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.Bacterial and Fungal DNA Extraction from Blood Samples: Automated Protocols
Automation in DNA isolation is a necessity for routine practice employing molecular diagnosis of infectious agents. To this end, the development of automated systems for the molecular diagnosis of microorganisms directly in blood samples is at its beginning. Important characteristics of systems demanded for routine use include high recovery of microbial DNA, DNA-free containment for the reduction of DNA contamination from exogenous sources, DNA-free reagents and consumables, ideally a walkaway system, and economical pricing of the equipment and consumables. Such full automation of DNA extraction evaluated and in use for se...
Source: Springer protocols feed by Microbiology - October 17, 2014 Category: Microbiology Source Type: news
Bacterial and Fungal DNA Extraction from Blood Samples: Manual Protocols
A critical point of molecular diagnosis of systemic infections is the method employed for the extraction of microbial DNA from blood. A DNA isolation method has to be able to fulfill several fundamental requirements for optimal performance of diagnostic assays. First of all, low- and high-molecular-weight substances of the blood inhibitory to downstream analytical reactions like PCR amplification have to be removed. This includes human DNA which is a known source of false-positive results and factor decreasing the analytical sensitivity of PCR assays by unspecific primer binding. At the same time, even extremely low amount...
Source: Springer protocols feed by Microbiology - October 17, 2014 Category: Microbiology Source Type: news
Molecular Detection of Antibiotic Resistance Genes from Positive Blood Cultures
Rapid detection of the bacterial causative agent causing sepsis must be coupled with rapid identification of the antibiotic resistant mechanism that the pathogen might possess. Real-time PCR (qPCR)-based assays have been extensively utilized in the clinical microbiology field as diagnostic tools for the rapid detection of specific nucleic acid (NA) targets. In this chapter, we will discuss the technical aspects of using an internally controlled qPCR assay for the rapid detection of Klebsiella pneumoniae carbapenemase gene (bla
KPC) in positive Bactec blood culture bottles. The multiplex qPCR (bla
...
Source: Springer protocols feed by Microbiology - October 17, 2014 Category: Microbiology Source Type: news
Biofilms of Thermophilic Bacilli Isolated from Dairy Processing Plants and Efficacy of Sanitizers
We describe how to set up a pilot-scale experiment for testing the efficacy of sanitizers against the thermophilic bacilli. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Culture-Independent Methods to Study Subaerial Biofilm Growing on Biodeteriorated Surfaces of Stone Cultural Heritage and Frescoes
Actinobacteria, cyanobacteria, algae, and fungi form subaerial biofilm (SAB) that can lead to material deterioration on artistic stone and frescoes. In studying SAB on cultural heritage surfaces, a general approach is to combine microscopy observations and molecular analyses. Sampling of biofilm is performed using specific adhesive tape and sampling of SAB and the substrate with sterile scalpels and chisels. Biofilm observations are carried out using optical and scanning electron microscopy. Specific taxa and EPS in biofilm can be readily visualized by fluorochrome staining and subsequent observation using fluorescence or ...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Biofilm-Growing Bacteria Involved in the Corrosion of Concrete Wastewater Pipes: Protocols for Comparative Metagenomic Analyses
The objective of this chapter is to describe the steps involved in the taxonomic and functional analysis of metagenome datasets from biofilm involved in microbial-induced concrete corrosion (MICC). (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Capturing Air–Water Interface Biofilms for Microscopy and Molecular Analysis
Described here is a simple and versatile technique for capturing small samples of the thin biofilm that is located at the meniscus of almost every air–water interface (AWI), an electrostatically distinct aquatic domain/habitat. The method uses a microscope slide (and other supporting surfaces) coated in the lab with a collodion membrane, which has a strong affinity for the upper surface of the AWI biofilm. The structural integrity of the biofilm is maintained during the capture process, and components of the biofilm are effectively separated from the subtending liquid. The captured thin biofilm can be analyzed in man...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Photodynamic Therapy as a Novel Antimicrobial Strategy Against Biofilm-Based Nosocomial Infections: Study Protocols
