Whole genome sequencing for mutation discovery in a single case of lysosomal storage disease (MPS type 1) in the dog.

Mucopolysaccharidosis (MPS) is a metabolic storage disorder caused by the deficiency of any lysosomal enzyme required for the breakdown of glycosaminoglycans. A 15-month-old Boston Terrier presented with clinical signs consistent with lysosomal storage disease including corneal opacities, multifocal central nervous system disease and progressively worsening clinical course. Diagnosis was confirmed at necropsy based on histopathologic evaluation of multiple organs demonstrating accumulation of mucopolysaccharides. Whole genome sequencing was used to uncover a frame-shift insertion affecting the alpha-L-iduronidase (IDUA) gene (c.19_20insCGGCCCCC), a mutation confirmed in another Boston Terrier presented 2 years later with a similar clinical picture. Both dogs were homozygous for the IDUA mutation and shared coat colors not recognized as normal for the breed by the American Kennel Club. In contrast, the mutation was not detected in 120 unrelated Boston Terriers as well as 202 dogs from other breeds. Recent inbreeding to select for recessive and unusual coat colors may have concentrated this relatively rare allele in the breed. The identification of the variant enables ante-mortem diagnosis of similar cases and selective breeding to avoid the spread of this disease in the breed. Boston Terriers carrying this variant represent a promising model for MPS I with neurological abnormalities in humans

Certain Adenylated Non-Coding RNAs, Including 5′ Leader Sequences of Primary MicroRNA Transcripts, Accumulate in Mouse Cells following Depletion of the RNA Helicase MTR4

RNA surveillance plays an important role in posttranscriptional regulation. Seminal work in this field has largely focused on yeast as a model system, whereas exploration of RNA surveillance in mammals is only recently begun. The increased transcriptional complexity of mammalian systems provides a wider array of targets for RNA surveillance, and, while many questions remain unanswered, emerging data suggest the nuclear RNA surveillance machinery exhibits increased complexity as well. We have used a small interfering RNA in mouse N2A cells to target the homolog of a yeast protein that functions in RNA surveillance (Mtr4p). We used high-throughput sequencing of polyadenylated RNAs (PA-seq) to quantify the effects of the mMtr4 knockdown (KD) on RNA surveillance. We demonstrate that overall abundance of polyadenylated protein coding mRNAs is not affected, but several targets of RNA surveillance predicted from work in yeast accumulate as adenylated RNAs in the mMtr4KD. microRNAs are an added layer of transcriptional complexity not found in yeast. After Drosha cleavage separates the pre-miRNA from the microRNA\u27s primary transcript, the byproducts of that transcript are generally thought to be degraded. We have identified the 5′ leading segments of pri-miRNAs as novel targets of mMtr4 dependent RNA surveillance

Classification and modeling of power line noise using machine learning techniques

