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Repetitive structures in biological sequences are emerging as an active focus of research and the unifying concept of "repeatome" (the ensemble of knowledge associated with repeating structures in genomic/proteomic sequences) has been recently proposed in order to highlight several converging trends. One main trend is the ongoing discovery that genomic repetitions are linked to many biological significant events and functions. Diseases (e.g. Huntington's disease) have been causally linked with abnormal expansion of certain repeating sequences in the human genome. Deletions or multiple copy duplications of genes (Copy Number Variations) are important in the aetiology of cancer, Alzheimer, and Parkinson diseases. A second converging trend has been the emergence of many different models and algorithms for detecting non-obvious repeating patterns in strings with applications to in genomic data. Borrowing methodologies from combinatorial pattern, matching, string algorithms, data structures, data mining and machine learning these new approaches break the limitations of the current approaches and offer a new way to design better trans-disciplinary research. The articles collected in this book provides a glance into the rich emerging area of repeatome research, addressing some of its pressing challenges. We believe that these contributions are valuable resources for repeatome research and will stimulate further research from bioinformatic, statistical, and biological points of view.
Algorithms --- Repetitive structures --- next generation sequencing --- tandem repeats --- transposable elements
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There are only few major key functions that lie beneath the fundamental architecture of metabolism and life. These are multiplication, variation and heredity. Only if these factors interact synergistically can Darwinian selection power the evolution of biodiversity. Transposable elements have always played a major role in this process. The genomes of all organisms consist of chromosomes that are built up of double-stranded nucleic acid chains on whose stability and integrity the existence of cells depend. While DNA repair warrants the chemical integrity of DNA and protects it from metabolic and environmental mutagens, meiotic recombination and transposable element activity appear to counteract the molecular guardians of genome stability. Transposable elements and their kind often make up the bulk of genomic DNA, often approaching 50% of the genome. By contrast, the classic genes represent as little as 1.8% of genomic DNA, in case of the human genome. This volume gives an overview on mobile DNA and how such contradiction to the obligatory stability of genomes can be understood. Obviously, an understanding can only be achieved by cutting deeply into the evolutionary history of life along with the evolution of transposable elements and dynamic genomes. This book therefore also celebrates Charles Darwin’s 200th birthday. The reader is challenged to view the role of movable DNA along historical roots from the levels of cells to populations to biological species integrating the accompanying molecular evolution of host, cell and genome interaction. One will witness even the reactivation of a long since dead, fossil transposable element and the infection of germline cells by the first established, mobile and endogenous insect retrovirus.
Genomes --Stability. --- Genomes. --- Molecular dynamics. --- Transposons. --- Transposons --- Genomes --- Molecular dynamics --- DNA Transposable Elements --- Interspersed Repetitive Sequences --- DNA --- Genome Components --- Repetitive Sequences, Nucleic Acid --- Nucleic Acids --- Base Sequence --- Nucleic Acids, Nucleotides, and Nucleosides --- Genome --- Genetic Structures --- Chemicals and Drugs --- Molecular Structure --- Biochemical Phenomena --- Genetic Phenomena --- Phenomena and Processes --- Chemical Phenomena --- Biochemistry --- Genetics --- Biology - General --- Biology --- Chemistry --- Physical Sciences & Mathematics --- Health & Biological Sciences --- Stability --- Molecular genetics. --- Tn elements --- Transposable elements --- Life sciences. --- Human genetics. --- Biochemistry. --- Cell biology. --- Life Sciences. --- Biochemistry, general. --- Cell Biology. --- Human Genetics. --- Mobile genetic elements --- Molecular biology --- Cytology. --- Heredity, Human --- Human biology --- Physical anthropology --- Cell biology --- Cellular biology --- Cells --- Cytologists --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Medical sciences --- Composition
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Translocation (Genetics) --- Plasmids --- periodicals --- Extrachromosomal Inheritance. --- Plasmids. --- Plasmides --- Cytoplasmic Inheritance --- Extranuclear Inheritance --- Inheritance, Cytoplasmic --- Inheritance, Extrachromosomal --- Inheritance, Extranuclear --- Paragenes --- DNA, Chloroplast --- Cytoplasmic inheritance --- Genetic vectors --- Mobile genetic elements --- Extrachromosomal DNA --- Extrachromosomal Inheritance --- periodicals. --- Episome --- Plasmid --- Episomes --- Virophages --- DNA Transposable Elements --- Translocation, Genetic. --- Chromosomal Translocation --- Translocation, Chromosomal --- Chromosomal Translocations --- Genetic Translocation --- Genetic Translocations --- Translocations, Chromosomal --- Translocations, Genetic --- Gene Rearrangement --- Translocation, Genetic --- Periodical.
