Exploring the use of internal and externalcontrols for assessing microarray technical performance

<p>Abstract</p> <p>Background</p> <p>The maturing of gene expression microarray technology and interest in the use of microarray-based applications for clinical and diagnostic applications calls for quantitative measures of quality. This manuscript presents a retrospective study characterizing several approaches to assess technical performance of microarray data measured on the Affymetrix GeneChip platform, including whole-array metrics and information from a standard mixture of external spike-in and endogenous internal controls. Spike-in controls were found to carry the same information about technical performance as whole-array metrics and endogenous "housekeeping" genes. These results support the use of spike-in controls as general tools for performance assessment across time, experimenters and array batches, suggesting that they have potential for comparison of microarray data generated across species using different technologies.</p> <p>Results</p> <p>A layered PCA modeling methodology that uses data from a number of classes of controls (spike-in hybridization, spike-in polyA+, internal RNA degradation, endogenous or "housekeeping genes") was used for the assessment of microarray data quality. The controls provide information on multiple stages of the experimental protocol (e.g., hybridization, RNA amplification). External spike-in, hybridization and RNA labeling controls provide information related to both assay and hybridization performance whereas internal endogenous controls provide quality information on the biological sample. We find that the variance of the data generated from the external and internal controls carries critical information about technical performance; the PCA dissection of this variance is consistent with whole-array quality assessment based on a number of quality assurance/quality control (QA/QC) metrics.</p> <p>Conclusions</p> <p>These results provide support for the use of both external and internal RNA control data to assess the technical quality of microarray experiments. The observed consistency amongst the information carried by internal and external controls and whole-array quality measures offers promise for rationally-designed control standards for routine performance monitoring of multiplexed measurement platforms.</p

Aptamers for pharmaceuticals and their application in environmental analytics

Aptamers are single-stranded DNA or RNA oligonucleotides, which are able to bind with high affinity and specificity to their target. This property is used for a multitude of applications, for instance as molecular recognition elements in biosensors and other assays. Biosensor application of aptamers offers the possibility for fast and easy detection of environmental relevant substances. Pharmaceutical residues, deriving from human or animal medical treatment, are found in surface, ground, and drinking water. At least the whole range of frequently administered drugs can be detected in noticeable concentrations. Biosensors and assays based on aptamers as specific recognition elements are very convenient for this application because aptamer development is possible for toxic targets. Commonly used biological receptors for biosensors like enzymes or antibodies are mostly unavailable for the detection of pharmaceuticals. This review describes the research activities of aptamer and sensor developments for pharmaceutical detection, with focus on environmental applications

Amyloid Plaques Beyond Aβ: A Survey of the Diverse Modulators of Amyloid Aggregation

Aggregation of the amyloid-β (Aβ) peptide is strongly correlated with Alzheimer’s disease (AD). Recent research has improved our understanding of the kinetics of amyloid fibril assembly and revealed new details regarding different stages in plaque formation. Presently, interest is turning toward studying this process in a holistic context, focusing on cellular components which interact with the Aβ peptide at various junctures during aggregation, from monomer to cross-β amyloid fibrils. However, even in isolation, a multitude of factors including protein purity, pH, salt content, and agitation affect Aβ fibril formation and deposition, often producing complicated and conflicting results. The failure of numerous inhibitors in clinical trials for AD suggests that a detailed examination of the complex interactions that occur during plaque formation, including binding of carbohydrates, lipids, nucleic acids, and metal ions, is important for understanding the diversity of manifestations of the disease. Unraveling how a variety of key macromolecular modulators interact with the Aβ peptide and change its aggregation properties may provide opportunities for developing therapies. Since no protein acts in isolation, the interplay of these diverse molecules may differentiate disease onset, progression, and severity, and thus are worth careful consideration

ICAR: endoscopic skull‐base surgery

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Storage and release of spermatozoa from the pre-uterine tube reservoir

In mammals, after coitus a small number of spermatozoa enter the uterine tube and following attachment to uterine tube epithelium are arrested in a non-capacitated state until peri-ovulatory signalling induces their detachment. Whilst awaiting release low numbers of spermatozoa continually detach from the epithelium and the uterine tube reservoir risks depletion. There is evidence of attachment of spermatozoa to uterine epithelium in several species which might form a potential pre-uterine tube reservoir. In this study we demonstrate that: (1) dog spermatozoa attach to uterine epithelium and maintain flagellar activity, (2) in non-capacitating conditions spermatozoa progressively detach with a variety of motility characteristics, (3) attachment is not influenced by epithelial changes occurring around ovulation, (4) attachment to uterine epithelium slows capacitation, (5) capacitated spermatozoa have reduced ability to attach to uterine epithelium, (6) under capacitating conditions increased numbers of spermatozoa detach and exhibit transitional and hyperactive motility which differ to those seen in non-capacitating conditions, (7) detachment of spermatozoa and motility changes can be induced by post-ovulation but not pre-ovulation uterine tube flush fluid and by components of follicular fluid and solubilised zona pellucida, (8) prolonged culture does not change the nature of the progressive detachment seen in non-capacitating conditions nor the potential for increased detachment in capacitating conditions. We postulate that in some species binding of spermatozoa to uterine epithelium is an important component of the transport of spermatozoa. Before ovulation low numbers of spermatozoa continually detach, including those which are non-capacitated with fast forward progressive motility allowing the re-population of the uterine tube, whilst around the time of ovulation, signalling from as-yet unknown factors associated with follicular fluid, oocytes and uterine tube secretion promotes the detachment of large numbers of capacitated spermatozoa with hyperactive motility that may contribute to the fertilising pool