Secondary metabolism of the forest pathogen Dothistroma septosporum : a thesis presented in the partial fulfilment of the requirements for the degree of Doctor of Philosophy (PhD) in Genetics at Massey University, Manawatu, New Zealand

Dothistroma septosporum is a fungus causing the disease Dothistroma needle blight (DNB) on more than 80 pine species in 76 countries, and causes serious economic losses. A secondary metabolite (SM) dothistromin, produced by D. septosporum, is a virulence factor required for full disease expression but is not needed for the initial formation of disease lesions. Unlike the majority of fungal SMs whose biosynthetic enzyme genes are arranged in a gene cluster, dothistromin genes are dispersed in a fragmented arrangement. Therefore, it was of interest whether D. septosporum has other SMs that are required in the disease process, as well as having SM genes that are clustered as in other fungi. Genome sequencing of D. septosporum revealed that D. septosporum has 11 SM core genes, which is fewer than in closely related species. In this project, gene cluster analyses around the SM core genes were done to assess if there are intact or other fragmented gene clusters. In addition, one of the core SM genes, DsNps3, that was highly expressed at an early stage of plant infection, was knocked out and the phenotype of this mutant was analysed. Then, evolutionary selection pressures on the SM core genes were analysed using the SM core gene sequences across 19 D. septosporum strains from around the world. Finally, phylogenetic analyses on some of the SM core genes were done to find out if these genes have functionally characterised orthologs. Analysis of the ten D. septosporum SM core genes studied in this project showed that two of them were pseudogenes, and five others had very low expression levels in planta. Three of the SM core genes showed high expression levels in planta. These three genes, DsPks1, DsPks2 and DsNps3, were key genes of interest in this project. But despite the different expression levels, evolutionary selection pressure analyses showed that all of the SM core genes apart from the pseudogenes are under negative selection, suggesting that D. septosporum might actively use most of its SMs under certain conditions. In silico predictions based on the amino acid sequences of the proteins encoded by SM core genes and gene cluster analyses showed that four of the SM core genes are predicted to produce known metabolites. These are melanin (DsPks1), cyclosporin (DsNps1), ferricrocin (DsNps2) and cyclopiazonic acid (DsHps1). Gene cluster analyses revealed that at least three of the D. septosporum SMs might be produced by fragmented gene clusters (DsPks1, DsNps1, DsNps2). This suggested that dothistromin might not be the only fragmented SM gene cluster in D. septosporum. According to phylogenetic analyses, some of the D. septosporum SM core genes have no orthologs among its class (Dothideomycetes), suggesting some of the D. septosporum SMs may be unique. One such example is the metabolite produced by DsNps3. Comparison of wild type and ΔDsNps3 D. septosporum strains showed that the ΔDsNps3 strain produces fewer spores, less hyphal surface network at an early stage of plant infection, and lower levels of fungal biomass in disease lesions compared to wild type, suggesting that the DsNps3 SM may be a virulence factor. Attempts to identify a metabolite associated with DsNps3, and to knockout another gene of key interest, DsPks2, for functional characterization were unsuccessful. Further work is required to confirm the gene clusters, characterise the SMs and their roles. However, the findings so far suggest that dothistromin is unlikely to be the only D. septosporum SM that is a virulence factor in since the DsNps3 SM also appears to be involved in virulence. Likewise the fragmented dothistromin cluster may not be the only one in the genome and there may be at least three more fragmented SM gene clusters

Surgical treatment with rhomboid excision and Limberg flap technique under spinal anesthesia of 23 young with pilonidal sinus disease

Aim: To present the experience of treatment with Limberg flap procedure under spinal anesthesia in 23 young patients with pilonidal sinus disease. Methods: This was a retrospective study of 23 young patients who underwent surgery for pilonidal sinus disease under spinal anesthesia between January 2011 and November 2017 in the Division of Pediatric Surgery. All patients were evaluated for age, sex, clinical diagnosis, and body mass index, and infection, duration of symptoms, treatment, healing time, recurrences, complications and results.  Results: Of the 23 patients, 4 (17%) were male, and 19 (83%) were female. The mean age of the patients was 15.21 ± 2.8 years and the mean symptom duration was 4 ± 2.6 months. In 13 patients (56.5%), there was one or more sagittal lines in the midline and the mean sinus number of the patients was 2.12 ± 0.60. Pain was the most important complaint affecting the quality of life of the patient. The mean body mass index was 26.33 ± 2.54 kg / m2, and 47.8% (n = 11) were high BMI and 53.2% were normal BMI. One patient had temporary headache and one patient had urinary retention. Wound infection occurred in 2 patients (8.6%). Recurrence was not observed in patients.  Conclusion: In this study, pilonidal sinus disease was treated with Limberg flap procedure under spinal anesthesia. The combination of these two applications in patients with pilonidal sinus may provide significant advantages, such as rapid recovery and short hospital stay, early return to daily activities, low complications, and recurrence rates

Learning spatio-temporal spike train encodings with ReSuMe, DelReSuMe, and Reward-modulated Spike-timing Dependent Plasticity in Spiking Neural Networks

