Chemical Tools For Imaging Manipulating And Tracking Biological Systems Diverse Methods For Prokaryotic And Eukaryotic Systems

Author :
Publisher : Academic Press
ISBN 13 : 0128201487
Total Pages : 360 pages
Book Rating : 4.80/5 ( download)

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Download or read book Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods for Prokaryotic and Eukaryotic Systems written by and published by Academic Press. This book was released on 2020-05-14 with total page 360 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods for Prokaryotic and Eukaryotic Systems, Volume 638, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Sample chapters from this new release include In vitro characterization of the colibactin-activating peptidase ClbP enables development of a fluorogenic activity probe, Using FDAA probes to study cell division in Bacillus subtilis, Chemoenzymatic synthesis of UDP-sugars, Chemical tools for selective activity profiling of bacterial penicillin-binding proteins, Chemical Probes Reveal and Extraseptal Mode of Cross-linking in Staphylococcus Aureus, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on retinoid signaling pathways

Author : Howard C. Hang
Publisher : John Wiley & Sons
ISBN 13 : 352734733X
Total Pages : 806 pages
Book Rating : 4.39/5 ( download)

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Download or read book Advanced Chemical Biology written by Howard C. Hang and published by John Wiley & Sons. This book was released on 2023-04-03 with total page 806 pages. Available in PDF, EPUB and Kindle. Book excerpt: Advanced Chemical Biology The modern approach to teaching chemical biology Advanced Chemical Biology is organized around the central dogma of life, progressing from genes to proteins and higher-order cellular structures, including core application areas such as imaging, chemical genetics, activity-based protein profiling, and natural product discovery and biosynthesis. Advanced topics and applications in, e. g., microbiology, developmental biology, and neurobiology, are covered in separate sections. Every chapter is homogeneous in style and layout, consisting of a short historical introduction followed by a description of the underlying concepts and a selection of recent examples of how the concept has been turned into practice. The subdivision of the contents into core and supplemental chapters enables a flexible use in teaching, both for a one-semester and a two-semester course. Written by authors and editors coming from the leading scientific institutions that have developed the concepts and technologies for this discipline, Advanced Chemical Biology includes specific information on topics like: DNA function, synthesis and engineering, chemical approaches to genome integrity, and RNA function, synthesis, and probing Chemical approaches to transcription and RNA regulation in vivo, chemical biology of genome engineering, and peptide/protein synthesis and engineering Directed evolution for chemical biology, chemical biology of cellular metabolism, chemical biology of lipids, and protein post-translational modifications Chemical glycobiology, chemical and enzymatic modification of proteins, genetic code expansion, bio-orthogonal chemistry, and cellular imaging With its broad scope and focus on turning concepts into applications, Advanced Chemical Biology is an excellent starting point for anyone entering the field and looking for a guide to the wide range of available methods and strategies that chemical biology has to offer. With a Foreword by Nobel Laureate Carolyn Bertozzi.

Author : Mark Anthony Sellmyer
Publisher :
ISBN 13 :
Total Pages : pages
Book Rating : 4.41/5 ( download)

