Unraveling the Aromatic Rule of Cyclic Superatomic Molecules in π-Conjugated Compounds.

The aromaticity of π-conjugated compounds has long been a confusing issue. Based on a recently emerged two-dimensional (2D) superatomic-molecule theory, a unified rule was built to decipher the aromaticity of cyclic superatomic molecules of π-conjugated compounds from the chemical bonding perspective. Herein, a series of planar [n]helicenes and [n]circulenes, composed of benzene, thiophene, or furfuran, are systemically studied and seen as superatomic molecules ◊On-2◊F2 or ◊On, where superatoms ◊F and ◊O denote π-conjugated units with 5 and 4 π electrons, respectively. The ascertained superatomic Lewis structures intuitively display aromaticity with each basic unit meeting the superatomic sextet rule of benzene, similar to classical valence bond theory, which is favored by the synthesized complex π-conjugated compounds comprising different numbers and kinds of subrings. The evolutionary trend of ring currents and chemical bonding suggests a local ribbon-like aromaticity in these π-conjugated compounds. Moreover, nonplanar helical π-conjugated compounds have the potential to evolve into spring-like periodic materials with excellent physical properties.

Enhanced Stability of Rhombic Dodecahedron Nb15- with Well-Organized Superatomic States.

Well-resolved Nbn- clusters are produced and reacted with ethene and propene via a downstream flow tube reactor. Interestingly, the Nbn- clusters readily react with ethene and propene to form dehydrogenation products; however, Nb15- shows up in the mass spectra with prominent mass abundance indicating its inertness to react with olefins. For this cluster, we conduct photoelectron velocity map imaging (VMI) experiments and verify the stability of Nb15- within a highly symmetrical rhombic dodecahedron structure. Theoretical studies show that the stability of the Nb15- cluster is correlated with its superatomic nature pertaining to both geometric and electronic shell closures. Notably, the superatomic 1s orbital is dominated by the 5s electron of the central Nb atom, while the other superatomic orbitals are contributed by s-d hybridization, especially a remarkable contribution of s-dz2 hybridization. Apart from the closed shells, the highly symmetric geometry of Nb15- is associated with a regular polyhedral structure directed by all rhombus facets, embodying a magic number for body-centered dodecahedra, indicative of enhanced stability as a double magic cluster free of olefin adsorption.

The Baseline Gut Microbiota Directs Dieting-Induced Weight Loss Trajectories.

BACKGROUND & AIMS: Elucidating key factors affecting personal responses to food is the first step toward implementing personalized nutrition strategies in for example weight loss programs. Here, we aimed to identify factors of importance for individual weight loss trajectories in a natural setting where participants were provided dietary advice but otherwise asked to self-manage the daily caloric intake and data reporting. METHODS: A 6-month weight-reduction program with longitudinal collection of dietary, physical activity, body weight, and fecal microbiome data as well as single-nucleotide polymorphism genotypes in 83 participants was conducted, followed by integration of the high-dimensional data to define the most determining factors for weight loss in a dietician-guided, smartphone-assisted dieting program. RESULTS: The baseline gut microbiota was found to outperform other factors as a predieting predictor of individual weight loss trajectories. Weight loss was also linked to the magnitude of changes in abundances of certain bacterial species during dieting. Ruminococcus gnavus (MGS0160) was significantly enriched in obese individuals and decreased during weight loss. Akkermansia muciniphila (MGS0120) and Alistipes obesi (MGS0342) were significantly enriched in lean individuals, and their abundance increased during dieting. Finally, Blautia wexlerae (MGS0575) and Bacteroides dorei (MGS0187) were the strongest predictors for weight loss when present in high abundance at baseline. CONCLUSION: Altogether, the baseline gut microbiota was found to excel as a central personal factor in capturing the relationship between dietary factors and weight loss among individuals on a dieting program.

The Covalent AuI-AuI Bond in (AuF)n (n = 2∼4): A Perspective to Understand the Closed-Shell AuI···AuI Interaction.

