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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.

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.

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)
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

Endoplasmic reticulum - shape and function in stress translation

Authors: --- --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889193448 Year: Pages: 110 DOI: 10.3389/978-2-88919-344-8 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2016-03-10 08:14:32
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The endoplasmic reticulum (ER) is a manufacturing unit in eukaryotic cells required for the synthesis of proteins, lipids, metabolites and hormones. Besides supporting cellular signalling networks by its anabolic function, the ER on its own or in communication with other organelles directly initiates signalling processes of physiological significance. Based on the intimate and immediate involvement in stress signalling the ER is considered as sensory organelle on which cells strongly rely to effectively translate environmental cues into adaptive stress responses. The transcellular distribution of the ER providing comprehensive cell-to-cell connections in multicellular organisms probably allows a concerted action of cell alliances and tissue areas towards environmental constraints. At the cellular level, stress adaptation correlates with the capability of the ER machinery to synthesise proteins participating in stress signalling as well as in the activation of ER membrane localised proteins to start cell-protective signalling processes. Importantly, depending on the stress insult, the ER either supports protective strategies or initiates cell death programmes. Recent, genetic, molecular and cell biological studies have drawn an initial picture of underlying signalling events activated by ER membrane localised proteins. In this Research Topic, we provided a platform for articles describing research on ER morphology and metabolism with a focus on stress translation. The Research Topic is sub-divided into the following sections: 1. ER in stress signalling and adaptation 2. ER structure and biosynthetic functions 3. Regulation of protein processing 4. Regulation of programmed cell death

Progenitor diversity and neural cell specification in the central nervous system

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889196838 Year: Pages: 107 DOI: 10.3389/978-2-88919-683-8 Language: English
Publisher: Frontiers Media SA
Subject: Neurology --- Science (General)
Added to DOAB on : 2016-04-07 11:22:02
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The central nervous system continuously perceives, integrates, processes and generates information. These complex functions rely on the detailed elaboration of its cellular network and on the myriads of individual, highly differentiated and specialized cell types, classically subdivided into neurons, astrocytes and oligodendrocytes. The specification of these individual populations begins early during development with less differentiated, yet already partly restricted, progenitor cells. Anatomically located in dedicated germinative niches, neural progenitors perceive the influence of diffusible molecules of various natures and concentrations. These signals result in the initial specialization of cohorts of progenitors that express unique combinations of transcription factors. It is now clearly established that both extrinsic and intrinsic signals act in concert to determine the fate potentials of these progenitor cohorts. This limitation increases over time, adult neural progenitors being more restricted than their developmental counterparts. Nevertheless, recent data have shown that the fate restriction of neural progenitors, as well as that of their progenies, can be overwritten upon selected intrinsic factor expression, not only during development but also in adulthood. This e-book is a collection of original research studies along with review articles that, together, provide insights into the vast spatiotemporal diversity of neural progenitors, and the various factors that govern their fate potential.

Making Science Fun - A Tribute to Our Colleague and Friend, Prof. Antonius G. Rolink (1953-2017)

