Genomic Hotspots for Adaptation: The Population Genetics of Müllerian Mimicry in the Heliconius melpomene Clade

Wing patterning in Heliconius butterflies is a longstanding example of both Müllerian mimicry and phenotypic radiation under strong natural selection. The loci controlling such patterns are “hotspots” for adaptive evolution with great allelic diversity across different species in the genus. We characterise nucleotide variation, genotype-by-phenotype associations, linkage disequilibrium, and candidate gene expression at two loci and across multiple hybrid zones in Heliconius melpomene and relatives. Alleles at HmB control the presence or absence of the red forewing band, while alleles at HmYb control the yellow hindwing bar. Across HmYb two regions, separated by ∼100 kb, show significant genotype-by-phenotype associations that are replicated across independent hybrid zones. In contrast, at HmB a single peak of association indicates the likely position of functional sites at three genes, encoding a kinesin, a G-protein coupled receptor, and an mRNA splicing factor. At both HmYb and HmB there is evidence for enhanced linkage disequilibrium (LD) between associated sites separated by up to 14 kb, suggesting that multiple sites are under selection. However, there was no evidence for reduced variation or deviations from neutrality that might indicate a recent selective sweep, consistent with these alleles being relatively old. Of the three genes showing an association with the HmB locus, the kinesin shows differences in wing disc expression between races that are replicated in the co-mimic, Heliconius erato, providing striking evidence for parallel changes in gene expression between Müllerian co-mimics. Wing patterning loci in Heliconius melpomene therefore show a haplotype structure maintained by selection, but no evidence for a recent selective sweep. The complex genetic pattern contrasts with the simple genetic basis of many adaptive traits studied previously, but may provide a better model for most adaptation in natural populations that has arisen over millions rather than tens of years

Challenge clusters facing LCA in environmental decision-making—what we can learn from biofuels

Purpose Bioenergy is increasingly used to help meet greenhouse gas (GHG) and renewable energy targets. However, bioenergy’s sustainability has been questioned, resulting in increasing use of life cycle assessment (LCA). Bioenergy systems are global and complex, and market forces can result in significant changes, relevant to LCA and policy. The goal of this paper is to illustrate the complexities associated with LCA, with particular focus on bioenergy and associated policy development, so that its use can more effectively inform policymakers. Methods The review is based on the results from a series of workshops focused on bioenergy life cycle assessment. Expert submissions were compiled and categorized within the first two workshops. Over 100 issues emerged. Accounting for redundancies and close similarities in the list, this reduced to around 60 challenges, many of which are deeply interrelated. Some of these issues were then explored further at a policyfacing workshop in London, UK. The authors applied a rigorous approach to categorize the challenges identified to be at the intersection of biofuels/bioenergy LCA and policy. Results and discussion The credibility of LCA is core to its use in policy. Even LCAs that comply with ISO standards and policy and regulatory instruments leave a great deal of scope for interpretation and flexibility. Within the bioenergy sector, this has led to frustration and at times a lack of obvious direction. This paper identifies the main challenge clusters: overarching issues, application and practice and value and ethical judgments. Many of these are reflective of the transition from application of LCA to assess individual products or systems to the wider approach that is becoming more common. Uncertainty in impact assessment strongly influences planning and compliance due to challenges in assigning accountability, and communicating the inherent complexity and uncertainty within bioenergy is becoming of greater importance. Conclusions The emergence of LCA in bioenergy governance is particularly significant because other sectors are likely to transition to similar governance models. LCA is being stretched to accommodate complex and broad policy-relevant questions, seeking to incorporate externalities that have major implications for long-term sustainability. As policy increasingly relies on LCA, the strains placed on the methodology are becoming both clearer and impedimentary. The implications for energy policy, and in particular bioenergy, are large

Structure of MHC class I-like MILL2 reveals heparan-sulfate binding and interdomain flexibility

