The consent problem within DNA biobanks

Large prospective biobanks are being established containing DNA, lifestyle and health information in order to study the relationship between diseases, genes and environment. Informed consent is a central component of research ethics protection. Disclosure of information about the research is an essential element of seeking informed consent. Within biobanks, it is not possible at recruitment to describe in detail the information that will subsequently be collected because people will not know which disease they will develop. It will also be difficult to describe the specific research that will be performed using the biobank, other than to stipulate categories of research or diseases that are not included. Potential subjects can only be given information about the sorts of research that will be performed and by whom. Organisations responsible for biobanks usually argue that this disclosure of information is adequate when seeking informed consent, especially if coupled with a right to withdraw, as it would not be feasible or it would be too expensive to seek consent renewal on a regular basis. However, there are concerns about this 'blanket consent' approach'. Consent waivers have also been proposed in which research subjects entrust their consent with an independent third party to decide whether subsequent research using the biobank is consistent with the original consent provided by the subject.     

Vascular plant 15N natural abundance in heath and forest tundra ecosystems is closely correlated with presence and type of mycorrhizal fungi in roots

In this study we show that the natural abundance of the nitrogen isotope 15, δ¹⁵N, of plants in heath tundra and at the tundra-forest ecocline is closely correlated with the presence and type of mycorrhizal association in the plant roots. A total of 56 vascular plant species, 7 moss species, 2 lichens and 6 species of fungi from four heath and forest tundra sites in Greenland, Siberia and Sweden were analysed for δ¹⁵N and N concentration. Roots of vascular plants were examined for mycorrhizal colonization, and the soil organic matter was analysed for δ¹⁵N, N concentration and soil inorganic, dissolved organic and microbial N. No arbuscular mycorrhizal (AM) colonizations were found although potential host plants were present in all sites. The dominant species were either ectomycorrhizal (ECM) or ericoid mycorrhizal (ERI). The δ¹⁵N of ECM or ERI plants was 3.5–7.7‰ lower than that of non-mycorrhizal (NON) species in three of the four sites. This corresponds to the results in our earlier study of mycorrhiza and plant δ¹⁵N which was limited to one heath and one fellfield in N Sweden. Hence, our data suggest that the δ¹⁵N pattern: NON/AM plants > ECM plants ≥ ERI plants is a general phenomenon in ecosystems with nutrient-deficient organogenic soils. In the fourth site, a␣birch forest with a lush herb/shrub understorey, the differences between functional groups were considerably smaller, and only the ERI species differed (by 1.1‰) from the NON species. Plants of all functional groups from this site had nearly twice the leaf N concentration as that found in the same species at the other three sites. It is likely that low inorganic N availability is a prerequisite for strong δ¹⁵N separation among functional groups. Both ECM roots and fruitbodies were ¹⁵N enriched compared to leaves which suggests that the difference in δ¹⁵N between plants with different kinds of mycorrhiza could be due to isotopic fractionation at the␣fungal-plant interface. However, differences in δ¹⁵N between soil N forms absorbed by the plants could also contribute to the wide differences in plant δ¹⁵N found in most heath and forest tundra ecosystems. We hypothesize that during microbial immobilization of soil ammonium the microbial N pool could become ¹⁵N-depleted and the remaining, plant-available soil ammonium ¹⁵N-enriched. The latter could be a main source of N for NON/AM plants which usually have high δ¹⁵N. In contrast, amino acids and other soil organic N compounds presumably are ¹⁵N-depleted, similar to plant litter, and ECM and ERI plants with high uptake of these N forms hence have low leaf δ¹⁵N. Further indications come from the δ¹⁵N of mosses and lichens which was similar to that of ECM plants. Tundra cryptogams (and ECM and ERI plants) have previously been shown to have higher uptake of amino acid than ammonium N; their low δ¹⁵N might therefore reflect the δ¹⁵N of free amino acids in the soil. The concentration of dissolved organic N was 3–16 times higher than that of inorganic N in the sites. Organic nitrogen could be an important N source for ECM and, in particular, ERI plants in heath and forest tundra ecosystems with low release rate of inorganic N from the soil organic matter. Received: 8 June 1997 / Accepted: 28 February 1998     

Complete genome sequence of the proteolytic Clostridium botulinum type A5 (B3') strain H04402 065

H04402 065 is one of a very small group of strains of proteolytic Clostridium botulinum that form type A5 neurotoxin. Here, we report the complete 3.9-Mb genome sequence and annotation of strain H04402 065, which was isolated from a botulism patient in the United Kingdom in 2004.     

