[Acquirement and evaluation of murine ventricular extracellular matrix].

Cardiac extracellular matrix (ECM), generated from the process of decellularization, has been widely considered as an ideal source of biological scaffolds. However, current ECM preparations are generally difficult to be applied to generate cardiac tissue. Our research was aimed to improve decellularization protocols to prepare cardiac ECM slices. Adult murine ventricular tissues were embedded in low melting agarose and cut into 300 µm slices, and then were divided randomly into three groups: normal cardiac tissue, SDS treated group (0.1% SDS) and SDS+Triton X-100 treated group (0.1% SDS+0.5% Triton X-100). Total RNA content and protein content quantification, HE staining and immunostaining were used to evaluate the removal of cell components and preservation of vital ECM components. Furthermore, murine embryonic stem cell-derived cardiomyocytes (mES-CMs) and mouse embryonic fibroblasts (MEFs) were co-cultured with ECM slices to evaluate biocompatibility. The relative residual RNA and protein contents of ECM slices significantly decreased after decellularization. HE staining showed that SDS+Triton X-100 treatment better destroyed cellular structure and removed nuclei of ECM slices, compared with SDS treatment. Immunostaining showed that collagen IV and laminin were better preserved and presented better similarity to original cardiac tissue in ECM slices acquired by SDS+Triton X-100 treatment. However, collagen IV and laminin were significantly decreased and arranged disorderly in SDS treated group. We observed effective survival (≥ 12 days) of MEFs and mES-CMs on ECM slices acquired by SDS+Triton X-100 treatment, and signs of integration, whereas those signs were not found in SDS treated group. We concluded that, compared with traditional SDS method, new combined protocol (SDS+Triton X-100) generated ECM slices with better component and structural preservation, as well as better biocompatibility.

The efficacy of parenteral fish oil in critical illness patients with sepsis: a prospective, non-randomized, observational study.

BACKGROUND AND OBJECTIVES: To investigate the clinical outcomes in septic patients receiving parenteral fish oil. METHODS AND STUDY DESIGN: A prospective, non-randomized, observational clinical study was carried out in 112 patients with sepsis from March, 2013 to May, 2015 in the surgical intensive care unit (SICU) of a tertiaryreferral hospital. The patients were put into one of two groups; either the control or the study group. Patients received the standard treatment of sepsis based on guidelines in the control group. In the study group, patients received parenteral nutrition (PN) containing fish oil. The Acute Physiology and Chronic Health Evaluation II (APACHE II) scores, the length of ICU and hospital stay, duration of mechanical ventilation, mortality, and readmission into the ICU were recorded. Tumor necrosis factor (TNF)-α and procalcitonin (PCT) levels were also evaluated. RESULTS: The study group showed a significant reduction for all-cause mortality (20.0% vs 10.0% in study and control groups, p=0.034) and APACHE II score on day 5 (p=0.015), day 7 (p=0.036) and day out of SICU (p=0.045) compared with the control group. The study group tended to show a shortened length of stay in the ICU compared to the control group. However, TNF-α and PCT level, 28 d mortality, the length of hospital stay and the duration of mechanical ventilation did not show statistical differences between the two groups. There were no drug-related adverse effects shown during the study. CONCLUSIONS: PN with fish oil is probably safe and may improve clinical outcome in critical ill patients with sepsis.

YGA: identifying distinct biological features between yeast gene sets.

The advance of high-throughput experimental technologies generates many gene sets with different biological meanings, where many important insights can only be extracted by identifying the biological (regulatory/functional) features that are distinct between different gene sets (e.g. essential vs. non-essential genes, TATA box-containing vs. TATA box-less genes, induced vs. repressed genes under certain biological conditions). Although many servers have been developed to identify enriched features in a gene set, most of them were designed to analyze one gene set at a time but cannot compare two gene sets. Moreover, the features used in existing servers were mainly focused on functional annotations (GO terms), pathways, transcription factor binding sites (TFBSs) and/or protein-protein interactions (PPIs). In yeast, various important regulatory features, including promoter bendability, nucleosome occupancy, 5'-UTR length, and TF-gene regulation evidence, are available but have not been used in any enrichment analysis servers. This motivates us to develop the Yeast Genes Analyzer (YGA), a web server that simultaneously analyzes various biological (regulatory/functional) features of two gene sets and performs statistical tests to identify the distinct features between them. Many well-studied gene sets such as essential, stress-response, TATA box-containing and cell cycle genes were pre-compiled in YGA for users, if they have only one gene set, to compare with. In comparison with the existing enrichment analysis servers, YGA tests more comprehensive regulatory features (e.g. promoter bendability, nucleosome occupancy, 5'-UTR length, experimental evidence of TF-gene binding and TF-gene regulation) and functional features (e.g. PPI, GO terms, pathways and functional groups of genes, including essential/non-essential genes, stress-induced/-repressed genes, TATA box-containing/-less genes, occupied/depleted proximal-nucleosome genes and cell cycle genes). Furthermore, YGA uses various statistical tests to provide objective comparison measures. The two major contributions of YGA, comprehensive features and statistical comparison, help to mine important information that cannot be obtained from other servers. The sophisticated analysis tools of YGA can identify distinct biological features between two gene sets, which help biologists to form new hypotheses about the underlying biological mechanisms responsible for the observed difference between these two gene sets. YGA can be accessed from the following web pages: http://cosbi.ee.ncku.edu.tw/yga/ and http://yga.ee.ncku.edu.tw/.