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Quantitative Assessment and Validation of Network Inference Methods in Bioinformatics

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889194780 Year: Pages: 191 DOI: 10.3389/978-2-88919-478-0 Language: English
Publisher: Frontiers Media SA
Subject: Biotechnology --- General and Civil Engineering --- Genetics --- Science (General)
Added to DOAB on : 2016-03-10 08:14:33
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Scientists today have access to an unprecedented arsenal of high-tech tools that can be used to thoroughly characterize biological systems of interest. High-throughput “omics” technologies enable to generate enormous quantities of data at the DNA, RNA, epigenetic and proteomic levels. One of the major challenges of the post-genomic era is to extract functional information by integrating such heterogeneous high-throughput genomic data. This is not a trivial task as we are increasingly coming to understand that it is not individual genes, but rather biological pathways and networks that drive an organism’s response to environmental factors and the development of its particular phenotype. In order to fully understand the way in which these networks interact (or fail to do so) in specific states (disease for instance), we must learn both, the structure of the underlying networks and the rules that govern their behavior. In recent years there has been an increasing interest in methods that aim to infer biological networks. These methods enable the opportunity for better understanding the interactions between genomic features and the overall structure and behavior of the underlying networks. So far, such network models have been mainly used to identify and validate new interactions between genes of interest. But ultimately, one could use these networks to predict large-scale effects of perturbations, such as treatment by multiple targeted drugs. However, currently, we are still at an early stage of comprehending methods and approaches providing a robust statistical framework to quantitatively assess the quality of network inference and its predictive potential. The scope of this Research Topic in Bioinformatics and Computational Biology aims at addressing these issues by investigating the various, complementary approaches to quantify the quality of network models. These “validation” techniques could focus on assessing quality of specific interactions, global and local structures, and predictive ability of network models. These methods could rely exclusively on in silico evaluation procedures or they could be coupled with novel experimental designs to generate the biological data necessary to properly validate inferred networks.

Plastid Proteostasis: Relevance of Transcription; Translation and Post-Translational Modifications

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453436 Year: Pages: 110 DOI: 10.3389/978-2-88945-343-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2018-02-27 16:16:45
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Due to their bacterial endosymbiotic origin plastids are organelles with both nuclear-encoded and plastid-encoded proteins. Therefore, a highly integrated modulation of gene expression between the nucleus and the plastome is needed in plant cell development. Plastids have retained for the most part a prokaryotic gene expression machinery but, differently from prokaryotes and eukaryotes, they have largely abandoned transcriptional control and switched to predominantly translational control of their gene expression. Some transcriptional regulation is known to occur, but the coordinate expression between the nucleus and the plastome takes place mainly through translational regulation. However, the regulatory mechanisms of plastid gene expression (PGE) are mediated by intricate plastid-nuclear interactions and are still far from being fully understood. Although, for example, translational autoregulation mechanisms in algae have been described for subunits of heteromeric protein complexes and termed control by epistasy of synthesis (CES), only few autoregulatory proteins have been identified in plant plastids. It should be noted of course that PGE in C. reinhardtii is different from that in plants in many aspects. Another example of investigation in this research area is to understand the interactions that occur during RNA binding between nucleus-encoded RNA-binding proteins and the respective RNA sequences, and how this influences the translation initiation process. In addition to this, the plastid retains a whole series of mechanisms for the preservation of its protein balance (proteostasis), including specific proteases, as well as molecular chaperones and enzymes useful in protein folding. After synthesis, plastid proteins must rapidly fold into stable three dimensional structures and often undergo co- and posttranslational modifications to perform their biological mission, avoiding aberrant folding, aggregation and targeting with the help of molecular chaperones and proteases. We believe that this topic is highly interesting for many research areas because the regulation of PGE is not only of wide interest for plant biologists but has also biotechnological implications. Indeed, plastid transformation turns out to be a very promising tool for the production of recombinant proteins in plants, yet some limitations must still be overcome and we believe that this is mainly due to our limited knowledge of the mechanisms in plastids influencing the maintenance of proteostasis.