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Transposable elements are DNA sequences with the capacity to move within a genome. Although their presence and impact has long been known, the recent genome-wide analysis of many eukaryotic genomes has uncovered their major role in genome dynamics and function. The present book explains how to recognize and study transposable elements, e.g. by using state-of-the-art strategies based on new-generation sequencing. Moreover, the impact of transposable elements on plant genome structure and function is reviewed in detail and illustrated in examples and case studies. The book is intended both for readers familiar with the field and for newcomers. With large-scale sequencing becoming increasingly available, more and more people will come across transposable element sequences in their data, and this volume will hopefully help to convince them that transposable elements are not just "junk" DNA, and may actually be the most interesting and fun part of their data!
Genetic regulation -- Congresses. --- Insertion elements, DNA -- Congresses. --- Mutagens -- Congresses. --- Plant molecular genetics -- Congresses. --- Insertion elements, DNA --- Mutagens --- Plant genetic regulation --- Transposons --- Plant molecular genetics --- Interspersed Repetitive Sequences --- Genome --- DNA --- Genetic Structures --- Repetitive Sequences, Nucleic Acid --- Genome Components --- Nucleic Acids --- Nucleic Acids, Nucleotides, and Nucleosides --- Genetic Phenomena --- Base Sequence --- Chemicals and Drugs --- Phenomena and Processes --- Molecular Structure --- Biochemical Phenomena --- Chemical Phenomena --- DNA Transposable Elements --- Genome, Plant --- Biology --- Health & Biological Sciences --- Genetics --- Transposons. --- Plant molecular genetics. --- Tn elements --- Transposable elements --- Life sciences. --- Nucleic acids. --- Plant biochemistry. --- Cell biology. --- Plant genetics. --- Life Sciences. --- Plant Genetics & Genomics. --- Plant Biochemistry. --- Nucleic Acid Chemistry. --- Cell Biology. --- Molecular genetics --- Plant genetics --- Plant molecular biology --- Mobile genetic elements --- Biochemistry. --- Cytology. --- Plant Genetics and Genomics. --- Biological chemistry --- Chemical composition of organisms --- Organisms --- Physiological chemistry --- Chemistry --- Medical sciences --- Plants --- Cell biology --- Cellular biology --- Cells --- Cytologists --- Polynucleotides --- Biomolecules --- Composition --- Phytochemistry --- Plant biochemistry --- Plant chemistry --- Biochemistry --- Botany --- Phytochemicals --- Plant biochemical genetics
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This manual is an indispensable tool for introducing advanced undergraduates and beginning graduate students to the techniques of recombinant DNA technology, or gene cloning and expression. The techniques used in basic research and biotechnology laboratories are covered in detail. Students gain hands-on experience from start to finish in subcloning a gene into an expression vector, through purification of the recombinant protein.The second edition has been completely re-written, with new laboratory exercises and all new illustrations and text, designed for a typical 15-week semester,
Molecular biology --- Technique --- DNA, Recombinant. --- Molecular Biology --- Protein Engineering. --- methods. --- Genetic Engineering, Protein --- Proteins, Genetic Engineering --- Genetic Engineering of Proteins --- Engineering, Protein --- Engineering, Protein Genetic --- Protein Genetic Engineering --- Recombinant DNA Research --- Recombination Joint --- Genes, Spliced --- Recombinant DNA --- DNA Research, Recombinant --- Joint, Recombination --- Research, Recombinant DNA --- Spliced Genes --- Molecular biochemistry --- Molecular biophysics --- Genetic Engineering --- Directed Molecular Evolution --- DNA Shuffling --- Molecular Farming --- Cloning, Molecular --- DNA Transposable Elements --- Genetic Vectors --- Genomic Library --- Gene Library --- Artificial Gene Fusion --- Biochemistry --- Biophysics --- Biomolecules --- Systems biology
