Gut symbionts alleviate MASH through a secondary bile acid biosynthetic pathway.

The gut microbiota has been found to play an important role in the progression of metabolic dysfunction-associated steatohepatitis (MASH), but the mechanisms have not been established. Here, by developing a click-chemistry-based enrichment strategy, we identified several microbial-derived bile acids, including the previously uncharacterized 3-succinylated cholic acid (3-sucCA), which is negatively correlated with liver damage in patients with liver-tissue-biopsy-proven metabolic dysfunction-associated fatty liver disease (MAFLD). By screening human bacterial isolates, we identified Bacteroides uniformis strains as effective producers of 3-sucCA both in vitro and in vivo. By activity-based protein purification and identification, we identified an enzyme annotated as ß-lactamase in B. uniformis responsible for 3-sucCA biosynthesis. Furthermore, we found that 3-sucCA is a lumen-restricted metabolite and alleviates MASH by promoting the growth of Akkermansia muciniphila. Together, our data offer new insights into the gut microbiota-liver axis that may be leveraged to augment the management of MASH.

Trojan horselike T6SS effector TepC mediates both interference competition and exploitative competition.

The type VI secretion system (T6SS) is a bacterial weapon capable of delivering antibacterial effectors to kill competing cells for interference competition, as well as secreting metal ion scavenging effectors to acquire essential micronutrients for exploitation competition. However, no T6SS effectors that can mediate both interference competition and exploitation competition have been reported. In this study, we identified a unique T6SS-1 effector in Yersinia pseudotuberculosis named TepC, which plays versatile roles in microbial communities. First, secreted TepC acts as a proteinaceous siderophore that binds to iron and mediates exploitative competition. Additionally, we discovered that TepC has DNase activity, which gives it both contact-dependent and contact-independent interference competition abilities. In conditions where iron is limited, the iron-loaded TepC is taken up by target cells expressing the outer membrane receptor TdsR. For kin cells encoding the cognate immunity protein TipC, TepC facilitates iron acquisition, and its toxic effects are neutralized. On the other hand, nonkin cells lacking TipC are enticed to uptake TepC and are killed by its DNase activity. Therefore, we have uncovered a T6SS effector, TepC, that functions like a "Trojan horse" by binding to iron ions to provide a valuable resource to kin cells, whereas punishing cheaters that do not produce public goods. This lure-to-kill mechanism, mediated by a bifunctional T6SS effector, may offer new insights into the molecular mechanisms that maintain stability in microbial communities.

Distinct roles of the two SEC scaffold proteins, AFF1 and AFF4, in regulating RNA Pol II transcription elongation.

The super elongation complex (SEC) containing P-TEFb plays a critical role in regulating transcription elongation. AFF1 and AFF4, members of the AF4/FMR2 family, act as central scaffold proteins of SEC and are associated with various human diseases. However, their precise roles in transcriptional control remain unclear. We here reveal differences in the genomic distribution patterns of AFF1 and AFF4 around transcription start sites (TSSs). AFF1 mainly binds upstream of the TSSs, while AFF4 is enriched downstream of the TSSs. Notably, disruption of AFF4 results in slow elongation and early termination in a subset of AFF4 bound active genes, whereas AFF1 deletion leads to fast elongation and transcriptional readthrough in the same gene subset. Additionally, AFF1 knockdown increases AFF4 levels at chromatin, and vice versa. In summary, these findings demonstrate that AFF1 and AFF4 function antagonistically to regulate Pol II transcription.

The super elongation complex (SEC) mediates phase transition of SPT5 during transcriptional pause release.

Release of promoter-proximally paused RNA Pol II into elongation is a tightly regulated and rate-limiting step in metazoan gene transcription. However, the biophysical mechanism underlying pause release remains unclear. Here, we demonstrate that the pausing and elongation regulator SPT5 undergoes phase transition during transcriptional pause release. SPT5 per se is prone to form clusters. The disordered domain in SPT5 is required for pause release and gene activation. During early elongation, the super elongation complex (SEC) induces SPT5 transition into elongation droplets. Depletion of SEC increases SPT5 pausing clusters. Furthermore, disease-associated SEC mutations impair phase properties of elongation droplets and transcription. Our study suggests that SEC-mediated SPT5 phase transition might be essential for pause release and early elongation and that aberrant phase properties could contribute to transcription abnormality in diseases.

