Biology subjects

Ellison, A.

Publications and source records attributed to Ellison, A..

10 recordsLinked to original sources

bioRxiv2026

Taylor's Law, Smith's Law, and Diversity Power Laws: A Novel Triple Power Law Methodology for Scaling Diversity and Heterogeneity

Taylor's power law (TPL) and Smith's power law (SPL) are two foundational scaling laws describing how variance scales with mean density and plot area, respectively. While TPL captures ecological heterogeneity (variation among interacting organisms), SPL captures environmental heterogeneity (variation in the abiotic template). Diversity scaling, traditionally approached through species-area relationships, has been extended to diversity-area relationships (DAR) using Hill numbers. Here we integrate TPL, SPL, and DPL, including three newly proposed models [diversity-mean, diversity-variance, and diversity-heterogeneity relationships (DHR)], into a unified triple power law methodology for scaling diversity and heterogeneity in microbial ecosystems. Using human gut and vaginal microbiome datasets, we systematically vary two orthogonal factors: scale (unit vs. multi-unit) and accrual (without vs. with sample accrual). Our results show that TPL and SPL are complementary: classic TPL captures cross-sectional heterogeneity at the community scale, while accrual TPL, a new extension based on sample accrual, captures heterogeneity accumulation at the metacommunity scale and appears less scale-dependent. SPL provides a tool for relating environmental heterogeneity to diversity, supporting the reciprocity principle with ecological heterogeneity. Among the four diversity power laws, DHR, using the variance-to-mean ratio as a direct heterogeneity metric, is most aligned with the diversity-heterogeneity nexus. The triple power law methodology reveals that heterogeneity scaling predicts diversity scaling in the majority of models, with the strongest predictive relationships observed for accrual TPL at higher diversity orders. Nevertheless, the commonly assumed scale-invariance proved elusive, occurring in fewer than 20% of the power law models tested. This framework may extend beyond microbiome ecosystem to any complex system where heterogeneity and diversity arise from interacting components, from ecosystems to economies to artificial intelligence.

ecology↗

bioRxiv2026

Chronic {triangleup}9-Tetrahydrocannabinol Vapor Self-Administration Modulates Gut Microbiota and the Immune and Endocannabinoid Systems in Female Sprague-Dawley Rats

Vaping of cannabis and its primary components, including {triangleup}9-tetrahydrocannabinol (THC), has increased during the last decade, especially among adolescents and adults. While the behavioral consequences of THC, including anxiety, depression, and associated impacts on reward-related signaling, are well documented, evaluation of additional pathways that have implications for neuronal function remains relatively unexplored. Further, despite evidence of the impact of THC on several physiologic processes, most studies have focused on the brain even though the endocannabinoid system with which THC interacts has widespread expression and functions throughout the body. To address these gaps, we obtained biological samples from adult female Sprague-Dawley rats (N=5-6 per group; all females) that were passively exposed to THC or vehicle vapor and then allowed to self-administer vaporized THC or vehicle intermittently for nine months. Animals were euthanized, and brain and peripheral organs were collected for analyses. We evaluated genes of endocannabinoid system-related receptors, modulators, ion channels, and metabolic enzymes, along with immune and microbiome-related pathways in 9 peripheral organs, 14 brain regions, and plasma. We observed that rats exposed to chronic intermittent THC vapor administration had widespread modulation of several endocannabinoid-system genes only in the brain, with most changes occurring in the dorsal striatum and hippocampus. In contrast, endocannabinoid-system gene expression in all evaluated peripheral organs remained unchanged after THC exposure. Similar findings occurred with immune-relevant genes, where il-1beta, il-6, ccl2, and mx1 were modulated only in the brain while expression in peripheral organs remained unchanged. Immune system modulation following chronic THC exposure significantly elevated plasma concentrations of IL-17A, gut microbiota dysbiosis, and global changes to circulating metabolites, including several amino acids, fatty acids, aminosugar, and nucleic acids. Our findings provide, for the first time, a whole-body evaluation of the molecular effects of chronic THC exposure throughout adulthood on the endocannabinoid and immune systems that have implications for cannabinoid-related behavioral effects.

