Evolutionary relationships and sequence-structure determinants in human SARS coronavirus-2 spike proteins for host receptor recognition

Coronavirus disease 2019 (COVID-19) is a pandemic infectious disease caused by novel severe acute respiratory syndrome coronavirus-2 (SARS CoV-2). The SARS CoV-2 is transmitted more rapidly and readily than SARS CoV. Both, SARS CoV and SARS CoV-2 via their glycosylated spike proteins recognize the human angiotensin converting enzyme-2 (ACE-2) receptor. We generated multiple sequence alignments and phylogenetic trees for representative spike proteins of SARS CoV and SARS CoV-2 from various host sources in order to analyze the specificity in SARS CoV-2 spike proteins required for causing infection in humans. Our results show that among the genomes analyzed, two sequence regions in the N-terminal domain “MESEFR” and “SYLTPG” are specific to human SARS CoV-2. In the receptor-binding domain, two sequence regions “VGGNY“ and ”EIYQAGSTPCNGV” and a disulfide bridge connecting 480C and 488C in the extended loop are structural determinants for the recognition of human ACE-2 receptor. The complete genome analysis of representative SARS CoVs from bat, civet, human host sources, and human SARS CoV-2 identified the bat genome (GenBank code: MN996532.1) as closest to the recent novel human SARS CoV-2 genomes. The bat SARS CoV genomes (GenBank codes: MG772933 and MG772934) are evolutionary intermediates in the mutagenesis progression toward becoming human SARS CoV-2.     

Divergent growth of Norway spruce on Babia Góra Mountain in the western Carpathians

Growth divergence – i.e. the expression of divergent growth trends of neighboring trees – has certain implications for dendrochronological research, for instance in the context of climate reconstructions but also in terms of estimating net ecosystem productivity. Thus, understanding the underlying mechanisms is essential to extend our fundamental dendroecological knowledge. In this context, the Picea genus plays an important role since several of its species were reported to exhibit growth divergence. Here, we investigate a well sampled Norway spruce (Picea abies (L.) Karst) data set for growth divergence comprising ring-width and Blue Intensity measurements from seven sites on Babia Góra Mountain, at the border between Poland and Slovakia. By means of Principal Component Gradient Analysis, inter-series correlations, and climate growth relationships, we are able to show that I) Norway spruce on Babia Góra expressed growth divergence since the 1970s, II) the definition of groups increased the strength of population signals and the stability of climate-growth relationships, and III) Blue Intensity appeared as a more robust proxy for environmental conditions. We discuss soil heterogeneity, genetics, and air pollution as possible underlying mechanisms, thereby indicating further research avenues to obtain a better understanding of growth divergence.     

A salt on the bioenergy and biological invasions debate: salinity tolerance of the invasive biomass feedstock Arundo donax

Arundo donax L., commonly known as giant reed, is promising biomass feedstock that is also a notorious invasive plant in freshwater ecosystems around the world. Heretofore, the salt tolerance of A. donax had not been quantified even though anecdotal evidence suggests halophytic qualities. To test whole-plant and leaf level responses, we established a pot experiment on 80 scions propagated from an A. donax population that has naturalized on the shore of the San Francisco Bay Estuary. To quantify growth and physiological responses to salinity (NaCl), A. donax scions were divided into eight treatments and grown for 60 days across a range of salinities (0–42 dS m⁻¹). Classic growth analysis showed >80% reduction in overall growth at the highest salinities. Yet, there was zero mortality indicating that A. donax is able to tolerate high levels of salt. Declining photosynthesis rates were strongly correlated (R² > 0.97) with decreasing stomatal conductance, which was in turn closely related to increasing salinity. Leaf gas exchange revealed that stomata and leaf limitations of carbon dioxide were three times greater at high salinities. Nonetheless, even when salinities were 38–42 dS m⁻¹ A. donax was able to maintain assimilation rates 7–12 μmol m⁻² s⁻¹. Further, by maintaining 50% relative growth at salinities ~12 dS m⁻¹ A. donax can now be classified as ‘moderately salt tolerant’. A. donax leaf gas exchange and whole-plant salt tolerance are greater than many important food crops (i.e. maize, rice), the bioenergy feedstock Miscanthus × giganteus, as well as some uncultivated plant species (i.e. Populus and Salix) that are indigenous in regions A. donax currently invades. The results of this study have implications for both agronomists wishing to expand A. donax to fields dominated by saline soils, and for others who are concerned about the spread of A. donax with altered stream hydrology or sea-level rise.     

Reprogramming of Stem Cell Activity to Convert Thorns into Branches

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Biotic and abiotic determinants of the formation of ant mosaics in primary Neotropical rainforests

1. Ants are widespread in tropical rainforests, including in the canopy where territorially dominant arboreal species represent the main part of the arthropod biomass. 2. By mapping the territories of dominant arboreal ant species and using a null model analysis and a pairwise approach this study was able to show the presence of an ant mosaic on the upper canopy of a primary Neotropical rainforest (c. 1 ha sampled; 157 tall trees from 28 families). Although Neotropical rainforest canopies are frequently irregular, with tree crowns at different heights breaking the continuity of the territories of dominant ants, the latter are preserved via underground galleries or trails laid on the ground. 3. The distribution of the trees influences the structure of the ant mosaic, something related to the attractiveness of tree taxa for certain arboreal ant species rather than others. 4. Small‐scale natural disturbances, most likely strong winds in the area studied (presence of canopy gaps), play a role by favouring the presence of two ant species typical of secondary formations: Camponotus femoratus and Crematogaster levior, which live in parabiosis (i.e. share territories and nests but lodge in different cavities) and build conspicuous ant gardens. In addition, pioneer Cecropia myrmecophytic trees were recorded.