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Duplicated passages of source code - code clones - are a common property of software systems. While clones are beneficial in some situations, their presence causes various problems for software maintenance. Most of these problems are strongly related to change and include, for example, the need to propagate changes across duplicated code fragments and the risk of inconsistent changes to clones that are meant to evolve identically. Hence, we need a sophisticated analysis of clone evolution to better understand, assess, and manage duplication in practice. This thesis introduces Clone Evolution Graphs as a technique to model clone relations and their evolution within the history of a system. We present our incremental algorithm for efficient and automated extraction of Clone Evolution Graphs from a system's history. The approach is shown to scale even for large systems with long histories making it applicable to retroactive analysis ofclone evolution as well as live tracking of clones during software maintenance.We have used Clone Evolution Graphs in several studies to analyze versatile aspects of clone evolution in open-source as well as industrial systems. Our results show that the characteristics of clone evolution are quite different between systems, highlighting the need for a sophisticated technique like Clone Evolution Graphs to track clones and analyze their evolution on a per-system basis. We have also shown that Clone Evolution Graphs are well-suited to analyze the change behavior of individual clones and can be used to identify problematic clones within a system. In general, the results of our studies provide new insights into how clones evolve, how they are changed, and how they are removed.
Principles of Cloning, Second Edition is the fully revised edition of the authoritative book on the science of cloning. The book presents the basic biological mechanisms of how cloning works and progresses to discuss current and potential applications in basic biology, agriculture, biotechnology, and medicine. Beginning with the history and theory behind cloning, the book goes on to examine methods of micromanipulation, nuclear transfer, genetic modification, and pregnancy and neonatal care of cloned animals. The cloning of various species—including mice, sheep, cattle, and non-mammals—is considered as well. The Editors have been involved in a number of breakthroughs using cloning technique, including the first demonstration that cloning works in differentiated cells done by the Recipient of the 2012 Nobel Prize for Physiology or Medicine – Dr John Gurdon; the cloning of the first mammal from a somatic cell – Drs Keith Campbell and Ian Wilmut; the demonstration that cloning can reset the biological clock - Drs Michael West and Robert Lanza; the demonstration that a terminally differentiated cell can give rise to a whole new individual – Dr Rudolf Jaenisch and the cloning of the first transgenic bovine from a differentiated cell – Dr Jose Cibelli. The majority of the contributing authors are the principal investigators on each of the animal species cloned to date and are expertly qualified to present the state-of-the-art information in their respective areas. - First and most comprehensive book on animal cloning, 100% revised - Describes an in-depth analysis of current limitations of the technology and research areas to explore - Offers cloning applications on basic biology, agriculture, biotechnology, and medicine
Transgenic methodologies continue to evolve and have dramatically influenced a cross section of disciplines. They are recognized as instrumental in expanding our understanding of gene expression, regulation and function. This book covers the aspects of gene transfer in animals-from molecular methods to whole animal considerations across a host of species. The book starts with an introduction of what are transgenic animals. Chapter 1 methods and applications related to transgenic application. Chapter 2 describes the Use of Transgenic Animals in Biotechnology as Prospects and Problems. Chapter 3 study about Transgenic Animals in Agriculture. Chapter 4 depicts about the Gene Replacement and Transgenic Animals. This chapter give insight on Specific Sites in Cloned Genes Can Be Altered in Vitro and DNA that can be transferred into Eukaryotic Cells in Various Ways. Chapter 5 discuss about basics of cloning. Chapter 6 tells about the Reproductive Cloning. Chapter 7 tells about the Cloning of Domestic Animals. Chapter 8 depicts about the Surface Epigenetic Reprogramming. Chapters 9 devoted to Animal Health Risks. This chapter focus on the critical biological systems approach to the analysis of clone animal. Chapter 10 describes the development of the Risk Assessment Methodology required for cloning.
This volume focuses on newly emerging technologies that facilitate the isolation and characterization of genes. The detailed protocols will be useful to the seasoned professional and easily understood by the novice. The vast majority of methods are applic
Sample: "What does language do? Or, what does culture do? Language and culture are non-genetic mechanisms for increasing the number of qualities across individuals, and language and culture also increase the capacity for intraspecific assortative mating across individuals in the human species (by increasing the number of dissimilarities and categories of similarities across individuals in the human species). It is interesting to consider functional analogies amongst animals and plants: Birdsong and feather colors in bird species, and the colors and shapes of angiosperm flowering plant species play similar functions in these species, i.e., they increase the number and differentiation of characteristics across individual organisms, thus increasing the capacity for assortative mating across individual organisms in bird species (intraspecific assortative mating), and increasing the capacity for assortative mating across angiosperm species and insect, bee, and bird species (interspecific assortative mating).""
Tremendous strides in decoding the human genome have been made over the last ten years. Large, chromosome-scale, genome-scale EST-sequencing and mapping techniques have dramatically expanded the base of identified genes and sequenced DNA. Gene isolation and cloning techniques that emerged earlier on, however, still remain effective mainstays for constructing dense transcript maps to isolate coding sequences and disease-associated genes contained within a specific chromosomal region. Positional Cloning by Exon Trapping and cDNA Selection examines two powerful methods for locating the coding region of a given gene by isolating gene fragments from individual clones or pools of genomic clones. This comprehensive guide details the exon-trapping and cDNA selection processes step by step-from isolating genomic templates and nuclear splicing, to verifying generated clones and sequenced data, to analyzing exon libraries and cDNA sublibraries. Procedures covered include: * Exon-trapping systems and descriptions of pSPL1 and pSPL3 vectors. * Exon amplification protocols for preparing vectors for cloning; subcloning genomic DNA into vectors; transformation, analysis, and transfection of sublibraries; RNA transcription; and PCR amplification and PCR product cloning. * Evaluation of exon libraries by PCR colony testing, identifying artifactual clones using Southern blot, and sequencing and mapping back candidate exons. * Isolation of genomic templates, such as COSMID-, P1-, PAC, and YAC DNA. * cDNA selection experiment protocols including cDNA screening, hybridization, and biotinylation; preparation of genomic and cDNA sources; and PCR cloning. * Clone analysis and analysis by hybridization. Positional Cloning by Exon Trapping and cDNA Selection offers researchers, scientists, and graduate students an invaluable tool for probing gene distribution and molecular organization. Most importantly, it provides a critical approach to isolating specific disease genes within a targeted genomic area.
GENE CLONING & DNA ANALYSIS.