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Author(s):  
V. E. Yeshenko ◽  
◽  
G. V. Koval

Formulation of the problem. Crop rotations of modern field agriculture should be developed according to the principle of classical fruit change, which is an important factor in the high productivity of individual crops on different agro-backgrounds, which can be different ways of the depth of the main tillage. Verification of the latter was the main task of our research. Conditions and methodology. Field studies were carried out in a stationary experiment on podzolized chernozem with a 5-field crop rotation with such an alternation of spring crops: soybeans – rapeseed – wheat – oil flax – barley. The experiment compared the effect of plowing and flat-cut loosening at 15–17, 20–22 and 25–27 cm on the weediness of crops, crop yield and the productivity of crop rotation in terms of the yield of feed units and assimilated protein. Research results. It has been established that a significant part of weed seeds after flat-cutting loosening is concentrated in a layer of 0–10 cm, from where, under favorable moisture conditions, it can germinate with the formation of seedlings, which can bloom before cold weather and replenish the stock of weed seeds in the soil. During moldboard plowing, weed seeds are evenly distributed over the entire arable layer, as a result of which it can be half as much in the 0-10 cm layer as after non-moldboard plowing. Therefore, the actual weediness of crops cultivated in crop rotation has always been higher after flat-cutting loosening: soybeans – by 22.1 %, rapeseed – by 72.6 %, and wheat, oil flax and barley – 15.0, respectively; 20.4 and 20.3%. On average for the crop rotation, this increase averaged 25.2 % over three years. A decrease in the depth of cultivation also caused contamination of crops, and its deepening as a whole in the crop rotation had a positive effect on the cleanliness of crops from weeds. The level of weediness of crops of cultivated crops at the beginning of the growing season should be considered a determining factor in the formation of the productivity of these crops due to the presence of a strong and very strong correlation between these indicators. Wheat was the most productive in terms of the yield of feed units, and soy was the most productive in terms of the yield of digestible protein. This applied to both methods or techniques of the main processing, and individual crops against the background of plowing had an advantage in both productivity indicators over flat-cut loosening. The productivity of crops and crop rotation was higher against the background of deep cultivation compared to medium and shallow cultivation. Conclusions. The use of flat-cut loosening instead of moldboard plowing, as well as a decrease in the depth of both methods of processing, is accompanied by a significant increase in the contamination of crops. As well as a decrease in the yield of the main products and a noticeable decrease in the productivity of a 5-field crop rotation in terms of the yield of feed units and assimilated protein.


PLoS ONE ◽  
2021 ◽  
Vol 16 (9) ◽  
pp. e0257886
Author(s):  
Xubiao Peng ◽  
Antti J. Niemi

Novel topological methods are introduced to protein research. The aim is to identify hot-spot sites where a bifurcation can alter the local topology of the protein backbone. Since the shape of a protein is intimately related to its biological function, a substitution that causes a bifurcation should have an enhanced capacity to change the protein’s function. The methodology applies to any protein but it is developed with the SARS-CoV-2 spike protein as a timely example. First, topological criteria are introduced to identify and classify potential bifurcation hot-spot sites along the protein backbone. Then, the expected outcome of asubstitution, if it occurs, is estimated for a general class of hot-spots, using a comparative analysis of the surrounding backbone segments. The analysis combines the statistics of structurally commensurate amino acid fragments in the Protein Data Bank with general stereochemical considerations. It is observed that the notorious D614G substitution of the spike protein is a good example of a bifurcation hot-spot. A number of topologically similar examples are then analyzed in detail, some of them are even better candidates for a bifurcation hot-spot than D614G. The local topology of the more recently observed N501Y substitution is also inspected, and it is found that this site is proximal to a different kind of local topology changing bifurcation.


2021 ◽  
Author(s):  
Gáspár Pándy-Szekeres ◽  
Mauricio Esguerra ◽  
Alexander S Hauser ◽  
Jimmy Caroli ◽  
Christian Munk ◽  
...  

