Development and validation of a deep interpretable network for continuous acute kidney injury prediction in critically ill patients.

Early detection of acute kidney injury (AKI) may provide a crucial window of opportunity to prevent further injury, which helps improve clinical outcomes. This study aimed to develop a deep interpretable network for continuously predicting the 24-hour AKI risk in real-time and evaluate its performance internally and externally in critically ill patients. A total of 21,163 patients' electronic health records sourced from Beth Israel Deaconess Medical Center (BIDMC) were first included in building the model. Two external validation populations included 3025 patients from the Philips eICU Research Institute and 2625 patients from Zhongda Hospital Southeast University. A total of 152 intelligently engineered predictors were extracted on an hourly basis. The prediction model referred to as DeepAKI was designed with the basic framework of squeeze-and-excitation networks with dilated causal convolution embedded. The integrated gradients method was utilized to explain the prediction model. When performed on the internal validation set (3175 [15 %] patients from BIDMC) and the two external validation sets, DeepAKI obtained the area under the curve of 0.799 (95 % CI 0.791-0.806), 0.763 (95 % CI 0.755-0.771) and 0.676 (95 % CI 0.668-0.684) for continuousAKI prediction, respectively. For model interpretability, clinically relevant important variables contributing to the model prediction were informed, and individual explanations along the timeline were explored to show how AKI risk arose. The potential threats to generalisability in deep learning-based models when deployed across health systems in real-world settings were analyzed.

Association between diastolic blood pressure during the first 24 h and 28-day mortality in patients with septic shock: a retrospective observational study.

BACKGROUND: Although the mean arterial pressure (MAP) target of 65 mmHg was achieved, diastolic blood pressure (DBP) was still low in some septic shock patients. The effects of DBP on the prognosis and optimal target for patients with septic shock are unclear. We sought to investigate the relationship between DBP and 28-day mortality in septic shock patients. METHODS: In this retrospective observational study, we obtained data from the Chinese Database in Intensive Care (CDIC). We included patients with an admission diagnosis of septic shock and shock was controlled. DBP was measured every 1 h, and the mean DBP during the first 24 h (mDBP24h) was recorded. The primary outcome was 28-day mortality. Multivariable logistic regression determined the relationship between mDBP24h and 28-day mortality. RESULTS: In total, 1251 patients were finally included. The 28-day mortality of included septic shock patients was 28.3%. The mDBP24h, not mSBP24h, was higher among 28-day survivors compared with non-survivors. 28-day mortality was inversely associated with mDBP24h (unadjusted OR 0.814 per 10 mmHg higher mDBP24h, P = 0.003), with a stepwise increase in 28-day mortality at lower mDBP24h. The 28-day mortality of patients with mDBP24h < 59 mmHg had an absolute risk reduction of 9.4% (P = 0.001). And mDBP24h < 59 mmHg was the remaining high risk factor inversely associated with 28-day mortality after multivariable adjustment (adjusted OR 1.915, 95% CI 1.037-3.536, P = 0.038), while mMAP24h and mSBP24h were not. CONCLUSION: In patients with septic shock after initial resuscitation, we observed an inverse association between mDBP24h and 28-day mortality. The poor outcomes in patients with mDBP24h < 59 mmHg provide indirect evidence supporting a further DBP goal of 59 mmHg for patients with septic shock after MAP of 65 mmHg was achieved.

Impact of renal complications on outcome in adult patients with acute fulminant myocarditis receiving venoarterial extracorporeal membrane oxygenation: an analysis of nationwide CSECLS database in China.

