Search

Exhaled nitric oxide (FeNO) is a simple, noninvasive, and reproducible test, and FeNO (50 ml/s) is often used to reflect airway inflammation. The peripheral small airway/alveolar nitric oxide (NO) concentration is derived from the output of NO at multiple flow rates. Concentration of alveolar NO (CANO), which has been reported to reflect peripheral small airway inflammation, may be related to parameters that reflect abnormal small airway function.This study aims to investigate the relationship among CANO levels, clinical features, and small airway function-related indicators in patients with stable asthma and to provide a simple method for monitoring small airway function in asthma.We recruited 144 patients with well-controlled, stable asthma, including 69 patients with normal small airway function (normal group) and 75 patients with small airway dysfunction (abnormal group). CANO and pulmonary function were measured.CANO was significantly higher in the abnormal group ([7.28 ± 3.25] ppb) than the normal group CANO ([2.87 ± 1.50] ppb). FEF25-75%pred ([55.0 ± 16.5]%), FEF50%pred ([46.4 ± 13.2]%), and FEF75%pred ([41.9 ± 13.1]%) in abnormal group were significantly lower compared with normal group ([89.9 ± 7.5]%), ([80.9 ± 6.8]%), and ([73.8 ± 5.0]%). CANO was negatively correlated and FEF25-75%pred, FEF50%pred, and FEF75%pred (r = -0.87, P 0.001; r = -0.82, P 0.001; r = -0.78, P 0.001). CANO was positively correlated with age (r = 0.27, P = 0.001). The area under the ROC curve was 0.875 for CANO. The optimal cutoff point of 5.3 ppb had sensitivity and specificity values of 72% and 92% in diagnosing small airway dysfunction.CANO has diagnostic value for small airway dysfunction, and the optimal cutoff value is 5.3 ppb. However, the diagnostic evidence is still insufficient, so it still needs further exploration for its value in detecting small airway dysfunction.

2'-Fucosyllactose (2'-FL) is one of the most important oligosaccharides in human milk. In this study, a glucose–glycerol mixed carbon source and the deletion of the genes arcA and iclR were attempted for the first time in engineered Escherichia coli to improve 2'-FL production. The highest 2'-FL titre of 5.04 g/L, almost 1.4 times higher than that in the control strain, was obtained in the arcA mutant strain using shake-flask culture. In addition, the arcA mutant showed a significantly reduced accumulation of acetate. However, the deletion of iclR and the double deletion of arcA/iclR provided no benefit in terms of 2'-FL biosynthesis. Overall, these results suggest that deletion of arcA could efficiently increase the 2'-FL yield in E. coli and could lay a foundation for more efficient and larger-scale production. Moreover, in shake-flask culture under optimal conditions, the 2'-FL titer reached a maximum value of 7.14 g/L.

RPA2A is a subunit of the conserved heterotrimeric replication protein A (RPA) in Arabidopsis, which is an essential replisome component that binds to single-stranded DNA during DNA replication. RPA2A controls a set of developmental processes, but the underlying mechanism is largely unknown. Here we show that RPA2A represses key flowering genes including FLOWERING LOCUS T (FT), AGAMOUS (AG) and AGAMOUS LIKE 71 (AGL71) to suppress floral transition by cooperating with the PRC2 complex. RPA2A is vigorously expressed in dividing cells and required for correct DNA replication. Mutation of RPA2A leads to early flowering, which is dependent on ectopic expression of key flowering genes including FT molecularly and genetically. RPA2A and PRC2 have common target genes including FT, AG and AGL71 supported using genetic analysis, transcriptome profiling and H3K27me3 ChIP-seq analysis. Furthermore, RPA2A physically interacts with PRC2 components CLF, EMF2 and MSI1, which recruits CLF to the chromatin loci of FT, AG and AGL71. Together, our results show that the replication protein RPA2A recruits PRC2 to key flowering genes through physical protein interaction, thereby repressing the expression of these genes to suppress floral transition in Arabidopsis.

