Insight into mitigation mechanisms of N2O emission by biochar during agricultural waste composting.

The effects and mitigation mechanisms of biochar added at different composting stages on N2O emission were investigated. Four treatments were set as follows: CK: control, BB10%: +10 % biochar at beginning of composting, BB5%&T5%: +5% biochar at beginning and + 5 % biochar after thermophilic stage of composting, BT10%: +10 % after thermophilic stage of composting. Results showed that treatment BB10%, BB5%&T5%, and BT10% reduced total N2O emissions by 55 %, 37 %, and 36 %, respectively. N2O emission was closely related to most physicochemical properties, while it was only related to amoA gene and hydroxylamine oxidoreductase. Different addition strategies of biochar changed the contributions of physicochemical properties, functional genes and enzymes to N2O emission. Organic matter and C/N contributed 23.7 % and 27.6 % of variations in functional gene abundances (P < 0.05), respectively. pH and C/N (P < 0.05) contributed 37.3 % and 17.3 % of variations in functional enzyme activities. These findings provided valuable insights into mitigating N2O emissions during composting.

Myriocin enhances the clearance of M. tuberculosis by macrophages through the activation of PLIN2.

Myriocin is an inhibitor of de novo synthesis of sphingolipids and ceramides. In this research, we showed myriocin could significantly reduce Mtb burden and histopathological inflammation in mice. However, the underlying mechanism remains unclear. RNA-seq analysis revealed a significant increase in gene expression of PLIN2/CD36/CERT1 after myriocin treatment. The reduced bactericidal burden was only reversed after silencing the lipid droplets (LDs) surface protein PLIN2. This suggests that myriocin enhances the ability of macrophages to clear Mtb depending on the PLIN2 gene, which is part of the PPARγ pathway. Indeed, we observed a significant increase in the number of LDs following myriocin treatment.IMPORTANCEMycobacterium tuberculosis has the ability to reprogram host cell lipid metabolism and alter the antimicrobial functions of infected macrophages. The sphingolipids, such as ceramides, are the primary host lipids utilized by the bacteria, making the sphingomyelinase/ceramide system critical in Mtb infections. Surprisingly, the antimicrobial effect of myriocin was found to be independent of its role in reducing ceramides, but instead, it depends on the lipid droplets surface protein PLIN2. Our findings provide a novel mechanism for how myriocin enhances Mtb clearance in macrophages.

Study on the correlation of C-reactive protein/albumin ratio with sudden sensorineural hearing loss complicated by hypertension: a prospective study.

BACKGROUND: Understanding the pathophysiology of sudden sensorineural hearing loss (SSNHL) and identifying its clinical symptoms and associated risk factors are crucial for doctors in order to create effective prevention and therapeutic methods for this prevalent otolaryngologic emergency. METHODS: This study focuses on investigating the correlation between the C-reactive protein/albumin ratio (CAR) and SSNHL complicated by hypertension. In this study, 120 patients diagnosed with SSNHL were divided into groups with and without hypertension, and propensity score matching was used to compare and analyze the severity, type, prognosis, and CAR levels in SSNHL. RESULTS: The results showed that the SSNHL group with hypertension had significantly higher CAR levels, age, hearing curve abnormalities, and more severe hearing loss compared to the control group with isolated SSNHL. These differences were statistically significant (p < 0.001). Among different subtypes of SSNHL, CAR levels increased progressively with the advancement of the condition, and these differences were also statistically significant (p < 0.001). CONCLUSION: In summary, in patients with SSNHL, those with hypertension had higher CAR levels than those without a history of hypertension, and they experienced more severe hearing loss. Moreover, there was a clear correlation between CAR levels and the extent of SSNHL, indicating that greater CAR levels in patients with SSNHL are connected to more severe hearing loss in various hearing patterns and perhaps indicative of a poorer prognosis.

Straw from Different Crop Species Recruits Different Communities of Lignocellulose-Degrading Microorganisms in Black Soil.

