School of BioSciences - Research Publications

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    A high-throughput KASP assay provides insights into the evolution of multiple resistant mutations in populations of the two-spotted spider mite Tetranychus urticae across China
    Shen, X-J ; Zhang, Y-J ; Wang, S-Y ; Chen, J-C ; Cao, L-J ; Gong, Y-J ; Pang, B-S ; Hoffmann, AA ; Wei, S-J (Wiley, 2023-05)
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    Testing for adaptive changes linked to range expansion following a single introduction of the fall webworm
    Dai, J-X ; Cao, L-J ; Chen, J-C ; Yang, F ; Shen, X-J ; Ma, L-J ; Hoffmann, AA ; Chen, M ; Wei, S-J (WILEY, 2023-06-05)
    Adaptive evolution following colonization can affect the impact of invasive species. The fall webworm (FWW) invaded China 40 years ago through a single introduction event involving a severe bottleneck and subsequently diverged into two genetic groups. The well-recorded invasion history of FWW, coupled with a clear pattern of genetic divergence, provides an opportunity to investigate whether there is any sign of adaptive evolution following the invasion. Based on genome-wide SNPs, we identified genetically separated western and eastern groups of FWW and correlated spatial variation in SNPs with geographical and climatic factors. Geographical factors explained a similar proportion of the genetic variation across all populations compared with climatic factors. However, when the two population groups were analysed separately, environmental factors explained more variation than geographical factors. SNP outliers in populations of the western group had relatively stronger response to precipitation than temperature-related variables. Functional annotation of SNP outliers identified genes associated with insect cuticle protein potentially related to desiccation adaptation in the western group and genes associated with lipase biosynthesis potentially related to temperature adaptation in the eastern group. Our study suggests that invasive species may maintain the evolutionary potential to adapt to heterogeneous environments despite a single invasion event. The molecular data suggest that quantitative trait comparisons across environments would be worthwhile.
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    Scientists' warning on climate change and insects
    Harvey, JA ; Tougeron, K ; Gols, R ; Heinen, R ; Abarca, M ; Abram, PK ; Basset, Y ; Berg, M ; Boggs, C ; Brodeur, J ; Cardoso, P ; de Boer, JG ; De Snoo, GR ; Deacon, C ; Dell, JE ; Desneux, N ; Dillon, ME ; Duffy, GA ; Dyer, LA ; Ellers, J ; Espindola, A ; Fordyce, J ; Forister, ML ; Fukushima, C ; Gage, MJG ; Garcia-Robledo, C ; Gely, C ; Gobbi, M ; Hallmann, C ; Hance, T ; Harte, J ; Hochkirch, A ; Hof, C ; Hoffmann, AA ; Kingsolver, JG ; Lamarre, GPA ; Laurance, WF ; Lavandero, B ; Leather, SR ; Lehmann, P ; Le Lann, C ; Lopez-Uribe, MM ; Ma, C-S ; Ma, G ; Moiroux, J ; Monticelli, L ; Nice, C ; Ode, PJ ; Pincebourde, S ; Ripple, WJ ; Rowe, M ; Samways, MJ ; Sentis, A ; Shah, AA ; Stork, N ; Terblanche, JS ; Thakur, MP ; Thomas, MB ; Tylianakis, JM ; Van Baaren, J ; Van de Pol, M ; Van der Putten, WH ; Van Dyck, H ; Verberk, WCEP ; Wagner, DL ; Weisser, WW ; Wetzel, WC ; Woods, HA ; Wyckhuys, KAG ; Chown, SL (WILEY, 2023-02)
    Abstract Climate warming is considered to be among the most serious of anthropogenic stresses to the environment, because it not only has direct effects on biodiversity, but it also exacerbates the harmful effects of other human‐mediated threats. The associated consequences are potentially severe, particularly in terms of threats to species preservation, as well as in the preservation of an array of ecosystem services provided by biodiversity. Among the most affected groups of animals are insects—central components of many ecosystems—for which climate change has pervasive effects from individuals to communities. In this contribution to the scientists' warning series, we summarize the effect of the gradual global surface temperature increase on insects, in terms of physiology, behavior, phenology, distribution, and species interactions, as well as the effect of increased frequency and duration of extreme events such as hot and cold spells, fires, droughts, and floods on these parameters. We warn that, if no action is taken to better understand and reduce the action of climate change on insects, we will drastically reduce our ability to build a sustainable future based on healthy, functional ecosystems. We discuss perspectives on relevant ways to conserve insects in the face of climate change, and we offer several key recommendations on management approaches that can be adopted, on policies that should be pursued, and on the involvement of the general public in the protection effort.
