Noncoding RNA-associated competing endogenous RNA networks in trastuzumab-induced cardiotoxicity.

Trastuzumab-induced cardiotoxicity (TIC) is a common and serious disease with abnormal cardiac function. Accumulating evidence has indicated certain non-coding RNAs (ncRNAs), functioning as competing endogenous RNAs (ceRNAs), impacting the progression of cardiovascular diseases. Nonetheless, the specific involvement of ncRNA-mediated ceRNA regulatory mechanisms in TIC remains elusive. The present research aims to comprehensively investigate changes in the expressions of all ncRNA using whole-transcriptome RNA sequencing. The sequencing analysis unveiled significant dysregulation, identifying a total of 43 circular RNAs (circRNAs), 270 long noncoding RNAs (lncRNAs), 12 microRNAs (miRNAs), and 4131 mRNAs in trastuzumab-treated mouse hearts. Subsequently, circRNA-based ceRNA networks consisting of 82 nodes and 91 edges, as well as lncRNA-based ceRNA networks comprising 111 nodes and 112 edges, were constructed. Using the CytoNCA plugin, pivotal genes-miR-31-5p and miR-644-5p-were identified within these networks, exhibiting potential relevance in TIC treatment. Additionally, KEGG and GO analyses were conducted to explore the functional pathways associated with the genes within the ceRNA networks. The outcomes of the predicted ceRNAs and bioinformatics analyses elucidated the plausible involvement of ncRNAs in TIC pathogenesis. This insight contributes to a better understanding of underlying mechanisms and aids in identifying promising targets for effective prevention and treatment strategies.

Immobilisation remediation of arsenic-contaminated soils with promising CaAl-layered double hydroxide and bioavailability, bioaccessibility, and speciation-based health risk assessment.

Arsenic (As)-contaminated soil poses great health risk to human mostly through inadvertent oral exposure. We investigated CaAl-layered double hydroxide (CaAl-LDH), a promising immobilising agent, for the remediation of As-contaminated Chinese soils. The effects on specific soil properties and As fractionation were analyzed, and changes in the health risk of soil As were accurately assessed by means of advanced in vivo mice model and in vitro PBET-SHIME model. Results showed that the application of CaAl-LDH significantly increased soil pH and concentration of Fe and Al oxides, and effectively converted active As fractions into the most stable residual fraction, guaranteeing long-term remediation stability. Based on in vivo test, As relative bioavailability was significantly reduced by 37.75%. Based on in vitro test, As bioaccessibility in small intestinal and colon phases was significantly reduced by 25.65% and 28.57%, respectively. Furthermore, As metabolism (reduction and methylation) by the gut microbiota inhabiting colon was clearly observed. After immobilisation with CaAl-LDH, the concentration of bioaccessible As(Ⅴ) in the colon fluid was significantly reduced by 61.91%, and organic As (least toxic MMA(V) and DMA(V)) became the main species, which further reduced the health risk of soil As. In summary, CaAl-LDH proved to be a feasible option for immobilisation remediation of As-contaminated soils, and considerable progress was made in relevant health risk assessment.

Description of Microbacterium dauci sp. nov., a plant growth hormone indoleacetic acid-producing and nitrogen-fixing bacterium isolated from carrot rhizosphere soil.

