Diversity of viroids infecting grapevines in the South African Vitis germplasm collection

DATA AVAILABILITY : All sequence data generated or analysed during this study have been Submitted to Genbank under Accession numbers provided in the supplementary information files (Table 6).Seven viroid species and one putative viroid species have been reported to infect grapevine namely, hop stunt viroid (HSVd), grapevine yellow speckle viroid 1 (GYSVd-1), grapevine yellow speckle viroid 2 (GYSVd-2), Australian grapevine viroid (AGVd), Japanese grapevine viroid (JGVd), grapevine latent viroid (GLVd), and citrus exocortis viroid (CEVd), as well as a grapevine hammerhead viroid-like RNA (GHVd), so far. In this study, RNA sequence (RNA-Seq) data, from 229 Vitis accessions from the field-maintained vineyard of the South African Vitis germplasm collection, were analysed to determine the diversity of the viroids present. Five of the seven known grapevine-infecting viroids and one putative grapevine-infecting viroid species were very commonly found, with 214 of the 229 samples containing at least one viroid species. HSVd, GYSVd-1, GYSVd-2, AGVd, and JGVd, as well as GHVd, were identified in the RNA-Seq data of the samples and confirmed using RT-PCR and Sanger sequencing. The HSVd sequences indicated the presence of two variants, with one showing multiple nucleotide insertions. AGVd and GYSVd-2 did not display significant sequence diversity, confirming past international studies. GYSVd-1 occurs as four major variants worldwide and representatives of all four variants were identified in this vineyard. This is the first report on the diversity of viroids infecting grapevine in South Africa and the first report of JGVd outside of Japan and GHVd in South Africa. Further studies are needed to fully assess the population and to identify potentially new viroid species.http://link.springer.com/journal/11262hj2024Forestry and Agricultural Biotechnology Institute (FABI)SDG-02:Zero Hunge

Compressed air energy storage with liquid air capacity extension

As renewable electricity generation capacity increases, energy storage will be required at larger scales. Compressed Air Energy Storage (CAES) at large scales, with effective management of heat, is recognised to have potential to provide affordable grid-scale energy storage. Where suitable geologies are unavailable, compressed air could be stored in pressurised steel tanks above ground, but this would incur significant storage costs. Liquid Air Energy Storage (LAES), on the other hand, does not need a pressurised storage vessel, can be located almost anywhere, has a relatively large volumetric exergy density at ambient pressure, and has relatively low marginal cost of energy storage capacity even at modest scales. However, it has lower roundtrip efficiency than compressed air energy storage technologies. This paper carries out thermodynamic analyses for an energy storage installation comprising a compressed air component supplemented with a liquid air store, and additional machinery to transform between gaseous air at ambient temperature and high pressure, and liquid air at ambient pressure. A roundtrip efficiency of 42% is obtained for the conversion of compressed air at 50 bar to liquid air, and back. The proposed system is more economical than pure LAES and more economical than a pure CAES installation if the storage duration is sufficiently long and if the high-pressure air store cannot exploit some large-scale geological feature

Identification of Incident CKD Stage 3 in Research Studies

In epidemiologic research, incident chronic kidney disease (CKD) is commonly determined by laboratory tests performed at planned study visits. Given the morbidity and mortality associated with CKD, persons with incident disease may be less likely to attend scheduled visits, affecting observed associations. The objective of this study was to quantify loss-to-follow-up by CKD status, and to determine whether supplementation with diagnostic code data improves capture of incident CKD

Abdominal aortic aneurysm is associated with a variant in low-density lipoprotein receptor-related protein 1

Abdominal aortic aneurysm (AAA) is a common cause of morbidity and mortality and has a significant heritability. We carried out a genome-wide association discovery study of 1866 patients with AAA and 5435 controls and replication of promising signals (lead SNP with a p value < 1 × 10-5) in 2871 additional cases and 32,687 controls and performed further follow-up in 1491 AAA and 11,060 controls. In the discovery study, nine loci demonstrated association with AAA (p < 1 × 10-5). In the replication sample, the lead SNP at one of these loci, rs1466535, located within intron 1 of low-density-lipoprotein receptor-related protein 1 (LRP1) demonstrated significant association (p = 0.0042). We confirmed the association of rs1466535 and AAA in our follow-up study (p = 0.035). In a combined analysis (6228 AAA and 49182 controls), rs1466535 had a consistent effect size and direction in all sample sets (combined p = 4.52 × 10-10, odds ratio 1.15 [1.10-1.21]). No associations were seen for either rs1466535 or the 12q13.3 locus in independent association studies of coronary artery disease, blood pressure, diabetes, or hyperlipidaemia, suggesting that this locus is specific to AAA. Gene-expression studies demonstrated a trend toward increased LRP1 expression for the rs1466535 CC genotype in arterial tissues; there was a significant (p = 0.029) 1.19-fold (1.04-1.36) increase in LRP1 expression in CC homozygotes compared to TT homozygotes in aortic adventitia. Functional studies demonstrated that rs1466535 might alter a SREBP-1 binding site and influence enhancer activity at the locus. In conclusion, this study has identified a biologically plausible genetic variant associated specifically with AAA, and we suggest that this variant has a possible functional role in LRP1 expression

