Mobile small RNAs and their role in regulating cytosine methylation of DNA

Small (s)RNAs of 21 to 24 nucleotides are associated with RNA silencing and methylation of DNA cytosine residues. All sizes can move from cell-to-cell and long distance in plants, directing RNA silencing in destination cells. Twenty-four nucleotide sRNAs are the predominant long-distance mobile species. Thousands move from shoot to root, where they target methylation of transposable elements both directly and indirectly. We derive several classes of interaction between small RNAs and methylation and use these to explore the mechanisms of methylation and gene expression that associate with mobile sRNA signaling.This work was supported by European Research Council Advanced Investigator Grant ERC-2013-AdG 340642 – TRIBE. Work in MGL’s laboratory is supported by La Trobe University

Experimental verification of dose enhancement effects in a lung phantom from inline magnetic fields.

BACKGROUND AND PURPOSE: To present experimental evidence of lung dose enhancement effects caused by strong inline magnetic fields. MATERIALS AND METHODS: A permanent magnet device was utilised to generate 0.95T-1.2T magnetic fields that encompassed two small lung-equivalent phantoms of density 0.3g/cm3. Small 6MV and 10MV photon beams were incident parallel with the magnetic field direction and Gafchromic EBT3 film was placed inside the lung phantoms, perpendicular to the beam (experiment 1) and parallel to the beam (experiment 2). Monte Carlo simulations of experiment 1 were also performed. RESULTS: Experiment 1: The 1.2T inline magnetic field induced a 12% (6MV) and 14% (10MV) increase in the dose at the phantom centre. The Monte Carlo modelling matched well (±2%) to the experimentally observed results. Experiment 2: A 0.95T field peaked at the phantom centroid (but not at the phantom entry/exit regions) details a clear dose increase due to the magnetic field of up to 25%. CONCLUSIONS: This experimental work has demonstrated how strong inline magnetic fields act to enhance the dose to lower density mediums such as lung tissue. Clinically, such scenarios will arise in inline MRI-linac systems for treatment of small lung tumours

Methods for discovering genomic loci exhibiting complex patterns of differential methylation.

BACKGROUND: Cytosine methylation is widespread in most eukaryotic genomes and is known to play a substantial role in various regulatory pathways. Unmethylated cytosines may be converted to uracil through the addition of sodium bisulphite, allowing genome-wide quantification of cytosine methylation via high-throughput sequencing. The data thus acquired allows the discovery of methylation 'loci'; contiguous regions of methylation consistently methylated across biological replicates. The mapping of these loci allows for associations with other genomic factors to be identified, and for analyses of differential methylation to take place. RESULTS: The segmentSeq R package is extended to identify methylation loci from high-throughput sequencing data from multiple experimental conditions. A statistical model is then developed that accounts for biological replication and variable rates of non-conversion of cytosines in each sample to compute posterior likelihoods of methylation at each locus within an empirical Bayesian framework. The same model is used as a basis for analysis of differential methylation between multiple experimental conditions with the baySeq R package. We demonstrate the capability of this method to analyse complex data sets in an analysis of data derived from multiple Dicer-like mutants in Arabidopsis. This reveals several novel behaviours at distinct sets of loci in response to loss of one or more of the Dicer-like proteins that indicate an antagonistic relationship between the Dicer-like proteins at at least some methylation loci. Finally, we show in simulation studies that this approach can be significantly more powerful in the detection of differential methylation than many existing methods in data derived from both mammalian and plant systems. CONCLUSIONS: The methods developed here make it possible to analyse high-throughput sequencing of the methylome of any given organism under a diverse set of experimental conditions. The methods are able to identify methylation loci and evaluate the likelihood that a region is truly methylated under any given experimental condition, allowing for downstream analyses that characterise differences between methylated and non-methylated regions of the genome. Futhermore, diverse patterns of differential methylation may also be characterised from these data

