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Systems Biology of Transcription Regulation

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199679 Year: Pages: 189 DOI: 10.3389/978-2-88919-967-9 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics --- Botany --- General and Civil Engineering --- Biotechnology
Added to DOAB on : 2016-01-19 14:05:46
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Transcription regulation is a complex process that can be considered and investigated from different perspectives. Traditionally and due to technical reasons (including the evolution of our understanding of the underlying processes) the main focus of the research was made on the regulation of expression through transcription factors (TFs), the proteins directly binding to DNA. On the other hand, intensive research is going on in the field of chromatin structure, remodeling and its involvement in the regulation. Whatever direction we select, we can speak about several levels of regulation. For instance, concentrating on TFs, we should consider multiple regulatory layers, starting with signaling pathways and ending up with the TF binding sites in the promoters and other regulatory regions. However, it is obvious that the TF regulation, also including the upstream processes, represents a modest portion of all processes leading to gene expression. For more comprehensive description of the gene regulation, we need a systematic and holistic view, which brings us to the importance of systems biology approaches.Advances in methodology, especially in high-throughput methods, result in an ever-growing mass of data, which in many cases is still waiting for appropriate consideration. Moreover, the accumulation of data is going faster than the development of algorithms for their systematic evaluation. Data and methods integration is indispensable for the acquiring a systematic as well as a systemic view. In addition to the huge amount of molecular or genetic components of a biological system, the even larger number of their interactions constitutes the enormous complexity of processes occurring in a living cell (organ, organism). In systems biology, these interactions are represented by networks. Transcriptional or, more generally, gene regulatory networks are being generated from experimental ChIPseq data, by reverse engineering from transcriptomics data, or from computational predictions of transcription factor (TF) – target gene relations. While transcriptional networks are now available for many biological systems, mathematical models to simulate their dynamic behavior have been successfully developed for metabolic and, to some extent, for signaling networks, but relatively rarely for gene regulatory networks. Systems biology approaches provide new perspectives that raise new questions. Some of them address methodological problems, others arise from the newly obtained understanding of the data. These open questions and problems are also a subject of this Research Topic.

The Proteins of Plastid Nucleoids - Structure, Function and Regulation

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

Chromatin & Transcriptional Tango on the Immune Dance Floor

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195107 Year: Pages: 144 DOI: 10.3389/978-2-88919-510-7 Language: English
Publisher: Frontiers Media SA
Subject: Allergy and Immunology --- Medicine (General)
Added to DOAB on : 2015-12-03 13:02:24
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Signaling through the cell surface antigen receptor is a hallmark of various stages of lymphocyte development and adaptive immunity. Besides the adaptive immune system, the innate immunity is equally important for protection. However, the mechanistic connection between signaling, chromatin changes and downstream transcriptional pathways in both innate and adaptive immune system remains incompletely understood in hematopoiesis. A related issue is how the enhancers communicate to the promoters in a stage specific fashion and in the context of chromatin. Because the factors that regulate chromatin are generally present and active in most cell types, how could cell type and/or stage specific chromatin architecture is achieved in response to a particular immune signal?The genetic loci that encode lymphocyte cell surface receptors are in an "unrearranged” or “germline” configuration during the early stages of development. Thus, in addition to expressing lineage and/or stage specific transcription factors during each developmental stage, lymphocytes also need to rearrange their cognate receptor loci in a strictly ordered fashion. Hence, there must be a tightly coordinated communication between the recombination machinery and the transcriptional machinery (including chromatin regulators) at every developmental step. Mature B cells also undergo classswitch recombination and somatic hypermutation. Importantly, along the way, these cells must avoid autoimmune responses and only those cells capable of recognizing foreignantigens are preserved to reach peripheral organs where they must function. The exquisite regulation that govern chromatin accessibility, recombination and transcription regulation in response to the environmental signals in the immune system is discussed here is a series of articles.

The Transcriptional Regulation of Memory

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198658 Year: Pages: 116 DOI: 10.3389/978-2-88919-865-8 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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The formation of various forms of memory involves a series of distinct cellular and molecular mechanisms, many of which are not fully understood. There are highly conserved pathways that are involved in learning, memory, and synaptic plasticity, which is the primary substrate for memory storage. The formation of short-term (across minutes) memory is mediated by local changes in synapses, while long-term (across hours to days) memory storage is associated with activation of transcription and synthesis of proteins that modify synaptic function. Transcription factors, which can either repress or activate transcription, play a vital role in driving protein synthesis underlying synaptic plasticity and memory, whereby protein synthesis provides the necessary building blocks to accommodate structural changes at the synapse that foster memory formation. Recent data implicate several families of transcription factors that appear critically important in the regulation of memory.In this Topic we will focus on the families of transcription factors thus far found to be critically involved in synaptic plasticity and memory formation. These include cAMP response element binding protein (CREB), Rel/nuclear factor B (Rel/NFB), CCAAT enhancer binding protein (C/EBP), and early growth response factor (Egr). In recent years, numerous studies have implicated epigenetic mechanisms, changes in gene activity and expression that occur without alteration in gene sequence, in the memory consolidation process. DNA methylation and chromatin remodeling are critically involved in learning and memory, supporting a role of epigenetic mechanisms. Here we provide more evidence of the importance of DNA methylation, histone posttranslational modifications and the role of histone acetylation and HDAC inhibitors in above mentioned processes.

