New methods used for the detection of DNA hybridisation process, including electrochemical, optical scattering, surface plasmon resonance, nanogravimetric, and fluorimetric are described and their application in assays assessing DNA damage is discussed in this book. The analyses of damage and alterations for the DNA in solution as well as for the DNA immobilised on core-shell gold nanoparticles and solid electrodes are presented. These methods enable evaluating the degree of DNA damage caused by toxicants and can be applied to studies of the interactions of atrazine and other herbicides and pesticides with DNA.

DNA (deoxyribonucleic acid) is the hereditary material in humans and almost all other organisms. DNA sequencing is a common and requisite practice for molecular biologists today working in all areas of biology, including microbiology. This book aims to provide clues for DNA sequencing projects directed to unsequenced organisms in which many transcripts wait to be discovered, either coding small RNAs or genes homologue to known genes coding for protein products. This book also looks at the adoption of the polymerase chain reaction (PCR) to generate DNA profiles from minute biological samples, and the use of mitochondrial DNA to obtain information from old bones and the applications of Y chromosomal polymorphisms in sexual assault cases. Present research focuses on genetic markers for external visible traits and on improving the utility of poor quality samples with degraded DNA. The other direction of forensic DNA research addresses the difficulty of obtaining a DNA profile in a degraded crime stain. The third topic covered in this book is DNA chips- a microchip that holds DNA probes that form half of the DNA double helix. This book examines the development of DNA chips, as the prototype for global technology genetics.

This volume contains papers presented at the 20th International Conference on Genome Informatics (GIW 2009) held at the Pacifico Yokohama, Japan from December 14 to 16, 2009. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein structure prediction, genetic regulatory networks, bioinformatic algorithms, comparative genomics, and biomolecular data integration and analysis. Boasting a history of 20 years, GIW is the longest-running international bioinformatics conference.A total of 18 contributed papers were selected for presentation at GIW 2009 and for inclusion in this book. In addition, this book contains abstracts from the five invited speakers: Sean Eddy (HHMI's Janelia Farm, USA), Minoru Kanehisa (Kyoto University, Japan), Sang Yup Lee (KAIST, Korea), Hideyuki Okano (Keio University, Japan) and Mark Ragan (University of Queensland, Australia).

A comprehensive, authoritative look at an emergent area in post-genomic science, Evolutionary genomics is an up-and-coming, complex field that attempts to explain the biocomplexity of the living world. "Evolutionary Genomics and Systems Biology" is the first full-length book to blend established and emerging concepts in bioinformatics, evolution, genomics, and structural biology, with the integrative views of network and systems biology.

Three key aspects of evolutionary genomics and systems biology are covered in clear detail: the study of genomic history, i.e., understanding organismal evolution at the genomic level; the study of macromolecular complements, which encompasses the evolution of the protein and RNA machinery that propels life; and the evolutionary and dynamic study of wiring diagrams--macromolecular components in interaction--in the context of genomic complements. The book also features: A solid, comprehensive treatment of phylogenomics, the evolution of genomes, and the evolution of biological networks, within the framework of systems biologyA special section on RNA biology--translation, evolution of structure, and micro RNA and regulation of gene expressionChapters on the mapping of genotypes to phenotypes, the role of information in biology, protein architecture and biological function, chromosomal rearrangements, and biological networks and diseaseContributions by leading authorities on each topic

"Evolutionary Genomics and Systems Biology" is an ideal book for students and professionals in genomics, bioinformatics, evolution, structural biology, complexity, origins of life, systematic biology, and organismal diversity, as well as those individuals interested in aspects of biological sciences as they interface with chemistry, physics, and computer science and engineering.

The problem of unraveling two intertwined strands during the duplication of DNA was recognized shortly after the proposal of the DNA double helix structure in 1953. A group of enzymes called DNA topoisomerases solve this problem by breaking and rejoining DNA molecules in a controlled manner, thereby allowing strands to be passed through each other and thus untangled - not just during DNA replication, but also during many other basic cellular processes. Because of their intimate involvement in the workings of the cell, topoisomerases are also the logical targets of many antibiotics (including Cipro) and anticancer agents. This book, written by James Wang, the discoverer of the first topoisomerase and a leader in the field since, presents ten chapters covering the historical backdrop of the DNA entanglement problem and the discovery of the DNA topoisomerases, how DNA topoisomerases perform their magic in DNA replication, transcription, genetic recombination and chromosome condensation, and how they are targets of therapeutic agents. The book should appeal to readers from undergraduates upwards with interests in the biological and clinical aspects of topoisomerase function, or in the mathematics and physics of topology.

