Biology subjects

Bell, D.

Publications and source records attributed to Bell, D..

3 recordsLinked to original sources

bioRxiv2018

Environmental DNA for the enumeration and management of Pacific salmon

Pacific salmon are a keystone resource in Alaska, generating annual revenues of well over [~]US$500 million/yr. Due to their anadromous life history, adult spawners distribute amongst thousands of streams, posing a huge management challenge. Currently, spawners are enumerated at just a few streams because of reliance on human counters and, rarely, sonar. The ability to detect organisms by shed tissue (environmental DNA, eDNA) promises a more efficient counting method. However, although eDNA correlates generally with local fish abundances, we do not know if eDNA can accurately enumerate salmon. Here we show that daily, and near-daily, flow-corrected eDNA rate closely tracks daily numbers of returning sockeye and coho spawners and outmigrating sockeye smolts. eDNA thus promises accurate and efficient enumeration, but to deliver the most robust numbers will need higher-resolution stream-flow data, at-least-daily sampling, and a focus on species with simple life histories, since shedding rate varies amongst jacks, juveniles, and adults.

ecology↗

bioRxiv2017

Cell-free prototyping strategies for enhancing the sustainable production of polyhydroxyalkanoates bioplastics

The polyhydroxyalkanoates are a group of microbially-produced biopolymers that have been proposed as sustainable alternatives to several oil-derived plastics. However, polyhydroxyalkanoates are currently more expensive to produce than oil-derived plastics and therefore, more efficient production processes would be desirable. Cell-free transcription-translation-based metabolic engineering strategies have been previously used to optimise several different biosynthetic pathways but not the polyhydroxyalkanoates biosynthetic pathways. Here we have developed several Escherichia coli cell-free transcription-translation-based systems for in vitro prototyping of polyhydroxyalkanoates biosynthetic operons, and also for screening relevant metabolite recycling enzymes. These cell-free transcription-translation reactions were customised through the addition of whey permeate, an industrial waste that has been previously used as a low-cost feedstock for optimising in vivo polyhydroxyalkanoates production. We found that the inclusion of an optimal concentration of whey permeate enhanced relative cell-free GFPmut3b production by ~20% compared to control reactions that did not include whey permeate. An analysis of pH in our cell-free reactions suggests that the observed increase in GFPmut3b production was likely through enhanced ATP generation, as a consequence of the glycolytic processing of lactose present in whey permeate. We also found that whey permeate enhanced cell-free reactions produced ~3M (R)-3HB-CoA, whilst, coupled cell-free biotransformation/transcription-translation reactions produced a ten-fold greater yield of (R)-3HB-CoA. These reactions were also used to characterise a Clostridium propionicum propionyl CoA transferase enzyme that can recycle Acetyl-CoA. Together our data demonstrate that cell-free approaches can be used to complement in vivo workflows for identifying additional strategies for optimising polyhydroxyalkanoates production.

synthetic biology↗

bioRxiv2017

A cell-free synthetic biochemistry platform for raspberry ketone production

Cell-free synthetic biochemistry provides a green solution to replace traditional petroleum or agricultural based methods for production of fine chemicals. 4-(4-hydroxyphenyl)-butan-2-one, also known as raspberry ketone, is the major fragrance component of raspberry fruit and is utilised as a natural additive in the food and sports industry. Current industrial processing standards involve chemical extraction with a yield of 1-4 mg per kilo of fruit. As such its market price can fluctuate up to $20,000 per kg. Metabolic engineering approaches to synthesise this molecule by microbial fermentation have only resulted in low yields of up to 5 mg L-1. In contrast, cell-free synthetic biochemistry offers an intriguing compromise to the engineering constraints provided by the living cell. Using purified enzymes or a two-step semisynthetic route, an optimised pathway was formed for raspberry ketone synthesis leading up to 100% yield conversion. The semi-synthetic route is potentially scalable and cost-efficient for industrial synthesis of raspberry ketone.

synthetic biology↗