A plant growth hormone indoleacetic acid-producing strain LX3-4T was isolated from a carrot rhizosphere soil sample collected in Shandong Province, China. It is Gram-stain-positive, non-motile, and has irregular short rod-shaped cells. LX3-4T shared high 16S rRNA gene sequence identity with Microbacterium oleivorans DSM 16091T (99.4%), M. testaceum NBRC 12675T (98.6%), M. marinum DSM 24947T (98.5%), M. resistens NBRC 103078T (98.4%), and M. paraoxydans NBRC 103076T (98.3%). Phylogenetic analysis based on the concatenated gene sequences of 16S rRNA gene, housekeeping genes gryB and rpoB also showed the distinction between strain LX3-4T and other Microbacterium species. Furthermore, analysis of the average nucleotide identities (ANI), the average amino acid identity (AAI), and the digital DNA-DNA hybridization (dDDH) values between strain LX3-4T and its relatives revealed that strain LX3-4T represents a distinct species. The genomic DNA G + C content of the strain is 69.5%. It can grow at 25-37 °C (optimum 37 °C), pH 5.0-10.0 (optimum pH 6.0-8.0), and the range of NaCl concentration is 0-7% (w/v) (optimum 1-5%). The colonies on agar plates are smooth, translucent, and pale yellow. The main cellular fatty acids of strain LX3-4T are anteiso-C15:0, anteiso-C17:0, and iso-C16:0. The predominant respiratory quinones are MK-12 and MK-11. Diphosphatidylglycerol, phosphatidylglycerol, an unidentified glycolipid, and an unidentified phosphoglycolipid are major polar lipids. The cell-wall sugar of strain LX3-4T is glucose. The cell-wall peptidoglycan contains glycine, alanine, lysine, and glutamic acid. In addition, this strain carries nitrogen fixation genes and can grow in nitrogen-free medium. Based on the polyphasic data, strain LX3-4T represents a novel species of the genus Microbacterium, for which the name Microbacterium dauci sp. nov. is proposed with strain LX3-4T (= CCTCC AB 2023103T = LMG 33159T) designated as the type strain.

A Four Amino Acid Metabolism-Associated Genes (AMGs) Signature for Predicting Overall Survival Outcomes and Immunotherapeutic Efficacy in Hepatocellular Carcinoma.

Metabolites are important indicators of cancer and mutations in genes involved in amino acid metabolism may influence tumorigenesis. Immunotherapy is an effective cancer treatment option; however, its relationship with amino acid metabolism has not been reported. In this study, RNA-seq data for 371 liver cancer patients were acquired from TCGA and used as the training set. Data for 231 liver cancer patients were obtained from ICGC and used as the validation set to establish a gene signature for predicting liver cancer overall survival outcomes and immunotherapeutic responses. Four reliable groups based on 132 amino acid metabolism-related DEGs were obtained by consistent clustering of 371 HCC patients and a four-gene signature for prediction of liver cancer survival outcomes was developed. Our data show that in different clinical groups, the overall survival outcomes in the high-risk group were markedly low relative to the low-risk group. Univariate and multivariate analyses revealed that the characteristics of the 4-gene signature were independent prognostic factors for liver cancer. The ROC curve revealed that the risk characteristic is an efficient predictor for 1-, 2-, and 3-year HCC survival outcomes. The GSVA and KEGG pathway analyses revealed that high-risk score tumors were associated with all aspects of the degree of malignancy in liver cancer. There were more mutant genes and greater immune infiltrations in the high-risk groups. Assessment of the three immunotherapeutic cohorts established that low-risk score patients significantly benefited from immunotherapy. Then, we established a prognostic nomogram based on the TCGA cohort. In conclusion, the 4-gene signature is a reliable diagnostic marker and predictor for immunotherapeutic efficacy.

Predicting adsorption of organic compounds onto graphene and black phosphorus by molecular dynamics and machine learning.

With an increase in production and application of various engineering nanomaterials (ENMs), they will inevitably be released into the environment. Adsorption of various organic chemicals onto ENMs will impact on their environmental behavior and toxicology. It is unrealistic to experimentally determine adsorption equilibrium constants (K) for the vast number of organics and ENMs due to high cost in expenditure and time. Herein, appropriate molecular dynamics (MD) methods were evaluated and selected by comparing experimental K values of seven organics adsorbed onto graphene with the MD-calculated ones. Machine learning (ML) models on K of organics adsorption onto graphene and black phosphorus nanomaterials were constructed based on a benchmark data set from the MD simulations. Lasso models based on Mordred descriptors outperformed ML models built by support vector machine, random forest, k-nearest neighbor, and gradient boosting decision tree, in terms of cross-validation coefficients (Q2 > 0.90). The Lasso models also outperformed conventional poly-parameter linear free energy relationship models for predicting logK. Compared with previous models, the Lasso models considered more compounds with different functional groups and thus have broader applicability domains. This study provides a promising way to fill the data gap in logK for chemicals adsorbed onto the ENMs.

Enhanced ferrate(VI) oxidation of organic pollutants through direct electron transfer.