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Download or read book Chemical Tools to Perturb and Observe Complex Biology written by Mark Anthony Sellmyer and published by . This book was released on 2010 with total page pages. Available in PDF, EPUB and Kindle. Book excerpt: A detailed understanding of living systems requires tools to examine and manipulate biological processes. Small molecules and optical imaging technologies are uniquely suited for this purpose. Small molecules enable the specific manipulation of biomolecular targets, and optical imaging permits the real-time observation of molecular and cellular processes in vivo. This dissertation describes a combination of chemical tool development and imaging strategies to address the following biological problems: 1) specific modification of the genome 2) exquisite control of protein function 3) observing cell-cell interactions in living animals. Chapter One describes a technology for targeted gene modification via the induction of double strand breaks in genomic DNA. The chapter begins with an overview of the field of gene targeting, and documents the design, synthesis, and testing of a novel method for high efficiency homologous recombination. The method relies on engineering two reagents, a small molecule DNA targeting element and a nuclease fusion protein. The targeting element, a peptide nucleic acid (PNA), was designed and synthesized to target DNA via Watson-Crick base pairing. The PNA also was covalently linked to the small molecule, trimethoprim, to recruit a DHFR nuclease fusion protein to a specific DNA site. Our studies show that the individual interactions of PNA/DNA and of PNA/nuclease can readily occur. Further, the ternary complex of PNA, DNA, and nuclease can form in solution. Chapters Two, Three, and Four describe the development and further characterization of a general method to perturb protein stability and function. Briefly, an unstable protein domain, termed a destabilizing domain (DD), can confer instability to a fused protein of interest and promote its rapid degradation. This instability can be rescued by the addition of a small molecule, Shield-1. Our work in Chapter Two describes the use of this system to regulate protein function in living mammals. In one example, we show that regulation of a secreted protein, the immunomodulatory cytokine IL-2, can control tumor burden in mouse models. Additionally, we used the DD to control the function of TNF-[Alpha] after systemic delivery to a tumor. Chapter Three expands on these in vivo efforts by employing the system to regulate secreted FGF2, an important modulator of bone formation, for skeletal tissue engineering. Shield-1 induction of FGF2 causes induction of bone formation in a calvarial-defect model. Chapter Four presents our observations on the behavior of the DD in various cellular environments --the cytoplasm, nucleus, endoplasmic reticulum, and mitochondria- and in the presence of small molecules that modulate protein production, degradation, and local protein quality control machinery. These data indicate that the levels of the DD, in the presence and absence ligand, is dependent on its subcellular locale and protein homeostasis machinery. The fifth chapter of this dissertation reports the development of a method to assess spatiotemporal cell-cell relationships in real-time and in living animals. The method is based on small-molecule diffusion of an activatable substrate between two populations of cells, thus allowing assessment of cell-cell proximity in vivo via bioluminescence imaging. One cell population catalyzes the release of a caged luciferin. The free luciferin can diffuse to a nearby population of cells expressing luciferase capable of light-emitting catalysis. Thus the luciferase cells in closest proximity to the "pool" of free luciferin emit the most light. We demonstrate the utility of this system in vitro and in vivo and are currently investigating its use for the detection of cancer and early metastatic disease in mouse models.

Author : Anna Kataki Anastasakou
Publisher :
ISBN 13 :
Total Pages : 452 pages
Book Rating : 4.56/5 ( download)

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Download or read book Molecular Recognition Tools for Chemistry in Living Systems written by Anna Kataki Anastasakou and published by . This book was released on 2021 with total page 452 pages. Available in PDF, EPUB and Kindle. Book excerpt: The introduction of unnatural functionality in biological systems, coupled with detection using bioorthogonal chemical reactions, revolutionized the field of chemical biology by enabling the investigation of biological processes in live cells and simple organisms. However, the translation to complex organisms has led to less-than-optimal results with high background noise due to cross reactivity with activated reagents. This dissertation investigates the utilization of non-covalent chemistry and bioorthogonal host-guest pairs to obtain more efficient labeling of living systems. Complexation between a host and guest is diffusion-limited, hence can be efficient in dilute environments. The cucurbit[n]uril scaffold has been utilized to determine the minimum binding affinity required for efficient bioorthogonal complexation and investigate how guest size and charge affects the introduction of guests as unnatural metabolites. Carboranes, a cucurbit[7]uril guest class that can be removed "on demand" from the host cavity, were found compatible with metabolic glycoengineering and were successfully incorporated on the cell surface. The cucurbit[7]uril-carborane system serves as the first example of bioorthogonal complexation of a metabolically-incorporated guest and answers fundamental questions required for the further development of bioorthogonal host-guest pairs. Finally, work in expanding the properties of unnatural functionality that can be tolerated by biological systems led to the development of fluorescent guest molecules that could be used independently or in conjunction with molecular recognition tools to investigate living systems.Chapter One is a review on the expansion of chemical reporters beyond bioorthogonal chemistry by metabolic incorporation of alternative moieties with novel functions. These chemical reporters expand on our ability to study and manipulate biological processes with non-invasive methods. Chapters Two details the synthetic methodologies for functionalized cucurbit[7]urils. The two main synthetic approaches to obtaining mono-functionalized cucurbit[7]urils were investigated and cucurbit[7]uril-payload conjugates were synthesized that were used in the remaining work on bioorthogonal complexation described in this dissertation. Chapter Three describes the discovery of carboranes as cucurbit[7]uril guests and their derivatization to increase their binding affinity and aqueous solubility. Ortho-carborane is presented as an stimuli-responsive guest that allows recycling cucurbit[7]uril-solid support constructs through multiple payload isolation rounds in cell lysate. Chapter Four introduces bioorthogonal complexation, namely the labeling of cell-surfaces using host-guest chemistry. A variety of cucurbit[7]uril guests were labeled with a cucurbit[7]- uril-fluorescein conjugate to determine the minimum binding affinity required for bioorthogonal complexation. Metabolic incorporation of a cucurbit[7]uril guest is also presented as a sialic acid derivative on the cell surface that can be similarly labeled with cucurbit[7]uril-fluorophore conjugates. Chapters Five explores the functionality of cucurbit[7]uril guests that can be tolerated by the sialic acid biosynthetic pathway along with in vitro and in vivo methods to analyze and determine successful metabolic incorporation. Chapters Six outlines the development of fluorescent guest molecules that can serve as independent fluorophores or in conjuction with bioorthogonal complexation. The mechanism of luminescence is investigated and preliminary in cellulo data is presented that point towards potential applications.

