Biology subjects

Adams, B.

Publications and source records attributed to Adams, B..

10 recordsLinked to original sources

bioRxiv2025

Characterising a species-rich and understudied tropical insect fauna using DNA barcoding

BackgroundWest Africa has high biodiversity that is relatively understudied, especially for insects. Studies of West African arthropod diversity can therefore help address important questions regarding conservation, ecosystem services, and insecticide use and other species-control interventions in agriculture and disease management. We intensively sampled arthropods in Ghana using complementary trapping methods, generated DNA barcodes, and classified sequences by Barcode Index Numbers (BINs, a species proxy). Using this dataset, we investigate assemblage composition, temporal activity patterns, and the state of regional biodiversity sampling. ResultsSequencing DNA from 95,996 individuals captured using Malaise, yellow pan, pitfall, Heath and Centre for Disease Control (CDC) traps, we identified 10,120 unique BINs. The rate of species accumulation did not approach an asymptote for any taxonomic group or trap type, indicating high biodiversity. The different trap types sampled different subsets of the local community, with greatest similarity between yellow pan and pitfall traps. More insects and species (BINs) were trapped during the day than at night. Our dataset shared more BINs in the Barcode of Life Database with South Africa than with any other country, although this predominantly reflects the limited sampling and DNA sequencing campaigns in Africa. ConclusionsThis study more than doubles the published BINs for West Africa, offering insights into the biodiversity of an ecologically important but understudied taxon and region. Using multiple trap types allowed a more complete assessment of the local arthropod assemblage. The public release of these data will support and stimulate further taxonomic and ecological work in the region.

ecology↗

bioRxiv2025

Plant host identity drives Andropogon gerardii rhizobiome assembly strategies under increasing abiotic stress

Predicted changes in precipitation threaten tallgrass prairies by altering the soil microbial communities that are essential for plant resilience. Andropogon gerardii, a dominant grass in tallgrass prairies, spans the contiguous North American precipitation gradient. However, it remains unclear to what extent the rhizosphere microbiomes (rhizobiomes) are influenced by the plant-host environmental interaction. To assess how environmental and host factors shape the rhizobiome, we surveyed A. gerardii populations across 25 remnant prairie sites (June-August 2023) within its native range in the United States, characterizing the microbiomes in the rhizosphere and soils using 16S amplicon sequencing. We demonstrated that while geographic location largely structured both rhizosphere and soil communities, regional precipitation (60-day rainfall) emerged as a primary driver of the microbial community assembly. We observed distinct microbial divides across the dry and wet regions of the North American "arid-humid divide." Importantly, we found the first compelling large-scale evidence that regional precipitation has a profound influence on rhizobiome assembly. In the most arid regions, rhizosphere microbial communities exhibited significantly more predicted stochasticity than those in the local soil and contained taxa related to host-benefiting functions. Our study suggests that intensified host-driven selection for specific microbial variants occurs under heightened abiotic stress, highlighting the hosts pivotal role in shaping its rhizobiome composition in challenging environments.

microbiology↗

bioRxiv2025

A Bayesian approach to include Indigenous Knowledge in habitat selection functions

Indigenous Knowledge (IK) of species-habitat relationships provides in-depth understanding of species presence. While IK and Western scientific data are rarely combined in the same model, Bayesian statistics provides a method to include IK as prior knowledge (priors) and combine it with Western data. In partnership with Inupiat hunters, we developed a method to include IK in Bayesian habitat selection functions as priors and show how habitat variables mapped by IK holders can be included as covariates. We explain how to include IK and show the effects of IK in a case study for ringed seals (natchiq in Inupiaq; Pusa hispida). We show that influence of IK can vary depending on the covariate, and how IK provides information at scales not available in Western data. Our work points to the importance of both Western science and IK data sources in models that may be used for conservation and management decisions.

ecology↗

bioRxiv2024

Interaction of plant-derived metabolites and rhizobiome functions enhances drought stress tolerance

