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The Proteins of Plastid Nucleoids - Structure, Function and Regulation

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199273 Year: Pages: 111 DOI: 10.3389/978-2-88919-927-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2016-01-19 14:05:46
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Plastids are plant cell-specific organelles of endosymbiotic origin that contain their own genome, the so-called plastome. Its proper expression is essential for faithful chloroplast biogenesis during seedling development and for the establishment of photosynthetic and other biosynthetic functions in the organelle. The structural organisation, replication and expression of this plastid genome, thus, has been studied for many years, but many essential steps are still not understood. Especially, the structural and functional involvement of various regulatory proteins in these processes is still a matter of research. Studies from the last two decades demonstrated that a plethora of proteins act as specific regulators during replication, transcription, post-transcription, translation and post-translation accommodating a proper inheritance and expression of the plastome. Their number exceeds by far the number of the genes encoded by the plastome suggesting that a strong evolutionary pressure is maintaining the plastome in its present stage. The plastome gene organisation in vascular plants was found to be highly conserved, while algae exhibit a certain flexibility in gene number and organisation. These regulatory proteins are, therefore, an important determinant for the high degree of conservation in plant plastomes. A deeper understanding of individual roles and functions of such proteins would improve largely our understanding of plastid biogenesis and function, a knowledge that will be essential in the development of more efficient and productive plants for agriculture. The latter represents a major socio-economic need of fast growing mankind that asks for increased supply of food, fibres and biofuels in the coming decades despite the threats exerted by global change and fast spreading urbanisation.

DNA Replication Controls

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ISBN: 9783038425724 9783038425731 Year: Volume: 2 Pages: X, 346 DOI: 10.3390/books978-3-03842-573-1 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology
Added to DOAB on : 2017-12-27 08:38:10
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The conditions for DNA replication are not ideal, owing to endogenous and exogenous replication stresses that lead to arrest of the replication fork. Arrested forks are among the most serious threats to genomic integrity because they can break or rearrange, leading to genomic instability, which is a hallmark of cancers and aging-related disorders. This title, “DNA Replication Controls”, presents series of new reviews and original research articles, providing a comprehensive guide to theoretical advancements in the field of DNA replication research in both prokaryotic and eukaryotic systems. The topics include DNA polymerases and helicases; replication initiation; replication timing; replication-associated DNA repair; and replication of difficult-to-replicate genomic regions, including telomeres, centromeres and highly-transcribed regions. This title also provides recent advancements in studies of cellular processes that are coordinated with DNA replication and how defects in the DNA replication program result in genetic disorders, including cancer. Written by leading experts in DNA replication regulation, this book will be an important resource for a wide variety of audiences, including junior graduate students and established investigators who have interests in DNA replication and genome maintenance mechanisms.

DNA Replication Controls

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ISBN: 9783038425687 9783038425694 Year: Volume: 1 Pages: X, 304 DOI: 10.3390/books978-3-03842-569-4 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology
Added to DOAB on : 2018-01-02 15:17:59
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The conditions for DNA replication are not ideal, owing to endogenous and exogenous replication stresses that lead to arrest of the replication fork. Arrested forks are among the most serious threats to genomic integrity because they can break or rearrange, leading to genomic instability, which is a hallmark of cancers and aging-related disorders.

DNA Replication Origins in Microbial Genomes

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197798 Year: Pages: 115 DOI: 10.3389/978-2-88919-779-8 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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DNA replication, a central event for cell proliferation, is the basis of biological inheritance. Complete and accurate DNA replication is integral to the maintenance of the genetic integrity of organisms. In all three domains of life, DNA replication begins at replication origins. In bacteria, replication typically initiates from a single replication origin (oriC), which contains several DnaA boxes and the AT-rich DNA unwinding element (DUE). In eukaryotic genomes, replication initiates from significantly more replication origins, activated simultaneously at a specific time. For eukaryotic organisms, replication origins are best characterized in the unicellular eukaryote budding yeast Saccharomyces cerevisiae and the fission yeast Schizosaccharomyces pombe. The budding yeast origins contain an essential sequence element called the ARS (autonomously replicating sequence), while the fission yeast origins consist of AT-rich sequences. Within the archaeal domain, the multiple replication origins have been identified by a predict-and-verify approach in the hyperthermophilic archaeon Sulfolobus. The basic structure of replication origins is conserved among archaea, typically including an AT-rich unwinding region flanked by several short repetitive DNA sequences, known as origin recognition boxes (ORBs). It appears that archaea have a simplified version of the eukaryotic replication apparatus, which has led to considerable interest in the archaeal machinery as a model of that in eukaryotes. The research on replication origins is important not only in providing insights into the structure and function of the replication origins but also in understanding the regulatory mechanisms of the initiation step in DNA replication. Therefore, intensive studies have been carried out in the last two decades. The pioneer work to identify bacterial oriCs in silico is the GC-skew analysis. Later, a method of cumulative GC skew without sliding windows was proposed to give better resolution. Meanwhile, an oligomer-skew method was also proposed to predict oriC regions in bacterial genomes. As a unique representation of a DNA sequence, the Z-curve method has been proved to be an accurate and effective approach to predict bacterial and archaeal replication origins. Budding yeast origins have been predicted by Oriscan using similarity to the characterized ones, while the fission yeast origins have been identified initially from AT content calculation. In comparison with the in silico analysis, the experimental methods are time-consuming and labor-intensive, but convincing and reliable. To identify microbial replication origins in vivo or in vitro, a number of experimental methods have been used including construction of replicative oriC plasmids, microarray-based or high-throughput sequencing-based marker frequency analysis, two-dimensional gel electrophoresis analysis and replication initiation point mapping (RIP mapping). The recent genome-wide approaches to identify and characterize replication origin locations have boosted the number of mapped yeast replication origins. In addition, the availability of increasing complete microbial genomes and emerging approaches has created challenges and opportunities for identification of their replication origins in silico, as well as in vivo and in vitro. The Frontiers in Microbiology Research Topic on DNA replication origins in microbial genomes is devoted to address the issues mentioned above, and aims to provide a comprehensive overview of current research in this field.

