Site-specific quantification of Adenosine-to-Inosine RNA editing by Endonuclease-Mediated qPCR.

RNA molecules contain diverse modified nucleobases that play pivotal roles in numerous biological processes. Adenosine-to-inosine (A-to-I) RNA editing, one of the most prevalent RNA modifications in mammalian cells, is linked to a multitude of human diseases. To unveil the functions of A-to-I RNA editing, accurate quantification of inosine at specific sites is essential. In this study, we developed an endonuclease-mediated cleavage and real-time fluorescence quantitative PCR method for A-to-I RNA editing (EM-qPCR) to quantitatively analyze A-to-I RNA editing at a single site. By employing this method, we successfully quantified the levels of A-to-I RNA editing on various transfer RNA (tRNA) molecules at position 34 (I34) in mammalian cells with precision. Subsequently, this method was applied to tissues from sleep-deprived mice, revealing a notable alteration in the levels of I34 between sleep-deprived and control mice. The proposed method sets a precedent for the quantitative analysis of A-to-I RNA editing at specific sites, facilitating a deeper understanding of the biological implications of A-to-I RNA editing.

Nomogram for predicting early hypophosphatemia in term infants.

BACKGROUND: Physiological processes rely on phosphate, which is an essential component of adenosine triphosphate (ATP). Hypophosphatasia can affect nearly every organ system in the body. It is crucial to monitor newborns with risk factors for hypophosphatemia and provide them with the proper supplements. We aimed to evaluate the risk factors and develop a nomogram for early hypophosphatemia in term infants. METHODS: We conducted a retrospective study involving 416 term infants measured serum phosphorus within three days of birth. The study included 82 term infants with hypophosphatemia (HP group) and 334 term infants without hypophosphatemia (NHP group). We collected data on the characteristics of mothers, newborn babies, and childbirth. Furthermore, univariate and multivariate logistic regression analyses were performed to identify independent risk factors for hypophosphatemia in term infants, and a nomogram was developed and validated based on the final independent risk factors. RESULTS: According to our analysis, the multivariate logistic regression analysis showed that male, maternal diabetes, cesarean delivery, lower serum magnesium, and lower birth weight were independent risk factors for early hypophosphatemia in term infants. In addition, the C-index of the developed nomogram was 0.732 (95% CI = 0.668-0.796). Moreover, the calibration curve indicated good consistency between the hypophosphatemia diagnosis and the predicted probability, and a decision curve analysis (DCA) confirmed the clinical utility of the nomogram. CONCLUSIONS: The analysis revealed that we successfully developed and validated a nomogram for predicting early hypophosphatemia in term infants.

Effects of Perfluorooctanoic Acid (PFOA) and Perfluorooctane Sulfonic Acid (PFOS) on Soil Microbial Community.

The extensive application of perfluoroalkyl and polyfluoroalkyl substances (PFASs) causes their frequent detection in various environments. In this work, two typical PFASs, perfluorooctanoic acid (PFOA) and perfluorooctanesulfonic acid (PFOS), are selected to investigate their effects on soil microorganisms. Microbial community structure and microbe-microbe relationships were investigated by high-throughput sequencing and co-occurrence network analysis. Under 90 days of exposure, the alpha-diversity of soil microbial communities was increased with the PFOS treatment, followed by the PFOA treatment. The exposure of PFASs substantially changed the compositions of soil microbial communities, leading to the enrichment of more PFASs-tolerant bacteria, such as Proteobacteria, Burkholderiales, and Rhodocyclales. Comparative co-occurrence networks were constructed to investigate the microbe-microbe interactions under different PFASs treatments. The majority of nodes in the PFOA and PFOS networks were associated with the genus Azospirillum and Hydrogenophaga, respectively. The LEfSe analysis further identified a set of biomarkers in the soil microbial communities, such as Azospirillum, Methyloversatilis, Hydrogenophaga, Pseudoxanthomonas, and Fusibacter. The relative abundances of these biomarkers were also changed by different PFASs treatments. Functional gene prediction suggested that the microbial metabolism processes, such as nucleotide transport and metabolism, cell motility, carbohydrate transport and metabolism, energy production and conversion, and secondary metabolites biosynthesis transport and catabolism, might be inhibited under PFAS exposure, which may further affect soil ecological services.

