Redox-Regulated and Guest-Driven Transformations of Aromatic Oligoamide Foldamers in Advanced Structures.

In this study, we demonstrate that an aromatic oligoamide sequence assembles into a trimeric helix-turn-helix architecture with a disulfide linkage, and upon cleavage of this linkage, it reconstructs into an antiparallel double helix. The antiparallel double helix is accessible to encapsulate a diacid guest within its cavity, forming a 2:1 host-guest complex. In contrast, hydrogen-bonding interactions between the trimeric-assembled structure and guests induce a conformational shift in the trimeric helix, resulting in a cross-shaped double-helix complex at a 2:2 host-guest ratio. Interconversions between the trimeric helix and the antiparallel double helix, along with their respective host-guest complexes, can be initiated through thiol/disulfide redox-mediated regulation.

Quantum plasmonics pushes chiral sensing limit to single molecules: a paradigm for chiral biodetections.

Chiral sensing of single molecules is vital for the understanding of chirality and their applications in biomedicine. However, current technologies face severe limitations in achieving single-molecule sensitivity. Here we overcome these limitations by designing a tunable chiral supramolecular plasmonic system made of helical oligoamide sequences (OS) and nanoparticle-on-mirror (NPoM) resonator, which works across the classical and quantum regimes. Our design enhances the chiral sensitivity in the quantum tunnelling regime despite of the reduced local E-field, which is due to the strong Coulomb interactions between the chiral OSs and the achiral NPoMs and the additional enhancement from tunnelling electrons. A minimum of four molecules per single-Au particle can be detected, which allows for the detection of an enantiomeric excess within a monolayer, manifesting great potential for the chiral sensing of single molecules.

Construction of a food-grade gene editing system based on CRISPR-Cas9 and its application in Lactococcus lactis NZ9000.

Clustered regularly interspaced short palindromic repeats-associated protein 9 (CRISPR/Cas9) system has been widely used in gene editing of various organisms. However, food-grade gene editing systems in lactic acid bacteria are still preliminary. Red/ET-dependent homologous recombination or CRISPR-based systems have been developed to gene editing in Lactococcus lactis, but these methods are overall inefficient. In the present study, a recombinant system based on CRISPR/Cas9 technology combined with Red/ET was developed using the plasmid pMG36e derived from Lactococcus lactis. Then, the developed recombinant system was applied to Lactococcus lactis. Knockout efficiency was significantly higher using the developed system (91%). In addition, this system showed the potential to be used as a high-throughput method for hierarchical screening. Finally, a gene-edited strain was obtained, and no antibiotics or exogenous genes were introduced using the developed gene editing system. Thus, the efficient system in lactic acid bacteria was constructed and optimized.

Study on Lactiplantibacillus plantarum R6-3 from Sayram Ketteki to prevent chronic unpredictable mild stress-induced depression in mice through the microbiota-gut-brain axis.

The prevention, mitigation and treatment of depression has become a global issue that needs to be solved urgently. Sayram Ketteki, a traditional natural fermented yoghurt from the region with the world's fourth highest life expectancy, has been known as the "longevity secret", whose longevity and anti-depression factors are speculated to come from its rich microorganisms. Therefore, for the first time, we systematically studied in depth the microbes of Sayram Ketteki, screened a new edible probiotic strain, Lactiplantibacillus plantarum R6-3, and explored its anti-depression effect in chronic unpredictable mild stress (CUMS)-induced depression in mice. It is encouraging that L. plantarum R6-3 was significantly superior to the classic anti-depressant drug, fluoxetine, in the performance of promoting sucrose preference test (SPT) behavior by 18% (p < 0.001), lowering the serum CORT content by 5.6% (p < 0.05), accelerating the brain-derived neurotrophic factor (BDNF) level by 5.9% (p < 0.01), increasing the serum IL-10 concentration by 2.3% (p < 0.05), up-regulating the expression of BDNF and phosphorylated-ERK by 74% (p < 0.01) and 45% (p < 0.001), respectively, and facilitating the secretion of fecal short-chain fatty acids (SCFAs), including n-butyric, n-valeric, and isovaleric acid by 47% (p < 0.01), 42% (p < 0.05) and 38% (p < 0.05), respectively. Through the microbiota-gut-brain axis, L. plantarum R6-3 promoted the secretion of intestinal SCFAs through regulation of the composition and function of the gut microbiota, and activated the production of the monoamine neurotransmitter, renewed the level of brain neurotrophic factor, and suppressed the hyperactivity of the hypothalamic-pituitary-adrenal (HPA) axis by adjusting the hippocampal BDNF/TrkB/ERK/CREB signaling pathway, thereby improving the immune and oxidative stress status, protecting hippocampal tissue from damage, maintaining a healthy weight and preventing CUMS-induced depressive behavior in mice. It has great prospects for the development of natural functional foods, the prevention and treatment of depression and in innovative microecological preparations.

