Exposing and exploiting host-parasite arms race clues in SARS-CoV-2: a principally new method for improved T cell immunogenicity prediction.

Computational prediction of T cell epitopes is a crucial component in the development of novel vaccines. T cells in a healthy vertebrate host can recognize as non-self only those peptides that are present in the parasite's proteins but absent in the host's proteins. This principle enables us to determine the current and past host specificity of a parasite and to predict peptides capable of eliciting a T cell response. Building upon the detailed mapping of T cell clone specificity for Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) antigens, we employed Monte Carlo tests to determine that empirically confirmed T cell-stimulating peptides have a significantly increased proportion of pentapeptides, hexapeptides and heptapeptides not found in the human proteome (P < 0.0001, Cohen's d > 4.9). We observed a lower density of potential pentapeptide targets for T cell recognition in the spike protein from the human-adapted SARS-CoV-2 ancestor compared to 10 other SARS-CoV-2 proteins originating from the horseshoe bat-adapted ancestor. Our novel method for predicting T cell immunogenicity of SARS-CoV-2 peptides is four times more effective than previous approaches. We recommend utilizing our theory-based method where efficient empirically based algorithms are unavailable, such as in the development of certain veterinary vaccines, and combining it with empirical methods in other cases for optimal results.

Micropropagation as a Tool for the Conservation of Autochthonous Sorbus Species of Czechia.

Members of the genus Sorbus are the only endemic tree species that occur in Czechia. They are important components of endangered plant communities. Their natural regeneration is usually problematic because of their mode of reproduction and because they can survive in rare populations with small numbers of individuals. The aim of this study was to develop a successful micropropagation protocol for selected Sorbus species, of which two are endemic (S. gemella and S. omissa) and two are hybrid (S. × abscondita and S. × kitaibeliana). We found significant differences in shoot induction and rooting ability between the Sorbus species under study. With the exception of S. × abscondita, N6-benzyladenine had a significantly greater effect on shoot regeneration, both in terms of shoot number and total shoot length, than meta-topolin. Root induction was key to the successful micropropagation of the Sorbus species studied. Our results show that four Sorbus species can be successfully rooted under ex vitro conditions, without a rooting powder treatment in a steamed peat-perlite substrate. Auxin-untreated microcuttings of S. gemella, S. × kitaibeliana and S. omissa, but not S. × abscondita, rooted better than ones treated with indole-3-butyric acid. This is the first time a micropropagation protocol for S. omissa, S. × abscondita and S. × kitaibeliana has been published.

Thus spoke peptides: SARS-CoV-2 spike gene evolved in humans and then shortly in rats while the rest of its genome in horseshoe bats and then in treeshrews.

SARS-CoV-2 is suspected to be the product of a natural or artificial recombination of two viruses - one adapted to the horseshoe bat and the other, donor of the spike protein gene, adapted to an unknown species. Here we used a new method to search for the original host of the ancestor of the SARS-CoV-2 virus and for the donor of its gene for the spike protein, the molecule responsible for binding to and entering human cells. We computed immunological T-distances (the number of different peptides that are present in the viral proteins but absent in proteins of the host) between 11 species of coronaviruses and 38 representatives of the main mammal clades. Analyses of pentapeptides, the presumed principal targets of T-cell non-self recognition, showed the smallest T-distance of the spike protein of SARS-CoV-2 to humans, while the rest of SARS-CoV-2 proteome to the horseshoe bat. This suggests that the ancestor of SARS-CoV-2 was adapted to bats, but the spike gene donor was adapted to humans. Further analyses suggest that the ancestral coronavirus adapted to bats was shortly passaged in treeshrews, while the donor of the spike gene was shortly passaged in rats before the recombination event.

Forest Attendance in the Times of COVID-19-A Case Study on the Example of the Czech Republic.

