Structural Evolution of Bacterial Polyphosphate Degradation Enzyme for Phosphorus Cycling.

Living organisms ranging from bacteria to animals have developed their own ways to accumulate and store phosphate during evolution, in particular as the polyphosphate (polyP) granules in bacteria. Degradation of polyP into phosphate is involved in phosphorus cycling, and exopolyphosphatase (PPX) is the key enzyme for polyP degradation in bacteria. Thus, understanding the structure basis of PPX is crucial to reveal the polyP degradation mechanism. Here, it is found that PPX structure varies in the length of ɑ-helical interdomain linker (ɑ-linker) across various bacteria, which is negatively correlated with their enzymatic activity and thermostability - those with shorter ɑ-linkers demonstrate higher polyP degradation ability. Moreover, the artificial DrPPX mutants with shorter ɑ-linker tend to have more compact pockets for polyP binding and stronger subunit interactions, as well as higher enzymatic efficiency (kcat/Km) than that of DrPPX wild type. In Deinococcus-Thermus, the PPXs from thermophilic species possess a shorter ɑ-linker and retain their catalytic ability at high temperatures (70 °C), which may facilitate the thermophilic species to utilize polyP in high-temperature environments. These findings provide insights into the interdomain linker length-dependent evolution of PPXs, which shed light on enzymatic adaption for phosphorus cycling during natural evolution and rational design of enzyme.

Numerical Study on the Effect of Coarse Aggregate Shape during Concrete Mixing Process.

The shape of coarse aggregate is an important factor determining the performance of concrete, and it also affects the whole mixing process. This article selected four typical coarse aggregates and simulated the motion behavior of the coarse aggregate and mortar in a dual horizontal axis mixer using discrete element software, EDEM. The mixing motion of coarse aggregates with different shapes and mortar was studied using average velocity, contact rate, and dispersion coefficient as indicators. The results show that the largest average speed in the mixing process was achieved with the spherical coarse aggregate. Flat coarse aggregates have the highest velocity in the vertical direction, while ellipsoidal coarse aggregates have the lowest velocity. The spherical coarse aggregate mixes best with mortar while the ellipsoidal coarse aggregate mixes worst with mortar. The results of the study could provide strategies for the concrete mixing process considering the shape of the aggregate.

An inorganic mineral-based protocell with prebiotic radiation fitness.

Protocell fitness under extreme prebiotic conditions is critical in understanding the origin of life. However, little is known about protocell's survival and fitness under prebiotic radiations. Here we present a radioresistant protocell model based on assembly of two types of coacervate droplets, which are formed through interactions of inorganic polyphosphate (polyP) with divalent metal cation and cationic tripeptide, respectively. Among the coacervate droplets, only the polyP-Mn droplet is radiotolerant and provides strong protection for recruited proteins. The radiosensitive polyP-tripeptide droplet sequestered with both proteins and DNA could be encapsulated inside the polyP-Mn droplet, and form into a compartmentalized protocell. The protocell protects the inner nucleoid-like condensate through efficient reactive oxygen species' scavenging capacity of intracellular nonenzymic antioxidants including Mn-phosphate and Mn-peptide. Our results demonstrate a radioresistant protocell model with redox reaction system in response to ionizing radiation, which might enable the protocell fitness to prebiotic radiation on the primitive Earth preceding the emergence of enzyme-based fitness. This protocell might also provide applications in synthetic biology as bioreactor or drug delivery system.

[Characteristics of Cadmium Concentration and Transport of Pueraria thornsonii in Farmland with Different Cadmium Pollution Degrees].

