Biology subjects

Carroll, E.

Publications and source records attributed to Carroll, E..

10 recordsLinked to original sources

bioRxiv2025

Diversification of pre-mating behaviors through temporal reordering of components

Many biological processes, including mating behavior, are structured as ordered sequences in which each step enables the next. Diversity of such processes usually arises through the addition or loss of components rather than through changes in their order, since reordering can disrupt functional integration. Here we show that reordering of the steps associated with termite nuptial pairing can generate behavioral diversity. In most termites, dispersed adults shed their wings before initiating tandem pairing, as wings interfere with communication between females and males. However, we found that in the Australian termite, Microcerotermes nervosus, tandem running occurs prior to wing shedding, and the act of tandem running itself facilitates dealation. Video tracking revealed that wing removal improves movement coordination, and comparative analysis of sympatric species showed that M. nervosus exhibits much higher tandem stability than others. These results suggest that enhanced movement coordination of this species may have potentiated step reordering. Our findings demonstrate that even functionally conserved sequences can be reorganized and that overcoming such constraints can open novel pathways for behavioral diversification.

animal behavior and cognition↗

bioRxiv2025

Observation of tandem running behavior in mating pairs of Asian dampwood termite, Hodotermopsis sjostedti

As a social insect, termite colonies can grow to a group of millions of individuals, yet all colonies start from a single mating pair. Recent studies indicate that the pair formation process shows a large diversity among species, especially in basal lineages. Thus, comparative information is integral to estimating the ancestral state of this essential stage of the termite life cycle. The Asian dampwood termite, Hodotermopsis sjostedti, has been well-studied as a model basal termite of caste differentiation processes. Yet, their pair formation remains undocumented. In this study, we found that mating pairs of H. sjostedti show clear tandem running behavior. Both females and males played a leading role, with females showing more leader roles, and they switched their leading roles even within the same pair. We also found that dish size affected tandem movement coordination; pairs showed faster and more stable tandem running in a larger dish. We provide a tracking dataset of 17 body parts, including antennal and leg movements during tandem runs, which can be utilized in future comparative studies. This study supports the idea that tandem running existed in the early ancestors of termites and sheds light on the origin of termite mate pairing.

animal behavior and cognition↗

bioRxiv2024

T cell epitope mapping reveals immunodominance of evolutionarily conserved regions within SARS-CoV-2 proteome.

As SARS-CoV-2 variants continue to emerge capable of evading neutralizing antibodies, it has become increasingly important to fully understand the breadth and functional profile of T cell responses to determine their impact on the immune surveillance of variant strains. Here, sampling healthy individuals, we profiled the kinetics and polyfunctionality of T cell immunity elicited by mRNA vaccination. Modeling of anti-spike T cell responses against ancestral and variant strains of SARS-CoV-2 suggested that epitope immunodominance and cross-reactivity are major predictive determinants of T cell immunity. To identify immunodominant epitopes across the viral proteome, we generated a comprehensive map of CD4+ and CD8+ T cell epitopes within non-spike proteins that induced polyfunctional T cell responses in convalescent patients. We found that immunodominant epitopes mainly resided within regions that were minimally disrupted by mutations in emerging variants. Conservation analysis across historical human coronaviruses combined with in silico alanine scanning mutagenesis of non-spike proteins underscored the functional importance of mutationally-constrained immunodominant regions. Collectively, these findings identify immunodominant T cell epitopes across the mutationally-constrained SARS-CoV-2 proteome, potentially providing immune surveillance against emerging variants, and inform the design of next-generation vaccines targeting antigens throughout SARS-CoV-2 proteome for broader and more durable protection. One Sentence SummaryPolyfunctional CD8+ and CD4+ T cells directed against SARS-CoV-2 target mutationally constrained regions of the viral proteome.

