Interactions of AtRGL1, a negative regulator of gibberellic acid signalling : a thesis presented in partial fulfilment of the requirements for the degree of Master of Science in Biochemistry, Massey University, Palmerston North, New Zealand

Arabidopsis thaliana AtRGL1 (repressor of ga1-3 like-1) is a negative regulator of the signal transduction pathway of the plant hormone gibberellin. AtRGL1 belongs to the DELLA subfamily within the GRAS family of plant regulatory proteins. There are four other DELLA proteins, including AtRGA (repressor of ga1-3) and AtRGL2, encoded by the A. thaliana genome. Previous studies provided evidence that the DELLA proteins are nuclear localised and are functionally divided into N- and C- terminal domains. The N-terminal domain perceives the gibberellin signal, while the C-terminal domain functions as a negative regulator of transcription and also as a possible dimerisation domain. Previous studies have also shown that AtRGA, AtRGL1, and AtRGL2 function together in the regulation of the development of the inflorescence and that AtRGL1 is primarily expressed in this tissue. To investigate how DELLA proteins function in gibberellin signalling. I sought plant proteins that interact with AtRGL1. Two proteins. p24 (24 kDa) and p64 (64 kDa), were isolated from wild-type plant nuclear extracts by affinity to the N-tenninal 121 amino acid residues of AtRGL1. The identity of these two proteins remains to be established. To investigate the interactions of the C-terminal domain of AtRGL1 an anti-AtRGL1 polyclonal antiserum was developed for co-immunoprecipitation experiments. However, AtRGL1 was not detectable in plant nuclear extracts from the inflorescence of wild-type plants, precluding this approach. The possibility of DELLA protein dimerisation was also investigated using AtRGA, AtRGL1, and AtRGL2 in yeast 2-hybrid experiments. Yeast 2-hybrid protein interaction results suggest that AtRGA, AtRGL1, and AtRGL2 do not form homo- or hetero-dimers. Complexities encountered with this approach could make these results invalid, so these interactions require further investigation

Prioritization of HCV treatment in the direct-acting antiviral era: an economic evaluation

BACKGROUND & AIMS: We determined the optimal HCV treatment prioritization strategy for interferon-free (IFN-free) HCV direct-acting antivirals (DAAs) by disease stage and risk status incorporating treatment of people who inject drugs (PWID). METHODS: A dynamic HCV transmission and progression model compared the cost-effectiveness of treating patients early vs. delaying until cirrhosis for patients with mild or moderate fibrosis, where PWID chronic HCV prevalence was 20, 40 or 60%. Treatment duration was 12weeks at £3300/wk, to achieve a 95% sustained viral response and was varied by genotype/stage in alternative scenarios. We estimated long-term health costs (in £UK=€1.3=$1.5) and outcomes as quality adjusted life-years (QALYs) gained using a £20,000 willingness to pay per QALY threshold. We ranked strategies with net monetary benefit (NMB); negative NMB implies delay treatment. RESULTS: The most cost-effective group to treat were PWID with moderate fibrosis (mean NMB per early treatment £60,640/£23,968 at 20/40% chronic prevalence, respectively), followed by PWID with mild fibrosis (NMB £59,258 and £19,421, respectively) then ex-PWID/non-PWID with moderate fibrosis (NMB £9,404). Treatment of ex-PWID/non-PWID with mild fibrosis could be delayed (NMB -£3,650). In populations with 60% chronic HCV among PWID it was only cost-effective to prioritize DAAs to ex-PWID/non-PWID with moderate fibrosis. For every one PWID in the 20% chronic HCV setting, 2 new HCV infections were averted. One extra HCV-related death was averted per 13 people with moderate disease treated. Rankings were unchanged with reduced drug costs or varied sustained virological response/duration by genotype/fibrosis stage. CONCLUSIONS: Treating PWID with moderate or mild HCV with IFN-free DAAs is cost-effective compared to delay until cirrhosis, except when chronic HCV prevalence and reinfection risk is very high