The MILL family, composed of MILL1 and MILL2, is a group of nonclassical MHC class I molecules that occur in some orders of mammals. It has been reported that mouse MILL2 is involved in wound healing; however, the molecular mechanisms remain unknown. Here, we determine the crystal structure of MILL2 at 2.15 Å resolution, revealing an organization similar to classical MHC class I. However, the α1-α2 domains are not tightly fixed on the α3-β2m domains, indicating unusual interdomain flexibility. The groove between the two helices in the α1-α2 domains is too narrow to permit ligand binding. Notably, an unusual basic patch on the α3 domain is involved in the binding to heparan sulfate which is essential for MILL2 interactions with fibroblasts. These findings suggest that MILL2 has a unique structural architecture and physiological role, with binding to heparan sulfate proteoglycans on fibroblasts possibly regulating cellular recruitment in biological events

Finishing the euchromatic sequence of the human genome

The sequence of the human genome encodes the genetic instructions for human physiology, as well as rich information about human evolution. In 2001, the International Human Genome Sequencing Consortium reported a draft sequence of the euchromatic portion of the human genome. Since then, the international collaboration has worked to convert this draft into a genome sequence with high accuracy and nearly complete coverage. Here, we report the result of this finishing process. The current genome sequence (Build 35) contains 2.85 billion nucleotides interrupted by only 341 gaps. It covers ∼99% of the euchromatic genome and is accurate to an error rate of ∼1 event per 100,000 bases. Many of the remaining euchromatic gaps are associated with segmental duplications and will require focused work with new methods. The near-complete sequence, the first for a vertebrate, greatly improves the precision of biological analyses of the human genome including studies of gene number, birth and death. Notably, the human enome seems to encode only 20,000-25,000 protein-coding genes. The genome sequence reported here should serve as a firm foundation for biomedical research in the decades ahead

Escherichia coli knock-out mutants with altered electron transfer activity in the Micredox® assay and in microbial fuel cells

Electron transfer from bacteria to external electron acceptors is a biologically important phenomenon that is increasingly being harnessed as useful technology such as in the Micredox® assay and in microbial fuel cells (MFCs). Optimisation of these systems is limited by incomplete knowledge of the underlying genetics of electron transfer. The Keio collection of single gene knock-out Escherichia coli strains is being tested to find genes involved in electron transfer from bacteria to external electron acceptors. Initially, 21 E. coli strains from the Keio collection were selected and tested for altered electro-activity using the Micredox® assay. The Micredox® assay provides a rapid measurement of electron transfer from cells to a soluble electron acceptor (potassium hexacyanoferrate(III)) and was previously developed as a general test for BOD and toxicant measurement. Of the 21 Keio strains, 10 were found to have significantly reduced electron transfer and two were found to have significantly increased electron transfer. The mutant with the lowest electron transfer rate (nuoA) and the highest electron transfer rate (arcA) were then tested for electron transfer in microbial fuel cells (MFCs). The arcA mutant had slightly higher electron transfer rates than the wild type in mediator-less MFC while the nuoA mutant strain had very similar electro-activity to the wild type. However, in a mediated MFC, the mutants were consistently different from the wild type. These results demonstrate that single gene deletion strains of E. coli can have significantly altered electron transfer capabilities, both in the Micredox® assay and in MFCs. Importantly, the Micredox® assay was found to be a rapid and easily scaled-up method to discover genes that are important in electron transfer

At-line measurement of lactose in dairy-processing plants

Environmental and process control applications have needs for sensors that operate continuously or repeatedly, making them applicable to batch measurement and flowing product stream measurement. Additionally, for lactose monitoring in dairy-processing plants, the sensors must have sufficient flexibility to handle a wide range of substrate concentration and be resilient to withstand wide pH excursions brought about by frequent exposure to clean-in-place chemicals that happen without any warning. This paper describes the development and trialling of an at-line lactose biosensor that meets the needs of the dairy industry for loss monitoring of lactose in dairy-processing plants by the combination of a third-generation enzyme biosensor with a sequential injection analyser. Results, both from grab sample analysis and an at-line factory prototype, are shown from their operation when installed at a Fonterra dairy factory (New Zealand) during the 2011-2012 season. Previous sensor fabrication methods were converted to a single-step process, and the flow-through cell was adapted to bubble-free operation. The lactose concentration in wastewater-processing streams was successfully monitored by taking and analysing samples every 2-3 min, semi-continuously, for 3 months by an unskilled operator. The Fonterra site flushes approximately 100-300,000 L of wastewater per hour from its lactose plant. In the 2011-2012 season, the daily mean lactose content of this wastewater varied significantly, from 0.0 to 8.0 % w/v (0-233,712 μM) and equated to substantial total losses of lactose over a 6-month period. These lactose losses represent lost saleable or useable product