Identification of volatile organic compounds in muscle tissues of different species based on Headspace-Gas-Chromatography Ion-Mobility spectrometry.

Species identification of unknown biological samples is crucial for forensic applications, especially in cases of explosion, disaster accidents, and body mutilation after murdering, as well as poaching, illegal trade in endangered animals, and meat food fraud. In this study, we identified 60 volatile organic compounds (VOCs) in fresh skeletal muscle tissues of seven different animal species (cattle, sheep, pigs, rabbits, rats, chickens and carp) and a human dead body by headspace-gas-chromatography ion-mobility spectrometry (HS-GC-IMS), and compared their differences by retention time, drift time and molecular weight. The results showed that these VOCs formed different gallery plot fingerprints in the skeletal muscle tissues of the human dead body and seven animal species. Principal component analysis (PCA) showed significantly different fingerprints between these species, and these fingerprints maintained good stability between the species and within the same species. Some VOCs have high species specificity, while VOCs of human fresh muscle tissues from different individual sources have little difference, demonstrating that all tested muscle tissue samples could be distinguished based on different VOCs. HS-GC-IMS has proved to be a rapid, high-throughput, highly sensitive and specific species identification method, which can be used for forensic species identification in criminal cases and disaster accidents, as well as detection in the field of food safety, such as meat fraud and adulteration.

Phase Separation Properties in Transcriptional Organization.

Transcription is of great importance to stress response, fate control, and development, involving the functional cooperation of a large number of transcription factors and cofactors. Transcription machineries assemble rapidly to respond to the physiological and functional needs of cells. Recently, phase-separated biomolecular condensates have emerged as a universal biophysical basis for the spatiotemporal coordination of various cellular activities, including transcription. Here, we summarize and discuss recent advances in understanding of how phase separation contributes to RNA polymerase II (Pol II)-mediated transcriptional regulation, with a focus on the physical properties and dynamics of transcriptional condensates.

Risk factors for infection complications after transrectal ultrasound-guided transperineal prostate biopsy.

BACKGROUND: To investigate the influence factors of infection complications of transrectal ultrasound-guided transperineal prostate biopsy. METHODS: A total of 2192 patients who underwent prostate biopsy under transperineal prostate biopsy were analyzed retrospectively from December 2010 to May 2020.We collected the clinical characteristics and the incidence of complications, and used univariate and multivariate logistic regression analyses to analyze independent risk factors for infection complications after transperineal prostate biopsy. RESULTS: Univariate analysis showed that the following factors were associated with the infection complications: diabetes, bacterial prostatitis, history of urinary retention, history of urinary infection, and number of cores. Furthermore, multivariate logistic analysis revealed that diabetes (OR 2.037, 95% CI 1.143-3.572, P = 0.021) and history of urinary retention (OR 2.563, 95% CI 1.284-3.901, P = 0.013) were independent risk factors for infection complications after transperineal prostate biopsy. CONCLUSIONS: Patients with diabetes and history of urinary retention were more likely to have infection complications after transperineal prostate biopsy.

The application of a targeted periprostatic nerve block in transperineal template-guided prostate biopsies.

