A new anti-CRISPR gene promotes the spread of drug-resistance plasmids in Klebsiella pneumoniae.

The Klebsiella pneumoniae (K. pneumoniae, Kp) populations carrying both resistance-encoding and virulence-encoding mobile genetic elements (MGEs) significantly threaten global health. In this study, we identified a new anti-CRISPR gene (acrIE10) on a conjugative plasmid with self-target sequence in K. pneumoniae with type I-E* CRISPR-Cas system. AcrIE10 interacts with the Cas7* subunit of K. pneumoniae I-E* CRISPR-Cas system. The crystal structure of the AcrIE10-KpCas7* complex suggests that AcrIE10 suppresses the I-E* CRISPR-Cas by binding directly to Cas7 to prevent its hexamerization, thereby preventing the surveillance complex assembly and crRNA loading. Bioinformatic and functional analyses revealed that AcrIE10 is functionally widespread across diverse species. Our study reports a novel anti-CRISPR and highlights its potential role in spreading resistance and virulence among pathogens.

FOXL2 regulates RhoA expression to change actin cytoskeleton rearrangement in granulosa cells of chicken pre-ovulatory follicles.

Forkhead box L2 (FOXL2) is an indispensable key regulator of female follicular development, and it plays important roles in the morphogenesis, proliferation, and differentiation of follicle granulosa cells (GCs), such as establishing normal estradiol signaling and regulating steroid hormone synthesis. Nevertheless, the effects of FOXL2 on GC morphology and the underlying mechanism remain unknown. Using FOXL2 ChIP-seq analysis, we found that FOXL2 target genes significantly enriched in the actin cytoskeleton-related pathways. We confirmed that FOXL2 inhibited the expression of RhoA, a key gene for actin cytoskeleton rearrangement, by binding to TCATCCATCTCT in RhoA promoter region. In addition, the overexpression of FOXL2 in GCs induced the depolymerization of F-actin and the disordered of the actin filaments, resulting in a slowdown in the expansion of GCs, while silencing FOXL2 inhibited F-actin depolymerization and stabilized the actin filaments, thereby accelerating GC expansion. RhoA/ROCK pathway inhibitor Y-27632 exhibited similar effects to FOXL2 overexpression, even reversed the actin polymerization in FOXL2 silencing GCs. This study revealed for the first time that FOXL2 regulated GC actin cytoskeleton by RhoA/ROCK pathway, thus affecting GC expansion. Our findings provide new insights for constructing the regulatory network of FOXL2 and propose a potential mechanism for facilitating rapid follicle expansion, thereby laying a foundation for further understanding follicular development.

Release of a ubiquitin brake activates OsCERK1-triggered immunity in rice.

Plant pattern-recognition receptors perceive microorganism-associated molecular patterns to activate immune signalling1,2. Activation of the pattern-recognition receptor kinase CERK1 is essential for immunity, but tight inhibition of receptor kinases in the absence of pathogen is crucial to prevent autoimmunity3,4. Here we find that the U-box ubiquitin E3 ligase OsCIE1 acts as a molecular brake to inhibit OsCERK1 in rice. During homeostasis, OsCIE1 ubiquitinates OsCERK1, reducing its kinase activity. In the presence of the microorganism-associated molecular pattern chitin, active OsCERK1 phosphorylates OsCIE1 and blocks its E3 ligase activity, thus releasing the brake and promoting immunity. Phosphorylation of a serine within the U-box of OsCIE1 prevents its interaction with E2 ubiquitin-conjugating enzymes and serves as a phosphorylation switch. This phosphorylation site is conserved in E3 ligases from plants to animals. Our work identifies a ligand-released brake that enables dynamic immune regulation.

Key parameters of physiological responses to acute heat stress in two commercial layers determined by Fisher discriminant analyses.

