Shu Hui Koh

Cryptostylis ovata is a terrestrial orchid endemic to southwestern Australia. The virus status of C. ovata has not been studied. Eighty-three C. ovata samples from 16 populations were collected, and sequencing was used to identify RNA viruses from them. In one population, all tested plants were co-infected with isolates of the exotic-to-Australia viruses Ornithogalum mosaic virus (OrMV) and bean yellow mosaic virus (BYMV). In another population, one plant was infected with BYMV. No viruses were detected in the remaining populations. The OrMV isolate shared 98–99% nucleotide identity with isolates identified from wild indigenous Lachenalia (Iridaceae) plants in South Africa. This suggests that the source of OrMV in C. ovata may be one or more bulbous iridaceous flowering plants of southern African origin that were introduced to Western Australia as ornamentals and that have since become invasive weeds. One BYMV isolate from C. ovata also exhibited 99% nucleotide identity with strains isolated from the exotic leguminous crop Lupinus angustifolius in Western Australia, suggesting possible spillover to indigenous species from this source. This study with C. ovata highlights the probable role of invasive weeds and exotic crops as sources of exotic virus spillovers to indigenous plants.

Scientific writing is a common challenge for university students, particularly those lacking proficiency in academic English. Despite being routinely evaluated on their understanding of concepts through scientific writing, students are not explicitly taught how to write scientifically. STEM education often prioritises the teaching of concepts and experimental theories, leaving students to independently decipher the expectations of advanced scientific writing at a tertiary level. However, first-year students often encounter difficulties discerning and executing the essential elements of scientific writing. To address this, we developed five high-quality, online interactive modules with the aim to augment the first-year experience and empower students to master the intricacies of scientific communication. These modules complement traditional in-class teaching and facilitate the acquisition of scientific writing skills by actively involving students through interactive unit-specific exercises and structured scaffolding of scientific writing concepts. By creating an inclusive learning environment aligned with Universal Design for Learning principles, we hope to bridge gaps in scientific communication skills. Preliminary data analysis, offers valuable insights into the effectiveness and potential impact of these modules, particularly on academic success and confidence. 

This article presents a “how-to” guide for redesigning an introductory physiology unit to emphasize the Core Concepts of Physiology. Detailed descriptions are provided of innovative, scalable, adjustments to content delivery, assessment, learning objectives, and activities. Staff reflections and student experience suggest a strong Core Concepts emphasis, while challenging, can promote critical thinking and develop an understanding of underlying chemical, physical and biological principles.
This article showcases the redesign of an introductory undergraduate vertebrate physiology unit at Murdoch University (BMS107) to promote student mastery of six Core Concepts of Physiology (Michael J, Cliff W, McFarland J, Modell H, Wright A, SpringerLink. The Core Concepts of Physiology: a New Paradigm for Teaching Physiology, 2017). Concepts were selected for their suitability in an introductory physiology unit and their ability to scaffold advanced physiology learning. Innovative curricular and pedagogical approaches were employed to 1) create a Core Concepts structure, 2) sell the Core Concepts approach to students, 3) foreground Core Concepts in learning materials, 4) actively engage students with Core Concepts, 5) revise, and 6) assess Core Concepts understanding. Median student marks and overall satisfaction with the unit were unaffected by the introduction of a Core Concepts approach. Notably, though, there was a 14% increase in student agreement with the statement “I received feedback that helped me to learn.” The challenge of the Core Concepts approach was articulated by students, but these novice learners also recognized Core Concepts as a mechanism to focus their understanding of physiology and promote critical thinking. For teaching staff, a Core Concepts approach was a reinvigorating opportunity to apply their expertise to the teaching of introductory physiology. We propose that a strong Core Concepts emphasis, while challenging, is highly rewarding for staff and provides students with a “disciplinary passport” that better prepares them to progress in diverse courses and professions. NEW & NOTEWORTHY This article presents a “how-to” guide for redesigning an introductory physiology unit to emphasize the Core Concepts of Physiology. Detailed descriptions are provided of innovative, scalable, adjustments to content delivery, assessment, learning objectives, and activities. Staff reflections and student experience suggest a strong Core Concepts emphasis, while challenging, can promote critical thinking and develop an understanding of underlying chemical, physical and biological principles.