BACKGROUND: Our study aims to evaluate the anesthetic efficacy of multiparametric magnetic resonance imaging/transrectal ultrasound (mpMRI/TRUS) fusion-guided targeted periprostatic nerve block (PNB) for transperineal template-guided prostate biopsy (TTPB). METHODS: The patients who underwent mpMRI/TRUS fusion-guided prostate biopsy from May 2018 to March 2019 were randomized into two groups using a random number table. The intervention group (n=47) and the control group (n=45) received targeted PNB and traditional PNB, respectively. Visual analog scale (VAS) and visual numeric scale (VNS) scores were used to assess the patients' pain and quantify their satisfaction. RESULTS: The total detection rate for prostate cancer was 45.7%, with a comparable positive rate between the intervention group (42.6%) and the control group (48.9%), which meant there was no significant difference between the groups (P=0.542). Patient age, prostate-specific antigen, prostate volume, suspicious lesions on mpMRI, number of cores, operation time, and biopsy time were comparable between the groups. The VAS scores during biopsy were significantly lower in the intervention group than in the control group [2 (1 to 3) vs. 2 (1 to 4), P=0.019]. Conversely, the VNS scores during biopsy were higher in the intervention group [3 (2 to 4) vs. 3 (2 to 3), P=0.015]. There were no significant differences in the pain scores or the satisfaction scores at 30 min after the procedure between the two groups. There were no significant differences between the groups for complications, such as hematuria, urinary retention, infection, hemospermia, and vasovagal reaction (P>0.05). CONCLUSIONS: Targeted PNB significantly relieved the pain and did not increase the incidence of complications for patients when compared with traditional PNB.

RNF219 interacts with CCR4-NOT in regulating stem cell differentiation.

Regulation of RNA stability plays a crucial role in gene expression control. Deadenylation is the initial rate-limiting step for the majority of RNA decay events. Here, we show that RING finger protein 219 (RNF219) interacts with the CCR4-NOT deadenylase complex. RNF219-CCR4-NOT exhibits deadenylation activity in vitro. RNA-seq analyses identify some of the 2-cell-specific genes and the neuronal genes significantly downregulated upon RNF219 knockdown, while upregulated after depletion of the CCR4-NOT subunit CNOT10 in mouse embryonic stem (ES) cells. RNF219 depletion leads to impaired neuronal lineage commitment during ES cell differentiation. Our study suggests that RNF219 is a novel interacting partner of CCR4-NOT and required for maintenance of ES cell pluripotency.

ENL initiates multivalent phase separation of the super elongation complex (SEC) in controlling rapid transcriptional activation.

Release of paused RNA polymerase II (Pol II) requires incorporation of the positive transcription elongation factor b (P-TEFb) into the super elongation complex (SEC), thus resulting in rapid yet synchronous transcriptional activation. However, the mechanism underlying dynamic transition of P-TEFb from inactive to active state remains unclear. Here, we found that the SEC components are able to compartmentalize and concentrate P-TEFb via liquid-liquid phase separation from the soluble inactive HEXIM1 containing the P-TEFb complex. Specifically, ENL or its intrinsically disordered region is sufficient to initiate the liquid droplet formation of SEC. AFF4 functions together with ENL in fluidizing SEC droplets. SEC droplets are fast and dynamically formed upon serum exposure and required for rapid transcriptional induction. We also found that the fusion of ENL with MLL can boost SEC phase separation. In summary, our results suggest a critical role of multivalent phase separation of SEC in controlling transcriptional pause release.

Association analysis of CHRNA3 polymorphisms with schizophrenia in a Chinese Han population: A case-control study.

Schizophrenia (SCZ) is a highly heritable, chronic, severe psychiatric disorder associated with significant financial costs to families and societies. In this case-control study, we investigated the associations between seven SNPs in CHRNA3 gene and the risk of SCZ.A total of 1071 (384 cases and 687 controls) unrelated subjects were recruited for our association study. Seven candidate tagging SNPs in CHRNA3 gene (rs3743077, rs1317286, rs938682, rs12914385, rs2869546, rs3743075, rs8040868) selected in HapMap database were genotyped by Sequenom MassARRAY. Finally, association analysis was conducted under various models.According to our results, in genetic model analysis, rs12914385 and rs8040868 are associated with decreased risk of SCZ in female subgroup; rs3743075 is associated with decreased risk of SCZ in subgroup with age <45; while rs3743077 and rs2869546 are associated with increased risk of SCZ. Haplotype analysis suggested that the 3 variants comprised 1 block, and that the haplotype Ars938682Crs12914385Crs2869546 was significantly correlated with an increased risk of SCZ in the subgroup with age ≥45.Our data indicate potential associations between CHRNA3polymorphisms and SCZ susceptibility, and the significant variants identified in our study may be used as genetic biomarkers for SCZ susceptibility in Chinese Han population.

