Biology subjects

Weaver, M.

Publications and source records attributed to Weaver, M..

9 recordsLinked to original sources

bioRxiv2026

The Brightly Coloured Invaders: A Characterisation of the Invasive Lema Beetle, Lema equestris (Coleoptera: Chrysomelidae), in Hawaii

Introduced to Hawaii in 2016, Lema equestris has become a garden pest commonly reported on Solanum americanum, which is grown as a native and cultural plant in Hawaii and supports native vertebrates elsewhere across Oceania. Originally identified as L. solani, the species was later found to have been misidentified. Here, molecular and morphological evidence is used to discriminate Hawaiian specimens from L. solani and support the updated identification of L. equestris. As a new invasive species, it is important to confirm host associations and determine whether it will prey on important species, such as endemic or endangered plants, in its new range or any potential range to which it could spread. To this end, feeding assays were performed with adults, first-instar larvae, and newly hatched naive larvae on 11 potential hosts, comprising mostly Solanum species: Solanum americanum, potato, tomato, tomatillo, poha (gooseberry), chili pepper, eggplant, tobacco, tree tobacco, cabbage, and Brazilian nightshade. While feeding was attempted on cabbage, poha berry, and Brazilian nightshade, no host besides S. americanum supported survival. Rearing was used to further characterize the biology and life history of L. equestris, including instar length and distinctive morphological traits for identifying each life stage. While many basic biological traits are confirmed here, much remains to be studied to better understand this species and why it has begun to spread.

zoology↗

bioRxiv2026

Applying PCR cycle autonormalization to improve PacBio full-length 16S rRNA sequencing

The bacterial 16S rRNA gene is widely used to characterize host-associated and environmental microbiomes, most commonly through sequencing short hypervariable regions. Recent improvements in PacBio sequencing chemistry and concatenation approaches can now enable high-throughput, full-length 16S rRNA gene sequencing with high accuracy and depth. However, PCR-induced errors remain a major limitation, particularly for full-length amplicons where error accumulation may be elevated due to a five-fold increase in sequence lengths. These challenges are exacerbated when samples vary widely in microbial biomass, making it difficult to select a single optimal number of PCR cycles. Here, we evaluated the effects of PCR cycle autonormalization on PacBio Kinnex full-length 16S rRNA gene sequencing across seven agriculturally relevant specimen types. We compared conventional PCR protocols (20, 24, and 30 cycles) with an autonormalization approach in which individual reactions were terminated during exponential amplification based on real-time fluorescence thresholds. Autonormalized reactions consistently retained a higher proportion of sequences following denoising and chimera removal, exhibited fewer substitution-based errors, and produced more even read distributions across samples. Meanwhile, overamplified reactions (30 cycles) showed elevated error rates and higher sequence removal, particularly in samples with greatest microbial biodiversity. Importantly, PCR protocol had minimal effects on overall community composition relative to specimen types. These results demonstrate that PCR cycle autonormalization improves data yield for full-length 16S rRNA sequencing while maintaining robust inferences, while facilitating streamlined workflows for heterogeneous samples. ImportanceAmplicon-based sequencing of the 16S rRNA gene is foundational tool in microbiome research, yet PCR amplification remains a major source of technical error. This challenge is magnified for full-length 16S rRNA sequencing and for workflows that process specimen types with widely varying microbial biomass. Selecting a single PCR cycle number can result in under-amplification of samples with low 16S rRNA copies or over-amplification and error accumulation in high-titer samples. Here, we show that PCR cycle autonormalization, implemented using iconPCR, substantially improves PacBio full-length 16S rRNA sequencing by reducing PCR-induced substitution errors and chimeras while maintaining consistent biological inference. Autonormalization also enables blind pooling of amplicons without post-PCR quantification or equimolar normalization, reducing hands-on time and sample loss. These benefits make cycle autonormalization particularly valuable for high-throughput and production-scale sequencing applications handling diverse specimen types.