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Biomedical engineering --- Biotechnology --- Microbiology --- Biomedical engineering. --- Biotechnology. --- Microbiology. --- Microbial biology --- Biology --- Microorganisms --- Chemical engineering --- Genetic engineering --- Clinical engineering --- Medical engineering --- Bioengineering --- Biophysics --- Engineering --- Medicine --- Bioengineering. --- DNA, Recombinant. --- Genetic Engineering. --- Recombinant DNA Research --- Recombination Joint --- Genes, Spliced --- Recombinant DNA --- DNA Research, Recombinant --- Joint, Recombination --- Research, Recombinant DNA --- Spliced Genes --- Cloning, Molecular --- DNA Transposable Elements --- Genetic Engineering --- Genetic Vectors --- Genomic Library --- Gene Library --- Artificial Gene Fusion --- Engineering, Genetic --- Intervention, Genetic --- Genetic Intervention --- Genetic Interventions --- Interventions, Genetic --- DNA, Recombinant --- Industrial Microbiology --- Organisms, Genetically Modified --- Animals, Genetically Modified --- Plants, Genetically Modified --- Bio engineering --- Biological Engineering --- Bio-Engineering --- Bio engineerings --- Bioengineerings --- Engineering, Biological --- engineering, Bio --- engineerings, Bio --- Bioenginyeria --- Biotecnologia --- Bioenginyeria. --- Biotecnologia.
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The great advances in information technology (IT) have implications for many sectors, such as bioinformatics, and has considerably increased their possibilities. This book presents a collection of 11 original research papers, all of them related to the application of IT-related techniques within the bioinformatics sector: from new applications created from the adaptation and application of existing techniques to the creation of new methodologies to solve existing problems.
machine learning --- metagenomics --- bioinformatics --- CTX-M --- data mining --- cluster --- clinical implications --- diabetes --- epidemiology --- forecast --- PART --- Decision table --- Weka --- real-life patients --- regression --- ear detection --- computer vision --- convolutional neural network --- image recognition --- video analysis --- gene clustering --- swarm intelligence --- biological functions detection --- informative genes --- fuel cell --- hydrogen energy --- intelligent systems --- hybrid systems --- Artificial Neural Networks --- power management --- Machine Learning --- personality assessment --- gradient boosting --- Affective Computing --- transposable elements --- metrics --- deep learning --- detection --- classification --- mitochondrial protein --- bi-directional LSTM --- plasmodium falciparum --- Particle Swarm Optimization --- Harmony Search --- parameter estimation --- Arabidopsis thaliana --- clinical data --- feature selection --- genetic programming --- evolutionary computation --- dynamic models --- evolutionary computing --- derivative-free optimization --- metabolism --- glycolysis --- yeast
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DNA --- RNA --- Genetic engineering --- DNA. --- Genetic engineering. --- RNA. --- DNA, Recombinant --- Genetic Engineering --- Antisense Elements (Genetics) --- Synthesis --- Synthesis. --- chemical synthesis --- Health Sciences --- Physiology --- Deoxyribonucleic acid --- Desoxyribonucleic acid --- Thymonucleic acid --- TNA (Nucleic acid) --- ds-DNA --- DNA, Double-Stranded --- Deoxyribonucleic Acid --- DNA, Double Stranded --- Double-Stranded DNA --- ds DNA --- Ribonucleic acid --- Ribose nucleic acid --- Designed genetic change --- Engineering, Genetic --- Gene splicing --- Genetic intervention --- Genetic surgery --- Deoxyribonucleic acid synthesis --- Anti-Sense Elements --- Anti-Sense Probes --- Antisense Probes --- Anti Sense Elements --- Anti Sense Probes --- Elements, Anti-Sense --- Probes, Anti-Sense --- Probes, Antisense --- Intervention, Genetic --- Genetic Intervention --- Genetic Interventions --- Interventions, Genetic --- Recombinant DNA Research --- Recombination Joint --- Genes, Spliced --- Recombinant DNA --- DNA Research, Recombinant --- Joint, Recombination --- Research, Recombinant DNA --- Spliced Genes --- Biotechnology --- Cloning, Molecular --- Industrial Microbiology --- Artificial Gene Fusion --- Organisms, Genetically Modified --- Animals, Genetically Modified --- Plants, Genetically Modified --- DNA Transposable Elements --- Genetic Vectors --- Genomic Library --- Gene Library --- Biopolymers --- Nucleic acids --- Ribose --- Genetic recombination --- Transgenic organisms --- Deoxyribose --- Genes --- DNA, Recombinant. --- Genetic Engineering. --- Antisense Elements (Genetics). --- chemical synthesis.