The biological degradation of plant residues in the soil or on the soil surface is an integral part of the natural life cycle of annual plants and does not have adverse effects on the environment. Crop straw is characterized by a complex structure and exhibits stability and resistance to rapid microbial decomposition. In this study, we conducted a microcosm experiment to investigate the dynamic succession of the soil microbial community and the functional characteristics associated with lignocellulose-degrading pathways. Additionally, we aimed to identify lignocellulose-degrading microorganisms from the straw of three crop species prevalent in Northeast China: soybean (Glycine max Merr.), rice (Oryza sativa L.), and maize (Zea mays L.). Our findings revealed that both the type of straw and the degradation time influenced the bacterial and fungal community structure and composition. Metagenome sequencing results demonstrated that during degradation, different straw types assembled carbohydrate-active enzymes (CAZymes) and KEGG pathways in distinct manners, contributing to lignocellulose and hemicellulose degradation. Furthermore, isolation of lignocellulose-degrading microbes yielded 59 bacterial and 14 fungal strains contributing to straw degradation, with fungi generally exhibiting superior lignocellulose-degrading enzyme production compared to bacteria. Experiments were conducted to assess the potential synergistic effects of synthetic microbial communities (SynComs) comprising both fungi and bacteria. These SynComs resulted in a straw weight loss of 42% at 15 days post-inoculation, representing a 22% increase compared to conditions without any SynComs. In summary, our study provides novel ecological insights into crop straw degradation by microbes.

Persistent Colonization of Ciprofloxacin-Resistant and Extended-Spectrum ß-Lactamase (ESBL)-Producing Salmonella enterica Serovar Kentucky ST198 in a Patient with Inflammatory Bowel Disease.

Objective: Salmonella enterica serovar Kentucky ST198 has emerged as a global threat to humans. In this study, we aimed to characterize the prolonged carriage of ciprofloxacin-resistant and extended-spectrum ß-lactamase (ESBL)-producing S. Kentucky ST198 in a single patient with inflammatory bowel disease (IBD). Methods: Three S. Kentucky strains were collected from a single patient with IBD on 11th January, 23rd January, and 8th February, 2022, respectively. Antimicrobial susceptibility testing, whole-genome sequencing, and phylogenetic analysis with 38 previously described Chinese S. Kentucky ST198 strains from patients and food were performed. Results: All three S. Kentucky isolates belonged to ST198. They carried identical 16 resistance genes, such as blaCTX-M-55, tet(A), and qnrS1, and had identical mutations within gyrA (S83F and D87N) and parC (S80I). Therefore, they exhibited identical multidrug-resistant profiles, including the clinically important antibiotics cephalosporins (ceftazidime and cefepime), fluoroquinolones (ciprofloxacin and levofloxacin), and third-generation tetracycline (tigecycline). Our three S. Kentucky strains were classified into the subclade ST198.2-2, and were genetically identical (2-6 SNPs) to each other. They exhibited a close genetic similarity (15-20 SNPs) to the isolate NT-h3189 from a patient and AH19MCS1 from chicken meat in China, indicating a possible epidemiological link between these S. Kentucky ST198 isolates from the patients and chicken meat. Conclusion: Long-term colonization of ciprofloxacin-resistant and ESBL-producing S. Kentucky ST198 in a single patient is a matter of concern. Due to the potential transfer of S. Kentucky ST198 from food sources to humans, ongoing surveillance of this particular clone in animals, animal-derived food products, and humans should be strengthened.

Terminal modifications independent cell-free RNA sequencing enables sensitive early cancer detection and classification.

Cell-free RNAs (cfRNAs) offer an opportunity to detect diseases from a transcriptomic perspective, however, existing techniques have fallen short in generating a comprehensive cell-free transcriptome profile. We develop a sensitive library preparation method that is robust down to 100 µl input plasma to analyze cfRNAs independent of their 5'-end modifications. We show that it outperforms adapter ligation-based method in detecting a greater number of cfRNA species. We perform transcriptome-wide characterizations in 165 lung cancer, 30 breast cancer, 37 colorectal cancer, 55 gastric cancer, 15 liver cancer, and 133 cancer-free participants and demonstrate its ability to identify transcriptomic changes occurring in early-stage tumors. We also leverage machine learning analyses on the differentially expressed cfRNA signatures and reveal their robust performance in cancer detection and classification. Our work sets the stage for in-depth study of the cfRNA repertoire and highlights the value of cfRNAs as cancer biomarkers in clinical applications.

