metaProbiotics: a tool for mining probiotic from metagenomic binning data based on a language model.

Beneficial bacteria remain largely unexplored. Lacking systematic methods, understanding probiotic community traits becomes challenging, leading to various conclusions about their probiotic effects among different publications. We developed language model-based metaProbiotics to rapidly detect probiotic bins from metagenomes, demonstrating superior performance in simulated benchmark datasets. Testing on gut metagenomes from probiotic-treated individuals, it revealed the probioticity of intervention strains-derived bins and other probiotic-associated bins beyond the training data, such as a plasmid-like bin. Analyses of these bins revealed various probiotic mechanisms and bai operon as probiotic Ruminococcaceae's potential marker. In different health-disease cohorts, these bins were more common in healthy individuals, signifying their probiotic role, but relevant health predictions based on the abundance profiles of these bins faced cross-disease challenges. To better understand the heterogeneous nature of probiotics, we used metaProbiotics to construct a comprehensive probiotic genome set from global gut metagenomic data. Module analysis of this set shows that diseased individuals often lack certain probiotic gene modules, with significant variation of the missing modules across different diseases. Additionally, different gene modules on the same probiotic have heterogeneous effects on various diseases. We thus believe that gene function integrity of the probiotic community is more crucial in maintaining gut homeostasis than merely increasing specific gene abundance, and adding probiotics indiscriminately might not boost health. We expect that the innovative language model-based metaProbiotics tool will promote novel probiotic discovery using large-scale metagenomic data and facilitate systematic research on bacterial probiotic effects. The metaProbiotics program can be freely downloaded at https://github.com/zhenchengfang/metaProbiotics.

SNAC1-OsERF103-OsSDG705 module mediates drought response in rice.

Drought stress profoundly hampers both plant growth and crop yield. To combat this, plants have evolved intricate transcriptional regulation mechanisms as a pivotal strategy. Through a genetic screening with rice genome-scale mutagenesis pool under drought stress, we identified an APETALA2/Ethylene Responsive Factor, namely OsERF103, positively responds to drought tolerance in rice. Combining chromatin immunoprecipitation sequencing and RNA sequencing analyses, we pinpointed c. 1000 genes directly influenced by OsERF103. Further results revealed that OsERF103 interacts with Stress-responsive NAC1 (SNAC1), a positive regulator of drought tolerance in rice, to synergistically regulate the expression of key drought-related genes, such as OsbZIP23. Moreover, we found that OsERF103 recruits a Su(var)3-9,enhancer of zeste and trithorax-domain group protein 705, which encodes a histone 3 lysine 4 (H3K4)-specific methyltransferase to specifically affect the deposition of H3K4me3 at loci like OsbZIP23 and other genes linked to dehydration responses. Additionally, the natural alleles of OsERF103 are selected during the domestication of both indica and japonica rice varieties and exhibit significant geographic distribution. Collectively, our findings have unfurled a comprehensive mechanistic framework underlying the OsERF103-mediated cascade regulation of drought response. This discovery not only enhances our understanding of drought signaling but also presents a promising avenue for the genetic improvement of drought-tolerant rice cultivars.

Wideband finely tunable, ultralow-phase noise microwave generation in a Brillouin cavity.

A novel, to the best of our knowledge, approach to generate frequency-tunable microwave sources with low-phase-noise based on a Brillouin laser frequency comb is proposed and experimentally demonstrated. The Brillouin laser frequency comb is generated by combining stimulated Brillouin scattering, frequency shifting optical injection locking, modulation sideband optical injection locking (MSOIL), and four-wave mixing effects. By beating the generated comb lines, the microwave is generated with an extremely low-level phase noise of -120 dBc/Hz at a 10-kHz offset. The frequency of the microwave signal can be finely tuned in steps of a Brillouin cavity mode spacing (i.e., 2 MHz) and coarsely adjusted to integer times the applied RF signal frequency in the MSOIL unit. Remarkably, the phase noise of the microwave source can be kept at almost the same low level during the whole tuning process over the frequency range of 30-75 GHz. The proposed tunable low-phase-noise microwave generation approach has great potential applications in communications, radars, and metrology.

Resuscitation of baijiu pit mud bacteria based on Rpf protein of Umezawaea beigongshangensis.