Genetic polymorphisms in very important pharmacogenomic variants in the Zhuang ethnic group of Southwestern China: A cohort study in the Zhuang population.

Pharmacogenomics, the study of the role of genetics in drug response, has recently become a focal point of research. Previous studies showed that genes associated with drug detoxification vary among different populations. However, pharmacogenomic information of the Zhuang ethnic group is scarce. The aim of the present study was to screen members of the Zhuang ethnicity in southwestern China for genotype frequencies of very important pharmacogenomic (VIP) variants and to determine the differences between the Zhuang ethnicity and other human populations.We genotyped 80 variants of VIP genes in 100 unrelated healthy Zhuang adults from the Yunnan province of China. Next, we analyzed the genotyping data with Structure and F-statistics (Fst).We compared our data with those of other populations using the HapMap data set, and observed that the frequency distribution of Zhuang population in Yunnan closely resembles that of JPT. Furthermore, population structure and Fst analysis showed that the Zhuang population is closely related to the Shaanxi Han population with respect to genetic background.Our study supplements existing information on Zhuang population pharmacogenomics and provides an extensive overview for developing personalized medicine.

Feedback between E2F1 and CIP2A regulated by human papillomavirus E7 in cervical cancer: implications for prognosis.

Previously, we found that cancerous inhibitor of protein phosphatase 2A (CIP2A) plays a key role in the malignant transformation of cervical cancer. Here, we further explore whether and how CIP2A is regulated by human papillomavirus E7 (HPV E7) and the prognostic value of CIP2A in cervical cancer. We demonstrated a positive feedback loop between the E2F transcription factor 1 (E2F1) and CIP2A at the transcription level in HeLa and SiHa cells by real-time PCR and western blot analysis. The feedback, regulated by HPV E7, was further confirmed by their sub-cellular co-expression seen on immunofluorescence and immunohistochemistry staining in vitro and in vivo. Moreover, CIP2A and E2F1 expression was greatly elevated in human cervical cancer tissue. CIP2A expression was tightly associated with tumor size, depth of invasion and lymph node metastasis in 184 cases of cervical cancer. Kaplan-Meier and Cox proportional-hazards regression analyses revealed poor overall and disease-free survival of patients with CIP2A-E2F1 co-expression, and high CIP2A-E2F1 co-expression was an independent risk factor for overall survival of patients. Therefore, CIP2A-E2F1 expression might be a valuable indicator to predict outcome and guide personal treatment in cervical cancer.

TRPA1 in the spinal dorsal horn is involved in post-inflammatory visceral hypersensitivity: in vivo study using TNBS-treated rat model.

INTRODUCTION: The transient receptor potential ankyrin-1 (TRPA1) channel, a pain transducer and amplifier, is drawing increasing attention in the field of visceral hypersensitivity, commonly seen in irritable bowel syndrome and inflammatory bowel disease. However, the role of TRPA1 in visceral nociception during post-inflammatory states is not well defined. Here, we explore the correlation between TRPA1 expression in the spinal dorsal horn (SDH) and persistent post-inflammatory visceral hypersensitivity. METHODS: We injected rats intracolonically with 2,4,6-trinitrobenzene sulfonic acid (TNBS) or vehicle (n=12 per group). Post-inflammatory visceral hypersensitivity was assessed by recording the electromyographic activity of the external oblique muscle in response to colorectal distension. TRPA1 expression and distribution in the spinal cord and colon were examined by Western blotting and immunohistochemistry. RESULTS: Animals exposed to TNBS had more abdominal contractions than vehicle-injected controls (P<0.05), which corresponded to a lower nociceptive threshold. Expression of TRPA1 in the SDH (especially in the substantia gelatinosa) and the colon was significantly greater in the TNBS-treated group than in controls (P<0.05). In the SDH, the number of TRPA1-immunopositive neurons was 25.75±5.12 in the control group and 34.25±7.89 in the TNBS-treated group (P=0.023), and integrated optical density values of TRPA1 in the control and TNBS-treated groups were 14,544.63±6,525.54 and 22,532.75±7,608.11, respectively (P=0.041). CONCLUSION: Our results indicate that upregulation of TRPA1 expression in the SDH is associated with persistent post-inflammatory visceral hypersensitivity in the rat and provides insight into potential therapeutic targets for the control of persistent visceral hypersensitivity.