Enhancing Discovery of Genetic Variants for Posttraumatic Stress Disorder Through Integration of Quantitative Phenotypes and Trauma Exposure Information

Funding Information: This work was supported by the National Institute of Mental Health / U.S. Army Medical Research and Development Command (Grant No. R01MH106595 [to CMN, IL, MBS, KJRe, and KCK], National Institutes of Health (Grant No. 5U01MH109539 to the Psychiatric Genomics Consortium ), and Brain & Behavior Research Foundation (Young Investigator Grant [to KWC]). Genotyping of samples was provided in part through the Stanley Center for Psychiatric Genetics at the Broad Institute supported by Cohen Veterans Bioscience . Statistical analyses were carried out on the LISA/Genetic Cluster Computer ( https://userinfo.surfsara.nl/systems/lisa ) hosted by SURFsara. This research has been conducted using the UK Biobank resource (Application No. 41209). This work would have not been possible without the financial support provided by Cohen Veterans Bioscience, the Stanley Center for Psychiatric Genetics at the Broad Institute, and One Mind. Funding Information: MBS has in the past 3 years received consulting income from Actelion, Acadia Pharmaceuticals, Aptinyx, Bionomics, BioXcel Therapeutics, Clexio, EmpowerPharm, GW Pharmaceuticals, Janssen, Jazz Pharmaceuticals, and Roche/Genentech and has stock options in Oxeia Biopharmaceuticals and Epivario. In the past 3 years, NPD has held a part-time paid position at Cohen Veterans Bioscience, has been a consultant for Sunovion Pharmaceuticals, and is on the scientific advisory board for Sentio Solutions for unrelated work. In the past 3 years, KJRe has been a consultant for Datastat, Inc., RallyPoint Networks, Inc., Sage Pharmaceuticals, and Takeda. JLM-K has received funding and a speaking fee from COMPASS Pathways. MU has been a consultant for System Analytic. HRK is a member of the Dicerna scientific advisory board and a member of the American Society of Clinical Psychopharmacology Alcohol Clinical Trials Initiative, which during the past 3 years was supported by Alkermes, Amygdala Neurosciences, Arbor Pharmaceuticals, Dicerna, Ethypharm, Indivior, Lundbeck, Mitsubishi, and Otsuka. HRK and JG are named as inventors on Patent Cooperative Treaty patent application number 15/878,640, entitled “Genotype-guided dosing of opioid agonists,” filed January 24, 2018. RP and JG are paid for their editorial work on the journal Complex Psychiatry. OAA is a consultant to HealthLytix. All other authors report no biomedical financial interests or potential conflicts of interest. Funding Information: This work was supported by the National Institute of Mental Health/ U.S. Army Medical Research and Development Command (Grant No. R01MH106595 [to CMN, IL, MBS, KJRe, and KCK], National Institutes of Health (Grant No. 5U01MH109539 to the Psychiatric Genomics Consortium), and Brain & Behavior Research Foundation (Young Investigator Grant [to KWC]). Genotyping of samples was provided in part through the Stanley Center for Psychiatric Genetics at the Broad Institute supported by Cohen Veterans Bioscience. Statistical analyses were carried out on the LISA/Genetic Cluster Computer (https://userinfo.surfsara.nl/systems/lisa) hosted by SURFsara. This research has been conducted using the UK Biobank resource (Application No. 41209). This work would have not been possible without the financial support provided by Cohen Veterans Bioscience, the Stanley Center for Psychiatric Genetics at the Broad Institute, and One Mind. This material has been reviewed by the Walter Reed Army Institute of Research. There is no objection to its presentation and/or publication. The opinions or assertions contained herein are the private views of