immunology↗

bioRxiv2024

Phylogenetic and functional diversity among Drosophila-associated metagenome-assembled genomes

Host-associated microbial communities can mediate interactions between their hosts and biotic and abiotic environments. While much work has been done to document how microbiomes vary across species and environments, much less is known about the functional consequences of this variation. Here, we test for functional variation among drosophilid-associated bacteria by conducting Oxford Nanopore long-read sequencing and generating metagenome-assembled genomes (MAGs) from six species of drosophilid fly collected in association with anthropogenic environments in North America, Europe, and Africa. Using phylogenetic analyses, we find that drosophilid flies harbor a diverse microbiome that includes core members closely related to the genera Gilliamella, Orbus, Entomomonas, Dysgonomonas, and others. Comparisons with publicly available bacterial genomes show that many of these genera are associated with phylogenetically diverse insect gut microbiomes. Using functional annotations and predicted secondary metabolite biosynthetic gene clusters, we show that MAGs belonging to different bacterial orders and genera vary in gene content and predicted functions including metabolic capacity and how they respond to environmental stressors. Our results provide evidence that wild drosophilid flies harbor phylogenetically and functionally diverse microbial communities. These findings highlight a need to quantify the abundance and function of insect-associated bacteria from the genera Gilliamella, Orbus, Entomomonas, and others on the performance of their insect hosts across diverse environments.

genomics↗

bioRxiv2023

A multiplex, prime editing framework for identifying drug resistance variants at scale

CRISPR-based genome editing has revolutionized functional genomics, enabling screens in which thousands of perturbations of either gene expression or primary genome sequence can be competitively assayed in single experiments. However, for libraries of specific mutations, a challenge of CRISPR-based screening methods such as saturation genome editing is that only one region (e.g. one exon) can be studied per experiment. Here we describe prime-SGE ("prime saturation genome editing"), a new framework based on prime editing, in which libraries of specific mutations can be installed into genes throughout the genome and functionally assessed in a single, multiplex experiment. Prime-SGE is based on quantifying the abundance of prime editing guide RNAs (pegRNAs) in the context of a functional selection, rather than quantifying the mutations themselves. We apply prime-SGE to assay thousands of single nucleotide changes in eight oncogenes for their ability to confer drug resistance to three EGFR tyrosine kinase inhibitors. Although currently restricted to positive selection screens by the limited efficiency of prime editing, our strategy opens the door to the possibility of functionally assaying vast numbers of precise mutations at locations throughout the genome.

genomics↗

bioRxiv2020

Different protein metabolic strategies for growth during food-induced physiological plasticity

Food-induced morphological plasticity, a type of developmental plasticity, is a well-documented phenomenon in larvae of the echinoid echinoderm, Dendraster excentricus. A recent study in our lab has shown that this morphological plasticity is associated with significant physiological plasticity for growth. The goal of the current study was to measure several aspects of protein metabolism in larvae growing at different rates to understand the mechanistic basis for this physiological growth plasticity. Larvae of D. excentricus were fed rations of 1,000 (low-fed) or 10,000 (high-fed) algal cells mL−1. Primary measurements of protein growth, algal ingestion, aerobic metabolism, alanine transport and protein synthesis were used to model growth and protein metabolism. Relative protein growth rates were 6.0 and 12.2 % day−1 for low- and high-fed larvae, respectively. The energetic cost of protein synthesis was similar between both treatments at 4.91 J (mg protein synthesized)−1. Larvae in both treatments used about 50% of their metabolic energy production to fuel protein synthesis. Mass-specific rates of protein synthesis were also similar. The most important difference between low- and high-fed larvae were mass-specific rates of protein degradation. Low-fed larvae had relatively low rates of degradation early in development that increased with larval age, surpassing high-fed degradation rates at 20 days post-fertilization. Changes in protein depositional efficiency during development were similar to those of larval growth efficiency, indicating that differences in protein metabolism are largely responsible for whole-organism growth plasticity. Mass-specific alanine transport rates were about 2-times higher in low-fed larvae, demonstrating that the longer arms of low-fed larvae may be a mechanism for acquiring more dissolved nutrients from their environment. In total, these results provide an explanation for the differences in growth efficiency between low- and high-fed larvae and demonstrate the importance of protein degradation pathways in establishing these growth differences. These observations, together with previous studies measuring morphological and physiological plastic responses, allow for a more integrated understanding of developmental plasticity in echinoid larvae.AbbreviationsDPFdays post-fertilizationPOpostoral armAEassimilation efficiencyGGEgross growth efficiencyNGEnet growth efficiencyPGEprotein growth efficiencyPDEprotein depositional efficiencyMBLmidline body lengthFAAfree amino acid poolRGRrelative growth rateBCAbicinchoninic assayBSAbovine serum albuminTCAtrichloroacetic acidBODbiological oxygen demandTORtarget of rapamycinDOMdissolved organic materialView Full Text

