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30 years of the Comet Assay: an overview with some new insights

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196494 Year: Pages: 174 DOI: 10.3389/978-2-88919-649-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
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By means of this ‘Frontiers in Genetics’ research topic, we are celebrating 30 years of the Comet Assay. The first paper on this single-cell gel electrophoresis assay was published in 1984 by O. Ostling and K.J. Johanson (Biochem. Biophys. Res. Commun. Vol.123: 291-298). The comet assay is a versatile and sensitive method for measuring single - and double-strand breaks in DNA. By including lesion-specific enzymes in the assay, its range and sensitivity are greatly increased, but it is important to bear in mind that their specificity is not absolute. The comet assay (with and without inclusion of lesion-specific enzymes) is widely used as a biomarker assay in human population studies - primarily to measure DNA damage, but increasingly also to assess the capacity of cells for DNA repair. Ostling and Johanson (Biochem. Biophys. Res. Commun., 1984) were also the first to report experiments to measure DNA repair, by simply following the decrease of DNA damage over time after challenging cells with ionising radiation. However, this approach is time-consuming and laborious as it requires an extended period of cell culture and is therefore not ideal for biomonitoring studies, which typically require high-throughput processing of many samples. As an alternative approach, the in vitro comet-based repair assay was developed: a cell extract is incubated with a DNA substrate containing specific lesions, and DNA incisions accumulate. The in vitro comet-based repair assay has been modified and improved over the past decade: it was first devised to measure base excision repair of oxidised purines in lymphocytes (Collins et al., Mutagenesis, 2001), but has since been adapted for other lesions and thus other repair pathways, as well as being applied to tissue samples in addition to cell suspensions. Even after 30 years, the comet assay is still in a growth phase, with many new users each year. Many questions are repeatedly raised, which may seem to have self-evident answers, but clearly, it is necessary to reiterate them for the benefit of the new audience, and sometimes being forced to think again about old topics can shed new light. Different applications of the comet assay are discussed in this special issue, including: genotoxicity testing in different organisms, human biomonitoring, DNA repair studies, environmental biomonitoring and clinical studies. Furthermore, we consider and where possible answer questions, including the ones raised by Raymond Tice at the 8th International Comet Assay Workshop in Perugia (Italy 2009): What is the spectrum of DNA damage detected by the various versions of the comet assay?; What are the limitations associated with each application?; What should be done to standardize the assay for biomonitoring studies?; Can the comet assay be used to monitor changes in global methylation status?; What cell types are suitable for detecting genotoxic substances and their effects in vivo and in vitro?; Can the assay be fully automated?; and more. So this ‘Frontiers in Genetics’ research topic is written for the beginner as well as for the experienced users of the comet assay.

Advances in Farm Animal Genomic Resources

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197354 Year: Pages: 293 DOI: 10.3389/978-2-88919-735-4 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
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The history of livestock started with the domestication of their wild ancestors: a restricted number of species allowed to be tamed and entered a symbiotic relationship with humans. In exchange for food, shelter and protection, they provided us with meat, eggs, hides, wool and draught power, thus contributing considerably to our economic and cultural development. Depending on the species, domestication took place in different areas and periods. After domestication, livestock spread over all inhabited regions of the earth, accompanying human migrations and becoming also trade objects. This required an adaptation to different climates and varying styles of husbandry and resulted in an enormous phenotypic diversity. Approximately 200 years ago, the situation started to change with the rise of the concept of breed. Animals were selected for the same visible characteristics, and crossing with different phenotypes was reduced. This resulted in the formation of different breeds, mostly genetically isolated from other populations. A few decades ago, selection pressure was increased again with intensive production focusing on a limited range of types and a subsequent loss of genetic diversity. For short-term economic reasons, farmers have abandoned traditional breeds. As a consequence, during the 20th century, at least 28% of farm animal breeds became extinct, rare or endangered. The situation is alarming in developing countries, where native breeds adapted to local environments and diseases are being replaced by industrial breeds. In the most marginal areas, farm animals are considered to be essential for viable land use and, in the developing world, a major pathway out of poverty. Historic documentation from the period before the breed formation is scarce. Thus, reconstruction of the history of livestock populations depends on archaeological, archeo-zoological and DNA analysis of extant populations. Scientific research into genetic diversity takes advantage of the rapid advances in molecular genetics. Studies of mitochondrial DNA, microsatellite DNA profiling and Y-chromosomes have revealed details on the process of domestication, on the diversity retained by breeds and on relationships between breeds. However, we only see a small part of the genetic information and the advent of new technologies is most timely in order to answer many essential questions. High-throughput single-nucleotide polymorphism genotyping is about to be available for all major farm animal species. The recent development of sequencing techniques calls for new methods of data management and analysis and for new ideas for the extraction of information. To make sense of this information in practical conditions, integration of geo-environmental and socio-economic data are key elements. The study and management of farm animal genomic resources (FAnGR) is indeed a major multidisciplinary issue. The goal of the present Research Topic was to collect contributions of high scientific quality relevant to biodiversity management, and applying new methods to either new genomic and bioinformatics approaches for characterization of FAnGR, to the development of FAnGR conservation methods applied ex-situ and in-situ, to socio-economic aspects of FAnGR conservation, to transfer of lessons between wildlife and livestock biodiversity conservation, and to the contribution of FAnGR to a transition in agriculture (FAnGR and agro-ecology).

