Valorization of lignin-derived compounds into poly(3-hydroxybutyrate-co-3-hydroxyvalerate) by engineered Halomonas sp. Y3.

Poly(3-hydroxybutyrate-co-3-hydroxyvalerate) (PHBV) is a biopolyester with great potential, but its high production cost via the propionate-dependent pathway has hindered its development. Herein, we engineer Halomonas sp. Y3 to achieve efficient conversion of various LDCs into PHBV without propionate supplement. Initially, we successfully achieve PHBV production without propionate supplement by overexpressing threonine synthesis. The resulting biopolyester exhibits a 3 HV proportion of up to 7.89 mol%, comparable to commercial PHBV (8 mol%) available from Sigma Aldrich (403105). To further enhance PHBV production, we rationally design the reconstruction of aromatic compound catabolism. The engineered strain Y3_18 efficiently assimilates all LDCs containing syringyl (S), guaiacyl (G), and p-hydroxyphenyl-type (H) units. From 1 g/L of S-, G-, and H-type LDCs, Y3_18 produces PHBV at levels of 449 mg/L, 488 mg/L, and 716 mg/L, respectively, with yields of 44.9 % (g/g), 48.8 % (g/g), and 71.6 % (g/g). Moreover, to improve PHBV yield from lignin, we integrate laccase-secretion and PHBV production modules. This integration leads to the accumulation of 425.84 mg/L of PHBV with a yield of 21.29 % (g/g) and a 3 HV proportion of 6.38 mol%. By harnessing the capabilities of Halomonas sp. Y3, we demonstrate an efficient and sustainable approach for PHBV production from a variety of LDCs.

JustRNA: a database of plant long noncoding RNA expression profiles and functional network.

Long noncoding RNAs (lncRNAs) are regulatory RNAs involved in numerous biological processes. Many plant lncRNAs have been identified, but their regulatory mechanisms remain largely unknown. A resource that enables the investigation of lncRNA activity under various conditions is required because the co-expression between lncRNAs and protein-coding genes may reveal the effects of lncRNAs. This study developed JustRNA, an expression profiling resource for plant lncRNAs. The platform currently contains 1 088 565 lncRNA annotations for 80 plant species. In addition, it includes 3692 RNA-seq samples derived from 825 conditions in six model plants. Functional network reconstruction provides insight into the regulatory roles of lncRNAs. Genomic association analysis and microRNA target prediction can be employed to depict potential interactions with nearby genes and microRNAs, respectively. Subsequent co-expression analysis can be employed to strengthen confidence in the interactions among genes. Chromatin immunoprecipitation sequencing data of transcription factors and histone modifications were integrated into the JustRNA platform to identify the transcriptional regulation of lncRNAs in several plant species. The JustRNA platform provides researchers with valuable insight into the regulatory mechanisms of plant lncRNAs. JustRNA is a free platform that can be accessed at http://JustRNA.itps.ncku.edu.tw.

Non-sterilized conversion of whole lignocellulosic components into polyhydroxybutyrate by Halomonas sp. Y3 with a dual anti-microbial contamination system.

Polyhydroxybutyrate (PHB) production from lignocellulosic biomass is challenging due to the need for whole components and energy-effective conversion. Herein, Halomonas sp. Y3, a ligninolytic bacterium with the capacity to produce PHB from lignin and cellulose- and hemicellulose-derived sugars, is employed to explore its feasibility. This strain shows high sugar tolerance up to 200 g/L of glucose and 120 g/L of xylose. A dual anti-microbial contamination system (DACS) containing alkali-halophilic system (AHS) and phosphite-urea system (PUS) is presented, successfully achieving a completely aseptic effect and resulting in a total of 8.2 g of PHB production from 100 g bamboo biomass. We further develop a stage-fed-batch fermentation to promote the complete utilization of xylose. Approximately 69.99 g of dry cell weight (DCW) and 46.45 g of PHB with 66.35 % are obtained from a total of 296.58 g of sugars and 5.70 g of lignin, showing a significant advancement for LCB bioconversion. We then delete the native phosphate transporters, rendering the strain unable to grow on phosphate-loaded media, effectively improving the strain biosafety without compromising its ability to produce PHB. Overall, our findings demonstrate the potential of Y3 as a classic bacterium strain for PHB production with potential uses in industry.