Functional Characterization of Insect Chemoreceptors: Receptivity Range, Expression and Evolution

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889198603 Year: Pages: 163 DOI: 10.3389/978-2-88919-860-3 Language: English
Publisher: Frontiers Media SA
Subject: Ecology --- Science (General)
Added to DOAB on : 2016-01-19 14:05:46
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Olfaction and taste are of critical importance to insects and other animals, since vital behaviours, including mate, food and host seeking, as well as predator and toxin avoidance, are guided by chemosensory cues. Mate and habitat choice are to a large extent determined by chemical signals, and chemoreceptors contribute accordingly to pre-mating isolation barriers and speciation. In addition to fundamental physiological, ecological and evolutionary consideration, the knowledge of insect taste and especially olfaction is also of great importance to human economies, since it facilitates a more informed approach to the management of insect pests of agricultural crops and forests, and insect vectors of disease. Chemoreceptors, which bind to external chemical signals and then transform and send the sensory information to the brain, are at the core of the peripheral olfactory and gustatory system and have thus been the focus of recent research in chemical ecology. Specifically, emphasis has been placed on functional characterization of olfactory receptor genes, which are derived from three large gene families, namely the odorant receptors, gustatory receptors and ionotropic receptors. Spatial expression patterns of olfactory receptors in diverse chemosensory tissues provide information on divergent functions, with regards to ecologically relevant behaviours. On the other hand, characterization of olfactory receptor activation profiles, or “deorphanization”, provides complimentary data on the molecular range of receptivity to the fundamental unit of the olfactory sense. The aim of this Research Topic is to give an update on the breadth and depth of research currently in progress related to understanding the molecular mechanisms of insect chemoreception, with specific emphasis on the olfactory receptors.

Genomic Approaches for Improvement of Understudied Grasses

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452422 Year: Pages: 165 DOI: 10.3389/978-2-88945-242-2 Language: English
Publisher: Frontiers Media SA
Subject: Botany --- Science (General)
Added to DOAB on : 2017-10-13 14:57:01
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Grasses are diverse, spanning native prairies to high-yielding grain cropping systems. They are valued for their beauty and useful for soil stabilization, pollution mitigation, biofuel production, nutritional value, and forage quality; grasses encompass the most important grain crops in the world. There are thousands of distinct grass species and many have promiscuous hybridization patterns, blurring species boundaries. Resources for advancing the science and knowledgebase of individual grass species or their unique characteristics varies, often proportional to their perceived value to society. For many grasses, limited genetic information hinders research progress. Presented in this research topic is a brief snapshot of creative efforts to apply modern genomics research methodologies to the study of several minor grass species.

Oncolytic Viruses - Genetically Engineering the Future of Cancer Therapy

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889453580 Year: Pages: 193 DOI: 10.3389/978-2-88945-358-0 Language: English
Publisher: Frontiers Media SA
Subject: Medicine (General) --- Oncology --- Allergy and Immunology
Added to DOAB on : 2018-02-27 16:16:45
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The ability to genetically engineer oncolytic viruses in order to minimize side effects and improve the selective targeting of tumor cells has opened up novel opportunities for treating cancer. Understanding the mechanisms involved and the complex interaction between the viruses and the immune system will undoubtedly help guide the development of new strategies. Theranostic biomarkers to monitor these therapies in clinical trials serve an important need in this innovative field and demand further research.

Relevance of Translational Regulation on Plant Growth and Environmental Responses

Authors: --- --- --- --- et al.
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889454136 Year: Pages: 138 DOI: 10.3389/978-2-88945-413-6 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Botany
Added to DOAB on : 2018-11-16 17:17:57
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Plants, as sessile organisms, are exposed to a large array of challenging external and internal alterations that may restrict plant growth. These limiting growth conditions activate plant signalling responses which eventually target the protein synthesis machinery to rapidly reprogram plant metabolism to adapt to the new situation. Thus, the control of mRNA translation is one key regulatory step of gene expression and it is an essential molecular mechanism used by plants to bring about impressive growth plasticity. Compared to the vast number of studies aimed to identify plant transcriptional changes upon hormonal or environmental cues, the subsequent steps of mRNA transport, stability, storage, and eventually translational regulation, have been less studied in plants. This lack of knowledge concerns not only the fate of protein-coding transcripts in plants, but also the biogenesis and maturation of rRNAs, tRNAs and the plant translation factors involved. In this eBook we have focused on how internal cues and external signals of either biotic or abiotic origin impact translation to adjust plant growth and development. We have collected altogether ten scientific contributions to extend the knowledge on plant post-transcriptional and translational events that regulate the production of proteins that execute the required cellular functions. We hope that this compilation of original research articles and reviews will provide the readers with a detailed update on the state of knowledge in this field, and also with additional motivation to improve plant growth adaptation to future environmental challenges.