BACKGROUND: Limited data are available on renal complications in patients with acute fulminant myocarditis (AFM) receiving venoarterial extracorporeal membrane oxygenation (VA-ECMO) support in China. To evaluate the impact of renal complications on outcomes in adult patients with AFM supported with VA-ECMO. METHODS: Data were extracted from Chinese Society of ExtraCorporeal Life Support (CSECLS) Registry database. Adult patients who were diagnosed with AFM receiving VA-ECMO support in the database were included. The primary outcome was 30-day mortality in patients with AFM supported with VA-ECMO. Logistic regression model was used to examine the impact of renal complications on 30-day mortality by adjusting confounders. RESULTS: A total of 202 patients were included. The median age was 38 years (IQR 29-48) and males (n = 103) represented 51.0% of the total accounted patients. The median ECMO duration was 142.9 h (IQR 112.1-188.8 h). 178 (88.1%) patients weaned from ECMO and 156 (71.9%) patients survived. 94(46.5%) patients developed renal complications while on ECMO course. Patients with renal complications had higher 30-day mortality (40.7% (37 of 94) vs 8.3% (9 of 108), P < 0.001) compared with those without. The development of renal complications was related to a 3.12-fold increase risk of 30-day mortality (adjusted OR 3.120, 95%CI 1.002-6.577, P = 0.049). Increasing age (adjusted OR1.025, 95% CI 1.008-1.298, P = 0.040) and higher SOFA score (adjusted OR 1.162, 95%CI 1.012-1.334, P = 0.034) were independent risk factors of renal complications. CONCLUSIONS: Our findings demonstrated that patients with AFM receiving VA-ECMO at high risk of developing renal complications. Advancing age and higher SOFA score was associated with increased risk of developing renal complications. The onset of renal complications was significantly associated with 30-day mortality.

MLACNN: an attention mechanism-based CNN architecture for predicting genome-wide DNA methylation.

Methylation is an important epigenetic regulation of methylation genes that plays a crucial role in regulating biological processes. While traditional methods for detecting methylation in biological experiments are constantly improving, the development of artificial intelligence has led to the emergence of deep learning and machine learning methods as a new trend. However, traditional machine learning-based methods rely heavily on manual feature extraction, and most deep learning methods for studying methylation extract fewer features due to their simple network structures. To address this, we propose a bottomneck network based on an attention mechanism and use new methods to ensure that the deep network can learn more effective features while minimizing overfitting. This approach enables the model to learn more features from nucleotide sequences and make better predictions of methylation. The model uses three coding methods to encode the original DNA sequence and then applies feature fusion based on attention mechanisms to obtain the best fusion method. Our results demonstrate that MLACNN outperforms previous methods and achieves more satisfactory performance.

The Structural Basis of African Swine Fever Virus pS273R Protease Binding to E64 through Molecular Dynamics Simulations.

Identification of novel drugs for anti-African swine fever (ASF) applications is of utmost urgency, as it negatively affects pig farming and no effective vaccine or treatment is currently available. African swine fever virus (ASFV) encoded pS273R is a cysteine protease that plays an important role in virus replication. E64, acting as an inhibitor of cysteine protease, has been established as exerting an inhibitory effect on pS273R. In order to obtain a better understanding of the interaction between E64 and pS273R, common docking, restriction docking, and covalent docking were employed to analyze the optimal bonding position between pS273R-E64 and its bonding strength. Additionally, three sets of 100 ns molecular dynamics simulations were conducted to examine the conformational dynamics of pS273R and the dynamic interaction of pS273R-E64, based on a variety of analytical methods including root mean square deviation (RMSD), root mean square fluctuation (RMSF), free energy of ligand (FEL), principal component analysis (PCA), and molecular mechanics/Poisson-Boltzmann surface area (MM/PBSA) analysis. The results show that E64 and pS273R exhibited close binding degrees at the activity center of ASFV pS273R protease. The data of these simulations indicate that binding of E64 to pS273R results in a reduction in flexibility, particularly in the ARM region, and a change in the conformational space of pS273R. Additionally, the ability of E64 to interact with polar amino acids such as ASN158, SER192, and GLN229, as well as charged amino acids such as LYS167 and HIS168, seems to be an important factor in its inhibitory effect. Finally, Octet biostratigraphy confirmed the binding of E64 and pS273R with a KD value of 903 uM. Overall, these findings could potentially be utilized in the development of novel inhibitors of pS273R to address the challenges posed by ASFV.