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889457519 Year: Pages: 211 DOI: 10.3389/978-2-88945-751-9 Language: English
Publisher: Frontiers Media SA
Subject: Medicine (General) --- Allergy and Immunology
Added to DOAB on : 2019-01-23 14:53:43
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This Research Topic honors the memory of Prof. Antonius “Ton” G. Rolink (April 19, 1953–August 06, 2017), our colleague, mentor and friend in immunology. It is now over a year since Ton left us. This article collection, authored by many of Ton’s friends and colleagues, reflects the huge contribution to cellular and molecular immunology that work emanating directly from Ton’s own hands and laboratory have made to the understanding of lymphocyte development. Ton’s hard work, expertise, generosity, passion for science and infectious humor were legendary and for all of those lucky enough to have been his colleague, he ensured that science was fun. We take this opportunity of thanking all contributors for submitting their manuscripts; we are sure that Ton would have enjoyed reading and making his own insightful comments on them. In the form of original research and review articles, these papers cover many of Ton’s scientific interests in different aspects of lymphocyte development in mouse and man. In the first section, Development of hematopoietic cells and lymphocytes, Klein et al. describe the accumulation of multipotent hematopoietic progenitors in peripheral lymphoid organs of IL-7xFlt3L double transgenic mice and Pang et al. the role of the transcription factor PU.1 on the development of Common Lymphoid Progenitors. In Early B cell development, Winkler and Mårtensson review the role of the Pre-B cell receptor in B cell development and papers by Hobeika et al. and Brennecke et al. describe models of inducible B cell development. For B cell selection, survival and tolerance, Smulski and Eibel review the role of BAFF and Kowalczyk-Quintans et al. analyse the role of membrane-bound BAFF. The impact of BIM on B cell homeostasis is discussed by Liu et al. The role of the MEK-ERK pathway in B cell tolerance is discussed by Greaves et al. and the transcriptional regulation of germinal center development is reviewed by Song and Matthias. For Hematological diseases, Ghia reviews how studies of B cell development help the understanding of Leukemia development, Kim and Schaniel review how iPS technology helps the understanding of hematological diseases and Hellmann et al. describe development of new therapeutic antibody drug conjugates. Finally, in T cell development, homeostasis and graft vs. host disease, Heiler et al. describe the therapeutic effects of IL-2/anti-IL-2 immune complexes in GvHD, Calvo-Asensio et al. describe the DNA damage response of thymocyte progenitors and Mori and Pieters review the role of Coronin 1 in T cell survival.

Salinity Tolerance in Plants

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ISBN: 9783039210268 / 9783039210275 Year: Pages: 422 DOI: 10.3390/books978-3-03921-027-5 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Biochemistry
Added to DOAB on : 2019-06-26 10:09:00
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Salt stress is one of the most damaging abiotic stresses because most crop plants are susceptible to salinity to different degrees. According to the FAO, about 800 million Has of land are affected by salinity worldwide. Unfortunately, this situation will worsen in the context of climate change, where there will be an overall increase in temperature and a decrease in average annual rainfall worldwide. This Special Issue presents different research works and reviews on the response of plants to salinity, focused from different points of view: physiological, biochemical, and molecular levels. Although an important part of the studies on the response to salinity have been carried out with Arabidopsis plants, the use of other species with agronomic interest is also notable, including woody plants. Most of the conducted studies in this Special Issue were focused on the identification and characterization of candidate genes for salt tolerance in higher plants. This identification would provide valuable information about the molecular and genetic mechanisms involved in the salt tolerance response, and it also supplies important resources to breeding programs for salt tolerance in plants.

Keywords

Arabidopsis --- Brassica napus --- ion homeostasis --- melatonin --- NaCl stress --- nitric oxide --- redox homeostasis --- Chlamydomonas reinhardtii --- bZIP transcription factors --- salt stress --- transcriptional regulation --- photosynthesis --- lipid accumulation --- Apocyni Veneti Folium --- salt stress --- multiple bioactive constituents --- physiological changes --- multivariate statistical analysis --- banana (Musa acuminata L.) --- ROP --- genome-wide identification --- abiotic stress --- salt stress --- MaROP5g --- rice --- genome-wide association study --- salt stress --- germination --- natural variation --- Chlamydomonas reinhardtii --- salt stress --- transcriptome analysis --- impairment of photosynthesis --- underpinnings of salt stress responses --- chlorophyll fluorescence --- J8-1 plum line --- mandelonitrile --- Prunus domestica --- redox signalling --- salicylic acid --- salt-stress --- soluble nutrients --- Arabidopsis thaliana --- VOZ --- transcription factor --- salt stress --- transcriptional activator --- chlorophyll fluorescence --- lipid peroxidation --- Na+ --- photosynthesis --- photosystem --- RNA binding protein --- nucleolin --- salt stress --- photosynthesis --- light saturation point --- booting stage --- transcriptome --- grapevine --- salt stress --- ROS detoxification --- phytohormone --- transcription factors --- Arabidopsis --- CDPK --- ion homeostasis --- NMT --- ROS --- salt stress --- antioxidant enzymes --- Arabidopsis thaliana --- ascorbate cycle --- hydrogen peroxide --- reactive oxygen species --- salinity --- SnRK2 --- RNA-seq --- DEUs --- flax --- NaCl stress --- EST-SSR --- Salt stress --- Oryza sativa --- proteomics --- iTRAQ quantification --- cell membrane injury --- root activity --- antioxidant systems --- ion homeostasis --- melatonin --- salt stress --- signal pathway --- SsMAX2 --- Sapium sebiferum --- drought, osmotic stress --- salt stress --- redox homeostasis --- strigolactones --- ABA --- TGase --- photosynthesis --- salt stress --- polyamines --- cucumber --- abiotic stresses --- high salinity --- HKT1 --- halophytes --- glycophytes --- poplars (Populus) --- salt tolerance --- molecular mechanisms --- SOS --- ROS --- Capsicum annuum L. --- CaDHN5 --- salt stress --- osmotic stress --- dehydrin --- Gossypium arboretum --- salt tolerance --- single nucleotide polymorphisms --- association mapping. --- n/a