The nature of closed-shell AuI···AuI attraction is still a conundrum in theoretical chemistry. However, for Au2F2 with a zigzag conformation, the d10-d10 closed-shell interaction between the AuF monomers is demonstrated as a coordinate covalent bond. Chemical bonding analysis reveals that the strong AuI···AuI attraction is caused by the participation of the extraordinary active 5d orbital of Au. Based on our study, one of the 5d orbitals of the Au atom is activated to hybridize with its 6s and 6p orbitals to form hybridized dsp2 orbitals, where each Au atom is both an electron donor (Lewis base) and acceptor (Lewis Acid) in dimerization. Actually, the closed-shell AuI···AuI interaction in the zigzag conformation of Au2X2 (X = F, Cl, Br, I, or NH2) is covalent. Our results provide a rather simple but clear-cut example, where mysterious AuI···AuI attractions can be possibly explained by the covalent bond theory.

Benchmark studies on the large errors of calculated binding energies in metallophilic interactions.

Aurophilicity is a d10-d10 closed-shell interaction, which is repulsively calculated by the Hartree-Fork (HF) method, whereas binding energies (Eb) are largely overestimated under the second-order Møller-Plesset (MP2) method, compared to the coupled cluster singles and doubles with perturbative triples [CCSD(T)] method. The unusual energy errors between different wave functional methods were also verified in other closed-shell metallophilic systems and even were taken as a label of metallophilic interaction. Here, we performed a benchmark study on a collection of structures with weak interactions, sp-sp bonds, sp-d bonds, and d-d bonds, to investigate the influence factor of the errors of HF and MP2 methods. It was found that the large energy errors of HF and MP2 methods were not specified for closed-shell interactions, and the errors could also be very large for many covalent bonds, which was strongly related to the azimuthal quantum number of interaction orbitals. Compared to the CCSD(T) method, the MP2 method weakens the s-s covalent interactions slightly, strengthens the p-p covalent interactions slightly, and overestimates the d-d covalent interactions largely (can be -170 kcal/mol for the Re-Re quadruple bond). This benchmark study suggests that the special energy errors in metallophilicity may result from the participation of d orbitals. Benchmark studies on various density functional methods were also given for calculating binding energies of d-d bonds.

Identification, Characteristics and Function of Phosphoglucomutase (PGM) in the Agar Biosynthesis and Carbon Flux in the Agarophyte Gracilariopsis lemaneiformis (Rhodophyta).

Agar is widely applied across the food, pharmaceutical and biotechnology industries, owing to its various bioactive functions. To better understand the agar biosynthesis in commercial seaweed Gracilariopsis lemaneiformis, the activities of four enzymes participating in the agar biosynthesis were detected, and phosphoglucomutase (PGM) was confirmed as highly correlated with agar accumulation. Three genes of PGM (GlPGM1, GlPGM2 and GlPGM3) were identified from the G. lemaneiformis genome. The subcellular localization analysis validated that GlPGM1 was located in the chloroplast and GlPGM3 was not significantly distributed in the organelles. Both the GlPGM1 and GlPGM3 protein levels showed a remarkable consistency with the agar variations, and GlPGM3 may participate in the carbon flux between (iso)floridoside, floridean starch and agar synthesis. After treatment with the PGM inhibitor, the agar and floridean starch contents and the activities of floridean starch synthase were significantly decreased; products identified in the Calvin cycle, the pentose phosphate pathway, the Embden-Meyerhof-Parnas pathway and the tricarboxylic acid cycle were depressed; however, lipids, phenolic acids and the intermediate metabolites, fructose-1,6-phosphate were upregulated. These findings reveal the essential role of PGM in regulating the carbon flux between agar and other carbohydrates in G. lemaneiformis, providing a guide for the artificial regulation of agar accumulation.

Correlation between alveolar cleft morphology and the outcome of secondary alveolar bone grafting for unilateral cleft lip and palate.