Copper inhibits postacidification of yogurt and affects its flavor: A study based on the Cop operon.

Yogurt and its related products are popular worldwide. During transportation and storage, Lactobacillus delbrueckii ssp. bulgaricus in yogurt continues to metabolize to form lactic acid, the postacidification phenomenon of yogurt. Postacidification of yogurt is a widespread phenomenon in the dairy industry. Many scholars have done research on controlling the postacidification process, but few report on the molecular mechanisms involved. In this study, we used a molecular-assisted approach to screen food additives that can inhibit postacidification and analyzed its effects on yogurt quality as well as its regulatory mechanism from multi-omics perspectives in combination. The copper ion was found to upregulate the expression of the LDB_RS05285 gene, and the copper transporter-related genes were regulated by copper. Based on the metabolic-level analysis, copper was found to promote lactose hydrolysis, accumulate a large amount of glucose and galactose, inhibit the conversion of glucose to lactic acid, and reduce the production of lactic acid. The significantly greater abundance of l-isoleucine and l-phenylalanine increased the abundance of 3-methylbutyraldehyde (∼1.2 times) and benzaldehyde (∼7.9 times) to different degrees, which contributed to the formation of the overall flavor of yogurt. Copper not only stabilizes the acidity of yogurt, but also it improves the flavor of yogurt. Through this established method involving quantitative and correlation analyses at the transcriptional and metabolic levels, this study provides guidance for the research and development of food additives that inhibit postacidification of yogurt and provide a reference for studying the changes of metabolites during storage of yogurt.

Niacin inhibits post-acidification of yogurt based on the mining of LDB_RS00370 biomarker gene.

The post-acidification of yogurt results in short shelf life, undesirable flavor, and sour taste, making it unacceptable to consumers. Many scholars have proposed several solutions to this problem. However, the existing methods of inhibiting post-acidification cannot fundamentally solve this problem. So exploring the molecular mechanism behind post-acidification can be a better approach to finding the solution. Therefore, we first evaluated the correlation between 69 candidate genes for post-acidification and changes in the acidity of yogurt fermented with different Lactobacillus bulgaricus, and mined a biomarker LDB_RS00370 for post-acidification. Subsequently, this biomarker was used for large-scale screening of food additives that could inhibit post-acidification, and niacin was found to be the most representative one. Finally, the mechanism of niacin inhibiting post-acidification of yogurt was analyzed by RNA-seq, which revealed that post-acidification might be inhibited by affecting protein synthesis and glycolysis. This study opens up a novel perspective on molecular prediction of the post-acidification process, which could provide guidance for precautions to be taken in yogurt production.

Mechanism of gastrointestinal adaptability and antioxidant function of infant-derived Lactobacillus plantarum BF_15 through genomics.

Lactobacillus plantarum is an essential probiotic in the human gastrointestinal tract. L. plantarum BF_15, a functional probiotic isolated from the feces of breast-fed infants, has been reported in many in vitro and in vivo studies with strong gastrointestinal adaptability and outstanding anti-oxidative activities. Therefore, the whole genome of L. plantarum BF_15 was sequenced. Several genes, encoding the gastrointestinal adaptability-related proteins, were identified, including genes related to gastrointestinal environment-induced stress resistance, adhesive performance, and ability to transport and metabolize resistant starch and oligosaccharides. Genes related to alleviating oxidative stress were also found. Further functional verification was carried out by RT-qPCR on the 10 and 12 key adhesion and antioxidant genes. Overall, this study might provide a critical basis for L. plantarum BF_15 as a potential candidate for probiotics. Supplementary Information: The online version contains supplementary material available at 10.1007/s10068-022-01132-w.

Switching plasmonic nanogaps between classical and quantum regimes with supramolecular interactions.

In the realm of extreme nanophotonics, nanogap plasmons support reliable field enhancements up to 1000, which provide unique opportunities to access a single molecule for strong coupling and a single atom for quantum catalysis. The quantum plasmonics are intriguing but difficult to modulate largely because of the lack of proper spacers that can reversibly actuate the sub-1-nm gaps. Here, we demonstrate that supramolecular systems made of oligoamide sequences can reversibly switch the gap plasmons of Au nanoparticles on mirror between classical and quantum tunneling regimes via supramolecular interactions. The results reveal detailed plasmon shift near the quantum tunneling limit, which fits well with both classical- and quantum-corrected models. In the quantum tunneling regime, we demonstrate that plasmonic hot electron tunneling can further blue shift the quantum plasmons because of the increased conductance in the nanogaps, making it a promising prototype of optical tunable quantum plasmonic devices.