Optimized protocol for double vaccine immunization against classical swine fever and porcine reproductive and respiratory syndrome.

BACKGROUND: Classical swine fever and porcine reproductive and respiratory syndrome have seriously affected the development of the swine breeding industry in China. Vaccine immunization remains the main way to prevent these infections. The aim of this study was to establish an optimized protocol for vaccine immunization against classical swine fever virus (CSFV) and porcine reproductive and respiratory syndrome virus (PRRSV). METHODS: Blood samples were collected from the anterior vena cava of pigs after immunization, and blood indices, secreted levels of specific antibodies and neutralizing antibodies associated with humoral immunity, the proliferation capacity of T lymphocytes as a measure of cellular immunity, and secreted levels of IFN-γ and TNF-α were determined. RESULTS: The results showed that simultaneous immunization against CSFV and PRRSV infections induced strong and specific humoral and T-cellular immune responses, high levels of cytokine IFN-γ secretion and delayed secretion of cytokine TNF-α. Moreover, significantly higher lymphocyte percentages and red blood cell and leukocyte counts were found in the group simultaneously immunized against CSFV and PRRSV. However, no statistically significant differences were observed in hemoglobin values, neutrophil counts, and median cell percentages among the S + PRRS, PRRS-S, and S-PRRS groups. CONCLUSION: This study demonstrated that simultaneous immunization against CSFV and PRRSV had the advantages of inducing a rapid, enhanced, and long-lasting immune response. These findings provide a theoretical basis for the establishment of a reasonable and optimized vaccine immunization protocol against CSFV and PRRSV in combination with a variety of other vaccine inoculations.

Clinical outcome and risk factors for acute fulminant myocarditis supported by venoarterial extracorporeal membrane oxygenation: An analysis of nationwide CSECLS database in China.

BACKGROUND: To assess the outcomes and risk factors for adult patients with acute fulminant myocarditis (AFM) supported with venoarterial extracorporeal membrane oxygenation (VA ECMO) in China mainland. METHODS: Data were extracted from Chinese Society of ExtraCorporeal Life Support (CSECLS) Registry database. Data from adult patients who were diagnosed with AFM and needed VA ECMO in the database were retrospectively analyzed. The primary outcome was 90-day mortality after ECMO initiation in patients with AFM supported with VA ECMO. Cox proportional hazard regression model was used to examine the risk factors associated with 90-day mortality. RESULTS: Among 221 patients enrolled and followed up to 90 days, 186 (84.2%) patients weaned from ECMO and 159 (71.9%) patients survived and discharged home. The median age was 38 years (IQR 29-49) and males (n = 115) represented 52.0% of the total accounted patients. The median ECMO duration was 134 h (IQR 96-177 h). The main adverse event during ECMO course was bleeding (16.3%), followed by infection (15.4%). In the multivariate Cox model analysis, cardiac arrest prior to ECMO initiation (adjusted HR 2.529; 95%CI: 1.341-4.767, p = 0.004), lower pH value (adjusted HR 0.016; 95%CI: 0.010-0.059, p < 0.001) and higher lactate concentration at 24 h after ECMO initiation (adjusted HR 1.146; 95%CI: 1.075-1.221, p < 0.001) were associated with 90-day mortality. CONCLUSIONS: 71.9% patients with AFM (clinical diagnosed) supported with VA ECMO survived. Cardiac arrest prior to ECMO, lower pH and higher lactate concentration at 24 h after ECMO initiation were correlated with 90-day mortality of AFM patients supported with VA ECMO.

Ferulic acid alleviates AFB1-induced duodenal barrier damage in rats via up-regulating tight junction proteins, down-regulating ROCK, competing CYP450 enzyme and activating GST.