BACKGROUND: Secondary alveolar bone grafting (SABG) is an integral part of the treatment for cleft lip and alveolus and cleft lip and palate. However, the outcome of SABG was not satisfactory as expected, factors that affecting the outcome were still controversial. The aims of this study were to summarize a new method for the classification of alveolar cleft morphology in patients with unilateral cleft lip and alveolus or unilateral cleft lip and palate, to evaluate the correlation between the morphology and SABG outcomes, to identify factors that might predict the outcomes. METHODS: The characteristics of the cleft morphologies of 120 patients who underwent SABG were observed using the preoperative Cone-Beam Computed Tomography (CBCT) images. 52 patients who had CBCT scans performed at least 6 months after SABG were included for the evaluation of outcomes. Both categorical and continuous evaluation methods were measured. Correlations between cleft morphology and SABG outcomes were assessed using the Pearson correlation coefficient in SPSS 27.0.0. RESULTS: A new method for the classification of cleft morphology was summarized:type I, prism type (labial defect size ≥ palatal defect size; nasal defect size ≥ occlusal defect size); type II, prism' type (labial defect ≥ palatal defect; nasal defect < occlusal defect); type III, inverted prism type (palatal defect ≥ labial defect); type IV, funnel type (presented as a significantly narrow defect area in the middle towards the vertical dimension); and type V, undefinable (extremely irregular morphology can't be defined as any of the above types). Categorical evaluation showed 8 failure, 11 poor, 12 moderate, and 21 good results, while the average bone filling rate was 59.24 ± 30.68%. There was a significant correlation between the cleft morphology and categorical/continuous evaluation outcome (p < 0.05). CONCLUSION: The new method for the classification of alveolar cleft morphology summarized in this study was comprehensive and convenient for clinical application. Both categorical and continuous methods should be used for radiographic assessments in patients undergoing SABG. The chances of a successful procedure might be better when the patient has type I or IV morphology, in which the shape is like a funnel in the relatively palatal or occlusal area towards the vertical dimension. A relatively great amount of bone resorption was observed in most patients. Trial registration Chinese clinical trial registry; registration number: ChiCTR2100054438.

Evolutionary engineering of Escherichia coli for improved anaerobic growth in minimal medium accelerated lactate production.

Anaerobic fermentation is a favorable process for microbial production of bulk chemicals like ethanol and organic acids. Low productivity is the bottleneck of several anaerobic processes which has significant impact on the technique competitiveness of production strain. Improving growth rate of production strain can speed up the total production cycle and may finally increase productivity of anaerobic processes. In this work, evolutionary engineering of wild-type strain Escherichia coli W3110 was adopted to improve anaerobic growth in mineral medium. Significant increases in exponential growth rate and stationary cell density were achieved in evolved strain WE269, and a 96.5% increase in lactate productivity has also been observed in batch fermentation of this strain with M9 minimal medium. Then, an engineered strain for lactate production (BW100) was constructed by using WE269 as a platform and 98.3 g/L lactate (with an optical purity of D-lactate above 95%) was produced in a 5-L bioreactor after 48 h with a productivity of 2.05 g/(L·h). Finally, preliminary investigation demonstrated that mutation in sucD (sucD M245I) (encoding succinyl-CoA synthetase); ilvG (ilvG Δ1bp) (encoding acetolactate synthase 2 catalytic subunit), and rpoB (rpoB T1037P) (encoding RNA polymerase ß subunit) significantly improved anaerobic growth of E. coli. Double-gene mutation in ilvG and sucD resumed most of the growth potential of evolved strain WE269. This work suggested that improving anaerobic growth of production host can increase productivity of organic acids like lactate, and specific mutation-enabled improved growth may also be applied to metabolic engineering for production of other bulk chemicals.

Anti-Diabetic Nephropathy Activities of Polysaccharides Obtained from Termitornyces albuminosus via Regulation of NF-κB Signaling in db/db Mice.

Termitornyces albuminosus is a kind of traditional Chinese edible fungus rich in nutrients and medicinal ingredients, and it has anti-oxidative, analgesic and anti-inflammatory effects. However, the hypoglycemic and nephroprotective effects of polysaccharides separated from T. albuminosus (PTA) have not been reported. The properties of PTA were analyzed in a BKS.Cg-Dock7m +/+ Leprdb/JNju (db/db) mouse model of diabetes. After the administration of PTA for eight weeks, the hypoglycemic and hypolipidemic activities of PTA in the db/db mice were assessed. The results of a cytokine array combined with an enzyme-linked immunosorbent assay confirmed the anti-oxidative and anti-inflammatory activities of PTA. An eight-week administration of PTA caused hypoglycemic and hypolipidemic functioning, as indicated by suppressed plasma glucose levels, as well as the modulation of several cytokines related to glycometabolism, in the sera and kidneys of the mice. PTA treatment also had a protective effect on renal function, restoring renal structures and regulating potential indicators of nephropathy. In the kidneys of the db/db mice, PTA treatment reduced the activation of protein kinase B, the inhibitor of κB kinase alpha and beta, and the inhibitor of κB alpha and nuclear factor-κB (NF-κB). We establish the hypoglycemic, hypolipidemic, and anti-diabetic nephropathy effects of PTA, and we find that the renal protection effects of PTA may be related to anti-inflammatory activity via the regulation of NF-κB signaling.