Human Polyomaviruses and Papillomaviruses

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ISBN: 9783038972204 9783038972211 Year: Pages: 196 DOI: 10.3390/books978-3-03897-221-1 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology --- Oncology
Added to DOAB on : 2018-09-21 09:25:07
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The interest in human polyomaviruses (HPyV) has seen a renaissance because of new species that have been isolated and their previously unknown association with diseases. Likewise, the increasing evidence for the association of human papillomaviruses (HPV) with oropharyngeal cancer has sparked the attention of researchers and clinicians. The Special Issue “Human Polyomaviruses and Papillomaviruses” presents studies describing the nuclear egress of BK polyomavirus mediated by the viral agnoprotein and the cellular -SNAP protein. In addition, a study examines the promoter activity of two different variants of human polyomavirus 9 in different cell lines. This Special Issue offers an interesting perspective on the epidemiology of HR-HPV in different cancers and on the mechanisms by which these viruses target host cell proteins to replicate their genome, express their genes, interfere with autophagy, and induce cancer. Other topics that are highlighted include the role of co-factors, such as smoking and co-infection, novel therapeutic strategies, and surface immunoregulatory proteins, chemokines, and cytokines as possible biomarkers to determine the stage of a tumor and to predict clinical outcomes.

Maintenance of Genome Integrity: DNA Damage Sensing, Signaling, Repair and Replication in Plants

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198207 Year: Pages: 129 DOI: 10.3389/978-2-88919-820-7 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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Environmental stresses and metabolic by-products can severely affect the integrity of genetic information by inducing DNA damage and impairing genome stability. As a consequence, plant growth and productivity are irreversibly compromised. To overcome genotoxic injury, plants have evolved complex strategies relying on a highly efficient repair machinery that responds to sophisticated damage perception/signaling networks. The DNA damage signaling network contains several key components: DNA damage sensors, signal transducers, mediators, and effectors. Most of these components are common to other eukaryotes but some features are unique to the plant kingdom. ATM and ATR are well-conserved members of PIKK family, which amplify and transduce signals to downstream effectors. ATM primarily responds to DNA double strand breaks while ATR responds to various forms of DNA damage. The signals from the activated transducer kinases are transmitted to the downstream cell-cycle regulators, such as CHK1, CHK2, and p53 in many eukaryotes. However, plants have no homologue of CHK1, CHK2 nor p53. The finding of Arabidopsis transcription factor SOG1 that seems functionally but not structurally similar to p53 suggests that plants have developed unique cell cycle regulation mechanism. The double strand break repair, recombination repair, postreplication repair, and lesion bypass, have been investigated in several plants. The DNA double strand break, a most critical damage for organisms are repaired non-homologous end joining (NHEJ) or homologous recombination (HR) pathway. Damage on template DNA makes replication stall, which is processed by translesion synthesis (TLS) or error-free postreplication repair (PPR) pathway. Deletion of the error-prone TLS polymerase reduces mutation frequencies, suggesting PPR maintains the stalled replication fork when TLS is not available. Unveiling the regulation networks among these multiple pathways would be the next challenge to be completed. Some intriguing issues have been disclosed such as the cross-talk between DNA repair, senescence and pathogen response and the involvement of non-coding RNAs in global genome stability. Several studies have highlighted the essential contribution of chromatin remodeling in DNA repair. DNA damage sensing, signaling and repair have been investigated in relation to environmental stresses, seed quality issues, mutation breeding in both model and crop plants and all these studies strengthen the idea that components of the plant response to genotoxic stress might represent tools to improve stress tolerance and field performance. This focus issue gives researchers the opportunity to gather and interact by providing Mini-Reviews, Commentaries, Opinions, Original Research and Method articles which describe the most recent advances and future perspectives in the field of DNA damage sensing, signaling and repair in plants. A comprehensive overview of the current progresses dealing with the genotoxic stress response in plants will be provided looking at cellular and molecular level with multidisciplinary approaches. This will hopefully bring together valuable information for both plant biotechnologists and breeders.

