Making gut microbiomes from scratch.

Studying the microbiome presents a challenge: how do we untangle the interactions of microbes at ecologically relevant scales? We highlight research by Afrizal et al. and Cheng et al., which help to solve this problem through the generation and characterization of complex synthetic communities derived from lab-grown microbes.

A practical method to screen and identify functioning biomarkers in nasopharyngeal carcinoma.

Nasopharyngeal carcinoma (NPC) is a rare malignancy, with the unique geographical and ethnically characteristics of distribution. Gene chip and bioinformatics have been employed to reveal regulatory mechanisms in current functional genomics. However, a practical solution addressing the unresolved aspects of microarray data processing and analysis have been long pursuit. This study developed a new method to improve the accuracy of identifying key biomarkers, namely Unit Gamma Measurement (UGM), accounting for multiple hypotheses test statistics distribution, which could reduce the dependency problem. Three mRNA expression profile of NPC were selected to feed UGM. Differentially expressed genes (DEGs) were identified with UGM and hub genes were derived from them to explore their association with NPC using functional enrichment and pathway analysis. 47 potential DEGs were identified by UGM from the 3 selected datasets, and affluent in cysteine-type endopeptidase inhibitor activity, cilium movement, extracellular exosome etc. also participate in ECM-receptor interaction, chemical carcinogenesis, TNF signaling pathway, small cell lung cancer and mismatch repair pathway. Down-regulation of CAPS and WFDC2 can prolongation of the overall survival periods in the patients. ARMC4, SERPINB3, MUC4 etc. have a close relationship with NPC. The UGM is a practical method to identify NPC-associated genes and biomarkers.

Dextran sulfate sodium mouse model of inflammatory bowel disease evaluated for systemic genotoxicity via blood micronucleus and Pig-a gene mutation assays.

Inflammatory bowel disease (IBD) is an important risk factor for gastrointestinal cancers. Inflammation and other carcinogenesis-related effects at distal, tissue-specific sites require further study. In order to better understand if systemic genotoxicity is associated with IBD, we exposed mice to dextran sulfate sodium salt (DSS) and measured the incidence of micronucleated cells (MN) and Pig-a mutant phenotype cells in blood erythrocyte populations. In one study, 8-week-old male CD-1 mice were exposed to 0, 1, 2, 3 or 4% w/v DSS in drinking water. The 4-week in-life period was divided into four 1-week intervals-alternately on then off DSS treatment. Low volume blood samples were collected for MN analysis at the end of each week, and cardiac blood samples were collected at the end of the 4-week period for Pig-a analyses. The two highest doses of DSS were observed to induce significant increases in reticulocyte frequencies. Even so, no statistically significant treatment-related effects on the genotoxicity biomarkers were evident. While one high-dose mouse showed modestly elevated MN frequencies during the DSS treatment cycles, it also exhibited exceptionally high reticulocyte frequencies (e.g. 18.7% at the end of the second DSS cycle). In a second study, mice were treated with 0 or 4% DSS for 9-18 consecutive days. Exposure was continued until rectal bleeding or morbidity was evident, at which point the treatment was terminated and blood was collected for MN analysis. The Pig-a assay was conducted on samples collected 29 days after the start of treatment. The initial blood specimens showed highly elevated reticulocyte frequencies in DSS-exposed mice (mean ± SEM = 1.75 ± 0.10% vs. 13.04 ± 3.66% for 0 vs. 4% mice, respectively). Statistical analyses showed no treatment-related effect on MN or Pig-a mutant frequencies. Even so, the incidence of MN versus reticulocytes in the DSS-exposed mice were positively correlated (linear fit R2 = 0.657, P = 0.0044). Collectively, these results suggest that in the case of the DSS CD-1 mouse model, systemic effects include stress erythropoiesis but not remarkable genotoxicity. To the extent MN may have been slightly elevated in a minority of individual mice, these effects appear to be secondary, likely attributable to stimulated erythropoiesis.

