The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity.

The RNA modification N6-methyladenosine (m6A) has critical roles in many biological processes1,2. However, the function of m6A in the early phase of mammalian development remains poorly understood. Here we show that the m6A reader YT521-B homology-domain-containing protein 1 (YTHDC1) is required for the maintenance of mouse embryonic stem (ES) cells in an m6A-dependent manner, and that its deletion initiates cellular reprogramming to a 2C-like state. Mechanistically, YTHDC1 binds to the transcripts of retrotransposons (such as intracisternal A particles, ERVK and LINE1) in mouse ES cells and its depletion results in the reactivation of these silenced retrotransposons, accompanied by a global decrease in SETDB1-mediated trimethylation at lysine 9 of histone H3 (H3K9me3). We further demonstrate that YTHDC1 and its target m6A RNAs act upstream of SETDB1 to repress retrotransposons and Dux, the master inducer of the two-cell stage (2C)-like program. This study reveals an essential role for m6A RNA and YTHDC1 in chromatin modification and retrotransposon repression.

Systematic calibration of epitranscriptomic maps using a synthetic modification-free RNA library.

Recent years have witnessed rapid progress in the field of epitranscriptomics. Functional interpretation of the epitranscriptome relies on sequencing technologies that determine the location and stoichiometry of various RNA modifications. However, contradictory results have been reported among studies, bringing the biological impacts of certain RNA modifications into doubt. Here, we develop a synthetic RNA library resembling the endogenous transcriptome but without any RNA modification. By incorporating this modification-free RNA library into established mapping techniques as a negative control, we reveal abundant false positives resulting from sequence bias or RNA structure. After calibration, precise and quantitative mapping expands the understanding of two representative modification types, N6-methyladenosine (m6A) and 5-methylcytosine (m5C). We propose that this approach provides a systematic solution for the calibration of various RNA-modification mappings and holds great promise in epitranscriptomic studies.

External Validation of the Assessment of Different NEoplasias in the adneXa Model Performance in Evaluating the Risk of Ovarian Carcinoma Before Surgery in China: A Tertiary Center Study.

OBJECTIVES: The Assessment of Different NEoplasias in the adneXa (ADNEX) model was developed by the International Ovarian Tumor Analysis group to assess the risk of an ovarian mass being malignant. This study aimed to externally validate the ADNEX model performance in a tertiary center in China. METHODS: This retrospective, single-center university hospital study assessed the model diagnostic accuracy. All patients were examined by transvaginal ultrasonography, and serum CA125 levels were measured. Moreover, clinicopathological information was collected. The diagnostic performance of the ADNEX model was calculated with and without CA125 as a predictor. RESULTS: We retrieved data of 335 patients, of which 53 were excluded based on the exclusion criteria. Of the included 282 patients, 178 (63.1%) had benign tumors, and 104 (36.9%) had malignant tumors. When CA125 was factored in, the area under the receiver operating characteristic curve (AUC) for the distinction between benign and malignant tumors was 0.93 (95% confidence interval [CI], 0.90-0.96), whereas it was 0.91 (95% CI, 0.88-0.95) without CA125. The concordance between the predicted risk of malignancy and the proportion of observed malignancies was well demonstrated by the calibration plots. CONCLUSIONS: The proper performance of the ADNEX model was verified externally in a tertiary center in China, showing a good distinction between tumour subtypes. Our findings suggest the ADNEX model is a valuable tool in clinical practice and may help in managing patients with adnexal masses.

The Diagnostic Value of Multi-Index Combined Detection in Patients with COVID-19.