Investigation of the Ecological Roles of Putative Keystone Taxa during Tailing Revegetation.

Metal contamination released from tailings is a global environmental concern. Although phytoremediation is a promising remediation method, its practice is often impeded by the adverse tailing geochemical conditions, which suppress biological activities. The ecosystem services provided by indigenous microorganisms could alter environmental conditions and facilitate revegetation in tailings. During the process, the keystone taxa of the microbial community are assumed an essential role in regulating the community composition and functions. The identity and the environmental functions of the keystone taxa during tailing revegetation, however, remain unelucidated. The current study compared the microbial community composition and interactions of two contrasting stibnite (Sb2S3) tailings, one revegetated and one unvegetated. The microbial interaction networks and keystone taxa were significantly different in the two tailings. Similar keystone taxa were also identified in other revegetated tailings, but not in their corresponding unvegetated tailings. Metagenome-assembled genomes (MAGs) indicated that the keystone taxa in the revegetated tailing may use both organic and inorganic energy sources (e.g., sulfur, arsenic, and antimony). They could also facilitate plant growth since a number of plant-growth-promoting genes, including phosphorus solubilization and siderophore production genes, were encoded. The current study suggests that keystone taxa may play important roles in tailing revegetation by providing nutrients, such as P and Fe, and promoting plant growth.

Acylated Aminooligosaccharides with Inhibitory Effects against α-Amylase from Streptomyces sp. HO1518.

Five new acylated aminooligosaccharides (1⁻5), together with one known related analogue (6), were isolated from Streptomyces sp. HO1518. Their structure was identified by extensive spectroscopic analysis, including 1D and 2D NMR data and high resolution electrospray ionization mass spectrometry (HRESIMS), and by comparison with those reported in the literature. All of the new compounds showed more promising porcine pancreatic α-amylase (PPA) inhibitory activities than the clinical drug acarbose, indicating them as potential pharmaceutical drug leads toward type II diabetes.

An efficient direct competitive nano-ELISA for residual BSA determination in vaccines.

A simple, fast, and highly sensitive direct competitive enzyme-linked immunosorbent assay (ELISA) based on bovine serum albumin (BSA) antigen labeled amine-terminated silicon dioxide (SiO2-NH-BSA) nanoparticles was developed to determine residual BSA in vaccines. As nano-ELISA using nanomaterials with a very high surface-to-volume ratio has emerged as a promising strategy, SiO2-NH-BSA nanoparticles were prepared in this study by the coupling of BSA to SiO2 nanoparticles modified with amidogen, followed by the quantification of BSA via a direct competitive binding of BSA-antigen-labeled SiO2 nanoparticles to anti-BSA antibody conjugated with horseradish peroxidase. The validation study showed that the linear range of this method was from 1 to 90 ng/mL (r = 0.998) and the limit of detection was 0.67 ng/mL. The intra-assay and interassay coefficients of variation were less than 10% at three concentrations (10, 40, and 70 ng/mL), and the recovery was 92.4%, indicating good specificity. As a proof of principle, this new method was applied in the analysis of residual BSA in five different vaccines. Bland-Altman plots revealed that there was no significant difference in the accuracy and precision between our new method and the most commonly used sandwich ELISA. From the results taken together, the new method developed in this study is more sensitive and facile with lower cost and thus demonstrated potential to be applied in the quality control of biological products. Graphical Abstract Illustration of the procedures of the direct competitive enzyme immunoassay.

EEG microstate analysis reveals large-scale brain network alterations in depressed adolescents with suicidal ideation.