This study aimed to elucidate the cadmium (Cd) concentration and transport characteristics of Pueraria thornsonii in farmland with different Cd pollution degrees, so as to provide a reference basis for phytoremediation of Cd-contaminated farmland. The multi-point experiments in farmland with different Cd pollution degrees[ω(Cd) 0.32-38.08 mg·kg-1] were conducted, and the biomass (dry weight), Cd content, accumulation, concentration, and transport of Cd in P. thornsonii tissues under the main growing period were assessed. According to the results, for P. thornsonii, the tuber dry weight ranged from 5.04 to 11.98 t·hm-2, biomass ranged from 13.21 to 29.07 t·hm-2, and Cd accumulation ranged from 15.74 to 106.03 g·hm-2in the study area. The pattern of Cd uptake by P. thornsonii showed that the main vine>leaf>lateral branches>basal part of sti>tuber. The Cd content in P. thornsonii tissues considerably increased with soil Cd content (P<0.05), whereas the biomass decreased significantly (P<0.05). The Cd concentration and transport factor of aboveground parts in P. thornsonii showed a trend of initially falling, then increasing and decreasing again, whereas the Cd enrichment and transport coefficient of tubers gradually decreased. Correlation analysis revealed that the amount of Cd in the soil was a major predictor of Cd accumulation in P. thornsonii. Under light to moderate Cd contamination, the commercial portion of P. thornsonii (arrowroot)[ω(Cd) 0.03-0.22 mg·kg-1] was less than the standard limit for medicinal plants (≤ 0.30 mg·kg-1). In P. thornsonii from moderately contaminated areas, the Cd concentration and transport factor of aboveground parts were 2.43-7.97 and 3.02-9.81, respectively. This indicates that P. thornsonii is a prospective plant ideal for remediating Cd-contaminated soil because of its high capacity to transfer and enrich Cd.

A pectic polysaccharide isolated from Achyranthes bidentata is metabolized by human gut Bacteroides spp.

Achyranthes bidentata (A. bidentata) is a famous traditional Chinese medicine (TGM) for treatment osteoporosis. Polysaccharides, a major factor for shaping the gut microbiota, are the primary ingredients of A. bidentata. However, bioactivity of A. bidentata polysaccharide on human gut microbiota (HGM) remains unknown. Here, a homogeneous pectic polysaccharide A23-1 with average molecular weight of 93.085 kDa was extracted and purified from A. bidentata. And A23-1 was compsed of rhamnose, glucuronic acid, galacturonic acid, glucose, galactose and arabinose in a molar ratio of 7.26: 0.76: 5.12: 2.54: 23.51: 60.81. GC-MS, partial acid hydrolysis and NMR results indicated the backbone of A23-1 was composed of 1, 2, 4-Rhap and 1, 4-GlapA, while the branches were composed of galactose, arabinose, glucose and glucuronic acid. Further, A23-1 was found to be degraded into monosaccharides and fragments. Taking Bacteroides thetaiotaomicron (BT) as a model, we suggested three polysaccharide utilization loci (PULs) might be involved in the A23-1 degradation. Degraded products generated by BO might not support the growth of probiotics. Besides, acetate and propionate as the main end products were generated by Bacteroides spp. and probiotics utilizing A23-1. These findings suggested A23-1 was possible one of food sources of human gut Bacteroides spp.

Characterization and heterologous expression of plasmalogen synthase MeHAD from Megasphaera elsdenii.

Plasmalogens (Pls) are vinyl-ether bond-containing glycerophospholipids or glycosyl diradyl glycerols, and are of great importance in the physiological functions and stability of cell membrane. Here, we identified and characterized that the plasmalogen synthase MeHAD from anaerobic Megasphaera elsdenii was responsible for vinyl-ether bond formation. Different from the 2-hydroxyacyl-CoA dehydratase (HAD) family plasmalogen synthase PlsA-PlsR which are encoded by two genes in Clostridium perfringens, the HAD homolog (MeHAD) encoded by a single gene MELS_0169 was found in M. elsdenii. By heterologous expression of the MeHAD gene into a nonplasmalogen-producing Escherichia coli strain, the expressed MeHAD was found to be located in the cell membrane region. Plasmalogens were detected in the recombinant strain using GC-MS and LC-MS, demonstrating that MeHAD was the key enzyme for plasmalogen synthesis. Moreover, the synthesized plasmalogens could enhance the oxidative stress-resistance and osmotic pressure-resistance of the recombinant strain, probably due to the ROS scavenging and decreased membrane permeability by the plasmalogens, respectively. The four-cysteine (Cys125, Cys164, Cys445 and Cys484) site-mutant of MeHAD, which were predicted binding to the [4Fe-4S] cluster, was unable to synthesize plasmalogens, indicating that the cysteines are important for the catalytic activity of MeHAD. Our results revealed the single gene encoded plasmalogen synthase in M. elsdenii and established a recombinant E. coli strain with plasmalogen production potential.