physiology↗

bioRxiv2017

Three Decades as an NSF REU Site: Lessons and Recommendations

NSFs Research Experiences for Undergraduates (REU) program supports thousands of undergraduate researchers annually. REU sites operate independently with regards to their research mission and structure, leading to a complex educational milieu distinct from traditional classrooms and labs. Overall, REU sites are perceived as providing highly formative experiences for developing researchers. However, given improved assessment practices over REUs three decades, best practices for student learning and evaluation of long-term impacts remain limited. To address this limitation, we recommend the use of systems-based theoretical frameworks when studying REU programs. We outline how one such framework, cultural-historical activity theory (CHAT), could inform the collection of assessment data. Among other strengths, CHAT guides collection of quantitative and qualitative information that can help characterize REU programs in an educationally meaningful context. Adoption of CHAT and similar approaches by REU Sites could improve dialogue among programs, encourage collaborations, and improve evidence-based practices.

scientific communication and education↗

bioRxiv2017

Spring frost controls spring tree phenology along elevational gradients on the southeastern Tibetan Plateau

Temperature is considered to be a main driver of spring phenology, whereas the role of climate extremes (such as spring frosts) has long been neglected. A large elevational gradient of mature forests on the Tibetan Plateau provides a powerful space-for-time natural experiment to explore driving forces of spring phenology. Combining 5-yr of in situ phenological observations of Smith fir (Abies georgei var. smithii) with concurrent air temperature data along two altitudinal gradients on the southeastern Tibetan Plateau, we tested the hypothesis that spring frost was a major factor regulating the timing of spring phenology. Onset of bud swelling and leaf unfolding in the study years occurred {approx} 18 or 17 days earlier, respectively, at the lowest (3800 m a.s.l.) elevation relative to upper treelines (4360 or 4380 m a.s.l.). The frequency of freezing events and last freezing date were critical factors in determining the timing of bud swelling along two altitudinal gradients, whereas onset of leaf unfolding was primarily controlled by the onset of bud swelling. This finding provides evidence for detrimental impacts of spring frost on spring phenology, which have been underappreciated in research on phenological sensitivity to climate but should be included in phenology models. It contributes to explain the declining global warming effects on spring phenophases, because climatic extreme events (e.g. spring frosts) tend to increase with warming.