Autophagy modulates amino acid signaling network in myotubes: differential effects on mTORC1 pathway and the integrated stress response.

Induction of autophagy and the integrated stress response is important for amino acid homeostasis. It remains unknown whether the autophagy coregulates both mechanistic target of rapamycin complex 1 (mTORC1) signaling and the integrated stress response. In mouse C2C12 myotubes, we found that amino acid limitation induced autophagy and that the subsequent release of amino acid is required to sustain mTORC1 signaling. Inhibition of autophagy by bafilomycin A1 or chloroquine treatment during amino acid scarcity abolished mTORC1 signaling, an effect that could be rescued by inhibiting protein synthesis or amino acid supplementation, respectively. Autophagy is required to sustain the balance of both essential and nonessential amino acids during amino acid starvation, and it has a predominant role over the ubiquitin-proteasome system in the regulation of mTORC1. Inhibition of autophagy was found to activate the integrated stress response, as well as eukaryotic initiation factor 2α (eIF2α) and its target genes independent of amino acid availability. Conversely, autophagy induction via mTOR inhibition is sufficient to reduce eIF2α phosphorylation. Thus, autophagy protects the eIF2α-mediated stress response independent of amino acid supply in cultured myotubes. Our results showed that autophagy uniquely modulates mTORC1 and the integrated stress response in an amino acid-dependent and -independent manner, respectively.

Intracerebral Hemorrhage Prognosis Classification via Joint-Attention Cross-Modal Network.

Intracerebral hemorrhage (ICH) is a critical condition characterized by a high prevalence, substantial mortality rates, and unpredictable clinical outcomes, which results in a serious threat to human health. Improving the timeliness and accuracy of prognosis assessment is crucial to minimizing mortality and long-term disability associated with ICH. Due to the complexity of ICH, the diagnosis of ICH in clinical practice heavily relies on the professional expertise and clinical experience of physicians. Traditional prognostic methods largely depend on the specialized knowledge and subjective judgment of healthcare professionals. Meanwhile, existing artificial intelligence (AI) methodologies, which predominantly utilize features derived from computed tomography (CT) scans, fall short of capturing the multifaceted nature of ICH. Although existing methods are capable of integrating clinical information and CT images for prognosis, the effectiveness of this fusion process still requires improvement. To surmount these limitations, the present study introduces a novel AI framework, termed the ICH Network (ICH-Net), which employs a joint-attention cross-modal network to synergize clinical textual data with CT imaging features. The architecture of ICH-Net consists of three integral components: the Feature Extraction Module, which processes and abstracts salient characteristics from the clinical and imaging data, the Feature Fusion Module, which amalgamates the diverse data streams, and the Classification Module, which interprets the fused features to deliver prognostic predictions. Our evaluation, conducted through a rigorous five-fold cross-validation process, demonstrates that ICH-Net achieves a commendable accuracy of up to 87.77%, outperforming other state-of-the-art methods detailed within our research. This evidence underscores the potential of ICH-Net as a formidable tool in prognosticating ICH, promising a significant advancement in clinical decision-making and patient care.

Effects of field soil warming on the growth and physiology of Juglans mandshurica seedlings.