Dickens’s Working Notes for 'Dombey and Son'

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ISBN: 9781783742257 9781783742233 Year: Volume: 1 Pages: 244 DOI: http://doi.org/10.11647/OBP.0092 Language: English
Publisher: Open Book Publishers
Subject: Languages and Literatures
Added to DOAB on : 2017-09-08 18:04:01
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This critical edition of the working notes for Dombey and Son (1848) is ideal for readers who wish to know more about Charles Dickens’s craft and creativity. Drawing on the author’s manuscript in the Victoria and Albert Museum, London—and containing hyperlinked facsimiles—Dickens’s Working Notes for Dombey and Son offers a new digital transcription with a fresh commentary by Tony Laing. Unique and innovative, this is the only edition to make Dickens’s working methods visible.John Mullan has called Dombey and Son Dickens’s 'first great novel.' Set amid the coming of the railways, it tells the story of a powerful man—typical of the commercial and banking magnates of the period—and the effect he has on his family and those around him. Laing presents the worksheets and other materials (transcribed for the first time) that together grew into the novel. Reading the book alongside this edition of the notes enlarges the understanding of Dickens’s art among teachers, students, researchers and Dickens enthusiasts.As cultural tastes shift from print to digital, Dickens’s Working Notes helps preserve Dickens’s work for the future. The magnifying and linking functions of the edition mean that the notes are more easily and usefully—not to mention accessibly—exhibited here than elsewhere. Laing gives present-day readers the chance not only to recapture the effect of serial publication but also to gain greater insight into the making of a work which, by general agreement and Dickens’s own admission, has a special place in his development as a novelist.

Cell Fate

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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)
Added to DOAB on : 2016-01-19 14:05:46
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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

Recent Progress in Understanding the Mechanism and Consequences of Retrotransposon Movement

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ISBN: 9783038425403 9783038425410 Year: Pages: VIII, 194 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Biology
Added to DOAB on : 2017-12-27 09:08:55
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Retrotransposons are present in essentially all eukaryotic genomes and come in two basic flavors: those that are bracketed by long terminal repeats (LTRs) and share a common ancestor with retroviruses, and non-LTR retrotransposons that have a distinct lineage and remain transpositionally active in humans. Both types of retrotransposons replicate through an RNA intermediate, stably integrate into the host genome and have accumulated to a very high copy number in mammals and certain plant species. Autonomous elements produce transcripts capable of undergoing reverse transcription, and minimally encode proteins with reverse transcriptase, integrase/endonucleolytic, and nucleic acid chaperone activities. Retrotransposons are currently distinguished from viruses, since the process of retrotransposition is not infectious. However, this boundary may prove to be provisional as we learn more about these mobile genetic elements. The goal of this Special Issue of Viruses is to highlight progress in understanding the mechanism and consequences of retrotransposon movement. Several active research areas may be covered in reviews and research articles, including the roles of cellular modulators and defense systems, retrotransposon expression and replication, retrotransposon-induced mutations and their association with human diseases, and how these widely disseminated elements mold eukaryotic genomes.

Plant Organ Abscission: From Models to Crops

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453283 Year: Pages: 271 DOI: 10.3389/978-2-88945-328-3 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2018-02-27 16:16:45
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Plant organ abscission is a developmental process regulated by the environment, stress, pathogens and the physiological status of the plant. In particular, seed and fruit abscission play an important role in seed dispersion and plant reproductive success and are common domestication traits with important agronomic consequences for many crop species. Indeed, in natural populations, shedding of the seed or fruit at the correct time is essential for reproductive success, while for crop species the premature or lack of abscission may be either beneficial or detrimental to crop productivity. The use of model plants, in particular Arabidopsis and tomato, have led to major advances in our understanding of the molecular and cellular mechanisms underlying organ abscission, and now many workers pursue the translation of these advances to crop species. Organ abscission involves specialized cell layers called the abscission zone (AZ), where abscission signals are perceived and cell separation takes place for the organ to be shed. A general model for plant organ abscission includes (1) the differentiation of the AZ, (2) the acquisition of AZ cells to become competent to respond to various abscission signals, (3) response to signals and the activation of the molecular and cellular processes that lead to cell separation in the AZ and (4) the post-abscission events related to protection of exposed cells after the organ has been shed. While this simple four-phase framework is helpful to describe the abscission process, the exact mechanisms of each stage, the differences between organ types and amongst diverse species, and in response to different abscission inducing signals are far from elucidated. For an organ to be shed, AZ cells must transduce a multitude of both endogenous and exogenous signals that lead to transcriptional and cellular and ultimately cell wall modifications necessary for adjacent cells to separate. How these key processes have been adapted during evolution to allow for organ abscission to take place in different locations and under different conditions is unknown. The aim of the current collection of articles is to present and be able to compare recent results on our understanding of organ abscission from model and crop species, and to provide a basis to understand both the evolution of abscission in plants and the translation of advances with model plants for applications in crop species.

