Incomplete genome doubling enables to consistently enhance plant growth for maximum biomass production by altering multiple transcript co-expression networks in potato.

KEY MESSAGE: Cytochimera potato plants, which mixed with diploid and tetraploid cells, could cause the highest and significantly increased biomass yield than the polyploid and diploid potato plants. Polyploidization is an important approach in crop breeding for agronomic trait improvement, especially for biomass production. Cytochimera contains two or more mixed cells with different levels of ploidy, which is considered a failure in whole genome duplication. Using colchicine treatment with diploid (Dip) potato (Solanum chacoense) plantlets, this study generated tetraploid (Tet) and cytochimera (Cyt) lines, which, respectively, contained complete and partial cells with genome duplication. Compared to the Dip potato, we observed remarkably enhanced plant growth and biomass yields in Tet and Cyt lines. Notably, the Cyt potato straw, which was generated from incomplete genome doubling, was of significantly higher biomass yield than that of the Tet with a distinctively altered cell wall composition. Meanwhile, we observed that one layer of the tetraploid cells (about 30%) in Cyt plants was sufficient to trigger a gene expression pattern similar to that of Tet, suggesting that the biomass dominance of Cyt may be related to the proportion of different ploidy cells. Further genome-wide analyses of co-expression networks indicated that down-regulation (against Dip) of spliceosomal-related transcripts might lead to differential alternative splicing for specifically improved agronomic traits such as plant growth, biomass yield, and lignocellulose composition in Tet and Cyt plants. In addition, this work examined that the genome of Cyt line was relatively stable after years of asexual reproduction. Hence, this study has demonstrated that incomplete genome doubling is a promising strategy to maximize biomass production in potatoes and beyond.

A theoretical and experimental investigation of the effect of sodium dodecyl sulfate on the structural and conformational properties of bovine ß-casein.

A predicted three-dimensional structure of bovine ß-casein was constructed using homology modeling with the aid of MODELLER and I-TASSER programs, with the validity and reliability of the models evaluated according to stereochemical qualities and small angle X-ray scattering. By comparing the results obtained from the two models using the CRYSOL program, an optimal model of the ß-casein structure derived from I-TASSER was selected and used in subsequent molecular dynamics (MD) analysis. 300 ns MD simulations of ß-casein in water and in the presence of different SDS concentrations at 300 K were performed. The results of the MD simulations indicated that SDS molecules played a dual role in modifying the conformation of ß-casein at 300 K. Concentrations of SDS below its CMC (1 mM), at which only the monomer form of SDS was present, induced ß-casein to lose its secondary structure by converting helices into random coils; however the conformation of the complex was still comparable with that of native ß-casein. In the presence of 10 mM SDS (above its CMC), the helical content of ß-casein was increased along with reduced random coils, and the structural rearrangement led to a more compact conformation. The latter change is likely related to the hydrophobic interactions that dominate the binding of the C-terminal region, along with the anchoring of sulfate groups of SDS on the positively charged N-terminal portion via electrostatic attraction. Hydrogen bonding supplemented the SDS-induced stabilization of ß-casein. A correlated "necklace and bead" model, in which the micelles nucleate on the protein hydrophobic sites, was proposed for the structure of ß-casein-SDS complexes.

Interactions of chlorogenic acid and isochlorogenic acid A with model lipid bilayer membranes: Insights from molecular dynamics simulations.

Because of the negative side-effects of synthetic preservatives, the naturally-occurring polyphenols aroused intense interest of researchers. It has been suggested that chlorogenic acid (CA) and isochlorogenic acid A (iso-CAA) were good candidates to replace the synthetic preservatives. Moreover, the bactericidal activity of iso-CAA was stronger than CA, and the anti-bacterial activities of iso-CAA and CA were highly membrane-dependent. However, the mechanisms were still unclear. Therefore, in the present study, we investigated the mechanisms of the interactions between the two polyphenols and lipid bilayers through molecular dynamics simulations. The results revealed that iso-CAA could be inserted much deeper into POPG lipid bilayer than CA. We also found that hydrophobic interactions and hydrogen bonds both contributed to the insertion of iso-CAA into the POPG lipid bilayer, and the quinic acid moiety was the key structure in iso-CAA to form hydrogen bonds with POPG lipid bilayer. We believed that these findings would provide more useful information to explain the stronger bactericidal activity of iso-CAA than CA at the atomic level.