BACKGROUND: Accumulating evidence showed abnormalities in brain network connectivity in depressive individuals with suicidal ideation (SI). We aimed to investigate the large-scale brain network dynamics in adolescents with SI and major depressive disorder (MDD). METHODS: We recruited 47 first-episode drug-naïve adolescents with MDD and SI, 26 depressed adolescents without SI (noSI), and 26 age-matched healthy controls (HC). The Columbia Suicidal Ideation Severity Scale (C-SSRS) was utilized to assess suicide ideation. We acquired 64-channel resting-state EEG recordings from all subjects and used microstate analysis to investigate the large-scale brain network dynamics. RESULTS: We observed a significant reduction in the occurrence and coverage of microstate B within the SI group when contrasted with the noSI group. Conversely, there was a significant increase in the occurrence and coverage of microstate A in the SI group as compared to the HC group. Additionally, we observed heightened transition probabilities from microstates D and C to microstate A in the SI group; meanwhile, transitions from microstate D to B were more prevalent in the noSI group. Furthermore, the noSI group exhibited a significant decline in the transition probabilities from microstate D to microstate C. LIMITATIONS: The cross-sectional nature limits the capacity to determine whether microstate dynamics have prognostic significance for SI. CONCLUSION: We provided evidence that depressed adolescents with SI have a distinct pattern in microstate dynamics compared to those without SI. These findings suggest that microstate dynamics might serve as a potential neurobiomarker for identifying SI in depressed adolescents.

Personality traits predict treatment outcome of an antidepressant in untreated adolescents with depression: An 8-week, open-label, flexible-dose study.

BACKGROUND: Antidepressant response in adults with major depressive disorder (MDD) is probably influenced by personality dimensions. However, personality dimensions in depression and their association with antidepressant treatment in adolescents are relatively unknown. We sought to investigate whether personality traits (PTs) can influence antidepressant treatment response in adolescents with depression. METHODS: Eighty-two adolescents with MDD who had completed the 8 weeks of treatment with selective serotonin reuptake inhibitors (SSRI) were enrolled. The Revised NEO Five-Factor Inventory (NEO-FFI-R) was used to measure their personality at baseline, and the 17-item Hamilton Depression Rating Scale (HAMD-17) and Children's Depression Rating Scale-Revised (CDRS-R) were used to evaluate depressive symptoms at baseline and 8 weeks. Moreover, logistic regression was performed to investigate the relationship between personality dimensions and antidepressant response. Receiver operating characteristic analyses were employed to determine the accuracy of a PT-based model in predicting the antidepressant response rate. RESULTS: Adolescents with MDD had significantly different PTs at baseline. Multivariable logistic regression analysis showed that extroversion scores were associated with response to antidepressant treatment, the lower the extroversion score, the better the response to antidepressant treatment, after correcting for variables with significant differences and trends or all potential confounding variables. It was also found that the combination of disease duration, extraversion-gregariousness, and agreeableness-trust effectively predicted antidepressant response in adolescents with MDD, with a sensitivity of 79.4 % and specificity of 68.7 %. CONCLUSION: Personality dysfunction in adolescents is associated with MDD. The antidepressant treatment response is influenced by the degree of extroversion in adolescents with MDD.

Therapeutic Window of Intravenous Immunoglobulin (IVIG) and its correlation with IVIG-resistant in Kawasaki Disease: a retrospective study.

OBJECTIVE: To investigate the optimal timing of initial intravenous immunoglobulin (IVIG) treatment in Kawasaki disease (KD) patients. METHODS: KD patients were classified as the early group (day 1-4), conventional group (day 5-7), conventional group (day 8-10), and late group (after day 10). Differences among the groups were analyzed by ANOVA and Chi-square analysis. Predictors of IVIG resistance and the optimal cut-off value were determined by multiple logistic regression analyses and receiver operating characteristic (ROC) curve analysis. RESULTS: There were no significant differences in IVIG resistance among the 4 groups (p = 0.335). The sensitivity analysis also confirmed no difference in the IVIG resistance between those who started the initial IVIG ≤ day 7 of illness and those who received IVIG >day 7 of illness (p = 0.761). In addition, patients who received IVIG administration more than 7 days from the onset had a higher proportion of coronary artery abnormalities (p = 0.034) and longer length of hospitalization (p = 0.033) than those who started IVIG administration less than 7 days. The optimal cut-off value of initial IVIG administration time for predicting IVIG resistance was >7 days, with a sensitivity of 75.25% and specificity of 82.41%. CONCLUSIONS: IVIG therapy within 7 days of illness is found to be more effective for reducing the risk of coronary artery abnormalities than those who received IVIG >day 7 of illness. IVIG treatment within the 7 days of illness seems to be the optimal therapeutic window of IVIG. However, further prospective studies with long-term follow-up are required.