A thesis submitted in ful lment of the requirements for the degree of Doctor of Philosophy in the School of Electrical and Information Engineering Faculty of Engineering and Built Environment June 2017The realization of robust, reliable and e cient data transmission have been the theme of recent research, most importantly in real channel such as the noisy, fading prone power line communication (PLC) channel. The focus is to exploit old techniques or create new techniques capable of improving the transmission reliability and also increasing the transmission capacity of the real communication channels. Multi-carrier modulation scheme such as Orthogonal Frequency Division Multiplexing (OFDM) utilizing conventional single-carrier modulation is developed to facilitate a robust data transmission, increasing transmission capacity (e cient bandwidth usage) and further reducing design complexity in PLC systems. On the contrary, the reliability of data transmission is subjected to several inhibiting factors as a result of the varying nature of the PLC channel. These inhibiting factors include noise, perturbation and disturbances. Contrary to the Additive White Gaussian noise (AWGN) model often assumed in several communication systems, this noise model fails to capture the attributes of noise encountered on the PLC channel. This is because periodic noise or random noise pulses injected by power electronic appliances on the network is a deviation from the AWGN. The nature of the noise is categorized as non-white non-Gaussian and unstable due to its impulsive attributes, thus, it is labeled as Non-additive White Gaussian Noise (NAWGN). These noise and disturbances results into long burst errors that corrupts signals being transmitted, thus, the PLC is labeled as a horrible or burst error channel. The e cient and optimal performance of a conventional linear receiver in the white Gaussian noise environment can therefore be made to drastically degrade in this NAWGN environment. Therefore, transmission reliability in such environment can be greatly enhanced if we know and exploit the knowledge of the channel's statistical attributes, thus, the need for developing statistical channel model based on empirical data. In this thesis, attention is focused on developing a recon gurable software de ned un-coded single-carrier and multicarrier PLC transceiver as a tool for realizing an optimized channel model for the narrowband PLC (NB-PLC) channel. First, a novel recon gurable software de ned un-coded single-carrier and multi-carrier PLC transceiver is developed for real-time NB-PLC transmission. The transceivers can be adapted to implement di erent waveforms for several real-time scenarios and performance evaluation. Due to the varying noise parameters obtained from country to country as a result of the dependence of noise impairment on mains voltages, topology of power line, place and time, the developed transceivers is capable of facilitating constant measurement campaigns to capture these varying noise parameters before statistical and mathematically inclined channel models are derived. Furthermore, the single-carrier (Binary Phase Shift Keying (BPSK), Di erential BPSK (DBPSK), Quadrature Phase Shift Keying (QPSK) and Di erential QPSK (DQPSK)) PLC transceiver system developed is used to facilitate a First-Order semi-hidden Fritchman Markov modeling (SHFMM) of the NB-PLC channel utilizing the e cient iterative Baum- Welch algorithm (BWA) for parameter estimation. The performance of each modulation scheme is evaluated in a mildly and heavily disturbed scenarios for both residential and laboratory site considered. The First-Order estimated error statistics of the realized First- Order SHFMM have been analytically validated in terms of performance metrics such as: log-likelihood ratio (LLR), error-free run distribution (EFRD), error probabilities, mean square error (MSE) and Chi-square ( 2) test. The reliability of the model results is also con rmed by an excellent match between the empirically obtained error sequence and the SHFMM regenerated error sequence as shown by the error-free run distribution plot. This thesis also reports a novel development of a low cost, low complexity Frequency-shift keying (FSK) - On-o keying (OOK) in-house hybrid PLC and VLC system. The functionality of this hybrid PLC-VLC transceiver system was ascertained at both residential and laboratory site at three di erent times of the day: morning, afternoon and evening. A First and Second-Order SHFMM of the hybrid system is realized. The error statistics of the realized First and Second-Order SHFMMs have been analytically validated in terms of LLR, EFRD, error probabilities, MSE and Chi-square ( 2). The Second-Order SHFMMs have also been analytically validated to be superior to the First-Order SHFMMs although at the expense of added computational complexity. The reliability of both First and Second-Order SHFMM results is con rmed by an excellent match between the empirical error sequences and SHFMM re-generated error sequences as shown by the EFRD plot. In addition, the multi-carrier (QPSK-OFDM, Di erential QPSK (DQPSK)-OFDM) and Di erential 8-PSK (D8PSK)-OFDM) PLC transceiver system developed is used to facilitate a First and Second-Order modeling of the NB-PLC system using the SHFMM and BWA for parameter estimation. The performance of each OFDM modulation scheme in evaluated and compared taking into consideration the mildly and heavily disturbed noise scenarios for the two measurement sites considered. The estimated error statistics of the realized SHFMMs have been analytically validated in terms of LLR, EFRD, error probabilities, MSE and Chi-square ( 2) test. The estimated Second-Order SHFMMs have been analytically validated to be outperform the First-Order SHFMMs although with added computational complexity. The reliability of the models is con rmed by an excellent match between the empirical data and SHFMM generated data as shown by the EFRD plot. The statistical models obtained using Baum-Welch to adjust the parameters of the adopted SHFMM are often locally maximized. To solve this problem, a novel Metropolis-Hastings algorithm, a Bayesian inference approach based on Markov Chain Monte Carlo (MCMC) is developed to optimize the parameters of the adopted SHFMM. The algorithm is used to optimize the model results obtained from the single-carrier and multi-carrier PLC systems as well as that of the hybrid PLC-VLC system. Consequently, as deduced from the results, the models obtained utilizing the novel Metropolis-Hastings algorithm are more precise, near optimal model with parameter sets that are closer to the global maxima. Generally, the model results obtained in this thesis are relevant in enhancing transmission reliability on the PLC channel through the use of the models to improve the adopted modulation schemes, create adaptive modulation techniques, develop and evaluate forward error correction (FEC) codes such as a concatenation of Reed-Solomon and Permutation codes and other robust codes suitable for exploiting and mitigating noise impairments encountered on the low voltage NB-PLC channel. Furthermore, the recon gurable software de ned NB-PLC transceiver test-bed developed can be utilized for future measurement campaign as well as adapted for multiple-input and multiple-output (MIMO) PLC applications.MT201

Classification and modeling of power line noise using machine learning techniques

