Analyzing capacitance-voltage measurements of vertical wrapped-gated nanowires

The capacitance of arrays of vertical wrapped-gate InAs nanowires are analyzed. With the help of a Poisson-Schr"odinger solver, information about the doping density can be obtained directly. Further features in the measured capacitance-voltage characteristics can be attributed to the presence of surface states as well as the coexistence of electrons and holes in the wire. For both scenarios, quantitative estimates are provided. It is furthermore shown that the difference between the actual capacitance and the geometrical limit is quite large, and depends strongly on the nanowire material.Comment: 15 pages, 6 Figures included, to appear in Nanotechnolog

Improving comparability between microarray probe signals by thermodynamic intensity correction

Signals from different oligonucleotide probes against the same target show great variation in intensities. However, detection of differences along a sequence e.g. to reveal intron/exon architecture, transcription boundary as well as simple absent/present calls depends on comparisons between different probes. It is therefore of great interest to correct for the variation between probes. Much of this variation is sequence dependent. We demonstrate that a thermodynamic model for hybridization of either DNA or RNA to a DNA microarray, which takes the sequence-dependent probe affinities into account significantly reduces the signal fluctuation between probes targeting the same gene transcript. For a test set of tightly tiled yeast genes, the model reduces the variance by up to a factor ∼1/3. As a consequence of this reduction, the model is shown to yield a more accurate determination of transcription start sites for a subset of yeast genes. In another application, we identify present/absent calls for probes hybridized to the sequenced Escherichia coli strain O157:H7 EDL933. The model improves the correct calls from 85 to 95% relative to raw intensity measures. The model thus makes applications which depend on comparisons between probes aimed at different sections of the same target more reliable

Response of young and adult birds to the same environmental variables and different spatial scales during post breeding period

Context: How do young birds achieve spatial knowledge about the environment during the initial stages of their life? They may follow adults, so gaining social information and learning; alternatively, young birds may acquire knowledge of the environment themselves by experiencing habitat and landscape features. If learning is at least partially independent of adults then young birds should respond to landscape composition at finer spatial scale than adults, who possess knowledge over a larger area. Objectives: We studied the responses of juvenile, immature and adult Caspian Gull Larus cachinnans to the same habitat and landscape variables, but at several spatial scales (ranging from 2.5 to 15\ua0km), during post-breeding period. Methods: We surveyed 61 fish ponds (foraging patches) in southern Poland and counted Caspian gulls. Results: Juvenile birds responded at finer spatial scales to the factors than did adults. Immature birds showed complicated, intermediate responses to spatial scale. The abundance of juvenile birds was mostly correlated with the landscape composition (positively with the cover of corridors and negatively with barriers). Adult abundance was positively related to foraging patch quality (fish stock), which clearly required previous spatial experience of the environment. The abundance of all age classes were moderately correlated with each other indicating that social behaviour may also contribute to the learning of the environment. Conclusions: This study shows that as birds mature, they respond differently to components of their environment at different spatial scales. This has considerable ecological consequences for their distribution across environments

Strong tuning of Rashba spin orbit interaction in single InAs nanowires

A key concept in the emerging field of spintronics is the gate voltage or electric field control of spin precession via the effective magnetic field generated by the Rashba spin orbit interaction. Here, we demonstrate the generation and tuning of electric field induced Rashba spin orbit interaction in InAs nanowires where a strong electric field is created either by a double gate or a solid electrolyte surrounding gate. In particular, the electrolyte gating enables six-fold tuning of Rashba coefficient and nearly three orders of magnitude tuning of spin relaxation time within only 1 V of gate bias. Such a dramatic tuning of spin orbit interaction in nanowires may have implications in nanowire based spintronic devices.Comment: Nano Letters, in pres

Cyclebase.org: version 2.0, an updated comprehensive, multi-species repository of cell cycle experiments and derived analysis results

Cell division involves a complex series of events orchestrated by thousands of molecules. To study this process, researchers have employed mRNA expression profiling of synchronously growing cell cultures progressing through the cell cycle. These experiments, which have been carried out in several organisms, are not easy to access, combine and evaluate. Complicating factors include variation in interdivision time between experiments and differences in relative duration of each cell-cycle phase across organisms. To address these problems, we created Cyclebase, an online resource of cell-cycle-related experiments. This database provides an easy-to-use web interface that facilitates visualization and download of genome-wide cell-cycle data and analysis results. Data from different experiments are normalized to a common timescale and are complimented with key cell-cycle information and derived analysis results. In Cyclebase version 2.0, we have updated the entire database to reflect changes to genome annotations, included information on cyclin-dependent kinase (CDK) substrates, predicted degradation signals and loss-of-function phenotypes from genome-wide screens. The web interface has been improved and provides a single, gene-centric graph summarizing the available cell-cycle experiments. Finally, key information and links to orthologous and paralogous genes are now included to further facilitate comparison of cell-cycle regulation across species. Cyclebase version 2.0 is available at http://www.cyclebase.org

Cyclebase.org—a comprehensive multi-organism online database of cell-cycle experiments

The past decade has seen the publication of a large number of cell-cycle microarray studies and many more are in the pipeline. However, data from these experiments are not easy to access, combine and evaluate. We have developed a centralized database with an easy-to-use interface, Cyclebase.org, for viewing and downloading these data. The user interface facilitates searches for genes of interest as well as downloads of genome-wide results. Individual genes are displayed with graphs of expression profiles throughout the cell cycle from all available experiments. These expression profiles are normalized to a common timescale to enable inspection of the combined experimental evidence. Furthermore, state-of-the-art computational analyses provide key information on both individual experiments and combined datasets such as whether or not a gene is periodically expressed and, if so, the time of peak expression. Cyclebase is available at http://www.cyclebase.org

A Deletion in the Canine POMC Gene Is Associated with Weight and Appetite in Obesity-Prone Labrador Retriever Dogs.