Anaerobic selenite-reducing bacteria and their metabolic potentials in Se-rich sediment revealed by the combination of DNA-stable isotope probing, metagenomic binning, and metatranscriptomics.

Microorganisms play a critical role in the biogeochemical cycling of selenium (Se) in aquatic environments, particularly in reducing the toxicity and bioavailability of selenite (Se(IV)). This study aimed to identify putative Se(IV)-reducing bacteria (SeIVRB) and investigate the genetic mechanisms underlying Se(IV) reduction in anoxic Se-rich sediment. Initial microcosm incubation confirmed that Se(IV) reduction was driven by heterotrophic microorganisms. DNA stable-isotope probing (DNA-SIP) analysis identified Pseudomonas, Geobacter, Comamonas, and Anaeromyxobacter as putative SeIVRB. High-quality metagenome-assembled genomes (MAGs) affiliated with these four putative SeIVRB were retrieved. Annotation of functional gene indicated that these MAGs contained putative Se(IV)-reducing genes such as DMSO reductase family, fumarate and sulfite reductases. Metatranscriptomic analysis of active Se(IV)-reducing cultures revealed significantly higher transcriptional levels of genes associated with DMSO reductase (serA/PHGDH), fumarate reductase (sdhCD/frdCD), and sulfite reductase (cysDIH) compared to those in cultures not amended with Se(IV), suggesting that these genes played important roles in Se(IV) reduction. The current study expands our knowledge of the genetic mechanisms involved in less-understood anaerobic Se(IV) bio-reduction. Additinally, the complementary abilities of DNA-SIP, metagenomics, and metatranscriptomics analyses are demonstrated in elucidating the microbial mechanisms of biogeochemical processes in anoxic sediment.

A resting-state electroencephalographic microstates study in depressed adolescents with non-suicidal self-injury.

Neuroimaging studies have revealed abnormal brain activities in depressed teenagers who engage in non-suicidal self-injury (NSSI). We used resting-state electroencephalography (EEG) microstate analysis, which indicates the brief overlap of brain network activation for exploring the characteristics of large-scale cortical activities in depressed adolescents engaged with NSSI to clarify the underlying temporal mechanism. A modified k-means cluster algorithm was used to segment 64-channel resting-state EEG data into microstates. Data from 27 healthy adolescents, 37 adolescents with major depressive disorder (MDD), and 53 adolescents with both MDD and NSSI were examined in this study. The resting-state microstate parameters were compared among groups using the one-way ANOVA and Spearman correlation. Then the associations between significantly different microstate parameters and the depressive severity and self-harming data in the patient groups were further analyzed. The MDD group had higher contribution (p < 0.01), occurrence (p < 0.01) of microstate A, and higher microstate E→A transition (p < 0.05) than the HC and the NSSI group. The MDD group showed a distinctly longer duration (p < 0.05) of microstate A and microstate A→C transition than the HC. The transition probability from B to C was increased in the NSSI group compared to the HC. In the MDD group, the HAMD correlated with the duration of microstate A (Spearman's rho = 0.34, p = 0.044), as the PHQ-9 correlated with its occurrence (Spearman's rho = 0.37, p = 0.028). This research revealed that whereas depressive adolescents with NSSI and MDD displayed similar patterns with healthy controls in EEG microstate, the MDD group did not. Additionally, the non-random transition from microstate E→A may protect against recent self-harm in adolescents with MDD.

[Mid-infrared and Raman spectral analysis of geometrically frustrated natural atacamite].