[Comparison of curative effect between Tianji robot assisted screw placement and traditional cannulated screw internal fixation for femoral neck fracture].

OBJECTIVE: To investigate the clinical efficacy and advantages of Tianji orthopedic robot assisted cannulated screw internal fixation for femoral neck fracture. METHODS: The clinical data of 41 patients with femoral neck fracture who underwent internal fixation with cannulated screws from January 2019 to January 2022 were retrospectively analyzed. According to different surgical methods, they were divided into Tianji robot group and traditional cannulated screw fixation group (traditional operation group). Among them, there were 18 patients in Tianji robot group including 8 males and 10 females with age of (56.00±4.22) years old, Garden typeⅠ (4 cases), type Ⅱ (11 cases), type Ⅲ (2 cases), and type Ⅳ (1 case). There were 23 patients in the traditional operation group, including 10 males and 13 females, aged (54.87±4.81) years old;there were 5 cases of Garden typeⅠ, 14 cases of type Ⅱ, 3 cases of type Ⅲ and 1 case of type Ⅳ. The operation time, intraoperative blood loss, fluoroscopy times, guide needle placement times, operation costs and other indicators were observed and compared between two groups. Harris score was used to evaluate hip joint function 12 months after operation. RESULTS: The wounds of all patients healed in Grade A without complications. There were significant differences between two groups in terms of operation time, times of intraoperative fluoroscopy, times of guide needle placement, amount of intraoperative bleeding, and operation cost (P<0.05). All 41 patients were followed up for at least 12 months. The fractures of both groups were healed. There was no infection, screw loosening, fracture displacement and femoral head necrosis in Tianji robot group during follow-up;Screw loosening occurred in 2 patients in the traditional operation group during follow-up. At 12 months after operation, Harris hip joint function score of Tianji robot group was higher than that of traditional operation group in daily activity, lameness, joint activity score and total score (P<0.05). CONCLUSION: Tianji robot assisted nail placement is a better method for the treatment of femoral neck fracture, which improves the surgical efficiency, is more accurate, has higher success rate of one-time nail placement, shorter operation time, less radiation, and has better hip joint function recovery after surgery.

Highly efficient polyhydroxyalkanoate production from lignin using genetically engineered Halomonas sp. Y3.

Lignin degradation represents a significant challenge in biological valorization, but it is suffering from insufficiency, putting barriers to efficient lignin conversion. Herein, the study first develops a highly efficient laccase secretion apparatus, enabling high enzyme activity of 184 U/mL, complementing the biochemical limits on lignin depolymerization well in Halomonas sp. Y3. Further engineering of PHA biosynthesis produces a significantly high PHA titer of 286, 742, and 868 mg/L from alkaline lignin, catechol, and protocatechuate, respectively. The integration of laccase-secretion and PHA production modules enables a record titer of 693 and 1209 mg/L in converting lignin and lignin-containing stream to PHA, respectively. The titer is improved furtherly to 740 and 1314 mg/L by developing a non-sterilized fermentation. This study advances a cheaper and greener production of valuable chemicals from lignin by constructing a biosynthetic platform for PHA production and provides novel insight into the lignin conversion by extremophilic microbes.

Funneling lignin-derived compounds into polyhydroxyalkanoate by Halomonas sp. Y3.

Lignin-derived compounds (LDCs) biological funneling for polyhydroxyalkanoate (PHA) synthesis has been attractive but elusive. Herein, the Halomonas sp. Y3 is isolated and developed for PHA production from LDCs. Of the tested 13 LDCs, 4-hydroxybenzoic acid (4-HBA), protocatechuate (PA), catechol (CAT), and vanillic acid (VA) exhibit a hyper-degradation and production with 87.2 %, 85.8 %, 84.7 %, and 83.4 % TOC removal rate and 535.2 mg/L, 506.5 mg/L, 435.6 mg/L, and 440.8 mg/L PHA concentration, respectively. The Halomonas sp. Y3 genome is sequenced by identifying numerous genes responsible for LDCs funneling, stress response, and PHA biosynthesis. An open unsterilized fermentation with optimal conditions of pH 9.0 and NaCl 60 g/L is investigated, achieving a completely aseptic effect and significantly improved PHA production from LDCs. Overall, the results indicate that the Halomonas sp. Y3 is an ideal candidate for LDC bioconversion and exhibits a great potential to realize black liquor valorization.