The COVID-19 pandemic affected people all over the world, including the Czech Republic (CZ). In the CZ, a number of measures were applied in 2020 to reduce the contact between people and their mobility. This article dealt with the importance of forests during the pandemic. Data from 2019 and 2020 were compared. The qualitative data were obtained from two nationwide surveys, the first focused on forest attendance and forest fruit collection (about 1000 respondents per year), the second on the motivation to visit the forests (about 3700 respondents per year). The quantitative data were obtained on the regional level by analysing data from mobility counters. The impact of government restrictions was assessed. Findings: (1) there was a significant increase in the number of people who frequently visited the forest in 2020; (2) in 2020, the amount of households that collected forest fruits increased and was the highest for the monitored period; (3) the increased forest attendance significantly corresponded to the government restrictions. The analysis confirmed the great importance of forests for the citizens and, at the same time, the increased pressure on the forests' use-forest attendance and forest crops picking-(especially suburban ones) in times of COVID-19 restrictions.

Parasitism as the main factor shaping peptide vocabularies in current organisms.

Self/non-self-discrimination by vertebrate immune systems is based on the recognition of the presence of peptides in proteins of a parasite that are not contained in the proteins of a host. Therefore, a reduction of the number of 'words' in its own peptide vocabulary could be an efficient evolutionary strategy of parasites for escaping recognition. Here, we compared peptide vocabularies of 30 endoparasitic and 17 free-living unicellular organisms and also eight multicellular parasitic and 16 multicellular free-living organisms. We found that both unicellular and multicellular parasites used a significantly lower number of different pentapeptides than free-living controls. Impoverished pentapeptide vocabularies in parasites were observed across all five clades that contain both the parasitic and free-living species. The effect of parasitism on a number of peptides used in an organism's proteins is larger than effects of all other studied factors, including the size of a proteome, the number of encoded proteins, etc. This decrease of pentapeptide diversity was partly compensated for by an increased number of hexapeptides. Our results support the hypothesis of parasitism-associated reduction of peptide vocabulary and suggest that T-cell receptors mostly recognize the five amino acids-long part of peptides that are presented in the groove of major histocompatibility complex molecules.

Biomass of speckled alder on an air-polluted mountain site and its response to fertilization.

The article summarizes outcomes of a biomass study conducted in a young speckled alder plantation on a cold mountain site. At this location, the previously existing old forest was clear felled because of damage from air pollution, and present-day surface humus is in need of restoration. The intention of this study was to quantify the biomass and nutrients accumulated by alders and their components and assess whether the initial fertilization resulted in increased biomass production and nutrient accumulation in the biomass. Besides the control, two fertilized treatments were installed. In the surface treatment (SUT), the amendment was applied as a base dressing in small circles around trees. In the planting-hole treatment (PHT), the amendment was incorporated into soil inside the planting holes. Five growth seasons after planting and fertilization, six alders from each treatment were harvested including roots. Their biomass was quantified and analyzed for macroelements. The greatest pool of dry mass (DM) was branches in the control and stem wood in the fertilized treatments. The greatest pools of macroelements were leaves and branches. The most pronounced effects of fertilization were recorded in the DM and consequently in the absolute quantities of nutrients. The DM of an average tree in the control, SUT, and PHT was 85, 226, and 231 g, respectively. The absolute contents of nutrients per tree in the fertilized treatments showed the following increases, as compared with the control: (N) 2.5-2.6 times; (P) 1.6-2.4 times; (K) 1.8-2.1 times; and (Mg) 1.8-2.0 times, respectively. Speckled alder responded positively to fertilization.

Consensus in landscape preference judgments: the effects of landscape visual aesthetic quality and respondents' characteristics.

Landscape's visual aesthetic quality (VAQ) has been widely regarded as a valuable resource worthy of protection. Although great effort has been devoted to determining the factors driving aesthetic preferences, public consensus in judgments has been neglected in the vast majority of such studies. Therefore, the aim of our study was to analyze three main possible sources of judgment variance: landscape VAQ, landscape type, and variability among respondents. Based upon an extensive perception-based investigation including more than 400 hikers as respondents, we found that variance in respondents' judgments differed significantly among assessed landscape scenes. We discovered a significant difference in judgment variances within each investigated respondent characteristic (gender, age, education level, occupational classification, and respondent's type of residence). Judgment variance was at the same time affected by landscape VAQ itself - the higher the VAQ, the better the consensus. While differences caused by characteristics indicate subjectivity of aesthetic values, the knowledge that people better find consensus for positively perceived landscapes provides a cogent argument for legal protection of valuable landscape scenes.