Using surveys of Affymetrix GeneChips to study antisense expression.

We have used large surveys of Affymetrix GeneChip data in the public domain to conduct a study of antisense expression across diverse conditions. We derive correlations between groups of probes which map uniquely to the same exon in the antisense direction. When there are no probes assigned to an exon in the sense direction we find that many of the antisense groups fail to detect a coherent block of transcription. We find that only a minority of these groups contain coherent blocks of antisense expression suggesting transcription. We also derive correlations between groups of probes which map uniquely to the same exon in both sense and antisense direction. In some of these cases the locations of sense probes overlap with the antisense probes, and the sense and antisense probe intensities are correlated with each other. This configuration suggests the existence of a Natural Antisense Transcript (NAT) pair. We find the majority of such NAT pairs detected by GeneChips are formed by a transcript of an established gene and either an EST or an mRNA. In order to determine the exact antisense regulatory mechanism indicated by the correlation of sense probes with antisense probes, a further investigation is necessary for every particular case of interest. However, the analysis of microarray data has proved to be a good method to reconfirm known NATs, discover new ones, as well as to notice possible problems in the annotation of antisense transcripts

Identifying the impact of G-quadruplexes on Affymetrix 3' arrays using cloud computing.

A tetramer quadruplex structure is formed by four parallel strands of DNA/ RNA containing runs of guanine. These quadruplexes are able to form because guanine can Hoogsteen hydrogen bond to other guanines, and a tetrad of guanines can form a stable arrangement. Recently we have discovered that probes on Affymetrix GeneChips that contain runs of guanine do not measure gene expression reliably. We associate this finding with the likelihood that quadruplexes are forming on the surface of GeneChips. In order to cope with the rapidly expanding size of GeneChip array datasets in the public domain, we are exploring the use of cloud computing to replicate our experiments on 3' arrays to look at the effect of the location of G-spots (runs of guanines). Cloud computing is a recently introduced high-performance solution that takes advantage of the computational infrastructure of large organisations such as Amazon and Google. We expect that cloud computing will become widely adopted because it enables bioinformaticians to avoid capital expenditure on expensive computing resources and to only pay a cloud computing provider for what is used. Moreover, as well as financial efficiency, cloud computing is an ecologically-friendly technology, it enables efficient data-sharing and we expect it to be faster for development purposes. Here we propose the advantageous use of cloud computing to perform a large data-mining analysis of public domain 3' arrays

Uncovering the expression patterns of chimeric transcripts using surveys of affymetrix GeneChips.

BACKGROUND: A chimeric transcript is a single RNA sequence which results from the transcription of two adjacent genes. Recent studies estimate that at least 4% of tandem human gene pairs may form chimeric transcripts. Affymetrix GeneChip data are used to study the expression patterns of tens of thousands of genes and the probe sequences used in these microarrays can potentially map to exotic RNA sequences such as chimeras. RESULTS: We have studied human chimeras and investigated their expression patterns using large surveys of Affymetrix microarray data obtained from the Gene Expression Omnibus. We show that for six probe sets, a unique probe mapping to a transcript produced by one of the adjacent genes can be used to identify the expression patterns of readthrough transcripts. Furthermore, unique probes mapping to an intergenic exon present only in the MASK-BP3 chimera can be used directly to study the expression levels of this transcript. CONCLUSIONS: We have attempted to implement a new method for identifying tandem chimerism. In this analysis unambiguous probes are needed to measure run-off transcription and probes that map to intergenic exons are particularly valuable for identifying the expression of chimeras

Adapting the Bass Guitar for One-Handed Playing

This paper presents a prototype system for adapting the bass guitar for one-handed musicians. We discuss existing solutions to accessible musical instruments, followed by the results of an online survey of bass guitarists, which informed the design of a prototype bass guitar adaptation. The adaptation comprises a foot-operated MIDI controller with a solenoid-actuated fretting mechanism, providing access to six frets across two strings of the bass. A study involving six bassists rehearsing and writing a bass guitar accompaniment with the adapted bass highlighted unexpected facets of bass guitar playing, and provided insights into the design of future accessible string instruments

Inhibition of the Bloom's and Werner's syndrome helicases by G-quadruplex interacting ligands.

G-Quadruplex DNAs are folded, non-Watson-Crick structures that can form within guanine-rich DNA sequences such as telomeric repeats. Previous studies have identified a series of trisubstituted acridine derivatives that are potent and selective ligands for G-quadruplex DNA. These ligands have been shown previously to inhibit the activity of telomerase, the specialized reverse transcriptase that regulates telomere length. The RecQ family of DNA helicases, which includes the Bloom's (BLM) and Werner's (WRN) syndrome gene products, are apparently unique among cellular helicases in their ability to efficiently disrupt G-quadruplex DNA. This property may be relevant to telomere maintenance, since it is known that the sole budding yeast RecQ helicase, Sgs1p, is required for a telomerase-independent telomere lengthening pathway reminiscent of the "ALT" pathway in human cells. Here, we show that trisubstituted acridine ligands are potent inhibitors of the helicase activity of the BLM and WRN proteins on both G-quadruplex and B-form DNA substrates. Inhibition of helicase activity is associated with both a reduction in the level of binding of the helicase to G-quadruplex DNA and a reduction in the degree to which the G-quadruplex DNA can support DNA-dependent ATPase activity. We discuss these results in the context of the possible utility of trisubstituted acridines as antitumor agents for the disruption of both telomerase-dependent and telomerase-independent telomere maintenance

Establishing a major cause of discrepancy in the calibration of Affymetrix GeneChips