Assessment of low-dose paranasal sinus CT imaging using a new deep learning image reconstruction technique in children compared to adaptive statistical iterative reconstruction V (ASiR-V).

PURPOSE: To compare the effects of deep learning image reconstruction (DLIR) and adaptive statistical iterative reconstruction V (ASiR-V) on image quality in low-dose computed tomography (CT) of paranasal sinuses in children. METHODS: Low-dose CT scans of the paranasal sinuses in 25 pediatric patients were retrospectively evaluated. The raw data were reconstructed with three levels of DLIR (high, H; medium, M; and low, L), filtered back projection (FBP), and ASiR-V (30% and 50%). Image noise was measured in both soft tissue and bone windows, and the signal-to-noise ratios (SNRs) and contrast-to-noise ratios (CNRs) of the images were calculated. Subjective image quality at the ethmoid sinus and nasal cavity levels of the six groups of reconstructed images was assessed by two doctors using a five-point Likert scale in a double-blind manner. RESULTS: The patients' mean dose-length product and effective dose were 36.65 ± 2.44 mGy·cm and 0.17 ± 0.03 mSv, respectively. (1) Objective evaluation: 1. Soft tissue window: The difference among groups in each parameter was significant (P < 0.05). Pairwise comparisons showed that the H group' s parameters were significantly better (P < 0.05) than those of the 50% post-ASiR-V group. 2. Bone window: No significant between-group differences were found in the noise of the petrous portion of the temporal bone or its SNR or in the noise of the pterygoid processes of the sphenoids or their SNRs (P > 0.05). Significant differences were observed in the background noise and CNR (P < 0.05). As the DLIR intensity increased, image noise decreased and the CNR improved. The H group exhibited the best image quality. (2) Subjective evaluation: Scores for images of the ethmoid sinuses were not significantly different among groups (P > 0.05). Scores for images of the nasal cavity were significantly different among groups (P < 0.05) and were ranked in descending order as follows: H, M, L, 50% post-ASiR-V, 30% post-ASiR-V, and FBP. CONCLUSION: DLIR was superior to FBP and post-ASiR-V in low-dose CT scans of pediatric paranasal sinuses. At high intensity (H), DLIR provided the best reconstruction effects.

Household cooking oil type and risk of oral micronucleus frequency in Chinese nonsmokers.

Household animal fat has been linked to increased incidence of cancers compared with vegetable fat. However, few epidemiological studies have associated these two cooking oil types with precancerous genotoxic effects, such as occurrence of micronuclei (MN). This study aimed to explore the association between oral MN frequency and household cooking oil type and whether the association can be attributed to polycyclic aromatic hydrocarbons (PAHs). We collected information about individual cooking oil use, measured genotoxic effects by MN tests and urinary PAHs metabolites (OHPAHs) in 245 nonsmokers. The associations between household cooking oil type and MN frequency and OHPAHs were analyzed using generalized linear models (GLMs) and logistic regression models, evaluating odds ratios and coefficient (95% confidence intervals) (ORs, 95% Cls; ß, 95% Cls). The odds of animal fat consumers, rather than vegetable fat consumers, was positively associated with higher MN frequency (OR = 1.94, P < 0.05). The associations were discovered in participants only using kitchen ventilation (OR = 2.04, P < 0.05). Animal fat consumers had higher total OHPAHs than vegetable fat consumers (1.58 ± 0.22 mg/mol, Cr vs 1.20 ± 0.12 mg/mol, Cr; P = 0.028). Significant correlations were observed between total OHPAHs quartiles and increased MN frequency (ß = 0.38, P-trend = 0.026). After stratifying by household cooking oil type, sensitivity analyses showed that the positive association between total OHPAHs quartiles and increased MN frequency was only observed in animal fat consumers (ß = 0.61, P-trend = 0.030). In conclusion, usage of household animal fat was associated with an increased odds of oral MN frequency in Chinese nonsmokers and the odds correlated with increased PAHs exposure. This finding supplemented evidence associating cooking oil type with genotoxic effects and explained its association with PAHs exposure.

