What Can Microbial Genetics Teach Sociobiology?
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Ecology and Evolution of Metabolic Cross-Feeding Interactions in Bacteria† Cite This: Nat
Natural Product Reports View Article Online REVIEW View Journal | View Issue Ecology and evolution of metabolic cross-feeding interactions in bacteria† Cite this: Nat. Prod. Rep.,2018,35,455 Glen D'Souza, ab Shraddha Shitut, ce Daniel Preussger,c Ghada Yousif,cde Silvio Waschina f and Christian Kost *ce Literature covered: early 2000s to late 2017 Bacteria frequently exchange metabolites with other micro- and macro-organisms. In these often obligate cross-feeding interactions, primary metabolites such as vitamins, amino acids, nucleotides, or growth factors are exchanged. The widespread distribution of this type of metabolic interactions, however, is at odds with evolutionary theory: why should an organism invest costly resources to benefit other individuals rather than using these metabolites to maximize its own fitness? Recent empirical work has fi fi Creative Commons Attribution 3.0 Unported Licence. shown that bacterial genotypes can signi cantly bene t from trading metabolites with other bacteria relative to cells not engaging in such interactions. Here, we will provide a comprehensive overview over the ecological factors and evolutionary mechanisms that have been identified to explain the evolution Received 25th January 2018 and maintenance of metabolic mutualisms among microorganisms. Furthermore, we will highlight DOI: 10.1039/c8np00009c general principles that underlie the adaptive evolution of interconnected microbial metabolic networks rsc.li/npr as well as the evolutionary consequences that result for cells living in such communities. 1 Introduction 2.5 Mechanisms of metabolite transfer This article is licensed under a 2 Metabolic cross-feeding interactions 2.5.1 Contact-independent mechanisms 2.1 Historical account 2.5.1.1 Passive diffusion 2.2 Classication of cross-feeding interactions 2.5.1.2 Active transport 2.2.1 Unidirectional by-product cross-feeding 2.5.1.3 Vesicle-mediated transport Open Access Article. -
New Insights Into the Co-Occurrences of Glycoside Hydrolase Genes Among Prokaryotic Genomes Through Network Analysis
microorganisms Article New Insights into the Co-Occurrences of Glycoside Hydrolase Genes among Prokaryotic Genomes through Network Analysis Alei Geng * , Meng Jin, Nana Li, Daochen Zhu , Rongrong Xie, Qianqian Wang, Huaxing Lin and Jianzhong Sun * Biofuels Institute, School of the Environment and Safety Engineering, Jiangsu University, Zhenjiang 212013, China; [email protected] (M.J.); [email protected] (N.L.); [email protected] (D.Z.); [email protected] (R.X.); [email protected] (Q.W.); [email protected] (H.L.) * Correspondence: [email protected] (A.G.); [email protected] (J.S.) Abstract: Glycoside hydrolase (GH) represents a crucial category of enzymes for carbohydrate uti- lization in most organisms. A series of glycoside hydrolase families (GHFs) have been classified, with relevant information deposited in the CAZy database. Statistical analysis indicated that most GHFs (134 out of 154) were prone to exist in bacteria rather than archaea, in terms of both occurrence frequencies and average gene numbers. Co-occurrence analysis suggested the existence of strong or moderate-strong correlations among 63 GHFs. A combination of network analysis by Gephi and functional classification among these GHFs demonstrated the presence of 12 functional categories (from group A to L), with which the corresponding microbial collections were subsequently labeled, respectively. Interestingly, a progressive enrichment of particular GHFs was found among several types of microbes, and type-L as well as type-E microbes were deemed as functional intensified Citation: Geng, A.; Jin, M.; Li, N.; species which formed during the microbial evolution process toward efficient decomposition of Zhu, D.; Xie, R.; Wang, Q.; Lin, H.; lignocellulose as well as pectin, respectively. -
Understanding Microbial Cooperation
