Cysteine tRNA acts as a stop codon readthrough-inducing tRNA in the human HEK293T cell line

Under certain circumstances, any of the three termination codons can be read through by a near-cognate tRNA; i.e., a tRNA whose two out of three anticodon nucleotides base pair with those of the stop codon. Unless programed to synthetize C-terminally extended protein variants with expanded physiological roles, readthrough represents an undesirable translational error. On the other side of a coin, a significant number of human genetic diseases is associated with the introduction of nonsense mutations (premature termination codons [PTCs]) into coding sequences, where stopping is not desirable. Here, the tRNA's ability to induce readthrough opens up the intriguing possibility of mitigating the deleterious effects of PTCs on human health. In yeast, the UGA and UAR stop codons were described to be read through by four readthrough-inducing rti-tRNAs-tRNATrp and tRNACys, and tRNATyr and tRNAGln, respectively. The readthrough-inducing potential of tRNATrp and tRNATyr was also observed in human cell lines. Here, we investigated the readthrough-inducing potential of human tRNACys in the HEK293T cell line. The tRNACys family consists of two isoacceptors, one with ACA and the other with GCA anticodons. We selected nine representative tRNACys isodecoders (differing in primary sequence and expression level) and tested them using dual luciferase reporter assays. We found that at least two tRNACys can significantly elevate UGA readthrough when overexpressed. This indicates a mechanistically conserved nature of rti-tRNAs between yeast and human, supporting the idea that they could be used in the PTC-associated RNA therapies.

Unraveling the palindromic and nonpalindromic motifs of retroviral integration site sequences by statistical mixture models

A weak palindromic nucleotide motif is the hallmark of retroviral integration site alignments. Given that the majority of target sequences are not palindromic, the current model explains the symmetry by an overlap of the nonpalindromic motif present on one of the half-sites of the sequences. Here, we show that the implementation of multicomponent mixture models allows for different interpretations consistent with the existence of both palindromic and nonpalindromic submotifs in the sets of integration site sequences. We further show that the weak palindromic motifs result from freely combined site-specific submotifs restricted to only a few positions proximal to the site of integration. The submotifs are formed by either palindrome-forming nucleotide preference or nucleotide exclusion. Using the mixture models, we also identify HIV-1-favored palindromic sequences in Alu repeats serving as local hotspots for integration. The application of the novel statistical approach provides deeper insight into the selection of retroviral integration sites and may prove to be a valuable tool in the analysis of any type of DNA motifs.

Kinetic Target-Guided Synthesis of Small-Molecule G-Quadruplex Stabilizers

The formation of a G-quadruplex motif in the promoter region of the c-MYC protooncogene prevents its expression. Accordingly, G-quadruplex stabilization by a suitable ligand may be a viable approach for anticancer therapy. In our study, we used the 4-(4-methylpiperazin-1-yl)aniline molecule, previously identified as a fragment library screen hit, as a template for the SAR-guided design of a new small library of clickable fragments and subjected them to click reactions, including kinetic target-guided synthesis in the presence of a G-quadruplex forming oligonucleotide Pu24. We tested the clickable fragments and products of click reactions for their G-quadruplex stabilizing activity and determined their mode of binding to the c-MYC G-quadruplex by NMR spectroscopy. The enhanced stabilizing potency of click products in biology assays (FRET, Polymerase extension assay) matched the increased yields of in situ click reactions. In conclusion, we identified the newly synthesized click products of bis-amino derivatives of 4-(4-methylpiperazin-1-yl)aniline as potent stabilizers of c-MYC G-quadruplex, and their further evolution may lead to the development of an efficient tool for cancer treatment.

Drivers of future alien species impacts: An expert-based assessment

Understanding the likely future impacts of biological invasions is crucial yet highly challenging given the multiple relevant environmental, socio-economic and societal contexts and drivers. In the absence of quantitative models, methods based on expert knowledge are the best option for assessing future invasion trajectories. Here, we present an expert assessment of the drivers of potential alien species impacts under contrasting scenarios and socioecological contexts through the mid-21st century. Based on responses from 36 experts in biological invasions, moderate (20%-30%) increases in invasions, compared to the current conditions, are expected to cause major impacts on biodiversity in most socioecological contexts. Three main drivers of biological invasions-transport, climate change and socio-economic change-were predicted to significantly affect future impacts of alien species on biodiversity even under a best-case scenario. Other drivers (e.g. human demography and migration in tropical and subtropical regions) were also of high importance in specific global contexts (e.g. for individual taxonomic groups or biomes). We show that some best-case scenarios can substantially reduce potential future impacts of biological invasions. However, rapid and comprehensive actions are necessary to use this potential and achieve the goals of the Post-2020 Framework of the Convention on Biological Diversity.