Water use implications of bioenergy cropping systems in Eastern England

Food and fuel security in the face of population growth and climate change represent key societal challenges. Extending an arable farm-level bio-economic optimisation model ‘MEETA’ to include dedicated energy crops (DECs) and water metrics, we quantify water use implications and trade-offs between greenhouse gas emissions, net energy and farm profitability. Drawing upon the limited available water use data for arable and energy crops applicable for East Anglia in the UK, six different farm scenarios were investigated. Profit maximisation produces a conventional crop mix, while maximising net energy and minimising greenhouse gas emissions result in crop mixes which impose financial penalties and lower water use in comparison to conventional cropping; average financial impacts of the associated reduced water use under these respective scenarios range from £0.12 to £0.28 per m3 of water. Confidence in these results and work on water use and management more generally would be improved through better data on inter-annual crop-water needs, temporal water availability relationships and water response functions. Water availability for UK crop production is largely perceived to be a non-limiting resource; however climate change predictions demonstrate that availability of water for UK crop production is of increasing concern for both farmers and society as a whole

Potential for Second Generation Biofuel Feedstock from English Arable Farms

Meeting the EU renewable fuel targets for 2020 will require a large increase in bioenergy feedstocks. To date, first generation biofuels have been the major response to meeting these targets. However, second generation biofuels from dedicated energy crops (e.g. miscanthus) or crop residues (e.g. straw) offer potential. Based on an on-farm survey of Farm Business Survey arable farmers in England and aggregated to national levels, we estimate that 5.27 Mt of cereal straw is produced annually on these farm types, of which farmers indicated that they would be willing to sell 2.5 Mt for bioenergy purposes, provided appropriate contractual conditions meet their needs. However, only 555Kt-840Kt would be obtained from straw currently incorporated into the soil. Timeliness of crop operations and benefits to soil were cited as key reasons for incorporating straw. A ‘good price’ represents the key incentive to encourage straw baling. With respect to dedicated energy crops, 81.6% (87.7%) would not consider growing miscanthus (SRC), while respectively, 17.2% (11.9%) would consider growing and 1.2% (0.4%) were currently growing these crops. Assuming 9.29% (average percentage of arable land set-aside between 1996-2005) of their utilised agricultural area to these crops, 89,900 ha (50,700 ha) of miscanthus (SRC) would be grown on English arable farms. Land quality issues, profitability and committing land for a long period of time were cited as both negative and positive reasons for farmer decisions about their level of willingness to grow these crops. Food and fuel policies must increasingly be integrated in order to meet societal goals without generating unintended consequences

Appraising freeze-drying for storage of bacteria and their ready access in a rapid toxicity assessment assay

Direct toxicity assessment (DTA) techniques seek to measure the impact of toxic chemicals on biological materials resident in the environment. This study features the use of freeze-dried bacterial cells in combination with a rapid DTA analyser, SciTOX™. The effects of three factors—cryoprotectant type, bacterial strain, and storage temperature— were tested in order to validate the shelf life of the freeze-dried cells. Three freeze-dried Gram-negative bacterial strains, Acinetobacter calcoaceticus, Escherichia coli and Pseudomonas putida, were tested by using the bacteria in the SciTox™ DTA assay and recording their responses to two standard toxicants: 2,4-dicholorophenol and 3,5- dichlorophenol. Each freeze-dried strain of bacteria was prepared in two forms—either pre-treatment with polyethylene glycol (PEG) or with sucrose/Tween 80—prior to storing at either 4 or −20 °C for three different storage periods (1, 2 or 3 months). While the sucrose/Tween 80 pre-treated freeze-dried cells exhibited better cell viability, we concluded that PEG was a more suitable cryoprotectant for the bacteria used in the DTA assay because of EC50 parity with fresh cell and zero-time freeze-dried cell assays. The results showed that freeze-dried cells, with appropriate materials and conditions, can give reproducible DTA results for up to 3 months. The availability of a biocomponent that can be activated by simple rehydration makes the deployment of this technology much easier for an end user