The pit mud in the Baijiu fermentation cellar is an abundant microbial resource that is closely related to the quality of baijiu. However, many naturally existing species might be in a viable but nonculturable (VBNC) state, posing challenges to the isolation and application of functional species. Herein, a previously isolated strain from baijiu mash, Umezawaea beigongshangensis, was found to contain the rpf gene that encodes resuscitation promotion factor (Rpf). Therefore, the gene was cloned and heterologously expressed, and the recombinant protein (Ub-Rpf 2) was purified. Ub-Rpf 2 was found to significantly promote the growth of resuscitated VBNC state Corynebacterium beijingensis and Sphingomonas beigongshangensis. To determine the resuscitation effect of Ub-Rpf 2 on real ecological samples, the protein was supplemented in pit mud for enrichment culture. Results revealed that specific families and genera were enriched in abundance upon Ub-Rpf 2 incubation, including a new family of Symbiobacteraceae and culturable Symbiobacterium genus. Furthermore, 14 species belonging to 12 genera were obtained in Ub-Rpf 2 treated samples, including a suspected novel species. This study lays a foundation for applying Rpf from U. beigongshangensis to exploit microbial resources in baijiu pit mud.

Synthesis of Aminomethylpyridine-Decorated Polyamidoamine Dendrimer/Apple Residue for the Efficient Capture of Cd(II).

Water contamination irritated by Cd(II) brings about severe damage to the ecosystem and to human health. The decontamination of Cd(II) by the adsorption method is a promising technology. Here, we construct aminomethylpyridine-functionalized polyamidoamine (PAMAM) dendrimer/apple residue biosorbents (AP-G1.0-AMP and AP-G2.0-AMP) for adsorbing Cd(II) from aqueous solution. The adsorption behaviors of the biosorbents for Cd(II) were comprehensively evaluated. The maximum adsorption capacities of AP-G1.0-AMP and AP-G2.0-AMP for Cd(II) are 1.40 and 1.44 mmol·g-1 at pH 6. The adsorption process for Cd(II) is swift and can reach equilibrium after 120 min. The film diffusion process dominates the adsorption kinetics, and a pseudo-second-order model is appropriate to depict this process. The uptake of Cd(II) can be promoted by increasing concentration and temperature. The adsorption isotherm follows the Langmuir model with a chemisorption mechanism. The biosorbents also display satisfied adsorption for Cd(II) in real aqueous media. The adsorption mechanism indicates that C-N, N═C, C-O, CONH, N-H, and O-H groups participate in the adsorption for Cd(II). The biosorbents display a good regeneration property and can be reused with practical value. The as-prepared biosorbents show great potential for removing Cd(II) from water solutions with remarkable significance.

Spartinivicinus marinus sp. nov., isolated from intertidal sediment.

A Gram-stain-negative, aerobic, flagellated, and long rod-shaped bacterium, designated strain SM1973T, was isolated from an intertidal sediment sample collected from the coast of Qingdao, PR China. Strain SM1973T grew at 15-37 °C and with 0-5.5 % NaCl. It reduced nitrate to nitrite and hydrolysed aesculin but did not hydrolyse casein and gelatin. The strain showed the highest 16S rRNA gene sequence similarity (98.2 %) to the type strain of Spartinivicinus ruber. The phylogenetic trees based on the 16S rRNA genes and single-copy orthologous clusters showed that strain SM1973T clustered with S. ruber, forming a separate lineage within the family Zooshikellaceae. The major cellular fatty acids were summed feature 3 (C16 : 1 ω7с and/or C16 : 1 ω6с) and C16 : 0. The major polar lipids were phosphatidylethanolamine, phosphatidylglycerol and diphosphatidylglycerol. The main respiratory quinone was ubiquinone-9. The genomic DNA G+C content of strain SM1973T was 40.4 mol%. Based on the polyphasic evidence presented in this paper, strain SM1973T is considered to represent a novel species within the genus Spartinivicinus, for which the name Spartinivicinus marinus sp. nov. is proposed. The type strain is SM1973T (=MCCC 1K04833T=KCTC 72846T).

All-printed multiplexed electrocatalytic biosensors with rationally designed nanoparticle inks.

