Methods in molecular biology
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This chapter will outline strategies and ideas for the commercialization a promising wound healing technology discovered in an academic setting. This would include, but not limited to addressing topics such as intellectual property protection, funding, technology development, and regulatory aspects (i.e., navigating through the FDA).
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By the combinations of high-throughput analytical technologies in the fields of transcriptomics, proteomics, and metabolomics, we are now able to gain comprehensive and quantitative snapshots of the intracellular processes. Dynamic intracellular activities and their regulations can be elucidated by systematic observation of these multi-omics data. ⋯ Moreover, interpretation of such multitude of data requires an intuitive pathway context. Here we describe such statistical methods for the integration and comparison of multi-omics data, as well as the computational methods for pathway reconstruction, ID conversion, mapping, and visualization that play key roles for the efficient study of multi-omics information.
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Studies of DNA methylation in Arabidopsis have rapidly advanced from the analysis of a single reference accession to investigations of large populations. The goal of emerging population studies is to detect differentially methylated regions (DMRs) at the genome-wide scale, and to relate this variation to gene expression and phenotypic diversity. Whole-genome bisulfite sequencing (WGBS-seq) has established itself as a gold standard in DNA methylation analysis due to its high accuracy and single cytosine measurement resolution. ⋯ However, detection can be susceptible to strong signal distortions resulting from a combination of dye bias and the CG content of effectively unmethylated genomic regions. We show that these issues can be easily bypassed by taking appropriate data preparation steps and applying suitable analysis tools. We conclude that MeDIP-chip is a reasonable alternative to WGBS-seq in emerging Arabidopsis population epigenetic studies.
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The various biochemical cascades that follow primary brain injury result in secondary brain injury which can adversely affect the clinical outcome. Over the last few years it has been well established that molecules like erythropoietin (Epo) have a neuroprotective role in experimental traumatic brain injury (TBI). Epo is shown to produce this effect by modulating multiple cellular processes, including apoptosis, inflammation, and regulation of cerebral blood flow. ⋯ Peptides that mimic a portion of the Epo molecule, including Helix B surface peptide and Epotris, have also been developed to isolate the neuroprotective activities. The TBI model in rodents most commonly used to study the effect of Epo and these derivatives in TBI is controlled cortical impact injury, which is a model of focal contusion following a high velocity impact to the parietal cortex. Following TBI, rodents are given Epo or an Epo derivative vs. placebo and the outcome is evaluated in terms of physiological parameters (cerebral blood flow, intracranial pressure, cerebral perfusion pressure), behavioral parameters (motor and memory), and histological parameters (contusion volumes, hippocampus cell counts).
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Animal models are important to develop therapies for individuals suffering from spinal cord injuries. For this purpose, rats are commonly preferred. ⋯ On the other hand, spinal cord is compressed or contused to mimic the human injury in blunt injury models for understanding as well as managing the secondary pathophysiologic processes following injury. Especially, contusions are thought to be biomechanically similar to vertebral fractures and/or dislocations and thus provide the most realistic experimental setting in which to test potential neuroprotective and regenerative strategies.