This completely revised edition explores novel discoveries in bacterial genomic research, with a focus on technical and computational improvements as well as methods used for bacterial pangenome analysis, which relies on microbiome studies and metagenomic data. Beginning with up-to-date sequencing methods, the book continues with sections covering methods for deep phylogenetic analysis, the role of metagenomic data in understanding the genomics of the many yet uncultured bacteria, progress in genome-to-phenome inference, as well as computational genomic tools. Written for the highly successful Methods in Molecular Biology series, chapters include the type of practical detail necessary for reproducible results in the lab. Authoritative and up-to-date, Bacterial Pangenomics: Methods and Protocols, Second Edition serves as an ideal guide for both highly qualified investigators in bacterial genomics and for less experienced researchers, including students and teachers, who could use a reference for approaching genomic analysis and genome data.

Optics at the Nanometer Scale: Imaging and Storing with Photonic Near Fields deals with the fundamentals of and the latest developments and applications of near-field optical microscopy, giving basic accounts of how and under what circumstances superresolution beyond the half- wavelength Rayleigh limit is achieved. Interferometric and fluorescence techniques are also described, leading to molecular and even atomic resolution using light. The storage of optical information at this level of resolution is also addressed.

Developing microscale chemistry experiments, using small quantities of chemicals and simple equipment, has been a recent initiative in the UK. Microscale chemistry experiments have several advantages over conventional experiments: They use small quantities of chemicals and simple equipment which reduces costs; The disposal of chemicals is easier due to the small quantities; Safety hazards are often reduced and many experiments can be done quickly; Using plastic apparatus means glassware breakages are minimised; Practical work is possible outside a laboratory. Microscale Chemistry is a book of such experiments designed for use in schools and colleges, and the ideas behind the experiments in it come from many sources, including chemistry teachers from all around the world. Current trends indicate that with the likelihood of further environmental legislation, the need for microscale chemistry teaching techniques and experiments is likely to grow. This book should serve as a guide in this process.

The scanning tunneling microscope and the atomic force microscope, both capable of imaging and manipulating individual atoms, were crowned with the Nobel Prize in Physics in 1986, and are the cornerstones of nanotechnology today. The first edition of this book has nurtured numerous beginners and experts since 1993. The second edition is a thoroughly updated version of this 'bible' in the field. The second edition includes a number of new developments in the field. Non-contact atomic-force microscopy has demonstrated true atomic resolution. It enables direct observation and mapping of individual chemical bonds. A new chapter about the underlying physics, atomic forces, is added. The chapter on atomic force microscopy is substantially expanded. Spin-polarized STM has enabled the observation of local magnetic phenomena down to atomic scale. A pedagogical presentation of the basic concepts is included. Inelastic scanning tunneling microscopy has shown the capability of studying vibrational modes of individual molecules. The underlying theory and new instrumentation are added. For biological research, to increase the speed of scanning to observe life phenomena in real time is a key. Advances in this direction are presented as well. The capability of STM to manipulate individual atoms is one of the cornerstones of nanotechnology. The theoretical basis and in particular the relation between tunneling and interaction energy are thoroughly presented, together with experimental facts.

This book covers several of the most important topics of current interest at the forefront of scanning probe microscopy. These include a realistic theory of atom-resolving atomic force microscopy (AFM), fundamentals of MBE growth of III-V compound semiconductors and atomic manipulation for future single-electron devices.

Knowledge of the microscopic structure of biological systems is the key to understanding their physiological properties. Most of what we now know about this subject has been generated by techniques that produce images of the materials of interest, one way or another, and there is every reason to believe that the impact of these techniques on the biological sciences will be every bit as important in the future as they are today. Thus the 21st century biologist needs to understand how microscopic imaging techniques work, as it is likely that sooner or later he or she will have to use one or another of them, or will otherwise become dependent on the information that they provide. The objective of this textbook is to introduce its readers to the many techniques now available for imaging biological materials, e.g. crystallography, optical microscopy and electron microscopy, at a level that will enable them to use them effectively to do research. Since all of these experimental methods are best understood in terms of Fourier transformations, this book explains the relevant concepts from this branch of mathematics, and then illustrates their elegance and power by applying them to each of the techniques presented. The book is derived from a one-term course in structural biology that the author gave for many years at Yale. It is intended for students interested either in doing structural research themselves, or in exploiting structural information produced by others. Over the years, the course was taken successfully by advanced undergraduates and by graduate students. Scientists interested in entering the structural biology field later in their careers may also find it useful.

The 14th conference in the series focused on the most recent advances in the study of the structural and electronic properties of semiconducting materials by the application of transmission and scanning electron microscopy. The latest developments in the use of other important microcharacterisation techniques were also covered and included the latest work using scanning probe microscopy and also X-ray topography and diffraction.

