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The Bacterial Nucleoid

Author: Olivier Espéli

Publisher: Humana Press

Published: 2017-08-25

Total Pages: 374

ISBN-13: 9781493970971

This volume presents state-of-the-art protocols for key experiments that have revolutionized our understanding of the bacterial nucleoid. This book is divided into five parts: Part I introduces molecular genetic methods to study bacterial nucleoids; Part II highlights the study of bacterial nucleoid with whole genome analysis method; Part III discusses molecular biology methods to study nucleoid structuring factors; Part IV looks at imaging bacterial nucleoid; and Part V explores biophysics of the bacterial nucleoid. 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. Thorough and cutting-edge, The Bacterial Nucleoid: Methods and Protocols is a valuable resource that provides a wealth of new information about this chromosome.

Prokaryotic Cytoskeletons

Author: Jan Löwe

Publisher: Springer

Published: 2017-05-11

Total Pages: 450

ISBN-13: 331953047X

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This book describes the structures and functions of active protein filaments, found in bacteria and archaea, and now known to perform crucial roles in cell division and intra-cellular motility, as well as being essential for controlling cell shape and growth. These roles are possible because the cytoskeletal and cytomotive filaments provide long range order from small subunits. Studies of these filaments are therefore of central importance to understanding prokaryotic cell biology. The wide variation in subunit and polymer structure and its relationship with the range of functions also provide important insights into cell evolution, including the emergence of eukaryotic cells. Individual chapters, written by leading researchers, review the great advances made in the past 20-25 years, and still ongoing, to discover the architectures, dynamics and roles of filaments found in relevant model organisms. Others describe one of the families of dynamic filaments found in many species. The most common types of filament are deeply related to eukaryotic cytoskeletal proteins, notably actin and tubulin that polymerise and depolymerise under the control of nucleotide hydrolysis. Related systems are found to perform a variety of roles, depending on the organisms. Surprisingly, prokaryotes all lack the molecular motors associated with eukaryotic F-actin and microtubules. Archaea, but not bacteria, also have active filaments related to the eukaryotic ESCRT system. Non-dynamic fibres, including intermediate filament-like structures, are known to occur in some bacteria.. Details of known filament structures are discussed and related to what has been established about their molecular mechanisms, including current controversies. The final chapter covers the use of some of these dynamic filaments in Systems Biology research. The level of information in all chapters is suitable both for active researchers and for advanced students in courses involving bacterial or archaeal physiology, molecular microbiology, structural cell biology, molecular motility or evolution. Chapter 3 of this book is open access under a CC BY 4.0 license.

Bacterial Chromatin

Author: Remus T. Dame

Publisher: Humana

Published: 2024-08-26

Total Pages: 0

ISBN-13: 9781071639290

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This second edition brings together new and updated methods to explore the structure and function of bacterial chromatin from molecular to the cellular scale. Chapters detail experimental protocols of in vivo and in vitro approaches, approaches to genome structure modeling, and data analysis. 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 key tips on troubleshooting and avoiding known pitfalls. Authoritative and cutting-edge, Bacterial Chromatin: Methods and Protocols, Second Edition aims to be a useful up-to-date reference work for researchers currently in the field and to those entering the field.

Bacterial Chromatin

Author: Claudio O. Gualerzi

Publisher: Springer Science & Business Media

Published: 2012-12-06

Total Pages: 236

ISBN-13: 3642712665

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This book brings together various contributions aimed at the elucida tion of the structural and functional organization of the bacterial nucleoid. Most of these papers, spanning the fields of physical chemistry through biochemistry to genetics, were presented at the session on bac terial chromatin during the Symposium "Selected topics on chromatin structure and function" held at the University of Camerino, Italy, at the end of May 1985. Times when the bacterial DNA was regarded as "naked" or, at most, complexed with polyamines, and when the absence of histones and organized chromatin was considered to be a distinct feature of the pro karyotic cell, now appear remote. Our concepts of how DNA is packaged in bacteria are changing rapidly. Studies on the structure of the bacterial nucleoid are not new. Recently, however, investigations in this field have flourished again, leading to some important contributions such as the elucidation of the three-dimensional structure of what appears to be the major protein constituent of the bacterial nucleoid or the development of methods to titrate the extent of DNA supercoiling within the bacterial cell.