Global Transcriptomic Analysis of the Response of Corynebacterium glutamicum to Vanillin.

Lignocellulosic biomass is an abundant and renewable resource for biofuels and bio-based chemicals. Vanillin is one of the major phenolic inhibitors in biomass production using lignocellulose. To assess the response of Corynebacterium glutamicum to vanillin stress, we performed a global transcriptional response analysis. The transcriptional data showed that the vanillin stress not only affected the genes involved in degradation of vanillin, but also differentially regulated several genes related to the stress response, ribosome/translation, protein secretion, and the cell envelope. Moreover, deletion of the sigH or msrA gene in C. glutamicum resulted in a decrease in cell viability under vanillin stress. These insights will promote further engineering of model industrial strains, with enhanced tolerance or degradation ability to vanillin to enable suitable production of biofuels and bio-based chemicals from lignocellulosic biomass.

The icmF3 locus is involved in multiple adaptation- and virulence-related characteristics in Pseudomonas aeruginosa PAO1.

The type VI secretion system (T6SS) is widely distributed in Gram-negative bacteria. Three separate T6SSs called H1-, H2-, and H3-T6SS have been discovered in Pseudomonas aeruginosa PAO1. Recent studies suggest that, in contrast to the H1-T6SS that targets prokaryotic cells, H2- and H3-T6SS are involved in interactions with both prokaryotic and eukaryotic cells. However, the detailed functions of T6SS components are still uncharacterized. The intracellular multiplication factor (IcmF) protein is conserved in type VI secretion systems (T6SS) of all different bacterial pathogens. Bioinformatic analysis revealed that IcmF3 in P. aeruginosa PAO1 is different from other IcmF homologs and may represent a new branch of these proteins with distinct functions. Herein, we have investigated the function of IcmF3 in this strain. We have shown that deletion of the icmF3 gene in P. aeruginosa PAO1 is associated with pleiotropic phenotypes. The icmF3 mutant has variant colony morphology and an hypergrowth phenotype in iron-limiting medium. Surprisingly, this mutant is also defective for the production of pyoverdine, as well as defects in swimming motility and virulence in a C. elegans worm model. The icmF3 mutant exhibits higher conjugation frequency than the wild type and increased biofilm formation on abiotic surfaces. Additionally, expression of two phenazine biosynthetic loci is increased in the icmF3 mutant, leading to the overproduction of pyocyanin. Finally, the mutant exhibits decreased susceptibility to aminoglycosides such as tobramycin and gentamicin. And the detected phenotypes can be restored completely or partially by trans complementation of wild type icmF3 gene. The pleiotropic effects observed upon icmF3 deletion demonstrate that icmF3 plays critical roles in both pathogenesis and environmental adaptation in P. aeruginosa PAO1.

Radiographic morphology of fallopian tubes in women of child-bearing potential: a descriptive study.

AIM: The aim of this study was to determine the radiographic morphological characteristics of fallopian tubes in women of child-bearing age. MATERIAL AND METHODS: From 2007 to 2008 we retrospectively collected records from women aged 19-45 years undergoing fertility evaluation who had normal salpingograms. Women were excluded if they had abnormal imaging on salpingogram, ultrasound, or hysteroscopy, and if they had any history of pelvic disease or pathology, were febrile, or were taking oral contraceptives at the time of the salpingogram. RESULTS: We analyzed the salpingograms from 100 women. The interstitial portion of the tube is funnel-shaped. The mean diameter of the proximal tubal opening was 1.07 ± 0.43 mm. The mean length of the interstitial portion was 5.27 ± 4.28 mm, and the mean internal diameters of the middle and distal segments of the interstitial portion were 0.50 ± 0.22 mm and 0.32 ± 0.12 mm, respectively. The narrowest part of the fallopian tube was the distal segment of the interstitial portion, which is significantly different from the internal diameter of the isthmus (0.46 ± 0.28 mm) (P < 0.01). CONCLUSIONS: This study provides detailed data of the normal fallopian tube that may be of value in the development of new contraceptive agents, as well as infertility treatments.