This updated volume provides stepwise instructions for the analysis of numerous clinically important analytes by mass spectrometry. Mass spectrometry offers clinical laboratory scientists a number of advantages including increased sensitivity and specificity, multiple component analysis, and limited need for specialized reagents. These techniques are essential in laboratory fields including endocrinology, biochemical genetics, drug analysis, proteomics, and pathogen identification. 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. Cutting-edge and practical, Clinical Applications of Mass Spectrometry in Biomolecular Analysis: Methods and Protocols, Second Edition is an ideal resource for clinical laboratory scientists who are already using or thinking of bringing mass spectrometry to their laboratories.

This first edited Volume on IgY-Technology, addresses the historical and dynamic development of IgY-applications. The authors cover the biological basis and theoretical context, methodological guidance, and applications of IgY-Technology. A focus is laid on the use of IgY-antibodies for prophylactic/therapeutic purposes in human and veterinary medicine. Aside from applications, the chapters also offer an evolutionary understanding of the IgY molecule, IgY receptors and practical prerequisites to produce IgY-antibodies. Guidance is given for every step of the process. Starting with an introduction to hens as a model species and including hen husbandry, hen egg-laying capacity and total IgY outcomes. Readers will also learn about immunization techniques, the advantages and limitations of different IgY extraction methods, as well as storage stability of the final product. The last part of the volume highlights hands-on aspects of applications, such as IgY delivery strategies, new methods to produce monoclonal IgY-antibodies or production of functional IgY fragments by phage-display as well as commercial exploitation of the technology. Thus, this book is a valuable resource and guide for Scientists, Clinicians and Health Product Developers in both human and veterinary medicine.

This volume provides a comprehensive reference for researchers aiming to bring new techniques and approaches to their scientific research using urodeles. Chapters are authored by leaders in the field and meant to guide readers through laboratory colony husbandry, traditional molecular techniques, experimental manipulation and surgeries, bioinformatics and genomics, transgenics and lineage-tracing, and physiological and organismal techniques. In addition to laboratory methods, this volume highlights techniques developed for field studies and work with wild-caught animals. Written in the 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 protocols, and notes on troubleshooting and avoiding known pitfalls. Authoritative and state-of-the-art, Methods in Salamander Research aims to be a practical guide for researchers interested in deploying new methodologies in their lab or in the field.

This book presents a detailed look at experimental and computational techniques for accurate structure determination of free molecules. The most fundamental property of a molecule is its structure - it is a prerequisite for determining and understanding most other important properties of molecules. The determination of accurate structures is hampered by a myriad of factors, subjecting the collected data to non-negligible systematic errors. This book explains the origin of these errors and how to mitigate and even avoid them altogether. It features a detailed comparison of the different experimental and computation methods, explaining their interplay and the advantages of their combined use. Armed with this information, the reader will be able to choose the appropriate methods to determine - to a great degree of accuracy - the relevant molecular structure.

Introduction to Statistical Analysis of Laboratory Data presents a detailed discussion of important statistical concepts and methods of data presentation and analysis * Provides detailed discussions on statistical applications including a comprehensive package of statistical tools that are specific to the laboratory experiment process * Introduces terminology used in many applications such as the interpretation of assay design and validation as well as fit for purpose procedures including real world examples * Includes a rigorous review of statistical quality control procedures in laboratory methodologies and influences on capabilities * Presents methodologies used in the areas such as method comparison procedures, limit and bias detection, outlier analysis and detecting sources of variation * Analysis of robustness and ruggedness including multivariate influences on response are introduced to account for controllable/uncontrollable laboratory conditions

The Nobel Prize of 1986 on Sc- ningTunnelingMicroscopysignaled a new era in imaging. The sc- ning probes emerged as a new - strument for imaging with a p- cision suf?cient to delineate single atoms. At ?rstthere were two -the ScanningTunnelingMicroscope,or STM,andtheAtomicForceMic- scope, or AFM. The STM relies on electrons tunneling between tip and sample whereas the AFM depends on the force acting on the tip when itwasplacednearthesample.These were quickly followed by the M- netic Force Microscope, MFM, and the Electrostatic Force Microscope, EFM.TheMFMwillimageasinglemagneticbitwithfeaturesassmallas10nm. WiththeEFMonecanmonitorthechargeofasingleelectron.Prof.PaulHansma atSantaBarbaraopenedthedoorevenwiderwhenhewasabletoimagebiological objects in aqueous environments. At this point the sluice gates were opened and amultitudeofdifferentinstrumentsappeared. There are signi?cant differences between the Scanning Probe Microscopes or SPM, and others such as the Scanning Electron Microscope or SEM. The probe microscopes do not require preparation of the sample and they operate in ambient atmosphere, whereas, the SEM must operate in a vacuum environment and the sample must be cross-sectioned to expose the proper surface. However, the SEM canrecord3Dimage andmovies, featuresthatarenotavailable withthescanning probes. TheNearFieldOpticalMicroscopeorNSOMisalsomemberofthisfamily.At thistimetheinstrumentsuffersfromtwolimitations;1)mostoftheopticalenergy is lost as it traverses the cut-off region of the tapered ?ber and 2) the resolution is insuf?cient for many purposes. We are con?dent that NSOM's with a reasonable opticalthroughputandaresolutionof10nmwillsoonappear.TheSNOMwillthen enterthemainstreamofscanningprobes. VI Foreword In the Harmonic Force Microscope or HFM, the cantilever is driven at the resonantfrequencywiththeamplitudeadjustedsothatthetipimpactsthesampleon each cycle. Theforcesbetween tipandsample generate multiple harmonics inthe motionofthecantilever.Thestrengthoftheseharmonicscanbeusedtocharacterize thephysicalpropertiesofthesurface.

