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Dissertation
Data-driven Inference of a TF-regulated Metabolic Network for photosynthetic organism modelling: Chlamydomonas Reinhardtii.
Authors: --- --- --- ---
Year: 2018 Publisher: Liège Université de Liège (ULiège)

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Abstract

Metabolic pathways involved in photosynthesis and biosynthesis of lipids, hydrogen or growth are typically regulated by complex interdependent mechanisms involving multiple fronts of omics (genomics, transcriptomics, proteomics, …). Here, we apply Constraint-Based Modelling (CBM) techniques on a genome-scale metabolic network reconstruction of C. reinhardtii, and improve the model by integrating constraints from a Transcriptional Regulation Network, thus taking into account cell gene expression shifts under envrionmental changes.


Dissertation
Thesis, COLLÉGIALITÉ
Authors: --- --- --- ---
Year: 2022 Publisher: Liège Université de Liège (ULiège)

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Abstract

Eosinophils are polymorphonuclear leukocytes mainly known for their role in protection against helminthic parasites. Beyond this immune function, eosinophils have been attributed diverse roles in health and disease. On the one hand, eosinophils contribute to immune and metabolic homeostasis and participate in tissue morphogenesis and regeneration. On the other hand, eosinophils are associated with tissue lesions in a variety of human diseases such as eosinophilic asthma, in which they are thought to play a pathogenic role. Indeed, the severity of eosinophilic asthma is positively correlated with the number of blood and tissue-infiltrating eosinophils, and biological therapies that eliminate or control the number of eosinophils improve control over exacerbations of severe forms of the disease. Nonetheless, mere counting of eosinophils is not a perfect predictor of the response of individual patients to anti-eosinophil targeted therapies. This led clinicians to posit that yet-to-identify factors may determine whether eosinophils are “good”, “bad” or “bystander” cells in asthma. Indeed, eosinophils are more labile than their classical vision as terminally differentiated effector cells posits. Eosinophils are able to adapt to their tissue microenvironment, which calls in the notion of plasticity.&#13;In this work, we address the question of whether and how the alarmin interleukin (IL)-33, a pro-inflammatory cytokine of the IL-1 family and major activator of eosinophils, could participate in the plasticity of eosinophils. Indeed, it has been shown that IL-33 induces a plastic response in macrophages, in which it first elicits a pro-inflammatory gene expression program and later reprograms macrophages into pro-resolving and pro-remodeling cells. Therefore, we studied the short- and long-term transcriptomic response of human blood eosinophils to IL-33 ex vivo. The results showed that IL-33 induced a short term, NF-κB-controlled pro-inflammatory program in eosinophils but no detectable long-term transcriptomic response. Thus, our results suggest that IL-33 signaling does not elicit a long-term plastic response in eosinophils.


Book
The Tumor Microenvironment of High Grade Serous Ovarian Cancer
Authors: --- --- ---
ISBN: 3038975559 3038975540 Year: 2019 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

The Special Issue on high grade serous ovarian cancer (HGSOC) and the contribution of the tumor microenviroment (TME) consists of reviews contributed by leaders in the OC field. As HGSOC metastases have a highly complex TME, there is an urgent need to better understand the TME in general, its distinct components in particular, and the role of the TME in the context of disease recurrence and development of chemoresistance. The Special Issue incorporates the current understanding of the different parts of thd TME components, including the cancer cells themselves, the cells surrounding the cancer cells or stromal cells, and the cells of the immune system, which are attracted to the site of metastases. In addition to these cells of the TME, the role of various cellular factors made by the cells of the TME are also the subject of the reviews. In addition, reviews in this Special Issue cover the complex relationships between the molecular mechanisms of HGSOC progression, including genomic, epigenomic and transcriptomic changes and changes in the immune cell landscape, as these may provide attractive new molecular targets for HGSOC therapy.


Book
Forest-Tree Gene Regulation in Response to Abiotic and Biotic Stress
Authors: ---
ISBN: 3036559485 3036559477 Year: 2022 Publisher: Basel MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

The forest ecosystem is the largest terrestrial ecosystem on earth. It not only has the highest biological productivity and the strongest ecological effect, but can also maintain carbon and oxygen balance and control temperature rise. With the rapid development of the economy, climate change has become the largest challenge to the continuation of forest ecosystem. With constantly changing climate, environmental conditions including CO2 concentration,temperature,intensity of rainfall and the probability of extreme weathers are all affected. In particular, extreme heat, extreme drought and intense fall will become more frequent and widespread. Climate change has a great impact on all ecosystems, especially forest ecosystems. As the largest carbon pool on the earth, these area play a very important role in mitigating global climate change. It is necessary to understand what changes have taken place in the growth and development of trees under climate change, the changes that have taken place in the regulation mechanism of trees when multiple stresses occur at the same time, and to determine the regulation mechanism of trees under new stresses? This book presents relevant results from scientific research in the fields of forest tree gene regulation in response to abiotic and biotic stresses that can contribute to the understanding of forest response mechanisms to different environmental signals and provide a new insight for tolerant tree improvement.


