Minimizing Cognitive Errors in Site-Specific Causal Assessments

Interest in causal investigations in aquatic systems has been a natural outgrowth of the increased use of biological monitoring to characterize the condition of resources. Although biological monitoring approaches are critical tools for detecting whether effects are occurring, they do not identify the cause of the observed effects. Formal approaches to causal evaluation can provide a mechanism to build on expert knowledge, increasing the likelihood that remedial efforts will achieve the desired environmental improvement. This paper examines how formal approaches to causal investigations minimize common errors. We reviewed common cognitive errors reported in the literature, and compared them with considerations suggested for strength-of-evidence approaches. Many of the causal considerations are directed toward distinguishing spurious correlations from true causal relationships. However, this is only one type of error; others include hypothesis dependence, confirmation bias, hypothesis tenacity and anchoring. We suggest three general principles for minimizing error in site-specific investigations: (1) Conduct the causal evaluation as a fair, transparent comparison among alternatives; (2) Carefully describe and quantify the conjunction of cause and effect; and (3) Consider that conjunction between cause and effect is spurious, or that a real conjunction was masked.     

Functionally important segments in proteins dissected using Gene Ontology and geometric clustering of peptide fragments

We have developed a geometric clustering algorithm using backbone ,ψ angles to group conformationally similar peptide fragments of any length. By labeling each fragment in the cluster with the level-specific Gene Ontology 'molecular function' term of its protein, we are able to compute statistics for molecular function-propensity and p-value of individual fragments in the cluster. Clustering-cum-statistical analysis for peptide fragments 8 residues in length and with only trans peptide bonds shows that molecular function propensities ≥20 and p-values ≤0.05 can dissect fragments within a protein linked to the molecular function.     

Gαo/i-stimulated proteosomal degradation of RGS20: A mechanism for temporal integration of Gs and Gi pathways

The G_s and G_i pathways interact to control the levels of intracellular cAMP. Although coincident signaling through G_s and G_i-coupled receptors can attenuate G_s-stimulated cAMP levels, it is not known if prior activation of the G_i pathway can affect signaling by G_s-coupled receptors. We have found that activated Gα_o/i interact with RGS20, a GTPase activating protein for members of the Gα_ο/i family. Interaction between Gα_o/i and RGS20 results in decreased cellular levels of RGS20. This decrease was induced by activated Gα_o and Gα_i2 but not by Gα_q, Gα_i1 or Gα_i3. The Gα_o/i-induced decrease in RGS20 can be blocked by proteasomal inhibitors lactacystin or MG132. Activated Gα_o stimulates the ubiquitination of RGS20. The serotonin-1A receptor that couples to G_o/i reduces the levels of RGS20 and this effect is blocked by lactacystin, suggesting that G_o/i promotes the degradation of RGS20. Expression of RGS20 attenuates the inhibition of β-adrenergic receptor-induced cAMP levels mediated by the serotonin-1A receptor. Prior activation of the serotonin-1A receptor results in loss of the RGS20-mediated attenuation, and the loss of attenuation is blocked when lactacystin is included during the prior treatment. These observations suggest that G_o/i-coupled receptors, by stimulating the degradation of RGS20, can regulate how subsequent activation of the G_s and G_i pathways controls cellular cAMP levels, thus allowing for signal integration.     

Engineering sugarcane cultivars with bovine pancreatic trypsin inhibitor (aprotinin) gene for protection against top borer (Scirpophaga excerptalis Walker)

