Survival of Rhizobium in monoculture and binary population with Rhizosphere bacteria

The survival of pure cultures of Rhizobium leguminosarum bv. pisum and Rhizobium trifolii and their interaction with associative diazotrophic and phosphate-mobilizing bacteria after inoculation of sterile soil were studied. The viable heterotypical diazotrophic and rhizobial phosphate-mobilizing association was shown to be formed whose efficiency was 14% (clover) and 28% (pea) higher compared to monorhizobial inoculates.     

Biologically Active Polypeptides and Hydrolytic Enzymes in Sea Anemones of Northern Temperate Waters

The content of biologically active polypeptides in aqueous and ethanol extracts of seven sea anemone species collected near Sakhalin Island (Sea of Okhotsk) and in Posyet Bay (Sea of Japan) was analyzed. Water extracts of the sea anemone Cribrinopsis similis showed the highest hemolytic activity, while ethanol extracts proved to have toxic properties. The levels of toxic and hemolytic activity of extracts of sea anemones inhabiting northern temperate waters were 2 to 3 orders of magnitude lower, compared to tropic species. The reason for this is likely to be the differences in the habitat conditions and biological traits of these animals. The water extracts of all species possessed proteolytic, phospholipase A2, and low DNAase activities, except Actinostola sp., whose aqueous extract contained a high activity alkaline DNAase. The species studied contained a wide range of proteinase inhibitors, O-glycosyl hydrolases (glycosidases and polysaccharide hydrolases). Water extracts of C. similis and Stomphia coccinea possessed the highest laminarinase activity. High activity of N-galactopyranosidase was found in water extracts of S. coccinea and Oulactis orientalis.     

XENet: Using a new graph convolution to accelerate the timeline for protein design on quantum computers

Graph representations are traditionally used to represent protein structures in sequence design protocols in which the protein backbone conformation is known. This infrequently extends to machine learning projects: existing graph convolution algorithms have shortcomings when representing protein environments. One reason for this is the lack of emphasis on edge attributes during massage-passing operations. Another reason is the traditionally shallow nature of graph neural network architectures. Here we introduce an improved message-passing operation that is better equipped to model local kinematics problems such as protein design. Our approach, XENet, pays special attention to both incoming and outgoing edge attributes. We compare XENet against existing graph convolutions in an attempt to decrease rotamer sample counts in Rosetta’s rotamer substitution protocol, used for protein side-chain optimization and sequence design. This use case is motivating because it both reduces the size of the search space for classical side-chain optimization algorithms, and allows larger protein design problems to be solved with quantum algorithms on near-term quantum computers with limited qubit counts. XENet outperformed competing models while also displaying a greater tolerance for deeper architectures. We found that XENet was able to decrease rotamer counts by 40% without loss in quality. This decreased the memory consumption for classical pre-computation of rotamer energies in our use case by more than a factor of 3, the qubit consumption for an existing sequence design quantum algorithm by 40%, and the size of the solution space by a factor of 165. Additionally, XENet displayed an ability to handle deeper architectures than competing convolutions.     

Conformational Stability and Hemolytic Activity of Actinoporin RTX-SII from the Sea Anemone <Emphasis Type="Italic">Radianthus macrodactylus</Emphasis>

The spatial organization of actinoporin RTX-SII from the sea anemone Radianthus macrodactylus on the level of tertiary and secondary structures was studied by UV and CD spectroscopy and intrinsic protein fluorescence. The specific and molar extinction coefficients of RTX-SII were determined. The percentages of canonical secondary structures of actinoporin were calculated. The tertiary structure of the polypeptide is well developed and its secondary structure is highly ordered and contains about 50% antiparallel folded beta-sheets. The irreversible thermal denaturation of RTX-SII was studied by CD spectroscopy; a conformational transition occurs at 53 degrees C. Above this temperature irreversible conformational changes are observed in the secondary and tertiary structures. This is accompanied by redistribution of the content of regular and distorted forms of beta-sheet and also by increase in the content of an unordered form. It is suggested that an intermediate is formed in the process of thermal denaturation. Acid-base titration of RTX-SII results in irreversible conformational changes at pH below 2.0 and above 12.0. As shown by intrinsic protein fluorescence, tyrosine residues of RTX-SII make a fundamental contribution to emission, and the total fluorescence depends more on temperature and ionic strength of the solution than tryptophan fluorescence. The data on conformational stability of actinoporin are correlated with data on its hemolytic activity. Activity of RTX-SII significantly decreases at increased temperature and slightly decreases at low pH. Hemolytic activity drastically increases at high pH. Increase in the actinoporin activity at pH above 10 seems to be caused by ionization of the molecule.     

Survival of Rhizobiumin a Monoculture and Binary Population with Rhizosphere Bacteria

The survival of pure cultures of Rhizobium leguminosarumbv. pisumand Rhizobium trifoliiand their interaction with associative diazotrophic and phosphate-mobilizing bacteria after inoculation of sterile soil were studied. The viable heterotypic diazotrophic and rhizobial phosphate-mobilizing association was formed whose efficiency was 14% (clover) and 28% (pea) higher compared to monorhizobial inoculates.