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This volume presents a comprehensive collection of methods that have been instrumental to the current understanding of bacterial persisters. Chapters in the book cover topics ranging from general methods for measuring persister levels in Escherichia coli cultures, protocols for the determination of the persister subpopulation in Candida albicans, quantitative measurements of Type I and Type II persisters using ScanLag, to in vitro and in vivo models for the study of the intracellular activity of antibiotics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bacterial Persistence: Methods and Protocols brings together the most respected researchers in bacterial persistence whose studies will remain vital to understanding this field for many years to come.
Book Synopsis Bacterial Persistence by : Jan Michiels
Download or read book Bacterial Persistence written by Jan Michiels and published by Humana. This book was released on 2015-10-15 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume presents a comprehensive collection of methods that have been instrumental to the current understanding of bacterial persisters. Chapters in the book cover topics ranging from general methods for measuring persister levels in Escherichia coli cultures, protocols for the determination of the persister subpopulation in Candida albicans, quantitative measurements of Type I and Type II persisters using ScanLag, to in vitro and in vivo models for the study of the intracellular activity of antibiotics. Written in the highly successful Methods in Molecular Biology series format, chapters include introductions to their respective topics, lists of the necessary materials and reagents, step-by-step, readily reproducible laboratory protocols, and tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bacterial Persistence: Methods and Protocols brings together the most respected researchers in bacterial persistence whose studies will remain vital to understanding this field for many years to come.
An examination of persistent bacterial infections in the light of ecological and evolutionary principles. - Focuses on the principles of parasitism and commensalism and our ability to distinguish the two states. - Explores the ways in which persistent infections differ from acute, self-limiting bacterial infections and how both differ from the nonpathogenic commensal state. - Addresses coevolution, host adaptation, natural selection, and other fundamental biological principles. - Serves as a resource for investigators and advanced students in the field of bacterial pathogenesis.
Book Synopsis Persistent Bacterial Infections by : James P. Nataro
Download or read book Persistent Bacterial Infections written by James P. Nataro and published by . This book was released on 2000 with total page 482 pages. Available in PDF, EPUB and Kindle. Book excerpt: An examination of persistent bacterial infections in the light of ecological and evolutionary principles. - Focuses on the principles of parasitism and commensalism and our ability to distinguish the two states. - Explores the ways in which persistent infections differ from acute, self-limiting bacterial infections and how both differ from the nonpathogenic commensal state. - Addresses coevolution, host adaptation, natural selection, and other fundamental biological principles. - Serves as a resource for investigators and advanced students in the field of bacterial pathogenesis.
This volume is a collection of chapters from the leading experts in the relatively new and burgeoning field of persister cell studies. Persisters play a leading role in the recalcitrance of chronic infections, and enable the development of classical antibiotic resistance. The focus of the book is on studies that provide an understanding of the mechanisms of persister formation, antibiotic tolerance and role in disease, at the molecular level.
Book Synopsis Persister Cells and Infectious Disease by : Kim Lewis
Download or read book Persister Cells and Infectious Disease written by Kim Lewis and published by Springer Nature. This book was released on 2019-11-13 with total page 295 pages. Available in PDF, EPUB and Kindle. Book excerpt: This volume is a collection of chapters from the leading experts in the relatively new and burgeoning field of persister cell studies. Persisters play a leading role in the recalcitrance of chronic infections, and enable the development of classical antibiotic resistance. The focus of the book is on studies that provide an understanding of the mechanisms of persister formation, antibiotic tolerance and role in disease, at the molecular level.