microbiology↗

bioRxiv2024

Utilizing full-length 16S rRNA sequencing to assess the impact of diet formulation and age on targeted gut microbiome colonization in laboratory and mass-reared Mediterranean fruit flies

Insect gut microbiomes have important roles in overall host health and how hosts function in the environment. In laboratory and mass-reared insects, gut microbiomes can differ in composition and function compared to wild conspecifics. For fruit flies, like the Mediterranean fruit fly (medfly; Ceratitis capitata), these changes can influence male performance and behavior. Overall, understanding factors that influence the ability of bacteria to colonize hosts is an important for the establishment of lost or novel microbiota into mass-reared insects. The goal of this study was to evaluate how host age and diet inoculation method influenced bacterial establishment in laboratory and mass-reared medfly. We used an Enterobacter strain with antibiotic resistance and coupled it with full-length PacBio 16S rRNA sequencing to track the establishment of a specific isolates under different adult dietary conditions. We also used two longstanding reared lines of medfly in our study. Our results identified that diet had a strong interaction with age. Host medfly fed a liquid diet with the target bacteria were able to be colonized regardless of age, but those fed a slurry-based diet and separate water source were more resilient. This was consistent for both fly rearing lines used in the study. 16S rRNA sequencing corroborated the establishment of the specific strain, but also revealed some species/strain-level variation of Enterobacter sequences associated with the flies. Additionally, our study illustrates that long-read 16S rRNA sequencing may afford improved characterization of species- and strain-level distribution of Enterobacteriaceae in insects. ImportanceInsects form intimate relationships with gut microorganisms that can help facilitate several important roles. The goals of our study were to evaluate factors that influence microbial establishment in lines of the Mediterranean fruit fly (medfly), an important pest species throughout the world. Mass-reared insects for sterile insect technique often possess gut microbiomes that substantially differ from wild flies, which can impact their performance in pest control contexts. Here, we show that liquid-based formulations can be utilized to manipulate the gut microbiota of mass-reared medfly. Furthermore, using near full-length 16S rRNA metabarcoding sequencing, we uncovered strain-level diversity of that was not immediately obvious using other approaches. This is a notable finding, as it suggests that full-length 16S rRNA approaches can have marked improvements for some taxa compared to fewer hypervariable regions at approximately the same cost. Our results provide new avenues for exploring and interrogating medfly-microbiome interactions.

microbiology↗

bioRxiv2024

PrimalScheme: open-source community resources for low-cost viral genome sequencing

Viral genome sequencing using the ARTIC protocol has been a vital tool for understanding the spread of epidemics including Ebola, Zika, Covid-19 and Mpox and has seen widespread adoption due to its low cost and high sensitivity. Here, we describe PrimalScheme, an open-source toolkit and website that allows users to easily design primer schemes for amplicon sequencing of viruses, and has generated over 67,000 primer schemes for the global community since 2017. In January 2020, PrimalScheme was used to rapidly generate a primer scheme for SARS-CoV-2, with primer pools distributed to researchers from 44 countries to help scale-up genomic surveillance efforts. Overall, these primers were used to generate an estimated 18M genome sequences and the protocols were viewed online [~]250K times. To complement PrimalScheme, we have built PrimalScheme Labs, a scheme repository which allows users to find and share primer schemes as well as establishing a set of data standards. Through improvements to the primer design process, including the use of discrete primer clouds, we have expanded the use of amplicon sequencing to include diverse virus species. We demonstrate the utility of this approach through a high diversity pan-genotype Measles virus (MeV) scheme. We also demonstrate its use on a high sensitivity, short amplicon Monkeypox virus (MPXV) scheme with over 1000 primers, showing high genome recovery on low-titre clinical samples. These developments have implications for sequencing from samples such as wastewater, for genomic surveillance of endemic pathogens and in preparing for future pandemics.

