Biology subjects

Pierce, S.

Publications and source records attributed to Pierce, S..

11 recordsLinked to original sources

bioRxiv2026

Maternal diet and genetics shape the human milk metabolome

Human milk contains a diverse array of metabolites that contribute to infant nutrition, immune development, and microbial colonization. The maternal factors shaping the milk metabolome, and the relative contribution of genetics or diet vs. other factors, remain poorly understood. Here, we profiled 458 milk metabolites in 349 one-month postpartum human milk samples and integrated metabolomic data with maternal diet, clinical, transcriptomic, and genomic measurements. Maternal diet was broadly associated with milk metabolite composition, with significant correlations identified between dietary features and 323 metabolites. Coffee consumption strongly predicted milk quinic acid and 1,3-dimethyluric acid abundance, while high-fiber dietary patterns were associated with metabolites including proline-betaine and N-acetylornithine. Integration of milk transcriptomic and metabolomic data via machine learning identified biologically plausible gene-metabolite pairs, including associations between QPRT expression and quinolinic acid, and DPEP1 and cysteine-glycine dipeptide. Genome-wide association analyses identified nine study-wide significant metabolite quantitative trait loci, including novel milk-specific associations near PDE6A affecting purine metabolites and near GNE affecting free sialic acid. Comparison with plasma metabolite studies demonstrated both shared and milk-specific genetic regulation of metabolites. Finally, we found that of all tested maternal features, diet explained the largest proportion of variation in the milk metabolome. Together, these findings demonstrate that the human milk metabolome reflects both maternal exposures and mammary gland-specific biology. This work establishes a framework for understanding how genetic and environmental factors shape milk composition.

genomics↗

bioRxiv2025

Integrating migratory marine connectivity into shark conservation

Understanding migratory connectivity is important for the conservation of highly mobile marine species that face escalating threats across the globe. Establishing baseline information on migratory connectivity is therefore needed to identify regions of conservation focus. Despite efforts to track migratory sharks and rays, information on transboundary movements is limited and often inaccessible to managers and policymakers. Here, we synthesised multimethod movement data for migratory Australian shark and ray species, investigating which species require international engagement to support their population recovery. Based on data from a systematic literature review, we built connectivity networks from telemetry and mark-recapture studies that provide a first baseline for transboundary migratory connectivity for Australian sharks and rays. Of the 31 shark and ray species reviewed, we identified 6 species that link the Australian Exclusive Economic Zone to other national jurisdictions via multispecies migratory connections through the Tasman Sea to New Zealand, through the Tasman and Coral Sea to New Caledonia, and north across the Timor Sea and Torres Strait to Indonesia and Papua New Guinea. White sharks (Carcharhinus carcharias) and whale sharks (Rhincodon typus) were the most data rich, whereas 14 shark and ray species had no movement information. There is a grave deficiency in available information for endangered or critically endangered migratory shark and ray populations, with 76% having only one or no published studies. This work supports future conservation strategies for migratory sharks that require robust international collaboration and the adoption of integrated and dynamic management approaches.

ecology↗

bioRxiv2023

Whale shark residency and small-scale movements around oil and gas platforms in Qatar

Artificial structures in the ocean can influence the movements and residency of migratory fishes. Whale sharks seasonally aggregate near oil and gas platforms in Qatar to feed on fish spawn, creating one of the largest aggregations for the species. We used passive acoustic telemetry to examine their fine-scale movements, residency, and seasonality and investigate whether the platforms influence their habitat use in the area. Tags had a mean retention of 161 {+/-}186 SD days and 32 of the 117 tags were recorded in multiple seasons in the acoustic array (21 stations). Most detections were recorded during the season that was established with other methods from May to September, confirming that this whale shark aggregation is seasonal. Whale sharks stayed up to 77 consecutive days in the array (mean = 16 {+/-} 12.51 days) and had a mean residency index Rmax of 0.31, highlighting the importance of this site to their ecology. While most detections were made at a receiver near a platform, other platforms had few detections and the distance from the centre of the aggregation was the main explanatory variable in a GLM, indicating that the platforms do not influence the whale sharks habitat use. Instead, they moved with the current during the morning, when they feed on fish eggs at the surface which also float with the current, and swam against the current in the late afternoon and at night to be at the presumed fish spawning site again in the early morning. Our results highlight the importance of this small feeding area for whale sharks which face a high threat level in the region.

animal behavior and cognition↗

bioRxiv2022

Cerebral malaria is regulated by host mediated changes in Plasmodium gene expression

