Construction of Aerobic/Anaerobic-Substrate-Induced Gene Expression Procedure for Exploration of Metagenomes From Subseafloor Sediments

Substrate-induced gene expression (SIGEX) is a high-throughput promoter-trap method. It is a function-based metagenomic screening tool that relies on transcriptional activation of a reporter gene green fluorescence protein (gfp) by a metagenomic DNA library upon induction with a substrate. However, its use is limited because of the relatively small size of metagenomic DNA libraries and incompatibility with screening metagenomes from anaerobic environments. In this study, these limitations of SIGEX were addressed by fine-tuning metagenome DNA library construction protocol and by using Evoglow, a green fluorescent protein that forms a chromophore even under anaerobic conditions. Two metagenomic libraries were constructed for subseafloor sediments offshore Shimokita Peninsula (Pacific Ocean) and offshore Joetsu (Japan Sea). The library construction protocol was improved by (a) eliminating short DNA fragments, (b) applying topoisomerase-based high-efficiency ligation, (c) optimizing insert DNA concentration, and (d) column-based DNA enrichment. This led to a successful construction of metagenome DNA libraries of approximately 6 Gbp for both samples. SIGEX screening using five aromatic compounds (benzoate, 3-chlorobenzoate, 3-hydroxybenzoate, phenol, and 2,4-dichlorophenol) under aerobic and anaerobic conditions revealed significant differences in the inducible clone ratios under these conditions. 3-Chlorobenzoate and 2,4-dichlorophenol led to a higher induction ratio than that for the other non-chlorinated aromatic compounds under both aerobic and anaerobic conditions. After the further screening of induced clones, a clone induced by 3-chlorobenzoate only under anaerobic conditions was isolated and characterized. The clone harbors a DNA insert that encodes putative open reading frames of unknown function. Previous aerobic SIGEX attempts succeeded in the isolation of gene fragments from anaerobes. This study demonstrated that some gene fragments require a strict in vivo reducing environment to function and may be potentially missed when screened by aerobic induction. The newly developed anaerobic SIGEX scheme will facilitate functional exploration of metagenomes from the anaerobic biosphere.

Supercritical CO2 Extraction of Narcissus poeticus L. Flowers for the Isolation of Volatile Fragrance Compounds

The flowers of Narcissus poeticus are used for the isolation of valuable fragrance substances. So far, as the majority of these substances consist of volatile and sensitive to heat compounds, there is a need of developing effective methods for their recovery. In this study, freeze-dried N. poeticus inflorescences were extracted with pure supercritical CO2 (SFE-CO2) and its mixture with 5% co-solvent ethanol (EtOH) at 40 °C. Extract yields varied from 1.63% (12 MPa) to 3.12% (48 MPa, 5% EtOH). In total, 116 volatile compounds were identified by GC-TOF/MS in the extracts, which were divided into 20 different groups. Benzyl benzoate (9.44–10.22%), benzyl linoleate (1.72–2.17%) and benzyl alcohol (0.18–1.00%) were the major volatiles among aromatic compounds. The amount of the recovered benzyl benzoate in N. poeticus SFE-CO2 extracts varied from 58.98 ± 2.61 (24 MPa) to 91.52 ± 1.36 (48 MPa) mg/kg plant dry weight (pdw). α-Terpineol dominated among oxygenated monoterpenes (1.08–3.42%); its yield was from 9.25 ± 0.63 (12 MPa) to 29.88 ± 1.25 (48 MPa/EtOH) mg/kg pdw. Limonene was the major monoterpene hydrocarbon; (3E)-hexenol and heneicosanol dominated among alcohols and phenols; dihydroactinidiolide and 4,8,12,16-tetramethyl heptadecan-4-olide were the most abundant lactones; heptanal, nonanal, (2E,4E)-decadienal and octadecanal were the most abundant aldehydes. The most important prenol lipids were triterpenoid squalene, from 0.86 ± 0.10 (24 MPa) to 7.73 ± 0.18 (48 MPa/EtOH) mg/kg pdw and D-α-tocopherol, from 1.20 ± 0.04 (12 MPa) to 15.39 ± 0.31 (48 MPa/EtOH) mg/kg pdw. Aliphatic hydrocarbons (waxes) constituted the main part (41.47 to 54.93%) in the extracts; while in case of a 5% EtOH the percentage of alkanes was the lowest. The fraction of waxes may be removed for the separation of higher value fragrance materials. In general, the results obtained are promising for a wider application of SFE-CO2 for the recovery of fragrance substances from N. poeticus flowers.