Poor numeracy/quantitative skills (QS) development is a widespread issue across Australian tertiary education. Lack of fundamental QS can impede students' progression in STEM degrees, and disadvantage individual students across other domains of life (e.g., financial literacy and active citizenship). Our ACDS-funded Diversity in Numbers (DiN) project seeks to evaluate a targeted, course-wide, just-in-time model for undergraduate development of QS. Digital numeracy modules will be designed to scaffold QS development through embedded interactive content and rich automated feedback. Each module targets a core QS concept (e.g., statistical testing, unit conversions, mathematical relationships) and is framed around a published article relevant to unit content, to expand student awareness of numbers as a tool across diverse fields of science. Given the ongoing under-representation of women, LGBTIQA+ people and other minorities in STEM, the selection of journal articles aims to increase students' appreciation of diversity from many different viewpoints, while developing their QS. At a broader level, the project aims to address the ongoing lack of diversity among STEM graduates and within the STEM workforce by enabling students to "see themselves" within published research. Here we will present the design of our research project to assess the success of our pilot DiN modules.

Samples of leaves exhibiting symptoms resembling those caused by virus infection were collected from ornamental street flowers in a rural town in Western Australia. Thirty-seven leaf samples were collected from plants of iris, tulip, lily, daffodil, stock and grape hyacinth. Shotgun sequencing of cDNA derived from leaf samples was done, and analysis showed that about 6% of the sequences obtained were of viral origin. Assembly of virus-like sequences revealed complete or partial genome sequences of 13 virus isolates representing 11 virus species. Eight of the isolates were of potyviruses, one was of a macluravirus, three were of potexviruses, and one was of a bunya-like virus. The complete genome of an isolate originally classified as ornithogalum mosaic virus was genetically divergent and differed in polyprotein cleavage motifs, and we propose that this isolate represents a distinct species. The implications of importing to Australia live plant propagules infected with viruses are discussed.

Tobamoviruses are serious pathogens because they have extremely stable virions, they are transmitted by contact, and they often induce severe disease in crops. Knowledge of the routes of transmission and resilience of tobamovirus virions is essential in understanding the epidemiology of this group of viruses. We used an isolate of the tobamovirus yellow tailflower mild mottle virus (YTMMV) to examine root-to-root transmission in soil and in a hydroponic growth environment. Root-to-root transmission occurred rarely, and when it occurred plants did not exhibit systemic movement of the virus from the roots to the shoots over a 30-day period. The resilience of YTMMV virions was tested in dried leaf tissue over time periods from one hour to one year under temperatures ranging from -80°C to 160°C. Infectivity was maintained for at least a year when incubated at -80°C, 22°C or at fluctuating ambient temperatures of 0.8°C to 44.4°C, but incubation under dry conditions at 160°C for >4 days eliminated infectivity. Exposure of virions to 0.1 M sodium hydroxide or 20% w/v skim milk solution for 30 min, treatments recommended for tobamovirus inactivation, did not abolish infectivity of YTMMV.

The south-west Australian floristic region is one of 36 United Nations global hotspots of international species diversity. Considering the high biodiversity of the flora, it is likely that the plant virus flora is also abundant and genetically diverse, although only 15 indigenous plant viruses have been described from the flora of Western Australia. Colonisation of Australia by foreign powers from the 1830s onwards saw the introduction of thousands of exotic plant species and their pathogens, including plant viruses. Clearance of the original flora for agriculture and housing has created interfaces between the new exotic flora of exotic crops, pastures, gardens and weeds and the remnants of the original one. The actions of humans and the creation of these interfaces between ecosystems have provided opportunities for exotic viruses to interact with indigenous plants, and for indigenous viruses to interact with exotic hosts. A component of this thesis describes studies to gain a greater understanding of the identity and evolution of the plant viruses present in the indigenous flora of Western Australia and how viruses are adapting to new host opportunities. A metagenomics approach was used to identify virus-like sequences from plant samples along transects that spanned interfaces between highly modified, partially modified and relatively unmodified sites. 78 novel viruses were identified. Most of these were from indigenous plants, and analysis of them confirmed our hypothesis that viruses of this indigenous flora are abundant, genetically diverse and largely unknown. None of the viruses found in indigenous plants also occurred in the exotic plants sampled, or vice versa. The exotic viruses, Catharanthus mosaic virus, barley yellow dwarf virus and white clover mosaic virus, were found in exotic plants at ecosystem interfaces, but not in indigenous plants, suggesting that viral movement across exotic-indigenous floral interfaces may not be widespread. Despite these findings, the continuing invasion by exotic viruses, as evidenced by our discovery in Australia of Catharanthus mosaic virus, demonstrates the failure of quarantine practices to prevent new viruses arriving, thereby posing potential threats to indigenous plants. An indigenous virus might extend its host range to infect exotic weeds or crop plants. We used yellow tailflower mild mottle virus (YTMMV) as a model to test how an indigenous virus might interact with exotic hosts it had never encountered before. YTMMV is a contact-transmissible tobamovirus isolated from endemic Anthocercis species (family Solanaceae). An isolate of YTMMV was passaged through plants of Nicotiana benthamiana, tomato and black nightshade, and its genome was sequenced after every passage to determine the presence of nonsynonymous (NS) and synonymous nucleotide substitutions. Only one fixed NS nucleotide substitution was observed in the intervening region (IR) of the viral genome, and it occurred only in tomato. The passages through tomato were repeated, and a different single NS substitution occurred adjacent to the NS substitution that occurred in the first passage experiment. This finding suggested that NS substitutions in the IR of YTMMV were being selected in tomato. Tobamovirus virions are famously stable under a range of treatments. An assessment of the durability of YTMMV virions under different treatments such as time under different temperature regimes, incubation in milk solution and sodium hydroxide was done. YTMMV was shown to be more resilient to inactivation using these treatments than related viruses, tobacco mosaic virus and green cucumber mild mosaic virus. The study into transmissibility and longevity of virions of YTMMV is a pre-emptive study that will be applicable should YTMMV spill over into crops. The study of plant virus biodiversity in the wild and at the interface of ecosystems will increase our understanding of how viruses influence ecosystems, particularly on resilience to biotic and abiotic stress tolerance, longevity and fecundity. The potential application of such knowledge to agriculture is important, but it is as yet unacknowledged because of the dearth of examples. A far greater research effort is needed to understand the roles viruses play in ecosystems and the molecular mechanisms by which these are achieved. These areas are where in-depth studies of wild plant-virus interactions will have their greatest impact.