genomics↗

bioRxiv2024

Protein-based cell population discovery and annotation for CITE-seq data identifies cellular phenotypes associated with critical COVID-19 severity

Technologies such as Cellular Indexing of Transcriptomes and Epitopes sequencing (CITE-seq) and RNA Expression and Protein sequencing (REAP-seq) augment unimodal single-cell RNA sequencing (scRNA-seq) by simultaneously measuring expression of cell-surface proteins using antibody derived oligonucleotide tags (ADT). These protocols have been increasingly used to resolve cellular populations that are difficult to infer from gene expression alone, and to interrogate the relationship between gene and protein expression at a single-cell level. However, the ADT-based protein expression component of these assays remains widely underutilized as a primary tool to discover and annotate cell populations, in contrast to flow cytometry which has used surface protein expression in this fashion for decades. Therefore, we hypothesized that computational tools used for flow cytometry data analysis could be harnessed and scaled to analyze ADT data. Here we apply Ozette Discovery, a recently-developed method for flow cytometry analysis, to re-analyze a large (>400,000 cells) published COVID-19 CITE-seq dataset. Using the protein expression data alone, Ozette Discovery is able to identify granular, robust, and interpretable cellular phenotypes in a high-throughput manner. In particular, we identify a population of CLEC12A+CD11b+CD14- myeloid cells that are specifically expanded in patients with critical COVID-19, and can only be resolved by their protein expression profiles. Using the longitudinal gene expression data from this dataset, we find that early expression of interferon response genes precedes the expansion of this subset, and that early expression of PRF1 and GZMB within specific Ozette Discovery phenotypes provides a RNA biomarker of critical COVID-19. In summary, Ozette Discovery demonstrates that taking a protein-centric approach to cell phenotype annotation in CITE-seq data can achieve the potential that dual RNA/protein assays provide in mixed samples: instantaneous in silico flow sorting, and unbiased RNA-seq profiling. HIGHLIGHTSO_LIOzette Discovery provides an alternative method for data-driven annotation of granular and homogeneous cell phenotypes in CITE-seq data using protein expression data alone. C_LIO_LIOur approach inherently accommodates for batch effects, and our novel background-normalization method improves the signal:noise ratio of these notoriously noisy protein measurements. C_LIO_LIWhile these subpopulations are not derived from RNA profiles, they have distinct and interpretable RNA signatures. C_LIO_LIWe find a population of CLEC12A+CD11b+CD14- myeloid cells associated with critical COVID-19 severity that can only be identified by their protein profiles, and identify early expression of interferon response genes in a CD4 T cell subset as a predictor of CLEC12A+CD11b+CD14- cell expansion. C_LIO_LIPeforming differential expression analysis within our identified phenotypes reveals predictors of COVID-19 severity that are not found with coarser annotations. C_LI

bioinformatics↗

bioRxiv2020

Pupil dilation and P3 reflect subjective surprise about decision outcome

Central to human and animal cognition is the ability to learn from feedback in order to optimize future rewards. Such a learning signal might be encoded and broadcasted by the brains arousal systems, including the noradrenergic locus coeruleus. Pupil responses and the positive slow wave component of event-related potentials reflect rapid changes in the arousal level of the brain. Here we ask whether and how these variables may reflect surprise: the mismatch between ones expectation about being correct and the outcome of a decision, when expectations fluctuate due to internal factors (e.g., engagement). We show that during an elementary decision-task in the face of uncertainty both physiological markers of phasic arousal reflect surprise. We further show that pupil responses and slow wave ERP are unrelated to each other, and that prediction error computations depend on feedback awareness. These results further advance our understanding of the role of central arousal systems in decision-making under uncertainty.

neuroscience↗

bioRxiv2019

Spatiotemporal characterization of periocular mesenchyme heterogeneity during anterior segment development

