OligoRAP – an Oligo Re-Annotation Pipeline to improve annotation and estimate target specificity

Background - High throughput gene expression studies using oligonucleotide microarrays depend on the specificity of each oligonucleotide (oligo or probe) for its target gene. However, target specific probes can only be designed when a reference genome of the species at hand were completely sequenced, when this genome were completely annotated and when the genetic variation of the sampled individuals were completely known. Unfortunately there is not a single species for which such a complete data set is available. Therefore, it is important that probe annotation can be updated frequently for optimal interpretation of microarray experiments. Results - In this paper we present OligoRAP, a pipeline to automatically update the annotation of oligo libraries and estimate oligo target specificity. OligoRAP uses a reference genome assembly with Ensembl and Entrez Gene annotation supplemented with a set of unmapped transcripts derived from RefSeq and UniGene to handle assembly gaps. OligoRAP produces alignments of each oligo with the reference assembly as well as with unmapped transcripts. These alignments are re-mapped to the annotation sources, which results in a concise, as complete as possible and up-to-date annotation of the oligo library. The building blocks of this pipeline are BioMoby web services creating a highly modular and distributed system with a robust, remote programmatic interface. OligoRAP was used to update the annotation for a subset of 791 oligos from the ARK-Genomics 20 K chicken array, which were selected as starting material for the oligo annotation session of the EADGENE/SABRE Post-analysis workshop. Based on the updated annotation about one third of these oligos is problematic with regard to target specificity. In addition, the accession numbers or ids the oligos were originally designed for no longer exist in the updated annotation for almost half of the oligos. Conclusion - As microarrays are designed on incomplete data, it is important to update probe annotation and check target specificity regularly. OligoRAP provides both and due to its design based on BioMoby web services it can easily be embedded as an oligo annotation engine in customised applications for microarray data analysis. The dramatic difference in updated annotation and target specificity for the ARK-Genomics 20 K chicken array as compared to the original data emphasises the need for regular updates

Influence of Superabsorbent Polymers on Properties of High-Performance Concrete with Active Supplementary Cementitious Materials of Nigeria

Concrete of strengths classes ≥ C55/67 referred to as high strength or highperformance concrete (HSC/HPC) are noted to be generally of low water/binder (W/B), made from binary or ternary cements with silica fume (SF) being a necessary constituent, and often requiring internal curing. Non-availability and high cost of SF in most sub-Saharan Africa like Nigeria however makes HSC/HPC production in this region very difficult and hence the continued search for alternative supplementary cementitious materials (SCM) with good performance properties as constituents of ternary/binary cements in HPC. This study thereby examines the strength properties of metastable calcined clay (MCC) based HPC cured internally with superabsorbent polymer (SAP) 0.2–0.3% (by weight of binder (bwob)). HPC mixtures of varied MCC and Rice husk ash (RHA) contents containing two SAP grain sizes labelled (SP1 ˂ 300 μm and SP2 ˂ 600 μm) were cast in 100 mm cubes and cured for varying ages (7, 14, 28 and 56 days) before testing. The hardened specimens were subjected to compressive strength and water absorption tests at the varied curing ages for the performance assessment of the binder types and SAP grain sizes in HPC with age. This study revealed the possibility of achieving Class 1 HPC (50–75 N/mm2) utilizing industry manufactured calcined clay and locally produced RHA in Nigeria. The compressive strength of HPCs increased as the curing age increases for both SCM type, SAP contents and grain sizes. RHA based HPCs however showed better strength performance at the early ages than the MCC based. SAP addition in MCC based HPCs led to slight decrease in compressive strength as the SAP contents increased while the RHA based HPCs on the other hand, revealed slight increase in compressive strength with increase in SAP contents

Critical Roles of Spätzle5 in Antimicrobial Peptide Production Against Escherichia coli in Tenebrio molitor Malpighian Tubules

The dimeric cytokine ligand Spätzle (Spz) is responsible for Toll pathway activation and antimicrobial peptide (AMP) production upon pathogen challenge in Tenebrio molitor. Here, we indicated that TmSpz5 has a functional role in response to bacterial infections. We showed that the highest expression of TmSpz5 is induced by Candida albicans. However, TmSpz5 knockdown reduced larval survival against Escherichia coli and Staphylococcus aureus. To evaluate the molecular mechanism underlying the observed survival differences, the role of TmSpz5 in AMP production was examined by RNA interference and microbial injection. T. molitor AMPs that are active against Gram-negative and -positive bacteria, including Tmtenecins, Tmattacins, Tmcoleoptericins, Tmtaumatin-like-proteins, and Tmcecropin-2, were significantly downregulated by TmSpz-5 RNAi in the Malpighian tubules (MTs) following a challenge with E. coli and S. aureus. However, upon infection with C. albicans the mRNA levels of most AMPs in the dsTmSpz5-injected group were similar to those in the control groups. Likewise, the expression of the transcription factors NF-κB, TmDorX2, and TmRelish were noticeably suppressed in the MTs of TmSpz5-silenced larvae. Moreover, E. coli-infected TmSpz5 knockdown larvae showed decreased antimicrobial activity in the MTs and hindgut compared with the control group. These results demonstrate that TmSpz5 has a defined role in T. molitor innate immunity by regulating AMP expression in MTs in response to E. coli

