Reproduction in selected New Zealand native ferns and their suitability for revegetation : a thesis presented in partial fulfilment of the requirements for the degree of Masters of Science in Plant Biology at Massey University, Palmerston North, New Zealand

The potential to use New Zealand native ferns for revegetation was assessed in laboratory , nursery and field experiments. Laboratory experiments indicated that the three native fern species. Blechnum novae-zelandiae. Cyathea medullaris and Dicksonia squarossa, had different maximum levels of spore germination. These differences also varied in response to seasonal changes in the environment. The effect of three soil conditioners on the germination of the same three species was minimal Gametophytes appeared to be tolerant of low levels of maceration, as they were able to continue to grow and develop normally. Additional laboratory experiments indicated that B. novae-zelandiae employs a mixed mating system, which utilizes an "antheridiogen" signal. The development of fern spores, laboratory propagated gametophytes and segmented rhizomes, was assessed in the nursery. Each experiment was applied with a hvdroseeding mix of paper fibre, tackifier. fertilizer and water Spore of B. novae-zelandiae. C. medullaris and D. squarossa failed to produce any long-lived gametophytes The survival of laboratory propagated gametophytes of B. novae-zelandiae. B. discolor and B. colensoi was low. However, a large proportion of surviving B. novae-zelandiae gametophytes produced sporophytes. B. novae-zelandiae rhizome segments produced healthy young ferns within 3 months of application. Field experiments were conducted on a sandstone/loess bank. 5 km east of Palmerston North. Aspects of the substrate were analysed including. pH. N, P and organic matter. The results indicated that the bank had a high soil pH, was deficient in several macronutrients and had no organic matter. Hydroseeding was applied using spore of the species B novae-zelandiae, C. medullaris and D. squarossa Hydroseeded spore failed to produce any visible gametophytes Rhizome experiments using B. novae-zelandiae and Microsorum pustulatum were also established. Low water availability resulted in poor rhizome establishment. The results suggest that there is great potential for utilizing native ferns in revegetation. Blechnum novae-zelandiae is the best species for revegetation in accordance to the results. Propagation via rhizome segmentation and gametophyte hydroseeding appear to be the most successful methods for establishing native ferns. This TIF project was carried out in conjunction with Rural Supply Technologies. Manaaki Whenua Landcare Research. Massey University and FoRST New Zealand

Partial stem resistance in Brassica napus to highly aggressive and genetically diverse Sclerotinia sclerotiorum isolates from Australia

Sclerotinia sclerotiorum is a fungal pathogen that causes stem rot in oilseed rape (Brassica napus). Previously, B. napus accessions with partial stem resistance to a Canadian S. sclerotiorum isolate (#321) were identified using a stem test in which flowering plants were inoculated with mycelium plugs. The present study examined the partial stem resistance of four of these accessions, PAK54, PAK93, DC21 and K22, following inoculation with Australian isolates. Mycelial compatibility groups and intergenic spacer (IGS) region haplotypes were identified among 71 isolates from Australian oilseed rape and lupin fields. Eleven genetically diverse isolates showed differences in aggressiveness when inoculated onto nine oilseed rape varieties and one Chinese accession. Isolates CU8.24, CU10.17 and CU11.19 were selected based on genetic diversity, growth rate in vitro and high aggressiveness in the initial screen and subsequently inoculated onto the four B. napus accessions. These accessions developed significantly smaller lesions compared with the susceptible control varieties (‘AV Garnet’ and ‘Westar’), with the average frequency of soft and collapsed lesions being less than 20% in PAK54, DC21 and K22, 29% in PAK93 and greater than 88% in the susceptible controls. Microscopic examination revealed that hyphae were typically confined to the stem cortex in the smallest lesions, but could be found in the stem pith in larger lesions. These results show that B. napus accessions PAK54, PAK93, DC21 and K22 can be used in Australia for development of varieties with partial stem resistance to S. sclerotiorum

The complete genome sequence of the phytopathogenic fungus Sclerotinia sclerotiorum reveals insights into the genome architecture of broad host range pathogens