Cerebral Malaria (CM), the deadliest complication of Plasmodium infection, is a complex and unpredictable disease. However, our understanding of the host and parasite factors that cause CM is limited. Using a mouse model of CM, experimental CM (ECM), we performed a three-way comparison between: ECM susceptible C57BL/6 mice infected with ECM-causing Plasmodium ANKA (Pb ANKA) parasites (ANKA(C57BL/6)); ECM resistant Balb/c mice infected with Pb ANKA (ANKA(Balb/c)); and C57BL/6 mice infected with Pb NK65 that does not cause ECM (NK65(C57BL/6)). All ANKA(C57BL/6) mice developed CM. In contrast in ANKA(Balb/c) and NK65(C57BL/6) infections do not result in CM and proceed similarly in terms of parasite growth, disease course and host immune response.. However, parasite gene expression in (ANKA(C57BL/6)) was remarkably different than in ANKA(Balb/c) but similar to the gene expression in NK65(C57BL/6). Thus, Pb ANKA has a ECM-specific gene expression profile that is only activated in susceptible hosts providing evidence that the host has a critical influence on the outcome of infection.

microbiology↗

bioRxiv2021

Plant secondary metabolite diversity reflects both phylogeny and ecological adaptation

A phylogenetic framework explaining plant secondary metabolite diversity is lacking, but metabolite classes could represent adaptations to habitat resource availability. We test the hypothesis that primary adaptive strategies (competitors, C; stress-tolerators, S; ruderals, R) are associated, respectively, with nitrogenous metabolites synthesized in persistent organs (alkaloids), nitrogen-lacking aromatic terpenes and phenolics, and nitrogenous compounds prevalent in reproductive tissues (cyanogenic glucosides and glucosinolates). A matrix was compiled of 1019 species for which secondary metabolite pathways and CSR strategies are known. Accounting for phylogenetic relatedness and native biomes, we found that most phytochemical pathways did not correlate with strategy axes, but certain key associations were evident. C-selection was positively associated with amino acid-derived phenylpropanoids (low phylogenetic relatedness; {lambda} <0.5) and pyrrolizidine alkaloids and galloyl derivatives (high {lambda}), and negatively with N-lacking linear monoterpenes (low {lambda}). Nitrogenous cyanogenic glucosides positively correlated with R-selection (low {lambda}). Terpenoids were widely distributed, but correlated positively with S- and negatively with R-selection (low {lambda}). Twenty-six correlations between phytochemicals and biomes (low {lambda}) were evident. Most secondary metabolite synthesis pathways are widespread, reflecting common roles and obligate defence, and strong phylogenetic effects are often evident. However, the character of phytochemical/adaptive strategy associations agrees with ecological theory and thus reflects adaptation.

ecology↗

bioRxiv2021

Size and shape regional differentiation during the development of the spine in the nine-banded armadillo (Dasypus novemcinctus)

Xenarthrans (armadillos, anteaters, sloths and their extinct relatives) are unique among mammals in displaying a distinctive specialization of the posterior trunk vertebrae - supernumerary vertebral xenarthrous articulations. This study seeks to understand how xenarthry develops through ontogeny and if it may be constrained to appear within pre-existing vertebral regions. Using 3D geometric morphometrics on the neural arches of vertebrae, we explore phenotypic, allometric, and disparity patterns of the different axial morphotypes during ontogeny of nine-banded armadillos. Shape-based regionalisation analyses showed that adult thoracolumbar column is divided into three regions according to the presence or absence of ribs and the presence or absence of xenarthrous articulations. A three-region-division was retrieved in almost all specimens through development, although younger stages (e.g. foetuses, neonates) have more region boundary variability. In size-based regionalisation analyses, thoracolumbar vertebrae are separated into two regions: a pre-diaphragmatic, pre-xenarthrous region, and a post-diaphragmatic xenarthrous region. We show that posterior thoracic vertebrae grow at a slower rate, while anterior thoracics and lumbar grow at a faster rate relatively, with rates decreasing anteroposterioly in the former and increasing anteroposterioly in the latter. We propose that different proportions between vertebrae and vertebral regions might result from differences in growth pattern and timing of ossification.

developmental biology↗

bioRxiv2020

The contribution of leaf sulfur content to the leaf economics spectrum explained by plant adaptive strategies

