Self-organized crystallization patterns from evaporating droplets of common wheat grain leakages as a potential tool for quality analysis.
Ontology highlight
ABSTRACT:
SUBMITTER: Kokornaczyk MO
PROVIDER: S-EPMC3201687 | biostudies-other | 2011
REPOSITORIES: biostudies-other
Similar Datasets
Project description:In the living cell, proteins are able to organize space much larger than their dimensions. In return, changes of intracellular space can influence biochemical reactions, allowing cells to sense their size and shape. Despite the possibility to reconstitute protein self-organization with only a few purified components, we still lack knowledge of how geometrical boundaries affect spatiotemporal protein patterns. Following a minimal systems approach, we used purified proteins and photolithographically patterned membranes to study the influence of spatial confinement on the self-organization of the Min system, a spatial regulator of bacterial cytokinesis, in vitro. We found that the emerging protein pattern responds even to the lateral, two-dimensional geometry of the membrane such that, as in the three-dimensional cell, Min protein waves travel along the longest axis of the membrane patch. This shows that for spatial sensing the Min system does not need to be enclosed in a three-dimensional compartment. Using a computational model we quantitatively analyzed our experimental findings and identified persistent binding of MinE to the membrane as requirement for the Min system to sense geometry. Our results give insight into the interplay between geometrical confinement and biochemical patterns emerging from a nonlinear reaction-diffusion system.
| S-EPMC3458403 | biostudies-literature
Project description:The effects of dwarfing alleles (reduced height, Rht) in near isogenic lines on wheat grain quality are characterised in field experiments and related to effects on crop height, grain yield and GA-sensitivity. Alleles included those that conferred GA-insensitivity (Rht-B1b, Rht-B1c, Rht-D1b, Rht-D1c) as well as those that retained GA-sensitivity (rht(tall), Rht8, Rht8 + Ppd-D1a, Rht12). Full characterisation was facilitated by including factors with which the effects of Rht alleles are known to interact for grain yield (i.e. system, [conventional or organic]; tillage intensity [plough-based, minimum or zero]; nitrogen fertilizer level [0-450 kg N/ha]; and genetic backgrounds varying in height [cvs Maris Huntsman, Maris Widgeon, and Mercia]. Allele effects on mean grain weight and grain specific weight were positively associated with final crop height: dwarfing reduced these quality criteria irrespective of crop management or GA-sensitivity. In all but two experiments the effects of dwarfing alleles on grain nitrogen and sulphur concentrations were closely and negatively related to effects on grain yield, e.g. a quadratic relationship between grain yield and crop height manipulated by the GA-insensitive alleles was mirrored by quadratic relationships for nitrogen and sulphur concentrations: the highest yields and most dilute concentrations occurred around 80cm. In one of the two exceptional experiments the GA-insensitive Rht-B1b and Rht-B1c significantly (P<0.05) reduced grain nitrogen concentration in the absence of an effect on yield, and in the remaining experiment the GA-sensitive Rht8 significantly reduced both grain yield and grain nitrogen concentration simultaneously. When Rht alleles diluted grain nitrogen concentration, N:S ratios and SDS-sedimentation volumes were often improved. Hagberg falling number (HFN) was negatively related to crop height but benefits from dwarfing were only seen for GA-insensitive alleles. For HFN, therefore, there was the strongest evidence for a direct pleiotropic effect of GA-insensitivity, rather than an effect consequential to yield and/or height.
| S-EPMC4873232 | biostudies-literature
Project description:We numerically investigate a diffusion-reaction model of an ombrotrophic peatland implementing a Turing instability relying on nutrient accumulation. We propose a systematic and quantitative sorting of the vegetation patterns, based on the statistical analysis of the numbers and filling factor of clusters of both Sphagnum mosses and vascular plants. In particular, we define the transition from Sphagnum-percolating to vascular plant-percolating patterns as the nutrient availability is increased. Our pattern sorting allows us to characterize the peatland pattern stability under climate stress, including strong drought.