Global climate change will increase surface soil temperature, with consequences on plant seedling growth and population dynamics. In this study, we carried out a field experiment to investigate the effects of 2 ℃ soil warming on the growth and physiological characteristics of 1- and 2-year-old seedlings of a dominant tree species in broadleaved Korean pine forest, Juglans mandshurica. The results showed that soil warming significantly increased basal diameter, root length, total leaf area, leaf dry weight, root dry weight, total biomass, apparent photosynthetic electron transfer rate (ETR), PSⅡ actual photochemical efficiency (ΦPSⅡ), and apparent photosynthetic electrophotochemical quenching coefficient (qP) of 1-year-old seedlings by 18.3%, 66.7%, 94.4%, 105.9%, 95.8%, 37.8%, 89.5%, 100.0%, and 71.4%, respectively. Soil warming significantly increased basal diameter, total leaf area, leaf dry weight, total biomass, leaf superoxide dismutase activity, peroxidase activity, catalase activity and free proline content, ETR, ΦPSⅡ, and qP of 2-year-old seedlings by 12.5%, 180.5%, 97.3%, 42.5%, 23.9%, 20.4%, 14.9%, 20.7%, 66.7%, 283.3% and 284.6%, respectively. There was an interaction between seedling age and soil warming on the root-shoot ratio and the ΦPSⅡ and qP in chlorophyll fluorescence parameters, in that soil warming significantly reduced the root-shoot ratio of 2-year-old seedlings and that the increase of chlorophyll fluorescence parameters of 2-year-old seedlings (4.1-4.6 times) was much higher than that of 1-year-old seedlings (1.5-1.8 times). Soil warming of 2 ℃ was beneficial to the growth of 1- and 2-year-old J. mandshurica seedlings and increased their regeneration potential. In particular, 2-year-old J. mandshurica seedlings responded to soil warming by increasing leaf area, improving leaf photochemical efficiency, and enhancing protective enzyme activity to increase resistance.

Study on the Suitability of Tea Cultivars for Processing Oolong Tea from the Perspective of Aroma Based on Olfactory Sensory, Electronic Nose, and GC-MS Data Correlation Analysis.

The oolong tea aroma is shown to consist of cultivar aroma and technical aroma in this study based on the aroma differences between oolong tea products of cultivars of different suitability, as determined by correlation analysis of olfactory, sensory, electronic nose, and GC-MS data. Human senses were significantly affected by the aroma components, which included eight terpene metabolites (ß-Ocimene, (Z)-Furan linalool oxide, linalool, (3E)-4,8-Dimethyl-1,3,7-nonatriene, (E)-Pyranoid linalool oxide, γ-Elemene, Humulene, (Z,E)-α-Farnesene), three carotenoid metabolites (ß-Ionone, (Z)-Geranylacetone and 6-methyl-5-Hepten -2-one), three lipid metabolites ((Z)-3-Hexenyl (Z)-3-hexenoate, Butanoic acid hexyl ester, and (Z)-Jasmone), four amino acid metabolites (Methyl salicylate, Geranyl isovalerate, indole, and Phenylethyl alcohol), and six thermal reaction products (2-Pentylfuran, Octanal, Decanal, (E,E)-2,4-Nonadienal, (Z)-2-Decenal, and (E)-2-Undecenal). Meanwhile, several aroma compounds (such as (E)-Nerolidol and α-Farnesene), mainly comprising the "technical aroma" formed in the processing mode, were noted to be less closely related to cultivar suitability. This study sheds light on the aroma characteristics of different tea cultivars for oolong tea processing.

Life History Recorded in the Vagino-cervical Microbiome Along with Multi-omes.

The vagina contains at least a billion microbial cells, dominated by lactobacilli. Here we perform metagenomic shotgun sequencing on cervical and fecal samples from a cohort of 516 Chinese women of reproductive age, as well as cervical, fecal, and salivary samples from a second cohort of 632 women. Factors such as pregnancyhistory, delivery history, cesarean section, and breastfeeding were all more important than menstrual cycle in shaping the microbiome, and such information would be necessary before trying to interpret differences between vagino-cervical microbiome data. Greater proportion of Bifidobacterium breve was seen with older age at sexual debut. The relative abundance of lactobacilli especially Lactobacillus crispatus was negatively associated with pregnancy history. Potential markers for lack of menstrual regularity, heavy flow, dysmenorrhea, and contraceptives were also identified. Lactobacilli were rare during breastfeeding or post-menopause. Other features such as mood fluctuations and facial speckles could potentially be predicted from the vagino-cervical microbiome. Gut and salivary microbiomes, plasma vitamins, metals, amino acids, and hormones showed associations with the vagino-cervical microbiome. Our results offer an unprecedented glimpse into the microbiota of the female reproductive tract and call for international collaborations to better understand its long-term health impact other than in the settings of infection or pre-term birth.

Tetrahedral Pt10- Cluster with Unique Beta Aromaticity and Superatomic Feature in Mimicking Methane.