Sclerotinia sclerotiorum is a phytopathogenic fungus with over 400 hosts including numerous economically important cultivated species. This contrasts many economically destructive pathogens that only exhibit a single or very few hosts. Many plant pathogens exhibit a “two-speed” genome. So described because their genomes contain alternating gene rich, repeat sparse and gene poor, repeat-rich regions. In fungi, the repeat-rich regions may be subjected to a process termed repeat-induced point mutation (RIP). Both repeat activity and RIP are thought to play a significant role in evolution of secreted virulence proteins, termed effectors. We present a complete genome sequence of S. sclerotiorum generated using Single Molecule Real-Time Sequencing technology with highly accurate annotations produced using an extensive RNA sequencing data set. We identified 70 effector candidates and have highlighted their in planta expression profiles. Furthermore, we characterized the genome architecture of S. sclerotiorum in comparison to plant pathogens that exhibit “two-speed” genomes. We show that there is a significant association between positions of secreted proteins and regions with a high RIP index in S. sclerotiorum but we did not detect a correlation between secreted protein proportion and GC content. Neither did we detect a negative correlation between CDS content and secreted protein proportion across the S. sclerotiorum genome. We conclude that S. sclerotiorum exhibits subtle signatures of enhanced mutation of secreted proteins in specific genomic compartments as a result of transposition and RIP activity. However, these signatures are not observable at the whole-genome scale

Electron inflow velocities and reconnection rates at earth's magnetopause and magnetosheath

Electron inflow and outflow velocities during magnetic reconnection at and near the dayside magnetopause are measured using satellites from NASA's Magnetospheric Multiscale (MMS) mission. A case study is examined in detail, and three other events with similar behavior are shown, with one of them being a recently published electron-only reconnection event in the magnetosheath. The measured inflow speeds of 200–400 km/s imply dimensionless reconnection rates of 0.05–0.25 when normalized to the relevant electron Alfvén speed, which are within the range of expectations. The outflow speeds are about 1.5–3 times the inflow speeds, which is consistent with theoretical predictions of the aspect ratio of the inner electron diffusion region. A reconnection rate of 0.04 ± 25% was obtained for the case study event using the reconnection electric field as compared to the 0.12 ± 20% rate determined from the inflow velocity.publishedVersio

Positional information resolves structural variations and uncovers an evolutionarily divergent genetic locus in accessions of Arabidopsis thaliana.

Genome sequencing of closely related individuals has yielded valuable insights that link genome evolution to phenotypic variations. However, advancement in sequencing technology has also led to an escalation in the number of poor quality–drafted genomes assembled based on reference genomes that can have highly divergent or haplotypic regions. The self-fertilizing nature of Arabidopsis thaliana poses an advantage to sequencing projects because its genome is mostly homozygous. To determine the accuracy of an Arabidopsis drafted genome in less conserved regions, we performed a resequencing experiment on a 3 ~71-kb genomic interval in the Landsberg erecta (Ler-0) accession. We identified novel structural variations (SVs) between Ler-0 and the reference accession Col-0 using a long-range polymerase chain reaction approach to generate an Illumina data set that has positional information, that is, a data set with reads that map to a known location. Positional information is important for accurate genome assembly and the resolution of SVs particularly in highly duplicated or repetitive regions. Sixty-one regions with misassembly signatures were identified from the Ler-0 draft, suggesting the presence of novel SVs that are not represented in the draft sequence. Sixty of those were resolved by iterative mapping using our data set. Fifteen large indels (>100 bp) identified from this study were found to be located either within protein-coding regions or upstream regulatory regions, suggesting the formation of novel alleles or altered regulation of existing genes in Ler-0. We propose future genome-sequencing experiments to follow a clone-based approach that incorporates positional information to ultimately reveal haplotype-specific differences between accessions

Mineralogy and petrology of comet 81P/wild 2 nucleus samples

The bulk of the comet 81P/Wild 2 (hereafter Wild 2) samples returned to Earth by the Stardust spacecraft appear to be weakly constructed mixtures of nanometer-scale grains, with occasional much larger (over 1 micrometer) ferromagnesian silicates, Fe-Ni sulfides, Fe-Ni metal, and accessory phases. The very wide range of olivine and low-Ca pyroxene compositions in comet Wild 2 requires a wide range of formation conditions, probably reflecting very different formation locations in the protoplanetary disk. The restricted compositional ranges of Fe-Ni sulfides, the wide range for silicates, and the absence of hydrous phases indicate that comet Wild 2 experienced little or no aqueous alteration. Less abundant Wild 2 materials include a refractory particle, whose presence appears to require radial transport in the early protoplanetary disk

BHPR research: qualitative1. Complex reasoning determines patients' perception of outcome following foot surgery in rheumatoid arhtritis

