Despite tremendous efforts, the exact structure of SARS-CoV-2 and related betacoronaviruses remains elusive. SARS-CoV-2 envelope is a key structural component of the virion that encapsulates viral RNA. It is composed of three structural proteins, spike, membrane (M), and envelope, which interact with each other and with the lipids acquired from the host membranes. Here, we developed and applied an integrative multi-scale computational approach to model the envelope structure of SARS-CoV-2 with near atomistic detail, focusing on studying the dynamic nature and molecular interactions of its most abundant, but largely understudied, M protein. The molecular dynamics simulations allowed us to test the envelope stability under different configurations and revealed that the M dimers agglomerated into large, filament-like, macromolecular assemblies with distinct molecular patterns. These results are in good agreement with current experimental data, demonstrating a generic and versatile approach to model the structure of a virus de novo.
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For the future circular economy, renewable carbon feedstocks manifest considerable promise for synthesizing sustainable and biodegradable polyhydroxyalkanoate (PHA). In this study, 16 wt% and 30 wt% PHA (cell dry weight) are respectively produced by thermophilic Caldimonas thermodepolymerans from beechwood xylan and wheat arabinoxylan as the sole carbon source. Moreover, an in silico study of the potential xylan-degrading proteins was conducted using proteome sequencing and CAZyme specialized bioinformatic tools. This study demonstrates the feasibility of utilizing complex polysaccharide substrates for PHA biosynthesis, thereby potentially eliminate additional processing steps and reducing overall production costs for sustainable plastic.
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BackgroundThe ROS1 G2032R mutation is the most common on-target resistance mutation in crizotinib treated ROS1-positive lung cancer patients. The aim of our study was to investigate resistance mechanisms in SCL34A2-ROS1G2032R positive Ba/F3 cells against second line treatment with lorlatinib.MethodsBa/F3 SLC34A2-ROS1G2032R cells were subjected to N-ethyl-N-nitrosourea (ENU) mutagenesis and clones were selected upon treatment with 1000 nM lorlatinib for 4 weeks. Resistant clones were analyzed for presence of on-target resistant mutations using Sanger sequencing. In addition, we generated subclones expressing SLC34A2-ROS1L2026M+G2032R and SLC34A2-ROS1L2026M in Ba/F3 cells. Sensitivity to ROS1 TKIs was determined by measuring cell viability and ROS1 phosphorylation. Molecular Dynamic simulations of the ATP binding pocket were performed for all ROS1 variants.ResultsThe ENU-screen of 41 lorlatinib resistant clones revealed one with a mutation in the kinase domain: L2026M. Cell viability assays of the ENU-induced resistant cell line and the Ba/F3 cells transfected with the mutant SCL34A2-ROS1 fusion gene constructs revealed a decreased sensitivity of SLC34A2-ROS1L2026M+G2032R cells for lorlatinib, crizotinib, entrectinib and repotrectinib compared to the single mutants. Consistent with these findings, we observed phosphorylation of ROS1 fusion protein in the double mutant cells which was not inhibited upon treatment with ROS1 TKIs. The single mutant cells showed as expected a clear reduction in phosphorylated ROS1 fusion protein . Molecular modeling to unravel the effect of the mutations demonstrated that the volume of the ATP-binding pocket was reduced in single and double mutants compared to wild type. The double L2026M+G2032R mutant displayed the smallest pocket.ConclusionsWe identified a novel on-target mutation after inducing lorlatinib resistance in SLC34A2-ROS1G2032R Ba/F3 cells. This SLC34A2-ROS1L2026M+G2032R cell line was also resistant to crizotinib, entrectinib and repotrectinib. The resistance can be explained by a smaller ATP binding pocket in the mutated ROS1 fusion protein preventing effective binding of the investigated TKIs.