Animal model studies on viral infections

Authors: ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194568 Year: Pages: 173 DOI: 10.3389/978-2-88919-456-8 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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Understanding viral replication and pathogenicity properties in infected individuals is a major mission of animal virology. Animal models are essential to analyze the in vivo viral characteristics and to develop countermeasures against viruses. To fight against a wide variety of viruses, basic studies with specific and/ or common approaches are required. This Research Topic collects articles that describe studies on numerous virus species at various stages toward animal experiments: (i) description/evaluation/ new challenges of animal model studies; (ii) experimental material/methods for animal model studies; (iii) observations for upcoming animal model studies.Numbers of DNA and RNA viruses such as HHV-6, HPV, Ebola virus, HCV, dengue virus, HTLV-1, HIV-1, SIV, and measles virus are covered by this special issue consisting of original research, methods, review, mini-review, and opinion articles. All readers would understand, we believe and hope, that animal model studies are critical for current virology as always.

Viral Replication Complexes: Structures, Functions, Applications and Inhibitors

ISBN: 9783038421672 9783038421689 Year: Pages: XVI, 428 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2016-07-14 07:43:51
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Viruses are obligate intracellular parasites that need to co-opt a living cell’s machinery for replication. At the heart of the viral replication machinery are the nucleic acid polymerases, which are responsible for efficiently copying the viral genome. This process must often be coordinated with other viral processes including protein translation and viral packaging. The nucleic acid polymerases may also be responsible for generating genetic diversity that is important for escape from the host’s defenses. The polymerases and other components of the replication machinery may serve as potential anti-viral targets. In this Special Issue, we seek to highlight recent advances into uncovering the structure and function of viral replication complexes. We are especially seeking to highlight the wide-range of methodologies used to gain structural insight into viral replication. Topics of interest include molecular mechanisms of nucleic acid polymerases, nucleic acid recognition and translocation, fidelity and error correction, interactions with lipid membranes, and coordination/regulation of transcription, translation and replication processes.

Epigenetic Modifications Associated with Abiotic and Biotic Stresses in Plants: An Implication for Understanding Plant Evolution

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453818 Year: Pages: 177 DOI: 10.3389/978-2-88945-381-8 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany --- Physiology
Added to DOAB on : 2018-11-16 17:17:57
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Alterations in gene expression are essential during growth and development phases and when plants are exposed to environmental challenges. Stress conditions induce gene expression modifications, which are associated with changes in the biochemical and physiological processes that help plants to avoid or reduce potential damage resulting from these stresses.After exposure to stress, surviving plants tend to flower earlier than normal and therefore transfer the accumulated epigenetic information to their progenies, given that seeds, where this information is stored, are formed at a later stage of plant development.DNA methylation is correlated with expression repression. Likewise, miRNA produced in the cell can reduce the transcript abundance or even prevent translation of mRNA. However, histone modulation, such as histone acetylation, methylation, and ubiquitination, can show distinct effects on gene expression. These alterations can be inherited, especially if the plants are consistently exposed to a particular environmental stress. Retrotransposons and retroviruses are foreign movable DNA elements that play an important role in plant evolution. Recent studies have shown that epigenetic alterations control the movement and the expression of genes harbored within these elements. These epigenetic modifications have an impact on the morphology, and biotic and abiotic tolerance in the subsequent generations because they can be inherited through the transgenerational memory in plants. Therefore, epigenetic modifications, including DNA methylation, histone modifications, and small RNA interference, serve not only to alter gene expression but also may enhance the evolutionary process in eukaryotes.In this E-book, original research and review articles that cover issues related to the role of DNA methylation, histone modifications, and small RNA in plant transgenerational epigenetic memory were published.The knowledge published on this topic may add new insight on the involvement of epigenetic factors in natural selection and environmental adaptation. This information may also help to generate a modeling system to study the epigenetic role in evolution.

Prozessentwicklung eines industrietauglichen Verfahrens zur Fertigung von vereinzelten LIGA-Mikrobauteilen

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Book Series: Schriften des Instituts für Mikrostrukturtechnik am Karlsruher Institut für Technologie / Hrsg.: Institut für Mikrostrukturtechnik ISSN: 18695183 ISBN: 9783731503262 Year: Volume: 30 Pages: VII, 211 p. DOI: 10.5445/KSP/1000045013 Language: GERMAN
Publisher: KIT Scientific Publishing
Subject: Technology (General)
Added to DOAB on : 2019-07-30 20:02:02
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This work deals with the development of an industry suited process aiming on the fabrication (based on the LIGA technique) of near net shape, single microparts. Those microparts should lead to new innovative ideas and thus to successful products on the market.

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