Hospital-acquired infections (HAIs), also known as nosocomial infections, are one of the most serious health-care issues currently influencing health-care costs. Among them, those sustained by microbial biofilm represent a major public health concern. Here, we describe the experimental protocols for microbial biofilm inactivation relying on antimicrobial photodynamic therapy (APDT) as a new strategy for the control of these kinds of infections. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Bacteriophage Attack as an Anti-biofilm Strategy
Bacteriophages are bacterial viruses. Bacteriophages replicate inside their target host whether this is in planktonic or biofilm forms. Here, we describe the methods used to control readily formed biofilms using bacteriophages. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Chip Calorimetry for Evaluation of Biofilm Treatment with Biocides, Antibiotics, and Biological Agents
Any growth or bioconversion in biofilms is accompanied by the release of heat. The heat (in J) is tightly related to the stoichiometry of the respective process via law of Hess, and the heat production rate (in W or J/s) is additionally related to the process kinetics. This heat and the heat production rate can nowadays be measured by modern calorimetry with extremely high sensitivity. Flow-through calorimetry allows the measurement of bioprocesses in biofilms in real time, without the need of invasive sample preparation and disturbing of biofilm processes. Furthermore, it can be applied for long-term measurements and is e...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Contribution of Confocal Laser Scanning Microscopy in Deciphering Biofilm Tridimensional Structure and Reactivity
Confocal laser scanning microscopy (CLSM) became in last years an invaluable technique to study biofilms since it enables researchers to explore noninvasively the dynamic architecture and the reactivity of these biological edifices. The constant development of fluorescent markers and genetic tools along with the improvement of spatial, spectral, and temporal resolution of imaging facilities offers new opportunities to better decipher microbial biofilm properties. In this contribution, we proposed to describe the contribution of CLSM to the study of biofilm architecture and reactivity throughout two different illustrative a...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Pharmacokinetics and Pharmacodynamics of Antibiotics in Biofilm Infections of Pseudomonas aeruginosa In Vitro and In Vivo
Although progress on biofilm research has been obtained during the past decades, the treatment of biofilm infections with antibiotics remains a riddle. The pharmacokinetic (PK) and pharmacodynamic (PD) profiles of an antimicrobial agent provide important information helping to establish an efficient dosing regimen and to minimize the development of antimicrobial tolerance and resistance in biofilm infections. Unfortunately, most previous PK/PD studies of antibiotics have been done on planktonic cells, and extrapolation of the results on biofilms is problematic as bacterial biofilms differ from planktonic grown cells in the...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Antibiotic Polymeric Nanoparticles for Biofilm-Associated Infection Therapy
Polymeric nanoparticles are highly attractive as drug delivery vehicles due to their high structural integrity, stability during storage, ease of preparation and functionalization, and controlled release capability. Similarly, lipid–polymer hybrid nanoparticles, which retain the benefits of polymeric nanoparticles plus the enhanced biocompatibility and prolonged circulation time owed to the lipids, have recently emerged as a superior alternative to polymeric nanoparticles. Drug nanoparticle complex prepared by electrostatic interaction of oppositely charged drug and polyelectrolytes represents another type of polymer...
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Efficacy Evaluation of Antimicrobial Drug-Releasing Polymer Matrices
To assay in vitro antimicrobial activity of substances such as antibiotics or antiseptics, standard methods both in liquid and on solid media are available. These procedures cannot be adequate for testing antimicrobial-releasing or biocidal polymer systems. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
Biofilm Matrix-Degrading Enzymes
Polymeric substances such as proteins, polysaccharides, and DNA constitute a major component of the biofilm matrix. Enzymes that depolymerize and degrade these components are useful tools for investigating the composition and function of the biofilm matrix. This chapter provides a brief overview of the most commonly used biofilm matrix-degrading enzymes and presents examples of their applications in biofilm research. (Source: Springer protocols feed by Microbiology)
Source: Springer protocols feed by Microbiology - March 27, 2014 Category: Microbiology Source Type: news