Global transcriptomic analysis of Lactobacillus delbrueckii subsp. bulgaricus ATCC11842 reveals the role of LDB_RS05285 in the post-acidification of yogurt.

During the storage of yogurt, acid-resistant bacteria continue to produce lactic acid (i.e., post-acidification process), leading to undesirable taste and flavor. Many methods have been proposed to inhibit post-acidification. However, the specific genes involved during this biological process have not yet been systematically studied. Hence, herein, we assessed the culture starter Lactobacillus delbrueckii subsp. bulgaricus ATCC11842 with regards to its transcriptomes under in vitro acid- and cold-culture conditions. Through differential gene expression analysis, we screened out 69 candidate genes that persistently responded to acid with or without cold stress. qPCR was then used to determine the in situ expression levels of these candidate genes at different stages of yogurt fermentation and storage. Genes whose expression levels did not change much from the end of fermentation to the early stage of yogurt storage were more likely to be post-acidification genes, as such stability indicated that they were not affected by cold stress. LDB_RS05285 was determined to be one such gene; the overexpression of this gene showed that the increase of gene expression could reduce the acid production of the strain without affecting normal growth. Therefore, the genetic manipulation techniques that increased the expression level of the LDB_RS05285 gene might have the potential to inhibit the post-acidification of yogurt. Thus, LDB_RS05285 plays an important role in the post-acidification process and would become a new target for regulating yogurt post-acidification.

Macrocyclic Aromatic Amide Foldamer: Synthesis, Twisted-to-Boxlike Conformational Switching, and Molecular Recognition.

In this study, a twisted macrocycle was synthesized via ring closure of a double-helical aromatic oligoamide foldamer with two disulfide bridges. Single-crystal X-ray structure and NMR spectroscopy demonstrate the twisted conformation of macrocycle both in the solid state and in solution. As a result of the rearrangement of hydrogen bonding preference, the twisted conformation could be transformed to boxlike through protonation of the pyridine segments of macrocycle. In addition, the NMR titration experiments revealed that flat aromatic guests (e. g., coronene and perylene) could bind to the boxlike macrocycle with a 1 : 1 binding stoichiometry. The addition of base to the host-guest complexes resulted in conformational reversal of the macrocycle from boxlike to twisted as well as the release of guest.

A Disulfide Switch Providing Absolute Handedness Control in Double Helices via Conversion from the Antiparallel to Parallel Helical Pattern.

A strategy to reversibly switch the parallel/antiparallel helical conformation of aromatic double helices through the formation/breakage of a disulfide bond is presented. Single-crystal X-ray structures, NMR, and circular dichroism spectroscopy demonstrate that the double helices with terminal thiol groups favor an antiparallel helical arrangement both in the solid state and in solution, while the P/M bias of helicity induced by chiral segments from another extremity of the sequence is weak in this structural motif. The antiparallel helices can be rearranged to parallel helices through the disulfide connection of the sequences. This change enhances the bias of helical handedness and results in absolute chirality control of the double helices. The handedness-mediated process can be governed by the oxidation-reduction cycle, thereby switching the structural arrangement and the enhancement of chiral bias. In addition, we find that the sequences can dimerize into an intermolecular double helix with the disulfide connection. And the helical handedness is also fully controlled due to the head-to-head structural motif.

Lactulose significantly increased the relative abundance of Bifidobacterium and Blautia in mice feces as revealed by 16S rRNA amplicon sequencing.

BACKGROUND: Lactulose was one of the earliest prebiotics to be identified. To assess the potential risk of large intakes of lactulose to the intestinal microbiota, mice were fed a diet containing lactulose (0%, 5% and 15%, w/w) for 2 weeks and the changes in the fecal microbiota were evaluated by 16S rRNA high-throughput sequencing. RESULTS: Lactulose intervention decreased the α-diversity of the fecal microbiota in both low-dose and high-dose groups. The relative abundance of Actinobacteria was significantly increased, while that of Bacteroidetes was significantly decreased after lactulose intervention. At the genus level, the relative abundance of Bifidobacterium belonging to Actinobacteria was significantly increased, and that of Alistipes belonging to Bacteroidetes was decreased in both low-dose and high-dose groups. The relative abundance of Blautia was significantly increased from 0.2% to 7.9% in the high-dose group and one strain of Blautia producta was isolated from the mice feces. However, the strain could not utilize lactulose. CONCLUSION: Overall, the microbial diversity was decreased after lactulose treatment, with significant increases in the relative abundance of Bifidobacterium. We also provide a strategy to increase the relative abundance of Blautia in the intestine by lactulose feeding at high doses, although the mechanism is not revealed. This will help us understand the prebiotic effect of lactulose on the host health. © 2021 Society of Chemical Industry.