Low-dose ketamine versus morphine in the treatment of acute pain in the emergency department: A meta-analysis of 15 randomized controlled trials.

OBJECTIVE: To compare the effectiveness and safety of ketamine and morphine in adult patients with acute pain in emergency department (ED) by using a meta-analysis method. METHODS: This study was based on the Cochrane methodology for conducting a meta-analysis. Only randomized controlled trials (RCTs) were eligible for this study, with an experimental group that received low-dose ketamine and a control group that received morphine. The participants were adults who had acute pain in the ED. The primary outcome measures were the numeric rating scale (NRS) and visual analog scale (VAS). The secondary outcome measures were the complete resolution of pain, NRS reduction ≥3 points, NRS reduction ≥50% or 60%, change of NRS score, change of VAS score, rescue analgesia, satisfaction and adverse events. Subgroup analysis was performed for studies with intravenous and intranasal administration of ketamine. The Review Manager Database was used to analyze the included studies. RESULTS: 15 RCTs involving 1768 patients were included. The ketamine group had lower NRS scores than morphine group at 30 min (MD, -0.77 [95% CI, -0.93 to -0.61]; p < 0.00001), while the morphine had better analgesic effects at 120 min after treatment (MD, 0.33 [95% CI, 0.15 to 051]; p = 0.0003). The subjects of complete resolution of pain in the ketamine group performed better than those in the morphine group at 15 min (RR 3.18, 95% CI 1.75 to 5.78; p = 0.0001). Compared with the morphine group, the ketamine group had a lower incidence of adverse events requiring intervention (RR, 0.34 [95% CI, 0.18 to 0.66]; p = 0.001). Subgroup analysis of intravenous ketamine showed that ketamine had lower VAS score than the morphine group at 30 min. However, also on the 30-min VAS score, intranasal ketamine analgesia was less effective than morphine. CONCLUSIONS: Ketamine had better analgesic effects in the early stages after treatment, while morphine maintained more durable effects. Compared with morphine, ketamine had a lower incidence of adverse events requiring intervention. The results of subgroup analysis showed that intravenous administration of ketamine was more effective than intranasal administration.

Correction: He et al. In Vivo Imaging Sheds Light on the Susceptibility and Permissivity of Carassius auratus to Cyprinid Herpesvirus 2 According to Developmental Stage. Viruses 2023, 15, 1746.

In the original publication [...].

Single-cell morphological and topological atlas reveals the ecosystem diversity of human breast cancer.

Digital pathology allows computerized analysis of tumor ecosystem using whole slide images (WSIs). Here, we present single-cell morphological and topological profiling (sc-MTOP) to characterize tumor ecosystem by extracting the features of nuclear morphology and intercellular spatial relationship for individual cells. We construct a single-cell atlas comprising 410 million cells from 637 breast cancer WSIs and dissect the phenotypic diversity within tumor, inflammatory and stroma cells respectively. Spatially-resolved analysis identifies recurrent micro-ecological modules representing locoregional multicellular structures and reveals four breast cancer ecotypes correlating with distinct molecular features and patient prognosis. Further analysis with multiomics data uncovers clinically relevant ecosystem features. High abundance of locally-aggregated inflammatory cells indicates immune-activated tumor microenvironment and favorable immunotherapy response in triple-negative breast cancers. Morphological intratumor heterogeneity of tumor nuclei correlates with cell cycle pathway activation and CDK inhibitors responsiveness in hormone receptor-positive cases. sc-MTOP enables using WSIs to characterize tumor ecosystems at the single-cell level.

In Vivo Imaging Sheds Light on the Susceptibility and Permissivity of Carassius auratus to Cyprinid Herpesvirus 2 According to Developmental Stage.