3Rs-friendly approach to exogenous metabolic activation that supports high-throughput genetic toxicology testing.

MultiFlow® DNA Damage-p53, γH2AX, Phospho-Histone H3 is a miniaturized, flow cytometry-based assay that provides genotoxic mode of action information by distinguishing clastogens, aneugens, and nongenotoxicants. Work to date has focused on the p53-competent human cell line TK6. While mammalian cell genotoxicity assays typically supply exogenous metabolic activation in the form of concentrated rat liver S9, this is a less-than-ideal approach for several reasons, including 3Rs considerations. Here, we describe our experiences with low concentration S9 and saturating co-factors which were allowed to remain in contact with cells and test chemicals for 24 continuous hours. We exposed TK6 cells in 96-well plates to each of 15 reference chemicals over a range of concentrations, both in the presence and absence of 0.25% v/v phenobarbital/ß-naphthoflavone-induced rat liver S9. After 4 and 24 hr of treatment cell aliquots were added to wells of a microtiter plate containing the working detergent/stain/antibody cocktail. After a brief incubation robotic sampling was employed for walk-away flow cytometric data acquisition. PROAST benchmark dose (BMD) modeling was used to characterize the resulting dose-response curves. For each of the 8 reference pro-genotoxicants studied, relative nuclei count, γH2AX, and/or p53 biomarker BMD values were order(s) of magnitude lower for 0.25% S9 conditions compared to 0% S9. Conversely, several of the direct-acting reference chemicals exhibited appreciably lower cytotoxicity and/or genotoxicity BMD values in the presence of S9 (eg, resorcinol). These results prove the efficacy of the low concentration S9 system, and indicate that an efficient and highly scalable multiplexed assay can effectively identify chemicals that require bioactivation to exert their genotoxic effects.

UGM: a more stable procedure for large-scale multiple testing problems, new solutions to identify oncogene.

Variations of gene expression levels play an important role in tumors. There are numerous methods to identify differentially expressed genes in high-throughput sequencing. Several algorithms endeavor to identify distinctive genetic patterns susceptable to particular diseases. Although these processes have been proved successful, the probability that the number of non-differentially expressed genes measured by false discovery rate (FDR) has a large standard deviation, and the misidentification rate (type I error) grows rapidly when the number of genes to be detected become larger. In this study we developed a new method, Unit Gamma Measurement (UGM), accounting for multiple hypotheses test statistics distribution, which could reduce the dependency problem. Simulated expression profile data and breast cancer RNA-Seq data were utilized to testify the accuracy of UGM. The results show that the number of non-differentially expressed genes identified by the UGM is very close to the real-evidence data, and the UGM also has a smaller standard error, range, quartile range and RMS error. In addition, the UGM can be used to screen many breast cancer-associated genes, such as BRCA1, BRCA2, PTEN, BRIP1, etc., provides better accuracy, robustness and efficiency, the method of identification differentially expressed genes in high-throughput sequencing.

In vitro evaluation of marrow clot enrichment on microstructure decoration, cell delivery and proliferation of porous titanium scaffolds by selective laser melting three-dimensional printing.