DNA microarray technology has become a useful technique in gene expression analysis for the development of new diagnostic tools and for the identification of disease genes and therapeutic targets for human cancers. Appropriate control for DNA microarray experiment and reliable analysis of the array data are key to performing the assay and utilizing the data correctly. The most difficult challenge has been the lack of a powerful method to analyze the data for all genes (more than 30,000 genes) simultaneously and to use the microarray data in a decision-making process. In this book, the authors describe DNA microarray technology and data analysis by pointing out current advantages and disadvantages of the technique and available analytical methods. Crucially, new ideas and analytical methods based on the authors' own experience in DNA microarray study and analysis are introduced. It is believed that this new way of interpreting and analyzing microarray data will bring us closer to success in decision-making using the information obtained through the DNA microarray technology.

"What underlying forces are responsible for the observed patterns of variability, given a collection of DNA sequences?" In approaching this question a number of probability models are introduced and anyalyzed.Throughout the book, the theory is developed in close connection with data from more than 60 experimental studies that illustrate the use of these results.

Transposons are segments of DNA that can relocate (transpose) to different positions within the genome of a single cell. In the years since their initial discovery in 1948 by Barbara McClintock, these mobile genetic elements have come to be widely recognised as ubiquitous components of genomes representing all major branches of life; furthermore, transposons have been developed into powerful tools for molecular biology, and, in particular, funcational genomes, in wide range of organisms. More recently, transposons have been developed into a technology platform for vertebrate genetics with application areas including gene therapy, transgenesis, somatic mutagenesis (cancer research), and germ line mutagenesis for gene discovery. This book presents new and important research from around the world in this field.

This volume contains 31 peer-reviewed papers based on the presentations at the 7th International Annual Workshop on Bioinformatics and Systems Biology (IBSB 2007) held at the Human Genome Center, Institute of Medical Science, University of Tokyo from July 31 to August 2, 2007. This workshop started in 2001 as an event for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following programs and partner institutions:* Boston (Charles DeLisi) - Graduate Program in Bioinformatics, Boston University* Berlin (Herman-Georg Holzhutter) - The International Research Training Group (IRTG) "Genomics and Systems Biology of Molecular Networks"* Kyoto/Tokyo (Minoru Kanehisa/Satoru Miyano) - Joint Bioinformatics Education Program of Kyoto University and University of Tokyo.This volume is dedicated to the memory of Prof. Dr. Dr. h.c. Reinhart Heinrich, a former Professor at Humboldt University Berlin and a co-founder of this workshop.

This volume contains papers presented at the 18th International Conference on Genome Informatics (GIW 2007) held at the Biopolis, Singapore from December 3 to 5, 2007. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein folding prediction, gene regulatory network, clustering algorithms, comparative genomics, and text mining. Boasting a history of 18 years, GIW is likely the longest-running international bioinformatics conference.A total of 16 papers were selected for presentation at GIW 2007 and inclusion in this book. The notable authors include Ming Li (University of Waterloo, Canada), Minoru Kanehisa (Kyoto University, Japan), Vladimir Kuznetsov (Genome Institute of Singapore), Tao Jiang (UC Riverside, USA), Christos Ouzounis (European Bioinformatics Institute, UK), and Satoru Miyano (University of Tokyo, Japan). In addition, this book contains abstracts from the five invited speakers: Frank Eisenhaber (Bioinformatics Institute, Singapore), Sir David Lane (Institute of Molecular and Cell Biology, Singapore), Hanah Margalit (The Hebrew University of Jerusalem, Israel), Lawrence Stanton (Genome Institute of Singapore), and Michael Zhang (Cold Spring Harbor Laboratory, USA).