Journal of Theoretical Biology 299 (2012) 31–41 Contents lists available at ScienceDirect Journal of Theoretical Biology journal homepage: www.elsevier.com/locate/yjtbi Understanding microbial cooperation James A. Damore, Jeff Gore à Department of Physics, Massachusetts Institute of Technology, 77 Massachusetts Ave., Cambridge, MA, United States article info abstract Available online 17 March 2011 The field of microbial cooperation has grown enormously over the last decade, leading to improved Keywords: experimental techniques and a growing awareness of collective behavior in microbes. Unfortunately, Evolutionary game theory many of our theoretical tools and concepts for understanding cooperation fail to take into account the Kin selection peculiarities of the microbial world, namely strong selection strengths, unique population structure, Hamilton’s rule and non-linear dynamics. Worse yet, common verbal arguments are often far removed from the math Multilevel selection involved, leading to confusion and mistakes. Here, we review the general mathematical forms of Price’s Price’s equation equation, Hamilton’s rule, and multilevel selection as they are applied to microbes and provide some intuition on these otherwise abstract formulas. However, these sometimes overly general equations can lack specificity and predictive power, ultimately forcing us to advocate for more direct modeling techniques. & 2011 Elsevier Ltd. All rights reserved. 1. Introduction do not hold, both methods resort to abstract generalities, making application difficult and prone to error. Cooperation presents a fundamental challenge to customary Microbes present a unique opportunity for scientists interested in evolutionary thinking. If only the fittest organisms survive, why the evolution of cooperation because of their well-characterized and would an individual ever pay a fitness cost for another organism simple genetics, fast generation times, and easily manipulated and to benefit? Traditionally, kin selection and group selection have measured interactions. -
Metabolic Modeling of Microbial Community Interactions for Health, En- Vironmental and Biotechnological Applications
Send Orders for Reprints to [email protected] 712 Current Genomics, 2018, 19, 712-722 REVIEW ARTICLE Metabolic Modeling of Microbial Community Interactions for Health, En- vironmental and Biotechnological Applications Kok Siong Ang1, Meiyappan Lakshmanan1, Na-Rae Lee2 and Dong-Yup Lee1,2,3,* 1Bioprocessing Technology Institute (BTI), A*STAR, Singapore 138668, Singapore; 2Department of Chemical and Bio- molecular Engineering, and NUS Synthetic Biology for Clinical and Technological Innovation (SynCTI), National Uni- versity of Singapore, Singapore 117585, Singapore; 3School of Chemical Engineering, Sungkyunkwan University, 2066 Seobu-ro, Jangan-gu, Suwon, Gyeonggi-do 16419, Republic of Korea Abstract: In nature, microbes do not exist in isolation but co-exist in a variety of ecological and bio- logical environments and on various host organisms. Due to their close proximity, these microbes in- teract among themselves, and also with the hosts in both positive and negative manners. Moreover, these interactions may modulate dynamically upon external stimulus as well as internal community changes. This demands systematic techniques such as mathematical modeling to understand the intrin- sic community behavior. Here, we reviewed various approaches for metabolic modeling of microbial A R T I C L E H I S T O R Y communities. If detailed species-specific information is available, segregated models of individual or- Received: June 25, 2017 ganisms can be constructed and connected via metabolite exchanges; otherwise, the community may Revised: November 08, 2017 be represented as a lumped network of metabolic reactions. The constructed models can then be simu- Accepted: November 11, 2017 lated to help fill knowledge gaps, and generate testable hypotheses for designing new experiments. -
Cooperation in Microbial Populations: Theory and Experimental Model Systems
Review Cooperation in Microbial Populations: Theory and Experimental Model Systems J. Cremer 1,A.Melbinger3,K.Wienand3,T.Henriquez2, H. Jung 2 and E. Frey 3 1 - Department of Molecular Immunology and Microbiology, Groningen Biomolecular Sciences and Biotechnology Institute, University of Groningen, 9747 AG Groningen, the Netherlands 2 - Microbiology, Department of Biology I, Ludwig-Maximilians-Universitat€ München, Grosshaderner Strasse 2-4, Martinsried, Germany 3 - Arnold-Sommerfeld-Center for Theoretical Physics and Center for Nanoscience, Ludwig-Maximilians-Universitat€ München, Theresienstrasse 37, D-80333 Munich, Germany Correspondence to E. Frey and H. Jung: [email protected], [email protected] https://doi.org/10.1016/j.jmb.2019.09.023 Edited by Ulrich Gerland Abstract Cooperative behavior, the costly provision of benefits to others, is common across all domains of life. This review article discusses cooperative behavior in the microbial world, mediated by the exchange of extracellular products called public goods. We