Identification of novel rheumatoid arthritis-associated MiRNA-204-5p from plasma exosomes.

Rheumatoid arthritis (RA) is an autoimmune disease characterized by infiltration of immune cells in the synovium. However, the crosstalk of immune cells and synovial fibroblasts is still largely unknown. Here, global miRNA screening in plasma exosomes was carried out with a custom microarray (RA patients vs. healthy controls = 9:9). A total of 14 exosomal miRNAs were abnormally expressed in the RA patients. Then, downregulated expression of exosomal miR-204-5p was confirmed in both the replication (RA patients vs. healthy controls = 30:30) and validation groups (RA patients vs. healthy controls = 56:60). Similar to the findings obtained in humans, a decreased abundance of exosomal miR-204-5p was observed in mice with collagen-induced arthritis (CIA). Furthermore, Spearman correlation analysis indicated that plasma exosomal miR-204-5p expression was inversely correlated with disease parameters of RA patients, such as rheumatoid factor, erythrocyte sedimentation rate, and C-reactive protein. In vitro, our data showed that human T lymphocytes released exosomes containing large amounts of miR-204-5p, which can be transferred into synovial fibroblasts, inhibiting cell proliferation. Overexpression of miR-204-5p in synovial fibroblasts suppressed synovial fibroblast activation by targeting genes related to cell proliferation and invasion. In vivo assays found that administration of lentiviruses expressing miR-204-5p markedly alleviated the disease progression of the mice with CIA. Collectively, this study identified a novel RA-associated plasma exosomal miRNA-204-5p that mediates the communication between immune cells and synovial fibroblasts and can be used as a potential biomarker for RA diagnosis and treatment.

A survey of current practices, attitudes and demands of anaesthesiologists regarding the depth of anaesthesia monitoring in China.

BACKGROUND: In this study, we aimed to analyse survey data to explore two different hypotheses; and for this purpose, we distributed an online survey to Chinese anaesthesiologists. The hypothetical questions in this survey include: (1) Chinese anaesthesiologists mainly use the depth of anaesthesia (DoA) monitors to prevent intraoperative awareness and (2) the accuracy of these monitors is the most crucial performance factor during the clinical daily practice of Chinese anaesthesiologists. METHODS: We collected and statistically analysed the response of a total of 12,750 anesthesiologists who were invited to participate in an anonymous online survey. The Chinese Society of Anaesthesiologists (CSA) trial group provided the email address of each anaesthesiologist, and the selection of respondents was random from the computerized system. RESULTS: The overall response rate was 32.0% (4037 respondents). Only 9.1% (95% confidence interval, 8.2-10.0%) of the respondents routinely used DoA monitors. Academic respondents (91.5, 90.3-92.7%) most frequently used DoA monitoring to prevent awareness, whereas nonacademic respondents (88.8, 87.4-90.2%) most frequently used DoA monitoring to guide the delivery of anaesthetic agents. In total, the number of respondents who did not use a DoA monitor and whose patients experienced awareness (61.7, 57.8-65.6%) was significantly greater than those who used one or several DoA monitors (51.5, 49.8-53.2%). Overall, the crucial performance factor during DoA monitoring was considered by 61.9% (60.4-63.4%) of the respondents to be accuracy. However, most respondents (95.7, 95.1-96.3%) demanded improvements in the accuracy of the monitors for DoA monitoring. In addition, broad application in patients of all ages (86.3, 85.2-87.4%), analgesia monitoring (80.4, 79.2-81.6%), and all types of anaesthetic agents (75.6, 74.3-76.9%) was reported. In total, 65.0% (63.6-66.5%) of the respondents believed that DoA monitors should be combined with EEG and vital sign monitoring, and 53.7% (52.1-55.2%) believed that advanced DoA monitors should include artificial intelligence. CONCLUSIONS: Academic anaesthesiologists primarily use DoA monitoring to prevent awareness, whereas nonacademic anaesthesiologists use DoA monitoring to guide the delivery of anaesthetics. Anaesthesiologists demand high-accuracy DoA monitors incorporating EEG signals, multiple vital signs, and antinociceptive indicators. DoA monitors with artificial intelligence may represent a new direction for future research on DoA monitoring.

