Pseudogene rescue: an adaptive mechanism of codon reassignment

Alterations to the genetic code – codon reassignments – have occurred many times in life’s history, despite the fact that genomes are coadapted to their genetic codes and therefore alterations are likely to be maladaptive. A potential mechanism for adaptive codon reassignment, which could trigger either a temporary period of codon ambiguity or a permanent genetic code change, is the reactivation of a pseudogene by a nonsense suppressor mutant transfer RNA. I examine the population genetics of each stage of this process and find that pseudogene rescue is plausible and also readily explains some features of extant variability in genetic codes.     

Roost tree characteristics determine use by the white‐striped freetail bat (Tadarida australis,Chiroptera: Molossidae) in suburban subtropical Brisbane,Australia

Abstract We examined factors affecting roost tree selection by the white‐striped freetail bat Tadarida australis (Chiroptera: Molossidae), a large insectivorous bat in suburban Brisbane, Australia. We compared biophysical characteristics associated with 34 roost trees and 170 control trees of similar diameter, height and tree senescence characters. Roost trees used by the white‐striped freetail bat had significantly higher numbers of hollows in the trunk and branches (P < 0.003) and were more likely to contain a large trunk cavity with an internal diameter of >30 cm (P < 0.001) than control trees. These trees also accommodated more species of hollow‐using fauna (P = 0.005). When comparing roost trees with control trees of similar diameters and heights, roost trees were on average at a later stage of tree senescence (P < 0.001). None of the roost trees were found in the large forest reserves fringing the Brisbane metropolitan area despite these areas being used for foraging by the white‐striped freetail bat. Although all tree locations in this study were in modified landscapes, roost trees tended to be surrounded by groups of trees and undergrowth. Roost trees provide important habitat requirements for hollow‐using fauna in suburban, rural and forested environments.     

Assessment of European streams with diatoms, macrophytes, macroinvertebrates and fish: a comparative metric-based analysis of organism response to stress

1. Periphytic diatoms, macrophytes, benthic macroinvertebrates and fish were sampled with standard methods in 185 streams in nine European countries to compare their response to degradation. Streams were classified into two main stream type groups (i.e. lowland, mountain streams); in addition, the lowland streams were grouped into four more specific stream types. 2. Principal components analysis with altogether 43 environmental parameters was used to construct complex stressor gradients for physical–chemical, hydromorphological and land use data. About 30 metrics were calculated for each sample and organism group. Metric responses to different stress types were analysed by Spearman Rank Correlation. 3. All four organism groups showed significant response to eutrophication/organic pollution gradients. Generally, diatom metrics were most strongly correlated to eutrophication gradients (85% and 89% of the diatom metrics tested correlated significantly in mountain and lowland streams, respectively), followed by invertebrate metrics (91% and 59%). 4. Responses of the four organism groups to other gradients were less strong; all organism groups responded to varying degrees to land use changes, hydromorphological degradation on the microhabitat scale and general degradation gradients, while the response to hydromorphological gradients on the reach scale was mainly limited to benthic macroinvertebrates (50% and 44% of the metrics tested correlated significantly in mountain and lowland streams, respectively) and fish (29% and 47%). 5. Fish and macrophyte metrics generally showed a poor response to degradation gradients in mountain streams and a strong response in lowland streams. 6. General recommendations on European bioassessment of streams were derived from the results.     

Symbiotic association of a pyrgomatid barnacle with a coral from a volcanic middle Miocene shoreline (Porto Santo,Madeira Archipelago,Portugal)

Abstract: The bioclaustration of the pyrgomatid barnacle Ceratoconcha aff. costata within the carbonate skeleton of a colonial hermatypical coral (Tarbellastrea reussiana) is described from a middle Miocene basaltic rocky palaeoshore on a small north‐eastern Atlantic islet of Porto Santo (Madeira Archipelago, Portugal). The resulting structure is named as a new trace fossil Imbutichnus igen. nov., characterized by a small, funnel‐like cavity, a circular to oval cross‐section, with a nearly cylindrical shape in the upper part and a conical shape towards the base. Imbutichnus costatum isp. nov. is defined as a bioclaustration structure produced by the overgrowth of a pyrgomatid barnacle by a coral. From an ethologic point of view, Imbutichnus is attributed to the Impedichnia category. In terms of palaeoecology, it is interpreted as the result of a parasitic relationship. This is also the oldest record of pyrgomatid barnacles in the eastern Atlantic and clearly demonstrates that the Miocene palaeogeographic range of Ceratoconcha was much wider than previously assumed.     

Long‐term impacts of invasive species on a native top predator in a large lake system

1. Declining abundances of forage fish and the introduction and establishment of non‐indigenous species have the potential to substantially alter resource and habitat exploitation by top predators in large lakes. 2. We measured stable isotopes of carbon (δ¹³C) and nitrogen (δ¹⁵N) in field‐collected and archived samples of Lake Ontario lake trout (Salvelinus namaycush) and five species of prey fish and compared current trophic relationships of this top predator with historical samples. 3. Relationships between δ¹⁵N and lake trout age were temporally consistent throughout Lake Ontario and confirmed the role of lake trout as a top predator in this food web. However, δ¹³C values for age classes of lake trout collected in 2008 ranged from 1.0 to 3.9‰ higher than those reported for the population sampled in 1992. 4. Isotope mixing models predicted that these changes in resource assimilation were owing to the replacement of rainbow smelt (Osmerus mordax) by round goby (Neogobius melanostomus) in lake trout diet and increased reliance on carbon resources derived from nearshore production. This contrasts with the historical situation in Lake Ontario where δ¹³C values of the lake trout population were dominated by a reliance on offshore carbon production. 5. These results indicate a reduced capacity of the Lake Ontario offshore food web to support the energetic requirements of lake trout and that this top predator has become increasingly reliant on prey resources that are derived from nearshore carbon pathways.     

Lipoteichoic acid is an important microbe-associated molecular pattern of Lactobacillus rhamnosus GG

Background

Receptors with a single transmembrane (TM) domain are essential for the signal transduction across the cell membrane. NMR spectroscopy is a powerful tool to study structure of the single TM domain. The expression and purification of a TM domain in Escherichia coli (E.coli) is challenging due to its small molecular weight. Although ketosteroid isomerase (KSI) is a commonly used affinity tag for expression and purification of short peptides, KSI tag needs to be removed with the toxic reagent cyanogen bromide (CNBr).

Result

The purification of the TM domain of p75 neurotrophin receptor using a KSI tag with the introduction of a thrombin cleavage site is described herein. The recombinant fusion protein was refolded into micelles and was cleaved with thrombin. Studies showed that purified protein could be used for structural study using NMR spectroscopy.

Conclusions

These results provide another strategy for obtaining a single TM domain for structural studies without using toxic chemical digestion or acid to remove the fusion tag. The purified TM domain of p75 neurotrophin receptor will be useful for structural studies.