Tobamovirus is a group of viruses that have become serious pathogens of crop plants. As part of a study informing risk of wild plant virus spill over to crops, we investigated the capacity of a solanaceous-infecting tobamovirus from an isolated indigenous flora to adapt to new exotic hosts. Yellow tailflower mild mottle virus (YTMMV) (genus Tobamovirus, family Virgaviridae) was isolated from a wild plant of yellow tailflower (Anthocercis littoria, family Solanaceae) and initially passaged through a plant of Nicotiana benthamiana, then one of Nicotiana glutinosa where a single local lesion was used to inoculate a N. benthamiana plant. Sap from this plant was used as starting material for nine serial passages through three plant species. The virus titre was recorded periodically, and 85% of the virus genome was sequenced at each passage for each host. Six polymorphic sites were found in the YTMMV genome across all hosts and passages. At five of these, the alternate alleles became fixed in the viral genome until the end of the experiment. Of these five alleles, one was a non-synonymous mutation (U1499C) that occurred only when the virus replicated in tomato. The mutant isolate harbouring U1499C, designated YTMMV-δ, increased its titre over passages in tomato and outcompeted the wild-type isolate when both were co-inoculated to tomato. That YTMMV-δ had greater reproductive fitness in an exotic host than did the wild type isolate suggests YTMMV evolution is influenced by host changes.

As part of an investigation into viruses of wild plants in Australia, a contiguous sequence of 3935 nucleotides was obtained after shotgun sequencing of RNA isolated from an asymptomatic wild legume, Gompholobium preissii. Phylogenetic analysis of the sequence revealed that it most closely resembled that of Trailing lespedeza virus 1 (TLV1), a virus isolated from a wild legume in America. The proposed virus, named Gompholobium virus A, and TLV1 are genetically closest to viruses in the genera Alphacarmovirus and Pelarspovirus, family Tombusviridae, but they share features distinguishing them from both groups.

Isolates of an Australian indigenous virus, Yellow tailflower mild mottle virus (YTMMV-Kalbarri), and an exotic virus, Pelargonium zonate spot virus (PZSV-SW13), are described from Anthocercis ilicifolia subsp. ilicifolia (red-striped tailflower, family Solanaceae), a species endemic to Western Australia. This is the first report of either virus from this plant species. The complete genome sequences of YTMMV-Kalbarri and of PZSV-SW13 were obtained. YTMMV-Kalbarri shared 97% nucleotide pairwise identity with the sequence of the type isolate YTMMV-Cervantes. The sequence PZSV-SW13 shared greatest sequence identity with the partial sequence of an Australian isolate of PZSV, also from a wild plant, and with a sunflower-derived isolate of PZSV from Argentina. An experimental host range study was done of YTMMV-Kalbarri using cultivated and wild solanaceous and non-solanaceous plants. Most solanaceous plants became systemically infected, with symptoms of systemic infection ranging from symptomless to whole plant necrosis. Based on these studies, it is suggested that YTMMV has the potential to become a pathogen of commercial species of Solanaceae. This study provides further evidence that PZSV is present in wild plants in Australia, in this case an indigenous host species, and possible routes by which it invaded Australia are discussed.