A structure defined pectin SA02B from Semiaquilegia adoxoides is metabolized by human gut microbes.

Polysaccharide is one of the major factors for shaping the gut microbiota. However, bioactivity of polysaccharide isolated from Semiaquilegia adoxoides on human gut microbiota remains unclear. Thus, we hypothesize gut microbes may act on it. Herein, pectin SA02B from the roots of Semiaquilegia adoxoides with molecular weight 69.26 kDa was elucidated. The backbone of SA02B was composed of alternate 1, 2-linked α-Rhap and 1, 4-linked α-GalpA, with branches of terminal (T) -, 1, 4-, 1, 3- and 1, 3, 6-linked ß-Galp, T-, 1, 5- and 1, 3, 5-linked α-Araf and T-, 1, 4-linked-ß-Xylp substituted at C-4 of 1, 2, 4-linked α-Rhap. Bioactivity screening showed SA02B promoted the growth of Bacteroides spp. which deconstructed it into monosaccharide. Simultaneously, we observed competition might exist between Bacteroides spp. and probiotics. Besides, we found that both Bacteroides spp. and probiotics could generate SCFAs grown on SA02B. Our findings highlight SA02B may deserve as a prebiotic to be explored to benefit the health gut microbiota.

Evidence and Impacts of Nanoplastic Accumulation on Crop Grains.

Nanoplastics are emerging pollutants of global concern. Agricultural soil is becoming a primary sink for nanoplastics generated from plastic debris. The uptake and accumulation of nanoplastics by crops contaminate the food chain and pose unexpected risks to human health. However, whether nanoplastics can enter grains and their impact on the grains of crop grown in contaminated soil is still unknown. Here, the translocation of polystyrene nanoplastics (PS-NPs) in crops, including peanut (Arachis hypogaea L.) and rice (Oryza sativa L.) is investigated. It is demonstrated PS-NPs translocation from the root and accumulation in the grains at the maturation stage. The treatment with PS-NPs (250 mg kg-1 ) increases the empty-shell numbers of rice grain by 35.45%, thereby decreasing the seed-setting rate of rice by 3.02%, and also decreases the average seed weight of peanuts by 3.45%. Moreover, PS-NPs exerted adverse effects on nutritional quality, such as decreasing the content of mineral elements, amino acids, and unsaturated fatty acids. To the knowledge, this is the first report of the presence of nanoplastics in the grains of crop plants grown in soil containing nanoplastics, and the results highlight the impact of nanoplastics on the yield and nutritional quality of crop grains.

Distinct lipid membrane interaction and uptake of differentially charged nanoplastics in bacteria.

BACKGROUND: Nanoplastics have been recently found widely distributed in our natural environment where ubiquitously bacteria are major participants in various material cycles. Understanding how nanoplastics interact with bacterial cell membrane is critical to grasp their uptake processes as well as to analyze their associated risks in ecosystems and human microflora. However, little is known about the detailed interaction of differentially charged nanoplastics with bacteria. The present work experimentally and theoretically demonstrated that nanoplastics enter into bacteria depending on the surface charges and cell envelope structural features, and proved the shielding role of membrane lipids against nanoplastics. RESULTS: Positively charged polystyrene nanoplastics (PS-NH2, 80 nm) can efficiently translocate across cell membranes, while negatively charged PS (PS-COOH) and neutral PS show almost no or much less efficacy in translocation. Molecular dynamics simulations revealed that the PS-NH2 displayed more favourable electrostatic interactions with bacterial membranes and was subjected to internalisation through membrane penetration. The positively charged nanoplastics destroy cell envelope of Gram-positive B. subtilis by forming membrane pore, while enter into the Gram-negative E. coli with a relatively intact envelope. The accumulated positively charged nanoplastics conveyed more cell stress by inducing a higher level of reactive oxygen species (ROS). However, the subsequently released membrane lipid-coated nanoplastics were nearly nontoxic to cells, and like wise, stealthy bacteria wrapped up with artifical lipid layers became less sensitive to the positively charged nanoplastics, thereby illustrating that the membrane lipid can shield the strong interaction between the positively charged nanoplastics and cells. CONCLUSIONS: Our findings elucidated the molecular mechanism of nanoplastics' interaction and accumulation within bacteria, and implied the shielding and internalization effect of membrane lipid on toxic nanoplastics could promote bacteria for potential plastic bioremediation.