Effects of prostaglandin E combined with continuous renal replacement therapy on septic acute kidney injury.

BACKGROUND: The effects of prostaglandin E (PGE) combined with continuous renal replacement therapy (CRRT) on renal function and inflammatory responses in patients with septic acute kidney injury (SAKI) remain unclear. AIM: To investigate the effects of PGE combined with CRRT on urinary augmenter of liver regeneration (ALR), urinary Na+/H+ exchanger 3 (NHE3), and serum inflammatory cytokines in patients with SAKI. METHODS: The clinical data of 114 patients with SAKI admitted to Yichang Second People's Hospital from May 2017 to January 2019 were collected. Fifty-three cases treated by CRRT alone were included in a control group, while the other 61 cases treated with PGE combined with CRRT were included in an experimental group. Their urinary ALR, urinary NHE3, serum inflammatory cytokines, renal function indices, and immune function indices were detected. Changes in disease recovery and the incidence of adverse reactions were observed. The 28-d survival curve was plotted. RESULTS: Before treatment, urinary ALR, urinary NHE3, blood urea nitrogen (BUN), serum creatinine (SCr), CD3+ T lymphocytes, CD4+ T lymphocytes, and CD4+/CD8+ T lymphocyte ratio in the control and experimental groups were approximately the same. After treatment, urinary ALR and NHE3 decreased, while BUN, SCr, CD3+ T lymphocytes, CD4+ T lymphocytes, and CD4+/CD8+ T lymphocyte ratio increased in all subjects. Urinary ALR, urinary NHE3, BUN, and SCr in the experimental group were significantly lower than those in the control group, while CD3+ T lymphocytes, CD4+ T lymphocytes, and CD4+/CD8+ T lymphocyte ratio were significantly higher than those in the control group (P < 0.05). After treatment, the levels of tumor necrosis factor-α, interleukin-18, and high sensitivity C-reactive protein in the experimental group were significantly lower than those in the control group (P < 0.05). The time for urine volume recovery and intensive care unit treatment in the experimental group was significantly shorter than that in the control group (P < 0.05), although there was no statistically significant difference in hospital stays between the two groups. The total incidence of adverse reactions did not differ statistically between the two groups. The 28-d survival rate in the experimental group (80.33%) was significantly higher than that in the control group (66.04%). CONCLUSION: PGE combined with CRRT is clinically effective for treating SAKI, and the combination therapy can significantly improve renal function and reduce inflammatory responses.

Rheumatoid arthritis-associated DNA methylation sites in peripheral blood mononuclear cells.

OBJECTIVES: To identify novel DNA methylation sites significant for rheumatoid arthritis (RA) and comprehensively understand their underlying pathological mechanism. METHODS: We performed (1) genome-wide DNA methylation and mRNA expression profiling in peripheral blood mononuclear cells from RA patients and health controls; (2) correlation analysis and causal inference tests for DNA methylation and mRNA expression data; (3) differential methylation genes regulatory network construction; (4) validation tests of 10 differential methylation positions (DMPs) of interest and corresponding gene expressions; (5) correlation between PARP9 methylation and its mRNA expression level in Jurkat cells and T cells from patients with RA; (6) testing the pathological functions of PARP9 in Jurkat cells. RESULTS: A total of 1046 DNA methylation positions were associated with RA. The identified DMPs have regulatory effects on mRNA expressions. Causal inference tests identified six DNA methylation-mRNA-RA regulatory chains (eg, cg00959259-PARP9-RA). The identified DMPs and genes formed an interferon-inducible gene interaction network (eg, MX1, IFI44L, DTX3L and PARP9). Key DMPs and corresponding genes were validated their differences in additional samples. Methylation of PARP9 was correlated with mRNA level in Jurkat cells and T lymphocytes isolated from patients with RA. The PARP9 gene exerted significant effects on Jurkat cells (eg, cell cycle, cell proliferation, cell activation and expression of inflammatory factor IL-2). CONCLUSIONS: This multistage study identified an interferon-inducible gene interaction network associated with RA and highlighted the importance of PARP9 gene in RA pathogenesis. The results enhanced our understanding of the important role of DNA methylation in pathology of RA.

