Biology subjects

Reed, K.

Publications and source records attributed to Reed, K..

3 recordsLinked to original sources

bioRxiv2026

Cell-specific dedifferentiation in Arabidopsis thaliana

Single somatic plant cells are capable of dedifferentiation and reversion to totipotency. However, understanding of dedifferentiation remains incomplete, limiting efforts to reprogram plant cell identities with engineered properties. Here, we describe the transcriptional dynamics of 125,091 Arabidopsis thaliana whole seedling protoplasts along a time course of dedifferentiation and varied chemical perturbations using single-cell RNA sequencing. We observed widespread cell-type-specific transcriptional reprogramming concomitant with cell wall digestion, including a guard cell-specific somatic embryogenic-like program initiated by ectopic LEC2 expression. Contrasting cell states between chemical perturbations across real time revealed that phytohormones antagonize cell aging, promote retention of transcriptional diversity, and selectively suppress wound responses. By dissecting time-resolved transcriptional dynamics, we discovered that dedifferentiation is accompanied by the activation of stem-cell and meristematic marker genes and associated with prevalent chromatin remodeling. Despite discovery of a shared regulatory program underlying early dedifferentiation, temporal modeling of diverse somatic cell types uncovered extensive bias in dedifferentiation potential, including epithem-derived dedifferentiated cells, variable dedifferentiation rates, and diversity in early reprogramming outcomes as a major source of in vitro heterogeneity. Taken together, these data showcase how initial somatic cell identity, phytohormone signaling, chromatin remodeling, and reprogramming heterogeneity combine to coordinate the early transcriptional events defining cellular dedifferentiation.

plant biology↗

bioRxiv2024

Purified diets containing high levels of soluble fiber and grain-based diets promote similar gastrointestinal morphometry yet distinct microbial communities

Grain-based diets (GBDs) are widely used in rodent studies but their utility is limited due to batch-to-batch variability resulting from inconsistent ingredients. Purified diets (PDs) are composed of only known and refined ingredients and offer a solution to the constraints of GBDs. However, unlike GBDs, PDs commonly used as control diets typically contain little to no soluble fiber. We therefore sought to identify a combination of fibers in PDs that best recapitulates the gastrointestinal morphometry and intestinal microbial composition of mice fed GBDs. Adult male mice (n=30) were randomly assigned to one of six diets--two GBDs and four PDs with varying insoluble and soluble fiber composition--for 28 days. 16S rRNA gene sequencing was used to compare microbial profiles across different gastrointestinal (GI) niches and diets. Gut microbiotas and cecal weights were distinct between mice fed the two GBDs, indicating that GBDs are unreliable controls in diet-based studies. Unexpectedly, intestinal microbial richness decreased as the amount of soluble fiber in the PDs increased and the addition of multiple soluble fibers did not rescue this effect. Mice fed PDs with high soluble fiber content ([≥] 75% of dietary fiber was soluble fiber) best recapitulated GI morphometry of mice fed GBDs, but intestinal microbial communities were distinct between PD- and GBD-fed mice. Although supplementing PDs with soluble fiber improved GI morphometry, further research to determine the optimal mixture of soluble and insoluble fibers is required to more closely mirror the intestinal microbial diversity observed in mice fed GBDs. ImportanceDietary fibers are essential for maintaining gut health. Insoluble fibers aid in fecal bulking and water retention while soluble fiber is a fermentative substrate for intestinal microbial communities. GBDs are commonly used in preclinical research but the variability in ingredients across batches impedes reproducibility. PDs, which are composed of highly refined ingredients, pose a potential solution but the most widely used low-fat control PDs contain no soluble fiber. This study intended to identify a PD with a combination of fibers that promotes murine gut health and microbial diversity. A PD with optimal fiber composition would aid in the standardization and reproducibility of studies investigating intestinal physiology and the gut microbiota.

microbiology↗

bioRxiv2019

APC2 is Critical for Ovarian WNT Signalling Control, Fertility and Tumour Suppression

Canonical WNT signalling plays a critical role in the regulation of ovarian development; mis-regulation of this key pathway in the adult ovary is associated with subfertility and tumourigenesis. The roles of Adenomatous polyposis coli 2 (APC2), a little-studied WNT signalling pathway regulator, in ovarian homeostasis, fertility and tumourigenesis have not previously been explored. Here, we demonstrate for the first time using constitutive APC2-knockout (Apc2-/-) mice, essential roles of APC2 in regulating ovarian WNT signalling and ovarian homeostasis. APC2-deficiency resulted in activation of ovarian WNT signalling and sub-fertility driven by intra-ovarian defects. Follicular growth was perturbed, resulting in a reduced rate of ovulation and corpora lutea formation, which could not be rescued by administration of gonadotrophins. Defects in steroidogenesis and follicular vascularity contributed to the subfertility phenotype. Tumour incidence was assessed in aged APC2-deficient mice, which also carried a hypomorphic Apc allele. APC2-deficiency in these mice resulted in predisposition to granulosa cell tumour (GCT) formation, accompanied by acute tumour-associated WNT-signalling activation and a histologic pattern and molecular signature seen in human adult GCTs. Hence, APC2 has an important tumour-suppressor activity within ovarian granulosa cells, most likely due to its role in regulating WNT-signalling. Importantly, given that the APC2-deficient tumours recapitulate the molecular signature and histological features of human adult GCTs, this APC2-deficient mouse has excellent potential as a pre-clinical model to study ovarian tumour biology and for therapeutic testing.

cancer biology↗