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Bioinformatics of Non-Coding RNAs with Applications to Biomedicine: Recent Advances and Open Challenges

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450961 Year: Pages: 95 DOI: 10.3389/978-2-88945-096-1 Language: English
Publisher: Frontiers Media SA
Subject: Biotechnology --- General and Civil Engineering
Added to DOAB on : 2017-07-06 13:27:36
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The recent discovery of small and long non-coding RNAs (ncRNAs) has represented a major breakthrough in the life sciences. These molecules add a new layer of complexity to biological processes and pathways by revealing a sophisticated and dynamic interconnected system whose structure is just beginning to be uncovered. Genetic and epigenetic aberrations affecting ncRNA gene sequences and their expression have been linked to a variety of pathological conditions, including cancer, cardiovascular and neurological diseases. Latest advances in the development of high throughput analysis techniques may help to shed light on the complex regulatory mechanisms in which ncRNA molecules are involved. Bioinformatics tools constitute a unique and essential resource for non-coding RNA studies, providing a powerful technology to organize, integrate and analyze the huge amount of data produced daily by wet biology experiments in order to discover patterns, identify relationships among heterogeneous biological elements and formulate functional hypotheses. This Research Topic reviews current knowledge, introduces novel methods, and discusses open challenges of this exciting and innovative field in connection with the most important biomedical applications. It consists of four reviews and six original research and methods articles, spanning the full scope of the Research Topic.

Keywords

bioinformatics --- ncRNA --- microRNA --- RNA Editing --- isomiRs --- networks --- RNAseq --- CLIPseq --- siRNA --- CRISPR

Metabolic Control of Brain Homeostasis

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452866 Year: Pages: 204 DOI: 10.3389/978-2-88945-286-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Neurology
Added to DOAB on : 2018-02-27 16:16:44
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Brain function is under metabolic control, which in turn determines the equilibrium of homeostatic systems that affect neuronal and glial networks on the molecular, cellular, and systems levels. The collection of articles ranges from molecules and mechanisms involved in regulating homeostasis and neuronal excitability to therapeutic mechanisms tailored to restore homeostatic function. It also features neurological diseases and novel treatment approaches that are based on metabolic and homeostatic interventions. Together, the collection of articles outlines novel strategies to restore brain function in neurology and highlights limitations of conventional pharmacological approaches. We suggest that restoration of molecular and biochemical networks could lead to a new era of therapeutic opportunities.

Biogenesis of the oxidative phosphorylation machinery in plants. From gene expression to complex assembly

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192786 Year: Pages: 98 DOI: 10.3389/978-2-88919-278-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Physiology --- Botany
Added to DOAB on : 2015-12-03 13:02:24
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Mitochondrial biogenesis is an extremely complex process. A hint of this complexity is clearly indicated by the many steps and factors required to assemble the respiratory complexes involved in oxidative phosphorylation. These steps include the expression of genes present in both the nucleus and the organelle, intricate post-transcriptional RNA processing events, the coordinated synthesis, transport and assembly of the different subunits, the synthesis and assembly of co-factors and, finally, the formation of supercomplexes or respirasomes. It can be envisaged, and current knowledge supports this view, that plants have evolved specific mechanisms for the biogenesis of respiratory complexes. For example, expression of the mitochondrial genome in plants has special features, not present in other groups of eukaryotes. Moreover, plant mitochondrial biogenesis and function should be considered in the context of the presence of the chloroplast, a second organelle involved in energetic and redox metabolism. It implies the necessity to discriminate between proteins destined for each organelle and requires the establishment of functional interconnections between photosynthesis and respiration. In recent years, our knowledge of the mechanisms involved in these different processes in plants has considerably increased. As a result, the many events and factors necessary for the correct expression of proteins encoded in the mitochondrial genome, the cis acting elements and factors responsible for the expression of nuclear genes encoding respiratory chain components, the signals and mechanisms involved in the import of proteins synthesized in the cytosol and the many factors required for the synthesis and assembly of the different redox co-factors (heme groups, iron-sulfur clusters, copper centers) are beginning to be recognized at the molecular level. However, detailed knowledge of these processes is still not complete and, especially, little is known about how these processes are interconnected. Questions such as how the proteins, once synthesized in the mitochondrial matrix, are inserted into the membrane and assembled with other components, including those imported from the cytosol, how the expression of both genomes is coordinated and responds to changes in mitochondrial function, cellular requirements or environmental cues, or which factors and conditions influence the assembly of complexes and supercomplexes are still open and will receive much attention in the near future. This Research Topic is aimed at establishing a collection of articles that focus on the different processes involved in the biogenesis of respiratory complexes in plants as a means to highlight recent advances. In this way, it intends to help to construct a picture of the whole process and, not less important, to expose the existing gaps that need to be addressed to fully understand how plant cells build and modulate the complex structures involved in respiration.

Methods in Computational Biology

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ISBN: 9783039211630 / 9783039211647 Year: Pages: 214 DOI: 10.3390/books978-3-03921-164-7 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Computer Science
Added to DOAB on : 2019-08-28 11:21:27
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Modern biology is rapidly becoming a study of large sets of data. Understanding these data sets is a major challenge for most life sciences, including the medical, environmental, and bioprocess fields. Computational biology approaches are essential for leveraging this ongoing revolution in omics data. A primary goal of this Special Issue, entitled “Methods in Computational Biology”, is the communication of computational biology methods, which can extract biological design principles from complex data sets, described in enough detail to permit the reproduction of the results. This issue integrates interdisciplinary researchers such as biologists, computer scientists, engineers, and mathematicians to advance biological systems analysis. The Special Issue contains the following sections:•Reviews of Computational Methods•Computational Analysis of Biological Dynamics: From Molecular to Cellular to Tissue/Consortia Levels•The Interface of Biotic and Abiotic Processes•Processing of Large Data Sets for Enhanced Analysis•Parameter Optimization and Measurement

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