Establishment of the ocular anterior segment (AS) is a critical event during development of the vertebrate visual system. Failure in this process leads to Anterior Segment Dysgenesis (ASD), which is characterized by congenital blindness and predisposition to glaucoma. The anterior segment is largely formed via a neural crest-derived population, the Periocular Mesenchyme (POM). In this study, we aimed to characterize POM behaviors and identities during zebrafish AS development. POM distributions and migratory dynamics were analyzed using transgenic zebrafish embryos (Tg[foxC1b:GFP], Tg[foxD3:GFP], Tg[pitx2:GFP], Tg[lmx1b.1:GFP], and Tg[sox10:GFP] throughout the course of early AS development (24-72hpf). In vivo imaging analysis revealed unique AS distribution and migratory behavior among the reporter lines, suggesting AS mesenchyme (ASM) is a heterogenous population. This was confirmed using double in situ hybridization. Furthermore, we generated ASM transcriptomic profiles from our reporter lines and using a four-way comparison analysis uncovered unique ASM subpopulation expression patterns. Taken together, our data reveal for the first time that AS-associated POM is not homogeneous but rather comprised of several unique subpopulations identifiable by their distributions, behaviors, and transcriptomic profiles.

developmental biology↗

bioRxiv2019

Pax2a regulates angiogenesis to facilitate fusion of the optic fissure

Vertebrate retinal development requires timely and precise fusion of the optic fissure (OF). Recent studies have suggested hyaloid vasculature to be involved in optic fissure fusion. In order to examine this link, we analyzed OF fusion and hyaloid vasculogenesis in the zebrafish pax2anoi mutant line. We determined that OF basement membrane (BM) remodeling, normally preceded by F-actin accumulation is mis-regulated in pax2a-/- embryos. Comparing transcriptomic profiles of pax2a-/- and wildtype eyes we discovered a novel connection between regulation of angiogenesis and fusion. Pax2a-/- eyes exhibited a significant reduction of talin1 expression, a regulator of hyaloid vasculature, in addition to increased expression of an anti-angiogenic protease, adamts1. Using 3D and live imaging we observed reduced OF hyaloid vascularization in pax2a-/- embryos. Additionally, pharmacological inhibition of VEGF signaling or adamts1 mRNA overexpression phenocopied the pax2a-/- vasculature, F-actin and BM remodeling phenotypes. Finally, we show that hyaloid vasculature expresses mmp2 which is necessary for remodeling the fissure BM. Taken together we propose a pax2a driven mechanism that restricts anti-angiogenic activity of adamts1 enabling hyaloid vasculature invasion of the OF and delivery of the BM remodeler mmp2.

developmental biology↗

bioRxiv2018

Mapping and dynamics of regulatory DNA during seed development

The genome is reprogrammed during development to produce diverse cell types, largely through altered expression and activity of key transcription factors. The accessibility and critical functions of epidermal cells have made them a model for connecting transcriptional events to development in a range of model systems. In Arabidopsis thaliana and many other plants, fertilization triggers differentiation of specialized epidermal seed coat cells that have a unique morphology caused by large extracellular deposits of pectin. Here, we used DNase I-seq to generate regulatory landscapes of A. thaliana seeds at two critical time points in seed coat maturation, enriching for seed coat cells with the INTACT method. We found over 3000 developmentally dynamic regulatory DNA elements and explored their relationship with nearby gene expression. The dynamic regulatory elements were enriched for motifs for several transcription factors families; most notably the TCP family at the earlier time point and the MYB family at the later one. To assess the extent to which the observed regulatory sites in seeds added to previously known regulatory sites in A. thaliana, we compared our data to 11 other data sets generated with seven-day-old seedlings for diverse tissues and conditions. Surprisingly, over a quarter of the regulatory, i.e. accessible, bases observed in seeds were novel. Notably, in this comparison, development exerted a stronger effect on the plant regulatory landscape than extreme environmental perturbations, highlighting the importance of extending studies of regulatory landscapes to other tissues and cell types during development.

plant biology↗