SNNs are referred to as the third generation of ANNs. Inspired from biological observations and recent advances in neuroscience, proposed methods increase the power of SNNs. Today, the main challenge is to discover efficient plasticity rules for SNNs. Our research aims are to explore/extend computational models of plasticity. We make various achievements using ReSuMe, DelReSuMe, and R-STDP based on the fundamental plasticity of STDP. The information in SNNs is encoded in the patterns of firing activities. For biological plausibility, it is necessary to use multi-spike learning instead of single-spike. Therefore, we focus on encoding inputs/outputs using multiple spikes. ReSuMe is capable of generating desired patterns with multiple spikes. The trained neuron in ReSuMe can fire at desired times in response to spatio-temporal inputs. We propose alternative architecture for ReSuMe dealing with heterogeneous synapses. It is demonstrated that the proposed topology exactly mimic the ReSuMe. A novel extension of ReSuMe, called DelReSuMe, has better accuracy using less iteration by using multi-delay plasticity in addition to weight learning under noiseless and noisy conditions. The proposed heterogeneous topology is also used for DelReSuMe. Another plasticity extension based on STDP takes into account reward to modulate synaptic strength named R-STDP. We use dopamine-inspired STDP in SNNs to demonstrate improvements in mapping spatio-temporal patterns of spike trains with the multi-delay mechanism versus single connection. From the viewpoint of Machine Learning, Reinforcement Learning is outlined through a maze task in order to investigate the mechanisms of reward and eligibility trace which are the fundamental in R-STDP. To develop the approach we implement Temporal-Difference learning and novel knowledge-based RL techniques on the maze task. We develop rule extractions which are combined with RL and wall follower algorithms. We demonstrate the improvements on the exploration efficiency of TD learning for maze navigation tasks

Zmiany stężeń hormonów tarczycy u pacjentów z rozpoznaniem śmierci mózgu mają związek z non-thyroidal illness syndrome

Introduction: Alterations in thyroid hormone levels occur in patients with acute neurological disease states. The aim of this study is to study changes in thyroid hormones in patients with brain death (BD). Material and methods: Eleven brain-dead patients were studied prospectively. Thyroid hormones were measured on admission to the intensive care unit, the day before BD diagnosis (BD before), and the day after BD diagnosis (BD day). Results: Thyroid stimulating hormone (TSH) and free triiodothyronine (fT3) concentrations were found to be significantly low on ad­mission, BD before, and BD day compared to age-matched healthy controls. TSH levels were shown to be increasing on BD day. Free thyroxine (fT4) levels were within normal limits in all cases except in one case having low fT4 levels with normal TSH levels. No statisti­cally significant changes were encountered between admission thyroid hormone levels and BD-before and BD-day thyroid hormone levels. Six patients were on steroid therapy when BD-before blood samples were drawn, and no difference in thyroid hormone levels was encountered between steroid users and non-users. Correlation analysis showed a positive correlation between GCS and TSH, but a negative association between fT3 and APACHE II. Conclusion: We have shown that patients with BD have altered thyroid hormones days before BD diagnosis, and these alterations con­tinue until the diagnosis of BD. The changes in thyroid hormones are compatible with non-thyroidal illness syndrome

An ultra-wideband SiGe BiCMOS LNA for w-band applications

This article presents the design steps and implementation of a W-band ultra-wideband low noise amplifier (LNA) for both automotive and imaging applications. Three amplifiers based on common-emitter topology with different configurations are manufactured using IHP 0.13 mu m SiGe BiCMOS 300/500 GHz (f(t)/f(max)) SG13G2 technology. A three-stage single-ended structure is proposed for ultra-wideband imaging purposes. As the results are analyzed, this 0.2 mm(2) LNA can operate in a 25 GHz of measured 3-dB bandwidth in W-band with 21 dB peak gain and 4.9 dB average noise figure using 1.5 V supply voltage. It consumes 50 mW of power in the edge operation conditions and the output 1 dB compression point is found as -4 dBm. To the authors' knowledge, this chip achieves one of the best overall performances compared to other W-band LNAs

Mass Culturing of Stem and Bulb Nematode (Ditylenchus dipsaci) for use in screenİng and İmpression Training on Carrot Discs

Stem and bulb nematode, Ditylenchus dipsaci, is a very important plant parasitic nematode, has a very wide host range and causes economic yield losses in many cultural plants in worldwide. Its races are very diverse and found in most temperate areas of the world. D. dipsaci is a migratory endoparasite, has the ability to enter into a dormancy stage. Genetic resistance offers one of the best control methods within the integrated pest management strategies for D. dipsaci. However mass rearing of stem and bulb nematode requires for the resistant studies including screening for this nematode species. The aim of study is focused on alternative rearing methods using carrot discs as a food source, culturing medium and provide a clearly outlined and visually informative guide. Carrot discs enable the rearing of high numbers of individuals of D. dipsaci for timely use in experiments and for screening purposes in under sterile conditions to provide a clean, same and pure source of inoculum. The carrot disc method has been shown to be suitable for stem and bulb nematode multiplication