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The transition to a biobased economy necessitates utilizing renewable resources as a sustainable alternative to traditional fossil fuels. Bioconversion is a way to produce many green chemicals from renewables, e.g., biopolymers like PHAs. However, fermentation and bioconversion processes mostly rely on expensive, and highly refined pure substrates. The utilization of crude fractions from biorefineries, especially herbaceous lignocellulosic feedstocks, could significantly reduce costs. This presentation shows the microbial production of PHA from such a crude stream by a wild-type thermophilic bacterium Schlegelella thermodepolymerans [1]. Specifically, it uses crude xylose-rich fractions derived from a newly developed biorefinery process for grassy biomasses (the ALACEN process). This new stepwise mild flow-through biorefinery approach for grassy lignocellulosic biomass allows the production of various fractions: a fraction containing esterified aromatics, a monomeric xylose-rich stream, a glucose fraction, and a native-like lignin residue [2]. The crude xylose-rich fraction was free of fermentation-inhibiting compounds meaning that the bacterium S.thermodepolymerans could effectively use it for the production of one type of PHA, polyhydroxybutyrate. Almost 90% of the xylose in the refined wheat straw fraction was metabolized with simultaneous production of PHA, matching 90% of the PHA production per gram of sugars, comparable to PHA yields from commercially available xylose. In addition to xylose, S. thermodepolymerans converted oligosaccharides with a xylose backbone (xylans) into fermentable xylose, and subsequently utilized the xylose as a source for PHA production. Since the xylose-rich hydrolysates from the ALACEN process also contain some oligomeric xylose and minor hemicellulose-derived sugars, optimal valorization of the C5-fractions derived from the refinery process can be obtained using S. thermodepolymerans. This opens the way for further exploration of PHA production from C5-fractions out of a variety of herbaceous lignocellulosic biomasses using the ALACEN process combined with S. thermodepolymerans. Overall, the innovative utilization of renewable resources in fermentation technology, as shown herein, makes a solid contribution to the transition to a biobased economy.[1] W. Zhou, D.I. Colpa, H. Permentier, R.A. Offringa, L. Rohrbach, G.J.W. Euverink, J. Krooneman. Insight into polyhydroxyalkanoate (PHA) production from xylose and extracellular PHA degradation by a thermophilic Schlegelella thermodepolymerans. Resources, Conservation and Recycling 194 (2023) 107006, ISSN 0921-3449, https://doi.org/10.1016/j.resconrec.2023.107006. [2] S. Bertran-Llorens, W.Zhou. M.A.Palazzo, D.I.Colpa, G.J.W.Euverink, J.Krooneman, P.J.Deuss. ALACEN: a holistic herbaceous biomass fractionation process attaining a xylose-rich stream for direct microbial conversion to bioplastics. Submitted 2023.
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The synthesis of total cellular proteins in Escherichia coli K12 was studied in batch culture following exposure of cells to low concentrations of monochlorophenol, pentachlorophenol and cadmium chloride. Changes in protein patterns were identified after pulse-chase labelling of proteins with [35S]methionine and subsequent two-dimensional gel electrophoresis (2D-PAGE). We demonstrated that besides the induction of some stress proteins, also a transient decrease in the rate of synthesis of other proteins occurred. Two of these proteins were identified as OmpF and aspartate transcarbamoylase (ATCase). Their transient repression appeared to be a general response to stress elicited by different pollutants and may therefore be used as a general and sensitive early warning system for pollutant stress.
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The invention relates to the use of modified starch obtainable by treating amylose containing starch in aqueous medium with an enzyme from the group of the α-1,4-α-1,4-glucosyl transferases (EC 2.4.1.25) or an enzyme the activity of which corresponds to that of enzymes from the group just mentioned, as an agent for forming a thermoreversible gel. The invention also relates to products in the form of a thermoreversible gel having as gel-forming substance a modified starch as defined. The invention further relates to the use of a modified starch as defined in the form of an aqueous solution.
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Control of plant growth is an important aspect of crop productivity and yield in agriculture. Overexpression of the At CHR12/ 23 genes in Arabidopsis thaliana reduced growth habit without other morphological changes. These two genes encode Snf2 chromatin remodelling ATPases. Here, we translate this approach to the horticultural crop tomato ( Solanum lycopersicum). We identified and cloned the single tomato ortholog of the two Arabidopsis Snf2 genes, designated Sl CHR1. Transgenic tomato plants (cv. Micro-Tom) that constitutively overexpress the coding sequence of Sl CHR1 show reduced growth in all developmental stages of tomato. This confirms that Sl CHR1 combines the functions of both Arabidopsis genes in tomato. Compared to the wild type, the transgenic seedlings of tomato have significantly shorter roots, hypocotyls and reduced cotyledon size. Transgenic plants have a much more compact growth habit with markedly reduced plant height, severely compacted reproductive structures with smaller flowers and smaller fruits. The results indicate that either GMO-based or non- GMO-based approaches to modulate the expression of chromatin remodelling ATPase genes could develop into methods to control plant growth, for example to replace the use of chemical growth retardants. This approach is likely to be applicable and attractive for any crop for which growth habit reduction has added value.
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There is a need to assess communication in daily life situations for people with speech and language disorders. Although language proficiency and communication in daily life are correlated, their relationship is far from linear or straightforward. This paper aims to demonstrate the usefulness of the construct of communicative participation by unravelling the relationship and overlap between participation and communication. We explored the relationship between communication, participation, and communicative participation by reviewing common definitions mentioned in the literature. Next, we evaluated to what extent communication plays a role in each of the World Health Organization’s International Classification of Functioning (ICF) “Activity and Participation” chapters by counting how many items in each chapter should be considered for describing communicative participation.
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