Characterization and Mapping of retr04, retr05 and retr06 Broad-Spectrum Resistances to Turnip Mosaic Virus in Brassica juncea, and the Development of Robust Methods for Utilizing Recalcitrant Genotyping Data

Turnip mosaic virus (TuMV) induces disease in susceptible hosts, notably impacting cultivation of important crop species of the Brassica genus. Few effective plant viral disease management strategies exist with the majority of current approaches aiming to mitigate the virus indirectly through control of aphid vector species. Multiple sources of genetic resistance to TuMV have been identified previously, although the majority are strain-specific and have not been exploited commercially. Here, two Brassica juncea lines (TWBJ14 and TWBJ20) with resistance against important TuMV isolates (UK 1, vVIR24, CDN 1, and GBR 6) representing the most prevalent pathotypes of TuMV (1, 3, 4, and 4, respectively) and known to overcome other sources of resistance, have been identified and characterized. Genetic inheritance of both resistances was determined to be based on a recessive two-gene model. Using both single nucleotide polymorphism (SNP) array and genotyping by sequencing (GBS) methods, quantitative trait loci (QTL) analyses were performed using first backcross (BC1) genetic mapping populations segregating for TuMV resistance. Pairs of statistically significant TuMV resistance-associated QTLs with additive interactive effects were identified on chromosomes A03 and A06 for both TWBJ14 and TWBJ20 material. Complementation testing between these B. juncea lines indicated that one resistance-linked locus was shared. Following established resistance gene nomenclature for recessive TuMV resistance genes, these new resistance-associated loci have been termed retr04 (chromosome A06, TWBJ14, and TWBJ20), retr05 (A03, TWBJ14), and retr06 (A03, TWBJ20). Genotyping by sequencing data investigated in parallel to robust SNP array data was highly suboptimal, with informative data not established for key BC1 parental samples. This necessitated careful consideration and the development of new methods for processing compromised data. Using reductive screening of potential markers according to allelic variation and the recombination observed across BC1 samples genotyped, compromised GBS data was rendered functional with near-equivalent QTL outputs to the SNP array data. The reductive screening strategy employed here offers an alternative to methods relying upon imputation or artificial correction of genotypic data and may prove effective for similar biparental QTL mapping studies.

Total ionizing dose effect on 2-D array data transfer ICs designed and fabricated by 0.18-µm CMOS technology

Circuits for CMOS two-dimensional (2-D) array data transfer are indispensable for applications such as space and nuclear fields. Issues include to be operated with higher speed, lower power, fewer size penalty and radiation hardness. To meet these requirements, two kinds of CMOS 2-D array data transfer circuits, such as a shift register type and a memory access type, are proposed and fabricated by the standard 0.18-µm CMOS process technology. In the both types, 16 µm pitch, 8×124 array data transfer operations were realized with data rate of more than 1 Gb/s. Furthermore, we conducted 60Co γ-ray irradiation experiments on those circuits. The current consumption ratio of the shift register type to the memory access type ranges from 150 to 200% as the dosage increases. The result indicate that the memory access type has better radiation hardness at 1 Gb/s than that of the shift register type.

KRSA: An R package and R Shiny web application for an end-to-end upstream kinase analysis of kinome array data

Phosphorylation by serine-threonine and tyrosine kinases is critical for determining protein function. Array-based platforms for measuring reporter peptide signal levels allow for differential phosphorylation analysis between conditions for distinct active kinases. Peptide array technologies like the PamStation12 from PamGene allow for generating high-throughput, multi-dimensional, and complex functional proteomics data. As the adoption rate of such technologies increases, there is an imperative need for software tools that streamline the process of analyzing such data. We present Kinome Random Sampling Analyzer (KRSA), an R package and R Shiny web-application for analyzing kinome array data to help users better understand the patterns of functional proteomics in complex biological systems. KRSA is an All-In-One tool that reads, formats, fits models, analyzes, and visualizes PamStation12 kinome data. While the underlying algorithm has been experimentally validated in previous publications, we demonstrate KRSA workflow on dorsolateral prefrontal cortex (DLPFC) in male (n = 3) and female (n = 3) subjects to identify differential phosphorylation signatures and upstream kinase activity. Kinase activity differences between males and females were compared to a previously published kinome dataset (11 female and 7 male subjects) which showed similar global phosphorylation signals patterns.

Determination of the source parameters of the 2011 Tohoku-Oki earthquake from three-component pre-P gravity signals recorded by dense arrays in Japan

Dynamic earthquake rupture causes mass redistribution around the fault, and the emitted propagating seismic waves are accompanied by bulk density perturbations. Both processes cause transient gravity changes prior to the arrival of P-waves. Such pre-P gravity signals have been detected in previous studies of several large earthquakes. However, the detections were limited to the vertical component of the signal owing to the high noise level in the horizontal records. In this study, we analyzed dense tiltmeter array data in Japan to search for the horizontal components of the signal from the 2011 Mw 9.1 Tohoku-Oki earthquake. Based on the synthetic waveforms computed for a realistic Earth model, we stacked the horizontal records and identified a signal that evidently exceeded the noise level. We further performed a waveform inversion analysis to estimate the source parameters. The horizontal tiltmeter data, combined with the vertical component of the broadband seismometer array data, yielded a constraint on the dip angle and magnitude of the earthquake in the ranges of 11.5°–15.3° and 8.75°–8.92°, respectively. Our results indicate that the analysis of the three components of the pre-P gravity signal avoids the intrinsic trade-off problem between the dip angle and seismic moment in determining the source mechanism of shallow earthquakes. Pre-P gravity signals open a new observation window for earthquake source studies. Graphical Abstract

Bayesian multiple target tracking

<p>This thesis addresses several challenges in Bayesian target tracking, particularly for array signal processing applications, and for multiple targets. The optimal method for multiple target tracking is the Bayes’ joint filter that operates by hypothesising all the targets collectively using a joint state. As a consequence, the computational complexity of the filter increases rapidly with the number of targets. The probability hypothesis density and the multi-Bernoulli filters that overcome this complexity do not possess a suitable framework to operate directly on phased sensor array data. Instead, such data is converted into beamformer images in which close targets may not be effectively resolved and much information is lost. This thesis develops a multiple signal classification (MUSIC) based multi-target particle filter that improves upon the filters mentioned above. A MUSIC based multi-Bernoulli particle filter is also developed, that operates more directly on array data. The above mentioned particle filters require a resampling step which impedes information accumulation over successive observations, and affects the detection of very covert targets. This thesis develops soft resampling and soft systematic resampling to overcome this problem without affecting the accuracy of approximation. Additionally, modified Kolmogorov-Smirnov testing is proposed, to numerically evaluate the accuracy of the particle filter approximation.</p>