BACKGROUND: To investigate the clinical value of multi-index combined detection in the diagnosis of new coronavirus disease 2019 (COVID-19). METHODS: A total of 63 laboratory confirmed patients treated in our hospital were selected as the COVID-19 group, including 28 severe patients and 35 non-severe patients. Another 50 healthy subjects undergoing physical examination simultaneously were selected as the healthy group. Here we performed a study on the laboratory characteristics and explored their efficacy for diagnosis of the disease. RESULTS: Compared with healthy people, the abnormal indicators of patients with COVID-19 are low levels of lymphocytes (LYM), red blood cells (RBC), hemoglobin (HGB), platelets (PLT), total protein (TP), and albumin (ALB), and high levels of monocytes (MON), aspartate aminotransferase (AST), gamma glutamyl transpeptidase (GGT), and C-reactive protein (CRP). The level of MON and CRP in severe patients were significantly increased compared with non-severe pneumonia patients, and indicators such as LYM and ALB were significantly reduced (p < 0.05). The sensitivity and specificity of the combined detection of LYM, MON, RBC, HGB, PLT, TP, ALB, AST, GGT, and CRP was 97.7% and 91.7%, which was higher than the single item (p < 0.05). The sensitivity and specificity of combined detection of LYM, MON, ALB, and CRP to predict the severity of COVID-19 were 96.4% and 73.0%, which were higher than those of separate detections (p < 0.05). CONCLUSIONS: The index of LYM, MON, RBC, HGB, PLT, TP, ALB, AST, GGT, and CRP can be used for the diagnosis of new COVID-19, and the indicators of LYM, MON, ALB, and CRP may be predictors of severe pneumonia. The combined detection of the laboratory indexes can diagnose COVID-19 and predict the severity more effectively and accurately.

Locating multiple information sources in social networks based on the naming game.

Identifying the source of information in a network plays a key role in controlling the impact of information. Herein, we study the problem of multiple source localization in the context of information propagation in social networks. We use the theory of the naming game to conduct observations. Moreover, we divide the observations into different sets based on the information provided by them and then estimate the source of each set. Finally, we combine the source of each observation set to obtain all the estimated information sources. The proposed method can locate sources without knowing the number of information sources. Simulations on four real data sets are provided to verify the performance of our method.

Recommending Queries by Extracting Thematic Experiences from Complex Search Tasks.

Since complex search tasks are usually divided into subtasks, providing subtask-oriented query recommendations is an effective way to support complex search tasks. Currently, most subtask-oriented query recommendation methods extract subtasks from plain form search logs consisting of only queries and clicks, providing limited clues to identify subtasks. Meanwhile, for several decades, the Computer Human Interface (CHI)/Human Computer Interaction (HCI) communities have been working on new complex search tools for the purpose of supporting rich user interactions beyond just queries and clicks, and thus providing rich form search logs with more clues for subtask identification. In this paper, we researched the provision of subtask-oriented query recommendations by extracting thematic experiences from the rich form search logs of complex search tasks logged in a proposed visual data structure. We introduce the tree structure of the visual data structure and propose a visual-based subtask identification method based on the visual data structure. We then introduce a personalized PageRank-based method to recommend queries by ranking nodes on the network from the identified subtasks. We evaluated the proposed methods in experiments consisting of informative and tentative search tasks.

Ultra pressure liquid chromatography-negative electrospray ionization mass spectrometry determination of twelve halobenzoquinones at ng/L levels in drinking water.

We report here the characterization of twelve halobenzoquinones (HBQs) using electrospray ionization (ESI) high resolution quadrupole time-of-flight mass spectrometry. The high resolution negative ESI spectra of the twelve HBQs formed two parent ions, [M + H(+) + 2e(-)], and the radical M(-•). The intensities of these two parent ions are dependent on their chemical structures and on instrumental parameters such as the source temperature and flow rate. The characteristic ions of the HBQs were used to develop an ultra pressure liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) method. At the UPLC flow rate (400 µL/min) and under the optimized ESI conditions, eleven HBQs showed the stable and abundant transitions [M + H(+) + 2e(-)] → X(-) (X(-) representing Cl(-), Br(-), or I(-)), while dibromo-dimethyl-benzoquinone (DBDMBQ) showed only the transition of M(-•) → Br(-). The UPLC efficiently separates all HBQs including some HBQ isomers, while the MS/MS offers exquisite limits of detection (LODs) at subng/mL levels for all HBQs except DBDMBQ. Combined with solid phase extraction (SPE), the method LOD is down to ng/L. The results from analysis of authentic samples demonstrated that the SPE-UPLC-MS/MS method is reliable, fast, and sensitive for the identification and quantification of the twelve HBQs in drinking water.