Soluble mediators released from PI-IBS patients' colon induced alteration of mast cell: involvement of reactive oxygen species.

BACKGROUND: Growing evidence suggests that patients with post-infectious irritable bowel syndrome (PI-IBS) have increased mast cell activation, and that mucosal soluble mediators are involved in the pathophysiology of visceral hyperalgesia. In addition, previous findings show that reactive oxygen species (ROS) and protease-activated receptors (PARs) are mediators of persistent hyperalgesia. AIMS: This article aims to investigate: (1) the ability of soluble factors from colonic biopsies to active peritoneal mast cells (PMCs) in vitro; (2) whether the effects of PMCs degranulation induced by soluble mediators are related to PARs activation; and (3) the ability of phenyl N-tert-butylnitrone (PBN), a ROS scavenger, to modify these alterations. METHODS: Supernatant (SUP) from colonic biopsies was collected and applied to PMCs for 12 h. Activation of PMCs was evaluated. The expression of PAR(2) in PMCs was examined by RT-PCR and double-immunofluorescence staining. PBN (10 mM) treatment was administered, then previous alterations were observed again. RESULTS: Stimulation with SUP of PI-IBS led to an increase in activation of PMCs. PAR(2)mRNA expression was significantly increased in PMCs induced by SUP of PI-IBS compared to healthy subjects. After being treated by PBN, the SUP-induced enhancement of PMCs activities could be weakened, and PAR(2)mRNA expression was significantly decreased. A similar result of immunoreactivity for PAR(2) was observed in PMCs. CONCLUSIONS: The study shows that ROS scavenger reverses the SUP of PI-IBS-induced enhancement of PMCs activities, and that these effects may be related to activation of PAR(2). These findings might pave the way to new therapeutic targets in PI-IBS.

Relationship between dental erosion and respiratory symptoms in patients with gastro-oesophageal reflux disease.

OBJECTIVES: Both dental erosion and respiratory symptoms are extra-oesophageal manifestations of gastro-oesophageal reflux disease (GERD). The aim of this study was to determine whether dental erosion was correlated with respiratory symptoms in GERD patients. METHODS: 88 GERD patients were recruited and assigned to three groups mainly according to the frequency of respiratory symptoms: Group I: never; Group II: occasional (1-2 days a week or less); Group III: frequent (3-5 days a week or more). All patients underwent medical evaluations, including medical history, questionnaire answering and alimentary tract examinations. Dental examinations were carried out on these patients and 36 healthy controls. Dental erosions were measured by modified method of Smith and Knight Tooth Wear Index (TWI). Location and severity of dental erosion were recorded. RESULTS: The prevalence of dental erosion in Group III (64.52%) was higher (p<0.05) than that in Groups I (36.67%) and II (44.44%). GERD patients were presented with dental erosion with TWI scores ranging from 1 to 4. Though proportion of dental erosion with Score 2 (7/20) in Group III was higher than that in Group I (2/11) and Group II (3/12), there was no statistical significance in the proportions of erosion scores among three patient groups. Correlation coefficient between airway symptoms and scores of dental erosion was 0.231 (p<0.05). Palatal erosion of upper incisor was seen in 8 persons (72.7%) in Group I, 9 persons (75%) in Group II and 16 persons (80%) in Group III (p>0.05). Labial erosion of upper incisors was found in 1 person in Groups I and II respectively and 4 persons in Group III. All patients with labial erosion on upper incisors had palatal erosion, except 1 patient in Group III. CONCLUSIONS: In GERD patients, dental erosions are more prevalent in patients with frequent respiratory symptoms than those in patients with occasional and without respiratory symptoms. Palatal erosion of upper incisor is the main manifestation in patients. Acid reflux is the main causative factor of dental erosion in GERD patients with airway symptoms.