Fe(VI) is a versatile agent for water purification, and various strategies have been developed to improve its pollutant removal efficiency. Herein, it was found that in addition to intermediate iron species [Fe(IV)/Fe(V)], direct electron transfer (DET) played a significant role in the abatement of organic pollutants in Fe(VI)/carbon quantum dots (CQDs) system. Around 86, 83, 73, 64, 52, 45 and 17% of BPA, DCF, SMX, 4-CP, phenol, p-HBA, and IBP (6 µM) could be oxidized by 30 µM of Fe(VI), whereas with the addition of CQDs (4 mg/L), the oxidation ratio of these pollutants increased to 98, 99, 80, 88, 87, 66 and 57%, respectively. The negative impact induced by solution pH and background constituents on Fe(VI) abatement of pollutants could be alleviated by CQDs, and CQDs acted as catalysts for mediating DET from organic pollutants to Fe(VI). Theoretical calculation revealed that iron species [Fe(VI)/Fe(V)/Fe(IV)] was responsible for the oxidation of 36% of phenol, while DET contributed to the oxidation of 64% of phenol in the Fe(VI)/CQDs system. Compared with iron species oxidation, the CQDs mediated DET from pollutants to Fe(VI) was more efficient for utilizing the oxidation capacity of Fe(VI). The DET mechanism presented in the study provides a prospective strategy for improving the pollution control potential of Fe(VI).

Novel quantitative structure activity relationship models for predicting hexadecane/air partition coefficients of organic compounds.

Predicting the logarithm of hexadecane/air partition coefficient (L) for organic compounds is crucial for understanding the environmental behavior and fate of organic compounds and developing prediction models with polyparameter linear free energy relationships. Herein, two quantitative structure activity relationship (QSAR) models were developed with 1272 L values for the organic compounds by using multiple linear regression (MLR) and support vector machine (SVM) algorithms. On the basis of the OECD principles, the goodness of fit, robustness and predictive ability for the developed models were evaluated. The SVM model was first developed, and the predictive capability for the SVM model is slightly better than that for the MLR model. The applicability domain (AD) of these two models has been extended to include more kinds of emerging pollutants, i.e., oraganosilicon compounds. The developed QSAR models can be used for predicting L values of various organic compounds. The van der Waals interactions between the organic compound and the hexadecane have a significant effect on the L value of the compound. These in silico models developed in current study can provide an alternative to experimental method for high-throughput obtaining L values of organic compounds.

Design and preparation of highly active TiO2 photocatalysts by modulating their band structure.

Titanium dioxide photocatalysts with high reduction potential and visible light response hold great promise in photochemical conversion. Here, we used a simple glycine doping method to synthesize novel N-TiO2@C photocatalysts with upward shifted conduction bands and narrowed band gaps as well as inhibited recombination of photoinduced electron-hole pairs. The N-TiO2@C photocatalysts exhibited higher visible light response and remarkably enhanced photocatalytic activity in the production of nicotinamide adenine dinucleotide (NADH) by photomediated reduction of NAD+ without any electron mediator. The yield of NADH was up to 70.3 % far greater than that of the undoped TiO2 (11.3 %), and it stabilized at ca. 60 % after 10 cycles. The viability of coupling NADH regeneration with enzymatic reaction (alcohol dehydrogenase) was established in aldehyde reduction where formaldehyde was specifically reduced to methanol. These findings shed new light on the modulation of the band structure of semiconductors and develop an electron mediator free strategy for NADH-dependent artificial photosynthesis through coupled photocatalytic and enzymatic approaches.

Efficient removal of TBBPA with a Z-scheme BiVO4-(rGO-Cu2O) photocatalyst under sunlight irradiation.