Biomass:polystyrene co-pyrolysis coupled with metal-modified zeolite catalysis for liquid fuel and chemical production

Biomass and waste polystyrene plastic (ratio 1:1) were co-pyrolysed followed by catalysis in a two-stage fixed bed reactor system to produce upgraded bio-oils for production of liquid fuel and aromatic chemicals. The catalysts investigated were ZSM-5 impregnated with different metals, Ga, Co, Cu, Fe and Ni to determine their influence on bio-oil upgrading. The results showed that the different added metals had a different impact on the yield and composition of the product oils and gases. Deoxygenation of the bio-oils was mainly via formation of CO2 and CO via decarboxylation and decarbonylation with the Ni–ZSM-5 and Co–ZSM-5 catalysts whereas higher water yield and lower CO2 and CO was obtained with the ZSM-5, Ga–ZSM-5, Cu–ZSM-5 and Fe–ZSM-5 catalysts suggesting hydrodeoxygenation was dominant. Compared to the unmodified ZSM-5, the yield of single-ring aromatic compounds in the product oil was increased for the Co–ZSM-5, Cu–ZSM-5, Fe–ZSM-5 and Ni–ZSM-5 catalysts. However, for the Ga–ZSM-5 catalyst, single-ring aromatic compounds were reduced, but the highest yield of polycyclic aromatic hydrocarbons was produced. A higher biomass to polystyrene ratio (4:1) resulted in a markedly lower oil yield with a consequent increased yield of gas.

A predictive model for the aggregation of polycyclic aromatic compounds

The physical aggregation of polycyclic aromatic compounds (PACs) is a key step in soot inception. In this work, we set out to elucidate which molecular properties influence the physical growth process and use machine learning to quantitatively relate these features to the propensity of these molecules to physically dimerize with other PACs. To this end, we first develop a dataset of PAC monomers along with their calculated free energies of dimerization emphasizing a set of PACs with a diverse range of properties. First, we augment existing calculations of dimerization energies with our own molecular dynamics simulations enhanced by well-tempered Metadyanmics. We then demonstrate that a machine learning model based on the least absolute shrinkage and selection operator (Lasso) is able to quantitatively learn how molecular features contribute to physical aggregation and predict the free energy of dimerization for new pairs of molecules. The model is able to accurately determine the stability for both homodimerization and heterodimerization cases. Our approach also provides a data driven method to determine the molecular features most important to predicting the dimer stability. From this, we determine that the PAC properties most influential to physical dimerization are size, shape, oxygenation, and presence of rotatable bonds. This work highlights the molecular complexity of the PAC monomers that must be accounted for in order to accurately represent physical aggregation. We anticipate that this approach will allow for more effective modeling of the PAC dimerization process as it facilitates the efficient prediction of dimerization propensity from easily calculable molecular features.

HS-SPME Combined with GC-MS/O to Analyze the Flavor of Strong Aroma Baijiu Daqu

Daqu has gained wide attention because it is an essential source of microorganisms and flavor in baijiu production. In this study, HS-SPME combined with GC-MS/O was used to analyze the volatile flavor components of Strong aroma baijiu Daqu. DI-GC-O was used to choose the best extraction fiber to extract the representative overall aroma profile of Daqu. A total of 139 compounds were identified in the six different maturity stages of Daqu, and these compounds are of different types and concentrations. HS-SPME combined with GC-MS/O was used to analyze the aroma active substances in the finished Daqu, and a total of 43 aroma compounds were identified. The OAVs of 21 aromatic compounds were calculated based on the quantitative analysis results of MHS-SPME. Eighteen compounds with OAVs ≥ 1 made significant contributions to the overall aroma of Daqu, including guaiacol, 4-ethyl-2-methoxy phenol, 2-ethyl-3,5-dimethylpyrazine, etc.

Impact of substitution on reactions and stability of one-electron oxidised phenyl sulfonates in aqueous solution

Functional groups can be used to modify the equilibrium position and tune the reactivity of one electron oxidised aromatic compounds.