Given the escalating global warming and the intense nature of modern poultry production, layers are becoming increasingly susceptible to heat stress. This stress disrupts the physiological processes of layers, which leads to reduced productivity and welfare. To address this issue, it is crucial to first evaluate the stress response systematically. However, such evaluations are still lacking in this field. The objective of this study was to accurately monitor the impact of thermal stress and identify common and key indicators that would support decision-making to maintain layer welfare and productivity under stress. We constructed two heat stress models to reflect moderate (32 °C) to severe (36 °C) stress effects and obtained a comprehensive profile of blood physiological parameters associated with the layers' responses to heat stress. We found that genetic differences had limited influence on their physiological responses to heat stress after 32 °C heat challenges. Using 8 selected and significantly changed parameters, layers' physiological status under heat stress could be accurately determined (judgmental accuracy of 98%). As ambient temperature increased to 36 °C, birds suffered more severe challenges that parameters changed in larger percentages. Additionally, breed variations of the physiological responses became apparent, a Fisher discriminant function based on 5 selected parameters could distinguish heat stress effects at 32 °C or 36 °C with 80% accuracy. The results obtained from this study provide two discriminant models for assessing heat stress and shed lights on developing effective and widely applicable heat stress mitigation strategies targeting these indicators.

Correction: Membrane technologies in toilet urine treatment for toilet urine resource utilization: a review.

[This corrects the article DOI: 10.1039/D1RA05816A.].

Structural basis for intrinsic transcription termination.

Efficient and accurate termination is required for gene transcription in all living organisms1,2. Cellular RNA polymerases in both bacteria and eukaryotes can terminate their transcription through a factor-independent termination pathway3,4-called intrinsic termination transcription in bacteria-in which RNA polymerase recognizes terminator sequences, stops nucleotide addition and releases nascent RNA spontaneously. Here we report a set of single-particle cryo-electron microscopy structures of Escherichia coli transcription intrinsic termination complexes representing key intermediate states of the event. The structures show how RNA polymerase pauses at terminator sequences, how the terminator RNA hairpin folds inside RNA polymerase, and how RNA polymerase rewinds the transcription bubble to release RNA and then DNA. These macromolecular snapshots define a structural mechanism for bacterial intrinsic termination and a pathway for RNA release and DNA collapse that is relevant for factor-independent termination by all RNA polymerases.

The structural mechanism for transcription activation by Caulobacter crescentus GcrA.

Canonical bacterial transcription activators bind to their cognate cis elements at the upstream of transcription start site (TSS) in a form of dimer. Caulobacter crescentus GcrA, a non-canonical transcription activator, can activate transcription from promoters harboring its cis element at the upstream or downstream of TSS in a form of monomer. We determined two cryo-EM structures of C. crescentus GcrA-bound transcription activation complexes, GcrA TACU and GcrA TACD, which comprise GcrA, RNAP, σ70 and promoter DNA with GcrA cis elements at either the upstream or downstream of TSS at 3.6 and 3.8 Å, respectively. In the GcrA-TACU structure, GcrA makes bipartite interactions with both σ70 domain 2 (σ702) and its cis element, while in the GcrA-TACD structure, GcrA retains interaction with σ702 but loses the interaction with its cis element. Our results suggest that GcrA likely forms a functionally specialized GcrA-RNAP-σA holoenzyme, in which GcrA first locates its cis element and then facilitates RNAP to load on core promoter at its proximal region. The sequence-specific interaction of GcrA and DNA is disrupted either at the stage of RPo formation or promoter escape depending on the location of GcrA cis elements relative to TSS.

Activation of Peracetic Acid with CuFe2O4 for Rhodamine B Degradation: Activation by Cu and the Contribution of Acetylperoxyl Radicals.