the authors and are not to be construed as official or as reflecting true views of the U.S. Department of the Army or the Department of Defense. We thank the investigators who comprise the PGC-PTSD working group and especially the more than 206,000 research participants worldwide who shared their life experiences and biological samples with PGC-PTSD investigators. We thank Mark Zervas for his critical input. Full acknowledgments are in Supplement 1. MBS has in the past 3 years received consulting income from Actelion, Acadia Pharmaceuticals, Aptinyx, Bionomics, BioXcel Therapeutics, Clexio, EmpowerPharm, GW Pharmaceuticals, Janssen, Jazz Pharmaceuticals, and Roche/Genentech and has stock options in Oxeia Biopharmaceuticals and Epivario. In the past 3 years, NPD has held a part-time paid position at Cohen Veterans Bioscience, has been a consultant for Sunovion Pharmaceuticals, and is on the scientific advisory board for Sentio Solutions for unrelated work. In the past 3 years, KJRe has been a consultant for Datastat, Inc. RallyPoint Networks, Inc. Sage Pharmaceuticals, and Takeda. JLM-K has received funding and a speaking fee from COMPASS Pathways. MU has been a consultant for System Analytic. HRK is a member of the Dicerna scientific advisory board and a member of the American Society of Clinical Psychopharmacology Alcohol Clinical Trials Initiative, which during the past 3 years was supported by Alkermes, Amygdala Neurosciences, Arbor Pharmaceuticals, Dicerna, Ethypharm, Indivior, Lundbeck, Mitsubishi, and Otsuka. HRK and JG are named as inventors on Patent Cooperative Treaty patent application number 15/878,640, entitled ?Genotype-guided dosing of opioid agonists,? filed January 24, 2018. RP and JG are paid for their editorial work on the journal Complex Psychiatry. OAA is a consultant to HealthLytix. All other authors report no biomedical financial interests or potential conflicts of interest. Publisher Copyright: © 2021 Society of Biological PsychiatryBackground: Posttraumatic stress disorder (PTSD) is heritable and a potential consequence of exposure to traumatic stress. Evidence suggests that a quantitative approach to PTSD phenotype measurement and incorporation of lifetime trauma exposure (LTE) information could enhance the discovery power of PTSD genome-wide association studies (GWASs). Methods: A GWAS on PTSD symptoms was performed in 51 cohorts followed by a fixed-effects meta-analysis (N = 182,199 European ancestry participants). A GWAS of LTE burden was performed in the UK Biobank cohort (N = 132,988). Genetic correlations were evaluated with linkage disequilibrium score regression. Multivariate analysis was performed using Multi-Trait Analysis of GWAS. Functional mapping and annotation of leading loci was performed with FUMA. Replication was evaluated using the Million Veteran Program GWAS of PTSD total symptoms. Results: GWASs of PTSD symptoms and LTE burden identified 5 and 6 independent genome-wide significant loci, respectively. There was a 72% genetic correlation between PTSD and LTE. PTSD and LTE showed largely similar patterns of genetic correlation with other traits, albeit with some distinctions. Adjusting PTSD for LTE reduced PTSD heritability by 31%. Multivariate analysis of PTSD and LTE increased the effective sample size of the PTSD GWAS by 20% and identified 4 additional loci. Four of these 9 PTSD loci were independently replicated in the Million Veteran Program. Conclusions: Through using a quantitative trait measure of PTSD, we identified novel risk loci not previously identified using prior case-control analyses. PTSD and LTE have a high genetic overlap that can be leveraged to increase discovery power through multivariate methods.publishersversionpublishe

