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Tissue-Specific DNA Methylation Patterns in Forensic Samples Detected by Pyrosequencing®
Joana Antunes, Kuppareddi Balamurugan, George Duncan, and Bruce McCord
In certain circumstances the outcome of a trial may hinge on the ability of a forensic laboratory to determine the identity of biological stains present at crime scenes. An example of such a situation would be the detection of blood, saliva, vaginal fluid, or other body fluid in a specific location whereby its presence would reinforce the victim’s or suspect’s version of the events that happened during the commission of a crime. However, current serological methods used for identifying body fluids may lack the sensitivity and specificity to identify these fluids, particularly for trace levels. New procedures using proteomic methods and RNA-based gene expression show promise in addressing this issue; however, concerns about stability and relative levels of gene expression remain. An alternative approach is to utilize patterns of epigenetic DNA methylation. DNA methylation is an epigenetic mechanism that regulates the specificity of genes being expressed or silenced in cells. Regions in the human genome referred to as tissue-specific differentially methylated regions account for unique patterns of DNA methylation that are specific for each cell type. This chapter addresses the application of bisulfite-modified PCR combined with Pyrosequencing® to detect tissue-specific DNA methylation patterns and perform trace serological analysis. The quantitative nature and precision available with Pyrosequencing presents major advantages in these studies as it permits detection of and contrast between cells with differential levels of methylation. The procedure can be applied to a variety of biological fluids which may be present at crime scenes.
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Group Selection
Omar T. Eldakar
This Encyclopedia is a comprehensive A-Z reference that defines sexuality from a broad biocultural perspective and show the diversity of human sexual behavior and belief systems.
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Engineering Cell-to-Cell Communication to Explore Fundamental Questions in Ecology and Evolution
Robert P. Smith, Lauren Boudreau, and L. You
Quorum sensing (QS) describes a chemical communication behavior that is nearly universal among bacteria. Individual cells release a diffusible small molecule (an autoinducer) into their environment. A high concentration of this autoinducer serves as a signal of high population density, triggering new patterns of gene expression throughout the population. However QS is often much more complex than this simple census-taking behavior. Many QS bacteria produce and detect multiple autoinducers, which generate quorum signal cross talk with each other and with other bacterial species. QS gene regulatory networks respond to a range of physiological and environmental inputs in addition to autoinducer signals. While a host of individual QS systems have been characterized in great molecular and chemical detail, quorum communication raises many fundamental quantitative problems which are increasingly attracting the attention of physical scientists and mathematicians. Key questions include: What kinds of information can a bacterium gather about its environment through QS? What physical principles ultimately constrain the efficacy of diffusion-based communication? How do QS regulatory networks maximize information throughput while minimizing undesirable noise and cross talk? How does QS function in complex, spatially structured environments such as biofilms? Previous books and reviews have focused on the microbiology and biochemistry of QS. With contributions by leading scientists and mathematicians working in the field of physical biology, this volume examines the interplay of diffusion and signaling, collective and coupled dynamics of gene regulation, and spatiotemporal QS phenomena. Chapters will describe experimental studies of QS in natural and engineered or microfabricated bacterial environments, as well as modeling of QS on length scales spanning from the molecular to macroscopic. The book aims to educate physical scientists and quantitative-oriented biologists on the application of physics-based experiment and analysis, together with appropriate modeling, in the understanding and interpretation of the pervasive phenomenon of microbial quorum communication.
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Chapter 12: Engineering Cell-to-Cell Communication to Explore Fundamental Questions in Ecology and Evolution
Robert P. Smith, Lauren Boudreau, and Lingchong You
Synthetic biology has created countless examples of gene circuits that lead to novel behavior in cells. While the technological applications of these circuits, in terms of their use in medicine, industry, and to study systems biology has been acknowledged, synthetic biology is increasingly used to explore questions in evolution and ecology. Traditionally, evolutionary and ecological studies have taken two separate approaches to address scientific questions. One traditional approach uses mathematical modeling to capture the essential aspects of the dynamic or relationship under study. Research is performed in silico, allowing the researcher to explore multiple parameters in a well-defined system, as compared to studying the relationship in its natural setting. However, predictions generated by mathematical models are often not verified experimentally, leading to questions regarding their validity. On the other hand, studying a single dynamic in a natural setting offers its own set of challenges. Here, the single dynamic of interest may be subject to multiple interacting factors, which may obscure its true contribution to the relationship under study. Synthetic biology thus offers a well-rounded intermediate between these two approaches; modeling predictions are verified in living, experimental systems. This dual approach has allowed for the study of ecological and evolutionary dynamics that would be nearly impossible to study in the natural environment. Indeed, the number of studies that have utilized synthetic biology to study such relationships is growing quickly.