focus on model species for which the production of a public good and the related growth disadvantage for the producing cells are well described. To unveil the biological and ecological factors promoting the emergence and stability of cooperative traits we take an interdisciplinary perspective and review insights gained from both mathematical models and well-controlled experimental model systems. Ecologically, we include crucial aspects of the microbial life cycle into our analysis and particularly consider population structures where ensembles of local communities (subpopulations) continuously emerge, grow, and disappear again. Biologically, we explicitly consider the synthesis and regulation of public good production. The discussion of the theoretical approaches includes general evolutionary concepts, population dynamics, and evolutionary game theory. -
Eco-Evolutionary Dynamics of Decomposition: Scaling up From
1 Eco-evolutionary dynamics of decomposition: scaling up from 2 microbial cooperation to ecosystem function 1,2* 3,4 2,5,6 3 Elsa Abs , H´el`eneLeman , and R´egisFerri`ere 1 4 Department of Ecology and Evolutionary Biology, University of California, Irvine, CA 5 92697, USA. 2 6 Interdisciplinary Center for Interdisciplinary Global Environmental Studies (iGLOBES), 7 CNRS, Ecole Normale Sup´erieure, Paris Sciences & Lettres University, University of 8 Arizona, Tucson AZ 85721, USA. 3 9 Numed Inria team, UMPA UMR 5669, Ecole Normale Sup´erieure, 69364 Lyon, France. 4 10 Centro de Investigaci´onen Matem´aticas, 36240 Guanajuato, M´exico. 5 11 Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ 85721, 12 USA. 6 13 Institut de Biologie (IBENS), Ecole Normale Sup´erieure, Paris Sciences & Lettres 14 University, CNRS, INSERM, 75005 Paris, France. 15 16 Keywords: Degradative exoenzyme, Evolutionary stability, Spatial structure, Scaling limits, Soil 17 carbon stock, Eco-evolutionary feedback, Adaptive dynamics. 18 Type of Article: Article 19 Number of words in the abstract: 165 20 Number of words in the main text: 2883 21 Number of references: 48 22 Number of figures: 5 23 Corresponding author: Elsa Abs. Phone: (520) 208-1112. Email address: [email protected] Elsa Abs: [email protected]: Corresponding author H´el`eneLeman: [email protected] R´egisFerri`ere:[email protected] 24 The decomposition of soil organic matter (SOM) is a critically important process in 25 global terrestrial ecosystems. SOM decomposition is driven by micro-organisms that 26 cooperate by secreting costly extracellular enzymes. This raises a basic puzzle: the 27 stability of microbial decomposition in spite of its evolutionary vulnerability to 28 `cheaters'|mutant strains that reap the benefits of cooperation while paying a lower 29 cost. -
Mechanisms of Microbial Genetics 443
Chapter 11 | Mechanisms of Microbial Genetics 443 Chapter 11 Mechanisms of Microbial Genetics Figure 11.1 Escherichia coli (left) may not appear to have much in common with an elephant (right), but the genetic blueprints for these vastly different organisms are both encoded in DNA. (credit left: modification of work by NIAID; credit right: modification of work by Tom Lubbock) Chapter Outline 11.1 The Functions of Genetic Material 11.2 DNA Replication 11.3 RNA Transcription 11.4 Protein Synthesis (Translation) 11.5 Mutations 11.6 How Asexual Prokaryotes Achieve Genetic Diversity 11.7 Gene Regulation: Operon Theory Introduction In 1954, French scientist and future Nobel laureate Jacques Monod (1910–1976) famously said, “What is true in E. coli is true in the elephant,” suggesting that the biochemistry of life was maintained throughout evolution and is shared in all forms of known life. Since Monod’s famous statement, we have learned a great deal about the mechanisms of gene regulation, expression, and replication in living cells. All cells use DNA for information storage, share the same genetic code, and use similar mechanisms to replicate and express it. Although many aspects of genetics are universally shared, variations do exist among contemporary genetic systems. We now know that within the shared overall theme of the genetic mechanism, there are significant differences among the three domains of life: Eukarya, Archaea, and Bacteria. Additionally, viruses, cellular parasites but not themselves living cells, show dramatic variation in their genetic material and the replication and gene expression processes. Some of these differences have allowed us to engineer clinical tools such as antibiotics and antiviral drugs that specifically inhibit the reproduction of pathogens yet are harmless to their hosts. -
