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Crop plants are continuously under attack by pathogens, both during pre and post-harvest stages, often causing economically important food losses. Chemical treatments can pose a serious treat to human health and the environment. Furthermore, there is an increasing market, especially in OECD countries for organic produce, for which most pesticides and inorganic fertilisers are unacceptable. There is therefore a pressing need to develop more effective, sustainable and environmentally friendly tools for disease control. The use of beneficial microorganisms for the control of plant pathogens is very attractive, and the availability of novel molecular techniques and a plethora of genomic information open unexplored avenues for plant protection approaches. Genome-enabled integration of research became a major strategy in the era of the 2000’s (the post-genomic era) and set the basis for a different way to understand interactions in plant-pathogen-beneficial microorganisms systems. In recent decades we have moved from the sequencing of single genomes, to the comparison of different genomes, their expression (from single organism to communities) and, more recently, we can apply novel techniques to edit a genome in a precise manner. Together with the complete sequencing of plant genomes, the genome sequences of plant pathogens as well as that of some beneficial organisms (bacteria, fungi, viruses), and the furnished information on their virulence, gave support to relatively new strategies such as transcriptome, proteome, metabolome and secretome analysis. Analyses of avirulence and resistance genes, their products and the cross-talking mechanisms, as well as proteins and metabolites – at an “omics” level – in highly performing beneficial microorganisms/pathogens interactions, represents a major contribution to plant protection, providing information at an unprecedented level of resolution. While single genomes are explored to infer the range of biological activities accomplished by a single organism or species, and comparative genomics allows evaluating the diversity and evolution of biochemical pathways adopted by individual species to perform a common function, information is being obtained about processes carried out by a diverse set of organisms interacting with each other. Environmental genomics, popularized by the metagenome concept, can generate billions of DNA sequences from a given environment furnishing a comparative assessment of a community in situ. Metagenomics (sequence-based approaches applied across genomes in an environment) provides information about functional capabilities and responses of organism (plant, pathogen and beneficial agent) assemblages in different niches, giving a different perspective in the management of plant diseases at a multitrophic level. Advances in functional genomics and genome editing approaches have recently provided new tools to manage the plant-pathogen-beneficial microorganism system, for preventing or controlling disease. The use of RNA-based technologies is extremely appealing, and these include artificial micro-RNA and transacting small interfering RNA, which are currently being used for generating plant virus-resistant plants, thus fostering plant virus control researches. Finally, targeted genome editing strategies – exemplified by, but not limited to, the CRISPR-Cas technique – are among the most modern ways for inducing targeted deletions, insertions and precise changes in the genome of host plants or pathogens, as well as in the genomes of beneficial microorganisms. The aim of the present Research Topic is to give an exhaustive and up to date overview of examples of genomic techniques (genome sequencing, genome comparison, transcriptomics, metagenomics, RNA based technologies and genome editing strategies) applied to plants, pathogens or beneficial microorganisms to promote the exploitation of these modern tools as a new frontier in plant disease management.

disease management --- NGS - next generation sequencing --- food security --- food safety --- post-genomic era

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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.

ovarian cancer --- transcriptomic --- stroma --- immune cells --- epigenetics --- recurrence --- immunotherapies --- chemoresistance --- fibroblasts --- metastasis --- genomic --- tumor microenvironment --- cancer stem cells

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Early in the 80’s date the first observations on the existence of hormonal steroids that may be synthesized and act in the nervous system. In order to refer to these endogenous steroids, proved important to control both central and peripheral nervous system, it was proposed the term “neurosteroids” (NSs). Over the years, their importance in regulating the physiological functions of neuronal and glial cells increased progressively. These steroids can be involved in several pathophysiological conditions such as depression, anxiety, premenstrual syndrome (PMS), schizophrenia and Alzheimer disease. Among the different classes of NSs, the progestagens revealed particularly important. The progesterone metabolite 5α-pregnan-3α-ol-20-one, also named tetrahydroprogesterone or allopregnanolone (ALLO) was one of the first most important steroid that was originally shown to act as neurosteroid. ALLO is synthesized through the action of the 5αR-3α-HSD, which converts P into DHP and subsequently, via a bidirectional reaction, into ALLO. NSs exert complex effects in the nervous system through ‘classic’, genomic, and ‘non-classic’, non-genomic actions. ALLO displays a rapid ‘non-genomic’ effect, which mainly involves the potent modulation of the GABA type A (GABA-A) receptor function. Recently a membrane receptor has been identified as target for ALLO effects, i.e. the membrane progesterone receptors (mPRs) that are able to activate a signalling cascade through G protein dependent mechanisms. By these ways, ALLO is able to modulate several cell functions, acting as neurogenic molecule on neural progenitor cells, as well as by activating proliferation and differentiation of glial cells in the central and peripheral nervous system. In this topic, we review the most recent acquisitions in the field of neurosteroids, focusing our attention on ALLO because its effects on the physiology of neurons and glial cells of the central and peripheral nervous system are intriguing and could potentially lead to the development of new strategies for neuroprotection and/or regeneration of injured nervous tissues and for the treatment of neuropsychiatric disorders.

