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New Insights into Microbial Ecology through Subtle Nucleotide Variation

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199884 Year: Pages: 133 DOI: 10.3389/978-2-88919-988-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Microbiology
Added to DOAB on : 2016-01-19 14:05:46
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The 16S ribosomal RNA gene commonly serves as a molecular marker for investigating microbial community composition and structure. Vast amounts of 16S rRNA amplicon data generated from environmental samples thanks to the recent advances in sequencing technologies allowed microbial ecologists to explore microbial community dynamics over temporal and spatial scales deeper than ever before. However, widely used methods for the analysis of bacterial communities generally ignore subtle nucleotide variations among high-throughput sequencing reads and often fail to resolve ecologically meaningful differences between closely related organisms in complex microbial datasets. Lack of proper partitioning of the sequencing data into relevant units often masks important ecological patterns. Our research topic contains articles that use oligotyping to demonstrate the importantance of high-resolution analyses of marker gene data, and providides further evidence why microbial ecologists should open the "black box" of OTUs identified through arbitrary sequence similarity thresholds.

Biochar as Soil Amendment: Impact on Soil Properties and Sustainable Resource Management

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ISBN: 9783039282746 9783039282753 Year: Pages: 252 DOI: 10.3390/books978-3-03928-275-3 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Agriculture (General)
Added to DOAB on : 2020-04-07 23:07:09
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The role of biochar in improving soil fertility is increasingly being recognized and is leading to recommendations of biochar amendment of degraded soils. In addition, biochars offer a sustainable tool for managing organic wastes and to produce added-value products. The benefits of biochar use in agriculture and forestry can span enhanced plant productivity, an increase in soil C stocks, and a reduction of nutrient losses from soil and non-CO2 greenhouse gas emissions. Nevertheless, biochar composition and properties and, therefore, its performance as a soil amendment are highly dependent on the feedstock and pyrolysis conditions. In addition, due to its characteristics, such as high porosity, water retention, and adsorption capacity, there are other applications for biochar that still need to be properly tested. Thus, the 16 original articles contained in this book, which were selected and evaluated for this Special Issue, provide a comprehensive overview of the biological, chemicophysical, biochemical, and environmental aspects of the application of biochar as soil amendment. Specifically, they address the applicability of biochar for nursery growth, its effects on the productivity of various food crops under contrasting conditions, biochar capacity for pesticide retention, assessment of greenhouse gas emissions, and soil carbon dynamics. I would like to thank the contributors, reviewers, and the support of the Agronomy editorial staff, whose professionalism and dedication have made this issue possible.

Cyanobacteria and Cyanotoxins: New Advances and Future Challenges

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ISBN: 9783039218387 / 9783039218394 Year: Pages: 246 DOI: 10.3390/books978-3-03921-839-4 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Public Health
Added to DOAB on : 2020-06-09 16:38:57
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Cyanobacteria are a group of ubiquitous photosynthetic prokaryotes. Their occurrence has been increasing worldwide, due to anthropogenic activities and climate change. Several cyanobacterial species are able to synthesize a high number of bioactive molecules, among them, cyanotoxins (microcystins, cylindrospermopsin, nodularin, etc.), which are considered a health concern. For risk assessment of cyanotoxins, more scientific knowledge is required to perform adequate hazard characterization, exposure evaluation and, finally, risk characterization of these toxins. This Special Issue “Cyanobacteria and Cyanotoxins: New Advances and Future Challenges” presents new research or review articles related to different aspects of cyanobacteria and cyanotoxins, and contributes to providing new toxicological data and methods for a more realistic risk assessment.

Keywords

cylindrospermopsin --- in vitro --- cytotoxicity --- oxidative stress --- genotoxicity --- microcystins --- taste-and-odor compounds --- water source --- drinking water treatment plant --- cyanobacterial thresholds --- arctic --- benthic mats --- cyanotoxins --- ELISA --- 16S rRNA gene --- apoptosis --- microcystin-LR (MC-LR) --- reproductive toxicity --- resveratrol --- sirtuin 1 (SIRT1) --- Aphanizomenon flos-aquae --- blue-green algae supplements --- cyanotoxins --- microcystin --- cylindrospermopsin --- saxitoxin --- cylindrospermopsin --- monoclonal antibody --- time-resolved fluoroimmunoassay --- method validation --- detection --- cyanobacteria --- cyanotoxins --- nutrient enrichment --- akinetes --- harmful algal blooms --- PCR --- phylogenetic analyses --- microcystin-LR --- Procambarus clarkii --- energy budget --- astaxanthin --- cylindrospermopsin --- anatoxin-a --- PSP toxins --- microcystins --- cyanobacteria --- Nostocales --- drinking water --- marine cyanobacteria --- cyanotoxins --- marine sponges --- secondary metabolites --- marine natural compounds --- bioassays --- Artemia salina --- Paracentrotus lividus --- hemolytic essay --- reservoir --- Yangtze estuary --- 16S rRNA gene sequencing --- shotgun metagenomic sequencing --- bacterial community --- microbial metabolisms --- [d-Leu1]Microcystin-LR --- Lithobates catesbeianus --- tadpoles --- exposure --- Histopathological evaluation --- microcystins --- cylindrospermopsin --- method validation --- UPLC-MS/MS --- lettuce --- genotoxicity --- mutagenicity --- Cylindrospermopsin --- Microcystin-LR --- mixture