At room temperature, the mid-infrared spectra of geometrically frustrated natural atacamite (hydroxyl copper chloride, beta-Cu2(OH)3Cl) in the range of 4 000-400 cm(-1) were measured by FTIR spectrometers, and meanwhile its Raman spectrum in the range of 4 000-95 cm(-1) was obtained by Jobin Yvon LabRAM HR800 Raman spectrometer. According to its crystal structure parameters, the authors confirmed the characteristic peaks of sample 4 000-2 500-1 000 cm(-1) in the functional group region and 1 000-550-200-95 cm(-1) in the fingerprint region, and also explored its microscopic origin Five distinct regions were assigned: the hydroxyl stretching vibration v(O-H) determined by the overall environment around the hydroxyl group; the overtones generated by the sum or multiplication of fundamental frequencies of hydroxyl bending vibration; the hydroxyl bending vibration modes delta(O-H) of the combination of delta(Cu-O-H) and delta(O-H...HCl); the vibration modes of strongly bonded planar CuO4 units; the vibration modes of weakly bonded linear-triatomic chain Cl-Cu-O/Cl. The bands were assigned in accordance with its crystal structure parameters, which is more reasonable to establish the relationship between its molecular structure and its respective spectral properties.

Methods for isolation of messenger RNA from biological samples.

RNA molecules contain many chemical modifications that can regulate a variety of biological processes. Messenger RNA (mRNA) molecules are critical components in the central dogma of molecular biology. The discovery of reversible chemical modifications in eukaryotic mRNA brings forward a new research field in RNA modification-mediated regulation of gene expression. The modifications in mRNA generally exist in low abundance. The use of highly pure mRNA is critical for the confident identification of new modifications as well as for the accurate quantification of existing modifications in mRNA. In addition, isolation of highly pure mRNA is the first step in many biological research studies. Therefore, the methods for isolating highly pure mRNA are important for mRNA-based downstream studies. A variety of methods for isolating mRNA have been developed in the past few decades and new methods continuously emerge. This review focuses on the methodologies and protocols for isolating mRNA populations. In addition, we discuss the advantages and limitations of these methods. We hope this paper will provide a general view of mRNA isolation strategies and facilitate studies that involve mRNA modifications and functions.

Direct decarboxylation of ten-eleven translocation-produced 5-carboxylcytosine in mammalian genomes forms a new mechanism for active DNA demethylation.

DNA cytosine methylation (5-methylcytosine, 5mC) is the most important epigenetic mark in higher eukaryotes. 5mC in genomes is dynamically controlled by writers and erasers. DNA (cytosine-5)-methyltransferases (DNMTs) are responsible for the generation and maintenance of 5mC in genomes. Active demethylation of 5-methylcytosine (5mC) is achieved by ten-eleven translocation (TET) dioxygenase-mediated oxidation of 5mC to 5-hydroxymethylcytosine (5hmC), 5-formylcytosine (5fC), and 5-carboxylcytosine (5caC). 5fC and 5caC are further processed by thymine DNA glycosylase (TDG)-initiated base excision repair (BER) to restore unmodified cytosines. The TET-TDG-BER pathway could cause the production of DNA strand breaks and therefore jeopardize the integrity of genomes. Here, we investigated the direct decarboxylation of 5caC in mammalian genomes by using metabolic labeling with 2'-fluorinated 5caC (F-5caC) and mass spectrometry analysis. Our results clearly demonstrated the decarboxylation of 5caC occurring in mammalian genomes, which unveiled that, in addition to the TET-TDG-BER pathway, the direct decarboxylation of TET-produced 5caC constituted a new pathway for active demethylation of 5mC in mammalian genomes.

Flexible and efficient perovskite quantum dot solar cells via hybrid interfacial architecture.

All-inorganic CsPbI3 perovskite quantum dots have received substantial research interest for photovoltaic applications because of higher efficiency compared to solar cells using other quantum dots materials and the various exciting properties that perovskites have to offer. These quantum dot devices also exhibit good mechanical stability amongst various thin-film photovoltaic technologies. We demonstrate higher mechanical endurance of quantum dot films compared to bulk thin film and highlight the importance of further research on high-performance and flexible optoelectronic devices using nanoscale grains as an advantage. Specifically, we develop a hybrid interfacial architecture consisting of CsPbI3 quantum dot/PCBM heterojunction, enabling an energy cascade for efficient charge transfer and mechanical adhesion. The champion CsPbI3 quantum dot solar cell has an efficiency of 15.1% (stabilized power output of 14.61%), which is among the highest report to date. Building on this strategy, we further demonstrate a highest efficiency of 12.3% in flexible quantum dot photovoltaics.

