Biology subjects

Sweet, M.

Publications and source records attributed to Sweet, M..

7 recordsLinked to original sources

bioRxiv2026

SeCAT (Sequence Consensus Amplicon Trimming): a simulation-informed Nextflow pipeline for cross-study harmonisation of 16S rRNA metabarcoding datasets

Global syntheses of 16S rRNA metabarcoding data rely on combining datasets, yet amplicon sequence variants generated with different primer pairs can rarely be compared directly. Existing approaches correct batch effects statistically or aggregate taxonomically; none first establishes whether the sequences are positionally comparable. We present SeCAT (Sequence Consensus Amplicon Trimming), a Nextflow pipeline that maps every studys variants onto a 16S rRNA full-length reference alignment, determines the largest window shared across studies, and tests by simulation whether trimming to that window degrades community structure before any data are merged. Applied to thirteen marine studies sequenced with three primer sets, twelve converged on a consensus window with a median trimmed read length of 249 bp (9,582 alignment columns). Degradation tests across twelve studies and six taxonomic ranks (72 study-rank combinations) returned 31 passes, 38 cautions and three confirmed failures. Eleven studies (682 samples after filtering) were harmonised (trimmed to the window and merged), collapsing 20,891 primer-specific variants into 12,667 MetaASVs, trimmed sequences deduplicated across studies. Harmonisation preserved community structure at family level (Mantel r = 1.00; Procrustes m{superscript 2} < 0.001) without adding between-study variance (|{Delta}R{superscript 2}| < 0.001). Alpha diversity, including observed richness, was recovered across all levels (intraclass correlations 0.93-1.00), whereas sequence-level congruence was moderate (Procrustes m{superscript 2} = 0.52), as expected where between-study similarity at sequence level exists only after harmonisation. The harmonised output supports synthesis from aggregated ranks down to exact sequences. By establishing positional comparability before merging, SeCAT opens the archive of primer-fragmented 16S rRNA surveys to sequence-level synthesis.

bioinformatics↗

bioRxiv2025

Cell and nuclear size are associated with chromosomal instability and tumorigenicity in cancer cells that undergo whole genome doubling

Whole genome doubling (WGD) is a frequent event in cancer evolution associated with chromosomal instability, metastasis, and poor prognosis. While the genomic consequences of WGD are well documented, the effects of non-genetic alterations that accompany WGD, such as changes to cell and nuclear size, on tetraploid (4N) cancer cell physiology are less understood. Here, we show that cell and nuclear volume do not always scale with DNA content after WGD in cancer cells, resulting in 4N cells that differ in size. We find that small size is associated with enhanced cell fitness, mitotic fidelity, and tumorigenicity in 4N cancer cells and with poor patient survival in WGD-positive human cancers. Overall, these results suggest that cell and nuclear size contribute to the tumorigenic potential of 4N cancer cells and could be an important prognostic marker in human tumors that undergo WGD. Statement of SignificanceWe report that WGD generates tetraploid cancer cells that vary in size, with larger cells displaying high chromosomal instability and smaller cells exhibiting high fitness and tumorigenicity. Furthermore, WGD status and cancer cell nuclear size in human tumors correlated with patient survival, demonstrating the clinical relevance of this association.

cancer biology↗

bioRxiv2023

The bacterial microbiome of symbiotic and menthol-bleached polyps of Galaxea fascicularis

AO_SCPLOWBSTRACTC_SCPLOWCoral reefs support the livelihood of half a billion people but are at high risk of collapse due to the vulnerability of corals to climate change and local anthropogenic stressors. While understanding coral functioning is essential to guide conservation efforts, research is challenged by the complex nature of corals. They exist as metaorganisms (holobionts), constituted by the association between the (coral) animal host, its obligate endosymbiotic algae (Symbiodiniaceae), and other microorganisms comprising bacteria, viruses, archaea, fungi and other protists. Researchers therefore increasingly turn to model organisms to unravel holobiont complexity, dynamics, and how these determine the health and fitness of corals. The coral Galaxea fascicularis is an emerging model organism for coral symbiosis research with demonstrated suitability to aquarium rearing and reproduction, and to manipulation of the host-Symbiodiniaceae symbiosis. However, little is known about the response of the G. fascicularis microbiome to menthol bleaching--the experimental removal of the Symbiodiniaceae which represents the first step in coral-algal symbiosis manipulation. For this, we characterized the bacterial microbiome of symbiotic and menthol-bleached G. fascicularis originating from the Red Sea and South China Sea (Hong Kong) that were long-term aquarium-reared in separate facilities. We found that the coral-associated microbiomes were composed of relatively few bacterial taxa (10-78 ASVs). Symbiotic polyps (clonal replicates) from the same colony had similar microbiomes, which were distinct from those of other colonies despite co-culturing in shared aquaria. A pattern of seemingly differential response of the bacterial microbiome to menthol bleaching between the two facilities emerged, warranting further investigation into the role of rearing conditions. Nevertheless, the changes in community composition overall appeared to be stochastic suggesting a dysbiotic state. Considering the importance of bleaching treatment of captive corals for symbiosis research, our results--although preliminary--contribute fundamental knowledge for the development of the Galaxea model for coral symbiosis research.