Background: Affymetrix GeneChips are a popular platform for performing whole-genome experiments on the transcriptome. There are a range of different calibration steps, and users are presented with choices of different background subtractions, normalisations and expression measures. We wished to establish which of the calibration steps resulted in the biggest uncertainty in the sets of genes reported to be differentially expressed.Results: Our results indicate that the sets of genes identified as being most significantly differentially expressed, as estimated by the z-score of fold change, is relatively insensitive to the choice of background subtraction and normalisation. However, the contents of the gene list are most sensitive to the choice of expression measure. This is irrespective of whether the experiment uses a rat, mouse or human chip and whether the chip definition is made using probe mappings from Unigene, RefSeq, Entrez Gene or the original Affymetrix definitions. It is also irrespective of whether both Present and Absent, or just Present, Calls from the MAS5 algorithm are used to filter genelists, and this conclusion holds for genes of differing intensities. We also reach the same conclusion after assigning genes to be differentially expressed using t-statistics, although this approach results in a large amount of false positives in the sets of genes identified due to the small numbers of replicates typically used in microarray experiments.Conclusion: The major calibration uncertainty that biologists need to consider when analysing Affymetrix data is how their multiple probe values are condensed into one expression measure

Signatures of Reductive Magnetic Mineral Diagenesis From Unmixing of First-Order Reversal Curves

Diagenetic alteration of magnetic minerals occurs in all sedimentary environments and tends to be severe in reducing environments. Magnetic minerals provide useful information about sedimentary diagenetic processes, which makes it valuable to use magnetic properties to identify the diagenetic environment in which the magnetic minerals occur and to inform interpretations of paleomagnetic recording or environmental processes. We use a newly developed first-order reversal curve (FORC) unmixing method on well-studied samples to illustrate how magnetic properties can be used to assess diagenetic processes in reducing sedimentary environments. From our analysis of multiple data sets, consistent magnetic components are identified for each stage of reductive diagenesis. Relatively unaltered detrital and biogenic magnetic mineral assemblages in surficial oxic to manganous diagenetic environments undergo progressive dissolution with burial into ferruginous and sulfidic environments, and largely disappear at the sulfate-methane transition (SMT). Below the SMT, a weak superparamagnetic to largely non-interacting stable single domain (SD) greigite component is observed in all studied data sets. Moderately interacting stable SD authigenic pyrrhotite and strongly interacting stable SD greigite are observed commonly in methanic environments. Recognition of these characteristic magnetic components enables identification of key diagenetic processes and should help to constrain interpretation of magnetic mineral assemblages in future studies. A key question for future studies concerns whether stable SD greigite forms in the sulfidic or methanic zones, where formation in deeper methanic sediments will cause greater delays in paleomagnetic signal recording. Authigenic pyrrhotite forms in methanic environments, so it will usually record a delayed paleomagnetic signal.European Research Council (320750) Australian Research Council (DP160100805

Influence of water intercalation and hydration on chemical decomposition and ion transport in methylammonium lead halide perovskites

The use of methylammonium (MA) lead halide perovskites \ce{CH3NH3PbX3} (X=I, Br, Cl) in perovskite solar cells (PSCs) has made great progress in performance efficiency during recent years. However, the rapid decomposition of \ce{MAPbI3} in humid environments hinders outdoor application of PSCs, and thus, a comprehensive understanding of the degradation mechanism is required. To do this, we investigate the effect of water intercalation and hydration of the decomposition and ion migration of \ce{CH3NH3PbX3} using first-principles calculations. We find that water interacts with \ce{PbX6} and MA through hydrogen bonding, and the former interaction enhances gradually, while the latter hardly changes when going from X=I to Br and to Cl. Thermodynamic calculations indicate that water exothermically intercalates into the perovskite, while the water intercalated and monohydrated compounds are stable with respect to decomposition. More importantly, the water intercalation greatly reduces the activation energies for vacancy-mediated ion migration, which become higher going from X=I to Br and to Cl. Our work indicates that hydration of halide perovskites must be avoided to prevent the degradation of PSCs upon moisture exposure

Domain State Diagnosis in Rock Magnetism: Evaluation of Potential Alternatives to the Day Diagram

The Day diagram is used extensively in rock magnetism for domain state diagnosis. It has been shown recently to be fundamentally ambiguous for ten sets of reasons. This ambiguity highlights the urgency for adopting suitable alternative approaches to identify the domain state of magnetic mineral components in rock magnetic studies. We evaluate ten potential alternative approaches here and conclude that four have value for identifying data trends, but, like the Day diagram, they are affected by use of bulk parameters that compromise domain state diagnosis in complex samples. Three approaches based on remanence curve and hysteresis loop unmixing, when “supervised” by independent data to avoid non-uniqueness of solutions provide valuable component-specific information that can be linked by inference to domain state. Three further approaches based on first-order reversal curve (FORC) diagrams provide direct domain state diagnosis with varying effectiveness. Environmentally important high coercivity hematite and goethite are represented with variable effectiveness in the evaluated candidate approaches. These minerals occur predominantly in non-interacting single domain particle assemblages in paleomagnetic contexts, so domain state diagnosis is more critical for ferrimagnetic minerals. Treating the high-coercivity component separately following normal rock magnetic procedures allows focus on the more vexing problem of diagnosing domain state in ferrimagnetic mineral assemblages. We suggest a move away from non-diagnostic methods based on bulk parameters and adoption of approaches that provide unambiguous component-specific domain state identification, among which various FORC-based approaches provide diagnostic information.European Research Council (ERC) Australian Research Council (ARC

The Midwives Service Scheme in Nigeria

Seye Abimbola and colleagues describe and evaluate their programme in Nigeria of recruiting midwives to rural areas to provide skilled attendance at birth, which is much poorer than in urban areas