A thesis submitted in ful lment of the requirements for the degree of Doctor of Philosophy in the School of Electrical and Information Engineering Faculty of Engineering and Built Environment June 2017The realization of robust, reliable and e cient data transmission have been the theme of recent research, most importantly in real channel such as the noisy, fading prone power line communication (PLC) channel. The focus is to exploit old techniques or create new techniques capable of improving the transmission reliability and also increasing the transmission capacity of the real communication channels. Multi-carrier modulation scheme such as Orthogonal Frequency Division Multiplexing (OFDM) utilizing conventional single-carrier modulation is developed to facilitate a robust data transmission, increasing transmission capacity (e cient bandwidth usage) and further reducing design complexity in PLC systems. On the contrary, the reliability of data transmission is subjected to several inhibiting factors as a result of the varying nature of the PLC channel. These inhibiting factors include noise, perturbation and disturbances. Contrary to the Additive White Gaussian noise (AWGN) model often assumed in several communication systems, this noise model fails to capture the attributes of noise encountered on the PLC channel. This is because periodic noise or random noise pulses injected by power electronic appliances on the network is a deviation from the AWGN. The nature of the noise is categorized as non-white non-Gaussian and unstable due to its impulsive attributes, thus, it is labeled as Non-additive White Gaussian Noise (NAWGN). These noise and disturbances results into long burst errors that corrupts signals being transmitted, thus, the PLC is labeled as a horrible or burst error channel. The e cient and optimal performance of a conventional linear receiver in the white Gaussian noise environment can therefore be made to drastically degrade in this NAWGN environment. Therefore, transmission reliability in such environment can be greatly enhanced if we know and exploit the knowledge of the channel's statistical attributes, thus, the need for developing statistical channel model based on empirical data. In this thesis, attention is focused on developing a recon gurable software de ned un-coded single-carrier and multicarrier PLC transceiver as a tool for realizing an optimized channel model for the narrowband PLC (NB-PLC) channel. First, a novel recon gurable software de ned un-coded single-carrier and multi-carrier PLC transceiver is developed for real-time NB-PLC transmission. The transceivers can be adapted to implement di erent waveforms for several real-time scenarios and performance evaluation. Due to the varying noise parameters obtained from country to country as a result of the dependence of noise impairment on mains voltages, topology of power line, place and time, the developed transceivers is capable of facilitating constant measurement campaigns to capture these varying noise parameters before statistical and mathematically inclined channel models are derived. Furthermore, the single-carrier (Binary Phase Shift Keying (BPSK), Di erential BPSK (DBPSK), Quadrature Phase Shift Keying (QPSK) and Di erential QPSK (DQPSK)) PLC transceiver system developed is used to facilitate a First-Order semi-hidden Fritchman Markov modeling (SHFMM) of the NB-PLC channel utilizing the e cient iterative Baum- Welch algorithm (BWA) for parameter estimation. The performance of each modulation scheme is evaluated in a mildly and heavily disturbed scenarios for both residential and laboratory site considered. The First-Order estimated error statistics of the realized First- Order SHFMM have been analytically validated in terms of performance metrics such as: log-likelihood ratio (LLR), error-free run distribution (EFRD), error probabilities, mean square error (MSE) and Chi-square ( 2) test. The reliability of the model results is also con rmed by an excellent match between the empirically obtained error sequence and the SHFMM regenerated error sequence as shown by the error-free run distribution plot. This thesis also reports a novel development of a low cost, low complexity Frequency-shift keying (FSK) - On-o keying (OOK) in-house hybrid PLC and VLC system. The functionality of this hybrid PLC-VLC transceiver system was ascertained at both residential and laboratory site at three di erent times of the day: morning, afternoon and evening. A First and Second-Order SHFMM of the hybrid system is realized. The error statistics of the realized First and Second-Order SHFMMs have been analytically validated in terms of LLR, EFRD, error probabilities, MSE and Chi-square ( 2). The Second-Order SHFMMs have also been analytically validated to be superior to the First-Order SHFMMs although at the expense of added computational complexity. The reliability of both First and Second-Order SHFMM results is con rmed by an excellent match between the empirical error sequences and SHFMM re-generated error sequences as shown by the EFRD plot. In addition, the multi-carrier (QPSK-OFDM, Di erential QPSK (DQPSK)-OFDM) and Di erential 8-PSK (D8PSK)-OFDM) PLC transceiver system developed is used to facilitate a First and Second-Order modeling of the NB-PLC system using the SHFMM and BWA for parameter estimation. The performance of each OFDM modulation scheme in evaluated and compared taking into consideration the mildly and heavily disturbed noise scenarios for the two measurement sites considered. The estimated error statistics of the realized SHFMMs have been analytically validated in terms of LLR, EFRD, error probabilities, MSE and Chi-square ( 2) test. The estimated Second-Order SHFMMs have been analytically validated to be outperform the First-Order SHFMMs although with added computational complexity. The reliability of the models is con rmed by an excellent match between the empirical data and SHFMM generated data as shown by the EFRD plot. The statistical models obtained using Baum-Welch to adjust the parameters of the adopted SHFMM are often locally maximized. To solve this problem, a novel Metropolis-Hastings algorithm, a Bayesian inference approach based on Markov Chain Monte Carlo (MCMC) is developed to optimize the parameters of the adopted SHFMM. The algorithm is used to optimize the model results obtained from the single-carrier and multi-carrier PLC systems as well as that of the hybrid PLC-VLC system. Consequently, as deduced from the results, the models obtained utilizing the novel Metropolis-Hastings algorithm are more precise, near optimal model with parameter sets that are closer to the global maxima. Generally, the model results obtained in this thesis are relevant in enhancing transmission reliability on the PLC channel through the use of the models to improve the adopted modulation schemes, create adaptive modulation techniques, develop and evaluate forward error correction (FEC) codes such as a concatenation of Reed-Solomon and Permutation codes and other robust codes suitable for exploiting and mitigating noise impairments encountered on the low voltage NB-PLC channel. Furthermore, the recon gurable software de ned NB-PLC transceiver test-bed developed can be utilized for future measurement campaign as well as adapted for multiple-input and multiple-output (MIMO) PLC applications.MT201