Advances in Genomics and Epigenomics of Social Insects

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450800 Year: Pages: 155 DOI: 10.3389/978-2-88945-080-0 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
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Social insects are among the most successful and ecologically important animals on earth. The lifestyle of these insects has fascinated humans since prehistoric times. These species evolved a caste of workers that in most cases have no progeny. Some social insects have worker sub-castes that are morphologically specialized for discrete tasks. The organization of the social insect colony has been compared to the metazoan body. Males in the order Hymenoptera (bees, ants and wasps) are haploid, a situation which results in higher relatedness between female siblings. Sociality evolved many times within the Hymenoptera, perhaps spurred in part by increased relatedness that increases inclusive fitness benefits to workers cooperating to raise their sisters and brothers rather than reproducing themselves. But epigenetic processes may also have contributed to the evolution of sociality. The Hymenoptera provide opportunities for comparative study of species ranging from solitary to highly social. A more ancient clade of social insects, the termites (infraorder Isoptera) provide an opportunity to study alternative mechanisms of caste determination and lifestyles that are aided by an array of endosymbionts. This research topic explores the use of genome sequence data and genomic techniques to help us explore how sociality evolved in insects, how epigenetic processes enable phenotypic plasticity, and the mechanisms behind whether a female will become a queen or a worker.

Advances in Systems Immunology and Cancer

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193134 Year: Pages: 108 DOI: 10.3389/978-2-88919-313-4 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Biology --- Biotechnology --- General and Civil Engineering --- Psychiatry --- Medicine (General) --- Physiology --- Neurology --- Science (General)
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Aims and Scope: The Research Topic is designed to feature the latest innovative and leading-edge research, reviews and opinions on the study of complex and dynamic processes related to the mammalian immune system and cancer. All papers were meticulously selected to present our readers the multidisciplinary approach to tackle the existing challenges faced in these important fields. From high throughput experimental methodologies to computational and theoretical approaches, the articles are intended to introduce physicists, chemists, computer scientists, biologists and immunologists the idea of systems biology approach to the understanding of mammalian immune system and cancer processes. Attention was given to works that developed more effective approaches to the treatment of proinflammatory disease and cancer. The strong interdisciplinary focus will discuss biological systems at the level from a few molecules to the entire organism. Specific focus domain includes: Innate and adaptive immunity, cancer and cancer stem cell, genomic, proteomic and metabolic analysis, imaging, biophysics of immune and cancer response, computational modeling, non-linear analysis, statistical analysis, translational and disease models Types of articles: Viewpoint, commentaries, research letters, research articles, review and methodologies

Advances in Wheat Genetics: From Genome to Field: Proceedings of the 12th International Wheat Genetics Symposium