Utilizing a customized metal cluster source in tandem with a flow tube reactor and a reflectron time-of-flight mass spectrometer, we have obtained well-resolved pure metal clusters Ptn- and observed their gas-phase reactions with a few small gas molecules. Interestingly, the remarkable inertness of Pt10- was repeatedly observed in different reactions. Meanwhile, we have determined the structure of Pt10- within a regular tetrahedron. Considering that Pt possesses 5d96s1 electron configuration, the tetrahedral Pt10- exhibits unexpected stability at neither a magic number of valence electrons nor a shell closure of geometric structure. Comprehensive theoretical calculations unveil the stability of Pt10- is significantly associated with the all-metal aromaticity. In addition to the classical total aromaticity, which is mainly due to 6s electrons, there is unique beta-aromaticity ascribed to spin-polarized beta 5d electrons pertaining to singly occupied multicenter bonds. Further, we demonstrate the superatomic feature of such a transition metal cluster Pt10-, as Pt6@Pt4-, in mimicking methane.

Different Withering Times Affect Sensory Qualities, Chemical Components, and Nutritional Characteristics of Black Tea.

The present study emphasizes the effect of withering time set at 4 ± 0.5 h (WT4), 6 ± 0.5 h (WT6), 8 ± 0.5 h (WT8), 10 ± 0.5 h (WT10), and 12 ± 0.5 h (WT12) on the sensory qualities, chemical components, and nutritional characteristics of black tea. The sensory evaluation revealed high total quality scores at WT8 and WT10. Polysaccharides, amino acids, and soluble sugars significantly increased with an increase in withering time, and an apparent peak value was obtained at WT10. However, polyphenols, flavonoids, glycosides, organic acids, catechins, alkanoids, and theaflavins decreased with an increase in withering time. With an increase in withering time, the content of aromatic substances showed a trend of increasing first and then decreasing. The peaks of alcohols, aldehydes, and acids appeared at 10 ± 0.5 h, 10 ± 0.5 h, and 8 ± 0.5 h, respectively. The content of esters, ketones, and hydrocarbons showed a downward trend with an increase in withering time. Aroma analysis revealed that withering time could not exceed 10 ± 0.5 h. Black tea withered up to WT10 showed enhanced inhibition of α-glucosidase and α-amylase activity with good sensorial attributes. Glucose uptake inhibition capacity increased up 6 ± 0.5 h and then decreased, while antioxidant capacity decreased with an increase in withering time. The overall results show that the 8 ± 0.5 h to 10 ± 0.5 h withering time could improve black tea quality and nutritional characteristics.

Simulating a combined lysis-cryptic and biological nitrogen removal system treating domestic wastewater at low C/N ratios using artificial neural network.

In this study, a combined alkaline (ALK) and ultrasonication (ULS) sludge lysis-cryptic pretreatment and anoxic/oxic (AO) system (AO + ALK/ULS) was developed to enhance biological nitrogen removal (BNR) in domestic wastewater with a low carbon/nitrogen (C/N) ratio. A real-time control strategy for the AO + ALK/ULS system was designed to optimize the sludge lysate return ratio (RSLR) under variable sludge concentrations and variations in the influent C/N (⩽ 5). A multi-layered backpropagation artificial neural network (BPANN) model with network topology of 1 input layer, 3 hidden layers, and 1 output layer, using the Levenberg-Marquardt algorithm, was developed and validated. Experimental and predicted data showed significant concurrence, verified with a high regression coefficient (R2 = 0.9513) and accuracy of the BPANN. The BPANN model effectively captured the complex nonlinear relationships between the related input variables and effluent output in the combined lysis-cryptic + BNR system. The model could be used to support the real-time dynamic response and process optimization control to treat low C/N domestic wastewater.

Network of Interactions Between Gut Microbiome, Host Biomarkers, and Urine Metabolome in Carotid Atherosclerosis.

