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Vibrio ecology, pathogenesis and evolution

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192892 Year: Pages: 239 DOI: 10.3389/978-2-88919-289-2 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Oceanography --- Science (General)
Added to DOAB on : 2015-12-10 11:59:07
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Vibrios are Gram-negative bacilli that occur naturally in marine, estuarine, and freshwater systems. Some species include human and animal pathogens capable of causing gastroenteritis, wound infections, cholera, and fatal septicemia. Over the past decades, cutting edge research on Vibrio genomics has promoted a tremendous advance in our knowledge of these pathogens. Significant developments include the discovery of emerging epidemic clones, tracking the spread of new strain variants, and an intensified appreciation of the role of mobile genetic elements in antibiotic resistance spread as well as pathogenesis. Furthermore, improved understanding of the interaction of Vibrios with a variety of living organisms in the aquatic environment has documented the significant role of environmental reservoirs in their seasonal cycle favoring persistence of the pathogen during inter-epidemic periods and enhancing disease transmission. This Research Topic is dedicated to our current understanding in these areas and will bring together leading experts in the field to provide a deep overview of Vibrios ecology and evolution, and will suggest the pathway of future research in this field.

Keywords

Vibrio --- Ecology --- Genome --- evolution --- Pathogenesis

Grappling with the Multifaceted World of the DNA Damage Response

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450572 Year: Pages: 306 DOI: 10.3389/978-2-88945-057-2 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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DNA damage is a major threat to genomic integrity and cell survival. It can arise both spontaneously and in response to exogenous agents. DNA damage can attack most parts of the DNA structure, ranging from minor and major chemical modifications, to single-strand breaks (SSBs) and gaps, to full double-strand breaks (DSBs). If DNA injuries are mis-repaired or unrepaired, they may ultimately result in mutations or wider-scale genome aberrations that threaten cell homeostasis. Consequently, the cells elicit an elaborate signalling network, known as DNA damage response (DDR), to detect and repair these cytotoxic lesions. This Research Topic was aimed at comprehensive investigations of basic and novel mechanisms that underlie the DNA damage response in eukaryotes.DNA damage is a major threat to genomic integrity and cell survival. It can arise both spontaneously and in response to exogenous agents. DNA damage can attack most parts of the DNA structure, ranging from minor and major chemical modifications, to single-strand breaks (SSBs) and gaps, to full double-strand breaks (DSBs). If DNA injuries are mis-repaired or unrepaired, they may ultimately result in mutations or wider-scale genome aberrations that threaten cell homeostasis. Consequently, the cells elicit an elaborate signalling network, known as DNA damage response (DDR), to detect and repair these cytotoxic lesions. This Research Topic was aimed at comprehensive investigations of basic and novel mechanisms that underlie the DNA damage response in eukaryotes.

Géométries du vivant

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ISSN: 9782213635019 ISBN: 9782213635019 9782722603264 Year: Language: French
Publisher: Collège de France
Added to DOAB on : 2015-05-20 10:31:46
License: OpenEdition licence for Books

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L’idée que je me fais d’une théorie en biologie est assez éloignée de cette biologie théorique, mise en équations de phénomènes observés ou photographiés. J’en ai une conception plus simple, plus concrète. Non pas cette description mathématique de ce qui est vu, mais un modèle évolutif, un outil bricolé, avec des mathématiques peut-être, mais aussi de la langue naturelle, et qui sert avant tout à comprendre ce qu’on ne voit pas, à deviner, sous le visible, l’invisible du vivant, sa « logique ...

Geometries of the Living

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ISBN: 9782722604377 Year: Language: English
Publisher: Collège de France
Added to DOAB on : 2016-04-04 11:23:49
License: OpenEdition licence for Books

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My idea of a theory in biology is quite different from the theoretical biology that is expressed as equations of observed or photographed phenomena. I have a simpler, more concrete conception. Not a mathematical description of what is seen, but an evolving model, a tool developed through bricolage, with mathematics perhaps, but also natural language: one that serves above all to understand the unseen; to guess, beneath the visible, the invisible dimensions of life forms, the underlying “logic”.