Overexpression of LILRA2 indicated poor prognosis of ovarian carcinoma: A new potential biomarker and therapeutic target.

OBJECTIVE: This study aimed to assess the role of leukocyte immunoglobulin-like receptor A2 (LILRA2) in ovarian carcinoma (OC) oncogenesis and prognosis. MATERIALS AND METHODS: Using the Cancer Genome Atlas, Genotype-Tissue Expression, and Gene Expression Omnibus databases, the association between clinicopathological profiles and LILRA2 expression was investigated using logistic regression analysis. Kaplan-Meier analysis, Cox regression analysis, and column plots predicted the clinical outcomes of patients with OC and determine the predictive value of LILRA2. The biological functions of LILRA2 were assessed using Gene Ontology and Kyoto Encyclopedia of Genes and Genomes analyses. We used single-sample Gene Set Enrichment Analysis to investigate the relationship between immune cell infiltration and LILRA2 expression. RESULTS: LILRA2 expression in OC tumors was significantly higher than in normal tissue (P < 0.05). The high LILRA2 expression in OC was correlated with lymphatic invasion (P = 0.014). The results showed consistency indices of 0.611 [95% confidence interval (CI), 0.572-0.649] and 0.623 (95% CI, 0.584-0.663) for the overall and disease-specific survival nomograms, respectively. Cox regression analysis showed that LILRA2 was an independent risk factor for overall survival (hazard ratio [HR], 1.511; P = 0.002) and disease-specific survival (HR, 1.537; P = 0.003). Functional annotation revealed enrichment with immunoglobulin-corresponding pathways when LILRA2 expression was high. CONCLUSION: By evaluating gene expression profiles, we demonstrated that LILRA2 has considerable potential to act as a therapeutic target and prognostic biomarker in OC.

Identification of ferroptosis-related genes in type 2 diabetes mellitus based on machine learning.

BACKGROUND: Type 2 diabetes mellitus (T2DM), which has a high incidence and several harmful consequences, poses a severe danger to human health. Research on the function of ferroptosis in T2DM is increasing. This study uses bioinformatics techniques identify new diagnostic T2DM biomarkers associated with ferroptosis. METHODS: To identify ferroptosis-related genes (FRGs) that are differentially expressed between T2DM patients and healthy individuals, we first obtained T2DM sequencing data and FRGs from the Gene Expression Omnibus (GEO) database and FerrDb database. Then, drug-gene interaction networks and competitive endogenous RNA (ceRNA) networks linked to the marker genes were built after marker genes were filtered by two machine learning algorithms (LASSO and SVM-RFE algorithms). Finally, to confirm the expression of marker genes, the GSE76895 dataset was utilized. The protein and RNA expression of some marker genes in T2DM and nondiabetic tissues was also examined by Western blotting, immunohistochemistry (IHC), immunofluorescence (IF) and quantitative real-time PCR (qRT-PCR). RESULTS: We obtained 58 differentially expressed genes (DEGs) associated with ferroptosis. GO and KEGG enrichment analyses showed that these DEGs were significantly enriched in hypoxia and ferroptosis. Subsequently, eight marker genes (SCD, CD44, HIF1A, BCAT2, MTF1, HILPDA, NR1D2, and MYCN) were screened by LASSO and SVM-RFE machine learning algorithms, and a model was constructed based on these eight genes. This model also has high diagnostic power. In addition, based on these eight genes, we obtained 48 drugs and constructed a complex ceRNA network map. Finally, Western blotting, IHC, IF, and qRT-PCR results of clinical samples further confirmed the results of public databases. CONCLUSIONS: The diagnosis and aetiology of T2DM can be greatly aided by eight FRGs, providing novel therapeutic avenues.

DNA damage repair-related gene signature for identifying the immune status and predicting the prognosis of hepatocellular carcinoma.