Previous studies reported that Aflatoxin B1 (AFB1) causes cell damage through its metabolite aflatoxin B1-8, 9-epoxide (AFBO), which is catalyzed by CYP450 enzymes. AFBO can be detoxified by glutathione S transferase (GST). Ferulic acid (FA) is known for its antioxidant capacity and intestinal protective function. However, the mechanism of AFB1 causing duodenal injury and the role of FA in AFB1-induced intestinal damage remains unclear. In this study, rats were exposed to AFB1 and treated with FA for 30 days. The results showed that I) FA alleviated the histopathological changes of duodenum and the ultrastructural changes of tight junctions between duodenal epithelial cells induced by AFB1. II) FA reduced the content of AFB1-ALB adduct in blood. III) The low expression of tight junction proteins (Claudin-1 and ZO-1) and the high expression of ROCK1 and ROCK2 induced by AFB1 were significantly reversed by FA. IV) The high expression of CYP2A6 and CYP3A4 were significantly down-regulated by FA, and the activity of GST was promoted by FA. V) The binding affinity of FA to CYP2A6 is very similar to the binding affinity of AFB1 to CYP2A6, which meaning that there is a competitive relationship between FA and AFB1 when conjugating to CYP2A6. These results suggested that FA proved effective in alleviating AFB1-induced duodenal barrier damage via up-regulating tight junction proteins, down-regulating ROCK, competing CYP450 enzyme, and activating GST in duodenal epithelial cells of rats.

Evaluation and Optimization of Microdrop Digital PCR for Detection of Serotype A and B Clostridium botulinum.

Clostridium botulinum is the causative pathogen of botulism. Laboratory detection of C. botulinum is essential for clinical therapy treatment of botulism due to the difficulty in diagnosis, especially in infant botulism. The extreme toxicity of botulinum neurotoxin (BoNT) requires a sensitive detection method. Due to the detection limit of real-time quantitative PCR (q-PCR), a more sensitive detection method, micro-drop digital PCR (ddPCR) was applied in C. botulinum main serotypes A and B. The following performance criteria were evaluated by ddPCR: analytical sensitivity; repeatability; and diagnostic specificity. The limit of detection (LOD) was 0.84 and 0.88 copies/µl for BoNT A and B genes, respectively, by ddPCR with high specificity, compared to 5.04×102 and 6.91×102 copies/µl by q-PCR. It was increased 10 times compared with q-PCR in spiked stool samples. This improvement in sensitivity was especially important in clinical samples as more positive samples were detected by digital PCR compared with q-PCR. Meanwhile, enrichment time for low bacteria content samples was shortened by four hours both in serotypes A and B C. botulinum by ddPCR compared with q-PCR, which are important for laboratory diagnosis and epidemiology work.

Pharmacokinetic/Pharmacodynamic Parameters of Linezolid in the Epithelial Lining Fluid of Patients With Sepsis.

The aim of this study was to investigate the pharmacokinetic/pharmacodynamic parameters of linezolid in both the plasma and epithelial lining fluid (ELF) of patients with pneumonia-induced sepsis. Blood specimens and bronchoalveolar lavage samples were collected at defined time points after administration of linezolid. The concentration in the ELF was calculated by urea dilution method. PK parameters were calculated, and probability of target attainment was evaluated by Monte Carlo simulations. Twenty-three patients were enrolled, 8 of whom had septic shock. The maximum concentration of linezolid was higher in the ELF than in the plasma (36.02 ± 13.17 vs 19.51±4.83 mg/L, P < .001) in all of the patients. In patients with septic shock, the maximum concentration in the ELF was significantly higher than that in the non-septic shock group (45.25 ± 11.70 vs 31.10 ± 11.38 mg/L, P = .01), while there was no significant difference in the plasma. The corresponding probability of target attainment values were 90.5% and 65.1% in ELF and plasma, respectively, with a minimum inhibitory concentration of 2 mg/L, which were 99.9% in the ELF in the patients with septic shock. Linezolid possesses an efficient penetration into the ELF of patients with pneumonia-induced sepsis with mechanical ventilation. When minimum inhibitory concentration ≤ 2 mg/L, 600 mg of linezolid every 12 hours could achieve the optimal therapeutic targets in the ELF rather than in the plasma of patients with pneumonia-induced sepsis.