Book
Advances in the Treatment of Renal Cell Carcinoma
Authors: ---
Year: 2022 Publisher: Basel MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

This Special Issue of Cancers focuses on new advances in the treatment of renal cell carcinoma, both surgical and pharmacological (and combinations of these), and novel approaches to tackle treatment resistance and improve our understanding of this phenomenon.


Book
Advances in the Molecular Mechanisms of Abscisic Acid and Gibberellins Functions in Plants
Author:
Year: 2021 Publisher: Basel, Switzerland MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

Gibberellins (GAs) and abscisic acid (ABA) are two phytohormones that antagonistically regulate plant growth, as well as several developmental processes from seed maturation and germination to flowering time, through hypocotyl elongation and root growth. In general, ABA and GAs inhibit and promote cell elongation and growth, respectively. Consequently, this mutual antagonism between GAs and ABA governs many developmental decisions in plants. In addition to its role as a growth and development modulator, ABA is primarily known for being a major player in the response and adaptation of plants to diverse abiotic stress conditions, including cold, heat, drought, salinity and flooding. Remarkably, different works have also recently pointed to a function for GAs in the control of some biological processes in response to stress. The selection of research and review papers of this book, mostly focused on ABA, covers a wide range of topics related to the most recent advances in the molecular mechanisms of ABA and GA functions in plants.


Book
Genetics of Biodegradation and Bioremediation
Authors: ---
Year: 2020 Publisher: Basel, Switzerland MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

Many biodegradation pathways, both aerobic and anaerobic, have already been characterised, and the phylogenetic relationships among catabolic genes within them have been studied. However, new biodegradation activities and their coding genes are continuously being reported, including those involved in the catabolism of emerging contaminants and those generally regarded as non-biodegradable. Gene regulation is also an important issue for the efficient biodegradation of contaminants. Specific induction by the substrate and over-imposed global regulatory networks adjust the expression of the biodegradation genes to meet bacterial physiological needs. New biodegradation pathways can be assembled in a particular strain or in a bacterial consortium by recruiting biodegradation genes from different origins through horizontal gene transfer. The abundance and diversity of biodegradation genes, analysed by either genomic or metagenomic approaches, constitute valuable indicators of the biodegradation potential of a particular environmental niche. This knowledge paves the way to systems metabolic engineering approaches to valorise biowaste for the production of value-added products.

Keywords

Research & information: general --- Biology, life sciences --- tetralin --- Sphingopyxis granuli strain TFA --- Rhodococcus sp. strain TFB --- redox proteins --- carbon catabolite repression --- plastics --- biodegradation --- sustainability --- upcycling --- biotransformations --- polyethylene terephthalate --- terephthalate --- ethylene glycol --- biphenyl --- bph gene --- integrative conjugative element --- genome sequence --- LysR --- transcription factor --- Acinetobacter --- LTTR --- benzoate --- muconate --- synergism --- biosensor --- naphthalene --- toluene --- hydrocarbons --- plant growth promotion --- bioremediation --- Pseudomonas --- soil pollution --- phytoremediation --- rhizoremediation --- diesel --- bacteria --- consortium --- metagenomics --- PAHs --- TPH --- regulation --- anaerobic --- Azoarcus --- promoter architecture --- bioethanol --- furfural --- ALE --- AraC --- sterols --- bile acids --- steroid hormones --- 9,10-seco pathway --- 4,5-seco pathway --- 2,3-seco pathway --- xenobiotics --- Carbaryl --- horizontal gene transfer --- mobile genetic elements --- transposons --- integrative conjugative elements --- pathway assembly --- evolution --- Sphingopyxis lindanitolerans --- pesticide --- complete genome sequence --- pangenome --- γ-HCH degradation --- lin genes --- testosterone --- steroid --- catabolism --- transcriptomic --- valorisation --- catabolic pathway --- mobile DNA --- anaerobic biodegradation --- gene regulation --- tetralin --- Sphingopyxis granuli strain TFA --- Rhodococcus sp. strain TFB --- redox proteins --- carbon catabolite repression --- plastics --- biodegradation --- sustainability --- upcycling --- biotransformations --- polyethylene terephthalate --- terephthalate --- ethylene glycol --- biphenyl --- bph gene --- integrative conjugative element --- genome sequence --- LysR --- transcription factor --- Acinetobacter --- LTTR --- benzoate --- muconate --- synergism --- biosensor --- naphthalene --- toluene --- hydrocarbons --- plant growth promotion --- bioremediation --- Pseudomonas --- soil pollution --- phytoremediation --- rhizoremediation --- diesel --- bacteria --- consortium --- metagenomics --- PAHs --- TPH --- regulation --- anaerobic --- Azoarcus --- promoter architecture --- bioethanol --- furfural --- ALE --- AraC --- sterols --- bile acids --- steroid hormones --- 9,10-seco pathway --- 4,5-seco pathway --- 2,3-seco pathway --- xenobiotics --- Carbaryl --- horizontal gene transfer --- mobile genetic elements --- transposons --- integrative conjugative elements --- pathway assembly --- evolution --- Sphingopyxis lindanitolerans --- pesticide --- complete genome sequence --- pangenome --- γ-HCH degradation --- lin genes --- testosterone --- steroid --- catabolism --- transcriptomic --- valorisation --- catabolic pathway --- mobile DNA --- anaerobic biodegradation --- gene regulation