Absolute handedness control of oligoamide double helices by chiral oxazolylaniline induction.

Aromatic oligoamide double helices bearing a chiral oxazolylaniline moiety at the C-terminus were synthesized and their helix handedness was completely controlled (de > 99%). The absolute helix sense and the de values were evaluated by using 1H NMR, X-ray crystallography, and circular dichroism (CD). Using crystal structure analysis, the high efficiency of helix handedness induction was attributed to the close location of the asymmetric carbon center to the helix orbits via intramolecular hydrogen bonding. The CD experiments also showed that there is no loss of chiral induction either in the interconversion of single and double helices or by elongation of the sequences.

Enhanced Efficacy of Gefitinib in Drug-Sensitive and Drug-Resistant Cancer Cell Lines after Arming with a Singlet Oxygen Releasing Moiety.

Attractive results have been achieved with small-molecule target-based drugs in the anticancer field; however, enhancing their treatment effect and solving the problem of drug resistance remain key concerns worldwide. Inspired by the specific affinity of gefitinib for tumour cells and the strong oxidation capacity of singlet oxygen, we combined a chemically generated singlet oxygen moiety with the small-molecule targeted drug gefitinib to improve its anticancer effect. We designed and synthesised a novel compound (Y5-1), in which a small-molecule targeted therapy agent (gefitinib) and a singlet oxygen (provided by an in vitro photodynamic reaction) thermally controlled releasing moiety are covalently conjugated. We demonstrated that the introduction of the singlet oxygen thermally controlled releasing moiety enhanced the anticancer activities of gefitinib. The results of this study are expected to provide a novel strategy to enhance the effect of chemotherapy drugs on drug-resistant cell lines.

Quadruple hybridization of quinoline-triazole oligomers.

A series of quinoline-triazole oligomers and their quadruple helical structures are demonstrated. The helical folding is mainly induced by the intramolecular hydrogen bonds, and solvophobic effects impel the aggregation, causing the quadruplex to be more stable in DMSO than in CDCl3 by four orders of magnitude. As a proof of concept, our studies reveal a tetramerization mechanism in which the single sequences first hybridize to dimers, and then two such dimers further aggregate into a quadruplex.

Epidermal Growth Factor Receptor-Targeted Delivery of a Singlet-Oxygen Sensitizer with Thermal Controlled Release for Efficient Anticancer Therapy.

Photodynamic therapy (PDT) utilizing light-induced singlet oxygen has achieved attractive results in anticancer fields; however, its development is hindered by limited light penetration depth, skin phototoxicity, tumor hypoxia, and PDT-induced hypoxia. Inspired by our previous research work and the limitations of PDT, we introduce a small-molecule-targeted drug erlotinib into the singlet-oxygen chemical source endoperoxide to achieve an EGFR-targeted PDT-mimetic sensitizer (Y3-1) for anticancer therapy. We demonstrated the erlotinib-based precise delivery of the singlet-oxygen chemical source (in vitro photosensitization) to EFGR-overexpressing tumor cells and tissues. Moreover, the anticancer assays validated that the enhanced anticancer efficacy (in vitro and in vivo) of Y3-1 was due to reversible singlet-oxygen thermal release. This study is expected to provide a smart strategy to break through the current roadblock in targeted PDT and achieve a more efficient anticancer therapy model.

Potential Functions of the Gastrointestinal Microbiome Inhabiting the Length of the Rat Digest Tract.

The rat is an important model animal used frequently in biological researches exploring the correlations between gut microbiome and a wide array of diseases. In this study, we used an extended ancestral-state reconstruction algorithm to predict the functional capabilities of the rat gastrointestinal microbiome. Our results indicate an apparent tendency toward metabolic heterogeneity along the longitudinal and transverse axes of the rat gastrointestinal tract (GIT). This heterogeneity was suggested by the enriched small-molecule transport activity and amino acid metabolism in the upper GIT, the aerobic energy metabolism in the stomach and the mucolysis-related metabolism in the lower GIT mucus layer. In contrast to prior results, many functional overlaps were observed when the gastrointestinal microbiomes of different hosts were compared. These overlaps implied that although both the biogeographic location and host genotype were prominent driving forces in shaping the gastrointestinal microbiota, the microbiome functions were similar across hosts when observed under similar physicochemical conditions at identical anatomical sites. Our work effectively complements the rat microbial biogeography dataset we released in 2017 and, thus, contributes to a better understanding and prediction of disease-related alterations in microbial community function.

