang Wei Huaqiao University Hend A. Alwathnani King Suad University Quaiser Saquib King Saud University Yanshuang Yu King Suad University Christopher Rensing Fujian Agriculture and Forestry University Suping Yang Huaqiao University Research article Keywords: Arsenic, As eux transporter, As methylation, Rhodopseudomonas palustris Posted Date: July 4th, 2019 DOI: https://doi.org/10.21203/rs.2.10508/v1 License: This work is licensed under a Creative Commons Attribution 4.0 International License. Read Full License Page 1/17 Abstract Background: Arsenic (As) methylation is regarded as a potential way to volatize and thereby remove As from the environment. However, most microorganisms conducting As methylation display low As volatilization eciency as As methylation is limited by As eux transporters as both processes compete for arsenite [As(III)]. In the study, we deleted arsB and acr3 from Rhodopseudomonas palustris CGA009, a good model organism for studying As detoxication, and further investigated the effect of As(III) eux transporters on As methylation. Results: Two mutants were obtained by gene deletion. Compared to the growth inhibition rate (IC50) [1.57±0.11 mmol/L As(III) and 2.67±0.04 mmol/L arsenate [As(V)] of wildtype R. palustris CGA009, the As(III) and As(V) resistance of the mutants decreased, and IC50 value of the R. palustris CGA009 ∆arsB mutant was 1.47±0.02 mmol/L As(III) and 2.12±0.03 mmol/L As(V), respectively, and that of the R. -
Title: WINOGRADSKY COLUMN AS a STRATEGY for MICROBIAL COMMUNITIES STUDY from MARINE and FRESHWATER ENVIRONMENTS
Title: WINOGRADSKY COLUMN AS A STRATEGY FOR MICROBIAL COMMUNITIES STUDY FROM MARINE AND FRESHWATER ENVIRONMENTS Authors: Copini, E.¹, de Almeida, B. N. C.¹, Canavese, C. M.¹, Cerávolo, M. S.¹, Antônio, E. S.¹, Almeida, F. P. R.¹, Camargo, M. D. C. ¹, dos Santos, G. A.¹, Machado, K. M. G.¹ Institution: ¹ Curso de Ciências Biológicas, Universidade Católica de Santos/ UniSantos (Av. Conselheiro Nébias 300, Santos, SP). Summary: Winogradsky column is widley used for microbial ecology studies and was employed to study microbial communities and assess the impact of the textile effluents in marine and freshwater environments. Soil and water samples were collected in Itaguaré, Bertioga, SP. The columns were prepared with the same nutrients (NPK, carbon and sulfur sources). Column Test received synthetic textile effluent (mixture of commercial dyes: yellow 0.1%, red 0.1% and blue 0.2%). Column without textile effluent was used as control. Incubation was carried out at room temperature, in the presence of indirect light. Visual observation was performed weekly for 2 months. Aerobic, microaerophile and anaerobic layers were processed: UFC count, isolation and characterization of axenic cultures (morphology, arrangement, response to Gram and O2 requirement, using enzymatic activities of catalase and cytochrome oxidase) and isolation of microrganisms that degrade dyes. They were used six different culture media (total bacteria, coliforms, anaerobic bacteria and red photosynthetic bacteria). Incubation at 28ºC and 37°C in the presence and absence of O2. The origin of the water and soil influence the formation of microbial communities. Prominent zonation was observed in freshwater columns, with extensive green and red zones, showing significant growth of phototrophics anaerobic bacteria.