BackgroundPlants evolved alongside microbes, enabling plants to better cope with abiotic and biotic stresses. The interactions between plant roots and local soil microbes are critical for environmental adaptation and plant health. Plants actively regulate the microbial community composition in their rhizospheres to recruit specific microorganisms that enhance their fitness in the ecosystem they inhabit. This study builds on prior research suggesting that plants have a "home field advantage" in recruiting microbes unique in their home environment, reflecting mutual recognition and the targeted recruitment of microbes. ResultsUsing gene- and genome-centric approaches, we assessed the functional potential of root-associated microbes and profiled the host metabolites to uncover the metabolic outputs potentially regulating host-microbe interactions. Our results showed that plants adapted to drier environments experience less stress, producing fewer stress-related metabolites and impacting the recruitment of microbes with genes linked to stress relief pathways. In particular, plant-derived trimethyllysine was highly associated with microbial populations capable of improving nutrient uptake, producing plant growth-promoting compounds, and modulating stress responses. ConclusionThis study highlights the critical interplay between host exudates and microbial substrate uptake as the primary mechanism of rhizosphere assembly. We demonstrate that plants actively produce metabolites to recruit microbial populations with the functional potential to enhance hosts ability to thrive in a stressful environment. This research provides insights into the mechanisms of plant-microbe communication, rhizosphere recruitment, and the complex interplay of plant-microbe interactions. Furthermore, it highlights promising avenues for manipulating rhizosphere microbiomes to support conservation agriculture in the face of climate change.

microbiology↗

bioRxiv2023

Disrupting traditions of science: Indigenous Knowledge to model species habitat use

While Indigenous Knowledge (IK) contains a wealth of information on the behaviour and habitat use of species, it is rarely included in the species-habitat models frequently used by Western species management authorities. As decisions from these authorities can limit access to species that are important culturally and for subsistence, exclusion of IK in conservation and management frameworks can negatively impact both species and Indigenous communities. In partnership with Inupiat hunters, we developed methods to statistically characterize IK of species-habitat relationships and developed models that rely solely on IK to identify species habitat use and important areas. We provide methods for different types of IK documentation and for dynamic habitat types (e.g., ice concentration). We apply the method to ringed seals (natchiq in Inupiaq) in Alaskan waters, a stock for which the designated critical habitat has been debated in part due to minimal inclusion of IK. Our work demonstrates how IK of species-habitat relationships, with the inclusion of dynamic habitat types, expands on existing mapping approaches and provides another method to identify species habitat use and important areas. The results of this work provide a straightforward and meaningful approach to include IK in species management, especially through co-management processes. "Agencies have a traditional way they do science and including Indigenous Knowledge is less traditional." - Taqulik Hepa, subsistence hunter and Director, North Slope Borough Department of Wildlife Management Statement of PositionalityThis study and the conversion and application of Indigenous Knowledge (IK) for habitat use models was initiated through discussions with the North Slope Borough Department of Wildlife Management (DWM). The DWM is an agency of the regional municipal government representing eight primarily Inupiat subsistence communities in Northern Alaska. One of the goals of the DWM is to "assure participation by Borough residents in the management of wildlife and fish... so that residents can continue to practice traditional methods of subsistence harvest of wildlife resources in perpetuity" (1). Additionally, this project was presented to the Ice Seal Committee (ISC) for review, input, and approval. The ISC is an Alaskan Native organization with representatives from five regions that cover ice-associated seal ranges and "was established to help preserve and enhance ice seal habitat; protect and enhance Alaska Native culture, traditions-particularly activities associated with the subsistence use of ice seals" (2). Both the DWM and the ISC have mandates to manage ice-associated seals considering both IK and Western scientific knowledge (1, 2), and this study was developed to meet those mandates. Inupiat hunters from Utqia[g]vik, Alaska (Figure 1) were collaborators on this project, five of whom are co-authors (B. Adams, B. Frantz, J. Gatten, Q. Harcharek, and R. Sarren), while the other hunter chose to remain anonymous for this publication. The other authors are not Indigenous: R. Gryba was a PhD candidate at the University of British Columbia, M. Auger-Methe and G. Henry are professors at the University of British Columbia, A. Von Duyke is a researcher at the DWM, and H. Huntington is an independent social scientist. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=78 SRC="FIGDIR/small/556613v2_fig1.gif" ALT="Figure 1"> View larger version (13K): org.highwire.dtl.DTLVardef@bf6ec5org.highwire.dtl.DTLVardef@149f2org.highwire.dtl.DTLVardef@9dc98aorg.highwire.dtl.DTLVardef@11aa42a_HPS_FORMAT_FIGEXP M_FIG O_FLOATNOFig. 1.C_FLOATNO Study area around Utqia[g]vik, Alaska (shown in the yellow triangle). C_FIG Significance StatementIndigenous Knowledge (IK) is an extensive source of information of species habitat use and behavior, but is still rarely included in statistical methods used for species conservation and management. Because current conservation practices are frequently still rooted in Western practices many Indigenous organizations are looking for ways for IK to be better included and considered. We worked with Inupiat hunters to develop a new statistical approach to characterize IK and use it as a sole data source in habitat models. This work expands on mapping approaches, that are valuable, but cannot be applied to dynamic habitat types (e.g., ice concentration). This work shows how IK can be meaningfully included in modelling and be considered in current approaches for species management.

