RNA extraction from self-assembling peptide hydrogels to allow qPCR analysis of encapsulated cells

Self-assembling peptide hydrogels offer a novel 3-dimensional platform for many applications in cell culture and tissue engineering but are not compatible with current methods of RNA isolation; owing to interactions between RNA and the biomaterial. This study investigates the use of two techniques based on two different basic extraction principles: solution-based extraction and direct solid-state binding of RNA respectively, to extract RNA from cells encapsulated in four β-sheet forming self-assembling peptide hydrogels with varying net positive charge. RNA-peptide fibril interactions, rather than RNA-peptide molecular complexing, were found to interfere with the extraction process resulting in low yields. A column-based approach relying on RNA-specific binding was shown to be more suited to extracting RNA with higher purity from these peptide hydrogels owing to its reliance on strong specific RNA binding interactions which compete directly with RNA-peptide fibril interactions. In order to reduce the amount of fibrils present and improve RNA yields a broad spectrum enzyme solution—pronase—was used to partially digest the hydrogels before RNA extraction. This pre-treatment was shown to significantly increase the yield of RNA extracted, allowing downstream RT-qPCR to be performed

Forty years on: clathrin-coated pits continue to fascinate

Clathrin mediated endocytosis (CME) is a fundamental process in cell biology and has been extensively investigated throughout the last several decades. Every cell biologist learns about it at some point during their education and the beauty of this process has led many of us to go deeper and make it the topic of our own research. Great progress has been made towards elucidating the mechanisms of CME and the field is becoming increasingly complex with several hundred new publications every year. This makes it easy to get lost in the vast amount of literature and to forget about the fundamentals of the field, based on the careful interpretation of simple observations made over 40 years ago. A study performed by Anderson, Brown and Goldstein in 1977 (Anderson et al., 1977) is a prime example of this. We therefore want to take a step back and examine how this seminal study was pivotal to our understanding of CME and its progression into ever increasing complexity over the last four decades

Structure-Based Discovery of A2A Adenosine Receptor Ligands

The recent determination of X-ray structures of pharmacologically relevant GPCRs has made these targets accessible to structure-based ligand discovery. Here we explore whether novel chemotypes may be discovered for the A(2A) adenosine receptor, based on complementarity to its recently determined structure. The A(2A) adenosine receptor signals in the periphery and the CNS, with agonists explored as anti-inflammatory drugs and antagonists explored for neurodegenerative diseases. We used molecular docking to screen a 1.4 million compound database against the X-ray structure computationally and tested 20 high-ranking, previously unknown molecules experimentally. Of these 35% showed substantial activity with affinities between 200 nM and 9 microM. For the most potent of these new inhibitors, over 50-fold specificity was observed for the A(2A) versus the related A(1) and A(3) subtypes. These high hit rates and affinities at least partly reflect the bias of commercial libraries toward GPCR-like chemotypes, an issue that we attempt to investigate quantitatively. Despite this bias, many of the most potent new ligands were novel, dissimilar from known ligands, providing new lead structures for modulation of this medically important target

Enabling smart spaces with OSGi

The use of Open Services gateway Initiative (OSGi) for enbaling pervasive computing spaces is discussed. OSGi promotes the dynamic discovery and collaboration of devices and services from different sources, by defining a standard execution environment and service interfaces. Running on top of a Java virtual machine, the framework provides a shared execution environment that installs, updates, and uninstalls bundles without needing to restart the system. It pointed out that OSGi presents a perfect infrastructure to integrate various devices and sensors and to cope with the dynamism inherent in future pervasive computing environments

The μJini proxy architecture for impromptu mobile services

Wireless hotspots and broadband coverage are permeating the globe giving rise to interesting spontaneous networking scenarios. The discovery and delivery of the most relevant and suitable services in a spontaneous network is a problem of paramount importance. In this paper, we propose an architecture that can support context-aware service discovery and delivery for resource-constrained mobile devices. At the heart of the architecture is the μJini proxy which mediates the discovery and delivery processes. Its delivery subsystem provides thin-client based adaptation for fat service delivery that does not fit into thin client devices. To demonstrate its effectiveness, we developed a proof-of-concept prototype, focusing first on J2ME smart-phones. © 2005 IEEE