Springer protocols feed by Microbiology 
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This is an RSS file. You can use it to subscribe to this data in your favourite RSS reader or to display this data on your own website or blog.In Vitro Screening of Antifungal Compounds Able to Counteract Biofilm Development
Fungi are able to grow as a single-species or a more complex biofilm attached to inert surfaces (catheters…) or tissues (lung…). This last form is a microbial niche which must be considered as a major risk factor of developing a human fungal infection. Nowadays, only a few therapeutic agents have been shown to be active against fungal biofilms in vitro and/or in vivo. So there is a real need to find new anti-biofilm molecules. Here we describe in detail some rapid, 96-well microtiter plate-based methods, for the screening of compounds with anti-biofilm activity against Candida spp. yeasts. Two approaches will...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Microbiological Methods for Target-Oriented Screening of Biofilm Inhibitors
In this report, we present two examples of target-based microbiological screenings for antimicrobials endowed with anti-biofilm activity, aimed respectively at the inhibition of the signal molecule cyclic di-GMP and of quorum sensing. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Animal Models to Evaluate Bacterial Biofilm Development
Medical biofilms have attracted substantial attention especially in the past decade. Animal models are contributing significantly to understand the pathogenesis of medical biofilms. In addition, animal models are an essential tool in testing the hypothesis generated from clinical observations in patients and preclinical testing of agents showing in vitro antibiofilm effect. Here, we describe three animal models — two non-foreign body Pseudomonas aeruginosa biofilm models and a foreign body Staphylococcus aureus model. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Imaging Bacteria and Biofilms on Hardware and Periprosthetic Tissue in Orthopedic Infections
Infection is a major complication of total joint arthroplasty (TJA) surgery, and even though it is now as low as 1 % in some hospitals, the increasing number of primary surgeries translates to tens of thousands of revisions due to prosthetic joint infection (PJI). In many cases the only solution is revision surgery in which the hardware is removed. This process is extremely long and painful for patients and is a considerable financial burden for the health-care system. A significant proportion of the difficulties in diagnosis and treatment of PJI are associated with biofilm formation where bacteria attach to the surface of...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Experimental Approaches to Investigating the Vaginal Biofilm Microbiome
Unraveling the complex ecology of the vaginal biofilm microbiome relies on a number of complementary techniques. Here, we describe the experimental approaches for studying vaginal microbial biofilm samples with a focus on specimen preparation for subsequent analysis. The techniques include fluorescence microscopy, fluorescence in situ hybridization, and scanning and transmission electron microscopy. Isolation of microbial DNA and RNA from these samples is covered along with a brief discussion of chemical analysis methods. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Field Emission Scanning Electron Microscopy of Biofilm-Growing Bacteria Involved in Nosocomial Infections
Scanning electron microscopy (SEM) provides useful information on the shape, size, and localization within the biofilm of single bacteria as well as on the steps of biofilm formation process, on bacterial interactions, and on production of extracellular polymeric substances. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Animal Models to Investigate Fungal Biofilm Formation
Microbial biofilms play an essential role in several infectious diseases and are defined as extensive communities of sessile organisms irreversibly associated with a surface, encased within a polysaccharide-rich extracellular matrix (ECM), and exhibiting enhanced resistance to antimicrobial drugs. Forming a biofilm provides the microbes protection from environmental stresses due to contaminants, nutritional depletion, or imbalances, but is dangerous to human health due to their inherent robustness and elevated resistance. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Nonmammalian Model Systems to Investigate Fungal Biofilms
Medical advances have resulted in an increase in the number of patients in immunocompromised states, vulnerable to infection, or individuals fitted with medical devices that form niches for microbial infections. These infections are difficult to treat and have significant morbidity and mortality rates. An important factor in the pathogenesis of fungal diseases is the development of biofilm-forming communities, enabling the invasion of host tissues and resistance to antimicrobial compounds. To investigate the genetic requirements for filamentation and seek compounds that inhibit the process, invertebrate hosts are employed ...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Methods for Dynamic Investigations of Surface-Attached In Vitro Bacterial and Fungal Biofilms