The heterogeneity of hepatocellular carcinoma (HCC) poses a challenge for accurate prognosis prediction. DNA damage repair genes (DDRGs) have an impact on a wide range of malignancies. However, the relevance of these genes in HCC prognosis has received little attention. In this study, we aimed to develop a prognostic signature to identify novel therapy options for HCC. We acquired mRNA expression profiles and clinical data for HCC patients from The Cancer Genome Atlas (TCGA) database. A polygenic prognostic model for HCC was constructed using selection operator Cox analysis and least absolute shrinkage. The model was validated using International Cancer Genome Consortium (ICGC) data. Overall survival (OS) between the high-risk and low-risk groups was compared using Kaplan‒Meier analysis. Independent predictors of OS were identified through both univariate and multivariate Cox analyses. To determine immune cell infiltration scores and activity in immune-related pathways, a single-sample gene set enrichment analysis was performed. The protein and mRNA expression levels of the prognostic genes between HCC and normal liver tissues were also examined by immunohistochemistry (IHC), immunofluorescence (IF) and quantitative real-time PCR (qRT-PCR). A novel ten-gene signature (CHD1L, HDAC1, KPNA2, MUTYH, PPP2R5B, NEIL3, POLR2L, RAD54B, RUVBL1 and SPP1) was established for HCC prognosis prediction. Patients in the high-risk group had worse OS than those in the low-risk group. Receiver operating characteristic curve analysis confirmed the predictive ability of this prognostic gene signature. Multivariate Cox analysis showed that the risk score was an independent predictor of OS. Functional analysis revealed a strong association with cell cycle and antigen binding pathways, and the risk score was highly correlated with tumor grade, tumor stage, and types of immune infiltrate. High expression levels of the prognostic genes were significantly correlated with increased sensitivity of cancer cells to antitumor drugs. IHC, IF and qRT-PCR all indicated that the prognostic genes were highly expressed in HCC relative to normal liver tissue, consistent with the results of bioinformatics analysis. Ten DDRGs were utilized to create a new signature for identifying the immunological state of HCC and predicting prognosis. In addition, blocking these genes could represent a promising treatment.

Efficacy and safety of Gemogenovatucel-T (Vigil) immunotherapy for advanced ovarian carcinoma: A systematic review and meta-analysis of randomized controlled trials.

In recent years, many clinical trials have shown the safety and efficacy of Gemogenovatucel-T (Vigil) in the treatment of advanced OC patients. The purpose of this study was to explore the safety and efficacy of Gemogenovatucel-T (Vigil) in the first-line maintenance of advanced ovarian carcinoma based on the randomized controlled trials (RCTs). Randomized controlled trials (RCTs) on Gemogenovatucel-T (Vigil) immunotherapy for advanced ovarian carcinoma were searched in PubMed, Embase, Cochrane Library and Web of Science up to December 31, 2021. The following study characteristics were investigated: baseline study characteristics, overall survival, recurrence free survival, recurrence free survival median time, and complication. A total of 36 articles were obtained, and seven suitable RCTs with a total sample size of 322 patients were eventually included in this meta-analysis. Overall survival (OS): from time of randomization: HR=0.48 (95% CI: 0.32 to 0.72), Z=3.55, P<0.001; from time of tissue procurement: HR=0.51 (95% CI: 0.33 to 0.78), Z=3.07, P=0.002. Recurrence free survival (RFS): from time of randomization: HR=0.43 (95% CI: 0.30 to 0.62), Z=4.61, P<0.001; from time of tissue procurement: HR=0.45 (95% CI: 0.31 to 0.65), Z=4.26, P<0.001. RFS median time: from time of randomization: HR=1.57 (95% CI: 1.16 to 2.11), Z=2.95, P=0.003; from time of tissue procurement: HR=2.16 (95% CI: 1.12 to 4.17), Z=2.29, P=0.022. This study found that Gemogenovatucel-T (Vigil) immunotherapy provided significant OS and RFS benefits, particularly in advanced OC patients with BRCA wild type. At the same time, treatment with the Gemogenovatucel-T (Vigil) is safer than other treatment modalities and does not have any toxic effects. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/, identifier (CRD42022300367).

Differential Expression of Duplicate Insulin-like Growth Factor-1 Receptors (igf1rs) in Medaka Gonads.