Cyprinid herpesvirus 2 (CyHV-2) is a virus that causes mass mortality in economically important Carassius spp. However, there have been no comprehensive studies into host susceptibility or permissivity with respect to developmental stage, and the major portal of viral entry into the host is still unclear. To help bridge these knowledge gaps, we developed the first ever recombinant strain of CyHV-2 expressing bioluminescent and fluorescent reporter genes. Infection of Carassius auratus hosts with this recombinant by immersion facilitated the exploitation of various in vivo imaging techniques to establish the spatiotemporal aspects of CyHV-2 replication at larval, juvenile, and adult developmental stages. While less susceptible than later developmental stages, larvae were most permissive to CyHV-2 replication, leading to rapid systemic infection and high mortality. Permissivity to CyHV-2 decreased with advancing development, with adults being the least permissive and, thus, also exhibiting the least mortality. Across all developmental stages, the skin was the most susceptible and permissive organ to infection at the earliest sampling points post-infection, indicating that it represents the major portal of entry into these hosts. Collectively these findings provide important fundamental insights into CyHV-2 pathogenesis and epidemiology in Carassius auratus with high relevance to other related economically important virus-host models.

WDR76 regulates 5-fluorouracil sensitivity in colon cancer via HRAS.

BACKGROUND: WD repeat domain 76 (WDR76) has been reported in multiple tumors, while without relation to chemotherapy resistance. 5-fluorouracil (5-FU) is widely adopted in treating colon cancer. However, the resistance of WDR76 and 5-FU in colon cancer remains unclear. METHODS: Limma package in R software was employed to analyze the differentially expressed genes. Western blot or quantitative real-time PCR (qRT-PCR) were run to assessed the gene expression. The cytotoxic effect was determined according to cell viability assay, colony formation assay in vitro. Cell apoptosis was assayed using flow cytometry. GSEA analysis was performed to identify pathways related to the target gene. Xenografted mice model was employed to evaluate the tumor growth. RESULTS: Bioinformatic analysis revealed the higher expression of WDR76 in 5-FU sensitive colon cancer cells compared to resistant colon cancer cells, accompanied by the decreased mRNA expression of WDR76 in 5-FU resistant colon cancer cells. The overexpressed WDR76 resulted in the apoptosis and the downregulated colony numbers in 5-FU resistant colon cancer cells, leading to the elevated sensitivity of 5-FU. Meanwhile, knockdown of WDR76 enhances the resistance of 5-FU in colon cancer both in vitro and vivo, which was reversed by a specific inhibitor of HRAS, Kobe006. An important molecular mechanism of 5-FU resistance lies the degradation of HRAS induced by WDR76. CONCLUSION: Our findings demonstrated a role of WDR76 as a promising target for reversing the resistance of colon cancer to 5-FU.

The co-occurrence network patterns and keystone species of microbial communities in cattle manure-corn straw composting.

Microbes often form complex ecological networks in various habitats. Co-occurrence network analysis allows exploring the complex community interactions beyond the community diversities. This study explores the interspecific relationships within and between bacterial and fungal communities during composting of cow manure using co-occurrence network analysis. Furthermore, the keystone taxa that potentially exert a considerable impact on the microbiome were revealed by network analysis. The networks in the present study harbored more positive links. Specifically, the interactions/coupling within bacterial communities was tighter and the response to changes in external environmental conditions was more quickly during the composting process, while the fungal network had a better buffer capacity for changes in external environmental conditions. Interestingly, this result was authenticated in the bacterial-fungal (BF) network and the Mantel test of major modules and environmental variables. More than that, the Zi-Pi plot revealed that the keystone taxa including "module hubs" and "connectors" were all detected in these networks, which could prevent the dissociation of modules and networks.

A fish herpesvirus highlights functional diversities among Zα domains related to phase separation induction and A-to-Z conversion.

Zalpha (Zα) domains bind to left-handed Z-DNA and Z-RNA. The Zα domain protein family includes cellular (ADAR1, ZBP1 and PKZ) and viral (vaccinia virus E3 and cyprinid herpesvirus 3 (CyHV-3) ORF112) proteins. We studied CyHV-3 ORF112, which contains an intrinsically disordered region and a Zα domain. Genome editing of CyHV-3 indicated that the expression of only the Zα domain of ORF112 was sufficient for normal viral replication in cell culture and virulence in carp. In contrast, its deletion was lethal for the virus. These observations revealed the potential of the CyHV-3 model as a unique platform to compare the exchangeability of Zα domains expressed alone in living cells. Attempts to rescue the ORF112 deletion by a broad spectrum of cellular, viral, and artificial Zα domains showed that only those expressing Z-binding activity, the capacity to induce liquid-liquid phase separation (LLPS), and A-to-Z conversion, could rescue viral replication. For the first time, this study reports the ability of some Zα domains to induce LLPS and supports the biological relevance of dsRNA A-to-Z conversion mediated by Zα domains. This study expands the functional diversity of Zα domains and stimulates new hypotheses concerning the mechanisms of action of proteins containing Zα domains.