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Megaplasmids are extrachromosomal genetic elements in the size range of 100 kb and larger. They are found in physiologically and phylogenetically diverse groups of bacteria and archaea. By definition, megaplasmids are not essential for the viability of their hosts under all growth conditions, but paradoxically many megaplasmids carry the genetic information for the defining and characteristic traits of the organism in which they reside. Microbial Megaplasmids reviews our knowledge of the extensively studied representatives, such as the catabolic plasmids of the pseudomonads, the rhizobial Sym plasmids, the Ti plasmids of the genus Agrobacterium and the giant enterobacterial virulence plasmids. It also presents snapshots of more recently discovered megaplasmids. The contribution of megaplasmids to the biology of their hosts is described, highlighting the interactions between megaplasmid and chromosomal genes.
Agriculture. --- Bacterial chromosomes. --- Bacteriology. --- Chromosomes, Bacterial. --- DNA Transposable Elements --genetics. --- DNA, Bacterial. --- Genome, Bacterial. --- Microbial genetics. --- Microbiology. --- Plant diseases. --- Plasmids --genetics. --- Plasmids. --- Microorganisms --- Paragenes --- Genetics --- Life sciences. --- Medical microbiology. --- Microbial genomics. --- Plant pathology. --- Life Sciences. --- Plant Pathology. --- Medical Microbiology. --- Microbial Genetics and Genomics. --- Applied Microbiology. --- Microbiology --- Botany --- Communicable diseases in plants --- Crop diseases --- Crops --- Diseases of plants --- Microbial diseases in plants --- Pathological botany --- Pathology, Vegetable --- Phytopathology --- Plant pathology --- Plants --- Vegetable pathology --- Agricultural pests --- Crop losses --- Diseased plants --- Phytopathogenic microorganisms --- Plant pathologists --- Plant quarantine --- Microbial biology --- Biology --- Genomics --- Microbial genetics --- Farming --- Husbandry --- Industrial arts --- Life sciences --- Food supply --- Land use, Rural --- Biosciences --- Sciences, Life --- Science --- Pathology --- Diseases and pests --- Diseases --- Wounds and injuries --- Cytoplasmic inheritance --- Genetic vectors --- Mobile genetic elements --- Extrachromosomal DNA
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This book brings together the papers published in the Special Issue "Recent advances in the understanding of molecular mechanisms of resistance in Noctuid pests" in the journal Insects in 2021. It contains 10 articles that are either original results or reviews. The focus is on insects of the noctuid family, as they are among the most devastating crop pests on the planet. Understanding the molecular mechanisms that allow these insects to become resistant to insecticides is essential for the implementation of sustainable control methods and resistance management strategies.
fall armyworm --- insecticide resistance --- target-site mutations --- Bt resistance --- corn strain --- rice strain --- resistance management --- Indonesia --- Kenya --- 1′S-1′-Acetoxychavicol acetate --- Alpinia galanga --- Spodoptera frugiperda --- Sf9 cells --- botanical pesticide --- Mythimna loreyi --- rice armyworm --- invasive pest --- LAMP --- diagnostic PCR --- Helicoverpa armigera --- transposable elements --- insertions sites --- insecticide resistance genes --- insect rearing --- dynamic energy budget (DEB) theory --- development --- temperature --- variability --- Bacillus thuringiensis --- Cry protein --- ATP-Binding Cassette --- ABC Transporter --- ATP switch model --- pore-forming toxin --- resistance --- genetics --- Noctuidae --- Helicoverpa --- Spodoptera --- Heliothis --- Chloridea --- Trichoplusia --- ABCC2 --- biological invasion --- Cytochrome P450 --- Fall armyworm --- cytochromes P450 --- carboxyl/cholinesterases --- glutathione S-transferases --- ATP-binding cassette transporters --- soybean looper --- reference genes --- Cry1F --- genotyping --- targeted sequencing --- resistance screen --- n/a --- 1'S-1'-Acetoxychavicol acetate
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