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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.

Modulating Prokaryotic Lifestyle by DNA-Binding Proteins

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451050 Year: Pages: 296 DOI: 10.3389/978-2-88945-105-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The Overview of the Topic was the following: “One of the most active areas of research in molecular microbiology has been the study of how bacteria modulate their genetic activity and its consequences. The prokaryotic world has received much interest not only because the resulting phenomena are important to cells, but also because many of the effects often can be readily measured. Contributing to the interest of the present topic is the fact that modulation of gene activity involves the sensing of intra- and inter-cellular conditions, DNA binding and DNA dynamics, and interaction with the replication/transcription machinery of the cell. All of these processes are fundamental to the operation of a genetic entity and condition their lifestyle. Further, the discoveries achieved in the bacterial world have been of ample use in eukaryotes. In addition to the fundamental interest of understanding modulation of prokaryotic lifestyle by DNA-binding proteins, there is an added interest from the healthcare point of view. As it is well known the antibiotic-resistance strains of pathogenic bacteria are a major world problem, so that there is an urgent need of innovative technologies to tackle it. Most of the acquired resistances are spread by processes of horizontal gene transfer mediated by mobile elements in which DNA replication and gene expression are of basic interest. There is an imperative of finding new alternatives to the ‘classical’ way of treatment of bacterial infections and these new alternatives include the discovery of new drugs and of new bacterial targets. Nevertheless, these new alternatives will find a dead-end if we are unable to obtain a better understanding of the basic processes modulating bacterial gene expression. Our goal to achieve with this Topic of Frontiers is to accelerate our understanding of protein-DNA interactions. First, the topic will bring together several very active researchers in the study of gene replication, gene regulation, the strategies applied by the different proteins that participate in these processes, and their consequences. We will also acquire an in-depth knowledge of some of the mechanisms of gene regulation, gene transfer and gene replication. Further, the readers of the papers will realize the importance of the topic and will learn the most recent thinking, results, and approaches in the area”. We are fully confident that we have exceeded our expectations. Now we are proud to present the final output of the Topic, which is the eBook. It includes 24 articles contributed by 118 authors. As of today, Monday, 16th, January 2017, the total number of readings has reached 19,284, 14,921 article views, and 2,944 article downloads.

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.

Kaposi's Sarcoma-Associated Herpesvirus

ISBN: 9783038420774 9783038420767 Year: Pages: 356 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Added to DOAB on : 2015-10-22 09:09:45
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The discovery of KSHV in 1994 was a historical landmark in tumor virology and human cancer research. Its subsequent identification as a cause of Kaposi sarcoma and in association with primary effusion lymphoma and multicentric Castleman disease soon attracted up to hundreds of research laboratories and thousands of virologists and oncologists to switch their research directions. To date, PubMed has collected nearly 5000 papers on KSHV from numerous journal publications in the world. These studies reiterate that the global fight against human cancers will continue to receive great support from our tremendous efforts in searching for new tumor-causing viruses and in understanding the basic biology of tumor viruses. To celebrate the 20th years of KSHV discovery, I am very proud to be an invited Guest Editor for a special issue on KSHV in the journal "Viruses" and happy to assemble all published articles from the special issue into this book, Kaposi Sarcoma Associated Herpesvirus. The collected articles cover almost all aspects of KSHV, including updated reviews and research articles on KSHV epidemiology and transmission, KSHV interaction with host cell receptors and cell entry, KSHV latency and latency-associated nuclear antigen (LANA), molecular biology of KSHV lytic reactivation and lytic switch control by KSHV ORF50 and other factors, KSHV post-transcriptional regulator ORF57, molecular biology of KSHV polyadenylated nuclear RNA (PAN RNA) and PAN as a lncRNA in epigenetic gene regulation of KSHV, viral mimics of cellular genes in KSHV infection and disease, KSHV targeted therapy, KSHV miRNAs and vGPCR, etc. In particular, I am greatly honored to have Yuan Chang and Patrick Moore to mark the first 20 years of KSHV research by recounting the historical stories leading to their astonish discovery and Science publication of KSHV that has led us where we are today. The book is also intended to assist Medical students and residents, dermatologists, hematologist, oncologists, and other related specialties to understand what we have known about KSHV and its infections and pathogenesis.