Dimethyl phthalate inhibits the growth of Escherichia coli K-12 by regulating sugar transport and energy metabolism.

Dimethyl phthalate (DMP) is one of the most widely used plasticizers, and it is easily released into the environment, posing a threat to microbes. In this study, the impact of DMP on the uptake and metabolism of sugars in E. coli K-12 was assessed using proteomics, computational simulation analysis, transcriptome analysis, and sugar utilization experiments. DMP contamination inhibited the growth of E. coli K-12 and downregulated the expression of proteins in ATP-binding cassette (ABC) transporters and the phosphotransferase (PTS) system of E. coli K-12, which are primarily involved in the transmembrane transport of sugars. DMP formed a stable complex with sugar transporters and changed the rigidity and stability of the proteins. Furthermore, DMP treatment decreased the utilization of L-arabinose, glucose, D-xylose, and maltose. Moreover, carbon metabolism and oxidative phosphorylation were also downregulated by DMP. Our study shows that DMP reduces the uptake of sugars and ATP production and subsequently inhibits the growth of E. coli K-12.

Citric Acid in Rice Root Exudates Enhanced the Colonization and Plant Growth-Promoting Ability of Bacillus altitudinis LZP02.

Exploration of the underlying mechanisms of plant-microbe interactions is very important. In the present study, citric acid in the root exudates of rice significantly enhanced the colonization of Bacillus altitudinis LZP02 in the rhizosphere. According to the results of transcriptome and reverse transcription-quantitative PCR or analyses, citric acid increased the expression of several genes involved in bacterial chemotaxis and biofilm formation in B. altitudinis LZP02. In addition, citric acid also increased the expression of several genes associated with S-adenosylmethionine biosynthesis and metabolism. Interestingly, the secretion of citric acid by rice roots could be increased by inoculation with B. altitudinis LZP02. The result indicated that citric acid might be a vital signal in the interaction between rice and B. altitudinis LZP02. Further verification showed that citric acid enhanced the plant growth-promoting ability of B. altitudinis LZP02. IMPORTANCE In a previous study, the mechanism by which citric acid in rice root exudates enhanced the colonization of Bacillus altitudinis LZP02 was discovered. The present study verified that citric acid increased the recruitment and rice growth-promoting ability of B. altitudinis LZP02. These findings serve as an interesting case for explaining the underlying mechanisms of plant-microbe interactions. Henceforth, citric acid and B. altitudinis LZP02 could be exploited for the development of sustainable agronomy.

Dimethyl phthalate destroys the cell membrane structural integrity of Pseudomonas fluorescens.

A Gram-negative bacteria (Pseudomonas fluorescens) was exposed to different concentrations (0, 20, and 40 mg/L) of dimethyl phthalate (DMP) for 8 h, and then Fourier transform infrared spectroscopy (FTIR) analysis, lipopolysaccharide content detection, analysis of fatty acids, calcein release test, proteomics, non-targeted metabolomics, and enzyme activity assays were used to evaluate the toxicological effect of DMP on P. fluorescens. The results showed that DMP exposure caused an increase in the unsaturated fatty acid/saturated fatty acid (UFA/SFA) ratio and in the release of lipopolysaccharides (LPSs) from the cell outer membrane (OM) of P. fluorescens. Moreover, DMP regulated the abundances of phosphatidyl ethanolamine (PE) and phosphatidyl glycerol (PG) of P. fluorescens and induced dye leakage from an artificial membrane. Additionally, excessive reactive oxygen species (ROS), malondialdehyde (MDA), and changes in antioxidant enzymes (i.e., catalase [CAT] and superoxide dismutase [SOD]) activities, as well as the inhibition of Ca2+-Mg2+-ATPase and Na+/K+-ATPase activities in P. fluorescens, which were induced by the DMP. In summary, DMP could disrupt the lipid asymmetry of the outer membrane, increase the fluidity of the cell membrane, and destroy the integrity of the cell membrane of P. fluorescens through lipid peroxidation, oxidative stress, and ion imbalance.