Ultralow thermal conductivity of turbostratically disordered MoSe2 ultra-thin films and implications for heterostructures.

Films containing 8, 16, 24, 32 and 64 MoSe2 layers were synthesized using the modulated elemental reactants method. X-ray reflectivity patterns showed that the annealed films were the targeted number of MoSe2 layers thick with atomically smooth interfaces. In-plane x-ray diffraction (XRD) scans contained only hk0 reflections for crystalline MoSe2 monolayers. Specular XRD patterns contained only 00l reflections, also indicating that the hk0 plane of the MoSe2 layers are parallel to the substrate. Both XRD and electron microscopy techniques indicated that the hk0 planes are rotationally disordered with respect to one another, with all orientations equally probable for large areas. The rotational disorder between MoSe2 layers is present even when analyzed spots are within 10 nm of one another. Cross-plane thermal conductivities of 0.07-0.09 W m-1 K-1 were measured by time domain thermoreflectance, with the thinnest films exhibiting the lowest conductivity. The structural analysis suggests that the ultralow thermal conductivity is a consequence of rotational disorder, which increases the separation between MoSe2 layers. The bonding environment of the Se atoms also becomes significantly distorted from C 3v symmetry due to the rotational disorder between layers. This structural disorder efficiently reduces the group velocity of the transverse phonon modes but not that of longitudinal modes. Since rotational disorder between adjacent layers in heterostructures is expected if the constituents have incommensurate lattices, this study indicates that these heterostructures will have very low cross-plane thermal conductivity.

Automatic microarray image segmentation with clustering-based algorithms.

Image segmentation, as a key step of microarray image processing, is crucial for obtaining the spot expressions simultaneously. However, state-of-art clustering-based segmentation algorithms are sensitive to noises. To solve this problem and improve the segmentation accuracy, in this article, several improvements are introduced into the fast and simple clustering methods (K-means and Fuzzy C means). Firstly, a contrast enhancement algorithm is implemented in image preprocessing to improve the gridding precision. Secondly, the data-driven means are proposed for cluster center initialization, instead of usual random setting. The third improvement is that the multi features, including intensity features, spatial features, and shape features, are implemented in feature selection to replace the sole pixel intensity feature used in the traditional clustering-based methods to avoid taking noises as spot pixels. Moreover, the principal component analysis is adopted for various feature extraction. Finally, an adaptive adjustment algorithm is proposed based on data mining and learning for further dealing with the missing spots or low contrast spots. Experiments on real and simulation data sets indicate that the proposed improvements made our proposed method obtains higher segmented precision than the traditional K-means and Fuzzy C means clustering methods.

In vitro fermentation of raffinose by the human gut bacteria.

Raffinose has become a major focus of research interest and recent studies have shown that besides beneficial bifidobacteria and lactobacilli, Escherichia coli, Enterococcus faecium and Streptococcus pneumoniae can also utilize raffinose and raffinose might lead to flatulence in some hosts. Therefore, it is required to find out the raffinose-metabolizing bacteria in the gut and the bacteria responsible for the flatulence. The BLASTP search results showed that the homologous proteins of glycosidases related to raffinose utilization are widely distributed in 196 of the 528 gut bacterial strains. Fifty-nine bacterial strains belonging to nine species of five genera were isolated from human feces and were found to be capable of utilizing raffinose; of these species, Enterococcus avium and Streptococcus salivarius were reported for the first time. High-performance liquid chromatography (HPLC) analysis of the supernatants of the nine species revealed that the bacteria could utilize raffinose in different manners. Glucose and melibiose were detected in the supernatants of Enterococcus avium E5 and Streptococcus salivarius B5, respectively. However, no resulting saccharides of raffinose degradation were detected in the supernatants of other seven strains, indicating that they had different raffinose utilization types from Enterococcus avium E5 and Streptococcus salivarius B5. Gas was produced with raffinose utilization by Escherichia coli, Enterococcus faecium, Streptococcus macedonicus, Streptococcus pasteurianus and Enterococcus avium. Thus, more attention should be paid to the raffinose-utilizing bacteria besides bifidobacteria and further studies are required to reveal the mechanisms of raffinose utilization to clarify the relationship between raffinose and gut bacteria.