Stem Cell Genetic Fidelity

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194902 Year: Pages: 110 DOI: 10.3389/978-2-88919-490-2 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General) --- Oncology --- Medicine (General)
Added to DOAB on : 2015-11-16 15:44:59
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The vision of this Frontiers in Oncology Research Topic on "Stem Cell Genetic Fidelity" had the goal of steeping a diverse range of research perspectives to a first comprehensive synthesis of thought on the questions of how tissue stem cells manage gene mutation rate and the significance of that management in mammalian evolution and biology, in particular as it relates to tissue cell renewal, carcinogenesis, and aging. The primary focus was determinants of mutation rate in distributed stem cells (DSCs), which encompass all naturally occurring stem cells at all stages of mammalian development. In particular, contributions were sought that considered a broad range of aspects of the immortal DNA strand hypothesis for DSC genetic fidelity. Though proposed in 1975, only in the last decade has this landmark concept in tissue cell biology emerged as a central discussion in DSC research with increasing scrutiny and discussion by an increasing number of laboratories of diverse research perspectives and experimental approaches. With this hypothesis presenting a formidable technical challenge for experimental investigation, as would be expected, both supportive and unsupportive reports have been lining up. In the case of supportive studies, neither the range of applicable tissues nor the responsible molecular mechanisms are known; and the essential genomic process, non-random DNA template strand inheritance by asymmetrically self-renewing DSCs, has been suggested to potentially have other cellular roles besides reducing mutation rate. A major aspiration of this Research Topic was to create the first comprehensive, critical synthesis of current insights and viewpoints on the impact of the immortal DNA strand hypothesis in the history of DSC mutation research. A wide range of article types was considered including historical perspectives, critical reviews, critical commentaries, new hypotheses, new research perspectives, technical advances, and original research reports. Although treatments of the immortal DNA strand hypothesis were the major focus, the desired synthesis required integration of related ideas on mechanisms of DSC mutagenesis and its impact in the evolution of mammals, the emergence of cancers, and stem cell aging. As such, investigators focused on issues in e.g., germ stem cell mutagenesis, effects of environmental mutagens on DSC mutation rate, DSC mutation and tissue aging, determinations of types of mutations in DSCs, and the role of DSC mutation in cancer initiation were invited. Similarly, although the specific goal of the Research Topic was to enlighten DSC genetic fidelity in humans and other mammalians, informing contributions based on studies in other model organisms were also welcomed. To achieve even better representation of current experience, advances, and ideas in this field of investigation, these early contributors were encouraged to extend the opportunity to others who shared their interest in advancing our understanding of the mutability of DSCs and its significance in human biology.

DNA Replication Stress

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ISBN: 9783039213894 9783039213900 Year: Pages: 368 DOI: 10.3390/books978-3-03921-390-0 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 16:10:12
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This Special Issue of International Journal of Molecular Sciences (IJMS) is dedicated to the mechanisms mediated at the molecular and cellular levels in response to adverse genomic perturbations and DNA replication stress. The relevant proteins and processes play paramount roles in nucleic acid transactions to maintain genomic stability and cellular homeostasis. A total of 18 articles are presented which encompass a broad range of highly relevant topics in genome biology. These include replication fork dynamics, DNA repair processes, DNA damage signaling and cell cycle control, cancer biology, epigenetics, cellular senescence, neurodegeneration, and aging. As Guest Editor for this IJMS Special Issue, I am very pleased to offer this collection of riveting articles centered on the theme of DNA replication stress. The blend of articles builds upon a theme that DNA damage has profound consequences for genomic stability and cellular homeostasis that affect tissue function, disease, cancer, and aging at multiple levels and through unique mechanisms. I thank the authors for their excellent contributions, which provide new insight into this fascinating and highly relevant area of genome biology.