Synbiotic Therapy Prevents Nosocomial Infection in Critically Ill Adult Patients: A Systematic Review and Network Meta-Analysis of Randomized Controlled Trials Based on a Bayesian Framework.

Background: The efficacy of synbiotics, probiotics, prebiotics, enteral nutrition or adjuvant peripheral parenteral nutrition (EPN) and total parenteral nutrition (TPN) in preventing nosocomial infection (NI) in critically ill adults has been questioned. We conducted a systematic review and network meta-analysis (NMA) of randomized controlled trials (RCTs) to evaluate and rank the effectiveness of these therapies on NI amongst critically ill adults. Methods: Four electronic databases were systematically searched up to June 30, 2019 for RCTs comparing the administration of probiotics, prebiotics, synbiotics, EPN and TPN in critically ill adults. The primary outcome was NI. The relative efficacy of all outcomes was determined by a Bayesian framework with random effects NMA. We estimated the odds ratio (OR) and mean difference (MD) and ranked the comparative effects of all regimens with the surface under the cumulative ranking probabilities. The study has been registered on PROSPERO (CRD42019147032). Results: Fifty-five RCTs (7,119 patients) were identified. Primary outcome showed that synbiotics had the best effect in preventing NI than EPN (OR 0.37; 95% CrI 0.22-0.61), probiotics followed (OR 0.52; 95% CrI 0.34-0.77), whereas TPN significantly increased NI (OR 2.29; 95% CrI 1.48-3.67). Subgroup analysis showed that TPN significantly increased NI in intensive care unit (ICU) patients (OR 1.57; 95% CrI 1.01-2.56) and severe acute pancreatitis (SAP) patients (OR 3.93; 95% CrI 1.74-9.15). Secondary outcomes showed that synbiotics were more effective in preventing hospital-acquired pneumonia (HAP) (OR 0.34; 95% CrI 0.11-0.85), catheter-related bloodstream infection (OR 0.08; 95% CrI 0.01-0.80), urinary tract infection (OR 0.27; 95% CrI 0.08-0.71) and sepsis (OR 0.34; 95% CrI 0.16-0.70) than EPN. Amongst the treatments, probiotics were most effective for shortening the mechanical ventilation duration (MD -3.93; 95% CrI -7.98 to -0.02), prebiotics were most effective for preventing diarrhea (OR 0.24; 95% CrI 0.05-0.94) and TPN was the least effective in shortening hospital length of stay (MD 4.23; 95% CrI 0.97-7.33). Conclusions: Amongst the five therapies, synbiotics not only prevented NI in critically ill adults but also demonstrated the best treatment results. By contrast, TPN did not prevent NI and ranked last, especially in ICU and SAP patients. Take-Home Message: Nosocomial infection is a leading cause of mortality in critically ill patients in the ICU. However, the efficacy of synbiotics, probiotics, prebiotics, enteral nutrition or adjuvant peripheral parenteral nutrition and total parenteral nutrition in preventing nosocomial infection in critically ill adults has been questioned. The network meta-analysis provides evidence that amongst the five therapies, synbiotics not only prevented NI in critically ill adults but also demonstrated the best treatment results. By contrast, TPN did not prevent NI and ranked last, especially in ICU and SAP patients. The results of this study will provide a new scientific basis and a new idea for the debate on the efficacy of synbiotics and other treatments in the improvement of prognosis in critically ill adult patients. Tweet: Synbiotic prevents nosocomial infection in critically ill adults, while total parenteral nutrition has the adverse curative.

Ferulic acid prevents aflatoxin B1-induced liver injury in rats via inhibiting cytochrome P450 enzyme, activating Nrf2/GST pathway and regulating mitochondrial pathway.