How has DNA come to be seen as a cosmic truth, representative of all life, potential for all cures, repository for all identity, and end to all stories? In "The Poetics of DNA," Judith Roof examines the rise of this powerful symbol and the implications of its ascendancy for the ways we think-about ourselves, about one another, and about the universe.
Descriptions of DNA, Roof argues, have distorted ideas and transformed nucleic acid into the answer to all questions of life. This hyperbolized notion of DNA, inevitably confused or conflated with the "gene," has become a vector through which older ways of thinking can merge with the new, advancing long-discredited and insidious ideas about such things as eugenics and racial selection and influencing contemporary debates, particularly the popular press obsession with the "gay gene." Through metaphors of DNA, she contends, racist and homophobic ideology is masked as progressive science.
Grappling with twentieth-century intellectual movements as well as contemporary societal anxieties, "The Poetics of DNA" reveals how descriptions of DNA and genes typify a larger set of epistemological battles that play out not only through the assumptions associated with DNA but also through less evident methods of magical thinking, reductionism, and pseudoscience.
For the first time, Roof exposes the ideology and cultural consequences of DNA and gene metaphors to uncover how, ultimately, they are paradigms used to recreate prejudices.
Judith Roof is professor of English and film studies at Michigan State University. She is the author of several books, including "All about Thelma and Eve: Sidekicks and Third Wheels."

This book provides an exceptionally friendly introduction to Perl that emphasizes good programming practices with repeated exposure to pattern matching as applied to biological sequence analysis (DNA analysis, Protein analysis). The full-length book is appropriate for postgraduates in either computer science or biology and especially relevant to new interdisciplinary courses involving students from multiple disciplines.

This book presents Perl programming with a uniquely interdisciplinary perspective for the bioinformatics classroom. The co-authors are a professor of computer science and a professor of biology who collaborate in developing software for DNA sequence analysis. A specialty of the authors is encouraging interdisciplinary undergraduate research. The book has been tested in the classroom as a text for both biology and computer science majors. Benefiting from years of teaching experience in both computer science and biology, the authors use an exceptionally friendly and pedagogically sound introduction to Perl that emphasizes good programming practices throughout. Concepts include a rich introduction to working with strings and files of sequence data, control structures, subroutines, and data structures (e.g., arrays and hash tables). A particularly unique feature of the text is the early and repeated exposure to and use of regular expressions in sequence analysis. All examples in the book are applied to biological sequence analysis (DNA analysis, Protein analysis). The full-length book is appropriate for majors in either computer science or biology and especially relevant for new interdisciplinary courses involving students from multiple disciplines.

This book focuses on the development and application of the latest advanced data mining, machine learning, and visualization techniques for the identification of interesting, significant, and novel patterns in gene expression microarray data.
Biomedical researchers will find this book invaluable for learning the cutting-edge methods for analyzing gene expression microarray data. Specifically, the coverage includes the following state-of-the-art methods:
- Gene-based analysis: the latest novel clustering algorithms to identify co-expressed genes and coherent patterns in gene expression microarray data sets
- Sample-based analysis: supervised and unsupervised methods for the reduction of the gene dimensionality to select significant genes. A series of approaches to disease classification and discovery are also described
- Pattern-based analysis: methods for ascertaining the relationship between (subsets of) genes and (subsets of) samples. Various novel pattern-based clustering algorithms to find the coherent patterns embedded in the sub-attribute spaces are discussed
- Visualization tools: various methods for gene expression data visualization. The visualization process is intended to transform the gene expression data set from high-dimensional space into a more easily understood two- or three-dimensional space.

DNA Fingerprinting is a method of identification that compares fragments of deoxyribonucleic acid (DNA). It is sometimes called DNA typing. DNA is the genetic material found within the cell nuclei of all living things. The techniques used in DNA fingerprinting also have applications in law and law enforcement, palaeontology, archaeology, various fields of biology, and medical diagnostics. In biological classification, it can help to show evolutionary change and relationships on the molecular level, and it has the advantage of being able to be used even when only very small samples are available. This new book details several applications of this break-through technique.

Microarray analysis is a highly efficient tool for assessing the expression of a large number of genes simultaneously, and offers a new means to classify cancer and other diseases. Gene expression profiling can also be used to predict clinical outcome and response to specific therapeutic agents. This survey spans recent applications of microarrays in clinical medicine, covering malignant disease including acute leukaemias, lymphoid malignancies and breast cancer, together with diabetes and heart disease. Investigators in oncology, pharmacology and related clinical sciences, as well as basic scientists, will value this review of a promising new diagnostic and prognostic technology.