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ISBN: 9784431556749 9784431556756 Year: Pages: 445 DOI: 10.1007/978-4-431-55675-6 Language: English
Publisher: Springer
Subject: Genetics --- Plant Sciences
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This proceedings is a collection of 46 selected papers that were presented at the 12th International Wheat Genetics Symposium (IWGS). Since the launch of the wheat genome sequencing project in 2005, the arrival of draft genome sequences has marked a new era in wheat genetics and genomics, catalyzing rapid advancement in the field. This book provides a comprehensive review of the forefront of wheat research, across various important topics such as germplasm and genetic diversity, cytogenetics and allopolyploid evolution, genome sequencing, structural and functional genomics, gene function and molecular biology, biotic stress, abiotic stress, grain quality, and classical and molecular breeding. Following an introduction, 9 parts of the book are dedicated to each of these topics. A final, 11th part entitled “Toward Sustainable Wheat Production” contains 7 excellent papers that were presented in the 12th IWGS Special Session supported by the OECD. With rapid population growth and radical climate changes, the world faces a global food crisis and is in need of another Green Revolution to boost yields of wheat and other widely grown staple crops. Although this book focuses on wheat, many of the newly developed techniques and results presented here can be applied to other plant species with large and complex genomes. As such, this volume is highly recommended for all students and researchers in wheat sciences and related plant sciences and for those who are interested in stable food production and food security.

Alterations of Epigenetics and MicroRNAs in Cancer and Cancer Stem Cell

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193455 Year: Pages: 79 DOI: 10.3389/978-2-88919-345-5 Language: English
Publisher: Frontiers Media SA
Subject: Biology --- Genetics --- Science (General)
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Studies have shown that alterations of epigenetics and microRNAs (miRNAs) play critical roles in the initiation and progression of human cancer. Epigenetic silencing of tumor suppressor genes in cancer cells is generally mediated by DNA hypermethylation of CpG island promoter and histone modification such as methylation of histone H3 lysine 9 (H3K9) and tri-methylation of H3K27. MiRNAs are small non-coding RNAs that regulate expression of various target genes. Specific miRNAs are aberrantly expressed and play roles as tumor suppressors or oncogenes during carcinogenesis. Important tumor suppressor miRNAs are silenced by epigenetic alterations, resulting in activation of target oncogenes in human malignancies. Stem cells have the ability to perpetuate themselves through self-renewal and to generate mature cells of various tissues through differentiation. Accumulating evidence suggests that a subpopulation of cancer cells with distinct stem-like properties is responsible for tumor initiation, invasive growth, and metastasis formation, which is defined as cancer stem cells. Cancer stem cells are considered to be resistant to conventional chemotherapy and radiation therapy, suggesting that these cells are important targets of cancer therapy. DNA methylation, histone modification and miRNAs may be deeply involved in stem-like properties in cancer cells. Restoring the expression of tumor suppressor genes and miRNAs by chromatin modifying drugs may be a promising therapeutic approach for cancer stem cells. In this Research Topic, we discuss about alterations of epigenetics and miRNAs in cancer and cancer stem cell and understand the molecular mechanism underlying the formation of cancer stem cell, which may provide a novel insight for treatment of refractory cancer.

Berry Antioxidants in Health and Disease

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ISBN: 9783038423492 9783038423485 Year: Pages: VIII, 156 DOI: 10.3390/books978-3-03842-349-2 Language: English
Publisher: MDPI AG - Multidisciplinary Digital Publishing Institute
Subject: Biology --- Genetics
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During the last decade, a high volume of work has been published on the health-promoting effects of berries (e.g., blueberries, cranberries, blackberries, etc.) that are rich in antioxidant phytochemicals, polyphenols. Consuming a diet rich in polyphenols has been documented to attenuate the risk of chronic diseases, such as cardiovascular disease, certain cancers, diabetes mellitus, and neurodegenerative disorders. Recent evidence also reveals that the biological effects of polyphenols extend beyond their traditional antioxidant role. This Special Issue includes 10 peer-reviewed papers, including original research papers and reviews. They present the most recent advances in the role of berry antioxidants, not only in maintaining health but also in preventing and/or reversing disease both in cell culture, animal models and in humans. Additionally, the molecular mechanisms and signaling pathways modulated by berry antioxidants are presented. Chapters include the role of berry antioxidants in whole fruit and leaves on the metabolic syndrome, obesity, diabetes and glucose intolerance, cancer, inflammation, oxidative stress and neuroprotection as well as cardiovascular disease. As a guest editor, I would like to acknowledge the authors of all chapters for their valuable contributions and reviewers for their thoughtful and constructive suggestions and time. Special thanks to the publishing team of the Antioxidants Journal for their professionalism, attention to detail and timely completion of this volume.