Inkjet printing, capable of rapid and template-free fabrication with high resolution and low material waste, is a promising method to construct electrochemical biosensor devices. However, the construction of fully inkjet-printed electrochemical biosensor remains a challenge owing to the lack of appropriate inks, especially the sensing inks of bioactive materials. Herein, we demonstrate a fully inkjet-printed, integrated and multiplexed electrochemical biosensor by combining rationally designed nanoparticle Inks. The stable gold (Au) nanoparticles ink with lower sintering temperature is prepared by using L-cysteine as stabilizer, and it is used to print the interconnects, the counter electrodes, and the working electrodes. The SU-8 ink is used to serve as dielectric layer for the biosensor, whereas the silver electrode is printed on the Au electrode by using commercially silver nanoparticles ink before it is chlorinated to prepare Ag/AgCl reference electrode. Moreover, we synthesize an inkjet-printable and electroactive ink, by the 'one-pot method', which is composed of conductive poly 6-aminoindole (PIn-6-NH2) and gold-palladium (Au-Pd) alloy nanoparticle (Au-Pd@PIn-6-NH2) to enhance the sensing performance of gold electrode towards hydrogen peroxide (H2O2). Especially, the amino groups in PIn-6-NH2can be further used to immobilizing glucose oxidase (GOx) and lactic acid oxidase (LOx) by glutaraldehyde to prepare printable sensing ink for the detection of glucose and lactate. The fully inkjet-printed electrochemical biosensor enabled by advanced inks can simultaneously detect glucose and lactate with good sensitivity and selectivity, as well as facile and scalable fabrication, showing great promise for metabolic monitoring.

Farnesoid X receptor is an important target for the treatment of disorders of bile acid and fatty acid metabolism in mice with nonalcoholic fatty liver disease combined with cholestasis.

BACKGROUND AND AIM: The prevalence of nonalcoholic fatty liver disease (NAFLD) has been rising globally. NAFLD patients combined with cholestasis have more obvious liver fibrosis, impaired bile acid (BA), and fatty acid (FA) metabolism and severer liver injury; however, its therapeutic options are limited, and the underlying metabolic mechanisms are understood. Here, we aimed to investigate the effects of farnesoid X receptor (FXR) on BA and FA metabolism in NAFLD combined with cholestasis and related signaling pathways. METHODS: A mouse model of NAFLD combined with cholestasis was established by joint intervention with high-fat diet (HFD) and alpha-naphthylisothiocyanate. The effects of FXR on BA and FA metabolism were evaluated by serum biochemical analysis. Liver damage was identified by histopathology. The expression of nuclear hormone receptor, membrane receptor, FA transmembrane transporter, and BA transporter protein in mice were measured by western blot. RESULTS: NAFLD mice combined with cholestasis developed more severe cholestasis and dysregulated BA and FA metabolism. Meanwhile, the expression of FXR protein was decreased in NAFLD mice combined with cholestasis compared to the controls. Fxr-/- mice showed liver injury. HFD aggravated the liver injury with decreased BSEP expression, increased expression of NTCP, LXRα, SREBP-1c, FAS, ACC1, and CD36, and significantly increased BA and FA accumulation. CONCLUSION: All the results suggested that FXR plays a key role in both FA and BA metabolism in NAFLD combined with cholestasis and thus may be a potential target for the treatment of disorders of BA and FA metabolism in NAFLD combined with cholestasis.

Dynamic stability of a blue multi-resonance thermally activated delayed fluorescence molecule without damaging the luminescence properties.

The instability of blue emitters is one of the shortcomings of organic light-emitting diodes (OLEDs) in industrial applications. This instability is intrinsically associated with the basic transitions and reactions in the excited states. In this work, using the framework of Fermi's golden rule and DFT/TDDFT, the mechanisms of the transitions and reactions of a typical boron based multi-resonance thermally activated delayed fluorescence emitter involving the excited states were investigated. A dynamic stability mechanism describing recycling between the dissociation of the molecular structure in the T1 state and restoration in the S0 state dominated by steric effects was discovered. Applying knowledge of this mechanism, a small modification was made to the molecular structure, and the stability was increased without degrading other luminescence properties such as the luminescence color, FWHM, reverse intersystem crossing, fluorescence quantum yield, and internal quantum yield.