Analysis of NGS Data from Immune Response and Viral Samples

This thesis is devoted to designing and applying advanced algorithmical and statistical tools for analysis of NGS data related to cancer and infection diseases. NGS data under investigation are obtained either from host samples or viral variants. Recently, random peptide phage display libraries (RPPDL) were applied to studies of host\u27s antibody response to different diseases. We study human antibody response to breast cancer and mouse antibody response to Lyme disease by sequencing of the whole antibody repertoire profiles which are represented by RPPDL. Alternatively, instead of sequencing immune response NGS can be applied directly to a viral population within an infected host. Specifically, we analyze the following RNA viruses: the human immunodeficiency virus (HIV) and the infectious bronchitis virus (IBV). Sequencing of RNA viruses is challenging because there are many variants inside population due to high mutation rate. Our results show that NGS helps to understand RNA viruses and explore their interaction with infected hosts. NGS also helps to analyze immune response to different diseases, trace changing of immune response at different disease stages

Genomic introgression mapping of field-derived multiple-anthelmintic resistance in Teladorsagia circumcincta

Preventive chemotherapy has long been practiced against nematode parasites of livestock, leading to widespread drug resistance, and is increasingly being adopted for eradication of human parasitic nematodes even though it is similarly likely to lead to drug resistance. Given that the genetic architecture of resistance is poorly understood for any nematode, we have analyzed multidrug resistant Teladorsagia circumcincta, a major parasite of sheep, as a model for analysis of resistance selection. We introgressed a field-derived multiresistant genotype into a partially inbred susceptible genetic background (through repeated backcrossing and drug selection) and performed genome-wide scans in the backcross progeny and drug-selected F2 populations to identify the major genes responsible for the multidrug resistance. We identified variation linking candidate resistance genes to each drug class. Putative mechanisms included target site polymorphism, changes in likely regulatory regions and copy number variation in efflux transporters. This work elucidates the genetic architecture of multiple anthelmintic resistance in a parasitic nematode for the first time and establishes a framework for future studies of anthelmintic resistance in nematode parasites of humans

Analysis of non-coding DNA from whole exome sequencing data

Next Generation Sequencing technologies have completely changed the way to study molecular bases underlying Rare Genetic Diseases (RGDs). Currently, sequencing of the exonic portion of the human genome – the exome (1%) – performed through Whole Exome Sequencing (WES) experiments represents the most used approach to discover molecular mechanisms underlying RGDs. To date, several tools have been developed to analyse and interpret data generated from WES. However, due to both technical and experimental limitations, its diagnostic rate is ~20-30%. In this context, we evaluated whether WES data contain information on non-coding sequences, focusing on microRNAs (miRNAs). Comparative analysis of capture design and experimental coverage allowed to disclose that in WES data reside information related to miRNA sequences that are efficiently captured by most exome enrichment kits. We therefore analysed WES of a cohort of 259 individuals, including patients affected by several genetic diseases and their unaffected relatives, searching for variants in miRNAs and performing functional annotation. Sanger sequence validation confirms the reliable call of variants mapping in miRNA sequences. To date, no dedicated tool is available to properly retrieve and analyse miRNAs from WES and WGS data. We therefore developed a tool, “AnnomiR”, that allows to systematically analyse miRNA variants and miRNAs, providing functional annotation retrieved from several databases. This tool can be integrated in a standard workflow of analysis for WES and WGS data. WES data contain a great amount of information that is generally discarded by commonly used workflow of analysis and that should be considered, as it could help in the comprehension of molecular mechanisms underlying RGDs. In this context, systematic study of miRNAs could help elucidating their role as disease-causative and phenotypic modifiers in a wide spectrum of human diseases, allowing to achieve a better characterisation of variability of the human genome related to these non-coding sequences