The life of microorganisms is characterized by two main tasks, rapid growth under conditions permitting growth and survival under stressful conditions. The environments, in which microorganisms dwell, vary in space and time. The microorganisms innovate diverse strategies to readily adapt to the regularly fluctuating environments. Phenotypic heterogeneity is one such strategy, where an isogenic population splits into subpopulations that respond differently under identical environments. Bacterial persistence is a prime example of such phenotypic heterogeneity, whereby a population survives under an antibiotic attack, by keeping a fraction of population in a drug tolerant state, the persister state. Specifically, persister cells grow more slowly than normal cells under growth conditions, but survive longer under stress conditions such as the antibiotic administrations. Bacterial persistence is identified experimentally by examining the population survival upon an antibiotic treatment and the population resuscitation in a growth medium. The underlying population dynamics is explained with a two state model for reversible phenotype switching in a cell within the population. We study this existing model with a new theoretical approach and present analytical expressions for the time scale observed in population growth and resuscitation, that can be easily used to extract underlying model parameters of bacterial persistence. In addition, we recapitulate previously known results on the evolution of such structured population under periodically fluctuating environment using our simple approximation method. Using our analysis, we determine model parameters for Staphylococcus aureus population under several antibiotics and interpret the outcome of cross-drug treatment. Next, we consider the expansion of a population exhibiting phenotype switching in a spatially structured environment consisting of two growth permitting patches separated by an antibiotic patch. The dynamic interplay of growth, death and migration of cells in different patches leads to distinct regimes in population propagation speed as a function of migration rate. We map out the region in parameter space of phenotype switching and migration rate to observe the condition under which persistence is beneficial. Furthermore, we present an extended model that allows mutation from the two phenotypic states to a resistant state. We find that the presence of persister cells may enhance the probability of resistant mutation in a population. Using this model, we explain the experimental results showing the emergence of antibiotic resistance in a Staphylococcus aureus population upon tobramycin treatment. In summary, we identify several roles of bacterial persistence, such as help in spatial expansion, development of multidrug tolerance and emergence of antibiotic resistance. Our study provides a theoretical perspective on the dynamics of bacterial persistence in different environmental conditions. These results can be utilized to design further experiments, and to develop novel strategies to eradicate persistent infections.
Book Synopsis Population Dynamics of Bacterial Persistence by : Pintu Patra
Download or read book Population Dynamics of Bacterial Persistence written by Pintu Patra and published by . This book was released on 2013 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: The life of microorganisms is characterized by two main tasks, rapid growth under conditions permitting growth and survival under stressful conditions. The environments, in which microorganisms dwell, vary in space and time. The microorganisms innovate diverse strategies to readily adapt to the regularly fluctuating environments. Phenotypic heterogeneity is one such strategy, where an isogenic population splits into subpopulations that respond differently under identical environments. Bacterial persistence is a prime example of such phenotypic heterogeneity, whereby a population survives under an antibiotic attack, by keeping a fraction of population in a drug tolerant state, the persister state. Specifically, persister cells grow more slowly than normal cells under growth conditions, but survive longer under stress conditions such as the antibiotic administrations. Bacterial persistence is identified experimentally by examining the population survival upon an antibiotic treatment and the population resuscitation in a growth medium. The underlying population dynamics is explained with a two state model for reversible phenotype switching in a cell within the population. We study this existing model with a new theoretical approach and present analytical expressions for the time scale observed in population growth and resuscitation, that can be easily used to extract underlying model parameters of bacterial persistence. In addition, we recapitulate previously known results on the evolution of such structured population under periodically fluctuating environment using our simple approximation method. Using our analysis, we determine model parameters for Staphylococcus aureus population under several antibiotics and interpret the outcome of cross-drug treatment. Next, we consider the expansion of a population exhibiting phenotype switching in a spatially structured environment consisting of two growth permitting patches separated by an antibiotic patch. The dynamic interplay of growth, death and migration of cells in different patches leads to distinct regimes in population propagation speed as a function of migration rate. We map out the region in parameter space of phenotype switching and migration rate to observe the condition under which persistence is beneficial. Furthermore, we present an extended model that allows mutation from the two phenotypic states to a resistant state. We find that the presence of persister cells may enhance the probability of resistant mutation in a population. Using this model, we explain the experimental results showing the emergence of antibiotic resistance in a Staphylococcus aureus population upon tobramycin treatment. In summary, we identify several roles of bacterial persistence, such as help in spatial expansion, development of multidrug tolerance and emergence of antibiotic resistance. Our study provides a theoretical perspective on the dynamics of bacterial persistence in different environmental conditions. These results can be utilized to design further experiments, and to develop novel strategies to eradicate persistent infections.
Bacteria are the most ubiquitous of all organisms. Responsible for a number of diseases and for many of the chemical cycles on which life depends, they are genetically adaptable. Vital to this adaptability is the existence of autonomous genetic elements-plasmids-which promote genetic exchange and recombination. The genes carried by any particular plasmid may be found in only a few individuals of any species but can also be shared with other species and thus constitute a horizontal gene pool. This book explains the various contributions that plasmids make to this pool: the replication, stable inheritance and transfer modules, the phenotypic markers they carry, the way they evolve, the ways they contribute to their host population and the approaches that we use to study and classify them. It also looks at what we know about their activity in natural communities and the way that they interact with other mobile elements to promote bacterial evolution.