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    HBO1 (KAT7) Does Not Have an Essential Role in Cell Proliferation, DNA Replication, or Histone 4 Acetylation in Human Cells
    Kueh, AJ ; Eccles, S ; Tang, L ; Garnham, AL ; May, RE ; Herold, MJ ; Smyth, GK ; Voss, AK ; Thomas, T (American Society for Microbiology, 2020-02-01)
    HBO1 (MYST2/KAT7) is essential for histone 3 lysine 14 acetylation (H3K14ac) but is dispensable for H4 acetylation and DNA replication in mouse tissues. In contrast, previous studies using small interfering RNA (siRNA) knockdown in human cell lines have suggested that HBO1 is essential for DNA replication. To determine if HBO1 has distinctly different roles in immortalized human cell lines and normal mouse cells, we performed siRNA knockdown of HBO1. In addition, we used CRISPR/Cas9 to generate 293T, MCF7, and HeLa cell lines lacking HBO1. Using both techniques, we show that HBO1 is essential for all H3K14ac in human cells and is unlikely to have a direct effect on H4 acetylation and only has minor effects on cell proliferation. Surprisingly, the loss of HBO1 and H3K14ac in HeLa cells led to the secondary loss of almost all H4 acetylation after 4 weeks. Thus, HBO1 is dispensable for DNA replication and cell proliferation in immortalized human cells. However, while cell proliferation proceeded without HBO1 and H3K14ac, HBO1 gene deletion led to profound changes in cell adhesion, particularly in 293T cells. Consistent with this phenotype, the loss of HBO1 in both 293T and HeLa principally affected genes mediating cell adhesion, with comparatively minor effects on other cellular processes.
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    The evolution of nest site use and nest architecture in modern birds and their ancestors
    Mainwaring, MC ; Medina, I ; Tobalske, BW ; Hartley, IR ; Varricchio, DJ ; Hauber, ME (ROYAL SOC, 2023-08-28)
    The evolution of nest site use and nest architecture in the non-avian ancestors of birds remains poorly understood because nest structures do not preserve well as fossils. Nevertheless, the evidence suggests that the earliest dinosaurs probably buried eggs below ground and covered them with soil so that heat from the substrate fuelled embryo development, while some later dinosaurs laid partially exposed clutches where adults incubated them and protected them from predators and parasites. The nests of euornithine birds-the precursors to modern birds-were probably partially open and the neornithine birds-or modern birds-were probably the first to build fully exposed nests. The shift towards smaller, open cup nests has been accompanied by shifts in reproductive traits, with female birds having one functioning ovary in contrast to the two ovaries of crocodilians and many non-avian dinosaurs. The evolutionary trend among extant birds and their ancestors has been toward the evolution of greater cognitive abilities to construct in a wider diversity of sites and providing more care for significantly fewer, increasingly altricial, offspring. The highly derived passerines reflect this pattern with many species building small, architecturally complex nests in open sites and investing significant care into altricial young. This article is part of the theme issue 'The evolutionary ecology of nests: a cross-taxon approach'.
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    Discovery of insecticide resistance in field-collected populations of the aphid pest, Acyrthosiphon kondoi Shinji
    Chirgwin, E ; Thia, JA ; Copping, K ; Umina, PA (JOHN WILEY & SONS LTD, 2024-03)
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    Deciphering the Interactions in the Root-Soil Nexus Caused by Urease and Nitrification Inhibitors: A Review
    Gupta, S ; Yildirim, S ; Andrikopoulos, B ; Wille, U ; Roessner, U (MDPI, 2023-06)
    Optimizing nitrogen (N) availability to plants is crucial for achieving maximum crop yield and quality. However, ensuring the appropriate supply of N to crops is challenging due to the various pathways through which N can be lost, such as ammonia (NH3) volatilization, nitrous oxide emissions, denitrification, nitrate (NO3−) leaching, and runoff. Additionally, N can become immobilized by soil minerals when ammonium (NH4+) gets trapped in the interlayers of clay minerals. Although synchronizing N availability with plant uptake could potentially reduce N loss, this approach is hindered by the fact that N loss from crop fields is typically influenced by a combination of management practices (which can be controlled) and weather dynamics, particularly precipitation, temperature fluctuations, and wind (which are beyond our control). In recent years, the use of urease and nitrification inhibitors has emerged as a strategy to temporarily delay the microbiological transformations of N-based fertilizers, thereby synchronizing N availability with plant uptake and mitigating N loss. Urease inhibitors slow down the hydrolysis of urea to NH4+ and reduce nitrogen loss through NH3 volatilization. Nitrification inhibitors temporarily inhibit soil bacteria (Nitrosomonas spp.) that convert NH4+ to nitrite (NO2−), thereby slowing down the first and rate-determining step of the nitrification process and reducing nitrogen loss as NO3− or through denitrification. This review aims to provide a comprehensive understanding of urease and nitrification inhibitor technologies and their profound implications for plants and root nitrogen uptake. It underscores the critical need to develop design principles for inhibitors with enhanced efficiency, highlighting their potential to revolutionize agricultural practices. Furthermore, this review offers valuable insights into future directions for inhibitor usage and emphasizes the essential traits that superior inhibitors should possess, thereby paving the way for innovative advancements in optimizing nitrogen management and ensuring sustainable crop production.
