title: Biochemical Characterisation of Reconstructed Ancestral CM-DAH7PS Enzymes

authors: McMillan, Joel Patrick

subjects: DAH7PS

abstract: Thermophily has been proposed to be a primitive trait (Stetter, 2006, Pace, 1991, Woese, 1987) which has led to suggestions that all contemporary thermophilic species are the direct descendants of ancient thermophilic organisms. Ancestral sequence reconstruction (ASR) is a modern molecular technique which has been used to study the evolution of thermophily, however these studies have produced conflicting results. Studies utilising ASR to investigate the evolution of thermophily with two different proteins, elongation factor Tu and thioredoxin, have suggested a primitive origin for thermophily. However a recent study by Hobbs et al. (2012), in which ancestral IPMDH enzymes were reconstructed and biochemically characterised in order to investigate the evolution of thermophily in the Bacillus genus, suggested that thermophily may have evolved at least twice within the Bacillus genus, indicating that thermophily may not be strictly a primitive trait. This finding needs to be supported by data from other reconstructed enzymes.

Four ancestral Bacillus 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase enzymes with chorismate mutase fused to their N-termini (CM-DAH7PS) were reconstructed to investigate whether a similar trend would be observed with a different enzyme. The ages of these ancestral Precambrian enzymes were estimated to be between 570 and 1,079 million years old. The three most recent ancestral enzymes were characterised and deemed biologically feasible as evidenced by the kinetic properties they display, which are similar to those displayed by two extant CM-DAH7PS enzymes from Bacillus subtilis and Bacillus stearothermophilus. The X-ray crystal structure of the most recent CM-DAH7PS ancestor has been solved and found to be very similar to previously solved DAH7PS structures. The optimal temperatures for activity of the ancestral DAH7PS enzymes were used to infer how thermophily may have evolved in the Bacillus genus. Interestingly, the results conflict with the findings of Hobbs et al. (2012). This suggests that the biochemical characteristics of ancestral enzymes may be highly susceptible to the biochemical properties of the contemporary species used in the inference or that different enzymes may result in different inferences being drawn regarding the evolution of thermophily.

text: Biochemical Characterisation of Reconstructed Ancestral CM-DAH7PS Enzymes Thermophily has been proposed to be a primitive trait (Stetter, 2006, Pace, 1991, Woese, 1987) which has led to suggestions that all contemporary thermophilic species are the direct descendants of ancient thermophilic organisms. Ancestral sequence reconstruction (ASR) is a modern molecular technique which has been used to study the evolution of thermophily, however these studies have produced conflicting results. Studies utilising ASR to investigate the evolution of thermophily with two different proteins, elongation factor Tu and thioredoxin, have suggested a primitive origin for thermophily. However a recent study by Hobbs et al. (2012), in which ancestral IPMDH enzymes were reconstructed and biochemically characterised in order to investigate the evolution of thermophily in the Bacillus genus, suggested that thermophily may have evolved at least twice within the Bacillus genus, indicating that thermophily may not be strictly a primitive trait. This finding needs to be supported by data from other reconstructed enzymes.

Four ancestral Bacillus 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase enzymes with chorismate mutase fused to their N-termini (CM-DAH7PS) were reconstructed to investigate whether a similar trend would be observed with a different enzyme. The ages of these ancestral Precambrian enzymes were estimated to be between 570 and 1,079 million years old. The three most recent ancestral enzymes were characterised and deemed biologically feasible as evidenced by the kinetic properties they display, which are similar to those displayed by two extant CM-DAH7PS enzymes from Bacillus subtilis and Bacillus stearothermophilus. The X-ray crystal structure of the most recent CM-DAH7PS ancestor has been solved and found to be very similar to previously solved DAH7PS structures. The optimal temperatures for activity of the ancestral DAH7PS enzymes were used to infer how thermophily may have evolved in the Bacillus genus. Interestingly, the results conflict with the findings of Hobbs et al. (2012). This suggests that the biochemical characteristics of ancestral enzymes may be highly susceptible to the biochemical properties of the contemporary species used in the inference or that different enzymes may result in different inferences being drawn regarding the evolution of thermophily.

year: 2012

title: The Non-Market Value of Biodiversity Enhancement in New Zealand's Planted Forests

authors: Yao, Richard

subjects: non-market value

abstract: This study investigates the non-market value of biodiversity enhancement in New Zealand’s planted forests using the stated choice experiments (CE) approach. This study focuses on two issues. One issue is policy orientated where we estimate the non-market value of biodiversity enhancement and the determinants of this value. The other issue is about the neutrality of major experimental design criteria used in CE. Specifically, we examine the impact of using different criteria on attribute non-attendance, choice variability, choice determinism and learning. 

To estimate the non-market value of biodiversity enhancement, a random parameters logit model with error components is used to analyse choice data collected from 209 respondents across New Zealand. The panel nature of the choice data set is exploited to calculate the marginal willingness-to-pay (WTP) for environmental attributes of each respondent. Panel random-effects regression models are subsequently employed to determine the factors that influence individual-specific WTP values. Results suggest that New Zealand taxpayers would be willing to pay $26.5 million per year for five years for a proposed biodiversity enhancement programme. Random effects regression analysis suggest that respondents living close to large planted forests (i.e., less than 10 kilometres away) would pay more for the programme. 

To study whether the selection of experimental design criterion affects attribute non-attendance and choice variability, we analyse a balanced sample with split designs. The balanced sample is composed of 1509 choice observations equally distributed across three experimental designs, namely: orthogonal, Bayesian D-efficient and optimal orthogonal. Results from latent class logit analysis suggest that tasks derived from the Bayesian D-efficient design (BDD) criterion are more attended than those derived from orthogonal and optimal orthogonal designs. Heteroskedastic logit analysis indicates that, unlike the two other designs, higher choice task complexity (as measured by entropy proxies) in the BDD does not increase choice variability of respondents. This is indicated by the absence of a significant increase in the variance of the Gumbel error in the choice data collected using BDD unlike the data collected using the two other criteria.

