Biology subjects

Tracey, D.

Publications and source records attributed to Tracey, D..

5 recordsLinked to original sources

bioRxiv2024

Regional Variations in Live Proportions of Southwest Pacific Cold-Water Coral Solenosmilia variabilis Reefs

Reef-building cold-water-corals (CWC) form deep-sea habitats that can create biodiversity hotspots. As live coral and dead intact framework provide disparate ecosystem services and are vulnerable to different anthropogenic stressors, it is important to quantify the proportions of each on CWC reefs. We analysed 1,160 images of Solenosmilia variabilis reefs at four sites off New Zealand (Valerie and Forde Guyots at the Louisville Seamount Chain & Ghoul and Gothic Seamounts at the Graveyard Seamount Complex) to determine the ratio of live coral to the whole reef area (termed live:reef). We found live:reef ratios are significantly different between sites at the offshore Louisville Seamount Chain and onshore Graveyard Seamount Complex. This could be driven by reef position relative to the aragonite saturation horizon (ASH) as corals in the Louisville Seamount Chain live below the ASH in colder and deeper waters than those at the Graveyard Seamount Complex, which live above the ASH. In the southwest Pacific, depth is a driver of live:reef ratios, with a larger proportion of live coral at shallow depths and dead intact framework at deeper depths. The live:reef ratios at Gothic Seamount within the Graveyard Seamount Complex remained stable between 2015 and 2020 despite significant differences in live coral, dead intact framework, and reef structure surface area. Our results indicate live:reef ratios can be used to estimate the amount of dead intact framework threatened by shoaling ASH due to ocean acidification at each site, which can help inform which sites could be protected as possible climate change refugia.

ecology↗

bioRxiv2022

Transcriptome-wide analysis of pseudouridylation in Drosophila melanogaster

Pseudouridine (Psi) is one of the most frequent post-transcriptional modification of RNA. Enzymatic Psi modification occurs on rRNA, snRNA, snoRNA, tRNA, non-coding RNA and has recently been discovered on mRNA. Transcriptomewide detection of Psi (Psi-seq) has yet to be performed for the widely studied model organism Drosophila melanogaster. Here, we optimized Psi-seq analysis for this species and have identified thousands of Psi modifications throughout the female fly head transcriptome. We find that Psi is widespread on both cellular and mitochondrial rRNAs. In addition, more than a thousand Psi sites were found on mRNAs. When pseudouridylated, mRNAs frequently had many Psi sites. Many mRNA Psi sites are present in genes encoding for ribosomal proteins, and many are found in mitochondrial encoded RNAs, further implicating the importance of pseudouridylation for ribosome and mitochondrial function. The 7SLRNA of the signal recognition particle is the non-coding RNA most enriched for Psi. The three mRNAs most enriched for Psi encode highly-expressed yolk proteins (Yp1, Yp2, Yp3). By comparing the pseudouridine profiles in the RluA-2 mutant and the w1118 control genotype, we identified Psi sites that were missing in the mutant RNA as potential RluA-2 targets. Finally, differential gene expression analysis of the mutant transcriptome indicates a major impact of loss of RluA-2 on the ribosome and translational machinery.

genomics↗

bioRxiv2021

DROP: Molecular voucher database for identification of Drosophila parasitoids

Molecular identification is increasingly used to speed up biodiversity surveys and laboratory experiments. However, many groups of organisms cannot be reliably identified using standard databases such as GenBank or BOLD due to lack of sequenced voucher specimens identified by experts. Sometimes a large number of sequences are available, but with too many errors to allow identification. Here we address this problem for parasitoids of Drosophila by introducing a curated open-access molecular reference database, DROP (Drosophila parasitoids). Identifying Drosophila parasitoids is challenging and poses a major impediment to realize the full potential of this model system in studies ranging from molecular mechanisms to food webs, and in biological control of Drosophila suzukii. In DROP (http://doi.org/10.5281/zenodo.4519656), genetic data are linked to voucher specimens and, where possible, the voucher specimens are identified by taxonomists and vetted through direct comparison with primary type material. To initiate DROP, we curated 154 laboratory strains, 856 vouchers, 554 DNA sequences, 16 genomes, 14 transcriptomes, and 6 proteomes drawn from a total of 183 operational taxonomic units (OTUs): 114 described Drosophila parasitoid species and 69 provisional species. We found species richness of Drosophila parasitoids to be heavily underestimated and provide an updated taxonomic catalogue for the community. DROP offers accurate molecular identification and improves cross-referencing between individual studies that we hope will catalyze research on this diverse and fascinating model system. Our effort should also serve as an example for researchers facing similar molecular identification problems in other groups of organisms.

genomics↗

bioRxiv2018

Proprioceptive neurons of larval Drosophila melanogaster show direction selective activity requiring the mechanosensory channel TMC.

Drosophila Transmembrane channel-like (Tmc) is a protein that functions in larval proprioception. The closely related TMC1 protein is required for mammalian hearing, and is a pore forming subunit of the hair cell mechanotransduction channel. In hair cells, TMC1 is gated by small deflections of microvilli that produce tension on extracellular tip-links that connect adjacent villi. How Tmc might be gated in larval proprioceptors, which are neurons having a morphology that is completely distinct from hair cells, is unknown. Here, we have used high-speed confocal microscopy to both measure displacements of proprioceptive sensory dendrites during larval movement, and to optically measure neural activity of the moving proprioceptors. Unexpectedly, the pattern of dendrite deformation for distinct neurons was unique and differed depending on the direction of locomotion: ddaE neuron dendrites were strongly curved by forward locomotion while the dendrites of ddaD were more strongly deformed by backward locomotion. Furthermore, GCaMP6f calcium signals recorded in the proprioceptive neurons during locomotion indicated tuning to the direction of movement. ddaE showed strong activation during forward locomotion while ddaD showed responses that were strongest during backwards locomotion. Peripheral proprioceptive neurons in animals mutant for Tmc showed a near complete loss of movement related calcium signals. As the strength of the responses of wild type animals was correlated with dendrite curvature, we propose that Tmc channels may be activated by membrane curvature in dendrites that are exposed to strain. Our findings begin to explain how distinct cellular systems rely on a common molecular pathway for mechanosensory responses.

neuroscience↗

bioRxiv2017

The Drosophila SK potassium channel negatively regulates nociception.

Inhibition of nociceptor activity is important for the prevention of spontaneous pain and hyperalgesia. To identify the critical K+ channels that regulate nociceptor excitability we performed a forward genetic screen using a Drosophila larval nociception paradigm. Knockdown of three K+ channel loci, the small conductance calcium-activated potassium channel (SK), seizure and tiwaz, resulted in marked hypersensitive nociception behaviors. In more detailed studies of SK, we found that hypersensitive phenotypes could be recapitulated with a genetically null allele. Importantly, the null mutant phenotype could be rescued with tissue specific expression of an SK cDNA in nociceptors. Optical recordings from nociceptive neurons showed a significant increase in mechanically activated Ca2+ signals in SK mutant nociceptors. SK showed expression in peripheral neurons. Interestingly SK proteins localized to axons of these neurons but were not detected in dendrites. Our findings suggest a major role for SK channels in the regulation of nociceptor excitation and they are inconsistent with the hypothesis that the important site of action is within dendrites.\n\nHighlights-Specific potassium channels regulate nociceptor excitability.\n-SK channels have a critical function in nociception.\n-SK channels specifically localize to sensory axons\n-SK channels are not detectable in sensory dendrites.

neuroscience↗