Medium-term effects of SARS-CoV-2 infection on multiple vital organs, exercise capacity, cognition, quality of life and mental health, post-hospital discharge.

BACKGROUND: The medium-term effects of Coronavirus disease (COVID-19) on organ health, exercise capacity, cognition, quality of life and mental health are poorly understood. METHODS: Fifty-eight COVID-19 patients post-hospital discharge and 30 age, sex, body mass index comorbidity-matched controls were enrolled for multiorgan (brain, lungs, heart, liver and kidneys) magnetic resonance imaging (MRI), spirometry, six-minute walk test, cardiopulmonary exercise test (CPET), quality of life, cognitive and mental health assessments. FINDINGS: At 2-3 months from disease-onset, 64% of patients experienced breathlessness and 55% reported fatigue. On MRI, abnormalities were seen in lungs (60%), heart (26%), liver (10%) and kidneys (29%). Patients exhibited changes in the thalamus, posterior thalamic radiations and sagittal stratum on brain MRI and demonstrated impaired cognitive performance, specifically in the executive and visuospatial domains. Exercise tolerance (maximal oxygen consumption and ventilatory efficiency on CPET) and six-minute walk distance were significantly reduced. The extent of extra-pulmonary MRI abnormalities and exercise intolerance correlated with serum markers of inflammation and acute illness severity. Patients had a higher burden of self-reported symptoms of depression and experienced significant impairment in all domains of quality of life compared to controls (p<0.0001 to 0.044). INTERPRETATION: A significant proportion of patients discharged from hospital reported symptoms of breathlessness, fatigue, depression and had limited exercise capacity. Persistent lung and extra-pulmonary organ MRI findings are common in patients and linked to inflammation and severity of acute illness. FUNDING: NIHR Oxford and Oxford Health Biomedical Research Centres, British Heart Foundation Centre for Research Excellence, UKRI, Wellcome Trust, British Heart Foundation

Discovery and functional prioritization of Parkinson's disease candidate genes from large-scale whole exome sequencing.

BACKGROUND: Whole-exome sequencing (WES) has been successful in identifying genes that cause familial Parkinson's disease (PD). However, until now this approach has not been deployed to study large cohorts of unrelated participants. To discover rare PD susceptibility variants, we performed WES in 1148 unrelated cases and 503 control participants. Candidate genes were subsequently validated for functions relevant to PD based on parallel RNA-interference (RNAi) screens in human cell culture and Drosophila and C. elegans models. RESULTS: Assuming autosomal recessive inheritance, we identify 27 genes that have homozygous or compound heterozygous loss-of-function variants in PD cases. Definitive replication and confirmation of these findings were hindered by potential heterogeneity and by the rarity of the implicated alleles. We therefore looked for potential genetic interactions with established PD mechanisms. Following RNAi-mediated knockdown, 15 of the genes modulated mitochondrial dynamics in human neuronal cultures and four candidates enhanced α-synuclein-induced neurodegeneration in Drosophila. Based on complementary analyses in independent human datasets, five functionally validated genes-GPATCH2L, UHRF1BP1L, PTPRH, ARSB, and VPS13C-also showed evidence consistent with genetic replication. CONCLUSIONS: By integrating human genetic and functional evidence, we identify several PD susceptibility gene candidates for further investigation. Our approach highlights a powerful experimental strategy with broad applicability for future studies of disorders with complex genetic etiologies

Characterisation of the interactions of RGL1 : a negative regulator of gibberellin signalling : a thesis presented in partial fulfilment of the requirements for the degree of Doctor of Philosophy in Biochemistry, Massey University, Palmerston North, New Zealand.

