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"Methods and Techniques"
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Cultivation of unculturable soil bacteria
Despite the abundance of bacterial species in soil, more than 99% of these species cannot be cultured by traditional techniques. In addition, the less than 1% of bacteria that can be cultured are not representative of the total phylogenetic diversity. Hence, identifying novel species and their new functions is still an important task for all microbiologists. Cultivating techniques have played an important role in identifying new species but are still low-throughput processes. This review discusses the issues surrounding cultivation, including achievements, limitations, challenges, and future directions.
Journal Article
The magic circle : principles of gaming & simulation
\"The purpose of this unique book is to outline the core of game science by presenting principles underlying the design and use of games and simulations\"--Page 4 of cover.
Book
Novel approaches toward preferential detection of viable cells using nucleic acid amplification techniques
This article elaborates on possible future directions for microbial viability assessment using nucleic acid-modifying compounds in combination with DNA- (and potentially RNA-) amplification technologies. Bacteria were traditionally considered viable when they could be cultured, whereas today's viability concept is based on the presence of some form of metabolic activity, responsiveness, RNA transcripts that tend to degrade rapidly after cell death, or of an intact membrane. The latter criterion was the focus of recent approaches to limit detection to intact cells using ethidium monoazide or propidium monoazide. Membrane integrity must, however, be considered as a very conservative criterion for microbial viability. The new concept presented here aims at limiting nucleic acid-based detection to cells with an active metabolism, which might be a more appropriate viability criterion. To selectively detect only cells with metabolic and respiratory activity (while excluding inactive dead cells from detection), we suggest the use of 'activity-labile compounds'. In addition to their potential usefulness for viability assessment, these new compounds could also be beneficial for selectively amplifying nucleic acids of cells that have metabolic activities of interest. This preferential detection of microorganisms with certain metabolic capabilities is referred to as 'molecular enrichment' in distinction to 'growth enrichment'.
Journal Article
Cultivating the uncultured: limits, advances and future challenges
Since the invention of the Petri dish, there have been continuous efforts to improve efficiency in microbial cultivation. These efforts were devoted to the attainment for diverse growth conditions, simulation of in situ conditions and achievement of high-throughput rates. As a result, prokaryotes catalysing novel redox reactions as well as representatives of abundant, but not-yet cultured taxa, were isolated. Significant insights into microbial physiology have been made by studying the small number of prokaryotes already cultured. However, despite these numerous breakthroughs, microbial cultivation is still a low-throughput process. The main hindrance to cultivation is likely due to the prevailing lack of knowledge on targeted species. In this review, we focus on the limiting factors surrounding cultivation. We discuss several cultivation obstacles, including the loss of microbial cell-cell communication following species isolation. Future research directions, including the refinement of culture media, strategies based on cell-cell communication and high-throughput innovations, are reviewed. We further propose that a combination of these approaches is urgently required to promote cultivation of uncultured species, thereby dawning a new era in the field.
Journal Article
Validating psychological constructs : historical, philosophical, and practical dimensions
\"This book critically examines the historical and philosophical foundations of construct validity theory (CVT), and how these have and continue to inform and constrain the conceptualization of validity and its application in research. CVT has had an immense impact on how researchers in the behavioural sciences conceptualize and approach their subject matter. Yet, there is equivocation regarding the foundations of the CVT framework as well as ambiguities concerning the nature of the 'constructs' that are its raison d'etre. The book is organized in terms of three major parts that speak, respectively, to the historical, philosophical, and pragmatic dimensions of CVT. The primary objective is to provide researchers and students with a critical lens through which a deeper understanding may be gained of both the utility and limitations of CVT and the validation practices to which it has given rise.\"-- Back cover.
Book
Improved whole-mount immunofluorescence protocol for consistent and robust labeling of adult Drosophila melanogaster adipose tissue
Energy storage and endocrine functions of the Drosophila fat body make it an excellent model for elucidating mechanisms that underlie physiological and pathophysiological organismal metabolism. Combined with Drosophila's robust genetic and immunofluorescence microscopy toolkits, studies of Drosophila fat body function are ripe for cell biological analysis. Unlike the larval fat body, which is easily removed as a single, cohesive sheet of tissue, isolating intact adult fat body proves to be more challenging, thus hindering consistent immunofluorescence labeling even within a single piece of adipose tissue. Here, we describe an improved approach to handling Drosophila abdomens that ensures full access of the adult fat body to solutions generally used in immunofluorescence labeling protocols. In addition, we assess the quality of fluorescence reporter expression and antibody immunoreactivity in response to variations in fixative type, fixation incubation time, and detergent used for cellular permeabilization. Overall, we provide several recommendations for steps in a whole-mount staining protocol that results in consistent and robust immunofluorescence labeling of the adult Drosophila fat body.
Journal Article
Composition, creative writing studies, and the digital humanities
\"In an era of blurred generic boundaries, multimedia storytelling, and open-source culture, creative writing scholars stand poised to consider the role that technology-and the creative writer's playful engagement with technology-has occupied in the evolution of its theory and practice. Composition, Creative Writing Studies and the Digital Humanities is the first book to bring these three fields together to open up new opportunities and directions for creative writing studies. Placing the rise of Creative Writing Studies alongside the rise of the digital humanities in Composition/Rhetoric, Adam Koehler shows that the use of new media and its attendant re-evaluation of fundamental assumptions in the field stands to guide Creative Writing Studies into a new era. Covering current developments in composition and the digital humanities, this book re-examines established assumptions about process, genre, authority/authorship and pedagogical practice in the creative writing classroom.\" -- Back cover.
Book
Lipid corrections in carbon and nitrogen stable isotope analyses: comparison of chemical extraction and modelling methods
1. Lipids have more negative δ¹³C values relative to other major biochemical compounds in plant and animal tissues. Although variable lipid content in biological tissues alters results and conclusions of δ¹³C analyses in aquatic food web and migration studies, no standard correction protocol exists. 2. We compared chemical extraction and mathematical correction methods for freshwater and marine fishes and aquatic invertebrates to better understand impacts of correction approaches on carbon (δ¹³C) and nitrogen (δ¹⁵N) stable isotope data. 3. Fish and aquatic invertebrate tissue δ¹³C values increased significantly following extraction for almost all species and tissue types relative to nonextracted samples. In contrast, δ¹⁵N was affected for muscle and whole body samples from only a few freshwater and marine species and had a limited effect for the entire data set. 4. Lipid normalization models, using C : N as a proxy for lipid content, predicted lipid-corrected δ¹³C for paired data sets more closely with parameters specific to the tissue type and species to which they were applied. 5. We present species- and tissue-specific models based on bulk C : N as a reliable alternative to chemical extraction corrections. By analysing a subset of samples before and after lipid extraction, models can be applied to the species and tissues of interest that will improve estimates of dietary sources using stable isotopes.
Journal Article