Three dynamic models for the investigation of in vitro biofilm formation are described in this chapter. In the 6-well plate assay presented here, the placing of the plate on a rotating platform provides shear, thereby making the system dynamic with respect to the static microtiter assay. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Quorum Sensing in Gram-Positive Bacteria: Assay Protocols for Staphylococcal agr and Enterococcal fsr Systems
A thiolactone/lactone peptide-mediated quorum sensing (QS) system is commonly employed in gram-positive bacteria to control the expression of a variety of phenotypes, including the production of virulence factors and biofilm formation. Here, we describe assay protocols for the well-studied QS systems (agr and fsr) of two representative gram-positive pathogens, Staphylococcus aureus and Enterococcus faecalis. These convenient assay systems are useful for the screening of QS inhibitors as well as for basic research to address the mechanism of these QS systems. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Aqueous Two-Phase System Technology for Patterning Bacterial Communities and Biofilms
We describe a novel method which makes use of polymer-based aqueous two-phase systems to pattern bacterial communities inside Petri dishes. This method allows us to culture submillimeter-sized bacterial communities in spatially distinct spots while maintaining a degree of chemical connectedness to each other through the aqueous phase. Given sufficient time, these bacterial cultures develop biofilms, each corresponding to the footprint of the droplet spot. This method can be used to study the interactions between bacterial communities and biofilms spotted adjacent to each other. Furthermore, it can be extended to study the ...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Multiplex Fluorescence In Situ Hybridization (M-FISH) and Confocal Laser Scanning Microscopy (CLSM) to Analyze Multispecies Oral Biofilms
Multiplex fluorescence in situ hybridization (M-FISH) constitutes a favorable microbiological method for the analysis of spatial distribution of highly variable phenotypes found in multispecies oral biofilms. The combined use of confocal laser scanning microscopy (CLSM) produces high-resolution three-dimensional (3D) images of individual bacteria in their natural environment. Here, we describe the application of M-FISH on early (Streptococcus spp., Actinomyces naeslundii) and late colonizers (Fusobacterium nucleatum, Veillonella spp.) of in situ-formed oral biofilms, the acquisition of CLSM images, as well as the qualitati...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Advanced Techniques for In Situ Analysis of the Biofilm Matrix (Structure, Composition, Dynamics) by Means of Laser Scanning Microscopy
The extracellular constituents in bioaggregates and biofilms can be imaged four dimensionally by using laser scanning microscopy. In this protocol we provide guidance on how to examine the various extracellular compartments in between microbial cells and communities associated with interfaces. The current options for fluorescence staining of matrix compounds and extracellular microhabitats are presented. Furthermore, practical aspects are discussed and useful notes are added. The chapter ends with a brief introduction to other approaches for EPS analysis and an outlook for future needs. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Quantitative Metaproteomics: Functional Insights into Microbial Communities
Quantitative metaproteomics aims to accurately determine the relative abundances of thousands of proteins in a microbial community. This approach can be used to provide a comprehensive view of metabolic activities of organisms in microbial communities and uncover significant changes in protein expression between communities at different developmental stages, environment types or in response to different perturbations. Here, we describe three strategies for quantitative metaproteomics, including label-free, 15N metabolic labeling, and isobaric chemical labeling. The measurements are all based on a shotgun proteomics workflo...
Source: Springer protocols feed by Microbiology - January 1, 2014 Category: Microbiology Source Type: news
Quantitative Microbial Metatranscriptomics
The direct retrieval and sequencing of environmental RNA is emerging as a powerful technique to elucidate the in situ activities of microbial communities. Here we provide a metatranscriptomic protocol describing environmental sample collection, rRNA depletion, mRNA amplification, cDNA synthesis, and bioinformatic analysis. In addition, the preparation of internal RNA standards and their addition to the sample are discussed, providing a method by which transcript numbers can be expressed as absolute abundances in the environment and more readily compared to other biogeochemical and ecological measurements. (Source: Springer...
Source: Springer protocols feed by Microbiology - January 1, 2014 Category: Microbiology Source Type: news