Astaxanthin and its gold nanoparticles mitigate cadmium toxicity in rice by inhibiting cadmium translocation and uptake.

Cadmium (Cd) is one of the main heavy metal in rice, Cd uptake by cereal crops from soil leads to toxicity in plants and pose serious health risks due to human body's accumulation through the food chain. Astaxanthin, a natural and anti-oxidative oxycarotenoid, is widely distributed in various microorganisms and seafood. In this study, we demonstrated that astaxanthin in the form of gold nanoparticles (Ast-AuNPs) can efficiently alleviate Cd toxicity to a greater extent in hydroponically grown rice plants than single astaxanthin. When supplemented with 100 µg/mL Ast-AuNPs in medium, the Cd level of rice was significantly reduced by 26.2% (in roots) and 85.9% (in leaves), respectively. We also found Ast-AuNPs supplement restores chlorophyll biosynthesis and mitigate Cd-induced oxidative stresses: the contents of superoxide anion (O2-), hydrogen peroxide (H2O2), and malondialdehyde (MDA) were significantly reduced while the activity of the antioxidant enzymes (superoxide dismutase, peroxidase, and catalase) was significantly elevated. Further study showed that the supplement of Ast-AuNPs inhibited Cd-induced gene expression of the metal transporter genes (OsHMA2, OsHMA3, OsIRT1, OsIRT2, OsNramp1, and OsNramp5) in rice roots. Moreover, Ast-AuNPs regulated the metabolism of free amino acids and increased the level of non-enzymatic antioxidants such as glutathione and ascorbic acid. Therefore, this study demonstrates that Ast-AuNPs could mitigate the Cd toxicity in rice seedlings by suppressing Cd uptake, scavenging of ROS, and enhancing the activity of antioxidants, and also expands the application of functional gold nanoparticles in the alleviation of heavy metal pollution in plants.

Colonized extremophile Deinococcus radiodurans alleviates toxicity of cadmium and lead by suppressing heavy metal accumulation and improving antioxidant system in rice.

Cadmium (Cd) and lead (Pb) are the major toxic heavy metals accumulated in rice and pose a serious threat to human health. The most important remediation strategy is to reduce the translocation of these heavy metals from polluted soil to rice. Bioremediation using microorganisms had been widely used for preventing environmental heavy metal pollution, and the interaction between microorganisms and plants is critical to reduce the heavy metal stress. In this study, we demonstrated that an extremophile Deinococcus radiodurans, especially its mutant strain-Δdr2577 which is deficient in cell surface-layer, could efficiently prevent the translocation and damages of Cd or Pb in rice. The bacterial cells efficiently removed Cd or Pb from culture medium. Following colonization of Δdr2577 cells in rice root, Cd level decreased to 71.6% in root and 60.9% in shoot, comparing to the plants treated with Cd alone; Pb level decreased to 73.3% in root and 56.9% in shoot, comparing to the plants treated with Pb alone. Meanwhile, the bacterial cells released their intracellular antioxidant-related molecules including glutamate and manganese ions into culture medium. Accumulation of glutamate and manganese ions detected in rice root and shoot ameliorate Cd/Pb-induced oxidative stress as indicated by reduced levels of ROS and enhanced activities of antioxidant enzymes in rice. Our results provide a potential application of an extremophile bacterium in alleviating heavy metal toxicity in rice. The main findings of the work reveal the interaction between the D. radiodurans and rice, as well as the alleviating mechanism of Cd and Pb toxicity through suppressing heavy metal accumulation and improving the antioxidant system in rice by the extremophile bacterium.