ecology↗

bioRxiv2023

Deep repertoire mining uncovers ultra-broad coronavirus neutralizing antibodies targeting multiple epitopes

Development of vaccines and therapeutics that are broadly effective against known and emergent coronaviruses is an urgent priority. Current strategies for developing pan-coronavirus countermeasures have largely focused on the receptor binding domain (RBD) and S2 regions of the coronavirus Spike protein; it has been unclear whether the N-terminal domain (NTD) is a viable target for universal vaccines and broadly neutralizing antibodies (Abs). Additionally, many RBD-targeting Abs have proven susceptible to viral escape. We screened the circulating B cell repertoires of COVID-19 survivors and vaccinees using multiplexed panels of uniquely barcoded antigens in a high-throughput single cell workflow to isolate over 9,000 SARS-CoV-2-specific monoclonal Abs (mAbs), providing an expansive view of the SARS-CoV-2-specific Ab repertoire. We observed many instances of clonal coalescence between individuals, suggesting that Ab responses frequently converge independently on similar genetic solutions. Among the recovered antibodies was TXG-0078, a public neutralizing mAb that binds the NTD supersite region of the coronavirus Spike protein and recognizes a diverse collection of alpha- and beta-coronaviruses. TXG-0078 achieves its exceptional binding breadth while utilizing the same VH1-24 variable gene signature and heavy chain-dominant binding pattern seen in other NTD supersite-specific neutralizing Abs with much narrower specificity. We also report the discovery of CC24.2, a pan-sarbecovirus neutralizing mAb that targets a novel RBD epitope and shows similar neutralization potency against all tested SARS-CoV-2 variants, including BQ.1.1 and XBB.1.5. A cocktail of TXG-0078 and CC24.2 provides protection against in vivo challenge with SARS-CoV-2, suggesting potential future use in variant-resistant therapeutic Ab cocktails and as templates for pan-coronavirus vaccine design.

immunology↗

bioRxiv2022

Isoform- and ligand-specific modulation of the adhesion GPCR ADGRL3/Latrophilin3 by a synthetic binder

Adhesion G protein-coupled receptors (aGPCRs) are cell-surface proteins with large extracellular regions that bind to multiple ligands to regulate key biological functions including neurodevelopment and organogenesis. Modulating a single function of a specific aGPCR isoform while affecting no other function and no other receptor is not trivial. Here, we engineered an antibody, termed LK30, that binds to the extracellular region of the aGPCR ADGRL3, and specifically acts as an agonist for ADGRL3 but not for its isoform, ADGRL1. The LK30/ADGRL3 complex structure revealed that the LK30 binding site on ADGRL3 overlaps with the binding site for an ADGRL3 ligand - teneurin. In cellular-adhesion assays, LK30 specifically broke the trans-cellular interaction of ADGRL3 with teneurin, but not with another ADGRL3 ligand - FLRT3. Our work provides proof of concept for the modulation of isoform- and ligand-specific aGPCR functions using unique tools, and thus establishes a foundation for the development of fine-tuned aGPCR-targeted therapeutics.