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Chapter 12: Forensic Animal DNA Analysis
Marilyn Menotti-Raymond, Victor A. David, Stephen J. O'Brien, Sree Kanthaswamy, Petar Projic, Vedrana Skaro, Gordan Lauc, and Adrian Linacre
Forensic DNA Applications: An Interdisciplinary Perspective was developed as an outgrowth of a conference held by the International Society of Applied Biological Sciences. The topic was human genome–based applications in forensic science, anthropology, and individualized medicine. Assembling the contributions of contributors from numerous regions around the world, this volume is designed as both a textbook for forensic molecular biology students and a reference for practitioners and those in the legal system.
The book begins with the history and development of DNA typing and profiling for criminal and civil purposes. It discusses the statistical interpretation of results with case examples, mitochondrial DNA testing, Y single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs), and X SNP and STR testing. It also explores low copy number DNA typing, mixtures, and quality assurance and control.
The second section examines the collection and preservation of biological evidence under a variety of different circumstances and the identification of human remains—including in mass disaster settings. It discusses applications to bioterrorism investigations, animal DNA testing in criminal cases, pedigree questions and wildlife forensic problems, applications in forensic entomology, and forensic botany.
The third section explores recent developments and new technologies, including the rigorous identification of tissue of origin, mtDNA profiling using immobilized probe strips, chips and next-generation sequencing, the use of SNPs to ascertain phenotypic characteristics, and the "molecular autopsy" that looks at aspects of toxicogenetics and pharmacogenetics.
The book concludes with a discussion on law, ethics, and policy. It examines the use of DNA evidence in the criminal justice system in both the United States and Europe, ethical issues in forensic laboratory practices, familial searches, DNA databases, ancestry searches, physical phenotyping, and report writing. The contributors also examine DNA applications in immigration and human trafficking cases and international perspectives on DNA databases.
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Pluripotent Adult Stem Cells: A Potential Revolution in Regenerative Medicine and Tissue Engineering
Tsz Kin Ng, Daniel Pelaez, Veronica R. Fortino, Jordan Greenberg, and Herman S. Cheung
Stem cells have generated a lot of excitement among the researchers, clinicians and the public alike. Various types of stem cells are being evaluated for their regenerative potential. Marginal benefit resulting by transplanting autologus stem cells (deemed to be absolutely safe) in various clinical conditions has been proposed to be a growth factor effect rather than true regeneration. In contrast, various pre-clinical studies have been undertaken, using differentiated cells from embryonic stem cells or induced pluripotent stem cells have shown promise, functional improvement and no signs of teratoma formation. The scientists are not in a rush to reach the clinic but a handful of clinical studies have shown promise. This book is a collection of studies/reviews, beginning with an introduction to the pluripotent stem cells and covering various aspects like derivation, differentiation, ethics, etc., and hence would provide insight into the recent standing on the pluripotent stem cells biology. The chapters have been categorized into three sections, covering subjects ranging from the generation of pluripotent stem cells and various means of their derivation from embryonic as well as adult tissues, the mechanistic understanding of pluripotency and narrating the potential therapeutic implications of these in vitro generated cells in various diseases, in addition to the associated pros and cons in the same.
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Chapter 13: Synthetic Microbial Consortia and their Applications
Robert P. Smith, Yu Tanouchi, and Lingchong You
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Synthetic Microbial Consortia and Their Applications
Robert P. Smith, Y. Tanouchi, and L. You
Synthetic Biology provides a framework to examine key enabling components in the emerging area of synthetic biology. Chapters contributed by leaders in the field address tools and methodologies developed for engineering biological systems at many levels, including molecular, pathway, network, whole cell, and multi-cell levels. The book highlights exciting practical applications of synthetic biology such as microbial production of biofuels and drugs, artificial cells, synthetic viruses, and artificial photosynthesis. The roles of computers and computational design are discussed, as well as future prospects in the field, including cell-free synthetic biology and engineering synthetic ecosystems.