Lysine acetylation, one of the major types of post-translational modifications, plays critical roles in regulating gene expression and protein function. Histone deacetylases (HDACs) are responsible for removing acetyl groups from lysines of both histone and non-histone proteins. While tremendous progress has been made in understanding the function and mechanism of HDACs in animals in the past two decades, nearly half of the HDAC studies in plants were reported within the past five years. In this review, we summarize the major findings on plant HDACs, with a focus on the model plant Arabidopsis thaliana, and highlight the components, regulatory mechanisms, and biological functions of HDAC complexes.

(1) Background: Ellagic acid (EA) acts as a product of gut microbiota transformation to prevent insulin resistance, which is limited by high-fat diet (HFD)-induced dysbiosis. The aim of this study was to investigate the synergistic effects and mechanisms of supplementation with the probiotic Weizmannia coagulans (W. coagulans) on the prevention of insulin resistance by EA; (2) Methods: C57BL/6J mice were divided into five groups (n = 10/group): low-fat-diet group, high-fat-diet group, EA intervention group, EA + W. coagulans BC77 group, and EA + W. coagulans BC2000 group; (3) Result: W. coagulans BC2000 showed a synergistic effect on EA’s lowering insulin resistance index and inhibiting high-fat diet-induced endotoxemia. The combined effect of BC2000 and EA activated the autophagy pathway in the mouse liver, a urolithin-like effect. This was associated with altered β-diversity of gut microbiota and increased Eggerthellaceae, a potential EA-converting family. Ellagic acid treatment alone and the combined use of ellagic acid and W. coagulans BC77 failed to activate the hepatic autophagy pathway; (4) Conclusions: W. coagulans BC2000 can assist EA in its role of preventing insulin resistance. This study provides a basis for the development of EA-rich functional food supplemented with W. coagulans BC2000.

Fern root (FR) was used in the biofuel production for the first time. However, fermentation of the enzymatic hydrolysate of FR starch (EHFS) directly to butanol by Clostridium acetobutylicum CGMCC1.0134 resulted in a low butanol production and yield with high content of starch residual. After adding yeast extract (YE) solution (with a 3 g/L final concentration in broth) into EHFS, the butanol production, productivity, and yield were raised by 174%, 250%, and 183%, respectively. Monitoring changes of free amino acid concentration in the fermentation broth indicated that aspartic acid families and serine families were stimulated to accumulate by YE addition. Gene expression analysis further revealed that ctfB coding CoA-transferase was induced by adding YE into EHFS. It was concluded that EHFS could be a promising substrate for butanol fermentation.

Histone deacetylases remove acetyl groups from histone proteins and play important roles in many genomic processes. How histone deacetylases perform specialized molecular and biological functions in plants is poorly understood. Here, we identify HIGH EXPRESSION OF OSMOTICALLY RESPONSIVE GENES 15 (HOS15) as a core member of the Arabidopsis (Arabidopsis thaliana) HISTONE DEACETYLASE9-POWERDRESS (HDA9-PWR) complex. HOS15 immunoprecipitates with both HDA9 and PWR. Mutation of HOS15 induces histone hyperacetylation and methylation changes similar to hda9 and pwr mutants. HOS15, HDA9, and PWR are coexpressed in all organs, and mutant combinations display remarkable phenotypic resemblance and nonadditivity for organogenesis and developmental phase transitions. Ninety percent of HOS15-regulated genes are also controlled by HDA9 and PWR. HDA9 binds to and directly represses 92 genes, many of which are responsive to biotic and abiotic stimuli, including a family of ethylene response factor genes. Additionally, HOS15 regulates HDA9 nuclear accumulation and chromatin association. Collectively, this study establishes that HOS15 forms a core complex with HDA9 and PWR to control gene expression and plant development.

In this study, carboxymethyl chitosan (CMCS) and N-acetylneuraminic acid (NeuAc) were used to develop C-NeuAc hydrogels to encapsulate Pediococcus pentosaceus QK-1. The mechanical properties, thermal stability, in vitro degradation, and pH sensitivity of the hydrogel were evaluated. The C-NeuAc concentration required for optimal hydrogel performance was 3% (w/v). Hydrogel swelling behaviour was effectively assessed by Fickian diffusion and Schott's second-order kinetic models. The hydrogel demonstrated excellent biocompatibility and low in vitro cytotoxicity. An in vitro assay revealed that the viability of Pediococcus pentosaceus QK-1 in C-NeuAc had decreased by only 1.41 log (CFU/ mL) after exposure to simulated acidic gastric fluid. Moreover, the survival rate of the encapsulated and free Pediococcus pentosaceus QK-1 cells were 80.1% and virtually zero, respectively, after passage through the gastrointestinal tract. It was empirically determined that low temperature and freeze-drying were the ideal condition and method to ensure storage longevity of the hydrogel-encapsulated probiotic. Hence, C-NeuAc hydrogel is highly desirable as a food-grade probiotic delivery vehicle.