In this study, reduced graphene oxide (rGO) was used to fabricate a Z-scheme BiVO4-(rGO-Cu2O) photocatalyst for the degradation of Tetrabromobisphenol A (TBBPA) under sunlight irradiation. The photocatalyst was synthesized using a three-step method BiVO4-(rGO-Cu2O) photocatalyst with an rGO loading of 1% and (rGO-Cu2O) to BiVO4 ratio of 50% achieved the best degradation effect for TBBPA removal. Electron paramagnetic resonance spectroscopy (EPR) confirmed that the charge transfer path of BiVO4-(rGO-Cu2O) follows that of Z-scheme photocatalysts. Moreover, the addition of rGO increases the charge transfer efficiency. High performance liquid chromatography-mass spectrometry (HPLC-MS) was used to detect and analyze intermediate products, allowing the proposal of the main degradation pathway of TBBPA. Photogenerated electrons of BiVO4-(rGO-Cu2O) were then transferred into the conduction band of Cu2O. Cu2O is located in the surface layer, which has the most effective contact area with pollutants, and therefore has a good outcome for the photocatalytic reduction of TBBPA. Photogenerated electrons (e-) and hydroxyl radicals (∙OH) are the main factors affecting TBBPA degradation. The degradation process of TBBPA includes electron reduction debromination, hydroxylation, and ß-cleavage. In our work, BiVO4-(rGO-Cu2O) was successfully synthesized to degrade TBBPA; this study brings forth a novel approach for the degradation of halogenated organic pollutants using a Z-scheme photocatalytic composite.

Bacillus arachidis sp. nov., Isolated from Peanut Rhizosphere Soil.

A novel facultatively aerobic bacterium designated SY8 was isolated from a peanut rhizosphere soil sample collected in Jiangsu Province, China. Cells are Gram-stain-positive, rod-shaped, and agar colonies are creamy, opaque, and usually rhizoidal. Strain growth occurs at 30 - 45 °C (optimum 30 °C), pH 4.0 - 10.0 (optimum pH 6.0) and 0 - 4% (w/v) NaCl (optimum 2%) in Luria-Bertani medium. Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain SY8 forms a distinct lineage in the clade of genus Bacillus and is related to Bacillus pseudomycoides DSM 12442 T (99.9%). Phylogenetic analysis of the concatenated gene sequences of 16S rRNA, gryB and rpoD also indicated that strain SY8 forms a distinct lineage in Bacillus. Calculation of the average nucleotide identities and the digital DNA-DNA hybridization values between strain SY8 and the related type Bacillus strains further revealed that strain SY8 represents a distinct species. The predominant cellular fatty acids are iso C15:0 (28.7%) and summed feature 3 (C16:1ω7c and/or C16:1ω6c) (10.3%). The major polar lipids consisted of diphosphatidyl glycerol, phosphatidyl glycerol, phosphatidyl ethanolamine, phosphatidylinositol, and three unidentified phospholipids. The major menaquinone of SY8 was MK-7. Based on phenotypic, phylogenetic, chemotaxonomic, and genomic features, strain SY8 represents a novel species of the genus Bacillus. The name Bacillus arachidis sp. nov. is proposed with strain SY8T (= CCTCC AB 2021100 T=LMG 32409 T) designated as the type strain.

Noncoding RNA-Associated Competing Endogenous RNA Networks in Doxorubicin-Induced Cardiotoxicity.

Accumulating evidence has indicated that noncoding RNAs (ncRNAs) are involved in doxorubicin-induced cardiotoxicity (DIC). However, the ncRNA-associated competing endogenous RNA (ceRNA)-mediated regulatory mechanisms in DIC remain unclear. In this study, we aimed to systematically investigate the alterations in expression levels of long noncoding RNA (lncRNA), circular RNA (circRNA), microRNA (miRNA), and mRNA in a DIC mouse model through deep RNA sequencing (RNA-seq). The results showed that 217 lncRNAs, 41 circRNAs, 11 miRNAs and 3633 mRNAs were aberrantly expressed. Moreover, the expression of 12 randomly selected transcripts was determined by real-time quantitative polymerase chain reaction to test the reliability of RNA-seq data. Based on the interaction between miRNAs and mRNAs, as well as lncRNAs/circRNAs and miRNAs, we constructed comprehensive lncRNA or circRNA-associated ceRNA networks in DIC mice. Moreover, we performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses for differentially expressed genes. In conclusion, these identified ceRNA interactions provide new insight into the underlying mechanism and may be crucial therapeutic targets of DIC.

Involvement of Abnormal Gut Microbiota Composition and Function in Doxorubicin-Induced Cardiotoxicity.

