Biology subjects

Carpenter, K.

Publications and source records attributed to Carpenter, K..

4 recordsLinked to original sources

bioRxiv2026

Multiomics dissection of the CO2-dependent fast growth of Picochlorum celeri

With a sub-3-micrometer cell and a 27-Mbp diploid genome, the small but mighty Picochlorum celeri doubles within three hours and exceeds 30 g m-2 d-1 outdoors with CO2 supplied. In climate-simulating photobioreactors, productivity declined from 39 g m-2 d-1 under 2.25% CO2 to near zero in air and resumed within hours of CO2 restoration with photosystem II photochemistry largely retained. We profiled the transcriptome, proteome, phosphoproteome, ubiquitinome, acetylome, metabolome and lipidome, including the first site-resolved green-algal ubiquitinome. In air, the Rubisco large subunit tripled to 7.6% of protein while its two small-subunit isoforms, 70% identical, exchanged near-reciprocally, a novel CO2-dependent switch that we propose retunes Rubisco to low CO2. Photorespiratory enzymes increased in abundance whereas proteins involved in external nitrogen assimilation decreased, consistent with increased reliance on internal nitrogen recycling as carbon fixation became limiting. Transcript and protein responses were nearly uncoupled, with cytosolic ribosomal proteins declining despite increased transcripts and plastid ribosomal proteins spared. Phosphorylation was extensively remodeled, as were the lysine modifications ubiquitination, acetylation and CO2-dependent carbamylation, where a CO2-competition assay identified 86 bicarbonate-protected lysines, including RbcL K252. CO2 limitation therefore imposes a reversible growth arrest that reduces cytosolic translational investment while preserving photosynthetic capacity for rapid recovery.

plant biology↗

bioRxiv2026

Ecological axes of skull diversification in a massive 1 vertebrate radiation

Eupercarian spiny-rayed fishes are one of the largest vertebrate radiations, rivaling mammals and occupying nearly every aquatic habitat. We present a densely sampled, time-calibrated phylogenomic framework for Eupercaria, supporting a revised classification, combined with the largest cranial phenomics dataset for fishes. Habitat and trophic ecology make independent, complementary contributions to skull shape. Most species cluster around a conserved generalized architecture, the Percomorph Pile, from which one clade of pufferfishes, anglerfishes, butterflyfishes, and surgeonfishes repeatedly invaded novel morphospace; exceptionally high rates on its deep branches indicate that rapid skull evolution arose early in this clade. Freshwater lineages converge on the ancestral condition, reflecting late arrival into systems occupied by older otophysans, whereas durophages show the greatest disparity and converge on derived forms. Cranial diversity was partitioned among subclades during the Cretaceous and later within them across the Cenozoic, showing that clade-level differences in evolutionary rates and ecological opportunity jointly shaped skull diversification.

evolutionary biology↗

bioRxiv2024

The effect of deferring feedback on rule-based and information-integration category learning.

Previous work has shown that deferring feedback significantly impairs two-dimensional information-integration category learning, often thought to recruit an implicit learning system, but leaves intact unidimensional rule-based learning, commonly assumed to engage an explicit system (Smith et al., 2014). These results were taken to support the influential COmpetition between Verbal and Implicit Systems (COVIS) dual-process theory. This conclusion has subsequently been challenged by the finding that this dissociation disappears when the number of relevant dimensions is matched between tasks (Le Pelley et al., 2019). However, as well as replacing a unidimensional rule-based task with a two-dimensional conjunction task, Le Pelley et al. also changed the stimuli that were used in their study making it unclear which of these alterations was driving the difference in results. The current paper directly examined how both category structure and stimulus type influence the deferred feedback effect. We replicated both the original sets of results but found that deferred feedback also impaired information-integration learning to a greater extent than a conjunction task when Smith et al.s original stimuli were used. This result suggests that the effect of deferred feedback on category learning is more complicated than has previously been documented and highlights the critical role the choice of stimuli has in determining whether the effect is obtained.

animal behavior and cognition↗

bioRxiv2022

A Translational Tissue Engineering Approach to Airway Reconstruction Leveraging Decellularized Meniscus and Cartilage Progenitor Cells

Severe subglottic stenosis develops in over 20,000 infants per year and requires laryngotracheal reconstruction (LTR) to enlarge the airway by implanting autologous cartilage from a rib graft. However, young children often lack sufficiently sized costal cartilage resulting in increased donor site morbidity and operative time, as well as an elevated risk for airway restenosis necessitating revision surgery. To overcome these limitations, we have created a first-of-its-kind scaffold based on porcine meniscal cartilage decellularization (MEND) by selectively digesting the elastin and blood vessels uniquely present in the meniscus to create microchannels that support cellular re-invasion. Here we demonstrated that MEND can be fully recellularized in 3 days with ear-derived cartilage progenitor cells (eCPCs) and reaches structural and functional maturation suitable for implant within 3 weeks of chondrogenic differentiation, a time frame compatible with clinical translation, a first in airway tissue engineering. To further this therapy toward clinical translation, we validated the eCPCs-MEND grafts in a New Zealand white rabbit LTR model. Our results demonstrated airway expansion, graft re-epitheliazation, neocartilage formation, and integration with adjacent native laryngotracheal cartilage, notably at a higher degree than the standard of care of autologous costal cartilage. No instances of adverse events of extrusion, granulation, infection, or calcification were observed in any of the 38 rabbits of our 3 months study. These results demonstrate the feasibility of our translational tissue engineering approach to laryngotracheal reconstruction and could overcome the autograft-associated limitations in pediatric patients and a decrease the risk of invasive revision surgery.

bioengineering↗