Interpretable pairwise distillations for generative protein sequence models

Many different types of generative models for protein sequences have been proposed in literature. Their uses include the prediction of mutational effects, protein design and the prediction of structural properties. Neural network (NN) architectures have shown great performances, commonly attributed to the capacity to extract non-trivial higher-order interactions from the data. In this work, we analyze two different NN models and assess how close they are to simple pairwise distributions, which have been used in the past for similar problems. We present an approach for extracting pairwise models from more complex ones using an energy-based modeling framework. We show that for the tested models the extracted pairwise models can replicate the energies of the original models and are also close in performance in tasks like mutational effect prediction. In addition, we show that even simpler, factorized models often come close in performance to the original models.     

Defoliation of a grass is mediated by the positive effect of dung deposition,moss removal and enhanced soil nutrient contents: results from a reindeer grazing simulation experiment

Herbivory is one of the key drivers shaping plant community dynamics. Herbivores can strongly influence plant productivity directly through defoliation and the return of nutrients in the form of dung and urine, but also indirectly by reducing the abundance of neighbouring plants and inducing changes in soil processes. However, the relative importance of these processes is poorly understood. We, therefore, established a common garden experiment to study plant responses to defoliation, dung addition, moss cover, and the soil legacy of reindeer grazing. We used an arctic tundra grazed by reindeer as our study system, and Festuca ovina, a common grazing‐tolerant grass species as the model species. The soil legacy of reindeer grazing had the strongest effect on plants, and resulted in higher growth in soils originating from previously heavily‐grazed sites. Defoliation also had a strong effect and reduced shoot and root growth and nutrient uptake. Plants did not fully compensate for the tissue lost due to defoliation, even when nutrient availability was high. In contrast, defoliation enhanced plant nitrogen concentrations. Dung addition increased plant production, nitrogen concentrations and nutrient uptake, although the effect was fairly small. Mosses also had a positive effect on aboveground plant production as long as the plants were not defoliated. The presence of a thick moss layer reduced plant growth following defoliation. This study demonstrates that grasses, even though they suffer from defoliation, can tolerate high densities of herbivores when all aspects of herbivores on ecosystems are taken into account. Our results further show that the positive effect of herbivores on plant growth via changes in soil properties is essential for plants to cope with a high grazing pressure. The strong effect of the soil legacy of reindeer grazing reveals that herbivores can have long‐lasting effects on plant productivity and ecosystem functioning after grazing has ceased.     

The Early Stages of Photosystem II Assembly Monitored by Measurements of Fluorescence Lifetime, Fluorescence Induction and Isoelectric Focusing of Chlorophyll-Proteins in Barley Etiochloroplasts

The relationship between functional and structural aspects ofPSII formation during greening of etiolated barley leaves hasbeen investigated using fluorescence lifetime measurements,fluorescence kinetics analysis and analysis of chlorophyll-proteincomplexes by IEF-PAGE. Two phases of different character couldbe distinguished in the course of the greening process in dark-grownplants. An early phase covering the first 3–4 h afterthe onset of illumination and a late phase covering the subsequentgreening. During the first phase the formation of PSII reactioncenters and their minor antenna components was observed as manifestedby the IEF-PAGE polypeptide pattern. This was accompanied byshortening of the slow and middle components of the fluorescencelifetime, as well as by the rapid drop in the amplitude of theslow component. A room temperature emission band at 676 nm wasassociated with uncoupled chlorophyll and with the slow fluorescencelifetime component during the first hours of greening. Duringthe late greening phase peripheral light-harvesting complexesof PSII were formed concomitantly to an increase in lifetimeand amplitude of the fast component and to a further decreasein the lifetime of the middle component. The gradual increasein PSII complexity during both phases of greening was also manifestedby changes in proportion and kinetic properties of PSII     

Diprenylated chalcones and other constituents from the twigs of Dorstenia barteri var. subtriangularis

The twigs of Dorstenia barteri var. subtriangularis yielded three diprenylated chalcones: (-)-3-(3,3-dimethylallyl)-5'-(2-hydroxy-3-methylbut-3-enyl)-4,2',4'-trihydroxychalcone, (+)-3-(3,3-dimethylallyl)-4',5'-[2'-(1-hydroxy-1-methylethyl)-dihydrofurano]-4,2'-dihydroxychalcone and 3,4-(6",6"-dimethyldihydropyrano)-4',5'-[2',-(1-hydroxy-1-methylethyl)-dihydrofurano]-2'-hydroxychalcone for which the names bartericins A, B and C, respectively, are proposed. Stipulin, beta-sitosterol and its 3-beta-D-glucopyranosyl derivative were also isolated. The structures of these secondary metabolites were determined on the basis of spectroscopic analysis, especially, NMR spectra in conjunction with 2D experiments, COSY, HMQC and HMBC. The structural relationship of bartericins B and C was further established by the chemical cyclization of one to the other.     

The mechanism of the angiotensin-converting enzyme inhibitor quinapril is not related to bradykinin level in heart tissue

In order to examine the effect of the angiotensin-converting enzyme inhibitor (ACEi) quinapril, we performed a sensitive and specific radioimmunoassay (RIA) to quantify bradykinin, BK-(1-9), in heart and kidney tissues. The BK-(1-9) level was unaffected in the heart of sham and water-deprived rats treated for 2h with quinapril (10mg/kg), but was significantly higher in the kidneys in the two groups. In these conditions, circulating and tissue angiotensin II (Ang II) levels were significantly decreased by quinapril. Moreover, our results indicated that acute treatment with this dose of quinapril induced kinin-mediated effects which were not related to its action on bradykinin degradation in rat hearts.