Biochemistry --- Chemistry --- Physical Sciences & Mathematics --- ganaxolone --- Non genomic action --- neurodegenerative disease --- Pain --- GABA A receptor --- Membrane progesterone receptor --- Tetrahydroprogesterone --- PKC epsilon --- neurosteroid --- neuropsychiatric disorder

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The importance of understanding metal–microbe interactions underlies a number of social–economic issues in the world. The antimicrobial resistance era has created a need for novel antimicrobials and within this fieldm metal and metalloid ions are promising solutions. Pollution sites, either co-contaminated with metals or with metals as the sole pollutant, contain microbes that are present as key participants, with both of these issues habing links to agriculture. Microbes also play key roles in the global geochemical cycle of many elements. Such statements solidify the need to understand metal–microbe interactions. Given that genomics has arguably become the most useful tool in biology, the application of this technology within the field of understanding metal resistance comes as no surprise. Whilst by no means comprehensive, this book provides examples of the applications of genomic approaches in the study of metal–microbe interactions. Here, we present a collection of manuscripts that highlights some present directions in the field. The book starts with a collection of three papers evaluating aspects of the genomics of the archetype metal resistant bacteria, Cuprividus metallidurans. This is followed by four studies that evaluate the mechanisms of metal resistance. The next two papers assess metal resistance in agricultural related situations, including a review on metal resistance in Listeria. The book concludes with a review on metal phytoremediation via Rhizobia and two subsequent studies of metal biotechnology relevance.

silver --- silver toxicity --- silver resistance --- Keio collection --- Escherichia coli --- antimicrobials --- Acidithiobacillus ferrooxidans --- copper resistance --- biomining --- envelope components --- proteomics --- lipopolysaccharide --- genomic island --- integrase --- Acinetobacter baumannii --- mobile genetic element --- Ensifer (Sinorhizobium) sp. M14 --- arsenic-oxidizing bacteria --- heavy metal resistance --- draft genome sequence --- comparative genomic analysis --- biosafety --- biotechnology for arsenic removal --- adsorption --- water treatment --- in situ (bio)remediation --- copper --- resistance --- swine --- phenotype microarray --- mobile genetic elements --- Cupriavidus --- metal --- soil bioremediation --- heavy-metals --- serpentine soils --- serpentine vegetation --- genome manipulation --- cis-hybrid strains --- heavy metals --- genomic islands --- genomic rearrangements --- metal resistance genes --- Mucilaginibacer rubeus --- Mucilaginibacter kameinonensis --- evolution --- CTnDOT --- Listeria monocytogenes --- cadmium --- arsenic --- gallium --- antimicrobial agents --- metal toxicity --- metal resistance --- metal-based antimicrobials --- platinum resistance --- RNA-Seq --- multireplicon --- Nanopore --- adaptive laboratory evolution --- n/a

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Rabbit livestock is especially important in the Mediterranean area and in the semi-arid zones of Africa, Asia, and America, representing a valuable alternative source of good animal protein of high quality (low fat and low cholesterol). However, rabbit husbandry should adapt to be a competitive and sustainable sector. In addition, it must maintain a balance between rabbit welfare, customer demands, and breeder requirements. Then, improvement in breeding systems is needed and may involve avoiding hormones and antibiotics in rabbit management; enhancing the efficiency of reproductive procedures such as artificial insemination systems and freezing of semen and embryos; extending the productive lifespan of does; improving genetic selection systems; and adjusting nutritional systems to optimize the physiological status of animals and the immune response. This Special Issue concerns all these challenges in increasing rabbit productivity and sustainability.

Oryctolagus cuniculus --- SNPs --- SLAF-seq --- genome-wide association study --- growth trait --- myeloperoxidase --- lysozyme --- rabbits --- viral infection --- rabbit hemorrhagic disease --- goji berries --- rabbit --- insulin resistance --- leptin --- non-esterified fatty acids --- pregnancy --- lactation --- body condition score --- principal component analysis --- gene expression --- endometrium --- oviduct --- spermatozoa --- seminal plasma --- inflammation --- angiogenesis --- corpus luteum --- reproduction --- genomic selection --- imputation --- litter size --- genomic simulation --- artificial insemination --- antibiotics --- antibacterial activity --- semen quality --- reproductive performance --- sperm quality --- cryopreservation --- animal model --- assisted reproductive technology --- CTSS --- granulosa cells --- proliferation --- apoptosis --- hormone secretion --- body composition --- fertility --- kits born alive --- rabbit does --- feed intake --- free tri-iodothyronine --- thyroxine --- insulin --- glucose --- corticosterone --- NEFA --- fetus --- placenta