Sequencing of candidate genes for obesity in Labrador retriever dogs identified a 14 bp deletion in pro-opiomelanocortin (POMC) with an allele frequency of 12%. The deletion disrupts the β-MSH and β-endorphin coding sequences and is associated with body weight (per allele effect of 0.33 SD), adiposity, and greater food motivation. Among other dog breeds, the deletion was only found in the closely related flat-coat retriever (FCR), where it is similarly associated with body weight and food motivation. The mutation is significantly more common in Labrador retrievers selected to become assistance dogs than pets. In conclusion, the deletion in POMC is a significant modifier of weight and appetite in Labrador retrievers and FCRs and may influence other behavioral traits.We are grateful to Rachel Moxon of Guide Dogs UK for collecting the assistance dog samples; Stephen J Sharp of the MRC Epidemiology Unit for his statistical advice; Jens Häggström, Karin Hultin Jäderlund and Berndt Klingeborn for the Swedish dog samples; Anne White for efforts to develop a canine beta MSH assay and adaptation of her original for figure 1b; and the Dogslife Consortium for samples from British Labrador retrievers (supported by an Institute Core Strategic Grant from the BBSRC to the Roslin Institute). A full list of the investigators who contributed to the Dogslife project is available from www.dogslife.ac.uk/who-runs-dogslife. AJG's academic post at the University of Liverpool is financially supported by Royal Canin. The work was primarily supported by the Wellcome Trust (Senior Investigator Award 095515/Z/11/Z and Strategic Award 100574/Z/12/Z), MRC (MRC Metabolic Diseases Unit, award 4050281695 and MRC_MC_UU_12012/5), and Dogs Trust. The authors would like to thank all the veterinary surgeons and nurses, owners and dogs who contributed samples.This is the final version of the article. It first appeared from Elsevier via https://doi.org/10.1016/j.cmet.2016.04.01

Paleopolyploidy in the Brassicales: Analyses of the Cleome Transcriptome Elucidate the History of Genome Duplications in Arabidopsis and Other Brassicales

The analysis of the Arabidopsis genome revealed evidence of three ancient polyploidy events in the evolution of the Brassicaceae, but the exact phylogenetic placement of these events is still not resolved. The most recent event is called the At-α (alpha) or 3R, the intermediate event is referred to as the At-β (beta) or 2R, and the oldest is the At-γ (gamma) or 1R. It has recently been established that At-γ is shared with other Rosids, including papaya (Carica), poplar (Populus), and grape (Vitis), whereas data to date suggest that At-α is Brassicaceae specific. To address more precisely when the At-α and At-β events occurred and which plant lineages share these paleopolyploidizations, we sequenced and analyzed over 4,700 normalized expressed sequence tag sequences from the Cleomaceae, the sister family to the Brassicaceae. Analysis of these Cleome data with homologous sequences from other Rosid genomes (Arabidopsis, Carica, Gossypium, Populus, and Vitis) yielded three major findings: 1) confirmation of a Cleome-specific paleopolyploidization (Cs-α) that is independent of the Brassicaceae At-α paleopolyploidization; 2) Cleome and Arabidopsis share the At-β duplication, which is lacking from papaya within the Brassicales; and 3) rates of molecular evolution are faster for the herbaceous annual taxa Arabidopsis and Cleome than the other predominantly woody perennial Rosid lineages. These findings contribute to our understanding of the dynamics of genome duplication and evolution within one of the most comprehensively surveyed clades of plants, the Rosids, and clarify the complex history of the At-α, At-β, and At-γ duplications of Arabidopsis

Dynamic probe selection for studying microbial transcriptome with high-density genomic tiling microarrays

<p>Abstract</p> <p>Background</p> <p>Current commercial high-density oligonucleotide microarrays can hold millions of probe spots on a single microscopic glass slide and are ideal for studying the transcriptome of microbial genomes using a tiling probe design. This paper describes a comprehensive computational pipeline implemented specifically for designing tiling probe sets to study microbial transcriptome profiles.</p> <p>Results</p> <p>The pipeline identifies every possible probe sequence from both forward and reverse-complement strands of all DNA sequences in the target genome including circular or linear chromosomes and plasmids. Final probe sequence lengths are adjusted based on the maximal oligonucleotide synthesis cycles and best isothermality allowed. Optimal probes are then selected in two stages - sequential and gap-filling. In the sequential stage, probes are selected from sequence windows tiled alongside the genome. In the gap-filling stage, additional probes are selected from the largest gaps between adjacent probes that have already been selected, until a predefined number of probes is reached. Selection of the highest quality probe within each window and gap is based on five criteria: sequence uniqueness, probe self-annealing, melting temperature, oligonucleotide length, and probe position.</p> <p>Conclusions</p> <p>The probe selection pipeline evaluates global and local probe sequence properties and selects a set of probes dynamically and evenly distributed along the target genome. Unique to other similar methods, an exact number of non-redundant probes can be designed to utilize all the available probe spots on any chosen microarray platform. The pipeline can be applied to microbial genomes when designing high-density tiling arrays for comparative genomics, ChIP chip, gene expression and comprehensive transcriptome studies.</p