Soil Microbial Communities and Enzyme Activities after Long-Term Application of Inorganic and Organic Fertilizers at Different Depths of the Soil Profile

Fertilization is a key factor for sustaining productivity in agroecosystems. A long-term experiment in cambisol following periodical application of several types of fertilization has been running at the experimental site since 1954. In this study, we determined the impact of applied inorganic and/or organic fertilizers on the activity of soil enzymes and on the structure of microorganisms at depths of 0-30 cm and 30-60 cm. Single-factor comparison showed that use of inorganic and/or organic fertilizer had an insignificant e_ect on the activities of soil enzymes (at depths 0-30 cm and 30-60 cm) and also on the structure of microbial communities at both depths studied. Only soil respirations exhibited stimulation by combined fertilization. The results, irrespective of sampling depth (0-60 cm), showed that application of combined organic and inorganic fertilization stimulated the activity of glucosidases and use of inorganic fertilizer inhibited the activity of arylsulphatases. Respirations were stimulated by application of organic fertilizer and combined fertilization. Nevertheless, principal component analyses, which calculate with multidimensional data, revealed di_erences in samples treated by sole mineral fertilizer compared to other variants, especially in the lower layer. In general, our results indicate that use of combined fertilization may improve biological characteristics in deeper parts of soil profile and possibly increase biological activity in agroecosystems.O

Novel Slippery Liquid-Infused Porous Surfaces (SLIPS) based on electrospun polydimethylsiloxane/polystyrene fibrous structures infused with natural blackseed oil

Hydrophobic fibrous slippery liquid-infused porous surfaces (SLIPS) were fabricated by electrospinning polydimethylsiloxane (PDMS) and polystyrene (PS) as a carrier polymer on plasma-treated polyethylene (PE) and polyurethane (PU) substrates. Subsequent infusion of blackseed oil (BSO) into the porous structures was applied for the preparation of the SLIPS. SLIPS with infused lubricants can act as a repellency layer and play an important role in the prevention of biofilm formation. The effect of polymer solutions used in the electrospinning process was investigated to obtain well-defined hydrophobic fibrous structures. The surface properties were analyzed through various optical, macroscopic and spectroscopic techniques. A comprehensive investigation of the surface chemistry, surface morphology/topography, and mechanical properties was carried out on selected samples at optimized conditions. The electrospun fibers prepared using a mixture of PDMS/PS in the ratio of 1:1:10 (g/g/mL) using tetrahydrofuran (THF) solvent showed the best results in terms of fiber uniformity. The subsequent infusion of BSO into the fabricated PDMS/PS fiber mats exhibited slippery behavior regarding water droplets. Moreover, prepared SLIPS exhibited antibacterial activity against Staphylococcus aureus and Escherichia coli bacterium strains.RP/CPS/2022/001, RP/CPS/2022/002; Qatar National Research Fund, QNRFQatar National Research Fund (a member of The Qatar Foundation) [NPRP13S-0123-200153, JSREP 07-022-3-010]; Ministry of Education, Youth and Sports of the Czech Republic DKRVO [RP/CPS/2022/001, RP/CPS/2022/002

Theater in the Self-Cleaning Cell: Intrinsically Disordered Proteins or Protein Regions Acting with Membranes in Autophagy

Intrinsically disordered proteins and protein regions (IDPs/IDPRs) are mainly involved in signaling pathways, where fast regulation, temporal interactions, promiscuous interactions, and assemblies of structurally diverse components including membranes are essential. The autophagy pathway builds, de novo, a membrane organelle, the autophagosome, using carefully orchestrated interactions between proteins and lipid bilayers. Here, we discuss molecular mechanisms related to the protein disorder-based interactions of the autophagy machinery with membranes. We describe not only membrane binding phenomenon, but also examples of membrane remodeling processes including membrane tethering, bending, curvature sensing, and/or fragmentation of membrane organelles such as the endoplasmic reticulum, which is an important membrane source as well as cargo for autophagy. Summary of the current state of knowledge presented here will hopefully inspire new studies. A profound understanding of the autophagic protein–membrane interface is essential for advancements in therapeutic interventions against major human diseases, in which autophagy is involved including neurodegeneration, cancer as well as cardiovascular, metabolic, infectious, musculoskeletal, and other disorders

Analysis of the native conformation of the LIR/AIM motif in the Atg8/LC3/GABARAP-binding proteins

<p>The Atg8/LC3/GABARAP family of proteins, a group that has structural homology with ubiquitin, connects with a large set of binding partners to function in macroautophagy (hereafter autophagy). This interaction occurs primarily via a conserved motif termed the LC3-interacting region (LIR), or the Atg8-interacting motif (AIM). The consensus sequence for this motif, [W/F/Y]xx[L/I/V], can be found in many proteins, but only some of them are physiological partners containing a functional LIR/AIM. Because the structure of many full-length partners has not been, or cannot be, solved, the structural context of the LIR/AIM within the native protein conformation is not obvious. Here we suggest that the functional LIR/AIM is a short linear motif (SLiM) protein-binding module, arising from an intrinsically disordered region. This finding enables the rapid elimination of some false Atg8/LC3/GABARAP-binding proteins, and connects the exponentially growing knowledge on disordered SLiMs with autophagy.</p

Identification of Atg3 as an intrinsically disordered polypeptide yields insights into the molecular dynamics of autophagy-related proteins in yeast

The mechanism of autophagy relies on complex cell signaling and regulatory processes. Each cell contains many proteins that lack a rigid 3-dimensional structure under physiological conditions. These dynamic proteins, called intrinsically disordered proteins (IDPs) and protein regions (IDPRs), are predominantly involved in cell signaling and regulation. Yet, very little is known about their presence among proteins of the core autophagy machinery. In this work, we characterized the autophagy protein Atg3 from yeast and human along with 2 variants to show that Atg3 is an IDPRs-containing protein and that disorder/order predicted for these proteins from their amino acid sequence corresponds to their experimental characteristics. Based on this consensus, we applied the same prediction methods to all known Atg proteins from Saccharomyces cerevisiae. The data presented here provide an insight into the structural dynamics of each Atg protein. They also show that intrinsic disorder at various levels has to be taken into consideration for about half of the Atg proteins. This work should become a useful tool that will facilitate and encourage exploration of protein intrinsic disorder in autophagy

Soil Microbial Communities and Enzyme Activities after Long-Term Application of Inorganic and Organic Fertilizers at Different Depths of the Soil Profile

Fertilization is a key factor for sustaining productivity in agroecosystems. A long-term experiment in cambisol following periodical application of several types of fertilization has been running at the experimental site since 1954. In this study, we determined the impact of applied inorganic and/or organic fertilizers on the activity of soil enzymes and on the structure of microorganisms at depths of 0&ndash;30 cm and 30&ndash;60 cm. Single-factor comparison showed that use of inorganic and/or organic fertilizer had an insignificant effect on the activities of soil enzymes (at depths 0&ndash;30 cm and 30&ndash;60 cm) and also on the structure of microbial communities at both depths studied. Only soil respirations exhibited stimulation by combined fertilization. The results, irrespective of sampling depth (0&ndash;60 cm), showed that application of combined organic and inorganic fertilization stimulated the activity of glucosidases and use of inorganic fertilizer inhibited the activity of arylsulphatases. Respirations were stimulated by application of organic fertilizer and combined fertilization. Nevertheless, principal component analyses, which calculate with multidimensional data, revealed differences in samples treated by sole mineral fertilizer compared to other variants, especially in the lower layer. In general, our results indicate that use of combined fertilization may improve biological characteristics in deeper parts of soil profile and possibly increase biological activity in agroecosystems