Sulfur is an essential macronutrient for plant metabolism. Terrestrial ecosystems have faced extensive anthropogenic sulfur depositions during the 20th century, but currently decreasing trend of sulfur emissions suggest that it could become limiting, although its relationship with plant economics remains unclear. We analysed leaf and nutrient traits for 740 vascular plant species growing in a wide range of environmental conditions. We aimed to determine whether leaf sulfur content (LSC) is associated with the leaf economics spectrum, and whether its distribution among functional types (life forms, leaf life span categories, and Grimes CSR (Competitive, Stress-tolerant, Ruderal) strategies) could help to elucidate adaptive differences within plant taxa. High LSC values corresponded mainly with R-, and to a lesser extent C-, strategy selection, hence the acquisitive extreme of plant economics. We found evidence of a relationship between nutrient stoichiometry and taxonomy, specifically at the acquisitive and conservative extremes of leaf economics. In general, LSC was significantly and positively correlated with leaf nitrogen content, but ruderal strategies in particular exhibited greater sulfur to nitrogen ratios. Faced with a dearth of LSC data, leaf nitrogen content could thus be used as a coarse proxy of LSC within the context of plant economics. Different ratios among sulfur and nitrogen may be expected for ruderal species, suggesting that deeper insights from CSR strategies can provide a bridge between plant stoichiometry and ecology.

ecology↗

bioRxiv2020

Clinicopathologic Correlates and Natural History of Atypical Chronic Myeloid Leukemia

There is limited data on the clonal mechanisms underlying leukemogenesis, prognostic factors, and optimal therapy for atypical chronic myeloid leukemia (aCML). We evaluated the clinicopathological features, outcomes, and responses to therapy of 65 patients with aCML. Median age was 67 years (range 46-89). The most frequently mutated genes included ASXL1 (83%), SRSF2 (68%), and SETBP1 (58%). Mutations in SETBP1, SRSF2, TET2, and GATA2 tended to appear within dominant clones, with frequent SRSF2 and SETBP1 codominance, while other RAS pathway mutations were more likely to appear as minor clones. Acquisition of new, previously undetectable mutations at transformation was observed in 63% of evaluable patients, the most common involving signaling pathway mutations. Hypomethylating agents were associated with the highest response rates and duration. With a median overall survival of 25 months (95% CI 20-30), intensive chemotherapy was associated with worse OS than other treatment modalities, and allogeneic stem cell transplantation was the only therapy associated with improved outcomes (HR 0.044, 95% CI 0.035-0.593, p=0.007). Age, platelet count, BM blast percentage, and serum LDH levels were independent predictors of survival and were integrated in a multivariable model which allowed to predict 1-year and 3-year survival.

cancer biology↗

bioRxiv2020

Only SF3B1 Mutation involving K700E (And Not Other Codons), Independently Predicts Overall Survival in Myelodysplastic Syndromes

BackgroundSF3B1 mutations (SF3B1mut) in myelodysplastic syndromes (MDS) frequently involve codon K700E and have a favorable prognosis. The prognostic effect of non-K700E SF3B1mut is uncertain. MethodsWe analyzed the clinical-pathologic features and outcomes of a single-institutional series of 94 SF3B1mut and 415 SF3B1wt newly diagnosed untreated MDS patients and explored the differences between K700E and non-K700E subgroups. FindingsNinety-four (19%) patients had SF3B1mut: median age, 74 years. Fifty-five (60%) patients carried K700E. Recurrent non-K700E mutations (39, 40%) included R625, H662 and K666. Compared to SF3B1mut K700E, non-K700E patients had a lower median ANC (1{middle dot}8 vs. 2{middle dot}4, p=0{middle dot}005) and were frequently "high" R-IPSS (revised International Prognostic Scoring System) [7(19%) vs. 2(4%), p=0{middle dot}031]. Non-K700E MDS frequently associated with RUNX1 (26% vs. 7%, p=0{middle dot}012) and exclusively with BCOR, IDH2, and SRSF2 mutations. There was no significant difference in karyotype or SF3B1 variant allele frequency. Most ([~]80%) were treated with hypomethylating agents. SF3B1mut had superior overall survival (OS) than SF3B1wt in all MDS categories [not-reached vs. 25{middle dot}2 months, p=0{middle dot}0003], low-grade MDS, and MDS with ring sideroblasts (MDS-RS). Compared to SF3B1wt, SF3B1mut K700E had superior outcomes in all MDS categories (25 months vs. not-reached, p=0{middle dot}0001), low-grade MDS, and MDS-RS, but no significant difference was seen with non-K700E. By multivariate analysis, absence of SF3B1mut K700E (not non-K700E) independently associated with prognosis. InterpretationSF3B1mut MDS show distinct clinical and mutational profiles, with K700E showing a significantly better OS compared to non-K700E mutations and SF3B1wt. Our study highlights the importance of SF3B1 mutation type in MDS risk assessment. Data Sharing StatementThe datasets generated during and/or analyzed during the current study are not publicly available due to patient privacy concerns but are available from the corresponding author on reasonable request. Research in ContextO_ST_ABSEvidence before this studyC_ST_ABSWe designed this study based on the collective evidence from a systematic search of the literature for outcomes of patients MDS with SF3B1 mutations (SF3B1mut) from January 2013 to June 2020. Both the International Working Group for the Prognosis of MDS (IWG-PM) proposal and 2016 revisions to the World Health Organization (WHO) Classification of Myelodysplastic Syndromes recognize SF3B1mut MDS with <5% blasts (or ring sideroblasts >5% for WHO) as a distinct sub-category, in the absence of other unfavorable features. This was largely based on favorable prognostic outcomes, a distinct gene expression profile, and association with ring sideroblasts. However, the natural history of SF3B1mut MDS is heterogeneous. A high proportion of SF3B1 mutations occur within codon K700, leading to large-scale mRNA downregulation due to branch point recognition error, while the rest occur outside of this codon. The downstream functional effects of SF3B1 mutations outside of the K700 codon are unclear. The clinical course of SF3B1mut MDS patients likely depends on the type of SF3B1 mutation and other features such as variant allele frequency, concomitant gene mutations, and karyotype. Until now, the effects of the different types of SF3B1 mutations were largely unknown. Added value of this studyIn this study, we report distinctive clinicopathologic characteristics and outcomes of MDS patients with SF3B1 mutations segregated based on mutation type: K700E vs. non-K700E. We show that [~]40% of SF3B1 mutated MDS patients have non-K700E mutations. Non-K700E SF3B1mut MDS have distinct clinico-pathologic features, such as lower ANC and frequent association with mutations in RUNX1, BCOR, IDH2, and SRSF2. There was no significant difference in karyotype or SF3B1 variant allele frequency. Importantly, K700E SF3B1mut MDS had superior overall survival compared to SF3B1wt, in all MDS, low-grade MDS, and MDS with ring sideroblasts, but no significant difference was seen with non-K700E. By multivariate analysis, absence of SF3B1mut K700E, but not non-K700E, independently associated with prognosis. Implications of all the available evidenceTo the best of our knowledge, this is the first study to report these findings from a single-institutional series of MDS primarily treated with hypomethylating agents. Our study highlights the importance of determining the SF3B1 mutation type in MDS risk assessment. These findings are important in light of the recent FDA approval of luspatercept based on the results of the MEDALIST trial that suggested sustained hematological responses in SF3B1mut MDS patients.