Objectives: Doxorubicin (Dox), a chemotherapeutic anthracycline agent for the treatment of a variety of malignancies, has a limitation in clinical application for dose-dependent cardiotoxicity. The purpose of this study was to explore the relationship between the composition/function of the gut microbiota and Dox-induced cardiotoxicity (DIC). Methods: C57BL/6J mice were injected intraperitoneally with 15 mg/kg of Dox, with or without antibiotics (Abs) administration. The M-mode echocardiograms were performed to assess cardiac function. The histopathological analysis was conducted by H&E staining and TUNEL kit assay. The serum levels of creatine kinase (CK), CK-MB (CK-MB), lactic dehydrogenase (LDH), and cardiac troponin T (cTnT) were analyzed by an automatic biochemical analyzer. 16S rRNA gene and metagenomic sequencing of fecal samples were used to explore the gut microbiota composition and function. Key Findings: Dox caused left ventricular (LV) dilation and reduced LV contractility. The levels of cardiomyocyte apoptosis and myocardial enzymes were elevated in Dox-treated mice compared with the control (Con) group. 16S rRNA gene sequencing results revealed significant differences in microbial composition between the two groups. In the Dox group, the relative abundances of Allobaculum, Muribaculum, and Lachnoclostridium were significantly decreased, whereas Faecalibaculum, Dubosiella, and Lachnospiraceae were significantly increased compared with the Con group at the genus level. Functional enrichment with Cluster of orthologous groups of proteins (COG) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that the Dox mice displayed different clusters of cellular processes and metabolism from the Con mice. The different species and their functions between the two groups were associated with the clinical factors of cardiac enzymes. Moreover, depletion of the gut microbiota could alleviate Dox-induced myocardial injury and cardiomyocyte apoptosis. Conclusions: The study here shows that composition imbalance and functional changes of the gut microbiota can be one of the etiological mechanisms underlying DIC. The gut microbiota may serve as new targets for the treatment of cardiotoxicity and cardiovascular diseases.

Simulating and Predicting Adsorption of Organic Pollutants onto Black Phosphorus Nanomaterials.

Layered black phosphorus (BP) has exhibited exciting application prospects in diverse fields. Adsorption of organics onto BP may influence environmental behavior and toxicities of both organic pollutants and BP nanomaterials. However, contributions of various intermolecular interactions to the adsorption remain unclear, and values of adsorption parameters such as adsorption energies (Ead) and adsorption equilibrium constants (K) are lacking. Herein, molecular dynamic (MD) and density functional theory (DFT) was adopted to calculate Ead and K values. The calculated Ead and K values for organics adsorbed onto graphene were compared with experimental ones, so as to confirm the reliability of the calculation methods. Polyparameter linear free energy relationship (pp-LFER) models on Ead and logK were developed to estimate contributions of different intermolecular interactions to the adsorption. The adsorption in the gaseous phase was found to be more favorable than in the aqueous phase, as the adsorbates need to overcome cohesive energies of water molecules onto BP. The affinity of the aromatics to BP was comparable to that of graphene. The pp-LFER models performed well for predicting the Ead and K values, with external explained variance ranging from 0.90 to 0.97, and can serve as effective tools to rank adsorption capacities of organics onto BP.

Disulfiram inhibits oxidative stress and NLRP3 inflammasome activation to prevent LPS-induced cardiac injury.

Sepsis-induced cardiac injury leads to the high rate of mortality, the therapeutics for this disorder are limited. Disulfiram (DSF) is an FDA-approved treatment for chronic alcohol addiction, and its cardio-protection is gradually discovered in recent years. In present study, mice were injected with lipopolysaccharide (LPS, 15 mg/kg) to induce a septic cardiac injury model, and aimed to investigate the protective effect of DSF on sepsis-induced cardiac injury and the underlying mechanisms. Results showed that DSF treatment alleviated the lowered left heart function and myocardial cell apoptosis induced by LPS. Moreover, we found that LPS increased myocardium lipid peroxidation, DNA damage and the activation of NLRP3 inflammasome, which were significantly reduced by DSF. These results suggested the protective role of DSF in LPS-induced cardiac injury, and the mechanism involved the inhibition on the oxidative stress and NLRP3 inflammasome activation. Given the potent cardiac protection effect of DSF, repurposing DSF in the clinic would represent a new strategy to protect and treat sepsis-induced cardiac injury.