Synthetic biology is the design and construction of new biological entities, such as enzymes, genetic circuits, and cells, or the redesign of existing biological systems. It builds on the advances in molecular, cell, and systems biology and seeks to transform biology in the same way that synthesis transformed chemistry and integrated circuit design transformed computing. The element that distinguishes synthetic biology from traditional molecular and cellular biology is the focus on the design and construction of core components that can be modeled, understood, and tuned to meet specific performance criteria and the assembly of these smaller parts and devices into larger integrated systems that solve specific biotechnology problems.
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Laboratory Exercises in Biology
Edward O. Keith, Charles Messing, Emily F. Schmitt Lavin, and Joshua Stephen Feingold
Third edition
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Chapter 19: Quantitative Analysis of the Spatiotemporal Dynamics of a Synthetic Predator–Prey Ecosystem
Stephen Payne, Robert P. Smith, and Lingchong You
A major focus in synthetic biology is the rational design and implementation of gene circuits to control dynamics of individual cells and, increasingly, cellular populations. Population-level control is highlighted in recent studies which attempt to design and implement synthetic ecosystems (or engineered microbial consortia). On the one hand, these engineered systems may serve as a critical technological foundation for practical applications. On the other hand, they may serve as well-defined model systems to examine biological questions of broad relevance. Here, using a synthetic predator-prey ecosystem as an example, we illustrate the basic experimental techniques involved in system implementation and characterization. By extension, these techniques are applicable to the analysis of other microbial-based synthetic or natural ecosystems.
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Helicosporidium
Aurelien Tartar
The Encyclopedia of Entomology brings together the talents of over 350 distinguished entomologists from 36 countries to provide a detailed, global overview of insects and their close relatives, including taxonomy, behavior, ecology, physiology, history, and management. All the major groups of arthropods are treated, as are many important families and individual species. The Encyclopedia also covers physiology, genetics, ecology, behavior, insect relationships with people, medical entomology, and pest management. Detailed listings are also complemented by more than 1100 illustrations. Featured in this important work are unique biographical sketches of the hundreds of entomologists who have made important contributions to the discipline since its origin.
Presented in three volumes and including a fully searchable and easily accessed online version, theEncyclopedia of Entomology is the most complete reference work in this field. In addition to being a must for Entomology departments around the world, the Encyclopedia also serves as a handy reference for scientists and students in related areas of science such as agronomy, animal science, botany, ecology, human disease, evolutionary biology, forestry, genetics, horticulture, parasitology, toxicology and zoology. -
Surveying coral reef fishes : a manual for data collection, processing, and interpretation of fish survey information for the tropical Northwest Atlantic
Emily F. Schmitt Lavin, Deena W. Feeley, and Kathleen M. Sullivan-Sealey
In order to utilize the untapped resources of volunteers, REEF and TNC, in active partnership, established the REEF Fish Survey Project. The Project involves the training and mobilization of a large corps of volunteers and is currently the only program with the technical and organizational ability to gather marine biodiversity data in a systematic and reliable manner. Objectives of the project are: 1.) to provide training and education opportunities for SCUBA divers and snorkelers to learn to identify and appreciate marine life 2.) to make data and summary reports readily accessible to the marine science, resource management, and conservation communities 3.) to promote the diving community as conservation-minded and active partner in the long-term protection of coral reefs and other marine systems 4.) to encourage support and implementation of effective marine conservation strategies developed through government, private or public frameworks
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Status of Reef Fishes in the Florida Keys National Marine Sanctuary: Regional Project Summary
Emily F. Schmitt Lavin
This report is a summary of the first 3 years of the Fish Survey Project in the Florida Keys, with comparisons among FKNMS sites and with other distant regions. It demonstrates some ways in which data from the Project can be used.
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Biology: The Living World
Peter Alexander, Mary J. Bahret, Judith Chaves, Gary Courtes, and Naomi D'Alessio
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