Sialyllactose (SL) is one of the most important acidic oligosaccharides in human milk, which plays an important role in the health of infants. In this work, an efficient multi-enzyme cascade was developed in a single whole cell to produce 3′-SL. We constructed two compatible plasmids with double cloning sites to co-express four genes. Different combinations were assessed to verify the optimal catalytic ability. Then, the conversion temperature, pH, and stability under the optimal temperature and pH were investigated. Moreover, the optimal conversion conditions and surfactant concentration were determined. By using the optimal conditions (35 °C, pH 7.0, 20 mM polyphosphate, 10 mM cytidine monophosphate (CMP), 20 mM MgCl2), 25 mL and 4 L conversion systems were carried out to produce 3′-SL. Similar results were obtained between different volume conversion reactions, which led the maximum production of 3′-SL to reach 53 mM from 54.2 mM of sialic acid (SA) in the 25 mL system and 52.8 mM of 3′-SL from 53.8 mM of SA in the 4 L system. These encouraging results demonstrate that the developed single whole-cell multi-enzyme system exhibits great potential and economic competitiveness for the manufacture of 3′-SL.

3-fucosyllactose (3-FL) and 2'-fucosyllactose (2'-FL), are two important fucosylated oligosaccharides in human milk. Extensive studies on 2'-FL enabled its official approval for use in infant formula. However, development of 3-FL has been somewhat sluggish due to its low content in human milk and poor yield in enlarged production. Here, an α-1,3-fucosyltransferase mutant was introduced into an engineered Escherichia coli (E. coli) capable of producing GDP-L-fucose, leading to a promising 3-FL titer in a 5.0-L bioreactor. To increase the availability of cofactors (NADPH and GTP) for optimized 3-FL production, zwf, pntAB, and gsk genes were successively overexpressed, finally resulting in a higher 3-FL level with a titer of 35.72 g/L and a yield of 0.82 mol 3-FL/mol lactose. Unexpectedly, the deletion of pfkA gene led to a much lower performance of 3-FL production than the control strain. Still, our strategy achieved the highest 3-FL level in E. coli to date.

Among the human milk oligosaccharides (HMOs), one of the most abundant oligosaccharides and has great benefits for human health is 3&prime, sialyllactose (3&prime, SL). Given its important physiological functions and the lack of cost-effective production processes, we constructed an in vitro multi-enzymatic cofactor recycling system for the biosynthesis of 3&prime, SL from a low-cost substrate. First, we constructed the biosynthetic pathway and increased the solubility of cytidine monophosphate kinase (CMK) with chaperones. We subsequently identified that &beta, galactosidase (lacZ) affects the yield of 3&prime, SL, and hence with the lacZ gene knocked out, a 3.3-fold increase in the production of 3&prime, SL was observed. Further, temperature, pH, polyphosphate concentration, and concentration of divalent metal ions for 3&prime, SL production were optimized. Finally, an efficient biotransformation system was established under the optimized conditions. The maximum production of 3&prime, SL reached 38.7 mM, and a molar yield of 97.1% from N-acetylneuraminic acid (NeuAc, sialic acid, SA) was obtained. The results demonstrate that the multi-enzymatic cascade biosynthetic pathway with cofactor regeneration holds promise as an industrial strategy for producing 3&prime, SL.