Promoter engineering to optimize recombinant periplasmic Fab′ fragment production in Escherichia coli

Fab’ fragments have become an established class of biotherapeutic over the last two decades. Likewise, developments in synthetic biology are providing ever more powerful techniques for designing bacterial genes, gene networks and entire genomes that can be used to improve industrial performance of cells used for production of biotherapeutics. We have previously observed significant leakage of an exogenous therapeutic Fab’ fragment into the growth medium during high cell density cultivation of an Escherichia coli production strain. In this study we sought to apply a promoter engineering strategy to address the issue of Fab’ fragment leakage and its consequent bioprocess challenges. We used site directed mutagenesis to convert the P_tac promoter, present in the plasmid, pTTOD‐A33 Fab’, to a P_tic promoter which has been shown by others to direct expression at a 35% reduced rate compared to P_tac. We characterized the resultant production trains in which either P_tic or P_tac promoters direct Fab’ fragment expression. The P_tic promoter strain showed a 25?30% reduction in Fab’ expression relative to the original P_tac strain. Reduced Fab’ leakage and increased viability over the course of a fed‐batch fermentation were also observed for the P_tic promoter strain. We conclude that cell design steps such as the P_tac to P_tic promoter conversion reported here, can yield significant process benefit and understanding with respect to periplasmic Fab’ fragment production. It remains an open question as to whether the influence of transgene expression on periplasmic retention is mediated by global metabolic burden effects or periplasm overcapacity. © 2016 American Institute of Chemical Engineers Biotechnol. Prog., 32:840–847, 2016     

Towards Monitoring Biodiversity in Amazonian Forests: How Regular Samples Capture Meso-Scale Altitudinal Variation in 25 km2 Plots

Background

Ecological monitoring and sampling optima are context and location specific. Novel applications (e.g. biodiversity monitoring for environmental service payments) call for renewed efforts to establish reliable and robust monitoring in biodiversity rich areas. As there is little information on the distribution of biodiversity across the Amazon basin, we used altitude as a proxy for biological variables to test whether meso-scale variation can be adequately represented by different sample sizes in a standardized, regular-coverage sampling arrangement.

Methodology/Principal Findings

We used Shuttle-Radar-Topography-Mission digital elevation values to evaluate if the regular sampling arrangement in standard RAPELD (rapid assessments (“RAP”) over the long-term (LTER [“PELD” in Portuguese])) grids captured patters in meso-scale spatial variation. The adequacy of different sample sizes (n = 4 to 120) were examined within 32,325 km²/3,232,500 ha (1293×25 km² sample areas) distributed across the legal Brazilian Amazon. Kolmogorov-Smirnov-tests, correlation and root-mean-square-error were used to measure sample representativeness, similarity and accuracy respectively. Trends and thresholds of these responses in relation to sample size and standard-deviation were modeled using Generalized-Additive-Models and conditional-inference-trees respectively. We found that a regular arrangement of 30 samples captured the distribution of altitude values within these areas. Sample size was more important than sample standard deviation for representativeness and similarity. In contrast, accuracy was more strongly influenced by sample standard deviation. Additionally, analysis of spatially interpolated data showed that spatial patterns in altitude were also recovered within areas using a regular arrangement of 30 samples.

Conclusions/Significance

Our findings show that the logistically feasible sample used in the RAPELD system successfully recovers meso-scale altitudinal patterns. This suggests that the sample size and regular arrangement may also be generally appropriate for quantifying spatial patterns in biodiversity at similar scales across at least 90% (≈5 million km²) of the Brazilian Amazon.     

Extensive hybridization in a contact zone between MacGillivray's warblers Oporornistolmiei and mourning warblers O. philadelphia detected using molecular and morphological analyses

There are many pairs of related western and eastern avian taxa in North America, and for many of these, little is known about their interactions in sympatry. One example is provided by MacGillivray's warblers Oporornis tolmiei and mourning warblers Oporornis philadelphia . There have been occasional reports of range contact and hybridization between these forms, but recent authors have doubted these reports. We show that these two species do in fact come into extensive range contact in the southern Peace Region of British Columbia, just east of the Rocky Mountains. We analyze whether patterns of variation in morphometric traits, eye-arcs, a mitochondrial DNA marker (COI), and a Z-chromosome marker (CHD1Z) are consistent with reproductive isolation or hybridization in this contact zone. Each trait shows strong differences between allopatric MacGillivray's warblers and allopatric mourning warblers, yet in the contact zone there are many birds with a combination of traits typical of both species. This is clearly seen in the molecular markers, for which 18 of 50 birds genotyped in the contact zone have both western and eastern alleles. These patterns strongly indicate the presence of an extensive hybrid zone between MacGillivray's and mourning warblers. Variation in each of the four traits is explained well by a single sigmoidal cline, with a width of roughly 150  km (or 130  km based only on the molecular markers). This is only the fourth hybrid zone known among North American wood-warblers (Parulidae).