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LuxR Solos are Becoming Major Players in Cell-Cell Communication in Bacteria

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199174 Year: Pages: 122 DOI: 10.3389/978-2-88919-917-4 Language: English
Publisher: Frontiers Media SA
Subject: Science (General) --- Biology
Added to DOAB on : 2016-01-19 14:05:46
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The most common quorum sensing (QS) system in Gram-negative bacteria occurs via N-acyl homoserine lactone (AHLs) signals. An archetypical system consists of a LuxI-family protein synthesizing the AHL signal which binds at quorum concentrations to the cognate LuxR-family transcription factors which then control gene expression by binding to specific sequences in target gene promoters. QS LuxR-family proteins are approximately 250 amino acids long and made up of two domains; at the N-terminus there is an autoinducer-binding domain whereas the C-terminus contains a DNA-binding helix-turn-helix (HTH) domain. QS LuxRs display surprisingly low similarities (18-25%) even if they respond to structurally similar AHLs. 95% of LuxRs share 9 highly conserved amino acid residues; six of these are hydrophobic or aromatic and form the cavity of the AHL-binding domain and the remaining three are in the HTH domain. With only very few exceptions, the luxI/R cognate genes of AHL QS systems are located adjacent to each other. The sequencing of many bacterial genomes has revealed that many proteobacteria also possess LuxRs that do not have a cognate LuxI protein associated with them. These LuxRs have been called orphans and more recently solos. LuxR solos are widespread in proteobacterial species that possess a canonical complete AHL QS system as well as in species that do not. In many cases more than one LuxR solo is present in a bacterial genome. Scientists are beginning to investigate these solos. Are solos responding to AHL signals? If present in a bacterium which possesses a canonical AHL QS system are solos an integral part of the regulatory circuit? Are LuxR solos eavesdropping on AHLs produced by neighboring bacteria? Have they evolved to respond to different signals instead of AHLs, and are these signals endogenously produced or exogenously provided? Are they involved in interkingdom signaling by responding to eukaryotic signals? Recent studies have revealed that LuxR solos are involved in several mechanisms of cell-cell communication in bacteria implicating them in bacterial intraspecies and interspecies communication as well as in interkingdom signaling by responding to molecules produced by eukaryotes. LuxR solos are likely to become major players in signaling since they are widespread among proteobacterial genomes and because initial studies highlight their different roles in bacterial communication. This Research Topic allows scientists studying or interested in LuxR solos to report their data and/or express their hypotheses and thoughts on this important and currently understudied family of signaling proteins.

Keywords

AHL --- LuxR solos --- Quorum Sensing --- signaling --- Bacteria

Agrobacterium biology and its application to transgenic plant production

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195749 Year: Pages: 165 DOI: 10.3389/978-2-88919-574-9 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General) --- Botany
Added to DOAB on : 2016-02-05 17:24:33
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The broad host range pathogenic bacterium Agrobacterium tumefaciens has been widely studied as a model system to understand horizontal gene flow, secretion of effector proteins into host cells, and plant-pathogen interactions. Agrobacterium-mediated plant transformation also is the major method for generating transgenic plants for research and biotechnology purposes. Agrobacterium species have the natural ability to conduct interkingdom genetic transfer from bacteria to eukaryotes, including most plant species, yeast, fungi, and even animal cells. In nature, A. tumefaciens causes crown gall disease resulting from expression in plants of auxin and cytokinin biosynthesis genes encoded by the transferred (T-) DNA. Gene transfer from A. tumefaciens to host cells requires virulence (vir) genes that reside on the resident tumor-inducing (Ti) plasmid. In addition to T-DNA, several Virulence (Vir) effector proteins are also translocated to host cells through a bacterial type IV secretion system. These proteins aid in T-DNA trafficking through the host cell cytoplasm, nuclear targeting, and T-DNA integration. Genes within native T-DNAs can be replaced by any gene of interest, making Agrobacterium species important tools for plant research and genetic engineering. In this research topic, we provided updated information on several important areas of Agrobacterium biology and its use for biotechnology purposes.