Comprehensive analyses of multi-omics data may provide insights into interactions between different biological layers concerning distinct clinical features. We integrated data on the gut microbiota, blood parameters and urine metabolites of treatment-naive individuals presenting a wide range of metabolic disease phenotypes to delineate clinically meaningful associations. Trans-omics correlation networks revealed that candidate gut microbial biomarkers and urine metabolite feature were covaried with distinct clinical phenotypes. Integration of the gut microbiome, the urine metabolome and the phenome revealed that variations in one of these three systems correlated with changes in the other two. In a specific note about clinical parameters of liver function, we identified Eubacteriumeligens, Faecalibacteriumprausnitzii and Ruminococcuslactaris to be associated with a healthy liver function, whereas Clostridium bolteae, Tyzzerellanexills, Ruminococcusgnavus, Blautiahansenii, and Atopobiumparvulum were associated with blood biomarkers for liver diseases. Variations in these microbiota features paralleled changes in specific urine metabolites. Network modeling yielded two core clusters including one large gut microbe-urine metabolite close-knit cluster and one triangular cluster composed of a gut microbe-blood-urine network, demonstrating close inter-system crosstalk especially between the gut microbiome and the urine metabolome. Distinct clinical phenotypes are manifested in both the gut microbiome and the urine metabolome, and inter-domain connectivity takes the form of high-dimensional networks. Such networks may further our understanding of complex biological systems, and may provide a basis for identifying biomarkers for diseases. Deciphering the complexity of human physiology and disease requires a holistic and trans-omics approach integrating multi-layer data sets, including the gut microbiome and profiles of biological fluids. By studying the gut microbiome on carotid atherosclerosis, we identified microbial features associated with clinical parameters, and we observed that groups of urine metabolites correlated with groups of clinical parameters. Combining the three data sets, we revealed correlations of entities across the three systems, suggesting that physiological changes are reflected in each of the omics. Our findings provided insights into the interactive network between the gut microbiome, blood clinical parameters and the urine metabolome concerning physiological variations, and showed the promise of trans-omics study for biomarker discovery.

Cloning and expression of a toxin gene from Pseudomonas fluorescens GcM5-1A.

Pseudomonas fluorescens GcM5-1A was isolated from the pine wood nematode (PWN), Bursaphelenchus xylophilus, obtained from wilted Japanese black pine, Pinus thumbergii, in China. In this paper, a genomic library of the GcM5-1A strain was constructed and a toxin-producing clone was isolated by bioassay. Nucleotide sequence analysis revealed an open reading frame of 1,290 bp encoding a protein of 429 amino acids with N-terminal putative signal peptide of 36 amino acids, which shared a similarity of 83, 82 and 80% identity with hypothetical protein PFLU2919 from P. fluorescens SBW25, Dyp-type peroxidase family protein from P. fluorescens Pf-5 and Tat-translocated enzyme from P. fluorescens Pf0-1, respectively. The gene encoding a full-length protein or without the putative signal peptide was cloned and expressed as a soluble protein in E. coli. The recombinant protein was purified to electrophoretic homogeneity by affinity chromatography using a Ni2+ matrix column. Its relative molecular weight was estimated to be 48.5 kDa by SDS-PAGE for full-length protein, and 45.0 kDa for the recombinant protein without putative signal peptide. Bioassay results showed that the recombinant protein with or without the putative signal peptide was toxic to both suspension cells and P. thunbergii seedlings. HPLC analysis demonstrated that components in branch extracts of P. thunbergii were significantly changed after addition of the recombinant full-length protein and hydrogen peroxide, which indicated that it is probably a peroxidase. This study offers information that can be used to determine the mechanism of pine wilt disease caused by the PWN.

Multiple d-d bonds between early transition metals in TM2Lin (TM = Sc, Ti) superatomic molecule clusters.

The synthesis and application of compounds with Cr-Cr and V-V d-d quintuple bonds (σ, 2π, 2δ) have led to new thinking about whether d-d multiple bonds also exist between early transition metals such as Sc-Sc and Ti-Ti. In this study, by extensive unbiased global search at the density functional theory level, the low-energy structures of 26e and 30e TM2Lin clusters were obtained. Based on the super valence bond (SVB) theory, the prolate double-core structure of TM2Lin clusters was regarded as a superatomic molecule, of which each half was regarded as an open-shell superatom, and the electronic shell-closure was realized by forming multiple bonds between superatoms. Then, the quintuple super bonds (2δ, 2π, σ) of the Li18Ti2, Li20Sc2, [Li17V2]+, [Li17Ti2]- clusters and the triple super bonds (2π, σ) of the Li24Sc2 and Li24Y2 clusters were confirmed via chemical-bonding analysis. This way of forming multiple bonds between early transition metals through superatomic bonding has promoted the experimental synthesis and application of early transition metal multiple bond compounds.