Using R in Taverna: RShell v1.2

Background: R is the statistical language commonly used by many life scientists in (omics) data by the open source workflow management system Taverna. However, Taverna had limited support for R, because it supported just a few data types and only a single output. Also, there was no support for graphical output and persistent sessions. Altogether this made using R in Taverna impractical.\ud \ud Findings: We have developed an R plugin for Taverna: RShell, which provides R functionality within workflows designed in Taverna. In order to fully support the R language, our RShell plugin directly uses the R interpreter. The RShell plugin consists of a Taverna processor for R scripts and an RShell Session Manager that communicates with the R server. We made the RShell processor highly configurable allowing the user to define multiple inputs and outputs. Also, various data types are supported, such as strings, numeric data and images. To limit data transport between multiple RShell processors, the RShell plugin also supports persistent sessions. Here, we will describe the architecture of RShell and the new features that are introduced in version 1.2, i.e.: i) Support for R up to and including R version 2.9; ii) Support for persistent sessions to limit data transfer; iii) Support for vector graphics output through PDF; iv) Syntax highlighting of the R code; v) Improved usability through fewer port types. Our new RShell processor is backwards compatible with workflows that use older versions of the RShell processor. We demonstrate the value of the RShell processor by a use-case workflow that maps oligonucleotide probes designed with DNA sequence information from Vega onto the Ensembl genome assembly.\ud \ud Conclusion: Our RShell plugin enables Taverna users to employ R scripts within their workflows in a highly configurable way

Single to Double Hump Transition in the Equilibrium Distribution Function of Relativistic Particles

We unveil a transition from single peaked to bimodal velocity distribution in a relativistic fluid under increasing temperature, in contrast with a non-relativistic gas, where only a monotonic broadening of the bell-shaped distribution is observed. Such transition results from the interplay between the raise in thermal energy and the constraint of maximum velocity imposed by the speed of light. We study the Bose-Einstein, the Fermi-Dirac, and the Maxwell-J\"uttner distributions, all exhibiting the same qualitative behavior. We characterize the nature of the transition in the framework of critical phenomena and show that it is either continuous or discontinuous, depending on the group velocity. We analyze the transition in one, two, and three dimensions, with special emphasis on two-dimensions, for which a possible experiment in graphene, based on the measurement of the Johnson-Nyquist noise, is proposed.Comment: 5 pages, 5 figure

Genetic variation in Pan species is shaped by demographic history and harbors lineage-specific functions

Chimpanzees (Pan troglodytes) and bonobos (Pan paniscus) are the closest living relatives of humans, but the two species show distinct behavioral and physiological differences, particularly regarding female reproduction. Despite their recent rapid decline, the demographic histories of the two species have been different during the past one to two million years, likely having an impact on their genomic diversity. Here, we analyze the inferred functional consequences of genetic variation across 69 individuals, making use of the most complete dataset of genomes in the Pan clade to date. We test to which extent the demographic history influences the efficacy of purifying selection in these species. We find that small historical effective population sizes (Ne) correlate not only with low levels of genetic diversity, but also with a larger number of deleterious alleles in homozygosity and an increased proportion of deleterious changes at low frequencies. To investigate the putative genetic basis for phenotypic differences between chimpanzees and bonobos, we exploit the catalog of putatively deleterious protein-coding changes in each lineage. We show that bonobo-specific non-synonymous changes are enriched in genes related to age at menarche in humans, suggesting that the prominent physiological differences in the female reproductive system between chimpanzees and bonobos might be explained, in part, by putatively adaptive changes on the bonobo lineage