Characterization of a recombinant d-allulose 3-epimerase from Agrobacterium sp. ATCC 31749 and identification of an important interfacial residue.

d-Allulose 3-epimerase (DAEase) catalyzes the epimerization between d-fructose and d-allulose. We had PCR-cloned and overexpressed the gene encoding Agrobacterium sp. ATCC 31749 DAEase (AsDAEase) in Escherichia coli. A high yield of active AsDAEase, 35,300U/L or 1350U/g of wet cells, was acquired with isopropyl ß-d-1-thiogalactopyranoside induction at 20°C for 20h. Although only six residues including residue 234 located in tetrameric interface are different between AsDAEase and A. tumefaciens DAEase (AtDAEase), the specific activity of purified AsDAEase is much larger than that of AtDAEase. The optimal pHs and optimal temperatures of the purified recombinant AsDAEase are 7.5-8.0 and 55-60°C, respectively. The half-life of the enzyme is 267min at 55°C in the presence of 0.1mM Co2+, and the equilibrium ratio between d-allulose and d-fructose is 30:70 at 55°C. Besides characterizing AsDAEase, mutation N234D was constructed to assess its influence on activity. The specific activity of the purified N234D AsDAEase is only 25.5% of wild-type's activity, suggesting residue N234 is an important interfacial residue which substantially affects enzyme activity. The high specific activity and high expression yield of AsDAEase suggest its prospect to be applied in d-allulose production.

Identification of expression quantitative trait loci (eQTLs) in human peripheral blood mononuclear cells (PBMCs) and shared with liver and brain.

PBMCs are essential for immunity and involved in various diseases. To identify genetic variations contributing to PBMCs transcriptome-wide gene expression, we performed a genome-wide eQTL analysis by using genome-wide SNPs data and transcriptome-wide mRNA expression data. To assess whether there are common regulation patterns shared among different tissues/organs, public datasets were utilized to identify common eQTLs shared with PBMCs in lymphoblastoid, monocytes, liver, and brain. Allelic expression imbalance (AEI) assay was employed to validate representative eQTLs identified. We identified 443 cis- and 2386 trans-eSNPs (FDR <0.05), which regulated 128 and 635 target genes, respectively. A transcriptome-wide expression regulation network was constructed, highlighting the importance of 28 pleiotropic eSNPs and 18 dually (cis- and trans-) regulated genes. Three genes, that is, TIPRL, HSPB8, and EGLN3, were commonly regulated by hundreds of eSNPs and constituted a very complex interaction network. Strikingly, the missense SNP rs371513 trans- regulated 25 target genes, which were functionally related to poly(A) RNA binding. Among 8904 eQTLs (P < 0.001) identified herein in PBMCs, a minority (163) was overlapped with lymphoblastoid, monocytes, liver, and/or brain. Besides, two cis-eSNPs in PBMC were confirmed by AEI. The present results demonstrated a comprehensive expression regulation network for human PBMCs and may provide novel insights into the pathogenesis of immunological diseases related to PBMCs.

Multiple correlation analyses revealed complex relationship between DNA methylation and mRNA expression in human peripheral blood mononuclear cells.

DNA methylation is an important regulator on the mRNA expression. However, a genome-wide correlation pattern between DNA methylation and mRNA expression in human peripheral blood mononuclear cells (PBMCs) is largely unknown. The comprehensive relationship between mRNA and DNA methylation was explored by using four types of correlation analyses and a genome-wide methylation-mRNA expression quantitative trait locus (eQTL) analysis in PBMCs in 46 unrelated female subjects. An enrichment analysis was performed to detect biological function for the detected genes. Single pair correlation coefficient (r T1) between methylation level and mRNA is moderate (-0.63-0.62) in intensity, and the negative and positive correlations are nearly equal in quantity. Correlation analysis on each gene (T4) found 60.1% genes showed correlations between mRNA and gene-based methylation at P < 0.05 and more than 5.96% genes presented very strong correlation (R T4 > 0.8). Methylation sites have regulation effects on mRNA expression in eQTL analysis, with more often observations in region of transcription start site (TSS). The genes under significant methylation regulation both in correlation analysis and eQTL analysis tend to cluster to the categories (e.g., transcription, translation, regulation of transcription) that are essential for maintaining the basic life activities of cells. Our findings indicated that DNA methylation has predictive regulation effect on mRNA with a very complex pattern in PBMCs. The results increased our understanding on correlation of methylation and mRNA and also provided useful clues for future epigenetic studies in exploring biological and disease-related regulatory mechanisms in PBMC.