The inhibitory activity of bovine pancreatic trypsin inhibitor (aprotinin), a natural polypeptide and a proteinase inhibitor, was demonstrated on gut proteinases of three lepidopteran borers of sugarcane using commercially available aprotinin. A synthetic gene coding for aprotinin, designed and codon optimized for better expression in plant system (Shantaram 1999), was transferred to two sugarcane cultivars namely CoC 92061 and Co 86032 through particle bombardment. Aprotinin gene expression was driven by maize ubiquitin promoter and the plant selection marker used was hygromycin resistance. The integration, expression and functionality of the transgene was confirmed by Southern, Western and insect bioassay, respectively. Southern analysis showed two to four integration sites of the transgene in the transformed plants. Independent transgenic events showed varied levels of transgene expression resulting in different levels (0.16–0.50%) of aprotinin. In in vivo bioassay studies, larvae of top borer Scirpophaga excerptalis Walker (Lepidoptera: Pyralidae) fed on transgenics showed significant reduction in larval weight which indicated impairment of their development. Results of this study show the possibility of deploying aprotinin gene for the development of transgenic sugarcane cultivars resistant to top borer.     

Rapid thermal adaptation in photosymbionts of reef‐building corals

Climate warming is occurring at a rate not experienced by life on Earth for 10 s of millions of years, and it is unknown whether the coral‐dinoflagellate (Symbiodinium spp.) symbiosis can evolve fast enough to ensure coral reef persistence. Coral thermal tolerance is partly dependent on the Symbiodinium hosted. Therefore, directed laboratory evolution in Symbiodinium has been proposed as a strategy to enhance coral holobiont thermal tolerance. Using a reciprocal transplant design, we show that the upper temperature tolerance and temperature tolerance range of Symbiodinium C1 increased after ~80 asexual generations (2.5 years) of laboratory thermal selection. Relative to wild‐type cells, selected cells showed superior photophysiological performance and growth rate at 31°C in vitro, and performed no worse at 27°C; they also had lower levels of extracellular reactive oxygen species (exROS). In contrast, wild‐type cells were unable to photosynthesise or grow at 31°C and produced up to 17 times more exROS. In symbiosis, the increased thermal tolerance acquired ex hospite was less apparent. In recruits of two of three species tested, those harbouring selected cells showed no difference in growth between the 27 and 31°C treatments, and a trend of positive growth at both temperatures. Recruits that were inoculated with wild‐type cells, however, showed a significant difference in growth rates between the 27 and 31°C treatments, with a negative growth trend at 31°C. There were no significant differences in the rate and severity of bleaching in coral recruits harbouring wild‐type or selected cells. Our findings highlight the need for additional Symbiodinium genotypes to be tested with this assisted evolution approach. Deciphering the genetic basis of enhanced thermal tolerance in Symbiodinium and the cause behind its limited transference to the coral holobiont in this genotype of Symbiodinium C1 are important next steps for developing methods that aim to increase coral bleaching tolerance.     

A dominant dwarf shrub increases diversity of herbaceous plant communities in a Trans-Himalayan rangeland

Plant communities are structured by both competition and facilitation. The interplay between the two interactions can vary depending on environmental factors, nature of stress, and plant traits. However, whether positive or negative interactions dominate in regions of high biotic and abiotic stress remains unclear. We studied herbaceous plant communities associated with a dwarf shrub Caragana versicolor in semi-arid, high altitude Trans-Himalayan rangelands of Spiti, India. We surveyed 120 pairs of plots (within and outside shrub canopies) across four watersheds differing in altitude, aspect, and dominant herbivores. Herbaceous communities within shrub canopies had 25% higher species richness, but similar abundance when compared to communities outside the canopy, with the shrub edge having higher diversity than the centre of the canopy. Grasses and erect forbs showed positive associations with the shrub, while prostrate plants occurred at much lower abundance within the canopy. Rare species showed stronger positive associations with Caragana than abundant species. Experimental removal of herbaceous vegetation from within shrub canopies led to 42% increase in flowering in Caragana, indicating a cost to the host shrubs. Our study indicates a robust pattern of a dwarf shrub facilitating local community diversity across this alpine landscape, increasing diversity at the plot level, facilitating rare species, and yet incurring a cost to hosts from the presence of herbaceous plants. Given these large influences of this shrub on the vegetation of these high altitude rangelands, we suggest that the shrub microhabitat be explicitly considered in any analyses of ecosystem health in such rangelands.