Biological Ontologies and Semantic Biology

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192779 Year: Pages: 106 DOI: 10.3389/978-2-88919-277-9 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Biotechnology --- General and Civil Engineering --- Genetics --- Science (General)
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As the amount of biological information and its diversity accumulates massively there is a critical need to facilitate the integration of this data to allow new and unexpected conclusions to be drawn from it. The Semantic Web is a new wave of web- based technologies that allows the linking of data between diverse data sets via standardised data formats (“big data”). Semantic Biology is the application of semantic web technology in the biological domain (including medical and health informatics). The Special Topic encompasses papers in this very broad area, including not only ontologies (development and applications), but also text mining, data integration and data analysis making use of the technologies of the Semantic Web. Ontologies are a critical requirement for such integration as they allow conclusions drawn about biological experiments, or descriptions of biological entities, to be understandable and integratable despite being contained in different databases and analysed by different software systems. Ontologies are the standard structures used in biology, and more broadly in computer science, to hold standardized terminologies for particular domains of knowledge. Ontologies consist of sets of standard terms, which are defined and may have synonyms for ease of searching and to accommodate different usages by different communities. These terms are linked by standard relationships, such as “is_a” (an eye “is_a” sense organ) or “part_of” (an eye is “part_of” a head). By linking terms in this way, more detailed, or granular, terms can be linked to broader terms, allowing computation to be carried out that takes these relationships into account.

Biology of Cognitive Aging: Model Systems, Technologies and Beyond

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451449 Year: Pages: 145 DOI: 10.3389/978-2-88945-144-9 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
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Welcome! We, humans, tend to experience forgetfulness when we get old. The forgetfulness may become more serious memory impairment, dementia. Presumably, we have known it for a long time, but we still do not know the mechanism behind. A normal part of forgetfulness is called age-related memory impairment (AMI), which is considered the first step towards mild cognitive impairment (MCI; transition state) and dementia (disease state). The majority of dementia is attributable to Alzheimer’s disease (AD). Progression to dementia occurs at a high rate in patients with AMI. This eBook covers exciting but yet challenging field of cognitive aging. AMI is specific to neural tissues of the brain and is considered to be segmental aging. It happens not only to humans but also to a variety of species. Learning and memory are vulnerable to aging in a wide variety of model species, including worms, fruit flies, insects, snails, fishes, and rodents. Aging specifically reduces the ability to learn new information but leaves “old” memories and procedural memory intact. A comparative approach including the use of model systems seems to facilitate understanding of the molecular mechanisms that lead to AMI and AD. We advocate research on model systems. This eBook also provides the first manuscript co-authored with an AD patient to create a feedback loop from patients incorporated into research. We also included a manuscript on the semi-automated system that was inspired by such a feedback. Those may place a nice flavor to this exciting series of comparative research on cognitive aging. We hope you enjoy this eBook. Warm regards, Shin Murakami, Ph.D.Welcome! We, humans, tend to experience forgetfulness when we get old. The forgetfulness may become more serious memory impairment, dementia. Presumably, we have known it for a long time, but we still do not know the mechanism behind. A normal part of forgetfulness is called age-related memory impairment (AMI), which is considered the first step towards mild cognitive impairment (MCI; transition state) and dementia (disease state). The majority of dementia is attributable to Alzheimer’s disease (AD). Progression to dementia occurs at a high rate in patients with AMI. This eBook covers exciting but yet challenging field of cognitive aging. AMI is specific to neural tissues of the brain and is considered to be segmental aging. It happens not only to humans but also to a variety of species. Learning and memory are vulnerable to aging in a wide variety of model species, including worms, fruit flies, insects, snails, fishes, and rodents. Aging specifically reduces the ability to learn new information but leaves “old” memories and procedural memory intact. A comparative approach including the use of model systems seems to facilitate understanding of the molecular mechanisms that lead to AMI and AD. We advocate research on model systems. This eBook also provides the first manuscript co-authored with an AD patient to create a feedback loop from patients incorporated into research. We also included a manuscript on the semi-automated system that was inspired by such a feedback. Those may place a nice flavor to this exciting series of comparative research on cognitive aging. We hope you enjoy this eBook. Warm regards, Shin Murakami, Ph.D.