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    Genomic exploration of coral-associated bacteria: identifying probiotic candidates to increase coral bleaching resilience in Galaxea fascicularis
    Doering, T ; Tandon, K ; Topa, SHH ; Pidot, SJJ ; Blackall, LLL ; van Oppen, MJH (BMC, 2023-08-19)
    BACKGROUND: Reef-building corals are acutely threatened by ocean warming, calling for active interventions to reduce coral bleaching and mortality. Corals associate with a wide diversity of bacteria which can influence coral health, but knowledge of specific functions that may be beneficial for corals under thermal stress is scant. Under the oxidative stress theory of coral bleaching, bacteria that scavenge reactive oxygen (ROS) or nitrogen species (RNS) are expected to enhance coral thermal resilience. Further, bacterial carbon export might substitute the carbon supply from algal photosymbionts, enhance thermal resilience and facilitate bleaching recovery. To identify probiotic bacterial candidates, we sequenced the genomes of 82 pure-cultured bacteria that were isolated from the emerging coral model Galaxea fascicularis. RESULTS: Genomic analyses showed bacterial isolates were affiliated with 37 genera. Isolates such as Ruegeria, Muricauda and Roseovarius were found to encode genes for the synthesis of the antioxidants mannitol, glutathione, dimethylsulfide, dimethylsulfoniopropionate, zeaxanthin and/or β-carotene. Genes involved in RNS-scavenging were found in many G. fascicularis-associated bacteria, which represents a novel finding for several genera (including Pseudophaeobacter). Transporters that are suggested to export carbon (semiSWEET) were detected in seven isolates, including Pseudovibrio and Roseibium. Further, a range of bacterial strains, including strains of Roseibium and Roseovarius, revealed genomic features that may enhance colonisation and association of bacteria with the coral host, such as secretion systems and eukaryote-like repeat proteins. CONCLUSIONS: Our work provides an in-depth genomic analysis of the functional potential of G. fascicularis-associated bacteria and identifies novel combinations of traits that may enhance the coral's ability to withstand coral bleaching. Identifying and characterising bacteria that are beneficial for corals is critical for the development of effective probiotics that boost coral climate resilience. Video Abstract.
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    Her6 and Prox1a are novel regulators of photoreceptor regeneration in the zebrafish retina.
    Veen, K ; Krylov, A ; Yu, S ; He, J ; Boyd, P ; Hyde, DR ; Mantamadiotis, T ; Cheng, LY ; Jusuf, PR ; Barsh, GS (Public Library of Science (PLoS), 2023-11)
    Damage to light-sensing photoreceptors (PRs) occurs in highly prevalent retinal diseases. As humans cannot regenerate new PRs, these diseases often lead to irreversible blindness. Intriguingly, animals, such as the zebrafish, can regenerate PRs efficiently and restore functional vision. Upon injury, mature Müller glia (MG) undergo reprogramming to adopt a stem cell-like state. This process is similar to cellular dedifferentiation, and results in the generation of progenitor cells, which, in turn, proliferate and differentiate to replace lost retinal neurons. In this study, we tested whether factors involved in dedifferentiation of Drosophila CNS are implicated in the regenerative response in the zebrafish retina. We found that hairy-related 6 (her6) negatively regulates of PR production by regulating the rate of cell divisions in the MG-derived progenitors. prospero homeobox 1a (prox1a) is expressed in differentiated PRs and may promote PR differentiation through phase separation. Interestingly, upon Her6 downregulation, Prox1a is precociously upregulated in the PRs, to promote PR differentiation; conversely, loss of Prox1a also induces a downregulation of Her6. Together, we identified two novel candidates of PR regeneration that cross regulate each other; these may be exploited to promote human retinal regeneration and vision recovery.