immunology↗

bioRxiv2024

Biocompatibility of KAPs-Depleted Residual Hair

This work is an in-depth investigation of the in vitro and in vivo biocompatibility of processed and treated residual human hair samples with intact cuticle layers. The specimens included oxidized hair with no melanin (BLH) and hair with medium-(M-KAP) and low-(L-KAP) levels of keratin associated proteins (KAPs), confirmed through gel electrophoresis, electron microscopy, and trichrome histological staining, in comparison to the untreated regular hair (REG) control. All hair groups, high KAPs (H-KAPs: REG and BLH), M-KAP, and L-KAP, were found to be non-cytotoxic in the adipose fibroblast cell lines response to their extracts based on the ISO 10993-5 medical device biomaterial testing standard. In vivo mouse subcutaneous implantation (ISO 10993-6, local effects) at 2 weeks showed that the samples caused a foreign body response (FBR) with a thin fibrous encapsulation at a mean value of 28% relative skin dermis thickness; but notably, the L-KAP implant mitigated a statistically significant decrease in FBR area compared to H-KAPs (REG and/or BLH) and a lower number of cells, including immune cells of mostly macrophages and mast cells on the biomaterials surface, normalized to implant and tissue coverage. In the bulk of the capsules, blood vessels and collagen extracellular matrix densities were similar among groups. These findings suggest that small globular KAPs diffuse out of the cortex to the host-biomaterial interface which induce a slightly elevated FBR but limited to the implants surface vicinity. On-going follow-up research focuses on purer keratin-based macromolecularly organized residual hair biomaterials, those with depleted KAPs, for drug-delivery gel implants as they are deemed the most biocompatible. Statement of SignificanceHuman hair is an abundant biological product that is regularly discarded and wasted but has the potential to be a clinical implantable allograft biomaterial. There are currently just two FDA class II-510(k)-approved medical devices from hair, limited to surface / skin wound care use, and no class III-PMA or biologics-BLA implants. Also, these products and those in research and development phases are based on soluble keratin and KAPs extracts utilizing tedious processing conditions and requiring oxidation reaction for reassembly into gels and scaffolds. Here we describe that the insoluble residual hair biomaterials with organized keratin structure, higher-degree of disulfide crosslinks, and particularly those with depleted KAPs have increased biocompatibility based on pre-clinical ISO 10993 standards. This novel natural biomaterials are now being developed as drug-delivery implantable gels for clinical applications.

bioengineering↗

bioRxiv2023

Subgenome dominance shapes novel gene evolution in the decaploid pitcher plant Nepenthes gracilis

Subgenome dominance after whole-genome duplication generates distinction in gene number and expression at the level of chromosome sets, but it remains unclear how this process may be involved in evolutionary novelty. Here, we generated a chromosome-scale genome assembly of the Asian pitcher plant Nepenthes gracilis to analyze how its novel traits (dioecy and carnivorous pitcher leaves) are linked to genomic evolution. We found a decaploid karyotype with five complete sets of syntenic chromosomes (2n = 10x = 80) yet with a clear indication of subgenome dominance and highly diploidized gene contents. The male-linked and pericentromerically located region on the putative sex chromosome was identified in a recessive subgenome and was found to harbor three transcription factors involved in flower and pollen development, including a likely neofunctionalized LEAFY duplicate. Transcriptomic and syntenic analyses of carnivory-related genes suggested that the paleopolyploidization events seeded genes that subsequently formed tandem clusters in recessive subgenomes with specific expression in the digestive zone of the pitcher, where specialized cells digest prey and absorb derived nutrients. Novel gene evolution in recessive subgenomes is likely to be prevalent because duplicates were enriched with Nepenthes-specific genes with tissue-specific expression, including those expressed in trapping pitchers. Thus, subgenome dominance likely contributed to evolutionary novelty by allowing recessive subgenomes experiencing relaxed purifying selection to serve as a preferred host of novel tissue-specific duplicates. Our results provide insight into how polyploids, which may frequently be evolutionary dead-ends, have given rise to novel traits in exceptionally thriving high-ploidy lineages.

plant biology↗

bioRxiv2022

The P450 Sterol Side Chain Cleaving Enzyme (P450scc) for Digoxin Biosynthesis in the Foxglove Plant Belongs to the CYP87A Family

Digoxin from the foxglove plant is a commonly prescribed plant natural product for treating heart failure and atrial fibrillation. Despite its medicinal prominence, how foxglove synthesizes digoxin is largely unknown, especially the cytochrome P450 sterol side chain cleaving enzyme (P450scc), which catalyzes the first and rate-limiting step in this pathway. Here we report the identification of the foxglove P450scc, the gatekeeping enzyme that channels sterols to digoxin. This enzyme converts both cholesterol and campesterol to pregnenolone, thus explaining how pregnenolone is synthesized in plants. Phylogenetic analysis indicates that this enzyme arose from a duplicated CYP87A gene and does not share clear homology with the mammalian P450scc. Identifying this long-speculated plant P450scc enzyme suggests that the digoxin biosynthetic pathway starts from both cholesterol and phytosterols, instead of just cholesterol as previously thought. The identification of this gatekeeping enzyme is a key step towards complete elucidation of digoxin biosynthesis and expanding the therapeutic applications of digoxin analogs in future work.

plant biology↗

bioRxiv2022

The Chemical Features of Polyanions Modulate Tau Aggregation and Conformational States