Author :
Publisher : Academic Press
ISBN 13 : 0128211520
Total Pages : 432 pages
Book Rating : 4.26/5 ( download)

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Download or read book Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods for Optical Imaging and Conjugation written by and published by Academic Press. This book was released on 2020-05-29 with total page 432 pages. Available in PDF, EPUB and Kindle. Book excerpt: Chemical Tools for Imaging, Manipulating, and Tracking Biological Systems: Diverse Methods for Optical Imaging and Conjugation, Volume 639, the latest release in the Methods in Enzymology series, continues the legacy of this premier serial with quality chapters authored by leaders in the field. Chapters in this new release include Fluorogenic detection of protein aggregates in live cells using the AggTag method, Synthesis and Application of Ratiometric Probes for Hydrogen Peroxide Detection, Chemical Tools for Multicolor Protein FRET with Tryptophan, Fluorescing Isofunctional Ribonucleosides for Adenosine Deaminase Activity and Inhibition, Temporal profiling establishes a dynamic S-palmitoylation cycle, Solvation-guided design of fluorescent probes for discrimination of amyloids, and much more. Provides the authority and expertise of leading contributors from an international board of authors Presents the latest release in the Methods in Enzymology series Includes the latest information on retinoid signaling pathways

Author : Bruce Alberts
Publisher :
ISBN 13 : 9780815332183
Total Pages : 0 pages
Book Rating : 4.81/5 ( download)

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Download or read book Molecular Biology of The Cell written by Bruce Alberts and published by . This book was released on 2002 with total page 0 pages. Available in PDF, EPUB and Kindle. Book excerpt:

Author : Alfred Hassner
Publisher : Elsevier
ISBN 13 : 1483287343
Total Pages : 462 pages
Book Rating : 4.48/5 ( download)

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Download or read book Organic Syntheses Based on Name Reactions and Unnamed Reactions written by Alfred Hassner and published by Elsevier. This book was released on 2013-10-22 with total page 462 pages. Available in PDF, EPUB and Kindle. Book excerpt: Synthetically useful organic reactions or reagents are often referred to by the name of the discoverer(s) or developer(s). Older name reactions are described in text books, but more recently developed synthetically useful reactions that may have been associated occasionally with a name are not always well known. For neither of the above are experimental procedures or references easy to find. In this monograph approximately 500 name reactions are included, of which over 200 represent newer name reactions and modern reagents. Each of these reactions are extremely useful for the contemporary organic chemistry researcher in industry or academic institutions. This book provides the information in an easily accessible form. In addition to seminal references and reviews, one or more examples for each name reaction are provided and a complete typical experimental procedure is included, to enable the student or researcher to immediately evaluate reaction conditions. Besides an alphabetical listing of reactions and reagents, cross references permit the organic practitioner to find those name reactions or reagents that enable specific transformations, such as, conversion of amines to nitriles, stereoselective reduction, fluoroalkylation, phenol alkynylation, asymmetric syntheses, allylic alkylation, nucleoside synthesis, cyclopentanation, hydrozirconation, to name a few. Emphasis has been placed on stereoselective and regioselective transformations as well as on enantioselective processes. The listing of reactions and reagents is supported by four indexes.