Single-atom spectroscopy of phosphorus dopants implanted into graphene

One of the keys behind the success of modern semiconductor technology has been the ion implantation of silicon, which allows its electronic properties to be tailored. For similar purposes, heteroatoms have been introduced into carbon nanomaterials both during growth and using post-growth methods. However, due to the nature of the samples, it has been challenging to determine whether the heteroatoms have been incorporated into the lattice as intended. Direct observations have so far been limited to N and B dopants, and incidental Si impurities. Furthermore, ion implantation of these materials is challenging due to the requirement of very low ion energies and atomically clean surfaces. Here, we provide the first atomic-resolution imaging and electron energy loss spectroscopy (EELS) evidence of phosphorus atoms in the graphene lattice, implanted by low-energy ion irradiation. The measured P L ₂‚₃-edge shows excellent agreement with an ab initio spectrum simulation, conclusively identifying the P in a buckled substitutional configuration. While advancing the use of EELS for single-atom spectroscopy, our results demonstrate the viability of phosphorus as a lattice dopant in sp ²-bonded carbon structures and provide its unmistakable fingerprint for further studies

Normal levels of p27Xic1 are necessary for somite segmentation and determining pronephric organ size

The Xenopus laevis cyclin dependent kinase inhibitor p27Xic1 has been shown to be involved in exit from the cell cycle and differentiation of cells into a quiescent state in the nervous system, muscle tissue, heart and retina. We show that p27Xic1 is expressed in the developing kidney in the nephrostomal regions. Using over-expression and morpholino oligonucleotide (MO) knock-down approaches we show normal levels of p27Xic1 regulate pronephros organ size by regulating cell cycle exit. Knock-down of p27Xic1 expression using a MO prevented myogenesis, as previously reported; an effect that subsequently inhibits pronephrogenesis. Furthermore, we show that normal levels of p27Xic1 are required for somite segmentation also through its cell cycle control function. Finally, we provide evidence to suggest correct paraxial mesoderm segmentation is not necessary for pronephric induction in the intermediate mesoderm. These results indicate novel developmental roles for p27Xic1, and reveal its differentiation function is not universally utilised in all developing tissues

The Hot and Energetic Universe: AGN feedback in galaxy clusters and groups

Mechanical feedback via Active Galactic Nuclei (AGN) jets in the centres of galaxy groups and clusters is a crucial ingredient in current models of galaxy formation and cluster evolution. Jet feedback is believed to regulate gas cooling and thus star formation in the most massive galaxies, but a robust physical understanding of this feedback mode is currently lacking. The large collecting area, excellent spectral resolution and high spatial resolution of Athena+ will provide the breakthrough diagnostic ability necessary to develop this understanding, via: (1) the first kinematic measurements on relevant spatial scales of the hot gas in galaxy, group and cluster haloes as it absorbs the impact of AGN jets, and (2) vastly improved ability to map thermodynamic conditions on scales well-matched to the jets, lobes and gas disturbances produced by them. Athena+ will therefore determine for the first time how jet energy is dissipated and distributed in group and cluster gas, and how a feedback loop operates in group/cluster cores to regulate gas cooling and AGN fuelling. Athena+ will also establish firmly the cumulative impact of powerful radio galaxies on the evolution of baryons from the epoch of group/cluster formation to the present day

The Hot and Energetic Universe: AGN feedback in galaxy clusters and groups

Mechanical feedback via Active Galactic Nuclei (AGN) jets in the centres of galaxy groups and clusters is a crucial ingredient in current models of galaxy formation and cluster evolution. Jet feedback is believed to regulate gas cooling and thus star formation in the most massive galaxies, but a robust physical understanding of this feedback mode is currently lacking. The large collecting area, excellent spectral resolution and high spatial resolution of Athena+ will provide the breakthrough diagnostic ability necessary to develop this understanding, via: (1) the first kinematic measurements on relevant spatial scales of the hot gas in galaxy, group and cluster haloes as it absorbs the impact of AGN jets, and (2) vastly improved ability to map thermodynamic conditions on scales well-matched to the jets, lobes and gas disturbances produced by them. Athena+ will therefore determine for the first time how jet energy is dissipated and distributed in group and cluster gas, and how a feedback loop operates in group/cluster cores to regulate gas cooling and AGN fuelling. Athena+ will also establish firmly the cumulative impact of powerful radio galaxies on the evolution of baryons from the epoch of group/cluster formation to the present day