Abstract Two-thirds of signaling substances, several sensory stimuli and over one-third of drugs act via receptors coupling to G proteins. Here, we present an online platform for G protein research with reference data and tools for analysis, visualization and design of scientific studies across disciplines and areas. This platform may help translate new pharmacological, structural and genomic data into insights on G protein signaling vital for human physiology and medicine. The G protein database is accessible at https://gproteindb.org.


2021 ◽  
Author(s):  
Violeta Muñoz-Fuentes ◽  
Hamed Haselimashhadi ◽  
Luis Santos ◽  
Henrik Westerberg ◽  
Helen Parkinson ◽  
...  

AbstractMost current biomedical and protein research focuses only on a small proportion of genes, which results in a lost opportunity to identify new gene-disease associations and explore new opportunities for therapeutic intervention. The International Mouse Phenotyping Consortium (IMPC) focuses on elucidating gene function at scale for poorly characterized and/or under-studied genes. A key component of the IMPC initiative is the implementation of a broad phenotyping pipeline, which is facilitating the discovery of pleiotropy. Characterizing pleiotropy is essential to identify gene-disease associations, and it is of particular importance when elucidating the genetic causes of syndromic disorders. Here we show how the IMPC is effectively uncovering pleiotropy and how the new mouse models and gene function hypotheses generated by the IMPC are increasing our understanding of the mammalian genome, forming the basis of new research and identifying new gene-disease associations.


IUCrJ ◽  
2021 ◽  
Vol 8 (5) ◽  
pp. 842-852
Author(s):  
Jisub Hwang ◽  
Sun-Ha Park ◽  
Chang Woo Lee ◽  
Hackwon Do ◽  
Seung Chul Shin ◽  
...  

MarR family proteins regulate the transcription of multiple antibiotic-resistance genes and are widely found in bacteria and archaea. Recently, a new MarR family gene was identified by genome analysis of the psychrophilic bacterium Paenisporosarcina sp. TG-14, which was isolated from sediment-laden basal ice in Antarctica. In this study, the crystal structure of the MarR protein from Paenisporosarcina sp. TG-14 (PaMarR) was determined at 1.6 Å resolution. In the crystal structure, a novel lipid-type compound (palmitic acid) was found in a deep cavity, which was assumed to be an effector-binding site. Comparative structural analysis of homologous MarR family proteins from a mesophile and a hyperthermophile showed that the DNA-binding domain of PaMarR exhibited relatively high mobility, with a disordered region between the β1 and β2 strands. In addition, structural comparison with other homologous complex structures suggests that this structure constitutes a conformer transformed by palmitic acid. Biochemical analysis also demonstrated that PaMarR binds to cognate DNA, where PaMarR is known to recognize two putative binding sites depending on its molar concentration, indicating that PaMarR binds to its cognate DNA in a stoichiometric manner. The present study provides structural information on the cold-adaptive MarR protein with an aliphatic compound as its putative effector, extending the scope of MarR family protein research.


PLoS ONE ◽  
2021 ◽  
Vol 16 (7) ◽  
pp. e0254118
Author(s):  
Cristina Cecchetti ◽  
Jannik Strauss ◽  
Claudia Stohrer ◽  
Claire Naylor ◽  
Edward Pryor ◽  
...  