Author : Mahendra Rai
Publisher : Springer Science & Business Media
ISBN 13 : 3642183123
Total Pages : 306 pages
Book Rating : 4.26/5 ( download)

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Download or read book Metal Nanoparticles in Microbiology written by Mahendra Rai and published by Springer Science & Business Media. This book was released on 2011-04-02 with total page 306 pages. Available in PDF, EPUB and Kindle. Book excerpt: Following an introduction to biogenic metal nanoparticles, this book presents how they can be biosynthesized using bacteria, fungi and yeast, as well as their potential applications in biomedicine. It is shown that the synthesis of nanoparticles using microbes is eco-friendly and results in reproducible metal nanoparticles of well-defined sizes, shapes and structures. This biotechnological approach based on the process of biomineralization exploits the effectiveness and flexibility of biological systems. Chapters include practical protocols for microbial synthesis of nanoparticles and microbial screening methods for isolating a specific nanoparticle producer as well as reviews on process optimization, industrial scale production, biomolecule-nanoparticle interactions, magnetosomes, silver nanoparticles and their numerous applications in medicine, and the application of gold nanoparticles in developing sensitive biosensors.

Author : Babin, Marcel
Publisher : UNESCO
ISBN 13 : 9231040421
Total Pages : 880 pages
Book Rating : 4.29/5 ( download)

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Download or read book Real-time Coastal Observing Systems for Marine Ecosystem Dynamics and Harmful Algal Blooms written by Babin, Marcel and published by UNESCO. This book was released on 2008-06-05 with total page 880 pages. Available in PDF, EPUB and Kindle. Book excerpt: The proliferation of harmful phytoplankton in marine ecosystems can cause massive fish kills, contaminate seafood with toxins, impact local and regional economies and dramatically affect ecological balance. Real-time observations are essential for effective short-term operational forecasting, but observation and modelling systems are still being developed. This volume provides guidance for developing real-time and near real-time sensing systems for observing and predicting plankton dynamics, including harmful algal blooms, in coastal waters. The underlying theory is explained and current trends in research and monitoring are discussed.Topics covered include: coastal ecosystems and dynamics of harmful algal blooms; theory and practical applications of in situ and remotely sensed optical detection of microalgal distributions and composition; theory and practical applications of in situ biological and chemical sensors for targeted species and toxin detection; integrated observing systems and platforms for detection; diagnostic and predictive modelling of ecosystems and harmful algal blooms, including data assimilation techniques; observational needs for the public and government; and future directions for research and operations.

Author : Institute of Medicine
Publisher : National Academies Press
ISBN 13 : 0309264324
Total Pages : 633 pages
Book Rating : 4.27/5 ( download)

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Download or read book The Social Biology of Microbial Communities written by Institute of Medicine and published by National Academies Press. This book was released on 2013-01-10 with total page 633 pages. Available in PDF, EPUB and Kindle. Book excerpt: Beginning with the germ theory of disease in the 19th century and extending through most of the 20th century, microbes were believed to live their lives as solitary, unicellular, disease-causing organisms . This perception stemmed from the focus of most investigators on organisms that could be grown in the laboratory as cellular monocultures, often dispersed in liquid, and under ambient conditions of temperature, lighting, and humidity. Most such inquiries were designed to identify microbial pathogens by satisfying Koch's postulates.3 This pathogen-centric approach to the study of microorganisms produced a metaphorical "war" against these microbial invaders waged with antibiotic therapies, while simultaneously obscuring the dynamic relationships that exist among and between host organisms and their associated microorganisms-only a tiny fraction of which act as pathogens. Despite their obvious importance, very little is actually known about the processes and factors that influence the assembly, function, and stability of microbial communities. Gaining this knowledge will require a seismic shift away from the study of individual microbes in isolation to inquiries into the nature of diverse and often complex microbial communities, the forces that shape them, and their relationships with other communities and organisms, including their multicellular hosts. On March 6 and 7, 2012, the Institute of Medicine's (IOM's) Forum on Microbial Threats hosted a public workshop to explore the emerging science of the "social biology" of microbial communities. Workshop presentations and discussions embraced a wide spectrum of topics, experimental systems, and theoretical perspectives representative of the current, multifaceted exploration of the microbial frontier. Participants discussed ecological, evolutionary, and genetic factors contributing to the assembly, function, and stability of microbial communities; how microbial communities adapt and respond to environmental stimuli; theoretical and experimental approaches to advance this nascent field; and potential applications of knowledge gained from the study of microbial communities for the improvement of human, animal, plant, and ecosystem health and toward a deeper understanding of microbial diversity and evolution. The Social Biology of Microbial Communities: Workshop Summary further explains the happenings of the workshop.