Dynamic Polyphosphate Metabolism Coordinating with Manganese Ions Defends against Oxidative Stress in the Extreme Bacterium Deinococcus radiodurans.

Deinococcus radiodurans is an extreme bacterium with unparalleled resistance to oxidative stresses. Accumulation of intracellular Mn2+ complexing with small metabolites is the key contributor to the tolerance of D. radiodurans against oxidative stress. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn complex in D. radiodurans remain unclear. We identified an evolutionarily ancient and negatively charged phosphate polymer (polyphosphate [PolyP]) in D. radiodurans We investigated PolyP metabolism in the response of D. radiodurans to oxidative stress. The genes dr1939, encoding polyphosphatase kinase (PPKDr; the subscript "Dr" refers to D. radiodurans), and dra0185, encoding exopolyphosphatase (PPXDr), were identified. PPXDr is a novel exopolyphosphatase with a cofactor preference to Mn2+, which enhances the dimerization and activity of PPXDr to allow the effective cleavage of PolyP-Mn. PPKDr and PPXDr exhibited different dynamic expression profiles under oxidative stress. First, ppkDr was upregulated leading to the accumulation of PolyP, which chelated large amounts of intracellular Mn ions. Subsequently, the expression level of ppkDr decreased while ppxDr was substantially upregulated and effectively hydrolyzed inactive PolyP-Mn to release phosphate (Pi) and Mn2+, which could form into Mn-Pi complexes to scavenge O2- and protect proteins from oxidative damage. Hence, dynamic cellular PolyP metabolites complexed with free Mn ions highlight a defense strategy of D. radiodurans in response to oxidative stress.IMPORTANCE The Mn-phosphate complex (Mn-Pi) plays a key role in the cellular resistance of radioresistant bacteria. The evolutionarily ancient polyphosphate polymers (polyphosphate [PolyP]) could effectively chelate Mn2+ and donate phosphates. However, the intracellular reservoir of Mn ions and homeostatic regulation of the Mn-Pi complex remain unclear. Here, we investigated the relationship of PolyP metabolites and Mn2+ homeostasis and how they function to defend against oxidative stress in the radioresistant bacterium Deinococcus radiodurans We found that PPXDr (the subscript "Dr" refers to D. radiodurans) is a novel exopolyphosphatase with a cofactor preference for Mn2+, mediating PolyP-Mn degradation into Pi and Mn ions. The formed Mn-Pi complexes effectively protect proteins. The dynamic PolyP metabolism coordinating with Mn ions is a defense strategy of D. radiodurans in response to oxidative stress. The findings not only provide new insights into the resistance mechanism of the extreme bacterium D. radiodurans but also broaden our understanding of the functions of PolyP metabolism in organisms.

Functionalized Gold and Silver Bimetallic Nanoparticles Using Deinococcus radiodurans Protein Extract Mediate Degradation of Toxic Dye Malachite Green.

BACKGROUND: Biodegradation of toxic organic dye using nanomaterial-based microbial biocatalyst is an ecofriendly and promising technique. MATERIALS AND METHODS: Here, we have investigated the novel properties of functionalized Au-Ag bimetallic nanoparticles using extremophilic Deinococcus radiodurans proteins (Drp-Au-AgNPs) and their degradation efficiency on the toxic triphenylmethane dye malachite green (MG). RESULTS AND DISCUSSION: The prepared Drp-Au-AgNPs with an average particle size of 149.8 nm were capped by proteins through groups including hydroxyl and amide. Drp-Au-AgNPs demonstrated greater degradation ability (83.68%) of MG than D. radiodurans cells and monometallic AuNPs. The major degradation product was identified as 4-(dimethylamino) benzophenone, which is less toxic than MG. The degradation of MG was mainly attributed to the capping proteins on Drp-Au-AgNPs. The bimetallic NPs could be reused and maintained MG degradation ability (>64%) after 2 cycles. CONCLUSION: These results suggest that the easily prepared Drp-Au-AgNPs have potential applications as novel nanomedicine for MG detoxification, and nanomaterial for biotreatment of a toxic polyphenyl dye-containing wastewater.

Energy-efficient multidimensional Hellinger modulation for SPAD-based optical wireless communications.