Genome Mining and Marine Microbial Natural Products

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ISBN: 9783039280902 9783039280919 Year: Pages: 202 DOI: 10.3390/books978-3-03928-091-9 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Microbiology --- Biology --- Science (General)
Added to DOAB on : 2020-01-30 16:39:46
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Two review papers, eight research articles, and one brief report were published in this Special Issue. They showed the rich resources that are present within the genomes of marine microorganisms and discussed the use of recently developed tools and technologies to exploit this genetic richness. Examples include the rational supply of precursors according to the relevant biosynthetic pathway and stress driven discovery together with the use of histone deacetylase inhibitors to facilitate the discovery of new bioactive molecules with potential biopharmaceutical applications. We believe that the content of this Special Issue reflects the current state-of-the-art research in this area and highlights the interesting strategies that are being employed to uncover increasing numbers of exciting novel compounds for drug discovery from marine genetic resources.

In-Cell NMR Spectroscopy: Biomolecular Structure and Function

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ISBN: 9783039282548 / 9783039282555 Year: Pages: 152 DOI: 10.3390/books978-3-03928-255-5 Language: eng
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2020-06-09 16:38:57
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This Special Issue examines state-of-the-art in-cell NMR spectroscopy as it relates to biological systems of increasing complexity. The compendia of research and recent innovations from prominent laboratories in the field of solid state and solution in-cell NMR spectroscopy, metabolomics and technology development are presented. The work establishes in-cell NMR spectroscopy as the premier method for determining the structures and interaction capabilities of biological molecules at high resolution within the delicately intricate interior of living cells, and the means of utilizing cells as living laboratories to directly assess the effects of exogenous and endogenous stimuli on cell physiology.]

The Interplay of Microbiome and Immune Response in Health and Diseases

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ISBN: 9783039216468 9783039216475 Year: Pages: 206 DOI: 10.3390/books978-3-03921-647-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Medicine (General) --- Internal medicine
Added to DOAB on : 2019-12-09 11:49:16
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[Increasing evidence suggests that microbiota and especially the gut microbiota (the microbes inhabiting the gut including bacteria, archaea, viruses, and fungi) plays a key role in human physiology and pathology. Recent findings indicate how dysbiosis—an imbalance in the composition and organization of microbial populations—could severely impact the development of different medical conditions (from metabolic to mood disorders), providing new insights into the comprehension of diverse diseases, such as IBD, obesity, asthma, autism, stroke, diabetes, and cancer. Given that microbial cells in the gut outnumber host cells, microbiota influences human physiology both functionally and structurally. Microbial metabolites bridge various—even distant—areas of the organism by way of the immune and hormone system. For instance, it is now clear that the mutual interaction between the gastrointestinal tract and the brain (gut–brain axis), often involves gut microbiota, indicating that the crosstalk between the organism and its microbial residents represents a fundamental aspect of both the establishment and maintenance of healthy conditions. Moreover, it is crucial to recognize that beyond the intestinal tract, microbiota populates other host organs and tissues (e.g., skin and oral mucosa). We have edited this eBook with the aim of publishing manuscripts focusing on the impact of microbiota in the development of different diseases and their associated treatments.]

Keywords

microbiota --- rheumatoid arthritis --- anti-TNF-? --- methotrexate --- etanercept --- disease activity --- microbiome --- health --- precision medicine --- genomics --- bacteriocins --- bacteriophages --- antibiotics --- gastrointestinal diseases --- dysbiosis --- gut barrier --- gut microbiota --- virus --- vaginal microbiota --- HIV --- HPV --- HSV2 --- cytokines --- chemokines --- innate immunity --- adaptive immunity --- microbiota --- autoimmunity --- etiopathogenesis --- Candida albicans --- 2,3-dihydroxy-4-methoxyBenzaldehyde --- melanin --- colitis --- anaerobic bacteria --- aerobic bacteria --- gut microbiota --- gut-liver axis --- chronic liver diseases --- fecal transplantation --- probiotics --- gut microbiota --- immunological niche --- dysbiosis --- cancer --- immune system --- cutaneous immunity --- microbiome --- Staphylococcus spp., T cells --- Staphylococcus aureus --- Staphylococcus epidermis --- commensals --- atopic dermatitis --- intravenous immunoglobulin G --- colitis --- dextran sulfate sodium --- mice --- inflammation --- cytokines --- Candida albicans --- Escherichia coli --- Enterococcus faecalis --- gut microbiota --- chemo free treatment --- lymphoid malignancies --- 16S rRNA gene --- chondroitin sulfate disaccharide --- co-occurrence network --- global network --- microbial interactions --- microbiome --- modularity --- superoxide dismutase --- gut microbiota --- macrophages --- TLR mimicry --- immune epigenetics --- metabolism --- sterile inflammation --- microbiota --- microbiome --- immunotherapy --- adoptive cell transfer (ACT) --- CAR T-cell --- TCR --- TIL --- checkpoint inhibitors --- immuno-oncology --- cancer --- diet --- n/a