International audience; Proteins in the Chromodomain-Helicase/ATPase-DNA-binding domain (CHD) family are divided into three groups. The function of group I CHD proteins in nucleosome positioning is well established, while that of group II members (represented by CHD3/Mi2) remains unclear. Using high-throughput approaches, we investigated the function of the group II rice (Oryza sativa) CHD protein CHR729 in nucleosome positioning, gene expression, histone methylation, and binding. Our data revealed that thechr729mutation led to increased nucleosome occupancy in the rice genome and altered the expression and histone H3K4me3 modification of many, mainly underexpressed, genes. Further analysis showed that the mutation affected both the deposition and depletion of H3K4me3 in distinct chromatin regions, with concomitant changes in H3K27me3 modification. Genetic and genomic analyses revealed that CHR729 and JMJ703, an H3K4 demethylase, had agonistic, antagonistic, and independent functions in modulating H3K4me3 and the expression of subsets of genes. In addition, CHR729 binding was enriched in H3K4me3-marked genic and H3K27me3-marked intergenic regions. The results indicate that CHR729 has distinct functions in regulating H3K4me3 and H3K27me3 modifications and gene expression at different chromatin domains and provide insight into chromatin regulation of bivalent genes marked by both H3K4me3 and H3K27me3.The chromodomain-helicase-DNA-binding factor CHR729 regulates nucleosome positioning and histone modification to control the expression of poised genes in rice.

International audience; Histone marks including histone modifications and histone variants may affect the processes of gene transcription and co-transcriptional RNA processing depending on their specific deposition patterns within genes. Here, we analyzed distribution patterns of rice histone marks and divided them into seven clusters according to their enrichment in promoter, transcription start site (TSS), and gene body regions. Expression levels of the genes in each cluster were explored to disclose the importance of histone marks in the processes of transcription. We show that a) H3K4me3 and histone acetylation marks show locally different distributions at TSS, implying that they may play different roles in transcription initiation. b) H3K36me1 enriched at TSS has a negative effect on transcription. c) Genes with high level of expression were marked by H3K36me3 at both the TSS and body regions. In addition, we found that H3K4me2, H3K23ac, H3K4ac, and H2A.Z show exon-biased enrichment, suggesting they may be chromatin marks involved in co-transcriptional splicing. Finally, we identified histone marks that discriminate constitutive expression genes (CEGs) from tissue-specific expressed genes (TSEGs). Taken together, the analysis revealed distribution patterns of different histone marks in rice to infer their potential roles in transcription and RNA processing. The results lay foundation for further understanding the mechanism by which histone marks are involved in the regulation of these processes in plants.

• Plant immune responses need to be tightly controlled for growth-defense balance. The mechanism underlying this tight control is not fully understood. Here we identify epigenetic regulation of nucleotide-binding leucine rich repeat or Nod-Like Receptor (NLR) genes as an important mechanism for immune responses. • Through a sensitized genetic screen and molecular studies, we identified and characterized HOS15 and its associated protein HDA9 as negative regulators of immunity and NLR gene expression. • The loss-function of HOS15 or HDA9 confers enhanced resistance to pathogen infection accompanied with increased expression of one-third of the 207 NLR genes in Arabidopsis thaliana. HOS15 and HDA9 are physically associated with some of these NLR genes and repress their expression likely through reducing the acetylation of H3K9 at these loci. In addition, these NLR genes are repressed by HOS15 under both pathogenic and non-pathogenic conditions but by HDA9 only under infection condition. • Together, this study uncovers a previously uncharacterized histone deacetylase complex in plant immunity and highlights the importance of epigenetic regulation of NLR genes in modulating growth-defense balance.

The ability of cells to perceive and translate versatile cues into differential chromatin and transcriptional states is critical for many biological processes1-5. In plants, timely transition to a flowering state is crucial for successful reproduction6-9. EARLY BOLTING IN SHORT DAY (EBS) is a negative transcriptional regulator that prevents premature flowering in Arabidopsis thaliana10,11. We found that EBS contains bivalent bromo-adjacent homology (BAH)-plant homeodomain (PHD) reader modules that bind H3K27me3 and H3K4me3, respectively. We observed co-enrichment of a subset of EBS-associated genes with H3K4me3, H3K27me3, and Polycomb repressor complex 2 (PRC2). Notably, EBS adopted an autoinhibition mode to mediate its switch in binding preference between H3K27me3 and H3K4me3. This binding balance was critical because disruption of either EBS-H3K27me3 or EBS-H3K4me3 interaction induced early floral transition. Our results identify a bivalent chromatin reader capable of recognizing two antagonistic histone marks, and we propose a distinct mechanism of interaction between active and repressive chromatin states.