To study whether the three experimental designs vary in terms of choice determinism and task order effects, a separate analysis of the balanced data set using heteroskedastic logit models is undertaken. Results show that higher levels of choice task complexity (as measured by attribute dispersion proxies) in BDD contribute to increasing choice determinism of respondents but not in the orthogonal design. Choice data collected using BDD choice tasks exhibit a steady learning effect, unlike the other designs which do not exhibit any form of continuous learning. 

We conclude that the BDD criterion provides choice tasks that are superior compared to the other two design criteria. Choice data collected using this criterion has a higher quality as indicated by more attended choice tasks, lower choice variability and a pattern of continuous learning. These results point to a higher behavioural efficiency of respondents in evaluating complex choice tasks. However, these results might be specific to the choice data collected in this current study. We suggest that future studies should further investigate the impacts of different experimental designs to verify the findings of this study.

text: The Non-Market Value of Biodiversity Enhancement in New Zealand's Planted Forests This study investigates the non-market value of biodiversity enhancement in New Zealand’s planted forests using the stated choice experiments (CE) approach. This study focuses on two issues. One issue is policy orientated where we estimate the non-market value of biodiversity enhancement and the determinants of this value. The other issue is about the neutrality of major experimental design criteria used in CE. Specifically, we examine the impact of using different criteria on attribute non-attendance, choice variability, choice determinism and learning. 

To estimate the non-market value of biodiversity enhancement, a random parameters logit model with error components is used to analyse choice data collected from 209 respondents across New Zealand. The panel nature of the choice data set is exploited to calculate the marginal willingness-to-pay (WTP) for environmental attributes of each respondent. Panel random-effects regression models are subsequently employed to determine the factors that influence individual-specific WTP values. Results suggest that New Zealand taxpayers would be willing to pay $26.5 million per year for five years for a proposed biodiversity enhancement programme. Random effects regression analysis suggest that respondents living close to large planted forests (i.e., less than 10 kilometres away) would pay more for the programme. 

To study whether the selection of experimental design criterion affects attribute non-attendance and choice variability, we analyse a balanced sample with split designs. The balanced sample is composed of 1509 choice observations equally distributed across three experimental designs, namely: orthogonal, Bayesian D-efficient and optimal orthogonal. Results from latent class logit analysis suggest that tasks derived from the Bayesian D-efficient design (BDD) criterion are more attended than those derived from orthogonal and optimal orthogonal designs. Heteroskedastic logit analysis indicates that, unlike the two other designs, higher choice task complexity (as measured by entropy proxies) in the BDD does not increase choice variability of respondents. This is indicated by the absence of a significant increase in the variance of the Gumbel error in the choice data collected using BDD unlike the data collected using the two other criteria.

To study whether the three experimental designs vary in terms of choice determinism and task order effects, a separate analysis of the balanced data set using heteroskedastic logit models is undertaken. Results show that higher levels of choice task complexity (as measured by attribute dispersion proxies) in BDD contribute to increasing choice determinism of respondents but not in the orthogonal design. Choice data collected using BDD choice tasks exhibit a steady learning effect, unlike the other designs which do not exhibit any form of continuous learning. 

We conclude that the BDD criterion provides choice tasks that are superior compared to the other two design criteria. Choice data collected using this criterion has a higher quality as indicated by more attended choice tasks, lower choice variability and a pattern of continuous learning. These results point to a higher behavioural efficiency of respondents in evaluating complex choice tasks. However, these results might be specific to the choice data collected in this current study. We suggest that future studies should further investigate the impacts of different experimental designs to verify the findings of this study.

year: 2012

title: Significance of an early date from an adzed tree stump in Northland

authors: Higham, Thomas F.G.

abstract: Ogle, Jones, Sutton and Wallace (1998) have recently investigated the radiocarbon dating of a tree stump ('Ogle's stump’) which had evidence of adze marks, near the site of Taumatawhana pa, Houhora, Northland. The conventional radiocarbon age of 938 ± 31 BP was obtained at the Institute of Geological and Nuclear Sciences Ltd (formerly INS) laboratory in 1971. Ogle et al.(1998) considered the 'inbuilt age' of the wood (see McFadgen, 1982) and assessed its contribution to the radiocarbon determination. In this brief paper we re-evaluate that methodology and question the conclusion of Ogle et al. (1998) that the date is reliable. We are particularly concerned with the comparison of the date with an associated radiocarbon result obtained by Elliot et al. (1995) from a nearby site at Lake Taumatawhana, which we think is misleading.

text: Significance of an early date from an adzed tree stump in Northland Ogle, Jones, Sutton and Wallace (1998) have recently investigated the radiocarbon dating of a tree stump ('Ogle's stump’) which had evidence of adze marks, near the site of Taumatawhana pa, Houhora, Northland. The conventional radiocarbon age of 938 ± 31 BP was obtained at the Institute of Geological and Nuclear Sciences Ltd (formerly INS) laboratory in 1971. Ogle et al.(1998) considered the 'inbuilt age' of the wood (see McFadgen, 1982) and assessed its contribution to the radiocarbon determination. In this brief paper we re-evaluate that methodology and question the conclusion of Ogle et al. (1998) that the date is reliable. We are particularly concerned with the comparison of the date with an associated radiocarbon result obtained by Elliot et al. (1995) from a nearby site at Lake Taumatawhana, which we think is misleading.

year: 1998