The RAG transposon is active through the deuterostome evolution and domesticated in jawed vertebrates.

RAG1 and RAG2 are essential subunits of the V(D)J recombinase required for the generation of the variability of antibodies and T cell receptors in jawed vertebrates. It was demonstrated that the amphioxus homologue of RAG1-RAG2 is encoded in an active transposon, belonging to the transposase DDE superfamily. The data provided support the possibility that the RAG transposon has been active through the deuterostome evolution and is still active in several lineages. The RAG transposon corresponds to several families present in deuterostomes. RAG1-RAG2 V(D)J recombinase evolved from one of them, partially due to the new ability of the transposon to interact with the cellular reparation machinery. Considering the fact that the RAG transposon survived millions of years in many different lineages, in multiple copies, and that DDE transposases evolved their association with proteins involved in repair mechanisms, we propose that the apparition of V(D)J recombination machinery could be a predictable genetic event.

Association of OCT4, SOX2, and NANOG expression with oral squamous cell carcinoma progression.

BACKGROUND: OCT4, SOX2, and NANOG are major transcription factors related to stem cell self-renewal and differentiation. The aim of this study was to examine the association of OCT4, SOX2, and NANOG expression levels with the development and prognosis of patients with oral squamous cell carcinoma (OSCC). MATERIALS AND METHODS: Expression levels of OCT4, SOX2, and NANOG were evaluated by immunohistochemistry with tissue microarray slides of 436 OSCC, 362 corresponding tumor-adjacent normal (CTAN) tissues, and 71 normal uvula epithelium tissues. The clinicopathologic and follow-up data of the OSCC patients were recorded. RESULTS: OCT4 expression was significantly higher in normal and CTAN tissues than in tumor tissue (both P < 0.001). SOX2 expression in CTAN tissue was significantly higher than that in normal (P = 0.021) and tumor tissues (P < 0.001). However, NANOG expression was significantly higher in CTAN (P = 0.014) and tumor tissues (P = 0.009) than in normal tissue. Higher OCT4 and SOX2 expressions were associated with earlier AJCC stage (P = 0.002 and P < 0.001), small tumor size (P = 0.017 and P = 0.001), and the absence of lymph node metastasis (P = 0.015 and P = 0.025). Higher levels of SOX2 expression were associated with better disease-specific survival (P = 0.002) even after adjustment for clinicopathologic factors. DISCUSSION: OCT4 and SOX2 are biomarkers of tumorigenesis and early stage OSCC. SOX2 is an independent prognostic factor for OSCC.

Reduction of global 5-hydroxymethylcytosine is a poor prognostic factor in breast cancer patients, especially for an ER/PR-negative subtype.

DNA methylation at the 5 position of cytosine (5 mC) is an epigenetic hallmark in cancer. The 5 mC can be converted to 5-hydroxymethylcytosine (5 hmC) through a ten-eleven-translocation (TET). We investigated the impact of 5 mC, 5 hmC, TET1, and TET2 on tumorigenesis and prognosis of breast cancer. Immunohistochemistry was used to assess the levels of 5 mC, 5 hmC, TET1, and TET2 in the corresponding tumor adjacent normal (n = 309), ductal carcinoma in situ (DCIS, n = 120), and invasive ductal carcinoma (IDC, n = 309) tissues for 309 breast ductal carcinoma patients. 5 mC, 5 hmC, TET1-n, and TET2-n were significantly decreased during DCIS and IDC progression. In IDC, the decrease of 5 hmC was correlated with the cytoplasmic mislocalization of TET1 (p < 0.001) as well as poor disease-specific survival (DSS) (adjusted hazard ratio [AHR] 1.95, p = 0.003) and disease-free survival (DFS) (AHR 1.91, p = 0.006). The combined decrease of 5 mC and 5 hmC was correlated with worse DSS (AHR 2.19, p = 0.008) and DFS (AHR 1.99, p = 0.036). Stratification analysis revealed that the low level of 5 mC was associated with poor DSS (AHR 1.89, p = 0.044) and DFS (AHR 2.02, p = 0.035) for the ER/PR-positive subtype. Conversely, the low level of 5 hmC was associated with worse DSS (AHR 2.77, p = 0.002) and DFS (AHR 2.69, p = 0.006) for the ER/PR-negative subtype. The decreases of 5 mC, 5 hmC, TET1-n, and TET2-n were biomarkers of tumor development. The global reduction of 5 hmC was a poor prognostic factor for IDC, especially for ER/PR-negative subtype.