ecology↗

bioRxiv2017

Red wood-ant nests are traps for fault-related CH4 micro-seepage

Methane (CH4) is common on Earth, forms the major commercial natural gas reservoirs, and is a key component of the global carbon cycle, but its natural sources are not well-characterized. We present a geochemical dataset acquired from a red wood-ant (RWA; Formica polyctena) nest in the Neuwied Basin, a part of the East Eifel Volcanic Field (EEVF), focusing on methane (CH4), stable carbon isotope of methane ({delta}13C-CH4), RWA activity patterns, earthquakes, and earth tides. Nest gas and ambient air were continuously sampled in-situ and analyzed to detect microbial, thermogenic, and abiotic fault-related micro-seepage. Methane degassing was not synchronized with earth tides. Elevated CH4 concentrations in nest gas appear to result from a combination of microbial activity and fault-related emissions moving via through fault networks through the RWA nest. Two {delta}13C-CH4 signatures were identified in nest gas: -69{per thousand} and -37{per thousand}. The -69{per thousand} signature of {delta}13C-CH4 within the RWA nest is attributed to microbial decomposition of organic matter. This finding supports previous findings that RWA nests are hot-spots of microbial CH4. Additionally, the -37% {delta}13C-CH4 signature is the first evidence that RWA nests also serve as traps for fault-related emissions of CH4. The -37{per thousand} {delta}13C-CH4 signature can be attributed either to thermogenic/fault-related or to abiotic/fault-related CH4 formation originating from e.g. low-temperature gas-water-rock reactions in a continental setting at shallow depths (microseepage). Sources of these micro-seeps could be Devonian schists (\"Sphaerosiderith Schiefer\") with iron concretions (\"Eisengallen\"), sandstones, or the iron-bearing \"Klerf Schichten\". We cannot exclude overlapping micro-seepage of magmatic CH4 from the Eifel plume. Given the abundance of RWA nests on the landscape, their role as sources of microbial CH4 and traps for abiotically-derived CH4 should be included in estimation of methane emissions that are contributing to climatic change.

ecology↗

bioRxiv2017

Assessment of the World Largest Afforestation Program: Success, Failure, and Future Directions

The Three-North Afforestation Program (TNAP), initiated in 1978 and scheduled to be completed in 2050, is the worlds largest afforestation project and covers 4.07 x 106 km2 (42.4%) of China. We systematically assessed goals and outcomes of the first 30 years of the TNAP using high-resolution remote sensing and ground survey data. With almost 23 billion dollars invested between 1978 and 2008, the forested area within the TNAP region increased by 1.20 x 107 ha, but the proportion of high quality forests declined by 15.8%. The establishment of shelterbelts improved crop yield by 1.7%, much lower than the 5.9% expected once all crop fields are fully protected by shelterbelts. The area subjected to soil erosion by water decreased by 36.0% from 6.72 x 107 to 4.27 x 107 ha; the largest reductions occurred in areas where soil erosion had been most severe and forests contributed more than half of this improvement. Desertification area increased from 1978 to 2000 but decreased from 2000 to 2008; the 30-year net reduction was 13.0% (4.05x106 ha), with 8.0% being accounted for by afforestation in areas with only slight, prior desertification. In addition to its direct impacts, the TNAP has enhanced peoples awareness of environmental protection and attracted consistent attention and long-term commitment from the Chinese government to the restoration and protection of fragile ecosystems in the vast Three-North region. The significant decline in forest quality, limited success in reducing desertification, and low coverage of shelterbelts are aspects of the TNAP in need of re-assessment, and additional ca. 34 billion dollars will be needed to ensure the completion of the TNAP.

ecology↗

bioRxiv2016

Critical minimum temperature limits xylogenesis and maintains treelines on the Tibetan Plateau

Physiological and ecological mechanisms that define treelines are still debated. It is suggested that the absence of trees above the treeline is caused by the low temperature that limits growth. Thus, we raise the hypothesis that there is a critical minimum temperature (CTmin) preventing xylogenesis at treeline. We tested this hypothesis by examining weekly xylogenesis across three and four growing seasons in two natural Smith fir (Abies georgei var. smithii) treeline sites on the south-eastern Tibetan Plateau. Despite differences in the timing of cell differentiation among years, minimum air temperature was the dominant climatic variable associated with xylem growth; the critical minimum temperature (CTmin) for the onset and end of xylogenesis occurred at 0.7{+/-}0.4 {degrees}C. A process-based-modeled chronology of tree-ring formation using this CTmin was consistent with actual tree-ring data. This extremely low CTmin permits Smith fir growing at treeline to complete annual xylem production and maturation and provides both support and a mechanism for treeline formation.

ecology↗