Roles of Neuropeptides in Sleep-Wake Regulation.

Sleep and wakefulness are basic behavioral states that require coordination between several brain regions, and they involve multiple neurochemical systems, including neuropeptides. Neuropeptides are a group of peptides produced by neurons and neuroendocrine cells of the central nervous system. Like traditional neurotransmitters, neuropeptides can bind to specific surface receptors and subsequently regulate neuronal activities. For example, orexin is a crucial component for the maintenance of wakefulness and the suppression of rapid eye movement (REM) sleep. In addition to orexin, melanin-concentrating hormone, and galanin may promote REM sleep. These results suggest that neuropeptides play an important role in sleep-wake regulation. These neuropeptides can be divided into three categories according to their effects on sleep-wake behaviors in rodents and humans. (i) Galanin, melanin-concentrating hormone, and vasoactive intestinal polypeptide are sleep-promoting peptides. It is also noticeable that vasoactive intestinal polypeptide particularly increases REM sleep. (ii) Orexin and neuropeptide S have been shown to induce wakefulness. (iii) Neuropeptide Y and substance P may have a bidirectional function as they can produce both arousal and sleep-inducing effects. This review will introduce the distribution of various neuropeptides in the brain and summarize the roles of different neuropeptides in sleep-wake regulation. We aim to lay the foundation for future studies to uncover the mechanisms that underlie the initiation, maintenance, and end of sleep-wake states.

Maize (Zea mays L.) genotypes induce the changes of rhizosphere microbial communities.

Plant-microbe interactions affect ecosystem function, and plant species influence relevant microorganisms. However, the different genotypes of maize that shape the structure and function of the rhizosphere microbial community remain poorly investigated. During this study, the structures of the rhizosphere microbial community among three genotypes of maize were analyzed at the seedling and maturity stages using high-throughput sequencing and bioinformatics analysis. The results demonstrated that Tiannuozao 60 (N) showed higher bacterial and fungal diversity in both periods, while Junlong1217 (QZ) and Fujitai519 (ZL) had lower diversity. The bacterial community structure among the three varieties was significantly different; however, fewer differences were found in the fungal community. The bacterial community composition of N and QZ was similar yet different from ZL at the seedling stage. The bacterial networks of the three cultivars were more complex than the fungal networks, and the networks of the mature stages were more complex than those of the seedling stages, while the opposite was true for the fungi. FAPROTAX functional and FUNGuild functional predictions revealed that different varieties of maize were different in functional abundance at the genus level, and these differences were related to breeding characteristics. This study suggested that different maize genotypes regulated the rhizosphere bacterial and fungal communities, which would help guide practices.

An Improved Chemotaxis Assay for the Rapid Identification of Rhizobacterial Chemoattractants in Root Exudates.

Chemotaxis identification is very important for the research and application of rhizosphere growth-promoting bacteria. We established a straightforward method to quickly identify the chemoattractants that could induce the chemotactic movement of rhizosphere growth-promoting bacteria on sterile glass slides via simple steps. Bacteria solution (OD600 = 0.5) and sterile chemoattractant aqueous solution were added dropwise on the glass slide at an interval of 1 cm. An inoculating loop was used to connect the chemoattractant aqueous solution to the bacterial solution. The slide was kept at room temperature for 20 min on the clean bench. Finally, the chemoattractant aqueous solution was collected for bacterial counting and microscopic observation. In this study, through multiple comparisons of experimental results, the method overcame multiple shortcomings of traditional bacterial chemotaxis methods. The method reduced the error of plate counting and shortened the experimental cycle. For the identification of chemoattractant substances, this new method can save 2-3 days compared to the traditional method. Additionally, this method allows any researcher to systematically complete a bacterial chemotaxis experiment within 1-2 days. The protocol can be considered a valuable resource for understanding plant-microbe interactions.