The Role of Aire, microRNAs and Cell-Cell Interactions on Thymic Architecture and Induction of Tolerance

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889197705 Year: Pages: 107 DOI: 10.3389/978-2-88919-770-5 Language: English
Publisher: Frontiers Media SA
Subject: Allergy and Immunology --- Medicine (General)
Added to DOAB on : 2016-04-07 11:22:02
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The focus of this eBook is to bring new insights into central immune tolerance. To fulfill that, much has been discussed about the master in the regulation of tolerance, the autoimmune regulator (Aire) gene the main thymus cell type that expresses this gene, the medullary thymic epithelial cells (mTECs). It includes one Editorial and 12 other excellent contributions in the format of mini reviews or original research papers covering one or more of these aspects: promiscuous gene expression (PGE), epigenetics, miRNAs, association of the Aire gene and miRNAs, thymocyte–TEC interaction, coxsackievirus and type 1 diabetes, exosomes in the thymus, thymic crosstalk, thymic B cells, T cell development, chemokines and migration of T cells, miRNAs and the thymic atrophy, cell–cell interactions, and thymus ontogeny. Authors raised hypothesis, discuss concepts, and show open questions. The remaining important issues to resolve questions within the central tolerance research are briefly discussed below.

Modulating Prokaryotic Lifestyle by DNA-Binding Proteins

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889451050 Year: Pages: 296 DOI: 10.3389/978-2-88945-105-0 Language: English
Publisher: Frontiers Media SA
Subject: Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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The Overview of the Topic was the following: “One of the most active areas of research in molecular microbiology has been the study of how bacteria modulate their genetic activity and its consequences. The prokaryotic world has received much interest not only because the resulting phenomena are important to cells, but also because many of the effects often can be readily measured. Contributing to the interest of the present topic is the fact that modulation of gene activity involves the sensing of intra- and inter-cellular conditions, DNA binding and DNA dynamics, and interaction with the replication/transcription machinery of the cell. All of these processes are fundamental to the operation of a genetic entity and condition their lifestyle. Further, the discoveries achieved in the bacterial world have been of ample use in eukaryotes. In addition to the fundamental interest of understanding modulation of prokaryotic lifestyle by DNA-binding proteins, there is an added interest from the healthcare point of view. As it is well known the antibiotic-resistance strains of pathogenic bacteria are a major world problem, so that there is an urgent need of innovative technologies to tackle it. Most of the acquired resistances are spread by processes of horizontal gene transfer mediated by mobile elements in which DNA replication and gene expression are of basic interest. There is an imperative of finding new alternatives to the ‘classical’ way of treatment of bacterial infections and these new alternatives include the discovery of new drugs and of new bacterial targets. Nevertheless, these new alternatives will find a dead-end if we are unable to obtain a better understanding of the basic processes modulating bacterial gene expression. Our goal to achieve with this Topic of Frontiers is to accelerate our understanding of protein-DNA interactions. First, the topic will bring together several very active researchers in the study of gene replication, gene regulation, the strategies applied by the different proteins that participate in these processes, and their consequences. We will also acquire an in-depth knowledge of some of the mechanisms of gene regulation, gene transfer and gene replication. Further, the readers of the papers will realize the importance of the topic and will learn the most recent thinking, results, and approaches in the area”. We are fully confident that we have exceeded our expectations. Now we are proud to present the final output of the Topic, which is the eBook. It includes 24 articles contributed by 118 authors. As of today, Monday, 16th, January 2017, the total number of readings has reached 19,284, 14,921 article views, and 2,944 article downloads.