Microbial Genetics 428L/528L - Laboratory Course Dr
MIC et al. 428/528L D. Baltrus Microbial Genetics 428L/528L - Laboratory Course Dr. David Baltrus Spring 2015 INTRODUCTION Welcome to the exciting world of Microbial Genetics. MIC428L/528L is going to be your opportunity to experience the hands-on experimental part of microbial genetics. It is important to remember that the field of Microbial Genetics consists of an extremely large area; in this laboratory we will expose you to some of the major theories and techniques used daily in thousands of microbial genetics research labs around the world. In fact, most of the experiments you will perform are used regularly in the research of Dr. Baltrus. Microbial Genetics 428L/528L is a constantly evolving course. Most students take the lecture (MIC428R/528R) and lab simultaneously. Although the laboratory runs concurrently with the lecture, it is impossible to match the laboratory exercises with the lecture material due to the different rates with which the information can be imparted to you and the limited laboratory periods available. At several points the laboratory utilizes techniques not yet covered in lecture. In addition, several laboratory periods are devoted to the DNA sequence analysis module taught in the Bioscience Learning Center (BLC) located in the Henry Koffler building. LABORATORY GOALS The overall goal of this laboratory course is to expose you to realistic microbial genetics research. Some laboratory periods will be short. Occasionally you will be required to come in during a non-scheduled lab time or day to continue the experimental protocol. Experience over the past several years re-enforces the maxim that your success and failure is directly related to your preparation and carefulness in the laboratory. -
Microbial Genetics and Genomics 11:680:480
COURSE SYLLABUS Microbial Genetics and Genomics 11:680:480 COURSE OVERVIEW: Microbial Genetics and Genomics 11:680:480 Spring Semester CONTACT INFORMATION: Instructor(s): Dr. Gerben Zylstra Office Location: Foran, Room 322 Email: [email protected] Office Hours: By arrangement COURSE WEBSITE, RESOURCES AND MATERIALS: • Canvas COURSE DESCRIPTION: Genetics of bacteria and phage, focusing on replication, repair, transcription, translation, gene regulation, genetic networks, plasmids, conjugation, transformation, microbial and phage interactions, and different types of phage and their lifestyles. LEARNING GOALS: Understand the biochemical mechanisms underpinning replication, transcription, and translation Appreciate the diversity of mechanisms used by bacteria to regulate gene expression Demonstrate knowledge of the biochemistry behind conjugation and transformation Recognize the diverse types and lifestyles of phage ASSIGNMENTS/RESPONSIBILITIES, GRADING & ASSESSMENT: Three exams each covering one third of the course (100 points each) and repeated questions from exam 1 and 2 on the third exam (40 points) ACCOMODATIONS FOR STUDENTS WITH DISABILITIES Please follow the procedures outlined at https://ods.rutgers.edu/students/registration-form. Full policies and procedures are at https://ods.rutgers.edu/ ABSENCE POLICY If you miss class please check with other students about what you missed. All lecture notes and all important announcements will be posted on Canvas. If you arrive late for class please come in quietly and find an open seat. -
Microbiology and Molecular Genetics 1
Microbiology and Molecular Genetics 1 For certification and completion of the BS degree, students will take MICROBIOLOGY AND one year of clinical internship in program accredited by the National Accrediting Agency for Clinical Laboratory Science (NAACLS) and MOLECULAR GENETICS affiliated with Oklahoma State University. Students have the options of the following hospitals/programs: Comanche County Memorial Hospital, Microbiology/Cell and Molecular Biology Lawton, OK; St. Francis Hospital, Tulsa, OK; Mercy Hospital, Ada, OK; Mercy Hospital, Ardmore, OK. Microbiology is the hands-on study of bacteria, viruses, fungi and algae and their many relationships to humans, animals, plants and the Medical Laboratory Science is unique in allowing students to enter environment. Cell and molecular biology bridges the fields of chemistry, the health profession directly after obtaining a BS degree. Clinical biochemistry and biology as it seeks to understand life and cellular laboratory scientists comprise the third-largest segment of the healthcare processes at the molecular level. Microbiologists apply their knowledge