Book Synopsis Horizontal Gene Pool by : Christopher M. Thomas
Download or read book Horizontal Gene Pool written by Christopher M. Thomas and published by CRC Press. This book was released on 2003-09-02 with total page 459 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacteria are the most ubiquitous of all organisms. Responsible for a number of diseases and for many of the chemical cycles on which life depends, they are genetically adaptable. Vital to this adaptability is the existence of autonomous genetic elements-plasmids-which promote genetic exchange and recombination. The genes carried by any particular plasmid may be found in only a few individuals of any species but can also be shared with other species and thus constitute a horizontal gene pool. This book explains the various contributions that plasmids make to this pool: the replication, stable inheritance and transfer modules, the phenotypic markers they carry, the way they evolve, the ways they contribute to their host population and the approaches that we use to study and classify them. It also looks at what we know about their activity in natural communities and the way that they interact with other mobile elements to promote bacterial evolution.
Persistent Viral Infections Edited by Rafi Ahmed Emory Vaccine Center, Atlanta, USA and Irvin S. Y. Chen UCLA School of Medicine, Los Angeles, USA During the past decade much of our attention has focused on diseases associated with viral persistence. Major breakthroughs in immunology, and the advent of molecular approaches to study pathogenesis have increased our understanding of the complex virus-host interactions that occur during viral persistence. Persistent Viral Infections focuses on: * The pathogenesis and immunology of chronic infections * Animal models that provide, or have the potential to provide, major insights This volume will be essential reading for virologists, immunologists, oncologists and neurologists.
Book Synopsis Persistent Viral Infections by : R. Ahmed
Download or read book Persistent Viral Infections written by R. Ahmed and published by Wiley-Blackwell. This book was released on 1999 with total page 754 pages. Available in PDF, EPUB and Kindle. Book excerpt: Persistent Viral Infections Edited by Rafi Ahmed Emory Vaccine Center, Atlanta, USA and Irvin S. Y. Chen UCLA School of Medicine, Los Angeles, USA During the past decade much of our attention has focused on diseases associated with viral persistence. Major breakthroughs in immunology, and the advent of molecular approaches to study pathogenesis have increased our understanding of the complex virus-host interactions that occur during viral persistence. Persistent Viral Infections focuses on: * The pathogenesis and immunology of chronic infections * Animal models that provide, or have the potential to provide, major insights This volume will be essential reading for virologists, immunologists, oncologists and neurologists.
Book Synopsis Population Antibiotic-resistance by : Sharon Lindsay
Download or read book Population Antibiotic-resistance written by Sharon Lindsay and published by . This book was released on 2005 with total page 388 pages. Available in PDF, EPUB and Kindle. Book excerpt:
The first and only comprehensive reference/solutions manual for managing food safety in low-moisture foods The first book devoted to an increasingly critical public health issue, Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods reviews the current state of the science on the prevalence and persistence of bacterial pathogens in low-moisture foods and describes proven techniques for preventing food contamination for manufacturers who produce those foods. Many pathogens, such as Salmonella, due to their enhanced thermal resistance in dry environments, can survive the drying process and may persist for prolonged periods in low-moisture foods, especially when stored in refrigerated environments. Bacterial contamination of low-moisture foods, such as peanut butter, present a vexing challenge to food safety, and especially now, in the wake of widely publicized food safety related events, food processors urgently need up-to-date, practical information on proven measures for containing the risk of contamination. While much has been written on the subject, until now it was scattered throughout the world literature in scientific and industry journals. The need for a comprehensive treatment of the subject has never been greater, and now this book satisfies that need. Discusses a wide variety of foods and evaluates multiple processing platforms from the standpoint of process validation of all food safety objectives for finished food products Takes a practical approach integrating the latest scientific and technological advances in a handy working resource Presents all known sources and risk factors for pathogenic bacteria of concern in the manufacturing environment for low-moisture/water activity products Characterizes the persistence and thermal resistance of bacterial pathogens in both the environment and most low-moisture food products Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods is a much-needed resource for food microbiologists and food industry scientists, as well as managers and executives in companies that produce and use low-moisture foods. It also belongs on the reference shelves of food safety regulatory agencies worldwide.