Advanced oxidation processes (AOPs) demonstrate great micropollutant degradation efficiency. In this study, CuFe2O4 was successfully used to activate peracetic acid (PAA) to remove Rhodamine B. Acetyl(per)oxyl radicals were the dominant species in this novel system. The addition of 2,4-hexadiene (2,4-HD) and Methanol (MeOH) significantly inhibited the degradation efficiency of Rhodamine B. The ≡Cu2+/≡Cu+ redox cycle dominated PAA activation, thereby producing organic radicals (R-O˙) including CH3C(O)O˙ and CH3C(O)OO˙, which accounted for the degradation of Rhodamine B. Increasing either the concentration of CuFe2O4 (0-100 mg/L) or PAA (10-100 mg/L) promoted the removal efficiency of this potent system. In addition, weakly acid to weakly alkali pH conditions (6-8) were suitable for pollutant removal. The addition of Humid acid (HA), HCO3-, and a small amount of Cl- (10-100 mmol·L-1) slightly inhibited the degradation of Rhodamine B. However, degradation was accelerated by the inclusion of high concentrations (200 mmol·L-1) of Cl-. After four iterations of catalyst recycling, the degradation efficiency remained stable and no additional functional group characteristic peaks were observed. Taking into consideration the reaction conditions, interfering substances, system stability, and pollutant-removal efficiency, the CuFe2O4/PAA system demonstrated great potential for the degradation of Rhodamine B.

Plant-derived Ren's oligopeptide has antiviral effects on influenza virus and SARS-CoV-2.

Influenza virus and SARS-CoV-2 virus are two important viruses that cause respiratory tract diseases. The high-frequency mutation of the two types of viruses leads to failure of the durable immune protection of vaccines, meanwhile it also poses continuous challenges to the development of antiviral drugs. Traditional Chinese medicine contains large number of biologically active compounds, and some of them contain broad-spectrum antiviral ingredients. In this study, we extracted antiviral active ingredients from medicinal and edible plants by biotransformation and enzymatic hydrolysis as a drug, and we named this drug Ren's oligopeptide. Further, we analyzed the antiviral activity of this drug and found that Ren's oligopeptide could inhibit the replication of influenza virus and SARS-CoV-2 virus with high anti-virus activities. In vitro experiments showed that the antiviral activity of the Ren's oligopeptide mainly targets the replication process after virus enters the cell. Therefore, Ren's oligopeptide is a promising drug against influenza and COVID-19.

Membrane technologies in toilet urine treatment for toilet urine resource utilization: a review.

Membrane technologies have broad potential in methods for separating, collecting, storing, and utilizing urine collected from toilets. Recovering urine from toilets for resource utilization instead of treating it in a sewage treatment plant not only reduces extra energy consumption for the degradation of N and P but also saves energy in chemical fertilizer production, which will contribute to carbon emission reduction of 12.19-17.82 kg kgN -1 in terms of N alone. Due to its high efficiency in terms of volume reduction, water recycling, nutrient recovery, and pollutant removal, membrane technology is a promising technology for resource utilization from urine collected from toilets. In this review, we divide membrane technologies for resource utilization from urine collected from toilets into four categories based on the driving force: external pressure-driven membrane technology, vapor pressure-driven membrane technology, chemical potential-driven membrane technology, and electric field-driven membrane technology. These technologies influence factors such as: recovery targets and mechanisms, reaction condition optimization, and process efficiency, and these are all discussed in this review. Finally, a toilet with source-separation is suggested. In the future, membrane technology research should focus on the practical application of source-separation toilets, membrane fouling prevention, and energy consumption evaluation. This review may provide theoretical support for the resource utilization of urine collected from toilets that is based on membrane technology.

Psychological symptoms in Chinese nurses may be associated with predisposition to chronic disease: a cross-sectional study of suboptimal health status.

