• Why barcode? High-throughput multiplex sequencing of mitochondrial genomes for molecular systematics

      Timmermans, MJTN; Dodsworth, S; Culverwell, CL; Bocak, L; Ahrens, D; Littlewood, T; Pons, J; Vogler, AP (Oxford University Press (OUP), 2010-09-28)
      Mitochondrial genome sequences are important markers for phylogenetics but taxon sampling remains sporadic because of the great effort and cost required to acquire full-length sequences. Here, we demonstrate a simple, cost-effective way to sequence the full complement of protein coding mitochondrial genes from pooled samples using the 454/Roche platform. Multiplexing was achieved without the need for expensive indexing tags (‘barcodes’). The method was trialled with a set of long-range polymerase chain reaction (PCR) fragments from 30 species of Coleoptera (beetles) sequenced in a 1/16th sector of a sequencing plate. Long contigs were produced from the pooled sequences with sequencing depths ranging from ∼10 to 100× per contig. Species identity of individual contigs was established via three ‘bait’ sequences matching disparate parts of the mitochondrial genome obtained by conventional PCR and Sanger sequencing. This proved that assembly of contigs from the sequencing pool was correct. Our study produced sequences for 21 nearly complete and seven partial sets of protein coding mitochondrial genes. Combined with existing sequences for 25 taxa, an improved estimate of basal relationships in Coleoptera was obtained. The procedure could be employed routinely for mitochondrial genome sequencing at the species level, to provide improved species ‘barcodes’ that currently use the cox1 gene only.
    • Yeomanite, Pb2O(OH)Cl, a new chain-structured Pb oxychloride from Merehead Quarry, Somerset, England

      Turner, RW; Siidra, OI; Rumsey, MS; Polekhovsky, YS; Kretser, YL; Krivovichev, SV; Spratt, J; Stanley, Christopher (2015-10)
    • Zinc isotopic compositions of breast cancer tissue

      Larner, F; Woodley, LN; Shousha, S; Moyes, A; Halliday, AN; Rehkämper, M; Coombes, RC; Strekopytov, S; Humphreys-Williams, Emma (The Royal Society of Chemistry, 2014-12-01)
      An early diagnostic biomarker for breast cancer is essential to improve outcome. High precision isotopic analysis, originating in Earth sciences, can detect very small shifts in metal pathways. For the first time, the natural intrinsic Zn isotopic compositions of various tissues in breast cancer patients and controls were determined. Breast cancer tumours were found to have a significantly lighter Zn isotopic composition than the blood, serum and healthy breast tissue in both groups. The Zn isotopic lightness in tumours suggests that sulphur rich metallothionein dominates the isotopic selectivity of a breast tissue cell, rather than Zn-specific proteins. This reveals a possible mechanism of Zn delivery to Zn-sequestering vesicles by metallothionein, and is supported by a similar signature observed in the copper isotopic compositions of one breast cancer patient. This change in intrinsic isotopic compositions due to cancer has the potential to provide a novel early biomarker for breast cancer.
    • Zircon-hosted apatite inclusions: A powerful tool for reconstruction of Cl contents in melts

      Tuffield, L; Buret, Y; Large, S; Spratt, J; Wilkinson, JJ (Mineral Deposits Studies Group, 2020-01)
      Chlorine in the exsolved volatile phase plays an important role in complexing with metals in the extraction and concentration of metals in magmatic-hydrothermal ore deposits. Therefore, tracking the concentration and evolution of Cl in the parent melt is of particular importance in understanding how such deposits form. In theory, the incorporation of Cl into apatite could be used to track the volatile content of melts; however, low closure temperatures and the rapid diffusion of halogens in apatite make it susceptible to sub-solidus re-equilibration by later thermal events and hydrothermal fluids. This susceptibility compromises its ability to retain the primary halogen signature. However, the common occurrence of apatite as an inclusion phase in zircon crystals, together with the refractory nature of zircon, open up the possibility that such inclusions may preserve primary Clmelt compositions [1]. The Rio-Blanco-Los Bronces porphyry copper district is located in central Chile and hosts several world class porphyry copper deposits as well as barren intrusions [2]. This makes it an excellent area for an investigation of the role of Clmelt in the formation of porphyry copper deposits, as well as the effect of sub-solidus re-equilibration of Cl in apatite. For this study we analysed apatite crystals that occur both in the groundmass and as inclusions in zircons in four samples from the Los Bronces porphyry copper district using EPMA for halogen and major elements and LA-ICP-MS for trace elements. These samples include a barren intrusion unrelated to mineralisation that precedes mineralisation by around 10 Ma, and pre-, syn- and post-mineralisation porphyries. Apatite inclusions hosted in zircon crystals typically exhibit a large range in Cl concentrations (<0.5 –2.5 wt.% Cl), with all inclusion data exhibiting polymodal distributions of Cl concentrations. By contrast, groundmass apatites from all samples are characterised by uniformly low Cl concentrations (<0.5 wt.% Cl). These results are consistent with the apatite crystals in the groundmass having experienced sub-solidus re-equilibration related to the pervasive hydrothermal alteration in the district. The wide range in Cl concentrations recorded by the apatite inclusions is interpreted to reflect changing Clmelt for the duration of apatite and zircon crystallisation, perhaps linked to volatile saturation and preferential partitioning of Cl into the aqueous phase. Additionally, the apatites hosted in zircon crystals show significant inter-sample variations, evolving from low Cl concentration (<0.5 wt. % Cl) in the barren intrusion, to higher Cl concentrations (0.5 – 2.5 wt.% Cl) in the samples closely temporally associated with porphyry Cu mineralisation. These data suggest that Clmelt was significantly higher (0.05 – 0.40 wt.% Clmelt) in the melts associated with porphyry copper mineralisation compared with the precursor barren magmatism (~0.04 wt.% Clmelt) [3]. We conclude that due to the rapid diffusion of halogens in apatite in the presence of melt or hydrothermal fluid, the study of apatite inclusions hosted in zircon crystals is required to reconstruct primary melt compositions and to track the evolution of Cl concentrations in porphyry-forming magmas. This study reveals high Clmelt concentrations in the magmas related to mineralisation in the Los Bronces district, a property that would have facilitated the efficient extraction and concentration of metals. References: [1] Brugge, E. et al. (2019). Proc. 15th SGA Biennial Meeting, Vol. 2, 983-986. [2] Toro, J.C. et al. (2012). SEG Special Publication 16:105-126. [3] Li, H. and Hermann, J. (2017) Am. Mineral. 102:580-594.