Crystalline matrix-activated spin-forbidden transitions of engineered organic crystals.

Spin-forbidden excitation is an efficient way to obtain triplet excitons directly from the ground state of organic semiconductors. According to perturbation theory under the framework of Fermi's golden rule, this process requires spin-orbit coupling (SOC) and the transition dipole moment (TDM) to be combined through an intermediate state that mixes the initial and final states. While previous research has focused mostly on enhancing SOC, little attention has been paid to engineering the coupling between SOC and the TDM in organic materials. In this study, a series of engineered crystals were designed by doping guest molecules into host organic crystals. The confinement of the guest molecule within a crystalline matrix of the host provides a strong intermolecular interaction to couple both SOC and the TDM. This in turn activates the spin-forbidden excitation directly from the ground state to a "dark" triplet state. Based on a comparison of different engineered crystals, strong intermolecular interaction is identified to induce a distortion of the ligands and further enhancing the spin-forbidden excitation. This work outlines a strategy for designing spin-forbidden excitation.

Correction: Crystalline matrix-activated spin-forbidden transitions of engineered organic crystals.

Correction for 'Crystalline matrix-activated spin-forbidden transitions of engineered organic crystals' by Heming Zhang et al., Phys. Chem. Chem. Phys., 2023, 25, 11102-11110, DOI: https://doi.org/10.1039/d3cp00187c.

Sinensetin ameliorates high glucose-induced diabetic nephropathy via enhancing autophagy in vitro and in vivo.

Diabetic nephropathy (DN) affects around 40% of people with diabetes, the final outcome of which is end-stage renal disease. The deficiency of autophagy and excessive oxidative stress have been found to participate in the pathogenesis of DN. Sinensetin (SIN) has been proven to have strong antioxidant capability. However, the effect of SIN on DN has not been studied. We examined the effect of SIN on cell viability and autophagy in the podocyte cell line, MPC5 cells, treated with high glucose (HG). For in vivo studies, DN mice models were established by intraperitoneal injected with streptozotocin (40 mg/kg) for 5 consecutive days and fed with a 60% high-fat diet, and SIN was given (10, 20, and 40 mg/kg) for 8 weeks via intraperitoneal injection. The results showed that SIN could protect MPC5 cells against HG-induced damage and significantly improve the renal function of DN mice. Moreover, SIN remarkably restored the autophagy activity of MPC5 cells which was inhibited under HG conditions. Consistent with this, SIN efficiently improved autophagy in the kidney tissue of DN mice. In brief, our findings demonstrated the protective effect of SIN on DN via restoring the autophagic function, which might provide a basis for drug development.

Role of cycle duration on the formation of quinoline-degraded aerobic granules in the aspect of sludge characteristics, extracellular polymeric substances and microbial communities.

This study investigated the culture and characteristics of quinoline-degraded aerobic granular sludge (AGS) under 8-h and 12-h cycle duration. According to results, the cultivation of an 8-h cycle duration enhanced the growth of quinoline-degraded AGS, as well as the settleability of sludge and the retention of biomass. Quinoline can be removed from mature AGS at a rate of more than 90%, but it is removed at a rate slightly higher when the AGS are cultured for 12-h. Compared to 12-h cycle duration, 8-h cycle duration result in a greater increase in the production of extracellular polymeric substances, particularly extracellular proteins. In these two systems, Acidovorax and Paracoccus dominated the quinoline degrading bacteria. In addition, analysis by non-metric multidimensional scaling (based on Bray-curtis distance) showed significant differences of community structure between the two reactors. Clostridia and Acidaminobacter are different bacteria with an 8-h cycle duration compared to 12 h. Relative abundance of nitrogen metabolism genes based on PICRUSt2 prediction, which explain the better total nitrogen removal for an 8-h cycle duration compared to a 12-h cycle duration. Finally, the KEGG pathway was analyzed in order to confirm the results of the microbial analysis.

Design, Synthesis, and Insecticidal Activities of Novel meta-Diamide Compounds Containing Ethyl Acetate and Their Derivatives.

