Biology subjects

Collins, S. M.

Publications and source records attributed to Collins, S. M..

12 recordsLinked to original sources

bioRxiv2026

A workflow to gather, clean, and standardize species occurrence records at scale for conservation applications

Biodiversity declines and pressing threats to wildlife necessitate data-driven approaches for conservation and management planning. Natural resource agencies, conservation practitioners, and researchers increasingly leverage digital species occurrence records. However, we still lack user-friendly and flexible tools to aggregate, clean, and standardize such data. These tools are particularly needed for speciose groups like invertebrates and plants whose natural histories are poorly or unevenly known. To provide such a tool and overcome limitations of existing options, we developed a workflow in R that encompasses the entire process of aggregating, cleaning, and standardizing occurrence records within one free software platform. It additionally can return information useful for assessing species' conservation status. Key features include user friendliness, flexibility in data sources and filtering, handling large volumes of data or multiple species, and high transparency. We demonstrate workflow functionality focusing on Texas native bees. We combined bee data from the Global Biodiversity Information Facility (GBIF) and several smaller datasets, then cleaned and standardized the combined dataset including removing duplicates. Processing 145,870 bee records took about an hour on a standard-configuration government computer. We used the resulting records in three case studies that demonstrated various uses conservation practitioners commonly implement. Case study 1 compiled a species list for Denton County, the second described phenology of bumble bees (Bombus genus) in the Dallas-Fort Worth Metroplex, and the third assessed conservation status of Bombus pensylvanicus. Our workflow greatly facilitates addressing a range of questions at various spatial and temporal scales from one vetted dataset that are tailored to the needs of a specific research objective, management question, municipality, or audience.

ecology↗

bioRxiv2025

Helix: a structure-aware deep learning model for accurate prediction of A-to-I RNA editing by endogenous ADARs

Adenosine deaminase acting on RNA (ADAR) converts adenosine to inosine within double-stranded RNA (dsRNA) and can be co-opted for therapeutic RNA editing by introducing dsRNA substrates in trans using programmable guide RNAs (gRNAs). However, ADARs natural promiscuity necessitates sophisticated gRNA designs to achieve efficient and specific editing. Here we present Helix, a predictive model that achieves highly accurate, zero-shot per-adenosine editing predictions for any target sequence. Helixs performance arises from two architectural choices: a transformer framework that scales effectively with increasing and imbalanced training data; and a structure-aware attention mechanism that incorporates predicted RNA secondary structure, a key determinant of ADAR activity. Helixs predictive accuracy enables seamless integration with DeepREAD, our previously reported generative model, in a noisy-student distillation framework termed DeepHelix. This workflow supports both zero-shot gRNA design and the generation of complex, constraint-based designs. We demonstrate DeepHelixs utility by designing gRNAs that efficiently edit a therapeutically relevant adenosine and by leveraging its flexible design space to engineer species cross-reactive gRNAs to accelerate pre-clinical development.

bioengineering↗

bioRxiv2025

Deciphering the role of histone modifications in memory and exhausted CD8 T cells

Exhausted CD8 T cells (TEX) arising during chronic infections and cancer have reduced functional capacity and limited fate flexibility that prevents optimal disease control and response to immunotherapies. Compared to memory (TMEM) cells, TEX have a unique open chromatin landscape underlying a distinct gene expression program. How TEX transcriptional and epigenetic landscapes are regulated through histone post-translational modifications (hPTMs) remains unclear. Here, we profiled key activating (H3K27ac and H3K4me3) and repressive (H3K27me3 and H3K9me3) histone modifications in naive CD8 T cells (TN), TMEM and TEX. We identified H3K27ac-associated super-enhancers that distinguish TN, TMEM and TEX, along with key transcription factor networks predicted to regulate these different transcriptional landscapes. Promoters of some key genes were poised in TN, but activated in TMEM or TEX whereas other genes poised in TN were repressed in TMEM or TEX, indicating that both repression and activation of poised genes may enforce these distinct cell states. Moreover, narrow peaks of repressive H3K9me3 were associated with increased gene expression in TEX, suggesting an atypical role for this modification. These data indicate that beyond chromatin accessibility, hPTMs differentially regulate specific gene expression programs of TEX compared to TMEM through both activating and repressive pathways.

immunology↗

bioRxiv2024

Local nesting resources rather than floral food alter ground-nesting bee communities in grazed habitats