The production of virginiamycin (VGM) from Streptomyces virginiae was improved by genome shuffling and ribosome engineering companied with a high-throughput screening method integrating deep-well cultivation and the cylinder-plate detecting. First, a novel high-throughput method was developed to rapidly screen large numbers of VGM-producing mutants. Then, the starting population of genome shuffling was obtained through ultraviolet (UV) and microwave mutagenesis, and four mutants with higher productivity of VGM were selected for genome shuffling. Next, the parent protoplasts were inactivated by UV and heat when a fusant probability was about 98%. Streptomycin resistance was used as an evolutionary pressure to extend positive effects on VGM synthesis. Finally, after five rounds of genome shuffling, a genetically stable strain G5-103 was obtained and characterized to be able to yield 251 mg/L VGM, which was 3.1- and 11.6-fold higher than that of the mutant strain UV 1150 and the wild-type strain, respectively.

Ribosome biogenesis is a fundamental process required for all cellular activities. Histone deacetylases play critical roles in many biological processes including transcriptional repression and rDNA silencing. However, their function in pre-rRNA processing remains poorly understood. Here, we discovered a previously uncharacterized role of Arabidopsis thaliana histone deacetylase HD2C in pre-rRNA processing via both canonical and noncanonical manners. HD2C interacts with another histone deacetylase HD2B and forms homo- and/or hetero-oligomers in the nucleolus. Depletion of HD2C and HD2B induces a ribosome-biogenesis deficient phenotype and aberrant accumulation of 18S pre-rRNA intermediates. Our genome-wide analysis revealed that HD2C binds and represses the expression of key genes involved in ribosome biogenesis. Using RNA immunoprecipitation and sequencing, we further uncovered a noncanonical mechanism of HD2C directly associating with pre-rRNA and small nucleolar RNAs to regulate rRNA methylation. Together, this study reveals a multifaceted role of HD2C in ribosome biogenesis and provides mechanistic insights into how histone deacetylases modulate rRNA maturation at the transcriptional and posttranscriptional levels.

Soybean milk is an economical substitute for dairy products. Pediococcus pentosaceus has been used as a food additive to improve taste, nutrition, and food safety. In this study, four P. pentosaceus strains (CICC 24444, QK-1, MQ-1 and RQ-1) isolated from various food sources and known to exhibit broad-spectrum antibacterial activities were used to ferment soybean milk, and their fermentation characteristics and the properties of the resulting beverages were evaluated. The results revealed that the P. pentosaceus strains can inhibited the growth of five types of pathogenic bacteria (Salmonella enterica subsp. enterica serotype Enteritidis, Yersinia enterocolitica, Shigella dysenteriae, Escherichia coli, and Staphylococcus aureus), and their in vitro survival rates in the simulated stomach and intestinal environments were above 90%, satisfying the probiotic requirements. Isomaltose oligosaccharide was used as a protective agent to resist low-temperature freeze-drying damage and ensure a high survival rate, and P. pentosaceus was directly injected into fermented soymilk. The acidification of fermented soybean milk was the weakest with P. pentosaceus QK-1, and the viable bacterial counts of all strains were stable after 28 days of storage. After fermentation, the antioxidant ability was enhanced. Arginine and β-alanine levels increased after fermentation, and the adjunct culture of P. pentosaceus QK-1 increased proline levels. Our data indicate that P. pentosaceus QK-1 is a suitable strain for the development of functional plant-based beverages.