Recently, the single photon avalanche diode optical wireless communication (SPAD OWC) has attracted much attention due to its potential underwater applications. For such system, the channel noise is additive Poisson noise (APN) rather than the commonly encountered additive white Gaussian noise (AWGN) and the corresponding maximum likelihood (ML) detection is hard to provide a useful insight into energy-efficient signal design. By using the previously proposed Hellinger distance design criterion, we design an energy-efficient multi-dimensional constellation within the nonnegative integer set by minimizing the average optical power for a fixed minimum Hellinger distance. Comprehensive simulations indicate that our designed constellation can substantially outperform the currently available pulse amplitude modulation (PAM) and squared PAM for SPAD OWC systems.

Clinical application of a novel computer-aided detection system based on three-dimensional CT images on pulmonary nodule.

The aim of this study was to investigate the clinical application effects of a novel computer-aided detection (CAD) system based on three-dimensional computed tomography (CT) images on pulmonary nodule. 98 cases with pulmonary nodule (PN) in our hospital from Jun, 2009 to Jun, 2013 were analysed in this study. All cases underwent PN detection both by the simple spiral CT scan and by the computer-aided system based on 3D CT images, respectively. Postoperative pathological results were considered as the "gold standard", for both two checking methods, the diagnostic accuracies for determining benign and malignant PN were calculated. Under simple spiral CT scan method, 63 cases is malignant, including 50 true positive cases and 13 false positive cases from the "gold standard"; 35 cases is benign, 16 true negative case and 19 false negative cases, the Sensitivity 1 (Se1)=0.725, Specificity1 (Sp1)=0.448, Agreement rate1 (Kappa 1)=0.673, J1 (Youden's index 1)=0.173, LR(+)1=1.616, LR(-)1=0.499. Kappa 1=0.673 between the 0.4 and 0.75, has a moderate consistency. Underwent computer-aided detection (CAD) based on 3D CT method, 67cases is malignant, including 62 true positive cases and 7 false positive cases; 31 cases is benign, 24 true negative case and 7 false negative cases, Sensitivity 2 (Se2)=0.899, Specificity2 (Sp2)=0.828, Agreement rate (Kappa 2)=0.877, J2 (Youden's index 2)=0.727, LR(+)2=5.212, LR(-)2=0.123. Kappa 2=0.877 >0.75, has a good consistency. Computer-aided PN detecting system based on 3D CT images has better clinical application value, and can help doctor carry out early diagnosis of lung disease (such as cancer, etc.) through CT images.

Photosynthetic physiological response of Radix Isatidis (Isatis indigotica Fort.) seedlings to nicosulfuron.

Radix Isatidis (Isatis indigotica Fort.) is one of the most important traditional Chinese medicine plants. However, there is no suitable herbicide used for weed control in Radix Isatidis field during postemergence stage. To explore the safety of sulfonylurea herbicide nicosulfuron on Radix Isatidis (Isatis indigotica Fort.) seedlings and the photosynthetic physiological response of the plant to the herbicide, biological mass, leaf area, photosynthetic pigment content, photosynthetic rate, chlorophyll fluorescence characteristics, and P700 parameters of Radix Isatidis seedlings were analyzed 10 d after nicosulfuron treatment at 5th leaf stage in this greenhouse research. The results showed that biological mass, total chlorophyll, chlorophyll a, and carotenoids content, photosynthetic rate, stomatal conductance, PS II maximum quantum yield, PS II effective quantum yield, PS II electron transport rate, photochemical quenching, maximal P700 change, photochemical quantum yield of PS I, and PS I electron transport rate decreased with increasing herbicide concentrations, whereas initial fluorescence, quantum yield of non-regulated energy dissipation in PS II and quantum yield of non-photochemical energy dissipation due to acceptor side limitation in PS I increased. It suggests that nicosulfuron ≥1 mg L-1 causes the damage of chloroplast, PS II and PS I structure. Electron transport limitations in PS I receptor side, and blocked dark reaction process may be the main cause of the significantly inhibited growth and decreased photosynthetic rate of Radix Isatidis seedlings.