Document sobre bioètica i edició genòmica en humans

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Book Series: Col·lecció de Bioètica ISBN: 9788447540730 Year: Pages: 52 Language: Catalan, Spanish, English
Publisher: Publicacions i Edicions de la Universitat de Barcelona
Subject: Genetics --- Philosophy --- Biotechnology
Added to DOAB on : 2018-10-22 12:29:11
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Aquest Document examina l’impacte de la utilització de les tècniques d’edició genòmica, tant en recerca bàsica com en el seu ús terapèutic i en l’anomenat «millorament» humà, amb l’objectiu de promoure un debat social informat que comporti propostes d’actuació assumibles per la col·lectivitat i que contribueixin a la construcció d’un marc jurídic, ètic i deontològic adequat.

Ubiquitin and Ubiquitin-Relative SUMO in DNA Damage Response

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889454419 Year: Pages: 183 DOI: 10.3389/978-2-88945-441-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2018-11-16 17:17:57
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DNA damage response (DDR) is a term that includes a variety of highly sophisticated mechanisms that cells have evolved in safeguarding the genome from the deleterious consequences of DNA damage. It is estimated that every single cell receives tens of thousands of DNA lesions per day. Failure of DDR to properly respond to DNA damage leads to stem cell dysfunction, accelerated ageing, various degenerative diseases or cancer. The sole function of DDR is to recognize diverse DNA lesions, signal their presence, activate cell cycle arrest and finally recruit specific DNA repair proteins to fix the DNA damage and thus prevent genomic instability. DDR is composed of hundreds of spatiotemporally regulated and interconnected proteins, which are able to promptly respond to various DNA lesions. So it is not surprising that mutations in genes encoding various DDR proteins cause embryonic lethality, malignancies, neurodegenerative diseases and premature ageing. The importance of DDR for cell survival and genome stability is unquestionable, but how the sophisticated network of hundreds of different DDR proteins is spatiotemporally coordinated is far from being understood. In the last ten years ubiquitin (ubiquitination) and the ubiquitin-relative SUMO (sumoylation) have emerged as essential posttranslational modifications that regulate DDR. Beside a plethora of ubiqutin and sumo E1-activating enzymes, E2-conjugating enzymes, E3-ligases and ubiquitin/sumo proteases involved in ubiquitination and sumoylation, the complexity of ubiqutin and sumo systems is additionally increased by the fact that both ubiquitin and sumo can form a variety of different chains on substrates which govern the substrate fate, such as its interaction with other proteins, changing its enzymatic activity or promoting substrate degradation. The importance of ubiquitin/SUMO systems in the orchestration of DDR is best illustrated in patients with mutations in E3-ubiquitin ligases BRCA1 or RNF168. BRCA1 is essential for proper function of DDR and its mutations lead to triple-negative breast and ovarian cancers. RNF168 is an E3 ubiquitin ligase, which creates the ubiquitin docking platform for recruitment of different DNA damage signalling and repair proteins at sites of DNA lesion, and its mutations cause RIDDLE syndrome characterized by radiosensitivity, immunodeficiency and learning disability. In addition, recently discovered the ubiquitin receptor protein SPRTN is part of the DNA replication machinery and its mutations cause early-onset hepatocellular carcinoma and premature ageing in humans. Despite more than 700 different enzymes directly involved in ubiquitination and sumoylation processes only few of them are known to play a role in DDR. Therefore, we feel that the role of ubiquitin and the ubiquitin-related SUMO in DDR is far from being understood, and that this is the emerging field that will hugely expand in the next decade due to the rapid development of a new generation of technologies, which will allow us a more robust and precise analyses of human genome, transcriptome and proteome. In this Research Topic we provide a comprehensive overview of our current understanding of ubiquitin and SUMO pathways in all aspects of DDR, from DNA replication to different DNA repair pathways, and demonstrate how alterations in these pathways cause genomic instability that is linked to degenerative diseases, cancer and pathological ageing.