Keywords

barley --- chromosome --- DNA replication pattern --- EdU --- mutagens --- DNA replication --- DNA damage --- DNA repair --- genome integrity --- A549 cells --- H1299 cells --- heterogeneity --- DNA damage response --- 8-chloro-adenosine --- DNA replication --- S phase --- origin firing --- TopBP1 --- ATR --- DNA fiber assay --- APE2 --- ATR-Chk1 DDR pathway --- Genome integrity --- SSB end resection --- SSB repair --- SSB signaling --- DNA replication stress --- genome stability --- ubiquitin --- replication fork restart --- translesion synthesis --- template-switching --- homologous recombination --- Fanconi Anemia --- G protein-coupled receptor (GPCR) --- aging --- DNA damage --- ?-arrestin --- G protein-coupled receptor kinase (GRK) --- interactome --- G protein-coupled receptor kinase interacting protein 2 (GIT2) --- ataxia telangiectasia mutated (ATM) --- clock proteins --- energy metabolism --- neurodegeneration --- cellular senescence --- ageing --- Alzheimer’s disease --- multiple sclerosis --- Parkinson’s disease --- lipofuscin --- SenTraGorTM (GL13) --- senolytics --- DNA replication --- DNA repair --- DNA damage response --- DNA translocation --- DNA helicase --- superfamily 2 ATPase --- replication restart --- fork reversal --- fork regression --- chromatin remodeler --- C9orf72 --- ALS --- motor neuron disease --- R loops, nucleolar stress --- neurodegeneration --- Difficult-to-Replicate Sequences --- replication stress --- non-B DNA --- Polymerase eta --- Polymerase kappa --- genome instability --- common fragile sites --- Microsatellites --- cancer --- DNA double-strand repair --- premature aging --- post-translational modification --- protein stability --- replication stress --- Werner Syndrome --- Werner Syndrome Protein --- dormant origins --- replicative stress --- replication timing --- DNA damage --- genome instability --- cancer --- Thermococcus eurythermalis --- endonuclease IV --- AP site analogue --- spacer --- DNA repair --- DNA repair --- double strand break repair --- exonuclease 1 --- EXO1 --- mismatch repair --- MMR --- NER --- nucleotide excision repair --- strand displacements --- TLS --- translesion DNA synthesis --- POL? --- mutation frequency --- mutations spectra --- SupF --- mutagenicity --- oxidative stress --- DNA damage --- DNA repair --- replication --- 8-oxoG --- epigenetic --- gene expression --- helicase --- cell cycle checkpoints --- genomic instability --- G2-arrest --- cell death --- repair of DNA damage --- adaptation --- n/a

Virus Bioinformatics

Authors: --- --- ---
ISBN: 9783039218820 9783039218837 Year: Pages: 330 DOI: 10.3390/books978-3-03921-883-7 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2020-04-07 23:07:08
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Virus bioinformatics is evolving and succeeding as an area of research in its own right, representing the interface of virology and computer science. Bioinformatic approaches to investigate viral infections and outbreaks have become central to virology research, and have been successfully used to detect, control, and treat infections of humans and animals. As part of the Third Annual Meeting of the European Virus Bioinformatics Center (EVBC), we have published this Special Issue on Virus Bioinformatics.

Keywords

bioinformatics --- virus --- comparative genomics --- software --- Base-By-Base --- BBB --- poxvirus --- ASFV --- MSA --- foot-and-mouth disease virus (FMDV) --- bovine soft palate --- nasopharynx --- transcriptomics --- proteomics --- bioinformatics --- virus-host interaction --- innate immune system --- interferon-stimulated genes (ISG) --- cellular immunity --- codon frequency distribution --- HPV58 --- minor capsid protein --- TLR agonist --- prophylaxis --- virus --- infection --- fluorescent reporter protein --- image quantification --- Hepatitis C virus --- Yellow Fever Virus --- polyomavirus --- Coxsackievirus B4 --- bivalve --- virome --- RNA-seq --- RNA viruses --- sncRNA --- ADAR --- RNAi --- Marek’s disease virus (MDV) --- RNA-seq --- transcriptome --- splicing --- polycistronic viral transcripts --- primary B cells --- RB1B --- CVI988/Rispens --- ICP0 --- DNA replication --- ori --- mitochondria --- Rickettsia --- gram-positive bacteria --- APMV --- Mimivirus --- giant virus --- eukaryogenesis --- flavivirus --- non-coding RNA --- secondary structure --- endogenous viral elements --- bioinformatics --- horizontal gene transfer --- virus-to-host gene transfer --- HMM --- tobacco mosaic virus --- Drosophila --- capsid protein --- deep sequencing --- virus genomics --- hepatitis C virus --- variant calling --- sequence interpretation --- drug resistance --- bioinformatics --- alignment --- assembly --- taxonomic classification --- time series --- data transformation --- DWT --- DFT --- PAA --- data compression --- compressive genomics --- RNAseq --- honey bees --- deformed wing virus --- quasispecies --- apiary pests --- recombination --- mRNA structure --- structure database --- secondary structure --- viral mRNA --- subVOG --- structurally related --- RNA structure --- structurally homogenous --- structurally related --- mRNA families --- Amebae viruses --- viral evolution --- protein domains --- mimivirus --- dsdna viruses --- translation machinery --- pandoravirus --- NCLDV --- virology --- virus bioinformatics --- software --- systems virology --- metagenomics --- virome --- viral taxonomy --- virus classification --- genome evolution --- bacteriophage --- virosphere --- chemical organization theory --- influenza A --- virus dynamics modeling --- complex networks analysis --- viral metagenome --- groundwater --- aquifer --- AquaDiva --- sequencing library preparation --- virus proteomics --- mass spectrometry --- virus diagnostics --- data analysis --- targeted proteomics --- peptide selection --- parallel reaction monitoring