Insulin-like growth factor-1 receptors (igf1rs) play important roles in regulating development, differentiation, and proliferation in diverse organisms. In the present study, subtypes of medaka igf1r, igf1ra, and igf1rb were isolated and characterized. RT-PCR results showed that igf1ra and igf1rb mRNA were expressed in all tissues and throughout embryogenesis. Using real-time PCR, the differential expression of igf1ra and igf1rb mRNA during folliculogenesis was observed. The results of in situ hybridization (ISH) revealed that both of them were expressed in ovarian follicles at different stages, and igf1rb was also expressed in theca cells and granulosa cells. In the testis, both igf1ra and igf1rb mRNA were highly expressed in sperm, while igf1rb mRNA was also obviously detected in spermatogonia. In addition, igf1ra mRNA was also present in Leydig cells in contrast to the distribution of igf1rb mRNA in Sertoli cells. Collectively, we demonstrated that differential igf1rs RNA expression identifies medaka meiotic germ cells and somatic cells of both sexes. These findings highlight the importance of the igf system in the development of fish gonads.

Research on the Constitutive Model of PTFE/Al/Si Reactive Material.

As a new type of energetic material, reactive materials are widely used at present; in particular, the metal/polymer mixtures type reactive materials show great advantages in engineering applications. This type of reactive material has good mechanical properties, and its overall performance is insensitive and high-energy under external impact loading. After a large number of previous studies, our team found that the energy release characteristics of PTFE/Al/Si reactive material are prominent. In order to master the mechanical properties of PTFE/Al/Si reactive materials, the quasi-static mechanical properties and dynamic mechanical properties were obtained by carrying out a quasi-static compression test and a dynamic SHPB test in this paper. Based on the experimental data, a Johnson-Cook constitutive model of PTFE/Al/Si reactive material considering strain hardening effect, strain rate hardening effect and thermal softening effect was constructed. The relevant research results will be used to guide future research on the reaction mechanism of PTFE/Al/Si reactive materials, in order to promote the engineering application of PTFE/Al/Si reactive materials.

Electrospray ionization tandem mass spectrometry analysis of the reactivity of structurally related bromo-methyl-benzoquinones toward oligonucleotides.

We report the use of electrospray ionization tandem mass spectrometry (ESI-MS/MS) as a tool for rapid screening of structurally related chemicals toward oligonucleotides using the binding of five bromobenzoquinones with single-stranded (ss) and double-stranded (ds) oligonucleotides (ODNs) as a model. We found that these compounds interact differentially with oligonucleotides depending on the extent of their bromination and methylation. Three dibromobenzoquinones, 2,6-dibromo-1,4-benzoquinone (2,6-DBBQ), 2,5-dibromo-1,4-benzoquinone (2,5-DBBQ), and 2,5-dimethyl-3,6-dibromo-1,4-benzoquinone (DMDBBQ), bound to ssODN to form 1:1 adducts, and the binding constant of DMDBBQ bound to ssODN was 100-fold lower than those of 2,6-DBBQ and 2,5-DBBQ to ssODN, indicating that methyl groups hindered interactions of the bromoquinones with ODNs. Collision-induced dissociation (CID) of the 1:1 and 1:2 adducts of ODN with 2,6-DBBQ and 2,5-DBBQ demonstrated neutral loss of DBBQ and charge separations. Incubation of two tetrabromobenzoquinones (TBBQ), 2,3,5,6-tetrabromo-1,4-benzoquinone and 3,4,5,6-tetrabromo-1,2-benzoquinone, with the same ODNs did not form any adducts of TBBQ with ssODN or dsODN; however, bromide-ODNs were detected. Fragmentation of the bromide-ODN adducts showed loss of the HBr molecule, supporting the presence of bromide on ODNs. High-resolution MS and MS/MS analysis of the mixtures of dinucleotides (AA, GG, CC, and TT) and TBBQ confirmed the presence of bromide on the dinucleotides, supporting the transfer of bromide to ODNs through interaction with TBBQ. This study presents evidence of differential interactions of structurally related bromo and methyl-benzoquinones with oligonucleotides and demonstrates a potential application of ESI-MS/MS analysis of chemical interactions with ODN for rapid screening of the reactivity of other structurally related environmental contaminants toward DNA.

Soluble Dietary Fiber Significance against Obesity in a Western China Population.

