Molecular dynamics simulations reveal the balance of forces governing the formation of a guanine tetrad—a common structural unit of G-quadruplex DNA

G-quadruplexes (G4) are nucleic acid conformations of guanine-rich sequences, in which guanines are arranged in the square-planar G-tetrads, stacked on one another. G4 motifs form in vivo and are implicated in regulation of such processes as gene expression and chromosome maintenance. The structure and stability of various G4 topologies were determined experimentally; however, the driving forces for their formation are not fully understood at the molecular level. Here, we used all-atom molecular dynamics to probe the microscopic origin of the G4 motif stability. By computing the free energy profiles governing the dissociation of the 3′-terminal G-tetrad in the telomeric parallel-stranded G4, we examined the thermodynamic and kinetic stability of a single G-tetrad, as a common structural unit of G4 DNA. Our results indicate that the energetics of guanine association alone does not explain the overall stability of the G-tetrad and that interactions involving sugar–phosphate backbone, in particular, the constrained minimization of the phosphate–phosphate repulsion energy, are crucial in providing the observed enthalpic stabilization. This enthalpic gain is largely compensated by the unfavorable entropy change due to guanine association and optimization of the backbone topology.     

Variability of polar scurvygrass Cochlearia groenlandica individual traits along a seabird influenced gradient across Spitsbergen tundra

In the resource-limited Arctic environment, vegetation developing near seabird colonies is exceptionally luxuriant. Nevertheless, there are very few detailed quantitative studies of any specific plant species responses to ornithogenic manuring. Therefore, we studied variability of polar scurvygrass Cochlearia groe nlandica individual biomass and leaf width along a seabird influenced gradient determining environmental conditions for vegetation in south-west Spitsbergen. We found seabird colony effect being a paramount factor responsible for augmented growth of C. groenlandica. The species predominated close to the colony and reached the highest mean values of individual biomass (1.4 g) and leaf width (26.6 mm) 10 m below the colony. Its abundance and size declined towards the coast. Both C. groenlandica individual traits significantly decreased with distance from the colony, soil water and organic matter content and increased with guano deposition, soil δ ¹⁵N, conductivity, acidity and nitrate, phosphate and potassium ion content. Our study supports the hypothesis that seabirds have fundamental importance for vegetation growth in poor Arctic environment. Highly plastic species such as C. groenlandica may be a useful instrument in detecting habitat condition changes, for instance resulting from climate change.     

Cretaceous roots of the amphisbaenian lizards

Amphisbaenians are highly specialized limbless burrowing lizards of controversial relationships. Among fossil lizards, the Eocene (47 Ma) Cryptolacerta is allegedly closest to the amphisbaenian ancestor, but this is put in doubt in this study. Similarities between Cryptolacerta and amphisbaenians, such as limb reduction and expansion of the skull roof, may be a result of parallel evolution. Instead, the Late Cretaceous lizard Slavoia with well‐developed limbs and several plesiomorphic skull characters is proposed to be the oldest known stem amphisbaenian. This is supported by two different phylogenetic analyses and observations on numerous specimens together representing almost the whole skeleton. Among the unique features, that Slavoia shares with amphisbaenians, the most significant are vomers strongly underlapping palatines and pterygoid quadrate ramus tightly wrapping around posteromedial surface of quadrate. The anatomy of Slavoia suggests that the reinforcement of the snout in amphisbaenian evolution preceded the elongation of the postorbital part of the skull, and that of the body, as well as modification of the limbs. Reduction of its hindlimbs was more advanced than that of the forelimbs. The ancient geological age of the central Asiatic Slavoia suggests that diversification of the main North American amphisbaenian groups may have resulted from a faunal dispersals from Asia after the Late Cretaceous.     