Parasites in the Tropic - A New Paradigm Shift

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889452088 Year: Pages: 84 DOI: 10.3389/978-2-88945-208-8 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General) --- Allergy and Immunology --- Medicine (General)
Added to DOAB on : 2017-10-13 14:57:01
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The highlight of this eBook is to bring new insights into parasites in the tropic. To achieve that, much has been discussed about risk assessment, infection rates, disease burden, hormones and mechanism of immune response, genetic expression and susceptibility as well as, therapeutic modalities. Authors raised hypothesis, discuss concepts, and show open questions. The remaining important issues to resolve questions within parasites in the tropic – a new paradigm shift are briefly discussed below. T. gondii, feline as the definitive host, is regarded as one of the most important parasites in the tropic. Human, as an accidental host, is the only species who still drinks raw milk or milk products particularly from animal sources. Based on the first paper, the author simplifies on how safe to drink milk to prevent the transmission of T. gondii by the insistence on heat treated milk before consumption. It is interesting to explore how hormone plays its role in Toxoplasma infection. Based on the second paper, the authors elucidated from thirty studies from humans, animals and cell cultures. Of these, it was shown that Toxoplasma infection was controlled by the presence of hormones found in different animal models. However, it is still premature to conclude which hormone that has a significant relationship with Toxoplasma infection. It estimates that one-third of the world population infected with T. gondii but the majority are asymptomatic. Based on the third paper, it demonstrated that people having low prevalent of Toxoplasma infection by having close contact with animals. This study will enhance positive attitudes for more people to be committed towards helping animals. For more than three decades, T. gondii has since been identified as one of the most important opportunistic parasitic pathogens in immunocompromised. Seroprevalence of chronic toxoplasmosis was detected in at least one-third of HIV-infected individuals in the regional hospital of southern Thailand, as reported from the fourth paper. Thailand has successfully formulated anti-retroviral therapy for HIV/AIDS patients and as a result reported a rare incidence of AIDS-related cerebral toxoplasmosis (CT) in this setting. Based on the fifth paper, the authors demonstrated low IL-10 (Th2 response) and IFN-γ (Th1 response) as well as high TNF-α were produced in ocular and cerebral toxoplasmosis in AIDS patients. This might be due to South American strains and/or the genetic susceptibility of the host.Due to high genetic diversity of T. gondii in Brazil, the sixth paper demonstrated that Calomys callosus survived chronically infected by T. gondii clonal type II strain and reinfected by Brazilian strains. However, congenital toxoplasmosis occurred leading to damaging effects of the developing fetus. The seventh paper conducted a questionnaire-based study on knowledge and practice on Toxoplasma infection among pregnant women from Malaysia, Philippines and Thailand. It clearly demonstrated that health education, a core value, is the cheapest and the best option to envisage the preventive strategies of feto-maternal toxoplasmosis from this region. For treatment modality of congenital toxoplasmosis, a novel experimental therapeutic synergism of diclazuril plus atovaquone combination shows a promising outcome with no toxicity in treating this condition, as demonstrated in the eighth paper. However, it warrants for future trials to prove its properties against T. gondii in different clinical scenarios of human toxoplasmosis for more effective therapeutic regimens. In the ninth paper, the author discussed the pathogenesis of maternal and congenital toxoplasmosis, the current treatment in clinical practice, and the experimental treatment approaches for promising future trials. Overall, this protozoan represents the most extraordinary example of parasite in the tropic and beyond scientific imagination. Hence, there are still many challenges ahead and waiting for more explorations on T. gondii, the parasite that never dies. Based on the findings from the tenth paper, it is interesting to identify common gene targets between Glossina p. gambiensis and Glossina m. morsitans that might shed some lights as a suitable candidate for controlling both acute and chronic forms of sleeping sickness. This therefore requires further investigations using proteomic analysis to ascertain the corresponding genes and its proteins as well as functional role that may help the search for more novel therapeutic agents.

Astrocytic-neuronal-astrocytic Pathway Selection for Formation and Degradation of Glutamate/GABA

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889192434 Year: Pages: 168 DOI: 10.3389/978-2-88919-243-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Biology --- Medicine (General) --- Internal medicine
Added to DOAB on : 2015-11-16 15:44:59
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Endocrinological research early recognized the importance of intercellular interactions and realized the importance of glutamatergic and GABAergic signaling. In turn this signalling depends on elaborate interactions between astrocytes and neurons, without which neurons would be unable to produce, reuse and metabolize transmitter glutamate and GABA. Details of these subjects are described in this Research Topic by key investigators in this field. It focuses on the intricate and extremely swift pathway producing these amino acid transmitters from glucose in brain but also discusses difficulties in determining expression of some of the necessary genes in astrocytes and related processes in pancreatic islets. However, it does not discuss how closely associated astrocytes and neurons are anatomically, enabling these interactions. This is elegantly shown in this cover image, kindly provided by Professor Andreas Reichenbach (University of Leipzig, Germany).

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