The aggregation of tau into insoluble fibrils is a defining feature of neurodegenerative tauopathies. However, tau has a positive overall charge and is highly soluble; so polyanions, such as heparin, are typically required to promote its aggregation in vitro. There are dozens of polyanions in living systems and it is not clear which ones might promote this process. Here, we systematically measure the ability of 30 diverse, anionic biomolecules to initiate tau aggregation, using either wild type (WT) tau or the disease associated P301S mutant. We find that polyanions from many different structural classes can promote fibril formation and that P301S tau is sensitive to a greater number of polyanions (19/30) than WT tau (16/30). We also find that some polyanions preferentially reduce the lag time of the aggregation reactions, while others enhance the elongation rate, suggesting that they act on partially distinct steps. From the resulting structure-activity relationships, the valency of the polyanion seems to be an important chemical feature, such that anions with low valency tend to be weaker aggregation inducers, even at the same overall charge. Finally, the identity of the polyanion influences fibril morphology, based on electron microscopy and limited proteolysis. These results provide insight into the crucial role of polyanion--tau interactions in modulating tau conformational dynamics with implications for understanding the tau aggregation landscape in a complex cellular environment.

biochemistry↗

bioRxiv2021

Cardenolide Increase in Foxglove During Stresses Corresponds to Cholesterol and Phytosterol Biosynthesis

Cardenolides are a group of steroidal metabolites found in Digitalis lanata with potent cardioactive effects on animals. In plants, cardenolides are involved in various stress responses. However, the molecular mechanism of cardenolide increase during stresses is mostly unknown. Here we show that cardenolides were increased upon methyl jasmonate (MJ), sorbitol, potassium (KCl) chloride, and salicylic acid analog (BTH: 2,1,3-benzothiadiazole) treatments. However, the expression of three known genes for cardenolide biosynthesis did not correlate well with these increases. Specifically, the expression of progesterone-5{beta}-reductases (P5{beta}R and P5{beta}R2) did not correlate with cardenolide increase. The expression of 3{beta}-hydroxysteroid dehydrogenase (3{beta}HSD) correlated with cardenolide levels only during the BTH treatment. Mining the D. lanata transcriptome identified genes involved in cholesterol and phytosterol biosynthesis: SSR1 (sterol sidechain reductase), SMO1, and SMO3 (sterol methyl oxidase). Surprisingly, the expression of all three genes correlated well with the cardenolide increase after BTH treatment. Phylogenetic analysis showed that SSR1 is likely involved in both cholesterol and phytosterol biosynthesis. In addition, SMO1 is likely specific to phytosterol biosynthesis, and SMO3 is specific to cholesterol biosynthesis. These results suggest that both cholesterol and phytosterol are involved in cardenolide biosynthesis. In summary, this work shows that cardenolides are important for stress responses in D. lanata and revealed a novel relationship between phytosterol and cardenolide biosynthesis.

plant biology↗

bioRxiv2020

A transient role of primary cilia in controlling direct versus indirect neurogenesis in the developing cerebral cortex

During the development of the cerebral cortex, neurons are generated directly from radial glial cells or indirectly via basal progenitors. The balance between these division modes determines the number and types of neurons formed in the cortex thereby affecting cortical functioning. Here, we investigate the role of primary cilia in this process. We show that a mutation in the ciliary gene Inpp5e leads to a transient increase in direct neurogenesis and subsequently to an overproduction of layer V neurons in newborn mice. Loss of Inpp5e also affects ciliary structure coinciding with increased Akt and mTOR signalling and reduced Gli3 repressor levels. Genetically re-storing Gli3 repressor rescues the decreased indirect neurogenesis in Inpp5e mutants. Overall, our analyses reveal how primary cilia determine neuronal subtype composition of the cortex by controlling direct vs indirect neurogenesis. These findings have implications for understanding cortical malformations in ciliopathies with INPP5E mutations.

developmental biology↗

bioRxiv2018

A barcoding approach to phylogenetic classification of Aedini mosquitoes (Aedes, Ochlerotatus)

Traditionally, entomologists have used morphological characteristics for mosquito taxonomy and systematics. However, this approach does not take into consideration the genetic relatedness of species. In 2000, the Aedes genus of mosquitoes in the tribe Aedini was split into two genera (Aedes and Ochlerotatus), thereby elevating Ochlerotatus from subgenus to genus rank, strictly based on morphology of adults. Herein, we use the genetic barcoding marker COI to generate a phylogeny of 65 species of Aedes, Ochlerotatus, and Anopheles outgroup from almost 900 sequences downloaded from BOLD systems. Our results reveal evidence of non-random, but polyphyletic clustering of Aedes and Ochlerotatus species, with a monophyletic outgroup. We do find support for the validity of Ochlerotatus as an evolutionary unit, although we find insufficient evidence to support its retention as a genus. We suggest that mosquito phylogenetic analyses incorporate a greater number of genetic markers to help clarify our understanding of Aedini species classifications, but caution that recent assessments based solely on morphology may be insufficient.

evolutionary biology↗