Springer protocols feed by Genetics/Genomics 
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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.A Fusion PCR Method for Expressing Genetic Tools in C. elegans
C. elegans offer a unique opportunity for understanding computation in neural networks. This is largely due to their relatively compact neural network for which a wiring diagram is available. Recent advances in genetic tools for interrogating neural activity (e.g., optogenetics) make C. elegans particularly compelling as they can be expressed in many different combinations in target individual neurons. Thus, the prospect to decipher principles underlying functionality in neural networks largely depends on the ease by which transgenic animals can be generated. Traditionally, to generate transgenic animals one would inject a...
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Genetic Methods for Cellular Manipulations in C. elegans
Neuron manipulation in vivo by ablation, activation, or inactivation, and regulation of gene expression, is essential for dissecting nervous system function. Here we describe genetic means for neuron manipulation in the nematode C. elegans, and provide protocols for generating transgenic animals containing these genetic tools. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Fundamentals of Comparative Genome Analysis in Caenorhabditis Nematodes
The genome of the nematode Caenorhabditis elegans was the first of any animal to be sequenced completely, and it remains the “gold standard” for completeness and annotations. Even before the C. elegans genome was completed, however, biologists began examining the generality of its features in the genomes of other Caenorhabditis species. With many such genomes now sequenced and available via WormBase, C. elegans researchers are often confronted with how to interpret comparative genomic data. In this article, we present practical approaches to addressing several common issues, including possible sources of error ...
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Library Construction for Mutation Identification by Whole-Genome Sequencing
Next-generation sequencing provides a rapid and powerful method for mutation identification. Herein is described a workflow for sample preparation to allow the simultaneous mapping and identification of candidate mutations by whole-genome sequencing in Caenorhabditis elegans. The protocol is designed for small numbers of worms to accommodate classes of mutations, such as lethal and sterile alleles, that are difficult to identify by traditional means. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
A Primer on Quantitative Modeling
Caenorhabditis elegans is particularly suitable for obtaining quantitative data about behavior, neuronal activity, gene expression, ecological interactions, quantitative traits, and much more. To exploit the full potential of these data one seeks to interpret them within quantitative models. Using two examples from the C. elegans literature we briefly explore several types of modeling approaches relevant to worm biology, and show how they might be used to interpret data, formulate testable hypotheses, and suggest new experiments. We emphasize that the choice of modeling approach is strongly dependent on the questions of in...
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
A Primer on Prototyping
Standard mechanical components, such as adapters or mounts, are ubiquitous in research laboratories, C. elegans labs included. Recently, in-house prototyping and fabricating both standard and custom mechanical parts has become simple and cost effective. Here we describe the basic steps, equipment, and considerations required for rapid prototyping of a handful of simple yet useful designs. These examples were chosen for their simplicity, as well as for demonstrating specific practicalities. They are thus appropriate as training exercises. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Sampling and Isolation of C. elegans from the Natural Habitat
Wild populations of the model organism C. elegans allow characterization of natural genetic variation underlying diverse phenotypic traits. Here we provide a simple protocol on how to sample and rapidly identify C. elegans wild isolates. We outline how to find suitable habitats and organic substrates, followed by describing isolation and identification of C. elegans live cultures based on easily recognizable morphological characteristics, molecular barcodes and/or mating tests. This protocol uses standard laboratory equipment and requires no prior knowledge of C. elegans biology. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
An Imaging System for C. elegans Behavior
Many experiments in C. elegans neurobiology and development benefit from automated imaging of worm behavior. Here we describe procedures for building a flexible and inexpensive imaging system using standard optical and mechanical components. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Tracking Single C. elegans Using a USB Microscope on a Motorized Stage
Locomotion and gross morphology have been important phenotypes for C. elegans genetics since the inception of the field and remain relevant. In parallel with developments in genome sequencing and editing, phenotyping methods have become more automated and quantitative, making it possible to detect subtle differences between mutants and wild-type animals. In this chapter, we describe how to calibrate a single-worm tracker consisting of a USB microscope mounted on a motorized stage and how to record and analyze movies of worms crawling on food. The resulting quantitative phenotypic fingerprint can sensitively identify differ...