The gibberellins are a family of phytohormones that promote many aspects of plant development. Central to the function of gibberellins are the DELLA regulatory proteins. The DELLA proteins actively repress cell differentiation and elongation, but are degraded upon perception of gibberellin, thus relieving repression of gibberellin responses. The GID1-family gibberellin receptors and DELLA-specific F-box proteins are essential for the gibberellin-induced degradation of the DELLA proteins. Importantly, the direct interaction between gibberellin-bound GID1-family gibberellin receptors and the N-terminal domain of DELLA proteins is a prerequisite for proteasomal degradation through recruitment of the F-box proteins. To increase understanding of gibberellin signalling, I have characterised a gibberellin-dependent GID1-DELLA-F-box protein signalling switch in Arabidopsis thaliana. First, I have characterised a suite of anti-DELLA antibodies for detection of four endogenous A. thaliana DELLA proteins, GIBBERELLIC ACID-INSENSITIVE (GAI), REPRESSOR OF GA1-3 (RGA), RGA-LIKE-1 (RGL1), and RGA-LIKE-2 (RGL2). Using these monoclonal antibodies against the conserved motifs of DELLA proteins, I showed that residues Asp/Glu/Leu/Leu within the signature DELLA motif are not essential for interaction of RGL1 with GID1A. Further, in vitro interaction assays allowed modelling a two-step conformational change within the N-terminal domain of RGL1 upon interaction with gibberellin-bound GID1A. Together with interaction assays in yeast two- and three-hybrid systems, these experiments provided three clues to the mechanism of GID1A-RGL1-SLY1 gibberellin signalling switch: i) N- to C- interdomain interactions of RGL1 regulate its accessibility to SLY1; ii) the N-terminal domain of RGL1 undergoes conformational rearrangement upon interaction with gibberellin-GID1A; iii) the conformational changes of the N-terminal domain of RGL1 primes the C-terminal domain for the recruitment of SLY1. I have also isolated two novel RGL1-interacting proteins, the myrosinase THIOGLUCOSIDE GLUCOHYDROLASE-2 (TGG2) and GERMIN-LIKE-PROTEIN-1 (GLP1), through affinity-purification from nuclear extract and mass spectrometry fingerprinting. Neither protein has yet been implicated in gibberellin signalling. Therefore, the identification of these novel components may help resolve several uncharacterised aspects of gibberellin signalling

Transparent, Flexible Silicon Nanostructured Wire Networks with Seamless Junctions for High-Performance Photodetector Applications

Optically transparent photodetectors are crucial in next-generation optoelectronic applications including smart windows and transparent image sensors. Designing photodetectors with high transparency, photoresponsivity, and robust mechanical flexibility remains a significant challenge, as is managing the inevitable trade-off between high transparency and strong photoresponse. Here we report a scalable method to produce flexible crystalline Si nanostructured wire (NW) networks fabricated from silicon-on-insulator (SOI) with seamless junctions and highly responsive porous Si segments that combine to deliver exceptional performance. These networks show high transparency (∼92% at 550 nm), broadband photodetection (350 to 950 nm) with excellent responsivity (25 A/W), optical response time (0.58 ms), and mechanical flexibility (1000 cycles). Temperature-dependent photocurrent measurements indicate the presence of localized electronic states in the porous Si segments, which play a crucial role in light harvesting and photocarrier generation. The scalable low-cost approach based on SOI has the potential to deliver new classes of flexible optoelectronic devices, including next-generation photodetectors and solar cells

Tau acts as an independent genetic risk factor in pathologically proven PD

MAPT has been repeatedly linked with Parkinson's disease (PD) in association studies. Although tau deposition may be seen in PD, its relevance to the pathogenesis of the condition remains unclear. The presence of tau-positive inclusions is, however, the defining feature of progressive supranuclear palsy (PSP), which may often be clinically misdiagnosed as idiopathic PD. On a genetic level, variants in MAPT are the strongest riskfactor for PSP. These facts raise the question whether the MAPT association in PD results from contamination with unrecognized cases of PSP. Using only neuropathologically provenPD, we show that the MAPT association remains and is independent of the PSP Association

Cervical lymph nodes and ovarian teratomas as germinal centres in NMDA receptor-antibody encephalitis

Autoantibodies against the extracellular domain of the N-methyl-D-aspartate receptor (NMDAR) NR1 subunit cause a severe and common form of encephalitis. To better understand their generation, we aimed to characterize and identify human germinal centres actively participating in NMDAR-specific autoimmunization by sampling patient blood, CSF, ovarian teratoma tissue and, directly from the putative site of human CNS lymphatic drainage, cervical lymph nodes. From serum, both NR1-IgA and NR1-IgM were detected more frequently in NMDAR-antibody encephalitis patients versus controls (both P