Structure and Function of the Bacterial Genome

Author: Charles J. Dorman

Publisher: John Wiley & Sons

Published: 2020-04-28

Total Pages: 437

ISBN-13: 1119308798

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Presents an integrated view of the expression of bacterial genetic information, genome architecture and function, and bacterial physiology and pathogenesis This book blends information from the very latest research on bacterial chromosome and nucleoid architecture, whole-genome analysis, cell signaling, and gene expression control with well-known gene regulation paradigms from model organisms (including pathogens) to give readers a picture of how information flows from the environment to the gene, modulating its expression and influencing the competitive fitness of the microbe. Structure and Function of the Bacterial Genome explores the governance of the expression of the genes that make a bacterium what it is, and updates the basics of gene expression control with information about transcription promoter structure and function, the role of DNA as a regulatory factor (in addition to its role as a carrier of genetic information), small RNAs, RNAs that sense chemical signals, ribosomes and translation, posttranslational modification of proteins, and protein secretion. It looks at the forces driving the conservation and the evolution of the dynamic genome and offers chapters that cover DNA replication, DNA repair, plasmid biology, recombination, transposition, the roles of repetitive DNA sequences, horizontal gene transfer, the defense of the genome by CRISPR-Cas, restriction enzymes, Argonaute proteins and BREX systems. The book finishes with a chapter that gives an integrated overview of genome structure and function. Blends knowledge of gene regulatory mechanisms with a consideration of nucleoid structure and dynamics Offers a 'DNA-centric' approach to considering transcription control Views horizontal gene transfer from a gene regulation perspective Assesses the opportunities and limitations of designing synthetic microbes or rewiring existing ones Structure and Function of the Bacterial Genome is an ideal book for graduate and undergraduate students studying microbial cell biology, bacterial pathogenesis, gene regulation, and molecular microbiology. It will also appeal to principal investigators conducting research on these and related topics and researchers in synthetic biology and other arms of biotechnology.

Management of Periprosthetic Joint Infections (PJIs)

Author: J.J. Chris Arts

Publisher: Woodhead Publishing

Published: 2016-10-25

Total Pages: 304

ISBN-13: 0081002424

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Management of Periprosthetic Joint Infections (PJIs): Management of PJIs discusses periprosthetic joint infection (PJI), a fairly rare occurrence that is nonetheless one of the most serious complications in joint replacement surgery. Intricate interactions between the pathogen, the host, and the implant can result in PJIs which are not only physically devastating for the patient, but also financially crippling for health authorities and insurance companies. Actions taken to minimize the risk of PJIs can be extremely challenging for the orthopaedic community. Consequently, new research, which is detailed in this comprehensive book, is being undertaken to minimize and manage these challenging infections. Provides essential background knowledge on the mechanisms and identification of PJIs Dedicated chapters focus on the complex, but vital eccentricities between PJIs in different areas of the body Contains contributions from a mixture of clinical and academic experts in the field, thus ensuring balanced coverage

The Bacterial Cell: Coupling between Growth, Nucleoid Replication, Cell Division and Shape

Author: Arieh Zaritsky

Publisher: Frontiers Media SA

Published: 2016-05-02

Total Pages: 326

ISBN-13: 2889198170

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Bacterial Physiology was inaugurated as a discipline by the seminal research of Maaløe, Schaechter and Kjeldgaard published in 1958. Their work clarified the relationship between cell composition and growth rate and led to unravel the temporal coupling between chromosome replication and the subsequent cell division by Helmstetter et al. a decade later. Now, after half a century this field has become a major research direction that attracts interest of many scientists from different disciplines. The outstanding question how the most basic cellular processes - mass growth, chromosome replication and cell division - are inter-coordinated in both space and time is still unresolved at the molecular level. Several particularly pertinent questions that are intensively studied follow: (a) what is the primary signal to place the Z-ring precisely between the two replicating and segregating nucleoids? (b) Is this coupling related to the structure and position of the nucleoid itself? (c) How does a bacterium determine and maintain its shape and dimensions? Possible answers include gene expression-based mechanisms, self-organization of protein assemblies and physical principles such as micro-phase separations by excluded volume interactions, diffusion ratchets and membrane stress or curvature. The relationships between biochemical reactions and physical forces are yet to be conceived and discovered. This e-book discusses the above mentioned and related questions. The book also serves as an important depository for state-of-the-art technologies, methods, theoretical simulations and innovative ideas and hypotheses for future testing. Integrating the information gained from various angles will likely help decipher how a relatively simple cell such as a bacterium incorporates its multitude of pathways and processes into a highly efficient self-organized system. The knowledge may be helpful in the ambition to artificially reconstruct a simple living system and to develop new antibacterial drugs.