Book
Advances in the Molecular Mechanisms of Abscisic Acid and Gibberellins Functions in Plants
Author:
Year: 2021 Publisher: Basel, Switzerland MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

Gibberellins (GAs) and abscisic acid (ABA) are two phytohormones that antagonistically regulate plant growth, as well as several developmental processes from seed maturation and germination to flowering time, through hypocotyl elongation and root growth. In general, ABA and GAs inhibit and promote cell elongation and growth, respectively. Consequently, this mutual antagonism between GAs and ABA governs many developmental decisions in plants. In addition to its role as a growth and development modulator, ABA is primarily known for being a major player in the response and adaptation of plants to diverse abiotic stress conditions, including cold, heat, drought, salinity and flooding. Remarkably, different works have also recently pointed to a function for GAs in the control of some biological processes in response to stress. The selection of research and review papers of this book, mostly focused on ABA, covers a wide range of topics related to the most recent advances in the molecular mechanisms of ABA and GA functions in plants.

Keywords

Research & information: general --- Biology, life sciences --- particle film technology --- xanthophylls --- VAZ cycle --- drought --- Vitis vinifera L. --- abscisic acid --- ABA --- ethylene --- pathogens --- plant immunity --- PYR1 --- salicylic acid --- Arabidopsis thaliana --- cell expansion --- gibberellins --- hypocotyl growth --- transcriptomic analysis --- plant hormones --- plant size --- receptor-like cytoplasmic kinase --- skotomorphogenesis --- Mediator complex --- transcription --- ABA signaling --- abiotic stress response --- grapevine --- stomata --- metabolism --- carbohydrates --- salinity --- chromatin remodeling --- guard cell --- osmotic stress --- protein phosphatase 2C --- stress memory --- transgenerational inheritance --- abscisic acid (ABA) --- flowering time --- Arabidopsis --- drought escape --- bZIP --- GIGANTEA --- CONSTANS --- FLOWERING LOCUS T --- FD --- citrus --- fruit maturation --- hormonal interplay --- sugars --- particle film technology --- xanthophylls --- VAZ cycle --- drought --- Vitis vinifera L. --- abscisic acid --- ABA --- ethylene --- pathogens --- plant immunity --- PYR1 --- salicylic acid --- Arabidopsis thaliana --- cell expansion --- gibberellins --- hypocotyl growth --- transcriptomic analysis --- plant hormones --- plant size --- receptor-like cytoplasmic kinase --- skotomorphogenesis --- Mediator complex --- transcription --- ABA signaling --- abiotic stress response --- grapevine --- stomata --- metabolism --- carbohydrates --- salinity --- chromatin remodeling --- guard cell --- osmotic stress --- protein phosphatase 2C --- stress memory --- transgenerational inheritance --- abscisic acid (ABA) --- flowering time --- Arabidopsis --- drought escape --- bZIP --- GIGANTEA --- CONSTANS --- FLOWERING LOCUS T --- FD --- citrus --- fruit maturation --- hormonal interplay --- sugars


Book
Advances in the Treatment of Renal Cell Carcinoma
Authors: ---
Year: 2022 Publisher: Basel MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

This Special Issue of Cancers focuses on new advances in the treatment of renal cell carcinoma, both surgical and pharmacological (and combinations of these), and novel approaches to tackle treatment resistance and improve our understanding of this phenomenon.

