Reference genome-independent assessment of mutation density using restriction enzyme-phased sequencing

<p>Abstract</p> <p>Background</p> <p>The availability of low cost sequencing has spurred its application to discovery and typing of variation, including variation induced by mutagenesis. Mutation discovery is challenging as it requires a substantial amount of sequencing and analysis to detect very rare changes and distinguish them from noise. Also challenging are the cases when the organism of interest has not been sequenced or is highly divergent from the reference.</p> <p>Results</p> <p>We describe the development of a simple method for reduced representation sequencing. Input DNA was digested with a single restriction enzyme and ligated to Y adapters modified to contain a sequence barcode and to provide a compatible overhang for ligation. We demonstrated the efficiency of this method at SNP discovery using rice and arabidopsis. To test its suitability for the discovery of very rare SNP, one control and three mutagenized rice individuals (1, 5 and 10 mM sodium azide) were used to prepare genomic libraries for Illumina sequencers by ligating barcoded adapters to <it>NlaIII </it>restriction sites. For genome-dependent discovery 15-30 million of 80 base reads per individual were aligned to the reference sequence achieving individual sequencing coverage from 7 to 15×. We identified high-confidence base changes by comparing sequences across individuals and identified instances consistent with mutations, i.e. changes that were found in a single treated individual and were solely GC to AT transitions. For genome-independent discovery 70-mers were extracted from the sequence of the control individual and single-copy sequence was identified by comparing the 70-mers across samples to evaluate copy number and variation. This <it>de novo </it>"genome" was used to align the reads and identify mutations as above. Covering approximately 1/5 of the 380 Mb genome of rice we detected mutation densities ranging from 0.6 to 4 per Mb of diploid DNA depending on the mutagenic treatment.</p> <p>Conclusions</p> <p>The combination of a simple and cost-effective library construction method, with Illumina sequencing, and the use of a bioinformatic pipeline allows practical SNP discovery regardless of whether a genomic reference is available.</p

Multimodal Imaging Reveals Bilateral Idiopathic Multiple Retinal Pigment Epithelial Detachments: A Case Report

Background: Retinal pigment epithelial detachment (RPED) is a nonspecific finding that is common in several ocular diseases; however, cases of bilateral idiopathic multiple RPEDs are rare. Less than 50 cases have been reported to date. Bilateral multiple RPEDs are usually idiopathic and benign in nature but can infrequently be associated with various ocular and systemic diseases, including central serous chorioretinopathy (CSC). The potential role of genetic factors in this condition remains elusive. We present a case where multimodal imaging assisted in revealing the diagnosis as well as discuss the potential implications of some of the genetic findings for this patient. Case report: A 30-year-old male presented with a chief complaint of mild, bilateral central blur of one-year duration. Health history was positive for type 2 diabetes mellitus. Conclusion: Multimodal ophthalmic imaging is useful in ruling out various differential diagnoses in posterior segment care, as well as monitoring for progressive changes such as sensory retinal detachment and choroidal neovascularization. Bilateral idiopathic multiple RPED is a rare condition that may represent an atypical form of CSC. There is currently no preferred treatment, besides observation, as visual prognosis is typically good

Mapping evapotranspiration with high-resolution aircraft imagery over vineyards using one- and two-source modeling schemes

Thermal and multispectral remote sensing data from low-altitude aircraft can provide high spatial resolution necessary for sub-field ( 10 m) and plant canopy (1 m) scale evapotranspiration (ET) monitoring. In this study, highresolution (sub-meter-scale) thermal infrared and multispectral shortwave data from aircraft are used to map ET over vineyards in central California with the two-source energy balance (TSEB) model and with a simple model having operational immediate capabilities called DATTUTDUT (Deriving Atmosphere Turbulent Transport Useful To Dummies Using Temperature). The latter uses contextual information within the image to scale between radiometric land surface temperature (TR) values representing hydrologic limits of potential ET and a non-evaporative surface. Imagery from 5 days throughout the growing season is used for mapping ET at the sub-field scale. The performance of the two models is evaluated using tower-based measurements of sensible (H) and latent heat (LE) flux or ET. The comparison indicates that TSEB was able to derive reasonable ET estimates under varying conditions, likely due to the physically based treatment of the energy and the surface temperature partitioning between the soil/cover crop inter-row and vine canopy elements. On the other hand, DATTUTDUT performance was somewhat degraded presumably because the simple scaling scheme does not consider differences in the two sources (vine and inter-row) of heat and temperature contributions or the effect of surface roughness on the efficiency of heat exchange. Maps of the evaporative fraction (EFDLE/(H CLE)) from the two models had similar spatial patterns but different magnitudes in some areas within the fields on certain days. Large EF discrepancies between the models were found on 2 of the 5 days (DOY 162 and 219) when there were significant differences with the tower-based ET measurements, particularly using the DATTUTDUT model. These differences in EF between the models translate to significant variations in daily water use estimates for these 2 days for the vineyards. Model sensitivity analysis demonstrated the high degree of sensitivity of the TSEB model to the accuracy of the TR data, while the DATTUTDUT model was insensitive to systematic errors in TR as is the case with contextual-based models. However, it is shown that the study domain and spatial resolution will significantly influence the ET estimation from the DATTUTDUT model. Future work is planned for developing a hybrid approach that leverages the strengths of both modeling schemes and is simple enough to be used operationally with high-resolution imagery

High-Speed CMOS-Free Purely Spintronic Asynchronous Recurrent Neural Network

Neuromorphic computing systems overcome the limitations of traditional von Neumann computing architectures. These computing systems can be further improved upon by using emerging technologies that are more efficient than CMOS for neural computation. Recent research has demonstrated memristors and spintronic devices in various neural network designs boost efficiency and speed. This paper presents a biologically inspired fully spintronic neuron used in a fully spintronic Hopfield RNN. The network is used to solve tasks, and the results are compared against those of current Hopfield neuromorphic architectures which use emerging technologies

Hemispherical power asymmetry: parameter estimation from CMB WMAP5 data

We reexamine the evidence of the hemispherical power asymmetry, detected in the CMB WMAP data using a new method. At first, we analyze the hemispherical variance ratios and compare these with simulated distributions. Secondly, working within a previously-proposed CMB bipolar modulation model, we constrain model parameters: the amplitude and the orientation of the modulation field as a function of various multipole bins. Finally, we select three ranges of multipoles leading to the most anomalous signals, and we process corresponding 100 Gaussian, random field (GRF) simulations, treated as observational data, to further test the statistical significance and robustness of the hemispherical power asymmetry. For our analysis we use the Internally-Linearly-Coadded (ILC) full sky map, and KQ75 cut-sky V channel, foregrounds reduced map of the WMAP five year data (V5). We constrain the modulation parameters using a generic maximum a posteriori method. In particular, we find differences in hemispherical power distribution, which when described in terms of a model with bipolar modulation field, exclude the field amplitude value of the isotropic model A=0 at confidence level of ~99.5% (~99.4%) in the multipole range l=[7,19] (l=[7,79]) in the V5 data, and at the confidence level ~99.9% in the multipole range l=[7,39] in the ILC5 data, with the best fit (modal PDF) values in these particular multipole ranges of A=0.21 (A=0.21) and A=0.15 respectively. However, we also point out that similar or larger significances (in terms of rejecting the isotropic model), and large best-fit modulation amplitudes are obtained in GRF simulations as well, which reduces the overall significance of the CMB power asymmetry down to only about 94% (95%) in the V5 data, in the range l=[7,19] (l=[7,79]).Comment: 24 pages, 10 figures; few typos corrected; published in JCA