Integrative multi-omics analysis revealed SNP-lncRNA-mRNA (SLM) networks in human peripheral blood mononuclear cells.

Long non-coding RNAs (lncRNAs) serve as important controller of cellular functions via regulating RNA transcription, degradation and translation. However, what are the regulation patterns of lncRNAs on downstream mRNA and how the upstream genetic variants regulate lncRNAs are largely unknown. We first performed a comprehensive expression quantitative trait locus (eQTL) analysis (MatrixeQTL package, R) using genome-wide lncRNA expression and SNP genotype data from human peripheral blood mononuclear cells (PBMCs) of 43 unrelated individuals. Subsequently, multi-omics integrative network analysis was applied to construct SNP-lncRNA-mRNA (SLM) interaction networks. The causal inference test (CIT) was used to identify lncRNA-mediated (epi-) genetic regulation on mRNA expressions. Our eQTL analysis detected 707 pairs of cis-effect associations (p < 5.64E-06) and 6657 trans-effect associations (p < 3.51E-08), respectively. We also found that top significant cis-eSNPs were enriched around the lncRNA transcription start site regions, and that enrichment patterns of cis-eSNPs differs among different lncRNA sizes (small, medium and large).The constructed SLM interaction networks (1 primary networks and four small separate networks) showed various complex interaction patterns. Especially, the in-depth CIT detected 50 significant lncRNA-mediated SLM trios, and some hotspots (e.g., SNPs: rs926370, rs7716167 and rs16880521; lncRNAs: HIT000061975 and ENST00000579057.1). This study represents the first effort of dissecting the SLM interaction patterns in PBMCs by multi-omics integrative network analysis and causal inference test for clearing the regulation chain. The results provide novel insights into the regulation patterns of lncRNA, and may facilitate investigations of PBMC-related immune physiological process and immunological diseases in the future.

Non-invasive evaluation of liver stiffness after splenectomy in rabbits with CCl4-induced liver fibrosis.

AIM: To investigate the diagnostic performance of liver stiffness measurement (LSM) by elastography point quantification (ElastPQ) in animal models and determine the longitudinal changes in liver stiffness by ElastPQ after splenectomy at different stages of fibrosis. METHODS: Liver stiffness was measured in sixty-eight rabbits with CCl4-induced liver fibrosis at different stages and eight healthy control rabbits by ElastPQ. Liver biopsies and blood samples were obtained at scheduled time points to assess liver function and degree of fibrosis. Thirty-one rabbits with complete data that underwent splenectomy at different stages of liver fibrosis were then included for dynamic monitoring of changes in liver stiffness by ElastPQ and liver function according to blood tests. RESULTS: LSM by ElastPQ was significantly correlated with histologic fibrosis stage (r = 0.85, P < 0.001). The optimal cutoff values by ElastPQ were 11.27, 14.89, and 18.21 kPa for predicting minimal fibrosis, moderate fibrosis, and cirrhosis, respectively. Longitudinal monitoring of the changes in liver stiffness by ElastPQ showed that early splenectomy (especially F1) may delay liver fibrosis progression. CONCLUSION: ElastPQ is an available, convenient, objective and non-invasive technique for assessing liver stiffness in rabbits with CCl4-induced liver fibrosis. In addition, liver stiffness measurements using ElastPQ can dynamically monitor the changes in liver stiffness in rabbit models, and in patients, after splenectomy.

Early complications after interventions in patients with acute pancreatitis.

