Functional interactions in vivo between suppressor tRNA and mutationally altered ribosomal protein S4

Summary Ribosomal mutants (rpsD) which are associated with a generally increased translational ambiguity were investigated for their effects in vivo on individual tRNA species using suppressor tRNAs as models. It was found that nonsense suppression is either increased, unaffected or decreased depending on the codon context and the rpsD allele involved as well as the nature of the suppressor tRNA. Missense suppression of AGA and AGG by glyT(SuAGA/G) tRNA as well as UGG by glyT(SuUGG-8) tRNA is unaffected whereas suppression of UGG by glyT(SuUGA/G) or glyV(SuUGA/G) tRNA is decreased in the presence of an rpsD mutation. The effects on suppressor tRNA are thus not correlated with the ribosomal ambiguity (Ram) phenotype of the rpsD mutants used in this study. It is suggested that the mutationally altered ribosomes are changed in functional interactions with the suppressor tRNA itself rather than with the competing translational release factor(s) or cognate aminoacyl tRNA. The structure of suppressor tRNA, particularly the anticodon loop, and the suppressed codon as well as the codon context determine the allele specific functional interactions with these ribosomal mutations.     

Hydrology shapes microbial communities and microbiome-mediated growth of an Everglades tree island species

Plant-associated microbiomes can improve plant fitness by ameliorating environmental stress, providing a promising avenue for improving outplantings during restoration. However, the effects of water management on these microbial communities and their cascading effects on primary producers are unresolved for many imperiled ecosystems. One such habitat, Everglades tree islands, has declined by 54% in some areas, releasing excess nutrients into surrounding wetlands and exacerbating nutrient pollution. We conducted a factorial experiment, manipulating the soil microbiome and hydrological regime experienced by a tree island native, Ficus aurea, to determine how microbiomes impact growth under two hydrological management plans. All plants were watered to simulate natural precipitation, but plants in the “unconstrained” management treatment were allowed to accumulate water above the soil surface, while the “constrained” treatment had a reduced stage to avoid soil submersion. We found significant effects of the microbiomes on overall plant performance and aboveground versus belowground investment; however, these effects depended on hydrological treatment. For instance, microbiomes increased investment in roots relative to aboveground tissues, but these effects were 142% stronger in the constrained compared to unconstrained water regime. Changes in hydrology also resulted in changes in the prokaryotic community composition, including a >20 log₂fold increase in the relative abundance of Rhizobiaceae, and hydrology-shifted microbial composition was linked to changes in plant performance. Our results suggest that differences in hydrological management can have important effects on microbial communities, including taxa often involved in nitrogen cycling, which can in turn impact plant performance.     

Acetyl-CoA cleavage pathway in a syntrophic propionate oxidizing bacterium growing on fumarate in the absence of methanogens

Abstract In an ompF'-'lacZ fusion system carried by the open reading frame vector pORF1 in a supE mutant of Escherichia coli K12, read-through of an amber codon was decreased at temperatures higher than 40°C. This effect of temperature was dependent on the nucleotide sequence surrounding the amber codon, which was inserted into a site between the ompF and lacZ cistrons. Upon a temperature shift-up from 30 to 42°C, β-galactosidase synthesis directed by this fusion showed a transient arrest.     

Recognition of 3′ nucleotide context and stop codon readthrough are determined during mRNA translation elongation

The nucleotide context surrounding stop codons significantly affects the efficiency of translation termination. In eukaryotes, various 3′ contexts that are unfavorable for translation termination have been described; however, the exact molecular mechanism that mediates their effects remains unknown. In this study, we used a reconstituted mammalian translation system to examine the efficiency of stop codons in different contexts, including several previously described weak 3′ stop codon contexts. We developed an approach to estimate the level of stop codon readthrough in the absence of eukaryotic release factors (eRFs). In this system, the stop codon is recognized by the suppressor or near-cognate tRNAs. We observed that in the absence of eRFs, readthrough occurs in a 3′ nucleotide context-dependent manner, and the main factors determining readthrough efficiency were the type of stop codon and the sequence of the 3′ nucleotides. Moreover, the efficiency of translation termination in weak 3′ contexts was almost equal to that in the tested standard context. Therefore, the ability of eRFs to recognize stop codons and induce peptide release is not affected by mRNA context. We propose that ribosomes or other participants of the elongation cycle can independently recognize certain contexts and increase the readthrough of stop codons. Thus, the efficiency of translation termination is regulated by the 3′ nucleotide context following the stop codon and depends on the concentrations of eRFs and suppressor/near-cognate tRNAs.     