High and Economical Nattokinase Production with Acetoin as a Useful Byproduct from Soybean Milk and Glucose.

Nattokinase (NK) is a potent fibrinolytic enzyme with wide pharmaceutical and nutraceutical applications. Safe and high NK-yielding strains are urgently needed. In this study, the best strain NDF was isolated from one of the 11 natto samples and then identified as Bacillus subtilis. The effects of carbon and nitrogen sources on NK production were investigated, and glucose and soybean milk were finally selected as the optimal carbon and nitrogen sources, respectively. Acetoin, a valuable compound with versatile usages, was detected as the main byproduct of carbon overflow. In a 6-L fermenter, NK and acetoin reached their peak concentrations simultaneously (10,220 IU/mL and 25.9 g/L, respectively) at 25 h in a culture medium containing 180 g/L of soybean milk and 105 g/L of glucose. The NK product was verified by sequencing of the aprN gene and SDS-PAGE analysis. Only very limited kinds of proteins were found in the supernatant of the fermentation broth, and NK was one of the main bands. This study has developed an economical and high NK production method with acetoin as a useful byproduct.

Disulfiram attenuates lipopolysaccharide-induced acute kidney injury by suppressing oxidative stress and NLRP3 inflammasome activation in mice.

OBJECTIVES: Disulfiram (DSF), an old drug for treating chronic alcohol addiction, has been reported to exhibit widely pharmacological actions. This study aimed to explore the protective effect of DSF on lipopolysaccharide (LPS)-induced acute kidney injury (AKI). METHODS: C57BL/6J mice were treated with 15 mg/kg LPS (i.p.) with or without DSF pre-treatment (i.p.). The histopathological analysis was conducted by H&E staining and TUNEL kit assay. An automatic biochemical analyser was used to determine the serum creatinine and blood urea nitrogen (BUN). Expressions of 8-OHdG, NLRP3 and IL-1ß in the kidney tissues were observed by IHC staining. The protein expressions of ß-actin, Bax, Bcl-2, NLRP3, caspase-1 (p20), pro-IL-1ß and IL-1ß were analysed by western blot. KEY FINDINGS: DSF attenuated the histopathologic deterioration of the kidney and inhibited the elevation of creatinine and BUN levels in mice. DSF inhibited LPS-induced cell apoptosis. Moreover, DSF treatment reversed the LPS-induced excessive oxidative stress. The NLRP3 inflammasome activation induced by the LPS, as indicated by up-regulation of NLRP3 expression, cleaved caspase-1 (p20) and IL-1ß, was also suppressed by DSF. CONCLUSIONS: The study here shows that DSF protects against the AKI induced by LPS at least partially via inhibiting oxidative stress and NLRP3 inflammasome activation.

Characterization and Regulation of the Acetolactate Synthase Genes Involved in Acetoin Biosynthesis in Acetobacter pasteurianus.

Acetoin is an important aroma-active chemical in cereal vinegars. Acetobacter pasteurianus was reported to make a significant contribution to acetoin generation in cereal vinegars. However, the related acetoin biosynthesis mechanism was largely unknown. Two annotated acetolactate synthase (ALS) genes of A. pasteurianus were investigated in this study to analyze their functions and regulatory mechanisms. Heterologous expression in Escherichia coli revealed that only AlsS1 exhibited ALS activity and had the optimal activity at 55 °C and pH 6.5. Two alsS-defective mutants of A. pasteurianus CICC 22518 were constructed, and their acetoin yields were both reduced, suggesting that two alsS genes participated in acetoin biosynthesis. A total 79.1% decrease in acetoin yield in the alsS1-defective mutant revealed that alsS1 took a major role. The regulator gene alsR disruptant was constructed to analyze the regulation effect. The decline of the acetoin yield and down-regulation of the alsD and alsS1 gene transcriptions were detected, but the alsS2 gene transcription was not affected. Acetoin was an important metabolite of lactate catabolism in A. pasteurianus. The coexistence of two alsS genes can help strains rapidly and securely assimilate lactate to deal with the lactate pressure in a vinegar brewing environment, which represented a new genetic mode of acetoin production in bacteria.