Membrane proteins have a range of crucial biological functions and are the target of about 60% of all prescribed drugs. For most studies, they need to be extracted out of the lipid-bilayer, e.g. by detergent solubilisation, leading to the loss of native lipids, which may disturb important protein-lipid/bilayer interactions and thus functional and structural integrity. Relipidation of membrane proteins has proven extremely successful for studying challenging targets, but the identification of suitable lipids can be expensive and laborious. Therefore, we developed a screen to aid the high-throughput identification of beneficial lipids. The screen covers a large lipid space and was designed to be suitable for a range of stability assessment methods. Here, we demonstrate its use as a tool for identifying stabilising lipids for three membrane proteins: a bacterial pyrophosphatase (Tm-PPase), a fungal purine transporter (UapA) and a human GPCR (A2AR). A2AR is stabilised by cholesteryl hemisuccinate, a lipid well known to stabilise GPCRs, validating the approach. Additionally, our screen also identified a range of new lipids which stabilised our test proteins, providing a starting point for further investigation and demonstrating its value as a novel tool for membrane protein research. The pre-dispensed screen will be made commercially available to the scientific community in future and has a number of potential applications in the field.


2021 ◽  
pp. 1-11
Author(s):  
Daniel Gómez-Pérez ◽  
Vasvi Chaudhry ◽  
Ariane Kemen ◽  
Eric Kemen

Amyloids have proven to be a widespread phenomenon rather than an exception. Many proteins presenting the hallmarks of this characteristic beta sheet-rich folding have been described to date. Particularly common are functional amyloids that play an important role in the promotion of survival and pathogenicity in prokaryotes. Here, we describe important developments in amyloid protein research that relate to microbe-microbe and microbe-host interactions in the plant microbiome. Starting with biofilms, which are a broad strategy for bacterial persistence that is extremely important for plant colonization. Microbes rely on amyloid-based mechanisms to adhere and create a protective coating that shelters them from external stresses and promotes cooperation. Another strategy generally carried out by amyloids is the formation of hydrophobic surface layers. Known as hydrophobins, these proteins coat the aerial hyphae and spores of plant pathogenic fungi, as well as certain bacterial biofilms. They contribute to plant virulence through promoting dissemination and infectivity. Furthermore, antimicrobial activity is an interesting outcome of the amyloid structure that has potential application in medicine and agriculture. There are many known antimicrobial amyloids released by animals and plants; however, those produced by bacteria or fungi remain still largely unknown. Finally, we discuss amyloid proteins with a more indirect mode of action in their host interactions. These include virulence-promoting harpins, signaling transduction that functions through amyloid templating, and root nodule bacteria proteins that promote plant-microbe symbiosis. In summary, amyloids are an interesting paradigm for their many functional mechanisms linked to bacterial survival in plant-associated microbial communities.


PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11330
Author(s):  
Julian Echave

Studying the effect of perturbations on protein structure is a basic approach in protein research. Important problems, such as predicting pathological mutations and understanding patterns of structural evolution, have been addressed by computational simulations that model mutations using forces and predict the resulting deformations. In single mutation-response scanning simulations, a sensitivity matrix is obtained by averaging deformations over point mutations. In double mutation-response scanning simulations, a compensation matrix is obtained by minimizing deformations over pairs of mutations. These very useful simulation-based methods may be too slow to deal with large proteins, protein complexes, or large protein databases. To address this issue, I derived analytical closed formulas to calculate the sensitivity and compensation matrices directly, without simulations. Here, I present these derivations and show that the resulting analytical methods are much faster than their simulation counterparts.


2021 ◽  
Vol 22 (8) ◽  
pp. 4076
Author(s):  
Lidia Sanchez-Moral ◽  
Neus Ràfols ◽  
Clara Martori ◽  
Tony Paul ◽  
Érica Téllez ◽  
...  

CD5L, a protein expressed and secreted mainly by macrophages, is emerging as a critical immune effector. In addition to its well-defined function as an anti-apoptotic protein, research over the last decade has uncovered additional roles that range from pattern recognition to autophagy, cell polarization, and the regulation of lipid metabolism. By modulating all these processes, CD5L plays a key role in highly prevalent diseases that develop by either acute or chronic inflammation, including several infectious, metabolic, and autoimmune conditions. In this review, we summarize the current knowledge of CD5L and focus on the relevance of this protein during infection- and sterile-driven inflammatory pathogenesis, highlighting its divergent roles in the modulation of inflammation.


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