Genome Informatics 2009:Genome Informatics Series Vol. 22

Authors: --- --- --- --- et al.
Book Series: Genome Informatics Series ISBN: 9781848165786 Year: Pages: 228 DOI: 10.1142/p718 Language: ENGLISH
Publisher: World Scientific Publishing Co.
Added to DOAB on : 2019-07-04 04:29:21

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This volume contains 17 peer-reviewed papers based on the presentations at the 9th Annual International Workshop on Bioinformatics and Systems Biology (IBSB 2009) held at the Life Science Engineering Building of Boston University from July 27 to 29, 2009. This workshop started in 2001 as a platform for doctoral students and young researchers to present and discuss their research results and approaches in bioinformatics and systems biology. It is part of a collaborative educational program involving leading institutions and leaders committed to the following institutions and programs:Boston University Graduate Program in BioinformaticsCharité – Universitätsmedizin BerlinFreie Universität BerlinGlobal COE Program — Center of Education and Research for Advanced Genome-Based Medicine, University of TokyoThe International Research Training Group (IRTG) Genomics and Systems Biology of Molecular NetworksInternational Research and Training Program on Bioinformatics and Systems Biology, Kyoto University Bioinformatics CenterMax-Delbrück Center for Molecular Medicine in BerlinMax Planck Institute for Molecular Genetics in BerlinMax Planck Institute of Molecular Plant Physiology in Potsdam

Genome Informatics 2009:Genome Informatics Series Vol. 23

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Book Series: Genome Informatics Series ISBN: 9781848165632 Year: Pages: 240 DOI: 10.1142/p715 Language: ENGLISH
Publisher: World Scientific Publishing Co.
Added to DOAB on : 2019-07-04 04:35:35

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This volume contains papers presented at the 20th International Conference on Genome Informatics (GIW 2009) held at the Pacifico Yokohama, Japan from December 14 to 16, 2009. The GIW Series provides an international forum for the presentation and discussion of original research papers on all aspects of bioinformatics, computational biology and systems biology. Its scope includes biological sequence analysis, protein structure prediction, genetic regulatory networks, bioinformatic algorithms, comparative genomics, and biomolecular data integration and analysis. Boasting a history of 20 years, GIW is the longest-running international bioinformatics conference.A total of 18 contributed papers were selected for presentation at GIW 2009 and for inclusion in this book. In addition, this book contains abstracts from the five invited speakers: Sean Eddy (HHMI's Janelia Farm, USA), Minoru Kanehisa (Kyoto University, Japan), Sang Yup Lee (KAIST, Korea), Hideyuki Okano (Keio University, Japan) and Mark Ragan (University of Queensland, Australia).

Genomics Research on Non-Model Plant Pathogens: Delivering Novel Insights into Rust Fungus Biology

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198146 Year: Pages: 166 DOI: 10.3389/978-2-88919-814-6 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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Fungi of the order Pucciniales cause rust diseases on many plants including important crops and trees widely used in agriculture, forestry and bioenergy programs; these encompass gymnosperms and angiosperms, monocots and dicots, perennial and annual plant species. These fungi are obligate biotrophs and -except for a few cases- cannot be cultivated outside their hosts in a laboratory. For this reason, standard functional and molecular genetic approaches to study these pathogens are very challenging and the means to study their biology, i.e. how they infect, develop and reproduce on plant hosts, are rather limited, even though they rank among the most devastating pathogens. Among fungal plant pathogens, rust fungi display the most complex lifecycles with up to five different spore forms and for many rust fungi, unrelated alternate hosts on which sexual and clonal reproduction are achieved. The genomics revolution and particularly the application of new generation sequencing technologies have greatly changed the way we now address biological studies and has in particular accelerated and made feasible, molecular studies on non-model species, such as rust fungi. The goal of this research topic is to gather articles that present recent advances in the understanding of rust fungi biology, their complex lifecycles and obligate biotrophic interactions with their hosts, through the means of genomics. This includes genome sequencing and/or resequencing of isolates, RNA-Seq or large-scale transcriptome analyses, genome-scale detailed annotation of gene families, and comparative analyses among the various rust fungi and, where feasible, with other obligate biotrophs or fungi displaying distinct trophic modes. This Research Topic provides a great opportunity to provide an up-to-date account of rust fungus biology through the lens of genomics, including state-of-the-art technologies developed to achieve this knowledge.

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.

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