Background: Foot surgery is common in patients with RA but research into surgical outcomes is limited and conceptually flawed as current outcome measures lack face validity: to date no one has asked patients what is important to them. This study aimed to determine which factors are important to patients when evaluating the success of foot surgery in RA Methods: Semi structured interviews of RA patients who had undergone foot surgery were conducted and transcribed verbatim. Thematic analysis of interviews was conducted to explore issues that were important to patients. Results: 11 RA patients (9 ♂, mean age 59, dis dur = 22yrs, mean of 3 yrs post op) with mixed experiences of foot surgery were interviewed. Patients interpreted outcome in respect to a multitude of factors, frequently positive change in one aspect contrasted with negative opinions about another. Overall, four major themes emerged. Function: Functional ability & participation in valued activities were very important to patients. Walking ability was a key concern but patients interpreted levels of activity in light of other aspects of their disease, reflecting on change in functional ability more than overall level. Positive feelings of improved mobility were often moderated by negative self perception ("I mean, I still walk like a waddling duck”). Appearance: Appearance was important to almost all patients but perhaps the most complex theme of all. Physical appearance, foot shape, and footwear were closely interlinked, yet patients saw these as distinct separate concepts. Patients need to legitimize these feelings was clear and they frequently entered into a defensive repertoire ("it's not cosmetic surgery; it's something that's more important than that, you know?”). Clinician opinion: Surgeons' post operative evaluation of the procedure was very influential. The impact of this appraisal continued to affect patients' lasting impression irrespective of how the outcome compared to their initial goals ("when he'd done it ... he said that hasn't worked as good as he'd wanted to ... but the pain has gone”). Pain: Whilst pain was important to almost all patients, it appeared to be less important than the other themes. Pain was predominately raised when it influenced other themes, such as function; many still felt the need to legitimize their foot pain in order for health professionals to take it seriously ("in the end I went to my GP because it had happened a few times and I went to an orthopaedic surgeon who was quite dismissive of it, it was like what are you complaining about”). Conclusions: Patients interpret the outcome of foot surgery using a multitude of interrelated factors, particularly functional ability, appearance and surgeons' appraisal of the procedure. While pain was often noted, this appeared less important than other factors in the overall outcome of the surgery. Future research into foot surgery should incorporate the complexity of how patients determine their outcome Disclosure statement: All authors have declared no conflicts of interes

Investigation of hospital discharge cases and SARS-CoV-2 introduction into Lothian care homes

Background The first epidemic wave of severe acute respiratory syndrome coronavirus-2 (SARS-CoV-2) in Scotland resulted in high case numbers and mortality in care homes. In Lothian, over one-third of care homes reported an outbreak, while there was limited testing of hospital patients discharged to care homes. Aim To investigate patients discharged from hospitals as a source of SARS-CoV-2 introduction into care homes during the first epidemic wave. Methods A clinical review was performed for all patients discharges from hospitals to care homes from 1st March 2020 to 31st May 2020. Episodes were ruled out based on coronavirus disease 2019 (COVID-19) test history, clinical assessment at discharge, whole-genome sequencing (WGS) data and an infectious period of 14 days. Clinical samples were processed for WGS, and consensus genomes generated were used for analysis using Cluster Investigation and Virus Epidemiological Tool software. Patient timelines were obtained using electronic hospital records. Findings In total, 787 patients discharged from hospitals to care homes were identified. Of these, 776 (99%) were ruled out for subsequent introduction of SARS-CoV-2 into care homes. However, for 10 episodes, the results were inconclusive as there was low genomic diversity in consensus genomes or no sequencing data were available. Only one discharge episode had a genomic, time and location link to positive cases during hospital admission, leading to 10 positive cases in their care home. Conclusion The majority of patients discharged from hospitals were ruled out for introduction of SARS-CoV-2 into care homes, highlighting the importance of screening all new admissions when faced with a novel emerging virus and no available vaccine

SARS-CoV-2 Omicron is an immune escape variant with an altered cell entry pathway

Vaccines based on the spike protein of SARS-CoV-2 are a cornerstone of the public health response to COVID-19. The emergence of hypermutated, increasingly transmissible variants of concern (VOCs) threaten this strategy. Omicron (B.1.1.529), the fifth VOC to be described, harbours multiple amino acid mutations in spike, half of which lie within the receptor-binding domain. Here we demonstrate substantial evasion of neutralization by Omicron BA.1 and BA.2 variants in vitro using sera from individuals vaccinated with ChAdOx1, BNT162b2 and mRNA-1273. These data were mirrored by a substantial reduction in real-world vaccine effectiveness that was partially restored by booster vaccination. The Omicron variants BA.1 and BA.2 did not induce cell syncytia in vitro and favoured a TMPRSS2-independent endosomal entry pathway, these phenotypes mapping to distinct regions of the spike protein. Impaired cell fusion was determined by the receptor-binding domain, while endosomal entry mapped to the S2 domain. Such marked changes in antigenicity and replicative biology may underlie the rapid global spread and altered pathogenicity of the Omicron variant