Influence of the gallate moiety on the interactions between green tea polyphenols and lipid membranes elucidated by molecular dynamics simulations.

Previous studies suggested that naturally occurring EGCG primarily acted on the bacterial cell membrane then damaged the membrane and the gallate moiety in EGCG was very important to its anti-bacterial activity. However, the detailed mechanisms were still poorly understood. In this paper, EGCG and EGC were selected to study the great contribution of gallate moiety on the anti-bacterial activities of polyphenols. The results indicated that EGCG could penetrate deeper into the POPG lipid bilayer and possess more potent structure-perturbing potency on the POPG lipid bilayer than EGC. We also found that EGCG had the ability to form hydrogen bonds with the deeper inside oxygen atoms in the POPG lipid bilayer and the gallate moiety was the key functional group for EGCG forming hydrogen bonds with the POPG lipid bilayer. Moreover, results from the binding free energy analysis demonstrated that the gallate moiety made great contribution to the high affinity between EGCG and the POPG lipid bilayer. We believed that these findings could yield useful insights into the influence mechanisms of gallate moiety on the anti-bacterial activities of polyphenols.

Modified lignocellulose and rich starch for complete saccharification to maximize bioethanol in distinct polyploidy potato straw.

Potato is a major food crop with enormous biomass straw, but lignocellulose recalcitrance causes a costly bioethanol conversion. Here, we selected the cytochimera (Cyt) potato samples showing significantly-modified lignocellulose and much increased soluble sugars and starch by 2-4 folds in mature straws. Under two pretreatments (8 min liquid hot water; 5% CaO) at minimized conditions, the potato Cyt straw showed complete enzymatic saccharification. Further performing yeast fermentation with all hexoses released from soluble sugars, starch and lignocellulose in the Cyt straw, this study achieved a maximum bioethanol yield of 24 % (% dry matter), being higher than those of other bioenergy crops as previously reported. Hence, this study has proposed a novel mechanism model on the reduction of major lignocellulose recalcitrance and regulation of carbon assimilation to achieve cost-effective bioethanol production under optimal pretreatments. This work also provides a sustainable strategy for utilization of potato straws with minimum waste release.

Using Amaranthus green proteins as universal biosurfactant and biosorbent for effective enzymatic degradation of diverse lignocellulose residues and efficient multiple trace metals remediation of farming lands.

Improving biomass enzymatic saccharification is effective for crop straw utilization, whereas phytoremediation is efficient for trace metal elimination from polluted agricultural soil. Here, we found that the green proteins extracted from Amaranthus leaf tissue could act as active biosurfactant to remarkably enhance lignocellulose enzymatic saccharification for high bioethanol production examined in eight grassy and woody plants after mild chemical and green-like pretreatments were performed. Notably, this study estimated that total green proteins supply collected from one-hectare-land Amaranth plants could even lead to additional 6400-12,400 tons of bioethanol, being over 10-fold bioethanol yield higher than those of soybean seed proteins and chemical surfactant. Meanwhile, the Amaranth green proteins were characterized as a dominated biosorbent for multiple trace metals (Cd, Pb, As) adsorption, being 2.9-6 folds higher than those of its lignocellulose. The Amaranth plants were also assessed to accumulate much more trace metals than all other plants as previously examined from large-scale contaminated soils. Furthermore, the Amaranth green proteins not only effectively block lignin to release active cellulases for the mostly enhanced biomass hydrolyzes, but also efficiently involve in multiple chemical bindings with Cd, which should thus address critical issues of high-costly biomass waste utilization and low-efficient trace metal remediation.

Molecular insights into the inhibitory mechanisms of gallate moiety on the Aß1-40 amyloid aggregation: A molecular dynamics simulation study.