Titanium alloy is a clinically approved material for bone substitution. Although three-dimensional printing (3DP) fabrication technique can build up porous Ti scaffolds with the designed shape and microstructure, the biomechanical performance of 3DP Ti scaffolds still need to be improved to increase the reliability of osseointegration capacity. To address this issue, rabbit bone marrow clot (MC) is used to modify 3DP Ti scaffolds by stem cell delivery and microenvironment decoration inside the pores of these scaffolds. Moreover, 3DP Ti scaffolds were built up using selective laser melting, and 3DP MC-Ti scaffolds were constructed through the enrichment of MC with Ti scaffolds in vitro. Results demonstrated that the obtained 3DP Ti scaffolds in current study has an average modulus of elasticity (ME) at 1294.48 MPa with average yield strength of 33.154 MPa. For MC-Ti scaffolds, MC enrichment obstructs the pores of 3DP scaffolds due to the large amount of fibrin and erythrocytes and leads to a decrease in ratio of live cells at 1-week culture. Cell proliferation and osteogenic differentiation performance of MC-Ti scaffolds were promoted with porous recanalization in the later 3 weeks. After 2 weeks in vitro culture, fivefold of cell number in MC-Ti scaffolds were observed than bone marrow-derived mesenchymal stem cell-seeded Ti scaffolds. Compared to Ti scaffolds, fourfold of deoxyribonucleic acid content, type I collagen-α1, osteocalcin, and alkaline phosphatase expression in MC-Ti scaffolds were observed after 4 weeks in vitro culture. Results suggested that the combination with MC is a highly efficient method that improves the biological performance of Ti scaffolds. © 2017 Wiley Periodicals, Inc. J Biomed Mater Res Part B: Appl Biomater, 106B: 2245-2253, 2018.

Application of 3D printing rapid prototyping-assisted percutaneous fixation in the treatment of intertrochanteric fracture.

The aim of the present study was to investigate the application of 3D printing (3DP) rapid prototyping (RP) technique-assisted percutaneous fixation in the treatment of femoral intertrochanteric fracture (ITF) using proximal femoral nail anti-rotation (PFNA). A total of 39 patients with unstable ITF were included in the current study. Patients were divided into two groups: 19 patients were examined using computed tomography scanning and underwent PFNA with SDP-RP whereas the other 20 patients underwent conventional PFNA treatment. Anatomical data were converted from the Digital Imaging and Communications in Medicine format to the stereolithography format using M3D software. The 3DP-RP model was established using the fused deposition modeling technique and the length and diameter of the main screw blade was measured during the simulation. The postoperative femoral neck-shaft angle (NSA), surgery duration, intraoperative and postoperative blood loss, and the duration of hospital stay were recorded and compared with the corresponding values in conventional surgery. No significant differences were observed in mean PFNA size between the implants used and the preoperative planning estimates. It was demonstrated that the 3DP-RP assisted procedure resulted in more effective reduction of the NSA. Furthermore, patients undergoing 3DP-RP experienced a significant reduction in duration of surgery (P<0.01), as well as reductions in intraoperative (P=0.02) and postoperative (P=0.03) blood loss, compared with conventional surgery. At 6 months post-surgery, no cases of hip varus/vague deformities or implant failure were observed in patients that underwent either the 3DP-RP-assisted or conventional procedure. The results of the present study suggest that the 3DP-RP technique is able to create an accurate model of the ITF, which facilitates surgical planning and fracture reduction, thus improving the efficiency of PFNA surgery for ITFs.

[MRNA expression of complement C3 and C4 in rat nasal mucosa with allergic rhinitis].

OBJECTIVE: To investigate the level of mRNA expression of complement C3 and C4 in rat nasal mucosa and to reveal the relationship with the pathogenesis of allergic rhinitis (AR) . METHODS: Twenty healthy SD rats were randomly divided into AR group and control group, 10 rats for each group. Ten rats was sensitized and intranasally challenged by ovalbumin and Al (OH)3 (as supplement) as allergic rhinitis models, and the control group was treated by saline. RT-PCR was performed to investigate the level of mRNA expression of complement C3 and C4 in nasal mucosa of both groups. RESULTS: C3 and C4 mRNA were detected in both groups. The relative intensity of gene expression was measured. The relative intensity of C3 mRNA expression was 6183+/-1376 in AR group, 4444+/-989 in control group, C4 mRNA was 4398 +/-948 in AR group, and 2771+/-407 in control group. Expression of C3 and C4 in AR group was higher than that of the controls ( P < 0. 05) . CONCLUSION: The high level of C3 and C4 mRNA expression in nasal mucosa of rats with allergic rhinitis suggests that C3 and C4 are involved in the immunopathology of allergic rhinitis. The result implies that complement system involved in the rat's allergic rhinitis is possibly activated through the classical pathway.