O_LIUnderstanding how the availability of both trophic and non-trophic resources impacts key ecosystem service providers is crucial for informing conservation efforts. Non-trophic resources such as shelter can play critical roles in ecosystem function and resilience by affecting predation and pathogen rates, reproductive success, and interspecific interactions. However, non-trophic resources are often overlooked. This holds true for insect pollinators; impacts of shelter on community dynamics and pollination remain poorly understood. C_LIO_LIBecause the majority of bee species spend most of their lives underground, we explored whether nesting habitat characteristics are key drivers of ground-nesting bee abundance, diversity, and community composition. We additionally compared impacts of aboveground versus belowground nesting habitat characteristics, as the latter have received significantly less attention. Nesting habitat characteristics we considered included bare ground cover; and soil texture, compaction, and depth. We also included floral abundance and richness. We focused on rangelands, natural or semi-natural grasslands that are managed for livestock grazing, where management can dramatically alter trophic and non-trophic resources. Thus, we also investigated impacts of grazing management on bee habitat. C_LIO_LIWe found that belowground, but not aboveground, nesting habitat characteristics were important for ground-nesting bee assemblages. Ground-nesting bee abundance and richness were highest at sites with sandier and less compacted soils. C_LIO_LIOur results suggest that livestock grazing management may indirectly impact ground-nesting bee abundance through impacts on floral abundance. Sites with longer grazing rest periods had higher floral abundance, and sites with higher floral abundance supported more ground-nesting bees (but not more bee species). C_LIO_LIPolicy implications: Our study highlights the importance of considering non-trophic resources in conservation and restoration management. Managers should be cautious in using an aboveground measure such as bare ground as an indicator of bee habitat quality. Rather, we recommend that belowground habitat characteristics such as soil texture and compaction be included in habitat quality assessments. Evidence-based rangeland conservation and restoration planning may need to manage for ground-nesting bees preferred levels of soil compaction. Additionally, management-insensitive habitat characteristics such as soil texture may be important considerations for site prioritization in pollinator habitat conservation and restoration efforts. C_LI

ecology↗

bioRxiv2024

Innate immune system signaling and CD11b+CD11c+CD103+ cell migration to the brain underlie changes in mouse behavior after microbial colonization.

Background and AimsAccumulating evidence suggests the microbiota is a key factor in disorders of gut-brain interaction (DGBI), by affecting host immune and neural systems. However, the underlying mechanisms remain elusive due to their complexity and clinical heterogeneity of patients with DGBIs. We aimed to identify neuroimmune pathways that are critical in microbiota-gut-brain communication during de novo gut colonization. MethodsWe employed a combination of gnotobiotic and state-of-the-art microbial tools, behavioral analysis, immune and pharmacological approaches. Germ-free wild type, MyD88-/- Ticam1-/- and SCID mice were studied before and after colonization with specific pathogen-free microbiota, Altered Schaedler Flora, E. coli or S. typhimurium (permanent or transient colonizers). TLR agonists and antagonists, CCR7 antagonist or immunomodulators were used to study immune pathways. We assessed brain c-Fos, brain-derived neurotrophic factor, and dendritic and glial cells by immunofluorescence, expression of neuroimmune genes by NanoString and performed brain proteomics. ResultsBacterial monocolonization, conventionalization or administration of microbial products to germ-free mice altered mouse behavior similarly, acting through Toll-like receptor or nucleotide-binding oligomerization domain signaling. The process required CD11b+CD11c+CD103+ cell activation and migration into the brain. The change in behavior did not require the continued presence of bacteria and was associated with activation of multiple neuro-immune networks in the gut and the brain. ConclusionsChanges in neural plasticity occur rapidly upon initial gut microbial colonization and involve innate immune signaling to the brain, mediated by CD11b+CD11c+CD103+ cell migration. The results identify a new target with therapeutic potential for DGBIs developing in context of increased gut and blood-brain barrier permeability. HighlightsO_LIMicrobiota impairment is a key factor in disorders of gut-brain interaction (DGBI) C_LIO_LIMicrobial colonization induces changes in brain and behavior via innate immunity C_LIO_LIMicrobial colonization activates multiple neuro-immune networks in gut and brain C_LIO_LIBehavioral change is mediated by CD11b+CD11c+CD103+ cells migration to the brain C_LI

animal behavior and cognition↗

bioRxiv2024

Geographic, ecological, and temporal patterns of seabird mortality during the 2022 HPAI H5N1 outbreak on the island of Newfoundland