Application of deep learning for predicting the treatment performance of real municipal wastewater based on one-year operation of two anaerobic membrane bioreactors.

In this study, data-driven deep learning methods were applied in order to model and predict the treatment of real municipal wastewater using anaerobic membrane bioreactors (AnMBRs). Based on the one-year operating data of two AnMBRs, six parameters related to the experimental conditions (temperature of reactor, temperature of environment, temperature of influent, influent pH, influent COD, and flux) and eight parameters for wastewater treatment evaluation (effluent pH, effluent COD, COD removal efficiency, biogas composition (CH4, N2, and CO2), biogas production rate, and oxidation-reduction potential) were selected to establish the data sets. Three deep learning network structures were proposed to analyze and reproduce the relationship between the input parameters and output evaluation parameters. The statistical analysis showed that deep learning closely agrees with the AnMBR experimental results. The prediction accuracy rate of the proposed densely connected convolutional network (DenseNet) can reach up to 97.44%, and the single calculation time can be reduced to within 1 s, suggesting the high performance of AnMBR treatment prediction with deep learning methods.

[Construction of genome BAC library for single Branchiostoma belcheri individual].

As one of the closest living invertebrate relatives of vertebrates, amphioxus (subphylum Cephalochordata) occupies a key position in animal evolution and is becoming the best available proxy and model animal for studying the last common ancestor of all chordates, especially vertebrates. As long-term continuous culturing of amphioxus in laboratory became reliable, for pushing this animal to be a more successful model system, whole-genome sequencing of one or more species derived from this branch will be another urgent issue needed to address. In the present study, we described the construction and characterization of a bacterial artificial chromosome (BAC) library, using a single individual of Chinese amphioxus (Branchiostoma belcheri). High quality genomic DNA extracted from the spermary was partially digested with EcoRand EcoRmethylase. Desirable DNA fragments were isolated by pulsed field gel electrophoresis (PFGE), ligated to linearized and phosphorylased carrier pCC1BAC, and then transformed to Escherichia coli EPI300. The constructed library consists of 44 706 clones with the average insert fragment size around 80 kb as estimated by PFGE. The representation of the library is about 9 equivalents to the amhioxus genome. These results indicate that the BAC library will be useful for functional genomic studies and facilitate the whole-genome sequencing of Chinese amphioxus.

An antibiotic decision-making tool for patients with pneumonia admitted to a medical intensive care unit.

Pneumonia is a leading cause of death in medical intensive care units (MICUs). Delayed or inappropriate antibiotic therapy largely increases morbidity and mortality. Multidrug-resistant (MDR) micro-organisms are major reasons for inappropriate antibiotic use. Currently there is no good antibiotic decision-making tool designed for critically ill patients. The objective of this study was to develop a convenient MDR prediction scoring system for patients admitted to MICUs with pneumonia. A retrospective cohort study was conducted using databases and chart reviews of pneumonia patients admitted to a 30-bed MICU from 2012 to 2013. Forward logistic regression was applied to identify independent MDR risk factors for prediction tool development. A total of 283 pneumonia episodes from 263 patients with positive cultures from blood or respiratory secretions were recruited, of which 154 (54.4%) were MDR episodes. Long-term ventilation (OR = 11.09; P = 0.026), residence in a long-term care facility (OR = 2.50; P = 0.005), MDR infection/colonisation during the preceding 90 days (OR = 2.08; P = 0.041), current hospitalisation ≥2 days (OR = 1.98; P = 0.019) and stroke (OR = 1.81; P = 0.035) were identified as independent predictors for MDR pneumonia. The area under the ROC curve of this prediction tool was much higher than that of ATS/IDSA classification (0.69 vs. 0.54; P <0.001). The prediction accuracy of this tool with risk score ≥1 for MDR infections was 63.7%. This simple five-item, one-step scoring tool for critically ill patients admitted to the MICU could help physicians provide timely appropriate empirical antibiotics.