Non‐specific amplification compromises environmental DNA metabarcoding with COI

1. Metabarcoding extra-organismal DNA from environmental samples is now a key technique in aquatic biomonitoring and ecosystem health assessment. However, choice of genetic marker and primer set is a critical consideration when designing experiments, especially so when developing community standards and legislative frameworks. Mitochondrial cytochrome c oxidase subunit I (COI), the standard DNA barcode marker for animals, with its extensive reference library, taxonomic discriminatory power, and predictable sequence variation, is the natural choice for many metabarcoding applications such as the bulk sequencing of invertebrates. However, the overall utility of COI for environmental sequencing of targeted taxonomic groups has yet to be fully scrutinised. 2. Here, by using a case study of marine and freshwater fishes from the British Isles, we quantify the in silico performance of twelve mitochondrial primer pairs from COI, cytochrome b, 12S and 16S, in terms of reference library coverage, taxonomic discriminatory power, and primer universality. We subsequently test in vitro three COI primer pairs and one 12S pair for their specificity, reproducibility, and congruence with independent datasets derived from traditional survey methods at five estuarine and coastal sites in the English Channel and North Sea coast. 3. Our results show that for aqueous extra-organismal DNA at low template concentrations, both metazoan and fish-targeted COI primers perform poorly in comparison to 12S, exhibiting low levels of reproducibility due to non-specific amplification of prokaryotic and non-target eukaryotic DNAs. 4. An ideal metabarcode would have an extensive reference library for which custom primer sets can be designed for either broad assessments of biodiversity or taxon specific surveys, but unfortunately, low primer specificity hinders the use of COI, while the paucity of reference sequences is problematic for 12S. The latter, however, can be mitigated by expanding the concept of DNA barcodes to include whole mitochondrial genomes generated by genome-skimming existing tissue collections

Natural Killer Cell Signal Integration Balances Synapse Symmetry and Migration

Imaging immune surveillance by natural killer (NK) cells has revealed that integration of activating and inhibitory signals determines whether or not NK cells stop to kill the target cell or retain a migratory configuration

Whole genome sequence and manual annotation of Clostridium autoethanogenum, an industrially relevant bacterium

Clostridium autoethanogenum is an acetogenic bacterium capable of producing high value commodity chemicals and biofuels from the C1 gases present in synthesis gas. This common industrial waste gas can act as the sole energy and carbon source for the bacterium that converts the low value gaseous components into cellular building blocks and industrially relevant products via the action of the reductive acetyl-CoA (Wood-Ljungdahl) pathway. Current research efforts are focused on the enhancement and extension of product formation in this organism via synthetic biology approaches. However, crucial to metabolic modelling and directed pathway engineering is a reliable and comprehensively annotated genome sequence

Palladium catalyzed arylation reactions of meta photocycloadducts

We describe the first application of a Heck arylation reaction being performed on a meta photocycloadduct. The resulting arylation/fragmentation process leads to the formation of a bridged bicyclic ketone and constitutes a dramatic increase in molecular complexity after just two synthetic operations

Palladium-mediated fragmentation reactions of meta photocycloadducts to afford arylated or oxidatively cyclised products

Whilst seeking to improve the yield of a Heck-style arylation/fragmentation reaction using a silyloxy substituted meta photocycloadduct, an alternative reaction pathway was discovered that led to the formation of the unique oxidatively cyclised compound 8. This tricyclic ether is believed to form as the result of the meta photocycloadduct structure fragmenting to give a -allyl palladium species and then subsequently being displaced by a neighbouring hydroxyl group. An attempt to develop an enantioselective version of this reaction via the desymmetrisation of a meso -allyl palladium intermediate was made using the meta photocycloadduct derived from anisole and Z-but-2-ene-1,4-diol, however no enantioenrichment of the products could be detected

Palladium-mediated fragmentation of meta photocycloadducts using carbon based electrophiles: Part 1

Substituted benzene derived meta photocycloadducts have been shown to undergo a fragmentation/arylation reaction under Heck reaction conditions to give bridged bicyclo[3.2.1] compounds in a highly atom-efficient manner. When an anisole derived meta photocycloadduct is used, a bridgehead ketone is generated. However, if an alkylbenzene derived meta photocycloadduct is used, a bridgehead alkene is formed. This strategy has been used to create novel enol ether and transient allyl silane compounds