ORCID Profile
0000-0001-9002-7933
Current Organisation
National University of Singapore
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Publisher: American Association for the Advancement of Science (AAAS)
Date: 22-12-2017
Abstract: The fungal pathogen Ug99 (named for its identification in Uganda in 1999) threatens wheat crops worldwide. Ug99 can kill entire fields of wheat and is undeterred by many of the disease-resistance genes that otherwise protect wheat crops. Two papers describe two peptides secreted by the fungus as it attacks the wheat (see the Perspective by Moscou and van Esse). Chen et al. show that fungal AvrSr50 binds to the plant's immune receptor Sr50, and Salcedo et al. show that fungal AvrSr35 binds to Sr35. Successful binding activates the plant's immune defenses. Removing or inactivating these Avr effectors leaves the plant defenseless and susceptible to disease. Science , this issue p. 1607 , p. 1604 see also p. 1541
Publisher: American Chemical Society (ACS)
Date: 17-08-2022
Abstract: Nanomedicine-based and unmodified drug interventions to address COVID-19 have evolved over the course of the pandemic as more information is gleaned and virus variants continue to emerge. For ex le, some early therapies (e.g., antibodies) have experienced markedly decreased efficacy. Due to a growing concern of future drug resistant variants, current drug development strategies are seeking to find effective drug combinations. In this study, we used IDentif.AI, an artificial intelligence-derived platform, to investigate the drug-drug and drug-dose interaction space of six promising experimental or currently deployed therapies at various concentrations: EIDD-1931, YH-53, nirmatrelvir, AT-511, favipiravir, and auranofin. The drugs were tested
Publisher: BMJ
Date: 09-06-2018
DOI: 10.1136/BJSPORTS-2017-098885
Abstract: Lateral ankle sprain injury is the most common musculoskeletal injury incurred by in iduals who participate in sports and recreational physical activities. Following initial injury, a high proportion of in iduals develop long-term injury-associated symptoms and chronic ankle instability. The development of chronic ankle instability is consequent on the interaction of mechanical and sensorimotor insufficiencies/impairments that manifest following acute lateral ankle sprain injury. To reduce the propensity for developing chronic ankle instability, clinical assessments should evaluate whether patients in the acute phase following lateral ankle sprain injury exhibit any mechanical and/or sensorimotor impairments. This modified Delphi study was undertaken under the auspices of the executive committee of the International Ankle Consortium. The primary aim was to develop recommendations, based on expert (n=14) consensus, for structured clinical assessment of acute lateral ankle sprain injuries. After two modified Delphi rounds, consensus was achieved on the clinical assessment of acute lateral ankle sprain injuries. Consensus was reached on a minimum standard clinical diagnostic assessment. Key components of this clinical diagnostic assessment include: establishing the mechanism of injury, as well as the assessment of ankle joint bones and ligaments. Through consensus, the expert panel also developed the International Ankle Consortium Rehabilitation-Oriented ASsessmenT (ROAST). The International Ankle Consortium ROAST will help clinicians identify mechanical and/or sensorimotor impairments that are associated with chronic ankle instability. This consensus statement from the International Ankle Consortium aims to be a key resource for clinicians who regularly assess in iduals with acute lateral ankle sprain injuries.
Publisher: Public Library of Science (PLoS)
Date: 28-12-2020
DOI: 10.1371/JOURNAL.PGEN.1009291
Abstract: Pathogen populations are expected to evolve virulence traits in response to resistance deployed in agricultural settings. However, few temporal datasets have been available to characterize this process at the population level. Here, we examined two temporally separated populations of Puccinia coronata f. sp. avenae ( Pca ), which causes crown rust disease in oat ( Avena sativa ) s led from 1990 to 2015. We show that a substantial increase in virulence occurred from 1990 to 2015 and this was associated with a genetic differentiation between populations detected by genome-wide sequencing. We found strong evidence for genetic recombination in these populations, showing the importance of the alternate host in generating genotypic variation through sexual reproduction. However, asexual expansion of some clonal lineages was also observed within years. Genome-wide association analysis identified seven Avr loci associated with virulence towards fifteen Pc resistance genes in oat and suggests that some groups of Pc genes recognize the same pathogen effectors. The temporal shift in virulence patterns in the Pca populations between 1990 and 2015 is associated with changes in allele frequency in these genomic regions. Nucleotide ersity patterns at a single Avr locus corresponding to Pc38 , Pc39 , Pc55 , Pc63 , Pc70 , and Pc71 showed evidence of a selective sweep associated with the shift to virulence towards these resistance genes in all 2015 collected isolates.
