Biology subjects

Hubbard, K.

Publications and source records attributed to Hubbard, K..

3 recordsLinked to original sources

bioRxiv2025

Diverse ssRNA viruses associated with Karenia brevis harmful algal blooms in Southwest Florida

Harmful algal blooms (HABs) caused by the dinoflagellate Karenia brevis frequently occur in the eastern Gulf of Mexico, where they negatively impact the environment, human health, and economy. Very little is known about viruses associated with K. brevis blooms, although viral infection of other HAB-forming phytoplankton species can play an important role in bloom dynamics. We used viral metagenomics to identify viruses in 11 pooled seawater samples collected from Southwest Florida, USA in 2021 during a severe, spatiotemporally dynamic K. brevis bloom. Assembled viral genomes were similar to published genomes from the order Picornavirales, family Marnaviridae, and genera Sogarnavirus, Bacillarnavirus, and Marnarnavirus. Viruses from these groups infect bloom-forming diatoms (Chaetoceros sp. and Rhizosolenia setigera) and the raphidophyte Heterosigma akashiwo. We also recovered unclassified Riboviria genomes related to a Symbiodinium positive-sense ssRNA virus sequenced from coral dinoflagellate symbionts. Reverse-transcriptase PCR assays were performed to monitor the occurrence of seven representative virus genomes in these 2021 samples and 43 seawater samples collected during a subsequent, typical bloom between November 2022 and May 2023. Over half of the samples contained multiple viruses, and at least one viral genome was detected in 44 of 54 samples, collected across seasons and years, highlighting the ubiquity of these viruses in this region. Alpha diversity was highest in the summer months and positively correlated with K. brevis cell counts. Multiple regression revealed month and the presence of unclassified Riboviria sequences most similar to dinoflagellate viruses as significant predictors of K. brevis cellular abundance. ImportanceHarmful algal blooms caused by the dinoflagellate Karenia brevis negatively impact the tourism, fisheries, and public health sectors. Anticipated impacts of climate change, nutrient pollution, and ocean acidification may sustain and/or exacerbate K. brevis blooms in the future, underscoring the need for proactive monitoring, communication, and mitigation strategies. This study represents a pioneering effort in monitoring viruses associated with K. brevis blooms. The findings lay the groundwork for studying the effects of environmental drivers on K. brevis blooms and their associated viruses, as well as for exploring the roles of viruses in bloom dynamics and potential applications of viruses as biocontrol agents for K. brevis blooms. Furthermore, the comparison of viral dynamics relative to local and regional bloom dynamics in this study helps inform future monitoring and modeling needs.

microbiology↗

bioRxiv2024

Who Grows There? A Course-based Undergraduate Research Experience to explore the human microbiome through 16S DNA metabarcoding

We describe a two week Course-based Undergraduate Research Experience (CURE) to introduce students to next-generation DNA sequencing, molecular biology methods and a bioinformatic workflow. The CURE is designed to take students with little to no technical and bioinformatic experience through key steps of the protocol through scaffolded laboratory and computational practicals. Our students extract and amplify human microbiome DNA using 16S ribosomal RNA specific primers, then construct a sequencing library for Oxford Nanopore based sequencing. They taxonomically assign the sequencing reads, and determine the ecological community composition using relevant software packages. Our students were able to successfully prepare sequencing libraries and analyse the data to produce relevant figures, demonstrating they met the learning objectives of the CURE. Students identified that they had developed higher level learning as defined by Blooms taxonomy, and that their confidence in practical work significantly increased as a result of doing the CURE. We share recommendations for implementation of the CURE in undergraduate curricula, and adaptations of the methods for use in schools outreach. Our CURE successfully provides training for students in genetic analysis in an enjoyable and relatively time and cost efficient manner, preparing them for future research or careers in modern molecular biology techniques.

scientific communication and education↗

bioRxiv2022

I Am A Scientist: Overcoming implicit bias in STEM through explicit representations of diversity in lectures

The lack of diversity in Science, Technology, Engineering and Mathematics (STEM) is a significant issue for the sector. Many organisations and educators have identified lack of representation of historically marginalised groups within teaching materials as a potential barrier to students feeling that a STEM career is something that they can aspire to. A key barrier to addressing the issue is providing accessible and effective evidence-based approaches for educators to implement. In this study, we explore the potential for adapting presentation slides within lectures to humanise the scientists involved, presenting their full names and photographs alongside a Harvard style reference. We adopt a questionnaire based methodology, and survey 161 undergraduates and postgraduates at a UK civic university. We first establish that students project implicit biases onto a hypothetical reference, with over 50% of students assuming the scientist was male and Western. We then explore what students think of the humanised slide design, concluding that most students see it as good pedagogical practice, with some students positively changing their perceptions about diversity in science. We were unable to compare responses by ethnicity, but find evidence that female and non-binary students are more likely to see this as good pedagogical practice, perhaps reflecting white male fragility in being exposed to initiatives designed to highlight diversity. We conclude that humanised powerpoint slides are a potentially effective tool to highlight diversity of scientists within existing research-led teaching, but highlight that this is only a small intervention that needs to sit alongside more substantive work to address the lack of diversity in STEM.

scientific communication and education↗