Background: Suboptimal health status (SHS) is a reversible state between ideal health and illness and it can be effectively reversed by risk prediction, disease prevention, and personalized medicine under the global background of predictive, preventive, and personalized medicine (PPPM) concepts. More and more Chinese nurses have been troubled by psychological symptoms (PS). The correlation between PS and SHS is unclear in nurses. The purpose of current study is to investigate the prevalence of SHS and PS in Chinese nurses and the relationship between SHS and PS along with predisposing factors as well as to discuss the feasibility of improving health status and preventing diseases according to PPPM concepts in Chinese nurses. Methods: A cross-sectional study was conducted with the cluster sampling method among 9793 registered nurses in Foshan city, China. SHS was evaluated with the Suboptimal Health Status Questionnaire-25 (SHSQ-25). Meanwhile, the PS of depression and anxiety were evaluated with Self-Rating Depression Scale (SDS) and Self-Rating Anxiety Scale (SAS) self-assessment questionnaires. The relationship between PS and SHS in Chinese nurses was subsequently analyzed. Results: Among the 9793 participants, 6107 nurses were included in the final analysis. The prevalence of SHS in the participants was 74.21% (4532/6107) while the symptoms of depression and anxiety were 47.62% (2908/6107) and 24.59% (1502/6107) respectively. The prevalence of SHS in the participants with depression and anxiety was significantly higher than those without the symptoms of depression (83.3% vs 16.7%, P < 0.001) and anxiety (94.2% vs 5.8%, P < 0.0001). The ratio of exercise habit was significantly lower than that of non-exercise habit (68.8% vs 78.4%, P < 0.001) in SHS group. Conclusions: There is a high prevalence of SHS and PS in Chinese nurses. PS in Chinese nurses are associated with SHS. Physical exercise is a protective factor for SHS and PS so that the exercise should be strongly recommended as a valuable preventive measure well in the agreement with PPPM philosophy. Along with SDS and SAS, SHSQ-25 should also be highly recommended and applied as a novel predictive/preventive tool for the health measures from the perspectives of PPPM in view of susceptible population and individual screening, the predisposition to chronic disease preventing, personalization of intervention, and the ideal health state restoring.

Co-metabolic degradation of refractory dye: A metagenomic and metaproteomic study.

Fructose was utilized as an additional co-substrate to systematically investigate the molecular mechanism of its boosting effect for the degradation of refractory dye reactive black 5 (RB5) by a natural bacterial flora DDMZ1. A decolorizing rate of 98% was measured for sample YE + FRU(200) (with 3 g/L fructose additionally to yeast extract medium, 10% (v/v) inoculation size of flora DDMZ1, 200 mg/L RB5) after 48 h. This result was 21% and 77%, respectively, higher than those of samples with only yeast extract or only fructose. Fructose was found to significantly stimulated both intracellular and extracellular azoreductase secretion causing enhanced activity. Metagenomic sequencing technology was used to analyze the functional potential of genes. A label-free quantitative proteomic approach further confirmed the encoding of functional proteins by the candidate genes. Subsequently, the molecular mechanism of RB5 degradation by candidate genes and functional proteins of the dominant species were proposed. This study provides important perspectives to the molecular mechanism of co-metabolic degradation of refractory pollutants by a natural bacterial flora.

Sugar sources as Co-substrates promoting the degradation of refractory dye: A comparative study.

Four sugar sources were used as co-substrates to promote the degradation of a selected refractory dye reactive black 5 (RB5) by the natural bacterial flora DDMZ1. The boosting performance of the four sugar sources on RB5 decolorization ranked as: fructose > sucrose > glucose > glucose + fructose. Kinetic results of these four co-metabolism systems agreed well with a first-order kinetic model. Four sugar sources stimulated the extracellular azoreductase secretion causing enhanced enzyme activity. An increased formation of low molecular weight intermediates was caused by the addition of sugar sources. The toxicity of RB5 degradation products was significantly reduced in the presence of sugar sources. The bacterial community structure differed remarkably as a result of sugar sources addition. For a fructose addition, a considerably enriched population of the functional species Burkholderia-Paraburkholderia and Klebsiella was noted. The results enlarge our knowledge of the microkinetic and microbiological mechanisms of co-metabolic degradation of refractory pollutants.

Structural basis for transcription antitermination at bacterial intrinsic terminator.