microbiology↗

bioRxiv2022

The reef-building coral Galaxea fascicularis: a new model system for coral symbiosis

Reef-building corals owe their evolutionary success to their symbiosis with unicellular algae (Symbiodiniaceae). However, increasingly frequent heat waves lead to coral mass-bleaching events and pose a serious threat to the survival of reef ecosystems. Despite significant efforts, a mechanistic understanding of coral-algal symbiosis functioning, what leads to its breakdown and what can prevent it, remains incomplete. The main obstacles are low amenability of corals to experimental handling and, owing to its obligatory nature, the difficulties of manipulating the coral-algal association. Indeed, many studies on the symbiotic partnership are conducted on other cnidarian model organisms and their results may therefore not be fully transferable to tropical reef-building corals. Here, we identify the tropical stony coral species Galaxea fascicularis as a novel candidate coral model system. Individual polyps of this species can be separated, enabling highly replicated genotype studies, and are well suited to experimental investigation of the symbiosis as they can be easily and effectively rid of their algal symbionts (bleached). We show that bleached adult individuals can reestablish symbiosis with non-native symbionts, and we report the completion of the gametogenic cycle ex-situ, with the successful spawning in aquaria over multiple years. These achievements help overcome several of the major limitations to direct research on corals and highlight the potential of G. fascicularis as an important new model system for investigations of symbiosis functioning and manipulation.

systems biology↗

bioRxiv2021

A framework for selectively breeding corals for assisted evolution

Coral cover on tropical reefs has declined during the last three decades due to the combined effects of climate change, destructive fishing, pollution, and land use change. Drastic reductions in greenhouse gas emissions combined with effective coastal management and conservation strategies are essential to slow this decline. Innovative approaches, such as selective breeding for adaptive traits combined with large-scale sexual propagation, are being developed with the aim of pre-adapting reefs to increased ocean warming. However, there are still major gaps in our understanding of the technical and methodological constraints to producing corals for such restoration interventions. Here we propose a framework for selectively breeding corals and rearing them from eggs to 2.5-year old colonies using the coral Acropora digitifera as a model species. We present methods for choosing colonies for selective crossing, enhancing early survivorship in ex situ and in situ nurseries, and outplanting and monitoring colonies on natal reefs. We used a short-term (7-day) temperature stress assay to select parental colonies based on heat tolerance of excised branches. From six parental colonies, we produced 12 distinct crosses, and compared survivorship and growth of colonies transferred to in situ nurseries or outplanted to the reef at different ages. We demonstrate that selectively breeding and rearing coral colonies is technically feasible at small scales and could be upscaled as part of restorative assisted evolution initiatives. Nonetheless, there are still challenges to overcome before selective breeding can be implemented as a viable conservation tool, especially at the post-settlement and outplanting phases. Although interdisciplinary approaches will be needed to overcome many of the challenges identified in this study, selective breeding has the potential to be a viable tool within reef managers toolbox to support the persistence of selected reefs in the face of climate change.

ecology↗

bioRxiv2019

Improving detection capabilities of a critically endangeredfreshwater invertebrate with environmental DNA using digital droplet PCR

Isogenus nubecula is a critically endangered Plecoptera species. Considered extinct in the UK, the species was recently rediscovered in one location of the river Dee in Wales after 22 years of absence. As many species belonging to the Perlodidae, this species can be a bio-indicator, utilised for assessing water quality and health status of a given freshwater system. However, conventional monitoring of invertebrates via kick-sampling for example, is an invasive and expensive (time consuming). Further, such methods require a high level of taxonomic expertise. Here, we compared the traditional kick-sampling method with the use of eDNA detection using qPCR and ddPCR-analyses. In spring 2018, we sampled eDNA from twelve locations on the river Dee. I. nubecula was detected using kick-sampling in five of these locations, three locations using both eDNA detection and kick-sampling and one location using eDNA detection alone - resulting in a total of six known and distinct populations of this critically endangered species. Interestingly, despite the eDNA assay being validated in vitro and in silico, and results indicating high sensitivity, qPCR analysis of the eDNA samples proved to be ineffective. In contrast, ddPCR analyses resulted in a clear detection of I. nubecula at four locations suggesting that inhibition most likely explains the big discrepancy between the obtained qPCR and ddPCR results. It is therefore important to explore inhibition effects on any new eDNA assay. We also highlight that ddPCR may well be the best option for the detection of aquatic organisms which are either rare or likely to shed low levels of eDNA into their environment.

ecology↗

bioRxiv2018

First detection of a highly invasive freshwater amphipod (Crangonyx floridanus) in the United Kingdom

The freshwater gammarid, Crangonyx floridanus, originates from North America but has invaded and subsequently spread rapidly throughout Japan. We provide here the first genetic and microscopic evidence that C. floridanus has now also reached the United Kingdom. We found this species in two locations separated by more than 200 km (Lake Windermere in the North of the UK and Smestow Brook, West Midlands). The current distribution of C. floridanus is currently unknown, however both sites are well connected to other river and channel systems therefore the chance of further spread is high. Genetic analyses of C. floridanus indicate that British inland waters are colonised by the same linage, which also has invaded Japan. We recommend further work to assess the distribution of this species and its impact on the local fauna and flora.

ecology↗