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Microfluidic Devices for Behavioral Analysis, Microscopy, and Neuronal Imaging in Caenorhabditis elegans
Microfluidic devices offer several advantages for C. elegans research, particularly for presenting precise physical and chemical environments, immobilizing animals during imaging, quantifying behavior, and automating screens. However, challenges to their widespread adoption in the field include increased complexity over conventional methods, operational problems (such as clogging, leaks, and bubbles), difficulty in obtaining or fabricating devices, and the need to characterize biological results obtained from new assay formats. Here we describe the preparation and operation of simple, reusable microfluidic devices for quan...
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Electron Tomography Methods for C. elegans
Methods for electron tomography of the nematode C. elegans are explained in detail, including a brief introduction to specimen preparation, methods for image collection, and a comparison of several general methods for producing dual-axis tomograms, with or without external fiducial reference objects. New electron tomograms highlight features in software for data display, annotation, and analysis. This chapter discusses the ultrastructural analysis of cells and tissues, rather than molecular studies. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
High-Pressure Freeze and Freeze Substitution Electron Microscopy in C. elegans
While traditional chemical fixation methods for C. elegans electron microscopy (EM) have provided invaluable anatomical and structural information, the development of high-pressure freeze (HPF) and freeze substitution (FS) protocols offers advantages for high-resolution imaging. Specimens prepared using HPF methodology exhibit fewer distortion artifacts due to fixation and dehydration, have improved antigenicity, and result in a more physiologically accurate structural representation of the worm. In the HPF technique, freely moving worms are frozen at high-pressure (2100 bar) and low temperature (−180 °C) within ...
Source: Springer protocols feed by Genetics/Genomics - October 2, 2015 Category: Genetics & Stem Cells Source Type: news
Precise Identification of Genome-Wide Transcription Start Sites in Bacteria by 5′-Rapid Amplification of cDNA Ends (5′-RACE)
Transcription start sites are commonly used to locate promoter elements in bacterial genomes. TSS were previously studied one gene at a time, often through 5′-rapid amplification of cDNA ends (5′-RACE). This technique has now been adapted for high-throughput sequencing and can be used to precisely identify TSS in a genome-wide fashion for practically any bacterium, which greatly contributes to our understanding of gene regulatory networks in microorganisms. (Source: Springer protocols feed by Genetics/Genomics)
Source: Springer protocols feed by Genetics/Genomics - September 15, 2015 Category: Genetics & Stem Cells Source Type: news
Functional Studies of DNA-Protein Interactions Using FRET Techniques
Protein-DNA interactions underpin life and play key roles in all cellular processes and functions including DNA transcription, packaging, replication, and repair. Identifying and examining the nature of these interactions is therefore a crucial prerequisite to understand the molecular basis of how these fundamental processes take place. The application of fluorescence techniques and in particular fluorescence resonance energy transfer (FRET) to provide structural and kinetic information has experienced a stunning growth during the past decade. This has been mostly promoted by new advances in the preparation of dye-labeled ...
Source: Springer protocols feed by Genetics/Genomics - September 15, 2015 Category: Genetics & Stem Cells Source Type: news
Probing of Nascent Riboswitch Transcripts
The study of biologically significant and native structures is vital to characterize RNA-based regulatory mechanisms. Riboswitches are cis-acting RNA molecules that are involved in the biosynthesis and transport of cellular metabolites. Because riboswitches regulate gene expression by modulating their structure, it is vital to employ native probing assays to determine how native riboswitch structures perform highly efficient and specific ligand recognition. By employing RNase H probing, it is possible to determine the accessibility of specific RNA domains in various structural contexts. Herein, we describe how to employ RN...
Source: Springer protocols feed by Genetics/Genomics - September 15, 2015 Category: Genetics & Stem Cells Source Type: news