Bacteriophages typically hijack the host bacterial transcriptional machinery to regulate their own gene expression and that of the host bacteria. The structural basis for bacteriophage protein-mediated transcription regulation-in particular transcription antitermination-is largely unknown. Here we report the 3.4 Å and 4.0 Å cryo-EM structures of two bacterial transcription elongation complexes (P7-NusA-TEC and P7-TEC) comprising the bacteriophage protein P7, a master host-transcription regulator encoded by bacteriophage Xp10 of the rice pathogen Xanthomonas oryzae pv. Oryzae (Xoo) and discuss the mechanisms by which P7 modulates the host bacterial RNAP. The structures together with biochemical evidence demonstrate that P7 prevents transcription termination by plugging up the RNAP RNA-exit channel and impeding RNA-hairpin formation at the intrinsic terminator. Moreover, P7 inhibits transcription initiation by restraining RNAP-clamp motions. Our study reveals the structural basis for transcription antitermination by phage proteins and provides insights into bacterial transcription regulation.

Unveiling the activating mechanism of tea residue for boosting the biological decolorization performance of refractory dye.

Conventional microbial treatments are challenged by new synthetic refractory dyes. In this work, tea residue was found serving as an effective activator to boost the decolorization performance of anthraquinone dye (reactive blue 19, RB19) by a new bacterial flora DDMY2. The unfermented West Lake Longjing tea residue showed the best enhancement performance. Seventeen main kinds of components in tea residue had been selected to take separate and orthogonal experiments on decolorization of RB19 by DDMY2. Results suggested epigallocatechin gallate (EGCG) in tea residue played important roles in boosting the treatment performance. Illumina MiSeq sequencing results confirmed that EGCG and tea residue pose similar impact on the change of DDMY2 community structure. Some functional bacterial genera unclassified_o_Pseudomonadales, Stenotrophomonas and Bordetella were enriched during the treatment of RB19 by EGCG and tea residue. These evidences suggested EGCG might be the key active component in tea residue that responsible for the enhancement effect on decolorization performance. These results revealed the activating mechanism of tea residue from the perspective of composition.

Fructose as an additional co-metabolite promotes refractory dye degradation: Performance and mechanism.

In this work, the performance and mechanism for the boosting effects of fructose as an additional co-metabolite towards the biological treatment of reactive black 5 were systematically investigated. A decolorization efficiency of 98% was obtained in sample FRU200 (with 3 g/L fructose added based on 3 g/L yeast extract), which was 21% higher than that without fructose. Several intermediates with low molecular weight generated in sample FRU200 and different metabolic pathways were deduced. The bacterial community structure significantly changed due to fructose addition. Label-free quantitative proteomic approach suggested that several up-regulated proteins in sample FRU200 might play essential roles during the degradation. Furthermore, the mechanisms of RB5 degradation by proteins/enzymes of the dominant species in flora DDMZ1 were proposed. This work deepens our understanding of the molecular and ecological mechanism of fructose as co-metabolite enhancing the biodegradation of refractory organic pollutants by a natural bacterial flora.

Highly efficient biodegradation of reactive blue 19 under the activation of tea residue by a newly screened mixed bacterial flora DDMY2.

In this study, a newly screened mixed bacterial flora DDMY2 had high decolorization capacity for anthraquinone dye reactive blue 19 (RB19) and the decolorization efficiency of 300 mg L-1 RB19 could reach up to 98% within 48 h in the presence of tea residue. Results indicated that RB19 could be efficiently decolorized by flora DDMY2 in wide ranges of pH values (5.0-9.0), temperatures (30-40 °C) and initial dye concentrations (50-500 mg L-1) under the activation of tea residue. Concentration of tea residue had been proved to significantly impact the decolorization performance. UV-vis spectrophotometry, Fourier transform infrared spectrometry and liquid chromatography/time-of-flight/mass spectrometry analysis showed three identified degradation products and the possible degradation pathway of RB19 was speculated. High-throughput sequencing analysis revealed the community structures of bacterial flora before and after domestication by tea residue. Based on the result, it was inferred that unclassified_o_Pseudomonadales, Brevibacillus, Stenotrophomonas and Bordetella activated by tea residue were responsible for the excellent decolorization performance. Results of this research deepen our understanding of the biodegradation process of anthraquinone dyes by bacterial flora and broaden the knowledge of utilizing tea residue as a bioactivator in biological treatment.