Book Synopsis Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods by : Richard Podolak
Download or read book Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods written by Richard Podolak and published by John Wiley & Sons. This book was released on 2017-09-05 with total page 276 pages. Available in PDF, EPUB and Kindle. Book excerpt: The first and only comprehensive reference/solutions manual for managing food safety in low-moisture foods The first book devoted to an increasingly critical public health issue, Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods reviews the current state of the science on the prevalence and persistence of bacterial pathogens in low-moisture foods and describes proven techniques for preventing food contamination for manufacturers who produce those foods. Many pathogens, such as Salmonella, due to their enhanced thermal resistance in dry environments, can survive the drying process and may persist for prolonged periods in low-moisture foods, especially when stored in refrigerated environments. Bacterial contamination of low-moisture foods, such as peanut butter, present a vexing challenge to food safety, and especially now, in the wake of widely publicized food safety related events, food processors urgently need up-to-date, practical information on proven measures for containing the risk of contamination. While much has been written on the subject, until now it was scattered throughout the world literature in scientific and industry journals. The need for a comprehensive treatment of the subject has never been greater, and now this book satisfies that need. Discusses a wide variety of foods and evaluates multiple processing platforms from the standpoint of process validation of all food safety objectives for finished food products Takes a practical approach integrating the latest scientific and technological advances in a handy working resource Presents all known sources and risk factors for pathogenic bacteria of concern in the manufacturing environment for low-moisture/water activity products Characterizes the persistence and thermal resistance of bacterial pathogens in both the environment and most low-moisture food products Control of Salmonella and Other Bacterial Pathogens in Low-Moisture Foods is a much-needed resource for food microbiologists and food industry scientists, as well as managers and executives in companies that produce and use low-moisture foods. It also belongs on the reference shelves of food safety regulatory agencies worldwide.
Bacterial persistence is a transient state of dormancy exhibited by a small subset of cells that allow them to survive antibiotic treatment. This is a ubiquitous phenomenon exhibited by all bacteria to all known classes of antibiotics which can result in chronic and relapsing infections. Persister cells are bacteria that are metabolically tolerant, not genetically resistant to antibiotics. However, because they confer survival in the presence of antibiotics, they pose a risk of developing resistance. Antibiotic resistance is currently a world-wide problem as resistant infections are becoming more numerous and the discovery rate of novel antibiotics is decreasing. Biofilms contain increased levels of persisters due to the nutrient limiting conditions in the interior of the biofilm due to limiting diffusion rates through the dense extracellular polymeric matrix. The specific mechanisms that lead to persistence are redundant making them difficult to overcome pharmacologically. Stress responses are thought to push the cell towards a dormant state in response to either accidental damage from cellular processes, or to antibiotics. Toxin-antitoxin systems have been shown to increase levels of persister cells increasing the lag time after inoculation from overnight cultures. Persisters are difficult to study because they appear at such low frequencies in metabolically heterogenous populations. Experimenters are thus forced to choose between scale and resolution as single-cell experiments fail to observe sufficient numbers of cells. Many labs utilize methods of enriching for persisters, though the largest problem is that persisters cannot be identified except by surviving antibiotic treatments. This thesis discusses novel methods that can be used to study persistence and chronic bacterial infection. Recent advances in CRISPR biotechnology have created a large toolbox of molecular techniques. CRISPR-Cas9 is best known for creating gene knockouts with ease, but an enzymatically inactivated Cas9 has been developed and repurposed as a tool for gene knockdown. The gene target can be customized by modifying the CRISPR gRNA that is responsible for targeting the Cas9 to a gene by base-pair complementarity. This technology was validated in our lab by confirming knockdown of lacZ expression with blue-white selection. A detailed method for creating gRNA was reproduced from the original paper. Novel gRNAs were designed and cloned into the CRISPRi system to target the stringent response genes relA and spoT. These genes control the levels of the alarmone (p)ppGpp in the cell which when in abundance downregulates genes associated with growth and division and upregulates genes associated with survival. Targeting these genes with CRISPRi was explored as a mechanism of decreasing persistence to antibiotics in preliminary experiments. A top-down analysis was also used to investigate genes associated with chronic infections in nontypeable Haemophilus influenzae (NTHi). A large NTHi genomic dataset containing the whole genome sequences for thousands of clinical isolates, for which clinical metadata are available, is a valuable asset of our lab. Recently, Facebook published a machine learning model for classifying protein variants that had been trained one 250,000,000 proteins. We applied this model to all unique protein sequences in our NTHI genomic collection. These data were used to examine each gene for clusters of variants that correlated with the clinical metadata. A pipeline was developed to assess the strength of correlation with categories including health state, infection type, and patient age. Top hits were identified from significant hits with particular interest in clusters containing a single category of metadata (e.g., only sick isolates).