Biomimetic Radical Chemistry and Applications

Author:
ISBN: 9783039283927 9783039283934 Year: Pages: 300 DOI: 10.3390/books978-3-03928-393-4 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology --- Science (General)
Added to DOAB on : 2020-04-07 23:07:09
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The enormous importance of free radical chemistry for a variety of biological events, including ageing and inflammation, has attracted a strong interest in understanding the related mechanistic steps at the molecular level. Modelling the free radical chemical reactivity of biological systems is an important research area. When studying free-radical-based chemical mechanisms, biomimetic chemistry and the design of established biomimetic models come into play to perform experiments in a controlled environment that is suitably designed to be in strict connection with cellular conditions. This Special Issue gives the reader a wide overview of biomimetic radical chemistry, where molecular mechanisms have been defined and molecular libraries of products are developed to also be used as traces for the discovery of some relevant biological processes. Several subjects are presented, with 12 articles and 6 reviews written by specialists in the fields of DNA, proteins, lipids, biotechnological applications, and bioinspired synthesis, having “free radicals” as a common denominator.

Keywords

type 2 diabetes --- glycogen phosphorylase --- anomeric spironucleosides --- 1,6-dioxa-4-azaspiro[4.5]decane --- [1,5]-radical translocation --- DNA --- guanine quadruplexes --- radicals --- electron holes --- oxidative damage --- photo-ionization --- time-resolved spectroscopy --- inhomogeneous reactions --- radiosensitizers --- stationary radiolysis --- pulse radiolysis --- modified nucleosides --- cellular response --- liposomal somatostatin --- retarded delivery --- free radicals --- isomerization --- trans lipid --- peroxidation --- photolysis --- laser flash photolysis --- ?-radiolysis --- singlet oxygen --- nucleosides --- free radicals --- reaction mechanism --- catalase activity --- iron(IV)-oxo --- hydrogen peroxide --- oxidation --- kinetic studies --- gold nanoparticles --- albumin --- EPR spectroscopy --- Raman spectroscopy --- circular dichroism --- beta cells --- diabetes --- confocal microscopy --- lipidomics --- membrane fluidity maps --- cell micropolarity maps --- DNA damage --- 5?,8-cyclopurines --- 8-oxo-dG --- free radicals --- pulse radiolysis --- gamma radiolysis --- Fenton reaction --- oligonucleotides --- oxidative DNA damage --- DNA replication stress --- replication fork stalling --- genomic and epigenomic instability --- DNA methylation --- histone modifications --- miRNAs --- iron porphyrin --- heme --- ATRPase --- iron-mediated ATRP --- bio-mimicking catalyst --- biomimetic radical reaction --- bioinspired chemical catalysis --- protein labeling --- DNA oxidation --- DNA hole transfer --- DNA --- quantum dynamics --- electron transfer --- charge transfer --- radical reaction --- azidoalkylation --- carboazidation --- sulfones --- azides --- Julia–Kocienski olefination --- DNA damage --- copper --- chemical nuclease --- intercalation --- free radical oxidation --- protein stability --- therapeutic proteins --- thiyl radicals --- oxidation --- fragmentation --- cross-link --- 2-thiouracil --- radiosensitizers --- ?OH and ?N3 radicals --- 2c-3e S?S-bonded intermediates --- pulse radiolysis --- TD-DFT methods --- thiobases --- nucleobase derivatives --- reactive aldehydes --- hydroxynonenal --- oxononenal --- free fatty acids --- mitochondrial uncoupling protein --- lipid bilayer membranes

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