Longitudinal transport timescales in a large dammed river - The Changjiang River.

As a key component of the global water cycle, river flow transports both freshwater and biotic/abiotic matters from land to sea, while in recent decades its rhythm has been strongly disturbed by human activities, especially damming. Yet little is known about the long-distance transport processes along the world's major fluvial systems and the impact of large dams on their timescales. Here, taking the Changjiang River (Yangtze River) as an example, we built a hydrodynamics-based model to investigate the water age and residence time in the mainstream from the upper reach ~700 km upstream of the Three Gorges Dam (TGD) to the estuary ~1900 km downstream of the TGD. We find that since the mainstream was dammed by the TGD, the water age increases significantly by approximately 2 to 5 times from the estuary to the dam. Downstream of the dam the longitudinal ageing rate of water becomes discordant in an annual cycle, and the replenished discharge in dry season accelerates the water transport. Due to the stationary assumption, the widely applied hydraulic residence time of water is substantially larger and smaller than the age-based dynamic residence time in the large reservoir during the impounding and releasing periods, respectively.

Halomonas bachuensis sp. nov., Isolated from Gobi Soil.

A novel aerobic bacterium designated DX6T was isolated from a Gobi soil sample collected in Bachu County, China. Cells are Gram-stain-negative and rod-shaped and colonies are creamy, circular and smooth. The growth range of NaCl concentration was 1-15% (optimum 2-10%, w/v). Growth occurs at 10-45 °C (optimum 37 °C) and pH 5.0-10.0 (optimum pH 7.0-9.0). Phylogenetic analysis of the 16S rRNA gene sequences indicated that strain DX6T formed a distinct lineage in the clade of genus Halomonas and is related to Halomonas desiderata DSM 9502T (98.3%), Halomonas kenyensis AIR-2T (97.7%), Halomonas daqingensis DQD2-30T (97.6%), Halomonas saliphila LCB169T (97.4%) and Halomonas endophytica MC28T (96.2%). Analysis of the housekeeping genes gryB and rpoD and calculation of the average nucleotide identities and the digital DNA-DNA hybridization values between strain DX6T and the related type Halomonas strains further revealed that strain DX6T represented a distinct species. The main respiratory quinones of strain DX6T were ubiquinone 9 (Q-9) and ubiquinone 8 (Q-8). The predominant cellular fatty acids were summed feature 8 (C18:1ω7c and/or C18:1ω6c), summed feature 3 (C16:1ω7c and/or C16:1ω6c) and C16:0. The major polar lipids consisted of diphosphatidylglycerol, phosphatidylglycerol, phosphatidylethanolamine, two unidentified phospholipids, an unidentified phosphatidylglycolipid, and four unidentified lipids. Based on the phenotypic, phylogenetic, chemotaxonomic and genomic features, strain DX6T represents a novel species of the genus Halomonas. The name Halomonas bachuensis sp. nov. is proposed with strain DX6T (= CCTCC AB 2020094T = KCTC 82196T) designated as the type strain.

Tetramethylpyrazine production from edible materials by the probiotic Bacillus coagulans.

2,3,5,6-Tetramethylpyrazine (TMP) has health care functions, especially for cardiovascular and cerebrovascular health. In this study, we found that Bacillus coagulans, a well-known probiotic, has the capability to produce acetoin, a precursor of TMP. The culture conditions and medium for the production of TMP by B. coagulans CICC 20138 were optimized. Then, a novel three-step process was successfully performed for the production of TMP from edible materials by B. coagulans. First, in the acetoin enrichment process, 12.61 ± 0.34 g/L acetoin was generated at 36 h. Second, in the spore enrichment process, various factors were optimized to make the bacteria produce more spores to improve the resistance to subsequent high-temperature reactions. Third, in the TMP enrichment process, the final concentration of TMP and B. coagulans spores contained in the product reached 2.54 ± 0.26 g/L and 8.81 × 108 CFU/mL at 46 h, respectively. This is the first report of using a probiotic bacterium to produce TMP. Using edible materials and the probiotic strain, this work provides a novel method for the production of a TMP food additive rich in B. coagulans spores.