Risk of hydroxychloroquine alone and in combination with azithromycin in the treatment of rheumatoid arthritis: a multinational, retrospective study

Background: Hydroxychloroquine, a drug commonly used in the treatment of rheumatoid arthritis, has received much negative publicity for adverse events associated with its authorisation for emergency use to treat patients with COVID-19 pneumonia. We studied the safety of hydroxychloroquine, alone and in combination with azithromycin, to determine the risk associated with its use in routine care in patients with rheumatoid arthritis. Methods: In this multinational, retrospective study, new user cohort studies in patients with rheumatoid arthritis aged 18 years or older and initiating hydroxychloroquine were compared with those initiating sulfasalazine and followed up over 30 days, with 16 severe adverse events studied. Self-controlled case series were done to further establish safety in wider populations, and included all users of hydroxychloroquine regardless of rheumatoid arthritis status or indication. Separately, severe adverse events associated with hydroxychloroquine plus azithromycin (compared with hydroxychloroquine plus amoxicillin) were studied. Data comprised 14 sources of claims data or electronic medical records from Germany, Japan, the Netherlands, Spain, the UK, and the USA. Propensity score stratification and calibration using negative control outcomes were used to address confounding. Cox models were fitted to estimate calibrated hazard ratios (HRs) according to drug use. Estimates were pooled where the I2 value was less than 0·4. Findings: The study included 956 374 users of hydroxychloroquine, 310 350 users of sulfasalazine, 323 122 users of hydroxychloroquine plus azithromycin, and 351 956 users of hydroxychloroquine plus amoxicillin. No excess risk of severe adverse events was identified when 30-day hydroxychloroquine and sulfasalazine use were compared. Self-controlled case series confirmed these findings. However, long-term use of hydroxychloroquine appeared to be associated with increased cardiovascular mortality (calibrated HR 1·65 [95% CI 1·12–2·44]). Addition of azithromycin appeared to be associated with an increased risk of 30-day cardiovascular mortality (calibrated HR 2·19 [95% CI 1·22–3·95]), chest pain or angina (1·15 [1·05–1·26]), and hear

Taxonomy and biology of Quambalaria spp. infecting eucalypts in South Africa

The genus Quambalaria (Microstromatales, Exobasidiomycetes) includes six species, five of which are pathogens of Eucalyptus and Corymbia species. The only exception is Q. cyanescens, which has been shown to be non-pathogenic to plants, but can be an opportunistic human pathogen. The symptoms on trees include shoot and leaf blight, which is characteristic of Q. eucalypti and Q. pitereka and stem cankers caused by Q. coyrecup. The studies in this dissertation arose from the discovery of a Quambalaria-like species infecting Eucalyptus seed capsules. The complete body of research on Quambalaria is reviewed here, focusing on the taxonomy, pathogenicity, host range and geographical distribution. The review revealed a lack of knowledge on basic aspects of its biology, especially in terms of its mating behaviour and sexual reproduction. For this reason, these two aspects in related in species of the Ustilaginomycetes were also considered. This revealed that whole genome sequences and some knowledge regarding mating genes in14 species of Ustilaginomycetes have been published. This knowledge provided a framework in which a whole genome sequence of a Quambalaria species could be explored for the presence of genes related to sexual reproduction. It is suggested that such knowledge could shed light on many unknown aspects of the reproduction and life cycle of Quambalaria species.Dissertation (MSc)--University of Pretoria, 2019.BiochemistryMSc (Microbiology)Unrestricte

First report of Citrus concave gum-associated virus (CCGaV) on apple (Malus spp.) in South Africa

DATA AVAILABILITY : Confirmed sequences deposited with Genbank numbers OR728660 to OR728683. The high throuput sequencing data are under accession number PRJNA1026321. The reviewer link to the data is: https://dataview.ncbi.nlm.nih.gov/object/PRJNA1026321?reviewer=2ee828113e7jbp0hp9mqljke31.No abstract available.The next generation sequencing of one sample was funded by the VirFree program from the European Union’s Horizon 2020 research and innovation programme under the Marie Skłodowska-Curie grant agreement No 734736.https://link.springer.com/journal/421612025-04-02hj2024Forestry and Agricultural Biotechnology Institute (FABI)SDG-15:Life on lan

A Reconfigurable and Biologically Inspired Paradigm for Computation Using Network-On-Chip and Spiking Neural Networks

FPGA devices have emerged as a popular platform for the rapid prototyping of biological Spiking Neural Networks (SNNs) applications, offering the key requirement of reconfigurability. However, FPGAs do not efficiently realise the biologically plausible neuron and synaptic models of SNNs, and current FPGA routing structures cannot accommodate the high levels of interneuron connectivity inherent in complex SNNs. This paper highlights and discusses the current challenges of implementing scalable SNNs on reconfigurable FPGAs. The paper proposes a novel field programmable neural network architecture (EMBRACE), incorporating low-power analogue spiking neurons, interconnected using a Network-on-Chip architecture. Results on the evaluation of the EMBRACE architecture using the XOR benchmark problem are presented, and the performance of the architecture is discussed. The paper also discusses the adaptability of the EMBRACE architecture in supporting fault tolerant computing