Therapeutic Window of Intravenous Immunoglobulin (IVIG) and its correlation with IVIG-resistant in Kawasaki Disease: a retrospective study

Abstract Objective: To investigate the optimal timing of initial intravenous immunoglobulin (IVIG) treatment in Kawasaki disease (KD) patients. Methods: KD patients were classified as the early group (day 1-4), conventional group (day 5-7), conventional group (day 8-10), and late group (after day 10). Differences among the groups were analyzed by ANOVA and Chi-square analysis. Predictors of IVIG resistance and the optimal cut-off value were determined by multiple logistic regression analyses and receiver operating characteristic (ROC) curve analysis. Results: There were no significant differences in IVIG resistance among the 4 groups (p = 0.335). The sensitivity analysis also confirmed no difference in the IVIG resistance between those who started the initial IVIG ≤ day 7 of illness and those who received IVIG >day 7 of illness (p = 0.761). In addition, patients who received IVIG administration more than 7 days from the onset had a higher proportion of coronary artery abnormalities (p = 0.034) and longer length of hospitalization (p = 0.033) than those who started IVIG administration less than 7 days. The optimal cut-off value of initial IVIG administration time for predicting IVIG resistance was >7 days, with a sensitivity of 75.25% and specificity of 82.41%. Conclusions: IVIG therapy within 7 days of illness is found to be more effective for reducing the risk of coronary artery abnormalities than those who received IVIG >day 7 of illness. IVIG treatment within the 7 days of illness seems to be the optimal therapeutic window of IVIG. However, further prospective studies with long-term follow-up are required.

Enhanced recovery after surgery programs versus traditional perioperative care in laparoscopic hepatectomy: A meta-analysis.

OBJECTIVE: Enhanced recovery after surgery (ERAS) programs are a series of measures being taken during the perioperation to alleviate surgical stress and accelerate the recovery rate of patients. Although several studies reported the efficacy of ERAS in liver surgery, the role of ERAS in laparoscopic hepatectomy is still unclear. This meta-analysis is aimed to evaluate the efficacy and safety of ERAS programs versus traditional care in laparoscopic hepatectomy. METHODS: We searched PubMed, EMBASE, the Cochrane Library, CNKI, Wang Fang Database and VIP Database for randomized controlled trials (RCTs) or clinical controlled trials (CCTs) concerning using ERAS in laparoscopic hepatectomy. Data collection ended in June 1st, 2016. The main end points were intraoperative blood loss, intraoperative blood transfusion, operative time, the cost of hospitalization, time to first flatus, the time to first diet after surgery, duration of postoperative hospital stay, total postoperative complication rate, gradeⅠcomplication rate, grade Ⅱ-Ⅴcomplication rate. RESULTS: 8 studies with 580 patients were eligible for analysis. There were 292 cases in ERAS group and 288 cases in traditional perioperative care (CTL) group. Compared with CTL group, ERAS group was associated with significantly accelerated of time to first diet after surgery (SMD = -1.79, 95%CI: -3.19 âˆ¼ -0.38, P = 0.01), time to first flatus (MD = -0.51, 95%CI: -0.91 âˆ¼ -0.12, P = 0.01). Meanwhile, it was associated with significantly decreased of duration of the postoperative hospital stay (MD = -3.31, 95%CI: -3.95 âˆ¼ -2.67, P < 0.00001), cost of hospitalization (MD = -1.0, 95%CI: -1.49 âˆ¼ -0.51, P < 0.0001), total postoperative complication rate (OR = 0.34, 95%CI: 0.15-0.75, P = 0.008), gradeⅠcomplication rate (OR = 0.37, 95%CI: 0.22-0.64, P = 0.0003) and gradeⅡ-Ⅴcomplication rate (OR = 0.49, 95%CI: 0.32-0.77, P = 0.002). Whereas there was no significantly difference in intraoperative blood loss (P > 0.05), intraoperative blood transfusion (P > 0.05), operative time (P > 0.05) between ERAS group and CTL group. CONCLUSION: Application of ERAS in laparoscopic hepatectomy is safe and effective, and it could accelerate the postoperative recovery and lighten the financial burden of patients.