Transcriptional Regulation: Molecules, Involved Mechanisms and Misregulation

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ISBN: 9783039212651 / 9783039212668 Year: Pages: 356 DOI: 10.3390/books978-3-03921-266-8 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-08-28 11:21:27
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Transcriptional regulation is a critical biological process involved in the response of a cell, a tissue or an organism to a variety of intra- and extra-cellular signals. Besides, it controls the establishment and maintenance of cell identity throughout developmental and differentiation programs. This highly complex and dynamic process is orchestrated by a huge number of molecules and protein networks and occurs through multiple temporal and functional steps. Of note, many human disorders are characterized by misregulation of global transcription since most of the signaling pathways ultimately target components of transcription machinery. This book includes a selection of papers that illustrate recent advances in our understanding of transcriptional regulation and focuses on many important topics, from cis-regulatory elements to transcription factors, chromatin regulators and non-coding RNAs, other than several transcriptome studies and computational analyses.

Keywords

major depressive disorder --- glioblastoma --- differentially expressed genes --- transcriptomics --- common pathway --- mouse --- miR-25-3p --- Akt1 --- AP-2? --- promoter --- cell metabolism --- p57Kip2 --- CDKN1C --- epigenetics --- disease --- cell differentiation --- placenta --- long non-coding RNA (lncRNA) --- human --- pregnancy --- high-throughput RNA sequencing (RNA-Seq) --- transcriptome --- Rsh regulon --- Novosphingobium pentaromativorans US6-1 --- sphingomonads --- RNA-seq --- N-acyl-l-homoserine lactone --- ppGpp --- selenium --- selenocysteine --- selenoproteins --- selenocysteine insertion sequence --- nonsense-mediated decay --- G-quadruplex --- transcriptional regulation --- promoter --- CRISPR/Cas9 --- PRDM gene family --- TCGA data analysis --- somatic mutations --- transcriptome profiling --- human malignancies --- tristetraprolin (TTP) --- tumorigenesis --- posttranscriptional regulation --- adenosine and uridine-rich elements (AREs) --- circRNA-disease associations --- pathway --- heterogeneous network --- Patau Syndrome --- cytogenetics --- FOXO1 --- transcription factor --- molecular pathways --- bioinformatics --- molecular docking --- and drug design --- transcription regulation --- gene expression --- causal inference --- enhancer activity --- insect --- transcription factors --- structures and functions --- research methods --- progress and prospects --- Pax3 --- Pteria penguin (Röding, 1798) --- tyrosinase --- melanin --- RNA interference --- liquid chromatograph-tandem mass spectrometer (LC-MS/MS) --- epigenetics --- gene expression --- nutrition --- transcription --- disorders --- mechanisms --- Crassostrea gigas --- Pacific oyster --- pediveliger larvae --- bioadhesive --- transcriptome --- gene expression --- interactome --- microscopy --- fertilization --- self-incompatibility --- transcriptome --- tea --- long non-coding RNAs --- cancer --- acute leukemia --- therapeutic targets --- Adiponectin --- cancer --- Adiponectin receptors --- obesity --- inflammatory response --- inflammation --- nutritional status --- n/a

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