Aflatoxin B1 (AFB1) causes oxidative stress and hepatocyte apoptosis through its epoxidized metabolite AFBO, which is catalyzed by CYP450 enzymes. Ferulic acid (FA) is a phenolic acid commonly found in plants and is known for its antioxidant capacity. However, the role of FA in AFB1-induced liver injury is still elusive. In this study, rats were exposed to AFB1 and simultaneously treated with FA for 30 days. The results showed that I) FA alleviated the histopathological changes induced by AFB1, inhibited the elevation of serological indexes induced by AFB1, and reduced the production of AFBO in liver. II) AFB1-induced increase in CYP450 expression was significantly reduced by FA. The molecular docking results of FA and CYP2A6 showed high fitness score and interaction. III) FA obviously inhibited the production of MDA, and significantly activated the Nrf2/GST pathway and antioxidant enzymes (SOD and GST). IV) AFB1-induced hepatocyte apoptosis, the high expression of p53, bax, cyt-c, caspase-9, caspase-3, and the low expression of bcl-2 were all restored by FA. It has been suggested from these results that FA proved effective against AFB1-induced liver damage in rats via inhibiting CYP450 enzyme, promoting antioxidant pathway Nrf2/GST, activating antioxidant enzymes (SOD and GST), and regulating the mitochondrial pathway.

[Chemokine receptor 7 promotes the paracrine of hepatocyte growth factor by mesenchymal stem cells via inhibitor of differentiation-1].

OBJECTIVE: To investigate the possible mechanism of mesenchymal stem cells (MSC) secreting hepatocyte growth factor (HGF). METHODS: (1) C57BL/6 mouse mesenchymal stem cells (mMSC) were cultured in vitro, and mMSC with high expression of chemokine receptor 7 (CXCR7) were transduced by lentivirus plasmid. Blank control group and empty carrier control group were set at the same time. After 20 generations of cell culture, the transfection efficiency was identified by fluorescence microscopy and flow cytometry. The mRNA expression levels of CXCR7 in mMSC were detected by real-time fluorescent quantitative reverse transcription-polymerase chain reaction (RT-PCR). (2) mMSC with passage number 4-6 were divided into MSC control group [MSC-blank group, 100 µg/L lipopolysaccharide (LPS) was added to wild-type MSC], highly expressed CXCR7 group (MSC-OE-CXCR7 group, 100 µg/L LPS was added to mMSC transduced by lentivirus plasmid with high expression of CXCR7), highly expressed CXCR7 control group (MSC-OENC-CXCR7 group, 100 µg/L LPS was added to mMSC transduced by no load lentivirus plasmid), CXCR4 inhibitor group (MSC-IE-CXCR4 group, 100 µg/L LPS was added to mMSC after 0.1 mg/L CXCR4 inhibitor TC14012 pretreatment for 24 hours), and CXCR4 inhibitor control group (MSC-IENC-CXCR4 group, 100 µg/L LPS was added to mMSC after DMEM culture medium with equal amount of TC14012 pretreatment for 24 hours). Cells in each group were collected after treatment with LPS, and mRNA expression of inhibitor of differentiation-1 (ID-1) was detected by RT-PCR. The cell supernatant was collected, and the levels of HGF were detected by enzyme linked immunosorbent assay (ELISA). RESULTS: (1) The high expression of CXCR7 for mMSC which were transduced through lentivirus plasmid were successfully constructed detected by fluorescence microscope and flow cytometry. Compared with the blank control group, the expression of CXCR7 mRNA in the lentivirus with high expression of CXCR7 group was significantly increased (2-ΔΔCt: 5.81±0.97 vs. 1.02±0.12, P < 0.05). There was no significant difference in CXCR7 mRNA expression between the empty carrier control group and the blank control group (2-ΔΔCt: 0.95±0.22 vs. 1.02±0.12, P > 0.05). (2) Compared with the MSC-blank group, high expression of CXCR7 in MSC-OE-CXCR7 group or inhibition of CXCR4 in MSC-IE-CXCR4 group could induce high expression of ID-1 mRNA in mMSC (2-ΔΔCt: 5.56±0.66, 2.47±0.58 vs. 1.00±0.10, both P < 0.05) and increase HGF exocrine level (ng/L: 632.02±149.98, 217.21±40.53 vs. 108.53±24.62, both P < 0.05). However, there were no significant differences in ID-1 mRNA expression and HGF exocrine level of mMSC among MSC-OENC-CXCR7 group, MSC-IENC-CXCR4 group and MSC-blank group [ID-1 mRNA (2-ΔΔCt): 1.01±0.27, 1.21±0.32 vs. 1.00±0.10, HGF (ng/L): 133.56±25.19, 107.11±25.30 vs. 108.53±24.62, both P > 0.05]. CONCLUSIONS: High expression of CXCR7 or inhibition of CXCR4 in MSC can increase the expression of ID-1 and promote the secretion of HGF, thus promoting pulmonary microvascular endothelial repair.

