Biology subjects

MacDonald, B.

Publications and source records attributed to MacDonald, B..

3 recordsLinked to original sources

bioRxiv2025

Activated Notch1 Redirects CD4-Fated CD4+ CD8+ Precursors to the CD8 Lineage During Thymocyte Selection Without Causing T Cell Leukemia

Positive selection of CD4/CD8 double-positive (DP) thymocytes generates helper and cytotoxic T lineages whose CD4 or CD8 co-receptor expression matches their {beta} T cell receptor (TCR{beta}) specificity MHCII or MHCI, respectively. Notch1 signaling is critical for early T cell development and was suggested to regulate CD4/CD8 lineage determination during DP thymocyte selection. However, early studies expressing activated Notch1 in pre-DP progenitors did not resolve this question. Here we showed that CD4-Cre-mediated activation of canonical Rbpj-dependent Notch1 signalling potently skews DP selection to the CD8 lineage. We used a tamoxifen-inducible "time-stamp" model coupled with phenotypic staging to show that that activated Notch1 decreases generation of Gata3+ CD4+CD8lo selection intermediates during the earliest stages of DP selection, thereby preventing ThPOK induction and emergence of CD4 lineage cells. Finally, activated Notch1 efficiently re-directed DP thymocytes expressing MHCII-specific TCR{beta} into the CD8 lineage. These studies show that activated Notch1 acts early during DP selection to skew selection of CD4-fated, MHCII-specific DP precursors to the CD8 lineage.

immunology↗

bioRxiv2022

Optimised DNA isolation from marine sponges for natural sampler DNA (nsDNA) metabarcoding

Marine sponges have recently been recognised as natural samplers of environmental DNA (eDNA) due to their effective water filtration and their ubiquitous, sessile and regenerative nature. However, laboratory workflows for metabarcoding of sponge tissue have not been optimised to ensure that these natural samplers achieve their full potential for community survey. We used a phased approach to investigate the influence of DNA isolation procedures on the biodiversity information recovered from sponges. In Phase 1, we compared three treatments of residual ethanol preservative in sponge tissue alongside five DNA extraction protocols. The results of Phase 1 informed which ethanol treatment and DNA extraction protocol should be used in Phase 2, where we assessed the effect of starting tissue mass on extraction success and whether homogenisation of sponge tissue is required. Phase 1 results indicated that ethanol preservative may contain unique and/or additional biodiversity information to that present in sponge tissue, but blotting tissue dry generally recovered more taxa and generated more sequence reads from the wild sponge species. Tissue extraction protocols performed best in terms of DNA concentration, taxon richness and proportional read counts, but the non-commercial tissue protocol was selected for Phase 2 due to cost-efficiency and greater recovery of target taxa. In Phase 2 overall, we found that homogenisation may not be required for sponge tissue and more starting material does not necessarily improve taxon detection. These results combined provide an optimised DNA isolation procedure for sponges to enhance marine biodiversity assessment using natural sampler DNA metabarcoding.

molecular biology↗

bioRxiv2020

Dissolved organic carbon (DOC) is essential to balance the metabolic demands of four dominant North-Atlantic deepsea sponges

Sponges are ubiquitous components of various deep-sea habitats, including cold water coral reefs and deep-sea sponge grounds. Despite being surrounded by oligotrophic waters, these ecosystems are known to be hotspots of biodiversity and carbon cycling. To assess the role of sponges in the carbon cycling of deep-sea ecosystems, we studied the energy budgets of six dominant deep-sea sponges (the hexactinellid species Vazella pourtalesi, and demosponge species Geodia barretti, Geodia atlantica, Craniella zetlandica, Hymedesmia paupertas and Acantheurypon spinispinosum) in an ex situ aquarium setup. Additionally, we determined morphological metrics for all species (volume, dry weight (DW), wet weight (WW), carbon (C) content, and ash-free dry weight (AFDW)) and provide species-specific conversion factors. Oxygen (O2) removal rates averaged 3.3 {+/-} 2.8 {micro}mol O2 DWsponge h-1 (all values mean {+/-} SD), live particulate (bacterial and phytoplankton) organic carbon (LPOC) removal rates averaged 0.30 {+/-} 0.39 {micro}mol C DWsponge h-1 and dissolved organic carbon (DOC) removal rates averaged 18.70 {+/-} 25.02 {micro}mol C DWsponge h-1. Carbon mass balances were calculated for four species (V. pourtalesi, G. barretti, G. atlantica and H. paupertas) and revealed that the sponges acquired 1.3-6.6 times the amount of carbon needed to sustain their minimal respiratory demands. These results indicate that irrespective of taxonomic class, growth form, and abundance of microbial symbionts, DOC is responsible for over 90 % of the total net organic carbon removal of deep-sea sponges and allows them to sustain in otherwise food-limited environments on the ocean floor.

ecology↗