Ideal Plant Architecture 1 (IPA1) encodes SQUAMOSA PROMOTER BINDING PROTEIN-LIKE 14 (SPL14) with a pleiotropic effect on regulating rice development and biotic stress responses. To investigate the role of IPA1 in early seedling development, we developed a pair of IPA1/ipal-NILs and found that seed germination and early seedling growth were retarded in the ipa1-NIL. Analysis of the soluble sugar content, activity of amylase, and expression of the α-amylase genes revealed that the starch metabolism was weakened in the ipa1-NIL germinating seeds. Additionally, the content of bioactive gibberellin (GA) was significantly lower than that in the IPA1-NIL seeds at 48 h of imbibition. Meanwhile, the expression of GA synthesis-related gene OsGA20ox1 was downregulated, whereas the expression of GA inactivation-related genes was upregulated in ipa1-NIL seeds. In addition, the expression of OsWRKY51 and OsWRKY71 was significantly upregulated in ipa1-NIL seeds. Using transient dual-luciferase and yeast one-hybrid assays, IPA1 was found to directly activate the expression of OsWRKY51 and OsWRKY71, which would interfere with the binding affinity of GA-induced transcription factor OsGAMYB to inhibit the expression of α-amylase genes. In summary, our results suggest that IPA1 negatively regulates seed germination and early seedling growth by interfering with starch metabolism via the GA and WRKY pathways.

Additional file 1. Flow diagram of lily rice wine production.

The objective of this study was to investigate the stability and degradation kinetics of N-acetylneuraminic acid (Neu5Ac). The pH of the solution strongly influenced the stability of Neu5Ac, which was more stable at neutral pH and low temperatures. Here, we provide detailed information on the degradation kinetics of Neu5Ac at different pH values (1.0, 2.0, 11.0 and 12.0) and temperatures (60, 70, 80 and 90 &deg, C). The study of the degradation of Neu5Ac under strongly acidic conditions (pH 1.0&ndash, 2.0) is highly pertinent for the hydrolysis of polysialic acid. The degradation kinetics of alkaline deacetylation were also studied. Neu5Ac was highly stable at pH 3.0&ndash, 10.0, even at high temperature, but the addition of H2O2 greatly reduced its stability at pH 5.0, 7.0 and 9.0. Although Neu5Ac has a number of applications in products of everyday life, there are no reports of rigorous shelf-life studies. This research provides kinetic data that can be used to predict product shelf lives at different temperatures and pH values.

The dynamic incorporation of histone variants influences chromatin structure and many biological processes. In Arabidopsis, the canonical variant H3.1 differs from H3.3 in four residues, one of which (H3.1Phe41) is unique and conserved in plants. However, its evolutionary significance remains unclear. Here, we show that Phe41 first appeared in H3.1 in ferns and became stable during land plant evolution. Unlike H3.1, which is specifically enriched in silent regions, H3.1F41Y variants gain ectopic accumulation at actively transcribed regions. Reciprocal tail and core domain swap experiments between H3.1 and H3.3 show that the H3.1 core, while necessary, is insufficient to restrict H3.1 to silent regions. We conclude that the vascular-plant-specific Phe41 is critical for H3.1 genomic distribution and may act collaboratively with the H3.1 core to regulate deposition patterns. This study reveals that Phe41 may have evolved to provide additional regulation of histone deposition in plants., The canonical histone variant H3.1 of vascular plants contains a conserved Phe residue at position 41 that is unique to the plant kingdom. Here, Lu et al. provide evidence that H3.1Phe41 acts collaboratively with the H3.1 core domain to restrict H3.1 deposition to silent regions of the genome.

To obtain an industrial strain with high ethanol fermentation efficiency under salted conditions, the wild strain H058 of Saccharomyces cerevisiae was mutated by means of nitrogen ions implantation. Mutagenic effects of strain H058 by low energy N + ion implantation were studied. A similar "saddle shape" survival curve due to ion beam irradiation appeared again in this study. By repeated screening, a high salt-tolerant and ethanol-producing strain M158 was obtained. Results showed that in medium contained 0, 1.5, 3.0, 4.5, 6.0% NaCl, M158 produced maximal ethanol of 98.3, 97.2, 96.4, 95.6 and 78.3 g/L at 54, 54, 54 and 72 h, respectively. However, the original strain H058 maximal ethanol of 95.2, 90.9, 84.8, 79.4 and 67.5 g/L at 60, 60, 66 and 72 h, respectively. In addition, the ethanol yield (g/g) in all of the NaCl concentrations for M158 is 0.492, 0.486, 0.482, 0.48 and 0.392 g/g, respectively, which were higher than those (0.476, 0.455, 0.424, 0.397 and 0.338 g/g, respectively) of the original strain H058. The higher production and shorter fermentation period suggest that strain M158 is a good salt-tolerant and ethanol-producing strain.