Fermi Gamma-ray Imaging of a Radio Galaxy

The Fermi Gamma-ray Space Telescope has detected the gamma-ray glow emanating from the giant radio lobes of the radio galaxy Centaurus A. The resolved gamma-ray image shows the lobes clearly separated from the central active source. In contrast to all other active galaxies detected so far in high-energy gamma-rays, the lobe flux constitutes a considerable portion (>1/2) of the total source emission. The gamma-ray emission from the lobes is interpreted as inverse Compton scattered relic radiation from the cosmic microwave background (CMB), with additional contribution at higher energies from the infrared-to-optical extragalactic background light (EBL). These measurements provide gamma-ray constraints on the magnetic field and particle energy content in radio galaxy lobes, and a promising method to probe the cosmic relic photon fields.Comment: 27 pages, includes Supplementary Online Material; corresponding authors: C.C. Cheung, Y. Fukazawa, J. Knodlseder, L. Stawar

Gene dispersion is the key determinant of the read count bias in differential expression analysis of RNA-seq data

Background: In differential expression analysis of RNA-sequencing (RNA-seq) read count data for two sample groups, it is known that highly expressed genes (or longer genes) are more likely to be differentially expressed which is called read count bias (or gene length bias). This bias had great effect on the downstream Gene Ontology over-representation analysis. However, such a bias has not been systematically analyzed for different replicate types of RNA-seq data. Results: We show that the dispersion coefficient of a gene in the negative binomial modeling of read counts is the critical determinant of the read count bias (and gene length bias) by mathematical inference and tests for a number of simulated and real RNA-seq datasets. We demonstrate that the read count bias is mostly confined to data with small gene dispersions (e.g., technical replicates and some of genetically identical replicates such as cell lines or inbred animals), and many biological replicate data from unrelated samples do not suffer from such a bias except for genes with some small counts. It is also shown that the sample-permuting GSEA method yields a considerable number of false positives caused by the read count bias, while the preranked method does not. Conclusion: We showed the small gene variance (similarly, dispersion) is the main cause of read count bias (and gene length bias) for the first time and analyzed the read count bias for different replicate types of RNA-seq data and its effect on gene-set enrichment analysis

Hip abduction weakness in elite junior footballers is common but easy to correct quickly: a prospective sports team cohort based study

Background: Hip abduction weakness has never been documented on a population basis as a common finding in a healthy group of athletes and would not normally be found in an elite adolescent athlete. This study aimed to show that hip abduction weakness not only occurs in this group but also is common and easy to correct with an unsupervised home based program. Methods: A prospective sports team cohort based study was performed with thirty elite adolescent under-17 Australian Rules Footballers in the Australian Institute of Sport/Australian Football League Under-17 training academy. The players had their hip abduction performance assessed and were then instructed in a hip abduction muscle training exercise. This was performed on a daily basis for two months and then they were reassessed.Results: The results showed 14 of 28 athletes who completed the protocol had marked weakness or a side-to-side difference of more than 25% at baseline. Two months later ten players recorded an improvement of ≥ 80% in their recorded scores. The mean muscle performance on the right side improved from 151 Newton (N) to 202 N (p<0.001) while on the left, the recorded results improved from 158 N to 223 N (p<0.001). Conclusions: The baseline values show widespread profound deficiencies in hip abduction performance not previously reported. Very large performance increases can be achieved, unsupervised, in a short period of time to potentially allow large clinically significant gains. This assessment should be an integral part of preparticipation screening and assessed in those with lower limb injuries. This particular exercise should be used clinically and more research is needed to determine its injury prevention and performance enhancement implications