The oral microbiome in an ecological perspective

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889195763 Year: Pages: 116 DOI: 10.3389/978-2-88919-576-3 Language: English
Publisher: Frontiers Media SA
Subject: Internal medicine --- Science (General)
Added to DOAB on : 2016-02-05 17:24:33
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The oral cavity harbors an immense diversity of microorganisms, including bacteria, fungi, archaea, protozoa and viruses. At health, oral microbial community is thought to be in a state of homeostasis, even after numerous perturbations (e.g., toothbrushing, food intake) a day. The breach in this homeostasis can occur for instance if the perturbations become too excessive (e.g., frequent carbohydrate intake leading to acidification of the community) or the host is compromised (e.g., inadequate immune response resulting in persistent inflammation of periodontal tissue). Aggressive antimicrobial therapy (e.g., antibiotics in case of periodontal disease or preventive antibiotic therapy before and after dental extractions) is commonly applied with all the negative consequences of this approach. So far little is known on the interplay between the environmental, host and microbial factors in maintaining an ecological balance. What are the prerequisites for a healthy oral ecosystem? Can we restore an unbalanced oral microbiome? How stable is the oral microbiome through time and how robust it is to external perturbations? Gaining new insights in the ecological factors sustaining oral health will lead to conceptually new therapies and preventive programs. Recent advances in high throughput technologies have brought microbiology as a science to a new era, allowing an open-ended approach instead of focusing on few opportunistic pathogens. With this topic we would like to integrate the current high-throughput ‘omics’ tools such as metagenomics, metatranscriptomics, metaproteomics or metabolomics with biochemical, physiological, genetic or clinical parameters within the oral microbial ecosystem. We aim to address questions underlying the regulation of the ecological balance in the oral cavity by including the following areas: • Ecology of oral microbiome at health • Ecology of oral microbiome under oral diseases • Ecology of oral microbiome during non-oral diseases • Shifts in the oral microbiome by therapeutic approaches (e.g., antimicrobials, replacement therapy, pre- and probiotics) • Modeling of oral ecological shifts (e.g., animal models, in vitro microcosm models) • Complex inter- and intra-kingdom interactions (e.g., bacterial-fungal-host) related to oral ecology • Environmental (e.g., diet, tobacco), host-related (e.g., immune response, saliva composition and flow) and biotic (e.g., bacterial competition) factors influencing oral ecology • Geographic variation in oral microbial ecology and diversity

Bacterial Exotoxins: How bacteria fight the immune system

Authors: --- ---
Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889199914 Year: Pages: 190 DOI: 10.3389/978-2-88919-991-4 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General) --- Allergy and Immunology --- Medicine (General)
Added to DOAB on : 2016-01-19 14:05:46
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The goal of this research topic was to gather current knowledge on the interaction of bacterial exotoxins and effector proteins with the host immune system. The following 16 research and review articles in this special issue describe mechanisms of immune modification and evasion and provide an overview over the complexity of bacterial toxin interaction with different cells of the immune system.

Insights into Microbe-Microbe Interactions in Human Microbial Ecosystems: Strategies to be Competitive

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Book Series: Frontiers Research Topics ISSN: 16648714 ISBN: 9782889450527 Year: Pages: 116 DOI: 10.3389/978-2-88945-052-7 Language: English
Publisher: Frontiers Media SA
Subject: Microbiology --- Science (General)
Added to DOAB on : 2017-07-06 13:27:36
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All parts of our body having communication with the external environment such as the skin, vagina, the respiratory tract or the gastrointestinal tract are colonized by a specific microbial community. The colon is by far the most densely populated organ in the human body. The pool of microbes inhabiting our body is known as “microbiota” and their collective genomes as “microbiome”. These microbial ecosystems regulate important functions of the host, and their functionality and the balance among the diverse microbial populations is essential for the maintenance of a “healthy status”. The impressive development in recent years of next generation sequencing (NGS) methods have made possible to determine the gut microbiome composition. This, together with the application of other high throughput omic techniques and the use of gnotobiotic animals has greatly improved our knowledge of the microbiota acting as a whole. In spite of this, most members of the human microbiota are largely unknown and remain still uncultured. The final functionality of the microbiota is depending not only on nutrient availability and environmental conditions, but also on the interrelationships that the microorganisms inhabiting the same ecological niche are able to establish with their partners, or with their potential competitors. Therefore, in such a competitive environment microorganisms have had to develop strategies allowing them to cope, adapt, or cooperate with their neighbors, which may imply notable changes at metabolic, physiological and genetic level. The main aim of this Research Topic was to contribute to better understanding complex interactions among microorganisms residing in human microbial habitats.All parts of our body having communication with the external environment such as the skin, vagina, the respiratory tract or the gastrointestinal tract are colonized by a specific microbial community. The colon is by far the most densely populated organ in the human body. The pool of microbes inhabiting our body is known as “microbiota” and their collective genomes as “microbiome”. These microbial ecosystems regulate important functions of the host, and their functionality and the balance among the diverse microbial populations is essential for the maintenance of a “healthy status”. The impressive development in recent years of next generation sequencing (NGS) methods have made possible to determine the gut microbiome composition. This, together with the application of other high throughput omic techniques and the use of gnotobiotic animals has greatly improved our knowledge of the microbiota acting as a whole. In spite of this, most members of the human microbiota are largely unknown and remain still uncultured. The final functionality of the microbiota is depending not only on nutrient availability and environmental conditions, but also on the interrelationships that the microorganisms inhabiting the same ecological niche are able to establish with their partners, or with their potential competitors. Therefore, in such a competitive environment microorganisms have had to develop strategies allowing them to cope, adapt, or cooperate with their neighbors, which may imply notable changes at metabolic, physiological and genetic level. The main aim of this Research Topic was to contribute to better understanding complex interactions among microorganisms residing in human microbial habitats.