AIM: To identify the possible predictors of early complications after the initial intervention in acute necrotizing pancreatitis. METHODS: We collected the medical records of 334 patients with acute necrotizing pancreatitis who received initial intervention in our center. Complications associated with predictors were analyzed. RESULTS: The postoperative mortality rate was 16% (53/334). Up to 31% of patients were successfully treated with percutaneous catheter drainage alone. The rates of intra-abdominal bleeding, colonic fistula, and progressive infection were 15% (50/334), 20% (68/334), and 26% (87/334), respectively. Multivariate analysis indicated that Marshall score upon admission, multiple organ failure, preoperative respiratory infection, and sepsis were the predictors of postoperative progressive infection (P < 0.05). Single organ failure, systemic inflammatory response syndrome upon admission, and C-reactive protein level upon admission were the risk factors of postoperative colonic fistula (P < 0.05). Moreover, preoperative Marshall score, organ failure, sepsis, and preoperative systemic inflammatory response syndrome were the risk factors of postoperative intra-abdominal bleeding (P < 0.05). CONCLUSION: Marshall score, organ failures, preoperative respiratory infection, sepsis, preoperative systemic inflammatory response syndrome, and C-reactive protein level upon admission are associated with postoperative complications.

Over-expression of microRNA-375 inhibits papillary thyroid carcinoma cell proliferation and induces cell apoptosis by targeting ERBB2.

MicroRNAs (miRs) played important roles in the cell proliferation, apoptosis and other biological processes in cancer. In the present study we found that miR-375 was significantly down-regulated in human papillary thyroid carcinoma (PTC) tissues and cell lines. In this study we try to investigate the biological activity of miR-375 in human PTC cells and try to find the potential target of miR-375. Our study indicated that over-expression of miR-375 could inhibit the PTC cells proliferation and this inhibition was caused by the induction of cell apoptosis. In vivo animal study indicated that over-expression of miR-375 could significantly decrease the migration and invasion of human PTC cell in vivo. These results exhibit over-expression of miR-375 in human PTC cells could inhibit the process of human PTC. Further study demonstrated ERBB2 was a direct target of miR-375, over-expression of miR-375 decrease the both mRNA and protein expression of ERBB2 in human PTC cells. These data indicate miR-375 play important roles in the process and development of human PTC. These finds suggested that appropriate application of miR-375 regulation might be a new sight for the treatment of human PTC in the future.

High glucose induces renal tubular epithelial injury via Sirt1/NF-kappaB/microR-29/Keap1 signal pathway.

OBJECTIVE: Diabetic nephropathy (DN) is a serious complication that commonly confronted by diabetic patients. A common theory for the pathogenesis of this renal dysfunction in diabetes is cell injury, inflammation as well as oxidative stress. In this content, the detailed molecular mechanism underlying high glucose induced renal tubular epithelial injury was elaborated. METHODS: An in vivo rat model of diabetes by injecting streptozotocin (STZ) and an in vitro high glucose incubated renal tubular epithelial cell (HK-2) model were used. Expression levels of Keap1, nuclear Nrf2 and p65 were determined by western blotting. Level of microR-29 (miR-29) was assessed using quantitative RT-PCR. Combination of p65 and miR-29 promotor was assessed using chromatin immunoprecipitation. Keap1 3'-UTR activity was detected using luciferase reporter gene assay. Cell viability was determined using MTT assay. RESULTS: In diabetic rat, miR-29 was downregulated and its expression is negatively correlated with both of serum creatinine and creatinine clearance. In high glucose incubated HK-2 cell, deacetylases activity of Sirt1 was attenuated that leads to decreased activity of nuclear factor kappa B (NF-κB). NF-κB was demonstrated to regulate miR-29 expression by directly binding to its promotor. The data of luciferase assay showed that miR-29 directly targets to Keap1 mRNA. While high glucose induced down regulation of miR-29 contributed to enhancement of Keap1 expression that finally reduced Nrf2 content by ubiquitinating Nrf2. Additionally, overexpression of miR-29 effectively relieved high glucose-reduced cell viability. CONCLUSION: High glucose induces renal tubular epithelial injury via Sirt1/NF-κB/microR-29/Keap1 signal pathway.