Gene duplications,divergence and recombination shape adaptive evolution of the fish ectoparasite Gyrodactylus bullatarudis

Determining the molecular basis of parasite adaptation to its host is an important component in understanding host–parasite coevolution and the epidemiology of parasitic infections. Here, we investigate short‐ and long‐term adaptive evolution in the eukaryotic parasite Gyrodactylus bullatarudis infecting Caribbean guppies (Poecilia reticulata), by comparing the reference genome of Tobagonian G. bullatarudis with other Platyhelminthes, and by analysing resequenced samples from local Trinidadian populations. At the macroevolutionary timescale, we observed duplication of G‐protein and serine proteases genes, which are probably important in host–parasite arms races. Serine protease also showed strong evidence of ongoing, diversifying selection at the microevolutionary timescale. Furthermore, our analyses revealed that a hybridization event, involving two divergent genomes, followed by recombination has dramatically affected the genetic composition of Trinidadian populations. The recombinant genotypes invaded Trinidad and replaced local parasites in all populations. We localized more than 300 genes in regions fixed in local populations for variants of different origin, possibly due to diversifying selection pressure from local host populations. In addition, around 70 genes were localized in regions identified as heterozygous in some, but not all, individuals. This pattern is consistent with a very recent spread of recombinant parasites. Overall, our results are consistent with the idea that recombination between divergent genomes can result in particularly successful parasites.     

The Crested Lark Galerida cristata as an example of a bird species that benefits from agricultural management in western Poland

ABSTRACT

Capsule: The Crested Lark Galerida cristata as an example of a species which selects habitats which have undergone agricultural intensification.

Aims: To describe habitat preferences of the Crested Lark in western Poland.

Methods: We surveyed 30 randomly chosen study plots (1?km²) in western Poland to detect breeding pairs of Crested Larks. Sentinel and direct observations in the field were used to provide habitat data. Generalized linear mixed models were used to determine what type of environments habitats were selected by the Crested Larks.

Results: We recorded a total of 106 pairs of Crested Larks in 30 study plots. Birds inhabited farmland environments, where their preferred habitats included buildings, silage, and arable land with cereals.

Conclusion: Silage, which is associated with agricultural intensification within agricultural landscapes, increased the chances of the occurrence of Crested Larks.     

Euthyroid Sick Syndrome as a Prognostic Indicator of COVID-19 Pulmonary Involvement,Associated With Poorer Disease Prognosis and Increased Mortality

ObjectiveThe prevalence of euthyroid sick syndrome (ESS) and its association with the prognosis of COVID-19 and mortality in patients with lung involvement in COVID-19 have not yet been elucidated.MethodsClinical and laboratory data of patients with COVID-19 with or without ESS were collected retrospectively and analyzed on admission. All subjects were admitted to the Department of Internal Diseases and Clinical Pharmacology at Bieganski Hospital between December 2020 and April 2021.ResultsIn total, 310 medical records of patients with COVID-19 were analyzed retrospectively. Among 215 enrolled patients, 82 cases of ESS were diagnosed. The patients with ESS had higher pro-inflammatory factor levels, longer hospitalizations, and a higher risk of requiring high-flow nasal oxygen therapy or intubation than the patients without ESS. The Kaplan-Meier curve indicated that the patients with ESS had a lower probability of survival when computed tomography showed ≤50% parenchymal involvement compared with that in patients without ESS. However, no differences in mortality were noted in those with more than 50% parenchymal involvement. The survival curve showed that ESS was associated with a higher risk of mortality during hospitalization.ConclusionESS is closely associated with a poor prognosis, including longer hospitalizations, more frequent intubation, transfer to the intensive care unit, and a higher mortality rate in patients with COVID-19. ESS is a potential prognostic predictor of survival, regardless of lung involvement in COVID-19.     

The Dundee Resource for Sequence Analysis and Structure Prediction

The Dundee Resource for Sequence Analysis and Structure Prediction (DRSASP; http://www.compbio.dundee.ac.uk/drsasp.html ) is a collection of web services provided by the Barton Group at the University of Dundee. DRSASP's flagship services are the JPred4 webserver for secondary structure and solvent accessibility prediction and the JABAWS 2.2 webserver for multiple sequence alignment, disorder prediction, amino acid conservation calculations, and specificity‐determining site prediction. DRSASP resources are available through conventional web interfaces and APIs but are also integrated into the Jalview sequence analysis workbench, which enables the composition of multitool interactive workflows. Other existing Barton Group tools are being brought under the banner of DRSASP, including NoD (Nucleolar localization sequence detector) and 14‐3‐3‐Pred. New resources are being developed that enable the analysis of population genetic data in evolutionary and 3D structural contexts. Existing resources are actively developed to exploit new technologies and maintain parity with evolving web standards. DRSASP provides substantial computational resources for public use, and since 2016 DRSASP services have completed over 1.5 million jobs.