Beyond a Ribosomal RNA Methyltransferase, the Wider Role of MraW in DNA Methylation, Motility and Colonization in Escherichia coli O157:H7.

MraW is a 16S rRNA methyltransferase and plays a role in the fine-tuning of the ribosomal decoding center. It was recently found to contribute to the virulence of Staphylococcus aureus. In this study, we examined the function of MraW in Escherichia coli O157:H7 and found that the deletion of mraW led to decreased motility, flagellar production and DNA methylation. Whole-genome bisulfite sequencing showed a genome wide decrease of methylation of 336 genes and 219 promoters in the mraW mutant including flagellar genes. The methylation level of flagellar genes was confirmed by bisulfite PCR sequencing. Quantitative reverse transcription PCR results indicated that the transcription of these genes was also affected. MraW was furtherly observed to directly bind to the four flagellar gene sequences by electrophoretic mobility shift assay (EMSA). A common flexible motif in differentially methylated regions (DMRs) of promoters and coding regions of the four flagellar genes was identified. Reduced methylation was correlated with altered expression of 21 of the 24 genes tested. DNA methylation activity of MraW was confirmed by DNA methyltransferase activity assay in vitro and repressed by DNA methylation inhibitor 5-aza-2'-deoxycytidine (5-aza). In addition, the mraW mutant colonized poorer than wild type in mice. We also found that the expression of mraZ in the mraW mutant was increased confirming the antagonistic effect of mraW on mraZ. In conclusion, mraW was found to be a DNA methylase and have a wide-ranging effect on E. coli O157:H7 including motility and virulence in vivo via genome wide methylation and mraZ antagonism.

Diagnostic value of circulating miR-21 for colorectal cancer: a meta-analysis.

BACKGROUND: MicroRNA-21 (miR-21) is highly expressed in the plasma of colorectal cancer (CRC) patients. Thus, miR-21 may be a useful novel diagnostic biomarker for CRC. This meta-analysis aims to verify the diagnostic value of circulating miR-21 in CRC patients. METHODS: A literature search was conducted for publications that evaluated the diagnostic value of miR-21 for CRC. The quality of each study was scored with the Quality Assessment of Diagnostic Accuracy Studies. The bivariate meta-analysis model was employed to summarize the sensitivity, specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), and diagnostic odds ratio (DOR). Receiver operating characteristic curves were used to check the overall test performance. RESULTS: Five publications with six studies involving 579 patients and 266 controls were included in this meta-analysis. The pooled sensitivity was 77.4% [95% confidence interval (CI): 67.2%-85.1%], specificity was 84.6% (95% CI: 79.7%-88.5%), PLR was 5.02 (95% CI: 3.73-6.75), NLR was 0.27 (95% CI: 0.18-0.40), and DOR was 18.77 (95% CI: 10.41-33.83). The area under the summary ROC curve was 0.86. In addition, the results became prominent in the CRC group when a study that explored the advanced adenoma was excluded. CONCLUSION: Circulating miR-21 may be a suitable diagnostic biomarker for CRC with moderate sensitivity and specificity. Further studies should evaluate the diagnostic value of miR-21 for CRC in the future.