Genomics in Aquaculture to Better Understand Species Biology and Accelerate Genetic Progress

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199570 Year: Pages: 151 DOI: 10.3389/978-2-88919-957-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Genetics
Added to DOAB on : 2016-01-19 14:05:46
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From a global perspective aquaculture is an activity related to food production with large potential for growth. Considering a continuously growing population, the efficiency and sustainability of this activity will be crucial to meet the needs of protein for human consumption in the near future. However, for continuous enhancement of the culture of both fish and shellfish there are still challenges to overcome, mostly related to the biology of the cultured species and their interaction with (increasingly changing) environmental factors. Examples of these challenges include early sexual maturation, feed meal replacement, immune response to infectious diseases and parasites, and temperature and salinity tolerance. Moreover, it is estimated that less than 10% of the total aquaculture production in the world is based on populations genetically improved by means of artificial selection. Thus, there is considerable room for implementing breeding schemes aimed at improving productive traits having significant economic impact. By far the most economically relevant trait is growth rate, which can be efficiently improved by conventional genetic selection (i.e. based on breeding values of selection candidates). However, there are other important traits that cannot be measured directly on selection candidates, such as resistance against infectious and parasitic agents and carcass quality traits (e.g. fillet yield and meat color). However, these traits can be more efficiently improved using molecular tools to assist breeding programs by means of marker-assisted selection, using a few markers explaining a high proportion of the trait variation, or genomic selection, using thousands of markers to estimate genomic breeding values. The development and implementation of new technologies applied to molecular biology and genomics, such as next-generation sequencing methods and high-throughput genotyping platforms, are allowing the rapid increase of availability of genomic resources in aquaculture species. These resources will provide powerful tools to the research community and will aid in the determination of the genetic factors involved in several biological aspects of aquaculture species. In this regard, it is important to establish discussion in terms of which strategies will be more efficient to solve the primary challenges that are affecting aquaculture systems around the world. The main objective of this Research Topic is to provide a forum to communicate recent research and implementation strategies in the use of genomics in aquaculture species with emphasis on (1) a better understanding of fish and shellfish biological processes having considerable impact on aquaculture systems; and (2) the efficient incorporation of molecular information into breeding programs to accelerate genetic progress of economically relevant traits.

Regulation of Cell Fate Determination in Plants

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193240 Year: Pages: 84 DOI: 10.3389/978-2-88919-324-0 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2016-03-10 08:14:32
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Plants are made up of a large number of distinct cell types that originate from a single fertilized egg cell. How the diversity of cell types arise in appropriate places is one of the most fascinating and attractive research areas of plant biology. During the past several decades, due to the development of new molecular techniques and tools, advances in optical microscopy, and availability of whole genome information and mutants in the model plant Arabidopsis and other plants, great advances have been made in understanding the mechanisms involved in cell fate determination in plants. Multiple mechanisms are used to generate cellular diversity. Asymmetric cell division is one of the primary mechanisms. As an example, asymmetric cell division enables one stem cell to generate a stem cell daughter and a daughter with a distinct identity. Initially equivalent cells can also differentiate to generate different cell types. This mechanism has been clearly demonstrated in the formation of multiple cell types during epidermis development in the shoot and root. Cell fate determination is influenced by both intrinsic factors, i.e, developmental regulators, as well as extrinsic signals, i.e., environmental stimuli. By using model systems like stomata, trichome, root hair and shoot and root apical meristem cells, ligands, receptors and transcription factors have been found to regulate cell fate determination. However, the details of signaling cassettes responsible for cell fate determination remain largely unknown. Plants are made up of a large number of distinct cell types that originate from a single fertilized egg cell. How the diversity of cell types arise in appropriate places is one of the most fascinating and attractive research areas of plant biology. During the past several decades, due to the development of new molecular techniques and tools, advances in optical microscopy, and availability of whole genome information and mutants in the model plant Arabidopsis and other plants, great advances have been made in understanding the mechanisms involved in cell fate determination in plants. This research topic contains 12 collected articles, including 2 Opinion Articles, 5 Reviews, 4 Mini Reviews, and 1 Original Research Article. Hopefully, these articles will expand our understanding of the regulation of cell fate determination in plants.

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