Biology subjects

Edwards, M. D.

Publications and source records attributed to Edwards, M. D..

3 recordsLinked to original sources

bioRxiv2024

Combined transcriptomic, connectivity, and activity profiling of the medial amygdala using highly amplified multiplexed in situ hybridization (hamFISH)

In situ transcriptomic technologies provide a promising avenue to link gene expression, connectivity, and physiological properties of neural cell types. Commercialized methods that allow the detection of hundreds of genes in situ, however, are expensive and therefore typically used for generating unimodal reference data rather than for resource-intensive multimodal analyses. A major bottleneck is the lack of a routine means to efficiently generate cell type data. Here, we have developed hamFISH (highly amplified multiplexed fluorescence in situ hybridization), which enables the sequential detection of 32 genes using multiplexed branched DNA amplification. We used hamFISH to profile the projection, activity, and transcriptomic diversity of the medial amygdala (MeA), a critical node for innate social and defensive behaviors in mice. In total, we profiled 643,834 cells and classified neurons into 16 inhibitory and 10 excitatory types, many of which were found to be spatially clustered. We then examined the organization of outputs of these cells and activation profiles during different social contexts. Therefore, by facilitating multiplexed detection of single molecule RNAs, hamFISH provides a streamlined and versatile platform for multimodal profiling of specific brain nuclei.

neuroscience↗

bioRxiv2024

Draft genome of Palmaria palmata and intraspecific genetic variations in the North-East Atlantic

The rhodophyte Palmaria palmata (L.) Weber & Mohr is one of the target species of a growing European seaweed industry due to its high content of protein and essential amino acids which makes it suitable for human food, dietary supplements, and as salmon feed. However, the lack of a published nuclear genome limits phylogenetics analyses and gene function investigations which could help the development of a breeding programme. We present the first draft genome of P. palmata that was obtained with PacBio HiFi long read sequencing with average coverage of 10x, consisting of an assembly of 1.05 Gb, N50=2.75Mb and BUSCO completeness of 72.1%. Additionally, a population study on the whole genome of 33 P. palmata individuals from across the Northern East Atlantic area found three main clusters consistent with their geographic distribution: (1) Denmark and Norway, (2) France and western Ireland, (3) Faroe Islands. All individuals from Northern Ireland share ancestry with western Ireland and Denmark, and some individuals from the Faroe Islands show admixture from Faroe, western Ireland and Northern Ireland. These results represent a fundamental step towards breeding and genetic studies to further explore the vastly unexploited economic potential of Palmaria palmata. Highlights- We report the first draft genome of Palmaria palmata, from PacBio HiFi long reads. - The size of the genome, 1.05 Gb, is among the largest so far among the Rhodophyta. - Busco completeness of 72.1% and contig N50 of 2.75 Mb indicate good quality. - The genomes of 33 more individuals from North Atlantic Europe have been sequenced. - Phylogenetic analysis found three clusters consistent with geographic distribution.

genomics↗

bioRxiv2020

CRYPTOCHROMES confer robustness, not rhythmicity, to circadian timekeeping

SummaryCircadian (approximately daily) rhythms are a pervasive property of mammalian cells, tissues, and behaviour, ensuring physiological and metabolic adaptation to solar time. Models of daily cellular timekeeping revolve around transcriptional feedback repression, whereby CLOCK and BMAL1 activate the expression of clock proteins PERIOD (PER) and CRYPTOCHROME (CRY), which in turn repress CLOCK/BMAL1 activity. CRY proteins are thus considered essential negative regulators of the oscillation; a function supported by behavioural arrhythmicity of CRY-deficient mice when kept under constant conditions. Challenging this interpretation, however, we find evidence for persistent circadian rhythms in mouse behaviour and cellular PER2 levels when CRY is absent. CRY-less oscillations are variable in their expression and have a shorter period than wild type controls. Importantly, we find classic circadian hallmarks such as temperature compensation and determination of period by casein kinase 1{delta}/{varepsilon} activity to be maintained. In the absence of CRY-mediated transcriptional feedback repression and rhythmic Per2 transcription, PER2 protein rhythms are sustained for several cycles, accompanied by circadian variation in protein stability. We suggest that, whereas circadian transcriptional feedback imparts robustness and functionality onto biological clocks, the core timekeeping mechanism is post-translational. Our findings suggest that PER proteins normally act as signalling hubs that transduce timing information to the nucleus, imparting daily rhythms upon the activity of transcriptional effectors. Highlights[tpltrtarr] PER/CRY-mediated negative feedback is dispensable for mammalian circadian timekeeping [tpltrtarr]Circadian variation in PER2 levels persists in the absence of rhythmic Per2 transcription [tpltrtarr]CK1 and GSK3 are plausible mechanistic components of a cytoscillator mechanism [tpltrtarr]CRY-mediated feedback repression imparts robustness to biological timekeeping In briefCircadian turnover of mammalian clock protein PERIOD2 persists in the absence of canonical transcriptional feedback repression and rhythmic clock gene activity, demanding a re-evaluation of cellular clock function and evolution.

cell biology↗