[89Zr]Oxinate4 for long-term in vivo cell tracking by positron emission tomography

Purpose 111In (typically as [111In]oxinate3) is a gold standard radiolabel for cell tracking in humans by scintigraphy. A long half-life positron-emitting radiolabel to serve the same purpose using positron emission tomography (PET) has long been sought. We aimed to develop an 89Zr PET tracer for cell labelling and compare it with [111In]oxinate3 single photon emission computed tomography (SPECT). Methods [89Zr]Oxinate4 was synthesised and its uptake and efflux were measured in vitro in three cell lines and in human leukocytes. The in vivo biodistribution of eGFP-5T33 murine myeloma cells labelled using [89Zr]oxinate4 or [111In]oxinate3 was monitored for up to 14 days. 89Zr retention by living radiolabelled eGFP-positive cells in vivo was monitored by FACS sorting of liver, spleen and bone marrow cells followed by gamma counting. Results Zr labelling was effective in all cell types with yields comparable with 111In labelling. Retention of 89Zr in cells in vitro after 24 h was significantly better (range 71 to >90 %) than 111In (43–52 %). eGFP-5T33 cells in vivo showed the same early biodistribution whether labelled with 111In or 89Zr (initial pulmonary accumulation followed by migration to liver, spleen and bone marrow), but later translocation of radioactivity to kidneys was much greater for 111In. In liver, spleen and bone marrow at least 92 % of 89Zr remained associated with eGFP-positive cells after 7 days in vivo. Conclusion [89Zr]Oxinate4 offers a potential solution to the emerging need for a long half-life PET tracer for cell tracking in vivo and deserves further evaluation of its effects on survival and behaviour of different cell types

Spatial dynamics and mixing of bluefin tuna in the Atlantic Ocean and Mediterranean Sea revealed using next generation sequencing

The Atlantic bluefin tuna is a highly migratory species emblematic of the challenges associated with shared fisheries management. In an effort to resolve the species’ stock dynamics, a genomewide search for spatially informative single nucleotide polymorphisms (SNPs) was undertaken, by way of sequencing reduced representation libraries. An allele frequency approach to SNP discovery was used, combining the data of 555 larvae and young-of-the-year (LYOY) into pools representing major geographical areas and mapping against a newly assembled genomic reference. From a set of 184,895 candidate loci, 384 were selected for validation using 167 LYOY. A highly discriminatory genotyping panel of 95 SNPs was ultimately developed by selecting loci with the most pronounced differences between western Atlantic and Mediterranean Sea LYOY. The panel was evaluated by genotyping a different set of LYOY (n = 326), and from these, 77.8% and 82.1% were correctly assigned to western Atlantic and Mediterranean Sea origins, respectively. The panel revealed temporally persistent differentiation among LYOY from the western Atlantic and Mediterranean Sea (FST = 0.008, p = .034). The composition of six mixed feeding aggregations in the Atlantic Ocean and Mediterranean Sea was characterized using genotypes from medium (n = 184) and large (n = 48) adults, applying population assignment and mixture analyses. The results provide evidence of persistent population structuring across broad geographic areas and extensive mixing in the Atlantic Ocean, particularly in the mid-Atlantic Bight and Gulf of St. Lawrence. The genomic reference and genotyping tools presented here constitute novel resources useful for future research and conservation efforts

Molecular Identification of Atlantic Bluefin Tuna (Thunnus thynnus, Scombridae) Larvae and Development of a DNA Character-Based Identification Key for Mediterranean Scombrids

The Atlantic bluefin tuna, Thunnus thynnus, is a commercially important species that has been severely over-exploited in the recent past. Although the eastern Atlantic and Mediterranean stock is now showing signs of recovery, its current status remains very uncertain and as a consequence their recovery is dependent upon severe management informed by rigorous scientific research. Monitoring of early life history stages can inform decision makers about the health of the species based upon recruitment and survival rates. Misidentification of fish larvae and eggs can lead to inaccurate estimates of stock biomass and productivity which can trigger demands for increased quotas and unsound management conclusions. Herein we used a molecular approach employing mitochondrial and nuclear genes (CO1 and ITS1, respectively) to identify larvae (n = 188) collected from three spawning areas in the Mediterranean Sea by different institutions working with a regional fisheries management organization. Several techniques were used to analyze the genetic sequences (sequence alignments using search algorithms, neighbour joining trees, and a genetic character-based identification key) and an extensive comparison of the results is presented. During this process various inaccuracies in related publications and online databases were uncovered. Our results reveal important differences in the accuracy of the taxonomic identifications carried out by different ichthyoplanktologists following morphology- based methods. While less than half of larvae provided were bluefin tuna, other dominant taxa were bullet tuna (Auxis rochei), albacore (Thunnus alalunga) and little tunny (Euthynnus alletteratus). We advocate an expansion of expertise for a new generation of morphology-based taxonomists, increased dialogue between morphology-based and molecular taxonomists and increased scrutiny of public sequence databases.Versión del editor4,411

SNP_flanking_sequences and alleles_from_GadMor_May2010_alignment

SNP flanking sequences and alleles from GadMor_May2010_alignment (Star B, et al. Nature 2011 Aug 10)

SNP_flanking_sequences_and_alleles_from_gadMor2_alignment

SNP flanking sequences and alleles from alignment with gadMor2 annotated genome assembly by Tørresen et al. 2017 (https://doi.org/10.6084/m9.figshare.3408247.v3)

Puncher_2019_NorthernSpawningCod_240IND_5077SNP

Genepop file containing genotypes (5,077 SNPs) of 240 adult Atlantic Cod (Gadus morhua) captured in the Northeastern Atlantic Ocean (2J3KL4VX). DNA was prepared using a ddRAD protocol and 125PE sequenced 60-96 individuals/lane on an Illumina HiSeq2500. SNPs were selected using STACKS and various software described in "Chromosomal inversions in the Atlantic cod genome: implications for management of Canada’s Northern cod stock." Please refer to publication for individual codes

Back to the future: What population genomics and paleogenomics reveal on spatio- temporal stock structure, connectivity and adaptation in the Atlantic bluefin tuna

A genotyping-by-sequencing approach was used to discover SNPs throughout the Atlantic Bluefin tuna genome while simultaneously analyzing population structure in the Gulf of Mexico, Atlantic and Mediterranean, including several previously uncharacterized sites. Genotyping revealed temporally persistent differentiation among baseline, early life stage samples from the western Atlantic and Mediterranean using panels of 80 and 25 SNPs (FST = 0.0091, p<0.001 and FST = 0.028, p<0.001, respectively) and an average self-assignment success rate of 83.8%. No clear pattern of structuring was detected among Mediterranean samples. The assignment (overall probability 82.2%) and mixture analyses of mixed feeding aggregations in the Atlantic Ocean and Mediterranean revealed an extensive mixing in the Atlantic Ocean, particularly in the Gulf of St. Lawrence, as well as a poleward shift in the distribution of eastern migrants in the Western Atlantic and ontogeny-dependent migratory behavior. Parallel ongoing researches are also exploiting Bluefin paleogenomic resources retrieved from Atlantic, Mediterranean and Marmara-Black Sea historical remains from late Iron Age, Ancient Roman, Byzantine and modern eras. Significant differences in geographic and temporal SNP allele frequencies are revealed at several functional genes. By comparing the contemporary and historical genetic codes we are making efforts to shed light on the evolution of the species genome in response to nearly two millennia of fisheries pressure, a changing climate and pollution of the sea