A Framework for Development and Communication of Absolute Environmental Sustainability Assessment Methods

An absolute environmental sustainability assessment (AESA) addresses whether a production or consumption activity can be considered environmentally sustainable in an absolute sense. This involves a comparison of its environmental pressure to its allocated environmental carrying capacity. AESA methods have been developed in multiple academic fields, each using their own set of concepts and terms with little communication across the fields. A recent growing interest in using AESA methods for decision support calls for a better common understanding of the constituents of an AESA method and how it can be communicated to scientific peers and to potential users. With this aim, we develop a framework for AESA methods, composed of a succession of four assessment steps and involving six methodological choices that must be made by the method developer or the user. We then use the framework to analyze and compare five selected AESA methods that focus on the release of phosphorus and nitrogen to the environment. In this manner, we show that the framework is able to systematically differentiate AESA methods that initially appear to be similar. Intended users of the framework include (1) method developers communicating new AESA methods to academic peers or potential method users and (2) researchers comparing a group of existing AESA methods and communicating their differences to their peers and to potential users looking for guidance on method selection.     

Rate of succession in restored wetlands and the role of site context

Question: Are changes in plant species composition, functional group composition and rates of species turnover consistent among early successional wetlands, and what is the role of landscape context in determining the rate of succession? Location: Twenty‐four restored wetlands in Illinois, USA. Methods: We use 4 years of vegetation sampling data from each site to describe successional trends and rates of species turnover in wetlands. We quantify: (1) the rate at which composition changes from early‐successional to late‐successional species and functional groups, as indicated by site movement in ordination space over time, and (2) the rate of change in the colonization and local extinction of individual species. We correlate the pace of succession to site area, isolation and surrounding land cover. Results: Some commonalities in successional trends were evident among sites. Annual species were replaced by clonal perennials, and colonization rates declined over time. However, differences among sites outweighed site age in determining species composition, and the pace of succession was influenced by a site's landscape setting. Rates of species turnover were higher in smaller wetlands. In addition, wetlands in agricultural landscapes underwent succession more rapidly, as indicated by a rapid increase in dominance by late‐successional plants. Conclusions: Although the outcome of plant community succession in restored wetlands was somewhat predictable, species composition and the pace of succession varied among sites. The ability of restoration practitioners to accelerate succession through active manipulation may be contingent upon landscape context.     

Intersectionality and trauma analysis in bioarchaeology

Intersectionality, the theory named by Kimberlé Crenshaw, outlines how multiple elements of an individual's social identity overlap to create and preserve societal inequalities and discrimination. Recently bioarchaeology's engagement with intersectionality has become increasingly explicit, as the field recognizes the lived experience of multiple axes of an individual's identity. Evidence of trauma can remain observable in an individual's skeleton for years, making it an ideal subject of study for intersectional analyses in bioarchaeology. Using contrasting case studies of two individuals who died in hospitals and were unclaimed after death, we explore the theoretical and methodological application of intersectionality to investigations of accidental and interpersonal trauma. Differences in identities and structural inequalities affect bone quality and health outcomes. As we demonstrate, a broken bone is the intersecting result of biological, histomorphological, sociocultural, and behavioral factors. This approach allows for a better acknowledgement of the inherent complexity of past lives, elevating and amplifying previously silenced voices. In this way, intersectionality in bioarchaeology demands social justice.     

Assimilation without groups?

In “Origins and Destinations”, Luthra, Soehl and Waldinger aim at “extending the canon” in research on immigrant integration. They do so by studying group and individual level characteristics across a large number of origin groups, thereby replacing group labels with theoretically relevant variables at the group level. In this review, three challenges in this endeavour are discussed: First of all, the analyses do not allow to disentangle the impact of group and individual level characteristics for all variables alike. Secondly, a primary data collection more tailored to the specifics of their conceptual framework is needed. This would many conclusions about how contexts of emigration and immigration truly matter above and beyond individual characteristic on a more solid ground. And third, the authors’ aim to abandon the use of origin group categories in empirical research on immigrant integration may come at a price.     

White families and race: colour-blind and colour-conscious approaches to white racial socialization

This paper examines the role that social context plays in mediating racial socialization in upper-middle-class white families. Outcomes of white racial socialization, as well as the process itself, depend in large part on the distinctive racial contexts designed by parents in which white children live and interact. I examine variation in white middle-school-aged children's common-sense racial knowledge and discuss the importance of exploring the social reproduction and reworking of racial ideologies and privilege in childhood.