Microbial Biofilms in Healthcare: Formation, Prevention and Treatment

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ISBN: 9783039284108 9783039284115 Year: Pages: 166 DOI: 10.3390/books978-3-03928-411-5 Language: English
Publisher: MDPI - Multidisciplinary Digital Publishing Institute
Subject: Science (General) --- Biology --- Microbiology
Added to DOAB on : 2020-04-07 23:07:09
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Biofilms are ubiquitous and their presence in industry can lead to production losses. However, nowhere do biofilms impact human health and welfare as much as those that are found contaminating the healthcare environment, surgical instruments, equipment, and medical implantable devices. Approximately 70% of healthcare-associated infections are due to biofilm formation, resulting in increased patient morbidity and mortality. Biofilms formed on medical implants are recalcitrant to antibiotic treatment, which leaves implant removal as the principal treatment option. In this book, we investigate the role of biofilms in breast and dental implant disease and cancer. We include in vitro models for investigating treatment of chronic wounds and disinfectant action against Candida sp. Also included are papers on the most recent strategies for treating biofilm infection ranging from antibiotics incorporated into bone void fillers to antimicrobial peptides and quorum sensing.

Emerging Marine Biotoxins

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ISBN: 9783039215133 9783039213498 Year: Pages: 206 DOI: 10.3390/books978-3-03921-349-8 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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The emergence of marine and freshwater toxins in geographical areas where they have never been reported before is a concern due to the considerable impact on (sea)food contamination, and consequently, on public health. Several groups of marine biotoxins, in particular tetrodotoxins, ciguatoxins, and palytoxins, are included among the relevant marine biotoxins that have recently emerged in several coastal areas. A similar situation has been observed in freshwater, where cyanobacterial toxins, such as microcystins, could end up in unexpected areas such as the estuaries where shellfish are cultivated. Climate change and the increased availability of nutrients have been considered as the key factors in the expansion of all of these toxins into new areas; however, this could also be due to more intense biological invasions, more sensitive analytical methods, or perhaps even an increased scientific interest in these natural contaminations. The incidences of human intoxications due to the consumption of seafood contaminated with these toxins have made their study an important task to accomplish in order to protect human health. This Special Issue has a focus on a wide variety of emerging biotoxin classes and techniques to identify and quantify them.

Dynamical Models of Biology and Medicine

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ISBN: 9783039212170 9783039212187 Year: Pages: 294 DOI: 10.3390/books978-3-03921-218-7 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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Mathematical and computational modeling approaches in biological and medical research are experiencing rapid growth globally. This Special Issue Book intends to scratch the surface of this exciting phenomenon. The subject areas covered involve general mathematical methods and their applications in biology and medicine, with an emphasis on work related to mathematical and computational modeling of the complex dynamics observed in biological and medical research. Fourteen rigorously reviewed papers were included in this Special Issue. These papers cover several timely topics relating to classical population biology, fundamental biology, and modern medicine. While the authors of these papers dealt with very different modeling questions, they were all motivated by specific applications in biology and medicine and employed innovative mathematical and computational methods to study the complex dynamics of their models. We hope that these papers detail case studies that will inspire many additional mathematical modeling efforts in biology and medicine

Keywords

hemodynamic model --- microcirculation load --- liquid-solid-porous media seepage coupling --- 2-combination --- graphical representation --- cell-based vector --- numerical characterization --- phylogenetic analysis --- intraguild predation --- random perturbations --- persistence --- stationary distribution --- global asymptotic stability --- quorum sensing --- chemostat --- mathematical model --- differential equations --- delay --- bifurcations --- dynamical system --- numerical simulation --- predator-prey model --- switched harvest --- limit cycle --- rich dynamics --- algae growth models --- uncertainty quantification --- asymptotic theory --- bootstrapping --- model comparison tests --- Raphidocelis subcapitata --- Daphnia magna --- spotting --- wildfire --- transport equations --- spotting distribution --- obesity --- mechano-electrochemical model --- articular cartilage --- cartilage degeneration --- cartilage loading --- optimal control --- hepatitis B --- delay differential equations (DDE) --- immune response --- drug therapy --- dynamic model --- flocculation --- global stability --- uniform persistence --- epidermis --- mathematical model --- bacterial inflammation --- bacterial competition --- chronic myeloid leukemia --- tyrosine kinase inhibitors --- immunomodulatory therapies --- combination therapy --- equilibrium points --- mathematical modeling --- prostate cancer --- androgen deprivation therapy --- data fitting --- generalized pseudo amino acid composition --- numerical characterization --- phylogenetic analysis --- identification of DNA-binding proteins --- n/a

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