Microarrays is an invaluable laboratory manual for anyone conducting experiments in the field of molecular biology or medical biochemistry who needs to understand and use microarray technologies. These technologies are especially appropriate in genome analysis, diagnostics, and studies involving differential gene expression.
Providing straightforward explanations, the authors demonstrate proven methods for biochip application and an overview of presently available instruments, biochips, and software. Chapters cover the different requirements for DNA and protein chips, as well as spotters and scanners. The book also covers high throughput screening, patent research, and the minimum requirements for setting up or expanding a microarray laboratory.
- Covers microarray applications, technology, and execution
- Written in an approachable yet informative tone
- Includes more than 100 detailed figures and graphs
- Examines the history of microarrays and their future potential
- Defines key terms from related disciplines
- Contains a full chapter on the importance of database research and patents
- Describes how to develop or improve one's own microarray laboratory

For over half a century, we have been in the thrall of the double-helicaln structure of DNA, which, in an instant, revealed that information can be transferred between generations by a simple rule, A pairs with T, G pairs with C. In its beautiful simplicity, this structure, along with the table of codons worked out in the following decade, had entranced us into believing that we can fully understand the information content of a DNA sequence, simply by treating it as text that is read in a linear fashion. While we have learned much based on this assumption, there is much we have missed. Far from a passive tape running through a reader, genomes contain information that appears in new forms which create regions with distinct behavior. Some are "gene rich," some mobile, some full of repeats and duplications, some sticking together across long evolutionary distances, some readily breaking apart in tumor cells. Even protein-coding regions can carry additional information, taking advantage of the flexible coding options provided by the degeneracy of the genetic code. The chapters in this volume touch on one or more of three interconnected themes; information can be implied, rather than explicit, in a genome; information can lead to focused and/or regulated changes in nucleotide sequences; information that affects the probability of distinct classes of mutation has implications for evolutionary theory.

This is the story of how three men won the Nobel Prize for their research on the humble nematode worm "C. elegans"; how their extraordinary discovery led to the sequencing of the human genome; how a global multibillion-dollar industry was born; and how the mysteries of life were revealed in a tiny, brainless worm.

In 1998 the nematode worm -- perhaps the most intensively studied animal on earth -- was the first multicellular organism ever to have its genome sequenced and its DNA mapped and read. "When we understand the worm, we will understand life," predicted John Sulston, one of the three Nobel laureates, and his prediction proved astonishingly accurate. Four years later, the research that led to this extraordinary event garnered three scientists a Nobel Prize. Along with Robert Horvitz and Sydney Brenner, Sulston discovered the phenomenon of programmed cell death in the worm, an essential concept that explains how biological development occurs in animal life and, as Horvitz later showed, how it occurs in human life. "C. elegans" is about as simple as an animal can be, but understanding its genetic organization is helping to reveal the mechanisms of life and, by extension, the mechanisms of our own lives. "In the Beginning Was the Worm" shows that in order to unlock the secrets of the human genome we must first understand the worm.

But this story is about more than just the worm. It is about how an eccentric group of impassioned scientists toiled in near anonymity for years, driven only by a deep passion for knowledge and scientific discovery. It is the story of countless hours of research, immense ambition, and one of the greatest discoveries in human history.

Flow cytometry is a sensitive and quantitative platform for the measurement of particle fluorescence. In flow cytometry, the particles in a sample flow in single file through a focused laser beam at rates of hundreds to thousands of particles per second. During the time each particle is in the laser beam, on the order of ten microseconds, one or more fluorescent dyes associated with that particle are excited. The fluorescence emitted from each particle is collected through a microscope objective, spectrally filtered, and detected with photomultiplier tubes.
Flow cytometry is uniquely capable of the precise and quantitative molecular analysis of genomic sequence information, interactions between purified biomolecules and cellular function. Combined with automated sample handling for increased sample throughput, these features make flow cytometry a versatile platform with applications at many stages of drug discovery. Traditionally, the particles studied are cells, especially blood cells; flow cytometry is used extensively in immunology.
This volume shows how flow cytometry is integrated into modern biotechnology, dealing with issues of throughput, content, sensitivity, and high throughput informatics with applications in genomics, proteomics and protein-protein interactions, drug discovery, vaccine development, plant and reproductive biology, pharmacology and toxicology, cell-cell interactions and protein engineering.