Objectives: This study aimed to investigate whether soluble dietary fibers (SDFs) could protect against obesity by influencing weight, body mass index (BMI), body fat rate (BFR), visceral fat rate (VFR), or waistline. Methods: We examined obese adult patients from western China at 0 and 3 weeks after an SDF diet. Index assessments of obesity including height, weight, BMI, BFR, VFR, and waistline were carried out. We used the Mann-Whitney U test to examine the difference between the usual diet and the SDF group. Results: Weight, BMI, BFR, and waistline were reduced in both the control group and the SDF group (P < 0.001). The reduction of the four indices in the SDF group was significantly higher than in the control group (P < 0.001). Higher intake of various SDFs has significantly reduced the weight, BMI, BFR, and waistline than the usual diet group in obesity. Conclusion: Our results indicated that increased intake of SDFs in the diet of obese patients would protect against obesity in the first 3 weeks.

Targeted RNA N6 -Methyladenosine Demethylation Controls Cell Fate Transition in Human Pluripotent Stem Cells.

Deficiency of the N6 -methyladenosine (m6 A) methyltransferase complex results in global reduction of m6 A abundance and defective cell development in embryonic stem cells (ESCs). However, it's unclear whether regional m6 A methylation affects cell fate decisions due to the inability to modulate individual m6 A modification in ESCs with precise temporal control. Here, a targeted RNA m6 A erasure (TRME) system is developed to achieve site-specific demethylation of RNAs in human ESCs (hESCs). TRME, in which a stably transfected, doxycycline-inducible dCas13a is fused to the catalytic domain of ALKBH5, can precisely and reversibly demethylate the targeted m6 A site of mRNA and increase mRNA stability with limited off-target effects. It is further demonstrated that temporal m6 A erasure on a single site of SOX2 is sufficient to control the differentiation of hESCs. This study provides a versatile toolbox to reveal the function of individual m6 A modification in hESCs, enabling cell fate control studies at the epitranscriptional level.

Characterization and determination of chloro- and bromo-benzoquinones as new chlorination disinfection byproducts in drinking water.

We report the characterization and determination of 2,6-dichloro-1,4-benzoquinone and three new disinfection byproducts (DBPs): 2,6-dichloro-3-methyl-1,4-benzoquinone, 2,3,6-trichloro-1,4-benzoquinone, and 2,6-dibromo-1,4-benzoquinone. These haloquinones are suspected bladder carcinogens and are likely produced during drinking water disinfection treatment. However, detection of these haloquinones is challenging, and consequently, they have not been characterized as DBPs until recently. We have developed an electrospray ionization tandem mass spectrometry technique based on our observation of unique ionization processes. These chloro- and bromo-quinones were ionized through a reduction step to form [M + H](-) under negative electrospray ionization. Tandem mass spectra and accurate mass measurements of these compounds showed major product ions, [M + H - HX](-), [M + H - HX - CO](-), [M + H - CO](-), and/or X(-) (where X represents Cl or Br). The addition of 0.25% formic acid to water samples was found to effectively stabilize the haloquinones in water and to improve the ionization for analysis. These improvements were rationalized from the estimates of pK(a) values (5.8-6.3) of these haloquinones. The method of tandem mass spectrometry detection, combined with sample preservation, solid phase extraction, and liquid chromatography separation, enabled the detection of haloquinones in chlorinated water samples collected from a drinking water treatment plant. The four haloquinones were detected only in drinking water after chlorination treatment, with concentrations ranging from 0.5 to 165 ng/L, but were not detectable in the untreated water. This method will be useful for future studies of occurrence, formation pathways, toxicity, and control of these new halogenated DBPs.

Electrospray ionization mass spectrometry characterization of interactions of newly identified water disinfection byproducts halobenzoquinones with oligodeoxynucleotides.