Keywords

Medicine --- renal cell carcinoma --- autophagy --- hydroxychloroquine --- chloroquine --- ROC-325 --- cysteine cathepsins --- cysteine cathepsin inhibitors --- lysosome --- renal cancer --- metastatic renal cell carcinoma --- immune-based combination therapies --- network meta-analysis --- PD-L1 --- predictive --- biomarker --- treatment --- TKIs --- mRCC --- biomarkers --- soluble factors --- immunotherapy --- renal cell carcinoma (RCC) --- sunitib resistance --- artesunate (ART) --- Traditional Chinese Medicine (TCM) --- growth inhibition --- ferroptosis --- reactive oxygen species (ROS) --- clear cell renal cell carcinoma --- ccRCC --- RCC --- kidney cancer --- evolution --- evolutionary trajectory --- metastatic --- second line therapy --- renal cell cancer --- immune checkpoint inhibitors --- tyrosine kinase inhibitors --- individualization --- genomic signature --- transcriptomic analysis --- renal cell carcinoma --- autophagy --- hydroxychloroquine --- chloroquine --- ROC-325 --- cysteine cathepsins --- cysteine cathepsin inhibitors --- lysosome --- renal cancer --- metastatic renal cell carcinoma --- immune-based combination therapies --- network meta-analysis --- PD-L1 --- predictive --- biomarker --- treatment --- TKIs --- mRCC --- biomarkers --- soluble factors --- immunotherapy --- renal cell carcinoma (RCC) --- sunitib resistance --- artesunate (ART) --- Traditional Chinese Medicine (TCM) --- growth inhibition --- ferroptosis --- reactive oxygen species (ROS) --- clear cell renal cell carcinoma --- ccRCC --- RCC --- kidney cancer --- evolution --- evolutionary trajectory --- metastatic --- second line therapy --- renal cell cancer --- immune checkpoint inhibitors --- tyrosine kinase inhibitors --- individualization --- genomic signature --- transcriptomic analysis


Book
Carotenoids and Human Health
Author:
ISBN: 3039218336 3039218328 Year: 2019 Publisher: MDPI - Multidisciplinary Digital Publishing Institute

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Abstract

Carotenoids are a group of approximately 600 compounds synthesized by photosynthetic organisms. These pigments are abundant in fruits and vegetables, as well as in certain animal products such as eggs and salmon, being responsible for their colorful appearance. The bioactive properties of certain carotenoids in human health are clear, as some of these compounds have antioxidant properties and serve as the only precursors of vitamin A in nature. The aim of this Special Issue entitled “Carotenoids and Human Health” is to provide the scientific community with an updated perspective of this exciting and growing research area. We compiled 19 papers from some of the most prominent scientists in the carotenoid field, including seven literature reviews and 12 original publication, covering topics such as cancer, obesity, vision, cognitive function, and skin health.

Keywords

membrane transporters --- RAR --- browning --- astaxanthin --- Vitamin A --- case-control study --- ?-carotene --- transcriptomic analysis --- new-born --- carotenes --- cancer-related cognitive impairment --- androgen --- beta-carotene --- eicosapentanoic acid --- mango by-products --- mangiferin --- cell culture --- chronic disease --- Akkermansia --- animal --- intestine --- carotenoids --- alcoholic fatty liver disease --- Phaeodactylum tricornutum --- carotenoid --- tomato --- colourless carotenoids --- preterm mothers --- inflammation --- ?-Cryptoxanthin --- adipocytes --- vitamin A --- gastric cancer --- food ingredients --- brain --- gut microbiota --- zeaxanthin --- nutricosmetics --- brown adipose tissue --- bioactive compounds --- breastfeeding --- aging --- oxidative stress --- retinoids --- phytofluene --- glaucoma --- H. pylori --- retinoid --- tomato extract --- retinol --- ?-cryptoxanthin --- microalgae --- fucoxanthin --- obesity --- macular pigment --- carotene --- photoprotection --- adipose tissue --- lutein --- metabolic syndrome --- Caenorhabditis elegans --- functional foods --- beta-cryptoxanthin --- retinoic acid --- nutrition --- lycopene --- bioavailability --- nutraceuticals --- adipocyte --- ?-tocopherol --- phytoene --- memory --- cosmeceuticals --- antioxidants --- mature milk --- RXR --- fat reduction --- xanthophylls --- colostrum --- smoking --- overweight --- provitamin A --- public health --- Korea --- ?-carotene oxygenase 1 --- cognition --- full-term mothers --- hippocampus --- alpha-carotene --- prostate cancer --- hypertension

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