Bioinformatics has ignited the imagination of scientists, entrepreneurs and the general public. At the meeting place of two fast growth disciplines, biology and computer science Bioinformatics is one of the cornerstones of the new biology. It is clearly pivotal to the translation of high throughput projects such the human genome project into useful knowledge. Yet despite all this attention, there is no consensus on what exactly is Bioinformatics. There are several canonical topics, such as gene structure prediction, protein functional classification or structure prediction. The present book explores new frontiers in bioinformatics, such as Glycomics or the computational modeling of genetic processes. We also discuss confounding factors that we find crucial to the development of the field, such as the ability to protect and restrict intellectual property in the field, or the challenges involved in educating bioinformatics users. Finally, we touch upon some fundamental questions, such as what information is and how it is captured in biological systems. By bringing to the readers such a broad spectrum of reviews, we hope to capture the vibrant spirit of this young science and to truly represent the fast pace with which it is still developing.

The most influential scientist of the last century, James Watson has been at dead center in the creation of modern molecular biology. This masterful biography brings to life the extraordinary achievements not only of Watson but also all those working on this cutting edge of scientific discovery, such as Walter Gilbert, Francis Crick, Francois Jacob, and David Baltimore. From the ruthless competition in the race to identify the structure of DNA to a near mutiny in the Harvard biology department, to clashes with ethicists over issues in genetics, Watson has left a wake of detractors as well as fans. Victor McElheny probes brilliantly behind the veil of Watson's own invented persona, bringing us close to the relentless genius and scientific impresario who triggered and sustained a revolution in science.

This is the story of how three men won the Nobel Prize for their research on the humble nematode worm "C. elegans"; how their extraordinary discovery led to the sequencing of the human genome; how a global multibillion-dollar industry was born; and how the mysteries of life were revealed in a tiny, brainless worm.

In 1998 the nematode worm -- perhaps the most intensively studied animal on earth -- was the first multicellular organism ever to have its genome sequenced and its DNA mapped and read. "When we understand the worm, we will understand life," predicted John Sulston, one of the three Nobel laureates, and his prediction proved astonishingly accurate. Four years later, the research that led to this extraordinary event garnered three scientists a Nobel Prize. Along with Robert Horvitz and Sydney Brenner, Sulston discovered the phenomenon of programmed cell death in the worm, an essential concept that explains how biological development occurs in animal life and, as Horvitz later showed, how it occurs in human life. "C. elegans" is about as simple as an animal can be, but understanding its genetic organization is helping to reveal the mechanisms of life and, by extension, the mechanisms of our own lives. "In the Beginning Was the Worm" shows that in order to unlock the secrets of the human genome we must first understand the worm.

But this story is about more than just the worm. It is about how an eccentric group of impassioned scientists toiled in near anonymity for years, driven only by a deep passion for knowledge and scientific discovery. It is the story of countless hours of research, immense ambition, and one of the greatest discoveries in human history.

Written for biologists and medical researchers who don't have any special training in data analysis and statistics, Guide to Analysis of DNA Microarray Data, Second Edition begins where DNA array equipment leaves off: the image produced by the microarray. The text deals with the questions that arise starting at this point, providing an introduction to microarray technology, then moving on to image analysis, data analysis, cluster analysis, and beyond.
With all chapters rewritten, updated, and expanded to include the latest generation of technology and methods, Guide to Analysis of DNA Microarray Data, Second Edition offers practitioners reliable information using concrete examples and a clear, comprehensible style. This Second Edition features entirely new chapters on:
* Image analysis
* Experiment design
* Automated analysis, integrated analysis, and systems biology
* Interpretation of results
Intended for readers seeking practical applications, this text covers a broad spectrum of proven approaches in this rapidly growing technology. Additional features include further reading suggestions for each chapter, as well as a thorough review of available analysis software.