The microanalytical technique of atom probe tomography (APT) permits the spatial coordinates and elemental identities of the individual atoms within a small volume to be determined with near atomic resolution. Therefore, atom probe tomography provides a technique for acquiring atomic resolution three dimensional images of the solute distribution within the microstructures of materials. This monograph is designed to provide researchers and students the necessary information to plan and experimentally conduct an atom probe tomography experiment. The techniques required to visualize and to analyze the resulting three-dimensional data are also described. The monograph is organized into chapters each covering a specific aspect of the technique. The development of this powerful microanalytical technique from the origins offield ion microscopy in 1951, through the first three-dimensional atom probe prototype built in 1986 to today's commercial state-of-the-art three dimensional atom probe is documented in chapter 1. A general introduction to atom probe tomography is also presented in chapter 1. The various methods to fabricate suitable needle-shaped specimens are presented in chapter 2. The procedure to form field ion images of the needle-shaped specimen is described in chapter 3. In addition, the appearance of microstructural features and the information that may be estimated from field ion microscopy are summarized. A brief account of the theoretical basis for processes of field ionization and field evaporation is also included.

This is the first book written on using Blender (an open-source visualization suite widely used in the entertainment and gaming industries) for scientific visualization. It is a practical and interesting introduction to Blender for understanding key parts.

This companion volume to "Fundamental Polymer Science" (Gedde and Hedenqvist, 2019) offers detailed insights from leading practitioners into experimental methods, simulation and modelling, mechanical and transport properties, processing, and sustainability issues. Separate chapters are devoted to thermal analysis, microscopy, spectroscopy, scattering methods, and chromatography. Special problems and pitfalls related to the study of polymers are addressed. Careful editing for consistency and cross-referencing among the chapters, high-quality graphics, worked-out examples, and numerous references to the specialist literature make "Applied Polymer Science" an essential reference for advanced students and practicing chemists, physicists, and engineers who want to solve problems with the use of polymeric materials.

Scanning Tunneling Microscopy and its Application presents a unified view of the rapidly growing field of STM,and its many derivatives. A thorough discussion of the various principles provides the background to tunneling phenomena and leads to the many novel scanning-probe techniques, such as AFM, MFM, BEEM, PSTM, etc. After having examined the available instrumentation and the methods for tip and surface preparations, the monograph provides detailed accounts of STM application to metal and semiconductor surfaces, adsorbates and surface chemistry, biology, and nanofabrication. It examines limitations of the present-day investigations and provides hints about possible further trends. This second edition includes important new developments in the field.

Scanning Probe Microscopy - Analytical Methods provides a comprehensive overview of the analytical methods on the nanometer scale based on scanning probe microscopy and spectroscopy. Numerous examples of applications of the chemical contrast mechanism down to the atomic scale in surface physics and chemistry are discussed with extensive references to original work in the recent literature.

In this book, the major paradigm-shifting discoveries made in the past century on key cellular nanomachines are described in great detail: their complex yet precise and elegant design and function, as well as the diseases linked to their dysfunction and the therapeutic approaches to overcome them. The major focus of this book is the "porosome" nanomachine, the universal secretory portal in cells. This is an ideal book for students, researchers, and professionals in the fields of nanoscience and nanotechnology.

Practical skills form the cornerstone of chemistry. However, the diversity of skills required in the laboratory means that a student's experience may be limited. While some techniques do require specific skills, many of them are transferable generic skills that are required throughout the subject area. Limited time constraints of the modern curriculum often preclude or minimise laboratory time. Practical Skills in Chemistry 3rd edition provides a general guidance for use in and out of practical sessions, covering a range of techniques from the basic to the more advanced. This 'one-stop' text will guide you through the wide range of practical, analytical and data handling skills that you will need during your studies. It will also give you a solid grounding in wider transferable skills such as teamwork, using information technology, communicating information and study skills. This edition has been enhanced and updated throughout to provide a complete and easy-to-read guide to the developing skills required from your first day through to graduation, further strengthening its reputation as the practical resource for students of chemistry and related discipline areas.

Although the specimen of choice in the US drug testing industry is urine, and serum in clinical medicine, interest has recently grown in the use of other matrices as drug testing media. This book provides researchers and forensic toxicologists with a convenient general text summarizing the state of knowledge today. Chapters focus specifically on the application of these practices to drugs of abuse. The up-to-date information provided is complemented with thorough references.