Book Synopsis Bacterial Persistence and Biofilms by : Phillip Richard Palmer
Download or read book Bacterial Persistence and Biofilms written by Phillip Richard Palmer and published by . This book was released on 2022 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt: Bacterial persistence is a transient state of dormancy exhibited by a small subset of cells that allow them to survive antibiotic treatment. This is a ubiquitous phenomenon exhibited by all bacteria to all known classes of antibiotics which can result in chronic and relapsing infections. Persister cells are bacteria that are metabolically tolerant, not genetically resistant to antibiotics. However, because they confer survival in the presence of antibiotics, they pose a risk of developing resistance. Antibiotic resistance is currently a world-wide problem as resistant infections are becoming more numerous and the discovery rate of novel antibiotics is decreasing. Biofilms contain increased levels of persisters due to the nutrient limiting conditions in the interior of the biofilm due to limiting diffusion rates through the dense extracellular polymeric matrix. The specific mechanisms that lead to persistence are redundant making them difficult to overcome pharmacologically. Stress responses are thought to push the cell towards a dormant state in response to either accidental damage from cellular processes, or to antibiotics. Toxin-antitoxin systems have been shown to increase levels of persister cells increasing the lag time after inoculation from overnight cultures. Persisters are difficult to study because they appear at such low frequencies in metabolically heterogenous populations. Experimenters are thus forced to choose between scale and resolution as single-cell experiments fail to observe sufficient numbers of cells. Many labs utilize methods of enriching for persisters, though the largest problem is that persisters cannot be identified except by surviving antibiotic treatments. This thesis discusses novel methods that can be used to study persistence and chronic bacterial infection. Recent advances in CRISPR biotechnology have created a large toolbox of molecular techniques. CRISPR-Cas9 is best known for creating gene knockouts with ease, but an enzymatically inactivated Cas9 has been developed and repurposed as a tool for gene knockdown. The gene target can be customized by modifying the CRISPR gRNA that is responsible for targeting the Cas9 to a gene by base-pair complementarity. This technology was validated in our lab by confirming knockdown of lacZ expression with blue-white selection. A detailed method for creating gRNA was reproduced from the original paper. Novel gRNAs were designed and cloned into the CRISPRi system to target the stringent response genes relA and spoT. These genes control the levels of the alarmone (p)ppGpp in the cell which when in abundance downregulates genes associated with growth and division and upregulates genes associated with survival. Targeting these genes with CRISPRi was explored as a mechanism of decreasing persistence to antibiotics in preliminary experiments. A top-down analysis was also used to investigate genes associated with chronic infections in nontypeable Haemophilus influenzae (NTHi). A large NTHi genomic dataset containing the whole genome sequences for thousands of clinical isolates, for which clinical metadata are available, is a valuable asset of our lab. Recently, Facebook published a machine learning model for classifying protein variants that had been trained one 250,000,000 proteins. We applied this model to all unique protein sequences in our NTHI genomic collection. These data were used to examine each gene for clusters of variants that correlated with the clinical metadata. A pipeline was developed to assess the strength of correlation with categories including health state, infection type, and patient age. Top hits were identified from significant hits with particular interest in clusters containing a single category of metadata (e.g., only sick isolates).
The Janeway's Immunobiology CD-ROM, Immunobiology Interactive, is included with each book, and can be purchased separately. It contains animations and videos with voiceover narration, as well as the figures from the text for presentation purposes.
Book Synopsis Janeway's Immunobiology by : Kenneth Murphy
Download or read book Janeway's Immunobiology written by Kenneth Murphy and published by Garland Science. This book was released on 2010-06-22 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: The Janeway's Immunobiology CD-ROM, Immunobiology Interactive, is included with each book, and can be purchased separately. It contains animations and videos with voiceover narration, as well as the figures from the text for presentation purposes.