Graphene for spintronics: giant Rashba splitting due to hybridization with Au

Graphene in spintronics has so far primarily meant spin current leads of high performance because the intrinsic spin-orbit coupling of its pi-electrons is very weak. If a large spin-orbit coupling could be created by a proximity effect, the material could also form active elements of a spintronic device such as the Das-Datta spin field-effect transistor, however, metal interfaces often compromise the band dispersion of massless Dirac fermions. Our measurements show that Au intercalation at the graphene-Ni interface creates a giant spin-orbit splitting (~100 meV) in the graphene Dirac cone up to the Fermi energy. Photoelectron spectroscopy reveals hybridization with Au-5d states as the source for the giant spin-orbit splitting. An ab initio model of the system shows a Rashba-split dispersion with the analytically predicted gapless band topology around the Dirac point of graphene and indicates that a sharp graphene-Au interface at equilibrium distance will account for only ~10 meV spin-orbit splitting. The ab initio calculations suggest an enhancement due to Au atoms that get closer to the graphene and do not violate the sublattice symmetry.Comment: 16 pages (3 figures) + supplementary information 16 pages (14 figures

Regulation of caspase-3 processing by cIAP2 controls the switch between pro-inflammatory activation and cell death in microglia.

Cell Death and Disease is an open-access journal published by Nature Publishing Group. This work is licensed under a Creative Commons Attribution 4.0 International Licence. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in the credit line; if the material is not included under the Creative Commons licence, users will need to obtain permission from the licence holder to reproduce the material.The activation of microglia, resident immune cells of the central nervous system, and inflammation-mediated neurotoxicity are typical features of neurodegenerative diseases, for example, Alzheimer's and Parkinson's diseases. An unexpected role of caspase-3, commonly known to have executioner role for apoptosis, was uncovered in the microglia activation process. A central question emerging from this finding is what prevents caspase-3 during the microglia activation from killing those cells? Caspase-3 activation occurs as a two-step process, where the zymogen is first cleaved by upstream caspases, such as caspase-8, to form intermediate, yet still active, p19/p12 complex; thereafter, autocatalytic processing generates the fully mature p17/p12 form of the enzyme. Here, we show that the induction of cellular inhibitor of apoptosis protein 2 (cIAP2) expression upon microglia activation prevents the conversion of caspase-3 p19 subunit to p17 subunit and is responsible for restraining caspase-3 in terms of activity and subcellular localization. We demonstrate that counteracting the repressive effect of cIAP2 on caspase-3 activation, using small interfering RNA targeting cIAP2 or a SMAC mimetic such as the BV6 compound, reduced the pro-inflammatory activation of microglia cells and promoted their death. We propose that the different caspase-3 functions in microglia, and potentially other cell types, reside in the active caspase-3 complexes formed. These results also could indicate cIAP2 as a possible therapeutic target to modulate microglia pro-inflammatory activation and associated neurotoxicity observed in neurodegenerative disorders

Circular Single-Stranded Synthetic DNA Delivery Vectors for MicroRNA

Single-stranded (ss) circular oligodeoxynucleotides were previously found to undergo rolling circle transcription (RCT) by phage and bacterial RNA polymerases (RNAPs) into tandemly repetitive RNA multimers. Here, we redesign them to encode minimal primary miRNA mimics, with the long term aim of intracellular transcription followed by RNA processing and maturation via endogenous pathways. We describe an improved method for circularizing ss synthetic DNA for RCT by using a recently described thermostable RNA ligase, which does not require a splint oligonucleotide to juxtapose the ligating ends. In vitro transcription of four templates demonstrates that the secondary structure inherent in miRNA-encoding vectors does not impair their RCT by RNAPs previously shown to carry out RCT. A typical primary-miRNA rolling circle transcript was accurately processed by a human Drosha immunoprecipitate, indicating that if human RNAPs prove to be capable of RCT, the resulting transcripts should enter the endogenous miRNA processing pathway in human cells. Circular oligonucleotides are therefore candidate vectors for small RNA delivery in human cells, which express RNAPs related to those tested here

Collapse of superconductivity in a hybrid tin-graphene Josephson junction array

When a Josephson junction array is built with hybrid superconductor/metal/superconductor junctions, a quantum phase transition from a superconducting to a two-dimensional (2D) metallic ground state is predicted to happen upon increasing the junction normal state resistance. Owing to its surface-exposed 2D electron gas and its gate-tunable charge carrier density, graphene coupled to superconductors is the ideal platform to study the above-mentioned transition between ground states. Here we show that decorating graphene with a sparse and regular array of superconducting nanodisks enables to continuously gate-tune the quantum superconductor-to-metal transition of the Josephson junction array into a zero-temperature metallic state. The suppression of proximity-induced superconductivity is a direct consequence of the emergence of quantum fluctuations of the superconducting phase of the disks. Under perpendicular magnetic field, the competition between quantum fluctuations and disorder is responsible for the resilience at the lowest temperatures of a superconducting glassy state that persists above the upper critical field. Our results provide the entire phase diagram of the disorder and magnetic field-tuned transition and unveil the fundamental impact of quantum phase fluctuations in 2D superconducting systems.Comment: 25 pages, 6 figure