Integrative analysis of competing endogenous RNA networks reveals the functional lncRNAs in heart failure.

Heart failure has become one of the top causes of death worldwide. It is increasing evidence that lncRNAs play important roles in the pathology processes of multiple cardiovascular diseases. Additionally, lncRNAs can function as ceRNAs by sponging miRNAs to affect the expression level of mRNAs, implicating in numerous biological processes. However, the functional roles and regulatory mechanisms of lncRNAs in heart failure are still unclear. In our study, we constructed a heart failure-related lncRNA-mRNA network by integrating probe re-annotation pipeline and miRNA-target interactions. Firstly, some lncRNAs that had the central topological features were found in the heart failure-related lncRNA-mRNA network. Then, the lncRNA-associated functional modules were identified from the network, using bidirectional hierarchical clustering. Some lncRNAs that involved in modules were demonstrated to be enriched in many heart failure-related pathways. To investigate the role of lncRNA-associated ceRNA crosstalks in certain disease or physiological status, we further identified the lncRNA-associated dysregulated ceRNA interactions. And we also performed a random walk algorithm to identify more heart failure-related lncRNAs. All these lncRNAs were verified to show a strong diagnosis power for heart failure. These results will help us to understand the mechanism of lncRNAs in heart failure and provide novel lncRNAs as candidate diagnostic biomarkers or potential therapeutic targets.

Performance and microbial community structures of hydrolysis acidification process treating azo and anthraquinone dyes in different stages.

In this study, performance of hydrolysis acidification process treating simulated dyeing wastewater containing azo and anthraquinone dyes in different stages was investigated. The decolorization ratio, CODCr removal ratio, BOD5/CODCr value, and volatile fatty acids (VFAs) production were almost better in stage 1 than that in stage 2. Fourier transform infrared spectroscopy (FTIR) and gas chromatography-mass spectrometry (GC-MS) confirmed the biodegradation of Reactive Black 5 (RB5) and Remazol Brilliant Blue R (RBBR) in hydrolysis acidification process. Polymerase chain reaction-denaturing gradient gel electrophoresis (PCR-DGGE) analyses revealed that significant difference of microbial community structures existed in stage 1 and 2. The dominant species in stage 1 was related to Bacteroidetes group, while the dominant species in stage 2 was related to Bacteroidetes and Firmicutes groups. From the results, it could be speculated that different dyes' structures might have significant influence on the existence and function of different bacterial species, which might supply information for bacteria screening and acclimation in the treatment of actual dyeing wastewater.

Modulation of gamma-secretase reduces beta-amyloid deposition in a transgenic mouse model of Alzheimer's disease.

Alzheimer's disease (AD) is characterized pathologically by the abundance of senile plaques and neurofibrillary tangles in the brain. We synthesized over 1200 novel gamma-secretase modulator (GSM) compounds that reduced Abeta(42) levels without inhibiting epsilon-site cleavage of APP and Notch, the generation of the APP and Notch intracellular domains, respectively. These compounds also reduced Abeta(40) levels while concomitantly elevating levels of Abeta(38) and Abeta(37). Immobilization of a potent GSM onto an agarose matrix quantitatively recovered Pen-2 and to a lesser degree PS-1 NTFs from cellular extracts. Moreover, oral administration (once daily) of another potent GSM to Tg 2576 transgenic AD mice displayed dose-responsive lowering of plasma and brain Abeta(42); chronic daily administration led to significant reductions in both diffuse and neuritic plaques. These effects were observed in the absence of Notch-related changes (e.g., intestinal proliferation of goblet cells), which are commonly associated with repeated exposure to functional gamma-secretase inhibitors (GSIs).