Concepts of Biology

Author: Samantha Fowler

Publisher:

Published: 2018-01-07

Total Pages: 618

ISBN-13: 9789888407453

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Concepts of Biology is designed for the single-semester introduction to biology course for non-science majors, which for many students is their only college-level science course. As such, this course represents an important opportunity for students to develop the necessary knowledge, tools, and skills to make informed decisions as they continue with their lives. Rather than being mired down with facts and vocabulary, the typical non-science major student needs information presented in a way that is easy to read and understand. Even more importantly, the content should be meaningful. Students do much better when they understand why biology is relevant to their everyday lives. For these reasons, Concepts of Biology is grounded on an evolutionary basis and includes exciting features that highlight careers in the biological sciences and everyday applications of the concepts at hand.We also strive to show the interconnectedness of topics within this extremely broad discipline. In order to meet the needs of today's instructors and students, we maintain the overall organization and coverage found in most syllabi for this course. A strength of Concepts of Biology is that instructors can customize the book, adapting it to the approach that works best in their classroom. Concepts of Biology also includes an innovative art program that incorporates critical thinking and clicker questions to help students understand--and apply--key concepts.

The Human Mitochondrial Genome

Author: Giuseppe Gasparre

Publisher: Academic Press

Published: 2020-07-23

Total Pages: 596

ISBN-13: 0128226420

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The Human Mitochondrial Genome: From Basic Biology to Disease offers a comprehensive, up-to-date examination of human mitochondrial genomics, connecting basic research to translational medicine across a range of disease types. Here, international experts discuss the essential biology of human mitochondrial DNA (mtDNA), including its maintenance, repair, segregation, and heredity. Furthermore, mtDNA evolution and exploitation, mutations, methods, and models for functional studies of mtDNA are dealt with. Disease discussion is accompanied by approaches for treatment strategies, with disease areas discussed including cancer, neurodegenerative, age-related, mtDNA depletion, deletion, and point mutation diseases. Nucleosides supplementation, mitoTALENs, and mitoZNF nucleases are among the therapeutic approaches examined in-depth. With increasing funding for mtDNA studies, many clinicians and clinician scientists are turning their attention to mtDNA disease association. This book provides the tools and background knowledge required to perform new, impactful research in this exciting space, from distinguishing a haplogroup-defining variant or disease-related mutation to exploring emerging therapeutic pathways. Fully examines recent advances and technological innovations in the field, enabling new mtDNA studies, variant and mutation identification, pathogenic assessment, and therapies Disease discussion accompanied by diagnostic and therapeutic strategies currently implemented clinically Outlines and discusses essential research protocols and perspectives for young scientists to pick up Features an international team of authoritative contributors from basic biologists to clinician-scientists

The Bacterial Cell: Coupling between Growth, Nucleoid Replication, Cell Division, and Shape, Volume 2

Author: Ariel Amir

Publisher: Frontiers Media SA

Published: 2019-11-14

Total Pages: 246

ISBN-13: 2889631567

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The 1st volume of our Research Topic "The Bacterial Cell: Coupling between Growth, Nucleoid Replication, Cell Division and Shape” was published as an eBook in May 2016 (see: http://journal.frontiersin.org/researchtopic/2905/the-bacterial-cell-coupling-between-growth-nucleoid-replication-cell-division-and-shape). As a sign of growing interest to the topic, two workshops followed the same year: "Stochasticity in the Cell Cycle" in Jerusalem (Israel) by the Hebrew University’s Institute of Advanced Studies and EMBO's "Cell Size Regulation" in Joachimsthal (Germany). From the time of launching the first edition, several new groups have entered the field, and many established groups have made significant advances using state-of-the-art microscopy and microfluidics. Combining these approaches with the techniques pioneered by quantitative microbiologists decades ago, these approaches have provided remarkable amounts of numerical data. Most of these data needed yet to be put into a broader theoretical perspective. Moreover, the molecular mechanisms governing coordination and progression of the main bacterial cell cycle processes have remained largely unknown. These outstanding fundamental questions and the growing interest to the field motivated us to launch the next volume titled “The Bacterial Cell: Coupling between Growth, Nucleoid Replication, Cell Division, and Shape, Volume 2” shortly after completion of the first edition in October 2016. The issue contains 17 contributions from a diverse array of scientists whose field of study spans microbiology, biochemistry, genetics, experimental and theoretical biophysics. The specific questions addressed in the issue include: What triggers initiation of chromosome replication? How is cell division coordinated with replication both spatially and temporally? How is cell size controlled and linked to the rate of mass growth? What role plays physical organization of the chromosomes in their segregation and in regulation of cell division? The publications covering these questions are divided into three topical areas: 1) Cell Cycle Regulation, 2) Growth and Division, and 3) Nucleoid Structure and Replication. New ideas and techniques put forward in these articles bring us closer to understand these fundamental cellular processes, but the quest to resolve them is far from being complete. Plans for the next edition are under way along with further meetings and workshops, e.g., an EMBO Workshop on Bacterial cell biophysics: DNA replication, growth, division, size and shape in Ein Gedi (Israel), May 2020. We hope that via such interdisciplinary exchange of ideas we will come closer to answering the above-mentioned complex and multifaceted questions.