Highly pathogenic avian influenza (HPAI) H5N1 caused mass seabird mortality across the North Atlantic in 2022. Following outbreaks in Europe, the first case in North America was detected on the island of Newfoundland (NFLD), Canada in November 2021, before spreading through all North American flyways. During the following breeding season, NFLD experienced the second-highest number of seabird mortalities in Canadian provinces. Surveys and citizen reports identified 13543 seabird mortalities from April to September 2022. Many carcasses occurred on the west coast of NFLD in May and June 2022. Reported mortalities peaked in July along the southeastern coast. In August and September, mortalities were concentrated along the northeastern coast. With the exception of two colony surveys, reported mortalities decreased in September. Most mortality was found among Northern Gannet (6622), Common Murre (5992), Atlantic Puffin (282), and Black-legged Kittiwake (217). Using comprehensive knowledge of seabird ecology, we formulated exploratory hypotheses regarding traits that could contribute to mortality. Species differences in mortality were most strongly associated with nesting density, timing of breeding, and at-sea overlap with allospecifics from other colonies. Unprecedented seabird mortality and ongoing transmission within the circulating avian influenza viruses highlight the need for continued monitoring and development of conservation strategies.

zoology↗

bioRxiv2023

Reduction of coastal lighting decreases seabird strandings

Leachs Storm-Petrels (Hydrobates leucorhous) are small, threatened seabirds with an extensive breeding range in the North Atlantic and North Pacific Oceans. The Atlantic population, which represents approximately 40 - 48% of the global population, is declining sharply. Positive phototaxis, the movement towards artificial light at night (ALAN), is considered to be a key contributing factor. Many seabirds exhibit positive phototaxis, which can result in stranding on land. The Leachs Storm-Petrel is the seabird most often found stranded around ALAN in the North Atlantic, though there is little experimental evidence showing that reducing ALAN will decrease the occurrence of stranded storm-petrels. During a two-year study at a large, brightly illuminated seafood processing plant adjacent to the Leachs Storm-Petrels largest colony, we compared the number of birds that stranded when the lights at the plant were turned on versus off. We recorded survival, performed carcass counts of both adults and juveniles, and released any rescued individuals. Turning the lights off reduced strandings by 39.15% (CI: 11.45% - 58.19%). The peak stranding period occurred from 25 September to 28 October, and most of the stranded birds were fledglings. These results provide evidence to support the widespread reduction and modification of coastal artificial light, especially during avian fledging and migration periods.

animal behavior and cognition↗

bioRxiv2023

Leach's Storm-Petrels fledge on the full moon and throughout the lunar cycle

Many seabirds are attracted to anthropogenic light, and the risk is greater for recent fledglings. Lunar phase predicts the probability of stranding, but it remains uncertain whether lunar phase is associated with when young seabirds fledge. Fledging behaviour of nocturnal, burrowing seabirds can be difficult to monitor using traditional methods but can provide insight into environmental factors that influence the risk of stranding. We used passive integrated transponder tags to monitor the fledging dates and times of Leachs Storm-Petrel chicks from four breeding seasons at a major colony in Newfoundland and Labrador, Canada. We also assessed whether lunar phase associated with fledging date. The median fledge time was 2.4 h after sunset (1.4 - 12.4 h). The median fledge date was 10 October, and fledging dates ranged from 13 September to 13 November. Most importantly, Leachs Storm-Petrels chicks did fledge during the full moon. These results provide insight into why storm-petrels are less attracted to anthropogenic light during high levels of natural illumination and can be used to inform periods of higher risk for stranding, thus allowing better concentration of conservation efforts.

animal behavior and cognition↗

bioRxiv2023

BeeDC: An R package and globally synthesised and flagged bee occurrence dataset

Species occurrence data are foundational for research, conservation, and science communication, but the limited availability and accessibility of reliable data represents a major obstacle, particularly for insects, which face mounting pressures. We present BeeBDC, a new R package, and a global bee occurrence dataset to address this issue. We combined >18.3 million bee occurrence records from multiple public repositories (GBIF, SCAN, iDigBio, USGS, ALA) and smaller datasets, then standardised, flagged, deduplicated, and cleaned the data using the reproducible BeeBDC R-workflow. Specifically, we harmonised species names (following established global taxonomy), country names, and collection dates and we added record-level flags for a series of potential quality issues. These data are provided in two formats, "cleaned" and "flagged-but-uncleaned". The BeeBDC package with online documentation provides end users the ability to modify filtering parameters to address their research questions. By publishing reproducible R workflows and globally cleaned datasets, we can increase the accessibility and reliability of downstream analyses. This workflow can be implemented for other taxa to support research and conservation.

ecology↗

bioRxiv2023

High pathogenicity avian influenza (H5N1) in Northern Gannets: Global spread, clinical signs, and demographic consequences

