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Author: Gregory K. Taylor Publisher: ISBN: Category : Languages : en Pages : 97
Book Description
Homing endonucleases, found in all forms of microbial life, facilitate the invasion of host genes often in concert with introns or inteins by generating double stranded breaks in conserved coding sequences. There are five homing endonuclease families distinct in their structural characteristics and each family appears to share a common ancestor with diverse host proteins of unrelated function. Such related proteins include restriction endonucleases, DNA mismatch repair proteins, transcription factors, four-way junction resolving enzymes, and colicins. Homing endonculeases are currently being computationally redesigned for applications in genome engineering and structures of three redesigned homing endonuclease variants are described. In these experiments, crystal structures uncovered unexpected shifts in the DNA backbone relative to the wild type endonucleases and have thus been informative in the redesign process. Recently, a sixth homing endonuclease family homologous to E. Coli DNA repair protein VSR was discovered. A series of biochemical and x-ray crystallographic experiments investigating binding specificity and catalytic mechanism of a representative family member I-Bth0305I are described. Finally, a database archiving experimentally characterized homing endonucleases and a web-base program supporting homing endonuclease target site search are discussed.
Author: Gregory K. Taylor Publisher: ISBN: Category : Languages : en Pages : 97
Book Description
Homing endonucleases, found in all forms of microbial life, facilitate the invasion of host genes often in concert with introns or inteins by generating double stranded breaks in conserved coding sequences. There are five homing endonuclease families distinct in their structural characteristics and each family appears to share a common ancestor with diverse host proteins of unrelated function. Such related proteins include restriction endonucleases, DNA mismatch repair proteins, transcription factors, four-way junction resolving enzymes, and colicins. Homing endonculeases are currently being computationally redesigned for applications in genome engineering and structures of three redesigned homing endonuclease variants are described. In these experiments, crystal structures uncovered unexpected shifts in the DNA backbone relative to the wild type endonucleases and have thus been informative in the redesign process. Recently, a sixth homing endonuclease family homologous to E. Coli DNA repair protein VSR was discovered. A series of biochemical and x-ray crystallographic experiments investigating binding specificity and catalytic mechanism of a representative family member I-Bth0305I are described. Finally, a database archiving experimentally characterized homing endonucleases and a web-base program supporting homing endonuclease target site search are discussed.
Author: Sahra-Taylor Mullineux Publisher: ISBN: Category : Languages : en Pages : 638
Book Description
Evolutionary relationships amongst strains of the fungal genus Leptographium and related taxa were inferred using the internal transcribed spacer (ITS) region of the nuclear ribosomal DNA repeat. To generate robust sequence alignments for phylogenetic analysis the relationship between DNA sequence variability and RNA structural conservation of ITS segments was examined. The results demonstrate that structural conservation of helical regions is facilitated by compensatory base changes, compensating insertions/deletions, and, possibly, RNA strand slippage. A high mol % G+C bias for ITS1 and ITS2 and structural constraints at the RNA level appear to limit the types of changes observed. Fifty strains of Leptographium were screened for the presence of introns within mitochondrial genes. Superimposing intron survey data onto the ITS-derived phylogenetic tree reveals that introns are absent from the small ribosomal RNA (rns) gene of all strains of L. procerum yet are found in all strains of L. lundbergii. Amongst members of L. wingfieldii, L. terebrantis, and L. truncatum intron distribution is stochastic and is not correlated to the evolutionary relationships amongst strains. A group II intron/LAGLIDADG homing endonuclease gene (HEG) composite element from the mt rns gene of L. truncatum strain CBS929.85 was characterized. Intron-catalyzed splicing was tested using ORF-less and ORF-containing precursor transcripts, and both versions of the intron readily self-splice under moderate temperature and ionic conditions (37 °C and 6 mM MgCl2). Cleavage activity of the intron-encoded protein (I-LtrII) was tested using an N-terminal His6-tagged and near native protein. The homing endonuclease cleaves double-stranded DNA 2 nucleotides upstream of the intron insertion site within the exon, generating 4 nucleotide 3' OH overhangs. Intron splicing is not enhanced by the addition of I-LtrII and RNA-binding assays indicate that the His6-tagged protein does not bind to the intron. Phylogenetic relationships amongst the rns gene, intron, and amino acid sequences were inferred. An evolutionary model of the composite element is proposed in which the HEG invaded a group II intron and mobilized it. The mobile genetic element may be transmitted vertically amongst L. lundbergii strains and horizontally through lateral gene transfer amongst strains of L. wingfieldii, L. terebrantis, and L. truncatum.
Author: Alfred Pingoud Publisher: Springer Science & Business Media ISBN: 3642188516 Category : Science Languages : en Pages : 462
Book Description
Restriction enzymes are highly specific nucleases which occur ubiquitously among prokaryotic organisms, where they serve to protect bacterial cells against foreign DNA. Many different types of restriction enzymes are known, among them multi-subunit enzymes which depend on ATP or GTP hydrolysis for target site location. The best known representatives, the orthodox type II restriction endonucleases, are homodimers which recognize palindromic sequences, 4 to 8 base pairs in length, and cleave the DNA within or immediately adjacent to the recognition site. In addition to their important biological role (up to 10 % of the genomes of prokaryotic organisms code for restriction/modification systems!), they are among the most important enzymes used for the analysis and recombination of DNA. In addition, they are model systems for the study of protein-nucleic acids interactions and, because of their ubiquitous occurence, also for the understanding of the mechanisms of evolution.