biochemistry↗

bioRxiv2022

Host adaptation drives genetic diversity in a vector-borne disease system

The range of hosts a pathogen can infect is a key trait influencing human disease risk and reservoir host infection dynamics. Borrelia burgdorferi sensu stricto (Bb), an emerging zoonotic pathogen, causes Lyme disease and is widely considered a host generalist, commonly infecting mammals and birds. Yet the extent of intraspecific variation in Bb host breadth, its role in determining host competence and potential implications to human infection remain unclear. We conducted a long-term study of Bb diversity, defined by the polymorphic ospC locus, across white-footed mice, passerine birds, and tick vectors leveraging long-read amplicon sequencing. Our results reveal strong variation in host breadth across Bb genotypes, exposing a spectrum of genotype-specific host-adapted phenotypes. We found support for multiple niche polymorphism maintaining Bb diversity in nature and little evidence of temporal shifts in genotype dominance, as would be expected under negative frequency-dependent selection. Passerine birds support the circulation of several human invasive strains in the local tick population and harbor greater Bb genotypic diversity compared to white-footed mice. Mouse-adapted Bb genotypes exhibited longer persistence in individual mice compared to non-adapted genotypes and infection communities infecting individual mice preferentially became dominated by mouse-adapted genotypes over time. We posit that intraspecific variation in Bb host breadth and specificity helps maintain overall species fitness in response to transmission by a generalist vector. Because pathogen genotypes vary in host breadth and result in diverse human disease manifestations, our findings indicate that a more nuanced definition of host competence incorporating local genotype frequency is warranted. SignificanceLyme disease is the most common vector-borne disease in the US with a causative agent (Borrelia burgdorferi) exhibiting high genetic diversity that partially correlates with human disease manifestations. Understanding the extent of host specificity in pathogens is critical for evaluating disease risk, but host specificity and mechanisms maintaining genetic diversity in Bb are unknown. We show that Bb genotypes exhibit variable host adaptation to white-footed mice and passerine birds, two common reservoir hosts, which appears to promote high intraspecific pathogen diversity. Conversely, we find limited evidence of negative frequency-dependent selection, an alternative mechanism for diversity maintenance. Our results reveal cryptic intraspecies host breadth variation and suggest that evaluating host competence depends on the frequency of host-adapted genotypes in local environments.

microbiology↗

bioRxiv2019

Parkinson’s disease: a systemic inflammatory disease accompanied by bacterial inflammagens

Parkinsons disease (PD) is a well-known neurodegenerative disease. Recently, the role of gingipains from Porphyromonas gingivalis was implicated in Alzheimers disease. Here we present evidence of systemic inflammation, accompanied by hypercoagulation; we also show that ginipains from P. gingivalis and its LPS may foster abnormal clotting, and that ginipains are present in PD blood, and thus that ginipains action on blood may be relevant to PD pathology. Bloods from both PD and healthy blood samples were analysed using thromboelastography (TEG), confocal and electron microscopies, and for cytokine and other circulating biomarkers. We also probed PD and healthy plasma clots with a polyclonal antibody for the bacterial protease, gingipain R1, from P. gingivalis. Low concentrations of recombinant gingipain R1 were also added to purified fluorescent fibrinogen. TEG, fibrin(ogen) amyloid formation and platelet ultrastructure analysis confirmed profound hypercoagulation, while the biomarker analysis confirmed significantly increased levels of circulating proinflammatory cytokines. We provide evidence for the presence of the protease, gingipain R1 in PD blood, implicating inflammatory microbial cell wall products in PD.

neuroscience↗

bioRxiv2018

Setting Starting Level for a Trial of an Biofilm-Disrupting Adjuvant

Combination therapy is beneficial treatment modality for multiple diseases. Cinnamon oil may be an advantageous agent in a number of combination therapies as cinnamon oil has antibacterial activity. Cinnamon oil has also been shown to be effective against biofilm cultures of Streptococcus mutans and Lactobacillus plantarum. Cinnamomum osmophloeum inhibits planktonic cultures of many gram-positive and gram-negative bacteria, including MRSA (methicillin-resistant Staphylococcus aureus). Subjecting S. epidermidis to cinnamon oil eliminates planktonic cells or staphylococci in biofilms. Cinnamon oil is an essential oil used throughout the food industry because of its pleasant and distinctive aroma. The purpose of this study is to estimate the amount of exposure to cinnamon through selected foods in the United States in order to propose an initial target level for pharmacokinetic studies of a novel combination drug.

pharmacology and toxicology↗