During 2021-22 High Pathogenicity Avian Influenza (HPAI) killed thousands of wild birds across Europe and North America, suggesting a change in infection dynamics and a shift to new hosts, including seabirds. Northern Gannets (Morus bassanus) appeared especially severely impacted, but limited understanding of how the virus spread across the metapopulation, or the demographic consequences of mass mortality limit our understanding of its severity. Accordingly, we collate information on HPAIV outbreaks across most North Atlantic gannet colonies and for the largest colony (Bass Rock, UK), provide impacts on population size, breeding success, adult survival, and preliminary results on serology. Unusually high numbers of dead gannets were first noted in Iceland during April 2022. Outbreaks in May occurred in many Scottish colonies, followed by colonies in Canada, Germany and Norway. By the end of June, outbreaks had occurred in five Canadian colonies and in the Channel Islands. Outbreaks in 12 UK and Ireland colonies appeared to follow a clockwise pattern with the last infected colonies recorded in late August/September. Unusually high mortality was recorded at 40 colonies (75% of global total colonies). Dead birds testing positive for HPAIV H5N1 were associated with 58% of these colonies. At Bass Rock, the number of occupied sites decreased by at least 71%, breeding success declined by [~]66% compared to the long-term UK mean and adult survival between 2021 and 2022 was 42% lower than the preceding 10-year average. Serological investigation detected antibodies specific to H5 in apparently healthy birds indicating that some gannets recover from HPAIV infection. Further, most of these recovered birds had black irises, suggestive of a phenotypic indicator of previous infection. Untangling the impacts of HPAIV infection from other key pressures faced by seabirds is key to establishing effective conservation strategies for threatened seabird populations, HPAIV being a novel and pandemic threat.

ecology↗

bioRxiv2022

Separation of heterogeneous Aggregatibacter actinomycetemcomitans outer membrane vesicles reveals that toxin sorting is driven by surface-associated DNA

Aggregatibacter actinomycetemcomitans is a Gram-negative oral bacterium associated with localized aggressive periodontitis as well as some systemic diseases. The strains of A. actinomycetemcomitans most closely associated with periodontal disease tend to produce more of a secreted leukotoxin (LtxA) than isolates from healthy carriers, suggesting a key role for this toxin in disease progression. LtxA is secreted via a type 1 secretion system, from the bacterial cytosol across both the inner and outer membranes in a single step into the supernatant, where it is able to interact with host cells. Upon secretion, some of the toxin associates with the bacterial cell membrane, enabling its release in association with the surface of outer membrane vesicles (OMVs), small, spherical vesicles derived from the outer membrane. We have previously observed that the highly leukotoxic A. actinomycetemcomitans strain JP2 produces two populations of OMVs, a highly abundant population of small (<100 nm in diameter) OMVs, and a less abundant population of large (>300 nm in diameter) OMVs. Here, we have investigated the association of LtxA with the two populations of OMVs varying in size. Our results indicate that surface-associated DNA drives the selective sorting of LtxA to large OMVs.

microbiology↗

bioRxiv2018

A Novel Household Water Insecurity Scale: Procedures and Psychometric Analysis among Postpartum Women in Western Kenya

Our ability to measure household-level food insecurity has revealed its critical role in a range of physical, psychosocial, and health outcomes. Currently, there is no analogous, standardized instrument for quantifying household-level water insecurity, which prevents us from understanding both its prevalence and consequences. Therefore, our objectives were to develop and validate a household water insecurity scale appropriate for use in our cohort in western Kenya. We used a range of qualitative techniques to develop a preliminary set of 29 household water insecurity questions, and administered those questions at 15 and 18 months postpartum, concurrent with a suite of other survey modules. These data were complemented by data on quantity of water used and stored, and microbiological quality. Inter-item and item-total correlations were performed to reduce scale items to 20. Exploratory factor and parallel analyses were used to determine the latent factor structure; a unidimensional scale was hypothesized and tested using confirmatory factor and bifactor analyses, along with multiple statistical fit indices. Reliability was assessed using Cronbachs alpha and the coefficient of stability, which produced a coefficient alpha of 0.97 at 15 and 18 months postpartum and a coefficient of stability of 0.62. Predictive, convergent and discriminant validity of the final household water insecurity scale were supported, based on relationships with food insecurity, perceived stress, per capita household water use, and time and money spent acquiring water. The resultant scale is a valid and reliable instrument. It can be used in this setting to test a range of hypotheses about the role of household water insecurity in numerous physical and psychosocial health outcomes, to identify the households most vulnerable to water insecurity, and to evaluate the effects of water-related interventions. To extend its applicability, we encourage efforts to develop a cross-culturally valid scale using robust qualitative and quantitative techniques.

epidemiology↗