Repetitive DNA Sequences

Authors: --- --- ---
ISBN: 9783039283668 9783039283675 Year: Pages: 206 DOI: 10.3390/books978-3-03928-367-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Genetics
Added to DOAB on : 2020-04-07 23:07:08
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Repetitive DNA is ubiquitous in eukaryotic genomes, and, in many species, comprises the bulk of the genome. Repeats include transposable elements that can self-mobilize and disperse around the genome, and tandemly-repeated satellite DNAs that increase in copy number due to replication slippage and unequal crossing over. Despite their abundance, repetitive DNA is often ignored in genomic studies due to technical challenges in their identification, assembly, and quantification. New technologies and methods are now providing the unprecedented power to analyze repetitive DNAs across diverse taxa. Repetitive DNA is of particular interest because it can represent distinct modes of genome evolution. Some repetitive DNA forms essential genome structures, such as telomeres and centromeres, which are required for proper chromosome maintenance and segregation, whereas others form piRNA clusters that regulate transposable elements; thus, these elements are expected to evolve under purifying selection. In contrast, other repeats evolve selfishly and produce genetic conflicts with their host species that drive adaptive evolution of host defense systems. However, the majority of repeats likely accumulate in eukaryotes in the absence of selection due to mechanisms of transposition and unequal crossing over. Even these neutral repeats may indirectly influence genome evolution as they reach high abundance. In this Special Issue, the contributing authors explore these questions from a range of perspectives.

Venom and Toxin as Targeted Therapy

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ISBN: 9783039211890 9783039211906 Year: Pages: 180 DOI: 10.3390/books978-3-03921-190-6 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology
Added to DOAB on : 2019-12-09 11:49:15
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Targeted therapy has developed significantly in the last one and half decades, prescribing specific medications for treatment of particular diseases, such as cancer, diabetes, and heart disease. One of the most exciting recent developments in targeted therapies was the isolation of disease-specific molecules from natural resources, such as animal venoms and plant metabolites/toxins, for use as templates for new drug motif designs. In addition, the study of venom proteins/peptides and toxins naturally targeted mammalian receptors and demonstrated high specificity and selectivity towards defined ion channels of cell membranes. Research has also focsed intensely on receptors. The focus of this Special Issue of Toxins addressed the most recent advances using animal venoms, such as frog secretions, bee/ant venoms and plant/fungi toxins, as medicinal therapy. Recent advances in venom/toxin/immunotoxins for targeted cancer therapy and immunotherapy, along with using novel disease-specific venom-based protein/peptide/toxin and currently available FDA-approved drugs for combinationtreatments will be discussed. Finally, we included an overview of select promising toad/snake venom-based peptides/toxins potentially able to address the forthcoming challenges in this field. Both research and review articles proposing novelties or overviews, respectively, were published in this Special Issue after rigorous evaluation and revision by expert peer reviewers.

Keywords

disintegrin --- blood vessel formation --- VEGF --- antioxidant enzymes --- oxidative stress biomarkers --- bicarinalin --- antimicrobial peptide --- Helicobacter pylori --- gastric cells --- bacterial adhesion --- SEM --- atopic dermatitis (AD) --- house dust mite extract (DFE) --- 2,4-dinitrochlorobenzene (DNCB) --- bee venom phospholipase A2 (bvPLA2) --- skin inflammation --- CD206 --- mannose receptor --- immunotoxin --- Moxetumomab pasudotox --- targeted therapy --- CD22 --- B cell non-Hodgkin lymphoma --- acute lymphoblastic leukemia --- mantle cell lymphoma --- ribosome-inactivating protein --- BLF1 --- eIF4A --- MYCN --- cancer --- neuroblastoma --- apoptosis --- antimicrobial peptide (AMP) --- dermaseptin --- anuran skin secretion --- drug design --- antimicrobial activity --- anticancer activity --- antiviral activity --- Bougainvillea --- bouganin --- cancer therapy --- immunotherapy --- immunotoxins --- ribosome-inactivating proteins --- rRNA N-glycosylase activity --- VB6-845 --- orellanine --- clearance --- fungal toxin --- half-life --- toad toxins --- Chansu --- Huachansu --- cane toad --- bufadienolides --- indolealkylamines --- inflammation --- cancer --- obsessive–compulsive disorder (OCD) --- snake venom --- cancer --- target therapy --- snake venom --- Malaysian cobras --- N. kaouthia --- N. sumatrana --- O. hannah --- anticancer --- Apis mellifera syriaca --- bee venom --- melittin --- LC-ESI-MS --- solid phase extraction --- in vitro effects --- frog --- mass spectrometry --- molecular cloning --- bombesin-related peptide --- smooth muscle --- Bee venom --- complement system --- decay accelerating factor --- atopic dermatitis --- complement dependent cytotoxicity --- membrane attack complex --- n/a

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