In this study, a series of meta-diamide compounds containing ethyl acetate group and their derivatives were designed and synthesized. Their insecticidal activities against Plutella xylostella, Spodoptera frugiperda and Alfalfa sprouts were evaluated. Preliminary bioassays showed that some of the title compounds exhibited excellent insecticidal activities. Especially compound ethyl N-(3-((2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)carbamoyl)-2-fluorophenyl)-N-(4-cyanobenzoyl)glycinate and ethyl N-(3-((2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)carbamoyl)-2-fluorophenyl)-N-(6-fluoronicotinoyl)glycinate showed 100 % mortality at 0.1 mg/L against Plutella xylostella and Spodoptera frugiperda, same to broflanilide. Their LC50 against Plutella xylostella is 0.286 mg/L and 0.0218 mg/L, respectively. Moreover, compound ethyl N-(3-((2-bromo-4-(perfluoropropan-2-yl)-6-(trifluoromethyl)phenyl)carbamoyl)-2-fluorophenyl)-N-(6-fluoronicotinoyl)glycinate displayed faster control efficacy than broflanilide at 0.1 mg/L. The results indicated that meta-diamide compounds containing ethyl acetate group could be developed as novel and promising insecticides.

A Cylindrical Near-Field Acoustical Holography Method Based on Cylindrical Translation Window Expansion and an Autoencoder Stacked with 3D-CNN Layers.

The performance of near-field acoustic holography (NAH) with a sparse sampling rate will be affected by spatial aliasing or inverse ill-posed equations. Through a 3D convolution neural network (CNN) and stacked autoencoder framework (CSA), the data-driven CSA-NAH method can solve this problem by utilizing the information from data in each dimension. In this paper, the cylindrical translation window (CTW) is introduced to truncate and roll out the cylindrical image to compensate for the loss of circumferential features at the truncation edge. Combined with the CSA-NAH method, a cylindrical NAH method based on stacked 3D-CNN layers (CS3C) for sparse sampling is proposed, and its feasibility is verified numerically. In addition, the planar NAH method based on the Paulis-Gerchberg extrapolation interpolation algorithm (PGa) is introduced into the cylindrical coordinate system, and compared with the proposed method. The results show that, under the same conditions, the reconstruction error rate of the CS3C-NAH method is reduced by nearly 50%, and the effect is significant.

Probing ultra-fast dephasing via entangled photon pairs.

We demonstrate how the Hong-Ou-Mandel (HOM) interference with polarization-entangled photons can be used to probe ultrafast dephasing. We can infer the optical properties like the real and imaginary parts of the complex susceptibility of the medium from changes in the position and the shape of the HOM dip. From the shift of the HOM dip, we are able to measure 22 fs dephasing time using a continuous-wave (CW) laser even with optical loss > 97 %, while the HOM dip visibility is maintained at 92.3 % (which can be as high as 96.7 %). The experimental observations, which are explained in terms of a rigorous theoretical model, demonstrate the utility of HOM interference in probing ultrafast dephasing.

Study on the relationship between hormone and Lp(a) in Chinese overweight/obese patients.

BACKGROUND: Obesity is a risk factor for metabolic diseases and often influences hormone change. Lipoprotein (a) (Lp(a)) is associated with various metabolic diseases, but there are few studies on the relationship between Lp(a) and hormones in obese patients. This study investigated the the relationship between Lp(a) and hormones in Chinese overweight/obese people. METHODS: A total of 410 overweight/obese patients (Body mass index (BMI) ≥ 25 kg/m2) were included and underwent sociodemographic data investigations and relevant clinical examinations. Lp(a) was analyzed by colorimetric enzymatic assays and hormone was measured with chemiluminescence immunoassay method. According to Lp(a) levels, they were categorized into 3 groups: the lower Lp(a) group (Lp(a) levels < 30 mg/dl), the moderate Lp(a) group (Lp(a) levels between 30 mg/dl and 120 mg/dl) and the higher Lp(a) group (Lp(a) levels > 120 mg/dl). The differences of hormone levels among the three groups were compared and the relationship between Lp(a) and hormones was analyzed by Spearman's rank correlation. RESULTS: The higher Lp(a) group had significantly lower testosterone (TES) levels compared with the lower and moderate Lp(a) groups in the case of gender, age and BMI matching. Lp(a) concentration was negatively correlated with TES levels in all participants and the negative association between Lp(a) and TES levels was also observed when the analysis was stratified by gender. Additionally, the TES was statistically related with Lp(a) levels in the multiple linear regression model (95% confidence interval: - 0.451 to - 0.079). CONCLUSIONS: TES levels was negatively associated with Lp(a) levels in Chinese overweight/obese patients.