professions and are an important member of the healthcare team, to infectious diseases and pathogenic mechanisms; food production working alongside doctors and nurses. Students who complete and preservation, industrial fermentations which produce chemicals, Microbiology/Cell and Molecular Biology with the MLS option enjoy a drugs, antibiotics, alcoholic beverages and various food products; 100% employment rate upon graduation. biodegradation of toxic chemicals and other materials present in the environment; insect pathology; the exciting and expanding field of Courses biotechnology which endeavors to utilize living organisms to solve GENE 5102 Molecular Genetics important problems in medicine, agriculture, and environmental science; Prerequisites: BIOC 3653 or MICR 3033 and one course in genetics or infectious diseases; and public health and sanitation. -
Biosc1280 2017 Syllabus 1-3-17
BIOSC 1280 MICROBIAL GENETIC ENGINEERING SPRING TERM 2017 SYLLABUS AND COURSE POLICIES LECTURERS: Dr. Karen Arndt Dr. Graham Hatfull A316 Langley Hall 378 Crawford Hall Office hours: by appointment Office hours: by appointment Phone: 624-6963 Phone: 624-4350 email: [email protected] email: [email protected] LECTURES: Mon., Wed., Fri. 11:00 – 11:50 a.m. Langley Hall, Room A214 COURSE DESCRIPTION Microbes – both prokaryotic and eukaryotic – are critical to our understanding of the fundamentals of biology at the molecular level as well as for understanding human diseases. Microbes such as bacteria and yeast are advantageous in that they can be grown to very large numbers in small volumes, making them ideal for genetic approaches that require the isolation of mutants with informative phenotypes and for understanding the roles that genes perform. In this course we will discuss fundamental aspects of microbial genetics in bacteria and yeast and how this information can be used to understand pathogenic and inherent human diseases. LEARNING OBJECTIVES Upon completing this course, you will be able to apply the theories of classical and modern molecular genetic analysis of prokaryotic and eukaryotic microorganisms to current problems in microbial genetics. PREREQUISITES Completion of BioSc1850 Microbiology, with a grade of C or better. Please consult with the instructors if you have not satisfied this requirement or the prerequisites for BioSc1850. TEXTBOOKS Required Molecular Genetics of Bacteria, fourth edition (2013), by Larry Snyder, Joseph Peters, Tina Henkin and Wendy Champness. Published by ASM Press, Washington D.C. This textbook contains readings and problems that are required for successful completion of the prokaryotic section of the course. -
Plant & Microbial Biology
Plant & Microbial Biology 1 PLANTBI 200A Plant Developmental Genetics Plant & Microbial 1.5 Unit Terms offered: Fall 2021, Fall 2020, Fall 2019 Biology The students will be provided with both the basic framework and current topics of plant developmental genetics. Overview Plant Developmental Genetics: Read More [+] Rules & Requirements The Department of Plant and Microbial Biology consists of the Division of Plant Biology and the Division of Microbial Biology. Programs at both the Prerequisites: Consent of instructor undergraduate and graduate levels have been designed to offer students maximum flexibility in defining their own areas of interest. In addition to Hours & Format departmental resources that are available in Koshland Hall, the facilities Fall and/or spring: 5 weeks - 4 hours of lecture and 2 hours of of the College of Natural Resources Biological Imaging Facility and the discussion per week United States Department of Agriculture Plant Gene Expression Center are available for the programs of the department. Additional Details The Division of Plant Biology Subject/Course Level: Plant and Microbial Biology/Graduate The Division of Plant Biology program emphasizes basic research and its Grading: Letter grade. application to plants and promotes the design of plant biotechnologies. With an increasing awareness of environmental problems, global Instructor: Hake changes, and emerging food needs, plants are a focal point for new research initiatives and educational training programs. Understanding the Plant Developmental Genetics: Read Less [-] biology of plants, their development, their responses to the environment, and the impact of human activities on the plant biosphere are many of PLANTBI 200B Genomics and Computational the challenges that will continue to fuel the expansion of plant biology Biology 1.5 Unit research well into the twenty-first century.