Using bio-physical modelling and population genetics for conservation and management of an exploited species, Pecten maximus L.

This is the final version. Available on open access from Wiley via the DOI in this recordData availability statement: The microsatellite data along with the site location data that support the findings of this study are openly available in FigShare at https://doi.org/10.6084/m9.figshare.12907430Connectivity between populations is important when considering conservation or the management of exploitation of vulnerable species. We investigated how populations of a broadcast-spawning marine species (scallop, Pecten maximus) that occur in discrete geographic locations were connected to each other. Population genetic insights were related to the outputs from a three-dimensional hydrodynamic model implemented with scallop larval behaviour to understand the extent to which these areas were linked by oceanographic processes and how this was altered by season and two contrasting years that had strongly different average temperature records (warm vs cold) to provide contrasting oceanographic conditions. Our results span from regional to shelf scale. Connectivity was high at a regional level (e.g. northern Irish Sea), but lower at scales >100 km between sites. Some localities were possibly isolated thus dependent on self-recruitment to sustain local populations. Seasonal timing of spawning and inter-annual fluctuations in seawater temperature influenced connectivity patterns, and hence will affect spatial recruitment. Summer rather than spring spawning increased connectivity among some populations, due to the seasonal strengthening of temperature-driven currents. Furthermore, the warm year resulted in higher levels of modelled connectivity than the cold year. The combination of genetic and oceanographic approaches provided valuable insights into the structure and connectivity at a continental shelf scale. This insight provides a powerful basis for defining conservation management units and the appropriate scale for spatial management. Temporal fluctuations in temperature impact upon variability in connectivity, suggesting that future work should account for ocean warming when investigating population resilience.Isle of Man GovernmentEuropean Fisheries FundEuropean Union Regional Development Fun

Investigating the effect of available redox protein ratios for the conversion of a steroid by a myxobacterial CYP260A1

Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/136683/1/feb212619.pdfhttps://deepblue.lib.umich.edu/bitstream/2027.42/136683/2/feb212619_am.pd

Ageing European lobsters (Homarus gammarus) using DNA methylation of evolutionarily conserved ribosomal DNA.

Crustaceans are notoriously difficult to age because of their indeterminate growth and the moulting of their exoskeleton throughout life. The poor knowledge of population age structure in crustaceans therefore hampers accurate assessment of population dynamics and consequently sustainable fisheries management. Quantification of DNA methylation of the evolutionarily conserved ribosomal DNA (rDNA) may allow for age prediction across diverse species. However, the rDNA epigenetic clock remains to be tested in crustaceans, despite its potential to inform both ecological and evolutionary understanding, as well as conservation and management practices. Here, patterns of rDNA methylation with age were measured across 5154 bp of rDNA corresponding to 355 quality-filtered loci in the economically important European lobster (Homarus gammarus). Across 0- to 51-month-old lobsters (n = 155), there was a significant linear relationship between age and percentage rDNA methylation in claw tissue at 60% of quality-filtered loci (n = 214). An Elastic Net regression model using 46 loci allowed for the accurate and precise age estimation of individuals (R 2 = 0.98; standard deviation = 1.6 months). Applying this ageing model to antennal DNA from wild lobsters of unknown age (n = 38) resulted in predicted ages that are concordant with estimates of minimum size at age in the wild (mean estimated age = 40.1 months; range 32.8–55.7 months). Overall, the rDNA epigenetic clock shows potential as a novel, nonlethal ageing technique for European lobsters. However, further validation is required across a wider range of known-age individuals and tissue types before the model can be used in fisheries management

Electron transfer ferredoxins with unusual cluster binding motifs support secondary metabolism in many bacteria

The proteins responsible for controlling electron transfer in bacterial secondary metabolism are not always known or characterised. Here we demonstrate that many bacteria contain a set of unfamiliar ferredoxin encoding genes which are associated with those of cytochrome P450 (CYP) monooxygenases and as such are involved in anabolic and catabolic metabolism. The model organism Mycobacterium marinum M contains eleven of these genes which encode [3Fe–4S] or [4Fe–4S] single cluster containing ferredoxins but which have unusual iron–sulfur cluster binding motif sequences, CXX?XXC(X)nCP, where ‘?’ indicates a variable amino acid residue. Rather than a cysteine residue, which is highly conserved in [4Fe–4S] clusters, or alanine or glycine residues, which are common in [3Fe–4S] ferredoxins, these genes encode at this position histidine, asparagine, tyrosine, serine, threonine or phenylalanine. We have purified, characterised and reconstituted the activity of several of these CYP/electron transfer partner systems and show that all those examined contain a [3Fe–4S] cluster. Furthermore, the ferredoxin used and the identity of the variable motif residue in these proteins affects the functionality of the monooxygenase system and has a significant influence on the redox properties of the ferredoxins. Similar ferredoxin encoding genes were identified across Mycobacterium species, including in the pathogenic M. tuberculosis and M. ulcerans, as well as in a wide range of other bacteria such as Rhodococcus and Streptomyces. In the majority of instances these are associated with CYP genes. These ferredoxin systems are important in controlling electron transfer across bacterial secondary metabolite production processes which include antibiotic and pigment formation among others