Alzheimer's disease is the most common form of neurodegenerative disease and the formation of Aß amyloid aggregates has been widely demonstrated to be the principal cause of Alzheimer's disease. Our previous study and other studies suggested that the gallate moiety played an obligatory role in the inhibition process of naturally occurring polyphenols on Aß amyloid fibrils formation. However, the detailed mechanisms were still unknown. Thus, in the present study, the gallic acid (GA) was specially selected and the molecular recognition mechanisms between GA molecules and Aß1-40 monomer were examined and analyzed by molecular dynamics simulation. The in silico experiments revealed that GA significantly prevented the conformational changes of Aß1-40 monomer with no ß-sheet structure during the whole 100 ns. By analyzing the binding sites of GA molecules to Aß1-40 monomer, we found that both hydrophilic and hydrophobic amino acid residues were participated in the binding of GA molecules to Aß1-40 monomer. Moreover, results from the binding free energy analysis further demonstrated that the strength of polar interactions was significantly stronger than that of nonpolar interactions. We believed that our results could help to elucidate the underlying mechanisms of gallate moiety on the anti-amyloidogenic effects of polyphenols at the atomic level.

A mechanism for efficient cadmium phytoremediation and high bioethanol production by combined mild chemical pretreatments with desirable rapeseed stalks.

Cadmium (Cd) is one of the most hazardous trace metals, and rapeseed is a major oil crop over the world with considerable lignocellulose residues applicable for trace metal phytoremediation and cellulosic ethanol co-production. In this study, we examined that two distinct rapeseed cultivars could accumulate Cd at 72.48 and 43.70 ug/g dry stalk, being the highest Cd accumulation among all major agricultural food crops as previously reported. The Cd accumulation significantly increased pectin deposition as a major factor for trace metal association with lignocellulose. Meanwhile, the Cd-accumulated rapeseed stalks contained much reduced wall polymers (hemicellulose, lignin) and cellulose degree of polymerization, leading to improved lignocellulose enzymatic hydrolysis. Notably, three optimal chemical pretreatments were performed for enhanced biomass enzymatic saccharification and bioethanol production by significantly increasing cellulose accessibility and lignocellulose porosity, along with a complete Cd release for collection and recycling. Hence, this study proposed a mechanism model interpreting why rapeseed stalks are able to accumulate much Cd and how the Cd-accumulated stalks are of enhanced biomass saccharification. It has also provided a powerful technology for both cost-effective Cd phytoremediation and value-added bioethanol co-production with minimum waste release.

Crystallization, thermal stability, barrier property, and aging resistance application of multi-functionalized graphene oxide/poly(lactide)/starch nanocomposites.

Poly(lactide)-starch matrix, blended with multi-functionalized graphene oxide, was synthesized by solution casting in this study. To improve its interface compatibility, the graphene oxide (GO) was grafted with maleic anhydride and subsequently modified by dodecyl amine. The chemical structure and morphology of functionalized GO (f-GO) were determined by Fourier transform infrared (FTIR) spectroscopy, X-ray photoelectron spectroscopy (XPS), and transmission electron microscopy (TEM). The crystallization property, surface wettability, morphology, thermal stability, and dynamic mechanical and aging resistance properties of the nanocomposite were determined. By XRD and morphological analysis, we observed the formation of well-dispersed nanocomposites. Thermo-gravimetric analysis revealed significant improvements in thermal stability. The isothermal and non-isothermal crystallization behavior of the PLA-starch-f-GO nanocomposites demonstrated that the f-GO that was added accelerated the heterogeneous nucleation of the nanocomposites. The surface hydrophobicity, UV-shielding capacity, and aging resistance properties of these nanocomposites were enhanced by the incorporation of the f-GO. The migration rate of plasticizer of the nanocomposites decreased compared with the group without f-GO. The storage modulus for these nanocomposites improved by dynamic mechanical analysis. These insights provide a strategy for constructing high-performance nanohybrids and broadening their application in the food packaging and pharmaceutical industries.