Author: William F. Martin Publisher: Walter de Gruyter GmbH & Co KG ISBN: 3110612410 Category : Science Languages : en Pages : 269
Book Description
Mitochondria are sometimes called the powerhouses of eukaryotic cells, because mitochondria are the site of ATP synthesis in the cell. ATP is the universal energy currency, it provides the power that runs all other life processes. Humans need oxygen to survive because of ATP synthesis in mitochondria. The sugars from our diet are converted to carbon dioxide in mitochondria in a process that requires oxygen. Just like a fire needs oxygen to burn, our mitochondria need oxygen to make ATP. From textbooks and popular literature one can easily get the impression that all mitochondria require oxygen. But that is not the case. There are many groups of organismsm known that make ATP in mitochondria without the help of oxygen. They have preserved biochemical relicts from the early evolution of eukaryotic cells, which took place during times in Earth history when there was hardly any oxygen avaiable, certainly not enough to breathe. How the anaerobic forms of mitochondria work, in which organisms they occur, and how the eukaryotic anaerobes that possess them fit into the larger picture of rising atmospheric oxygen during Earth history are the topic of this book.
Author: Feng Zhang Publisher: Springer ISBN: 1493925563 Category : Science Languages : en Pages : 171
Book Description
Over the past 50 years, biotechnology has been the major driving force for increasing crop productivity. Particularly, advances in plant genetic engineering technologies have opened up vast new opportunities for plant researchers and breeders to create new crop varieties with desirable traits. Recent development of precise genome modification methods, such as targeted gene knock-out/knock-in and precise gene replacement, moves genetic engineering to another level and offers even more potentials for improving crop production. The work provides an overview of the latest advances on precise genomic engineering technologies in plants. Topics include recombinase and engineered nucleases-mediated targeted modification, negative/positive selection-based homologous recombination and oligo nucleotide-mediated recombination. Finally, challenges and impacts of the new technologies on present regulations for genetic modification organisms (GMOs) will be discussed.
Author: Janusz M. Bujnicki Publisher: John Wiley & Sons ISBN: 9780470741900 Category : Science Languages : en Pages : 302
Book Description
The growing flood of new experimental data generated by genome sequencing has provided an impetus for the development of automated methods for predicting the functions of proteins that have been deduced by sequence analysis and lack experimental characterization. Prediction of Protein Structures, Functions and Interactions presents a comprehensive overview of methods for prediction of protein structure or function, with the emphasis on their availability and possibilities for their combined use. Methods of modeling of individual proteins, prediction of their interactions, and docking of complexes are put in the context of predicting gene ontology (biological process, molecular function, and cellular component) and discussed in the light of their contribution to the emerging field of systems biology. Topics covered include: first steps of protein sequence analysis and structure prediction automated prediction of protein function from sequence template-based prediction of three-dimensional protein structures: fold-recognition and comparative modelling template-free prediction of three-dimensional protein structures quality assessment of protein models prediction of molecular interactions: from small ligands to large protein complexes macromolecular docking integrating prediction of structure, function, and interactions Prediction of Protein Structures, Functions and Interactions focuses on the methods that have performed well in CASPs, and which are constantly developed and maintained, and are freely available to academic researchers either as web servers or programs for local installation. It is an essential guide to the newest, best methods for prediction of protein structure and functions, for researchers and advanced students working in structural bioinformatics, protein chemistry, structural biology and drug discovery.
Author: Publisher: Academic Press ISBN: 012816574X Category : Medical Languages : en Pages : 228
Book Description
Cellular and Animal Models in Human Genomics Research provides an indispensable resource for applying comparative genomics in the annotation of disease-gene associated variants that are identified by human genomic sequencing. The book presents a thorough overview of effective protocols for the use of cellular and animal modeling methods to turn lists of plausible genes into causative biomarkers. With chapters written by international experts, the book first addresses the fundamental aspects of using cellular and animal models in genetic and genomic studies, including in-depth examples of specific models and their utility, i.e., yeast, worms, flies, fish, mice and large animals. Protocols for properly conducting model studies, genomic technology, modeling candidate genes vs. genetic variants, integrative modeling, utilizing induced pluripotent stem cells, and employing CRISPR-Cas9 are also discussed in-depth. - Provides a thorough, accessible resource that helps researchers and students employ cellular and animal models in their own genetic and genomic studies - Offers guidance on how to effectively interpret the results and significance of genetic and genomic model studies for human health - Features chapters from international experts in the use of specific cellular and animal models, including yeast, worms, flies, fish, mice, and large animals, among other organisms
Author: Boriana Marintcheva Publisher: Academic Press ISBN: 0128105151 Category : Science Languages : en Pages : 298
Book Description
Harnessing the Power of Viruses explores the application of scientific knowledge about viruses and their lives to solve practical challenges and further advance molecular sciences, medicine and agriculture. The book contains virus-based tools and approaches in the fields of: i) DNA manipulations in vitro and in vivo; ii) Protein expression and characterization; and iii) Virus- Host interactions as a platform for therapy and biocontrol are discussed. It steers away from traditional views of viruses and technology, focusing instead on viral molecules and molecular processes that enable science to better understand life and offer means for addressing complex biological phenomena that positively influence everyday life. The book is written at an intermediate level and is accessible to novices who are willing to acquire a basic level of understanding of key principles in molecular biology, but is also ideal for advanced readers interested in expanding their biological knowledge to include practical applications of molecular tools derived from viruses. - Explores virus-based tools and approaches in DNA manipulation, protein expression and characterization and virus-host interactions - Provides a dedicated focus on viral molecules and molecular processes that enable science to better understand life and address complex biological phenomena - Includes an overview of modern technologies in biology that were developed using viral components/elements and knowledge about viral processes
Author: Gregory K. Taylor
Author: Gregory K. Taylor
Author: Sahra-Taylor Mullineux
Author: Alfred Pingoud
Author: William F. Martin
Author: 
Author: Feng Zhang
Author: Janusz M. Bujnicki
Author: 
Author: 
Author: Boriana Marintcheva