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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

Authors: --- --- --- --- et al.
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 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.

Cell Fate

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198528 Year: Pages: 102 DOI: 10.3389/978-2-88919-852-8 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
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The fundamental question of how an undifferentiated progenitor cell adopts a more specialized cell fate that then contributes to the development of specialized tissues, organs, organ systems and ultimately a unique individual of a given species has intrigued cell and developmental biologists for many years. Advances in molecular and cell biology have enabled investigators to identify genetic and epigenetic factors that contribute to these processes with increasing detail and also to define the various molecular characteristics of each cell fate with greater precision. Understanding these processes have also provided greater insights into disorders in which the normal mechanisms of cell fate determination are altered, such as in cancer and inherited malformations. With these advances have come techniques that facilitate the manipulation of cell fate, which have the potential to revolutionize the field of medicine by facilitating the repair and/or regeneration of diseased organs. Given the rapid advances that are occurring in the field, the articles in this eBook are both relevant and timely. These articles originally appeared online as part of the Research Topic “Cell Fate” overseen by my colleagues Dr. Lin, Dr. Buttitta, Dr. Maves, Dr. Dilworth, Dr. Paladini and myself and have been viewed extensively. Because of their popularity, they are now made available as an eBook, in a more easily downloadable form. Michael T. Chin

Comprehensive Systems Biomedicine

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193745 Year: Pages: 113 DOI: 10.3389/978-2-88919-374-5 Language: English
Publisher: Frontiers Media SA
Subject: Genetics --- Science (General)
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Systems Biomedicine is a field in perpetual development. By definition a translational discipline, it emphasizes the role of quantitative systems approaches in biomedicine and aims to offer solutions to many emerging problems characterized by levels and types of complexity and uncertainty unmet before. Many factors, including technological and societal ones, need to be considered. In particular, new technologies are providing researchers with the data deluge whose management and exploitation requires a reinvention of cross-disciplinary team efforts. The advent of “omics” and high-content imaging are examples of advances de facto establishing the necessity of systems approaches. Hypothesis-driven models and in silico validation tools in support to all the varieties of experimental applications call for a profound revision. The focus on phases like mining and assimilating the data has substantially increased so to allow for interpretable knowledge to be inferred. Notably, to be able to tackle the newly generated data dimensionality, heterogeneity and complexity, model-free and data-driven intensive applications are increasingly shaping the computational pipelines and architectures that quant specialists set aside of the high-throughput genomics, transcriptomics, proteomics platforms. As for the societal aspects, in many advanced societies health care needs now more than in the past to address the problem of managing ageing populations and their complex morbidity patterns. In parallel, there is a growing research interest on the impact that cross-disciplinary clinical, epidemiological and quantitative modelling studies can have in relation to outcomes potentially affecting the quality of life of many people. Complex systems, including those characterizing biomedicine, are assessed in both their functionality and stability, and also relatively to the capacity of generating information from diversity, variation, and complexity. Due to the combined interactions and effects, such systems embed prediction power available for instance in both target identification or marker discovery, or more generally for conducting inference about patients’ pathological states, i.e. normal versus disease, diagnostic or prognostic analysis, and preventive assessment (e.g., risk evaluation). The ultimate goal, personalized medicine, will be achieved based on the confluence of the system’s predictive power to patient-specific profiling.

DNA helicases: expression, functions and clinical implications

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195756 Year: Pages: 78 DOI: 10.3389/978-2-88919-575-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
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Helicases are the proteins that bind to double- or single-stranded DNA and/or RNA chains to unwind higher order structures, usually consuming energy from the hydrolysis of ATP molecules. The biological roles of helicases are associated with a variety of DNA and/or RNA metabolisms, including DNA-replication, -repair, -recombination, RNA processing, and transcription. Dysfunctions of helicases cause various diseases, such as xeroderma pigmentosum (XP), premature aging syndrome, cancer and immunodeficiency, in humans. Moreover, recent genetic analyses revealed that mutations in helicase-encoding genes are frequently found in patients of specific diseases. Some helicases regulate cellular senescence by controlling integrity of genomes, and others play a role in neuromuscular functions presumably by modulating processing of mRNAs. However, the molecular mechanisms of how helicases are regulated in order to maintain our health are not yet fully understood. In this research topic, we will focus on the expression and functions of helicases and their encoding genes, reviewing recent research progresses that provide new insights into development of clinical and pharmaceutical treatments targeting helicases.

Keywords

Aging --- Cancer --- DNA Repair --- helicases --- Telomere

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