Comparative analysis of the prion protein gene sequences in African lion.

The prion protein gene of African lion (Panthera Leo) was first cloned and polymorphisms screened. The results suggest that the prion protein gene of eight African lions is highly homogenous. The amino acid sequences of the prion protein (PrP) of all samples tested were identical. Four single nucleotide polymorphisms (C42T, C81A, C420T, T600C) in the prion protein gene (Prnp) of African lion were found, but no amino acid substitutions. Sequence analysis showed that the higher homology is observed to felis catus AF003087 (96.7%) and to sheep number M31313.1 (96.2%) Genbank accessed. With respect to all the mammalian prion protein sequences compared, the African lion prion protein sequence has three amino acid substitutions. The homology might in turn affect the potential intermolecular interactions critical for cross species transmission of prion disease.

Amino acid sequence of the Pekingese dog prion protein gene.

Prion diseases are neurodegenerative disorders in humans and various animals associated with a proteinaceous infectious pathogen, designated prion. Canine species seem to be resistant to the infection and no natural prion disease has been documented in dogs. The polymorphisms within the open reading frame of the prion protein gene are associated with the susceptibility of the species, and species barriers, to prion diseases. In the present study, the open reading frame of the prion protein (Prnp) gene from 16 Pekingese dogs was cloned and screened for polymorphisms. One nucleotide polymorphism (G489C) was found; the G to C nucleotide substitution results in a glutamic to aspartic acid change at codon 163. The amino acid sequence of the Pekingese Prnp gene showed the highest homology with that of greyhounds (AF042843), when compared with other Prnp genes in GenBank. Glu/Asp163 and asparagine 107 in canine prion protein genes were replaced by asparagine and serine, respectively, in all the prion protein genes examined. These substitutes might in turn affect the potential intermolecular interactions critical for cross-species transmission of prion disease and might influence the canine susceptibility to prion infection.

Amino acid sequence of the Amur tiger prion protein.

Prion diseases are fatal neurodegenerative disorders in human and animal associated with conformational conversion of a cellular prion protein (PrP(C)) into the pathologic isoform (PrP(Sc)). Various data indicate that the polymorphisms within the open reading frame (ORF) of PrP are associated with the susceptibility and control the species barrier in prion diseases. In the present study, partial Prnp from 25 Amur tigers (tPrnp) were cloned and screened for polymorphisms. Four single nucleotide polymorphisms (T423C, A501G, C511A, A610G) were found; the C511A and A610G nucleotide substitutions resulted in the amino acid changes Lysine171Glutamine and Alanine204Threoine, respectively. The tPrnp amino acid sequence is similar to house cat (Felis catus ) and sheep, but differs significantly from other two cat Prnp sequences that were previously deposited in GenBank.

Quantification of prion gene expression in brain and peripheral organs of golden hamster by real-time RT-PCR.

Determination of tissue-specific expression of cellular prion protein (PrPc) is essential for understanding its poorly explained role in organisms. Herein we report on quantification of PrP mRNA in golden hamsters, a popular experimental model for studying mechanisms of transmissible spongiform encephalopathies (TSE), by real-time RT-PCR. Total RNA was isolated from four different regions of the brain and six peripheral organs of eight golden hamsters. PrP mRNA copy numbers were determined using absolute standard curve method with real-time quantitative PCR instrument. It was found that high mRNA levels were present in all four regions of the brain examined, including obex, neocortex, cerebellum, and thalamus. In peripheral organs examined, inguinal lymph node showed high level of the expression similar to that in overall brain; spleen, heart, liver, and lung showed moderate levels of the expression; and kidney showed the lowest expression. Our result is consistent with the potential involvement of different organs in prion diseases and offers essential data for further study of TSE mechanism in this animal model.