Elevated serum Meteorin-like levels in patients with hyperthyroidism.

BACKGROUND: Meteorin-like (Metrnl) is a newly discovered adipomyokine that regulates systemic energy homeostasis. Both thyroid hormones and Metrnl increase energy expenditure and induce browning of adipose tissue. Thus, the aim of this study was to investigate serum Metrnl levels in hyperthyroid patients and the association of serum Metrnl levels with hyperthyroidism. METHODS: The study included 88 patients with newly diagnosed untreated overt hyperthyroidism and 100 age- and sex- matched healthy controls. Serum Metrnl levels were determined using the enzyme-linked immunosorbent assay (ELISA) method. RESULTS: Serum Metrnl levels were significantly elevated in patients with hyperthyroidism compared with controls. Linear regression analyses indicated that serum Metrnl levels were independently associated with FT3 (ß = 0.324, P = 0.001), FT4 (ß = 0.293, P = 0.001), and TSH (ß = -0.234, P = 0.006) after full adjustment. Additionally, further logistic regression analyses revealed that the highest Metrnl tertile was significantly associated with hyperthyroidism compared with the lowest tertile (P for trend < 0.001). The relationship remained significant even after adjusting for potential confounders. Meanwhile, each one-unit increase in circulating Metrnl was independently associated with hyperthyroidism (OR 1.021, 95%CI 1.007-1.036, P < 0.01). CONCLUSION: Serum Metrnl levels were elevated in patients with hyperthyroidism and were independently associated with hyperthyroidism.

Load-dependent detachment kinetics plays a key role in bidirectional cargo transport by kinesin and dynein.

Bidirectional cargo transport along microtubules is carried out by opposing teams of kinesin and dynein motors. Despite considerable study, the factors that determine whether these competing teams achieve net anterograde or retrograde transport in cells remain unclear. The goal of this work is to use stochastic simulations of bidirectional transport to determine the motor properties that most strongly determine overall cargo velocity and directionality. Simulations were carried out based on published optical tweezer characterization of kinesin-1 and kinesin-2, and for available data for cytoplasmic dynein and the dynein-dynactin-BicD2 (DDB) complex. By varying dynein parameters and analyzing cargo trajectories, we find that net cargo transport is predicted to depend minimally on the dynein stall force, but strongly on dynein load-dependent detachment kinetics. In simulations, dynein is dominated by kinesin-1, but DDB and kinesin-1 are evenly matched, recapitulating recent experimental work. Kinesin-2 competes less well against dynein and DDB, and overall, load-dependent motor detachment is the property that most determines a motor's ability to compete in bidirectional transport. It follows that the most effective intracellular regulators of bidirectional transport are predicted to be those that alter motor detachment kinetics rather than motor velocity or stall force.

Sporosarcina beigongshangi sp. nov., isolated from pit mud of Baijiu.

A Gram-positive, aerobic and short rod-shaped bacterium designated REN13T, was isolated from pit mud of Baijiu, in Sichuan province, China. Strain REN13T could grow at 10-50 â„ƒ, pH 6.0-9.0 and 0-2% (w/v) NaCl, with the optimal growth occurred at 28 â„ƒ, pH 7.0, and 2% (w/v) NaCl. 16S rRNA gene sequence analysis showed that strain REN13T was closely related to Sporosarcina globispora DSM 4T (98.6%). The DNA G + C content of strain REN13T was 41.1 mol %. DDH and ANI value between strain REN13T and S. globispora DSM 4T was 24.4% and 67.6%, respectively. The major fatty acids were iso-C15:0 and antesio-C15:0. The respiratory quinone was MK-7, and the polar lipids were phosphatidylethanolamine, phospholipids, phosphatidylglycerol and diphosphatidylglycerol. Based on the above polyphasic taxonomic analysis, strain REN13T represents a novel species of the genus Sporosarcina, for which the name Sporosarcina beigongshangi sp. nov. is proposed. The type strain is strain REN13T (= JCM 34409T = GDMCC 1.2151T).