Four halobenzoquinones, 2,6-dibromo-1,4-benzoquinone, 2,6-dichloro-1,4-benzoquinone, 2,6-dichloro-3-methyl-1,4-benzoquinone, and 2,3,6-trichloro-1,4-benzoquinone, were recently identified as drinking water disinfection byproducts. Understanding their interactions with biomolecules could provide useful insights into their potential toxic effects. We report here electrospray ionization mass spectrometry characterization of the interactions between these new halobenzoquinone disinfection byproducts and oligodeoxynucleotides. The study demonstrates that 2,6-dibromo-1,4-benzoquinone exhibits much stronger binding to single- and double-stranded oligodeoxynucleotides than chlorobenzoquinones. The binding affinity of 2,6-dibromo-1,4-benzoquinone to oligodeoxynucleotides is similar to that of ethidium bromide, a well-known intercalator and carcinogen. Tandem mass spectrometry characterization confirms the formation of 1:1 and 2:1 complexes of 2,6-dibromo-1,4-benzoquinone binding to oligodeoxynucleotides. Collision-induced dissociation analysis of these adducts demonstrates neutral loss and charge separation, suggesting that 2,6-dibromo-1,4-benzoquinone binds to oligodeoxynucleotides through partial intercalation and H-bonding modes. The three chlorobezoquinones also form 1:1 adducts with the oligodeoxynucleotides, but their binding to the oligodeoxynucleotides was much weaker compared to that of 2,6-dibromo-1,4-benzoquinone. The relative binding affinity of the studied disinfection byproducts to oligodeoxynucleotides is in the order of 2,6-dibromo-1,4-benzoquinone≫2,6-dichloro-1,4-benzoquinone > 2,6-dichloro-3-methyl-1,4-benzoquinone ∼ 2,3,6-trichloro-1,4-benzoquinone, indicating potential structural effects on the interactions of halobenzoquinones with oligodeoxynucleotides.

Electroacupuncture Prevents Osteoarthritis of High-Fat Diet-Induced Obese Rats.

The effects of acupuncture on osteoarthritis (OA) pathogenesis have been demonstrated in vitro and in animal models. However, the potential for acupuncture to mediate protective effects on obese-induced OA has not been examined. Here, we investigated the effects of different acupuncture patterns on OA pathogenesis in high-fat diet- (HFD-) induced obese rats. After 12-week diet-induced obesity, obese rats were treated with three acupuncture protocols for 2 weeks, including ST36, GB34, and ST36+GB34. The results showed that the three acupuncture protocols both prevented obesity-induced cartilage matrix degradation and MMP expression and mitigated obesity-induced systemic and local inflammation but had different regulatory effects on lipid metabolism and gut microbiota disorder of obese-induced OA rats. Furthermore, the three acupuncture protocols increased the microbial diversity and altered the structure of community of feces in obese rats. We found that ST36 and GB34 could inhibit proinflammatory shift in the gut microbiome with an increase in the ratio of Bacteroidetes/Firmicutes and promote the recovery of relative abundance of Clostridium, Akkermansia, Butyricimonas, and Lactococcus. Although both ST36 and GB34 had an anti-inflammatory effect on serum inflammatory mediators, only the acupuncture protocol with both ST36 and GB34 could effectively inhibit LPS-mediated joint inflammation in obesity rats. Therefore, relieving obesity-related chronic inflammation, lipid metabolism disorder, and gut microbiota disorder may be an important mechanism for acupuncture with ST36 and GB34 to promote OA recovery.

Single-base mapping of m6A by an antibody-independent method.

N 6-methyladenosine (m6A) is one of the most abundant messenger RNA modifications in eukaryotes involved in various pivotal processes of RNA metabolism. The most popular high-throughput m6A identification method depends on the anti-m6A antibody but suffers from poor reproducibility and limited resolution. Exact location information is of great value for understanding the dynamics, machinery, and functions of m6A. Here, we developed a precise and high-throughput antibody-independent m6A identification method based on the m6A-sensitive RNA endoribonuclease recognizing ACA motif (m6A-sensitive RNA-Endoribonuclease-Facilitated sequencing or m6A-REF-seq). Whole-transcriptomic, single-base m6A maps generated by m6A-REF-seq quantitatively displayed an explicit distribution pattern with enrichment near stop codons. We used independent methods to validate methylation status and abundance of individual m6A sites, confirming the high reliability and accuracy of m6A-REF-seq. We applied this method on five tissues from human, mouse, and rat, showing that m6A sites are conserved with single-nucleotide specificity and tend to cluster among species.