cancer biology↗

bioRxiv2019

Computer vision to automatically assess infant neuromotor risk

An infants risk of developing neuromotor impairment is primarily assessed through visual examination by specialized clinicians. Therefore, many infants at risk for impairment go undetected, particularly in under-resourced environments. There is thus a need to develop automated, clinical assessments based on quantitative measures from widely-available sources, such as video cameras. Here, we automatically extract body poses and movement kinematics from the videos of at-risk infants (N=19). For each infant, we calculate how much they deviate from a group of healthy infants (N=85 online videos) using Naive Gaussian Bayesian Surprise. After pre-registering our Bayesian Surprise calculations, we find that infants that are at higher risk for impairments deviate considerably from the healthy group. Our simple method, provided as an open source toolkit, thus shows promise as the basis for an automated and low-cost assessment of risk based on video recordings.

animal behavior and cognition↗

bioRxiv2017

Three-dimensional mobility and muscle attachments in the pectoral limb of the Triassic cynodont Massetognathus pascuali

The musculoskeletal configuration of the mammalian pectoral limb has been heralded as a key anatomical feature leading to the adaptive radiation of mammals, but limb function in the cynodont outgroup remains unresolved. Conflicting reconstructions of abducted and adducted posture are based on mutually-incompatible interpretations of ambiguous osteology. We reconstruct the pectoral limb of the Triassic non-mammalian cynodont Massetognathus pascuali in three dimensions, by combining skeletal morphology from micro-computed tomography with muscle anatomy from an extended extant phylogenetic bracket. Conservative tests of maximum range of motion suggest a degree of girdle mobility, as well as substantial freedom at the shoulder and the elbow joints. The glenoid fossa supports a neutral pose in which the distal end of the humerus points 45{degrees} posterolaterally from the body wall, intermediate between classically \"sprawling\" and \"parasagittal\" limb postures. Massetognathus is reconstructed as having a near-mammalian complement of shoulder muscles, including an incipient rotator cuff (m. subscapularis, m. infraspinatus, m. supraspinatus, and m. teres minor). Based on close inspection of the morphology of the glenoid fossa, we hypothesize a posture-driven scenario for the evolution of the therian ball-and-socket shoulder joint. The musculoskeletal reconstruction presented here provides the anatomical scaffolding for more detailed examination of locomotor evolution in the precursors to mammals.

paleontology↗