Publisher: Cold Spring Harbor Laboratory
Date: 02-07-2021
DOI: 10.1101/2021.06.23.21259321
Abstract: We aimed to harness IDentif.AI 2.0, a clinically actionable AI platform to rapidly pinpoint and prioritize optimal combination therapy regimens against COVID-19. A pool of starting candidate therapies was developed in collaboration with a community of infectious disease clinicians and included EIDD-1931 (metabolite of EIDD-2801), baricitinib, ebselen, selinexor, masitinib, nafamostat mesylate, telaprevir (VX-950), SN-38 (metabolite of irinotecan), imatinib mesylate, remdesivir, lopinavir, and ritonavir. Following the initial drug pool assessment, a focused, 6-drug pool was interrogated at 3 dosing levels per drug representing nearly 10,000 possible combination regimens. IDentif.AI 2.0 paired prospective, experimental validation of multi-drug efficacy on a SARS-CoV-2 live virus (propagated, original strain, B.1.351 and B.1.617.2 variants) and Vero E6 assay with a quadratic optimization workflow. Within 3 weeks, IDentif.AI 2.0 realized a list of combination regimens, ranked by efficacy, for clinical go/no-go regimen recommendations. IDentif.AI 2.0 revealed EIDD-1931 to be a strong candidate upon which multiple drug combinations can be derived. IDentif.AI 2.0 rapidly revealed promising drug combinations for clinical translation. It pinpointed dose-dependent drug synergy behavior to play a role in trial design and realizing positive treatment outcomes. IDentif.AI 2.0 represents an actionable path towards rapidly optimizing combination therapy following pandemic emergence. - When novel pathogens emerge, the immediate strategy is to repurpose drugs. - Good drugs delivered together in suboptimal combinations and doses can yield low or no efficacy, leading to misperception that the drugs are ineffective. - IDentif.AI 2.0 does not use in silico modeling or pre-existing data. - IDentif.AI 2.0 pairs optimization with prospectively acquired experimental data using a SARS-CoV-2/Vero E6 assay. - IDentif.AI 2.0 pinpoints EIDD-1931 as a foundation for optimized anti-SARS-CoV-2 combination therapies.
Publisher: Springer Science and Business Media LLC
Date: 07-11-2019
DOI: 10.1038/S41467-019-12927-7
Abstract: Parasexuality contributes to ersity and adaptive evolution of haploid (monokaryotic) fungi. However, non-sexual genetic exchange mechanisms are not defined in dikaryotic fungi (containing two distinct haploid nuclei). Newly emerged strains of the wheat stem rust pathogen, Puccinia graminis f. sp. tritici ( Pgt ), such as Ug99, are a major threat to global food security. Here, we provide genomics-based evidence supporting that Ug99 arose by somatic hybridisation and nuclear exchange between dikaryons. Fully haplotype-resolved genome assembly and DNA proximity analysis reveal that Ug99 shares one haploid nucleus genotype with a much older African lineage of Pgt , with no recombination or chromosome reassortment. These findings indicate that nuclear exchange between dikaryotes can generate genetic ersity and facilitate the emergence of new lineages in asexual fungal populations.
Publisher: Oxford University Press (OUP)
Date: 22-06-2022
DOI: 10.1093/G3JOURNAL/JKAC149
Abstract: Advances in sequencing technologies as well as development of algorithms and workflows have made it possible to generate fully phased genome references for organisms with nonhaploid genomes such as dikaryotic rust fungi. To enable discovery of pathogen effectors and further our understanding of virulence evolution, we generated a chromosome-scale assembly for each of the 2 nuclear genomes of the oat crown rust pathogen, Puccinia coronata f. sp. avenae (Pca). This resource complements 2 previously released partially phased genome references of Pca, which display virulence traits absent in the isolate of historic race 203 (isolate Pca203) which was selected for this genome project. A fully phased, chromosome-level reference for Pca203 was generated using PacBio reads and Hi-C data and a recently developed pipeline named NuclearPhaser for phase assignment of contigs and phase switch correction. With 18 chromosomes in each haplotype and a total size of 208.10 Mbp, Pca203 has the same number of chromosomes as other cereal rust fungi such as Puccinia graminis f. sp. tritici and Puccinia triticina, the causal agents of wheat stem rust and wheat leaf rust, respectively. The Pca203 reference marks the third fully phased chromosome-level assembly of a cereal rust to date. Here, we demonstrate that the chromosomes of these 3 Puccinia species are syntenous and that chromosomal size variations are primarily due to differences in repeat element content.
Publisher: BMJ
Date: 10-09-2019
No related grants have been discovered for Alexandria Remus.