| S-EPMC6365544 | biostudies-literature
Project description:The grain hardness index (HI) is one of the important reference bases for wheat quality and commodity properties; therefore, it is essential and useful to identify loci associated with the HI in wheat breeding. The grain hardness index of the natural population including 150 common wheat genotypes was measured in this study. The phenotypic data diversity of HI based on four environments and the best linear unbiased prediction (BLUP) was analyzed. The results showed that the grain HI of the natural population ranged from 15.00 to 83.00, the variation range was from 5.10% to 24.44%, and the correlation coefficient was 0.872-0.980. BLUP value was used to grade and assign the grain HI to hard wheat, mixed wheat, and soft wheat, and the assigned phenotypes were used for genome-wide association analysis. Two types of grain hardness index phenotypic values were used for genome-wide association analysis (GWAS) using a 55K SNP array. A total of five significant association loci (p < 0.001) were excavated, among which four loci could be detected in three or more environments. They were distributed on chromosomes 1A and 7D, and the phenotypic contribution rate was 7.52% to 10.66%. A total of 48 sites related to grain hardness were detected by the assignment method, among which five were stable genetic sites, distributed on chromosomes 1A(2), 3B(1), 4B(1), and 7D(1), with phenotypic contribution rates ranging from 7.63% to 11.12%. Of the five loci detected by the assignment method, two stable loci were co-located in the phenotypic mapping results of the hardness index. One of the loci was consistent with previous reports and located on chromosome 1A, and one locus was unreported on chromosome 7D. Therefore, it may be a feasible attempt to use the assignment method to conduct genome-wide association analysis of the grain hardness index. In this study, a total of five genetic loci for grain hardness stability were excavated, and two of the loci were located in the two phenotypic values, two of which were not reported.
| S-EPMC10047947 | biostudies-literature
Project description:Microbial communities organize into spatial patterns that are largely governed by interspecies interactions. This phenomenon is an important metric for understanding community functional dynamics, yet the use of spatial patterns for predicting microbial interactions is currently lacking. Here we propose supervised deep learning as a new tool for network inference. An agent-based model was used to simulate the spatiotemporal evolution of two interacting organisms under diverse growth and interaction scenarios, the data of which was subsequently used to train deep neural networks. For small-size domains (100 µm × 100 µm) over which interaction coefficients are assumed to be invariant, we obtained fairly accurate predictions, as indicated by an average R2 value of 0.84. In application to relatively larger domains (450 µm × 450 µm) where interaction coefficients are varying in space, deep learning models correctly predicted spatial distributions of interaction coefficients without any additional training. Lastly, we evaluated our model against real biological data obtained using Pseudomonas fluorescens and Escherichia coli co-cultures treated with polymeric chitin or N-acetylglucosamine, the hydrolysis product of chitin. While P. fluorescens can utilize both substrates for growth, E. coli lacked the ability to degrade chitin. Consistent with our expectations, our model predicted context-dependent interactions across two substrates, i.e., degrader-cheater relationship on chitin polymers and competition on monomers. The combined use of the agent-based model and machine learning algorithm successfully demonstrates how to infer microbial interactions from spatially distributed data, presenting itself as a useful tool for the analysis of more complex microbial community interactions.
| S-EPMC7298420 | biostudies-literature
Project description:Biological functions rely on ordered structures and intricately controlled collective dynamics. This order in living systems is typically established and sustained by continuous dissipation of energy. The emergence of collective patterns of motion is unique to nonequilibrium systems and is a manifestation of dynamic steady states. Mechanical resilience of animal cells is largely controlled by the actomyosin cortex. The cortex provides stability but is, at the same time, highly adaptable due to rapid turnover of its components. Dynamic functions involve regulated transitions between different steady states of the cortex. We find that model actomyosin cortices, constructed to maintain turnover, self-organize into distinct nonequilibrium steady states when we vary cross-link density. The feedback between actin network structure and organization of stress-generating myosin motors defines the symmetries of the dynamic steady states. A marginally cross-linked state displays divergence-free long-range flow patterns. Higher cross-link density causes structural symmetry breaking, resulting in a stationary converging flow pattern. We track the flow patterns in the model actomyosin cortices using fluorescent single-walled carbon nanotubes as novel probes. The self-organization of stress patterns we have observed in a model system can have direct implications for biological functions.
| S-EPMC5990313 | biostudies-literature
Project description:Protein patterning is vital for many fundamental cellular processes. This raises two intriguing questions: Can such intrinsically complex processes be reduced to certain core principles and, if so, what roles do the molecular details play in individual systems? A prototypical example for protein patterning is the bacterial Min system, in which self-organized pole-to-pole oscillations of MinCDE proteins guide the cell division machinery to midcell. These oscillations are based on cycling of the ATPase MinD and its activating protein MinE between the membrane and the cytoplasm. Recent biochemical evidence suggests that MinE undergoes a reversible, MinD-dependent conformational switch from a latent to a reactive state. However, the functional relevance of this switch for the Min network and pattern formation remains unclear. By combining mathematical modeling and in vitro reconstitution of mutant proteins, we dissect the two aspects of MinE's switch, persistent membrane binding and a change in MinE's affinity for MinD. Our study shows that the MinD-dependent change in MinE's binding affinity for MinD is essential for patterns to emerge over a broad and physiological range of protein concentrations. Mechanistically, our results suggest that conformational switching of an ATPase-activating protein can lead to the spatial separation of its distinct functional states and thereby confer robustness on an intracellular protein network with vital roles in bacterial cell division.