Nanovortex-Driven All-Dielectric Optical Diffusion Boosting and Sorting Concept for Lab-on-a-Chip Platforms

The ever-growing field of microfluidics requires precise and flexible control over fluid flows at reduced scales. Current constraints demand a variety of controllable components to carry out several operations inside microchambers and microreactors. In this context, brand-new nanophotonic approaches can significantly enhance existing capabilities providing unique functionalities via finely tuned light-matter interactions. A concept is proposed, featuring dual on-chip functionality: boosted optically driven diffusion and nanoparticle sorting. High-index dielectric nanoantennae is specially designed to ensure strongly enhanced spin-orbit angular momentum transfer from a laser beam to the scattered field. Hence, subwavelength optical nanovortices emerge driving spiral motion of plasmonic nanoparticles via the interplay between curl-spin optical forces and radiation pressure. The nanovortex size is an order of magnitude smaller than that provided by conventional beam-based approaches. The nanoparticles mediate nanoconfined fluid motion enabling moving-part-free nanomixing inside a microchamber. Moreover, exploiting the nontrivial size dependence of the curled optical forces makes it possible to achieve precise nanoscale sorting of gold nanoparticles, demanded for on-chip separation and filtering. Altogether, a versatile platform is introduced for further miniaturization of moving-part-free, optically driven microfluidic chips for fast chemical analysis, emulsion preparation, or chemical gradient generation with light-controlled navigation of nanoparticles, viruses or biomolecules.

Competition among native and invasive Phragmites australis populations: An experimental test of the effects of invasion status, genome size, and ploidy level

Among the traits whose relevance for plant invasions has recently been suggested are genome size (the amount of nuclear DNA) and ploidy level. So far, research on the role of genome size in invasiveness has been mostly based on indirect evidence by comparing species with different genome sizes, but how karyological traits influence competition at the intraspecific level remains unknown. We addressed these questions in a common-garden experiment evaluating the outcome of direct intraspecific competition among 20 populations of Phragmites australis, represented by clones collected in North America and Europe, and differing in their status (native and invasive), genome size (small and large), and ploidy levels (tetraploid, hexaploid, or octoploid). Each clone was planted in competition with one of the others in all possible combinations with three replicates in 45-L pots. Upon harvest, the identity of 21 shoots sampled per pot was revealed by flow cytometry and DNA analysis. Differences in performance were examined using relative proportions of shoots of each clone, ratios of their aboveground biomass, and relative yield total (RYT). The performance of the clones in competition primarily depended on the clone status (native vs. invasive). Measured in terms of shoot number or aboveground biomass, the strongest signal observed was that North American native clones always lost in competition to the other two groups. In addition, North American native clones were suppressed by European natives to a similar degree as by North American invasives. North American invasive clones had the largest average shoot biomass, but only by a limited, nonsignificant difference due to genome size. There was no effect of ploidy on competition. Since the North American invaders of European origin are able to outcompete the native North American clones, we suggest that their high competitiveness acts as an important driver in the early stages of their invasion.

Seasonal drivers of understorey temperature buffering in temperate deciduous forests across Europe

AIM

Forest understorey microclimates are often buffered against extreme heat or cold, with important implications for the organisms living in these environments. We quantified seasonal effects of understorey microclimate predictors describing canopy structure, canopy composition and topography (i.e., local factors) and the forest patch size and distance to the coast (i.e., landscape factors).

LOCATION

Temperate forests in Europe.

TIME PERIOD

2017-2018.

MAJOR TAXA STUDIED

Woody plants.

METHODS

We combined data from a microclimate sensor network with weather-station records to calculate the difference, or offset, between temperatures measured inside and outside forests. We used regression analysis to study the effects of local and landscape factors on the seasonal offset of minimum, mean and maximum temperatures.

RESULTS

The maximum temperature during the summer was on average cooler by 2.1 °C inside than outside forests, and the minimum temperatures during the winter and spring were 0.4 and 0.9 °C warmer. The local canopy cover was a strong nonlinear driver of the maximum temperature offset during summer, and we found increased cooling beneath tree species that cast the deepest shade. Seasonal offsets of minimum temperature were mainly regulated by landscape and topographic features, such as the distance to the coast and topographic position.

MAIN CONCLUSIONS

Forest organisms experience less severe temperature extremes than suggested by currently available macroclimate data; therefore, climate-species relationships and the responses of species to anthropogenic global warming cannot be modelled accurately in forests using macroclimate data alone. Changes in canopy cover and composition will strongly modulate the warming of maximum temperatures in forest understories, with important implications for understanding the responses of forest biodiversity and functioning to the combined threats of land-use change and climate change. Our predictive models are generally applicable across lowland temperate deciduous forests, providing ecologically important microclimate data for forest understories.