Cancer-associated defects in the DNA damage response: drivers for malignant transformation and potential therapeutic targets

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199495 Year: Pages: 107 DOI: 10.3389/978-2-88919-949-5 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
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For this eBook, and the associated Research Topic in Frontiers in Genetics, entitled: ‘Cancer-associated defects in the DNA damage response: drivers for malignant transformation and potential therapeutic targets’ we have selected 10 papers that each discusses important, yet distinct aspects of the response to DNA damage in normal cells and cancer cells. Using an evolutionary conserved signaling network called the ‘DNA damage response (DDR)’ cells maintain the integrity of their genome, and thus safeguard cellular functioning and the ability to create viably progeny. Initially, the DDR appeared to consist of few linear kinase-driven pathways. However, research over the past decades in model organisms, as well as in the human system has revealed that the DDR is a complex signaling network, wired by multiple parallel pathways and displaying extensive crosstalk. Besides phosphorylation, multiple other post-translational modifications, including ubiquitination and sumoylation, are involved to achieve chromatin remodeling and initiation of DNA repair. Also, rather than being a cell-intrinsic phenomenon, we increasingly appreciate that cell-cell communication is involved. The recognition and repair of DNA damage is essential to maintain normal physiology. Multiple pathological conditions have been attributed to defective DNA repair, most notably accelerated aging, neurodegeneration and cancer. In the context of cancer, through repair of DNA damage or elimination of irreparably damaged cells, the DDR clearly has a tumor-suppressive role. Indeed, many tumor cells show partially inactivated DDR signaling, which allows proliferation in the context of DNA damage-inducing oncogenes. Simultaneously, loss of specific DDR signaling nodes creates a specific dependence of tumor cells on their remaining DDR components, and thus creates therapeutic opportunities. Especially in the context of cancer treatment, numerous targeted agents are under investigation, either to potentiate the cytotoxic effects of chemo-radiotherapy, or to induce synthetic lethality with cancer-specific alterations, with the treatment of BRCA1/2 mutant cancers with PARP1 inhibitors as a prototype example. We have selected four review articles that provide insight into the key components and the wiring of the DDR and DNA repair. Torgovnick and Schumacher review the involvement of DNA repair in the initiation and treatment of cancer, Brinkmann et al., describe the involvement of ubiquitination in DNA damage signaling and Jaiswal and Lindqvist discuss how cell-extrinsic signaling participates in communication of DNA damage to neighboring cells. In addition, Shatneyeva and colleagues review the connection between the cellular response to DNA damage and escape from immune surveillance. Concerning the therapeutic application of targeting the DDR and DNA repair, three articles were included. Krajewska and van Vugt review the wiring of homologous recombination and how this offers therapeutic opportunities. Additionally, Knittel and colleagues describe how genetic loss of the central DDR component ATM in chronic lymphocytic leukemia can be exploited therapeutically by targeting certain parallel DNA repair pathways. Syljuasen and colleagues report on how targeting of the DDR can be used as a therapeutic strategy in lung cancer. Finally, three chapters describe newly identified regulators of the cellular response to DNA damage. Von Morgen et al. describe the R2TP complex, Lezzi and Fanciluuli review the involvement of Che-1/AATF in the DDR, and Ohms and co-authors describe how retrotransposons are at the basis of increased genomic instability. Altogether, these articles describe how defective responses to DNA damage underlie disease - and especially in the context of cancer -can be exploited to better treat disease.

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