| S-EPMC5939084 | biostudies-literature
Project description:Key messageWe evaluated the potential of wheat wild relatives for the improvement in grain quality characteristics including micronutrients (Fe, Zn) and gluten and identified diploid wheats and the timopheevii lineage as the most promising resources. Domestication enabled the advancement of civilization through modification of plants according to human requirements. Continuous selection and cultivation of domesticated plants induced genetic bottlenecks. However, ancient diversity has been conserved in crop wild relatives. Wheat (Triticum aestivum L.; Triticum durum Desf.) is one of the most important staple foods and was among the first domesticated crop species. Its evolutionary diversity includes diploid, tetraploid and hexaploid species from the Triticum and Aegilops taxa and different genomes, generating an AA, BBAA/GGAA and BBAADD/GGAAAmAm genepool, respectively. Breeding and improvement in wheat altered its grain quality. In this review, we identified evolutionary patterns and the potential of wheat wild relatives for quality improvement regarding the micronutrients Iron (Fe) and Zinc (Zn), the gluten storage proteins α-gliadins and high molecular weight glutenin subunits (HMW-GS), and the secondary metabolite phenolics. Generally, the timopheevii lineage has been neglected to date regarding grain quality studies. Thus, the timopheevii lineage should be subject to grain quality research to explore the full diversity of the wheat gene pool.
| S-EPMC9729140 | biostudies-literature
Project description:Heat stress during the grain-filling period is the main abiotic stress factor limiting grain yield and quality in wheat (Triticum aestivum L.). In this study, 64 wheat genotypes were exposed to heat stress during reproduction caused by delayed sowing in two growing seasons. Grain yield, 1000 grain weight (GW), grain hardness (GH), and grain-quality related traits were investigated. Heat stress caused a significant decrease in GW through reducing starch content (SC) and a non-compensating rise in protein content (PC), and thereby resulted in lower yield. In addition, significant increases in flour water absorption (WA), Zeleny sedimentation volume (ZT), ash content (AC), lipid content (LC), loaf volume (LV), wet gluten content (WG), dry gluten content (DG), gluten index (GI), and amylopectin content (APC) were found following heat stress. In contrast, decreases in grain moisture content (MC) and amylose content (AMC) induced by heat stress were observed. The heat-tolerant genotypes were superior in grain yield, GW, SC, AMC, and MC. While the sensitive genotypes contained higher PC, LV, GI and AMP. A group of wheat genotypes characterized with a higher yield, AMC, GW, and SC as well as lower PC, WA, GH, ZT, and LV; and was found to be the most heat tolerant by principal component analysis. Lighter weight and smaller grains produce a smaller starchy endosperm with lower quality (less amylose) and higher grain protein content in heat stress compared to normal conditions. Heat stress caused by delayed sowing improves some of the baking-quality related traits.
| S-EPMC9442411 | biostudies-literature
Project description:A thermal contact transfer technique is presented for the fabrication of nanoscaled to microscaled patterns of polymer-insulated metal structures on ceramic surfaces using metal-coated, thermoplastic stamps. The thermally activated formation of polymer-metal-polymer (PMP) heterostructures occurs spontaneously when a metal-coated thermoplastic stamp is compressed against a ceramic substrate and subsequently heated. The presented technique exploits the dynamics of ultrathin polymer films localized at interfaces and interfacial forces to prompt local reorganization of polymer stamp materials during processing. Intercalation of polymer stamp materials into the metal-substrate interface yields a cohesive polymer layer that binds the metal layer to the substrate. Disproportionate adhesion between the bulk polymer and the polymer layer at the stamp-metal interface leaves a capping layer upon separation of the stamp from the substrate. Here we demonstrate this technique with single use, bilevel polymer stamps which afford transfer of two distinct general products. The transfer of insulated submicrometer wide wires from the raised stamp features affords patterns of trilayered PMP structures with uniform wire dimensions. Concomitant transfer from the recessed stamp features allows fabrication of multilayered PMP architectures with sub-100 nm spacing from microstructured polymer stamps. Thus, patterns with two different insulated nanowire widths are readily fabricated in a single stamping process. A variety of ceramic substrates, thermoplastic materials, and metals can be used; e.g., inexpensive gold-coated CD or DVD media can be used as stamps, where the combination of materials dictates the relative interfacial forces and the processing parameters.
| S-EPMC6180330 | biostudies-literature