Tri©DB: an integrated platform of knowledgebase and reporting system for cancer precision medicine.

BACKGROUND: With the development of cancer precision medicine, a huge amount of high-dimensional cancer information has rapidly accumulated regarding gene alterations, diseases, therapeutic interventions and various annotations. The information is highly fragmented across multiple different sources, making it highly challenging to effectively utilize and exchange the information. Therefore, it is essential to create a resource platform containing well-aggregated, carefully mined, and easily accessible data for effective knowledge sharing. METHODS: In this study, we have developed "Consensus Cancer Core" (Tri©DB), a new integrative cancer precision medicine knowledgebase and reporting system by mining and harmonizing multifaceted cancer data sources, and presenting them in a centralized platform with enhanced functionalities for accessibility, annotation and analysis. RESULTS: The knowledgebase provides the currently most comprehensive information on cancer precision medicine covering more than 40 annotation entities, many of which are novel and have never been explored previously. Tri©DB offers several unique features: (i) harmonizing the cancer-related information from more than 30 data sources into one integrative platform for easy access; (ii) utilizing a variety of data analysis and graphical tools for enhanced user interaction with the high-dimensional data; (iii) containing a newly developed reporting system for automated annotation and therapy matching for external patient genomic data. Benchmark test indicated that Tri©DB is able to annotate 46% more treatments than two officially recognized resources, oncoKB and MCG. Tri©DB was further shown to have achieved 94.9% concordance with administered treatments in a real clinical trial. CONCLUSIONS: The novel features and rich functionalities of the new platform will facilitate full access to cancer precision medicine data in one single platform and accommodate the needs of a broad range of researchers not only in translational medicine, but also in basic biomedical research. We believe that it will help to promote knowledge sharing in cancer precision medicine. Tri©DB is freely available at www.biomeddb.org , and is hosted on a cutting-edge technology architecture supporting all major browsers and mobile handsets.

Advances in the Study of the Mechanism by Which Selenium and Selenoproteins Boost Immunity to Prevent Food Allergies.

Selenium (Se) is an essential micronutrient that functions in the body mainly in the form of selenoproteins. The selenoprotein contains 25 members in humans that exhibit a number of functions. Selenoproteins have immunomodulatory functions and can enhance the ability of immune system to regulate in a variety of ways, which can have a preventive effect on immune-related diseases. Food allergy is a specific immune response that has been increasing in number in recent years, significantly reducing the quality of life and posing a major threat to human health. In this review, we summarize the current understanding of the role of Se and selenoproteins in regulating the immune system and how dysregulation of these processes may lead to food allergies. Thus, we can explain the mechanism by which Se and selenoproteins boost immunity to prevent food allergies.

Cysteine supplementation enhanced inhibitor tolerance of Zymomonas mobilis for economic lignocellulosic bioethanol production.

Inhibitors in lignocellulosic hydrolysates are toxic to Zymomonas mobilis and reduce its bioethanol production. This study revealed cysteine supplementation enhanced furfural tolerance in Z. mobilis with a 2-fold biomass increase. Transcriptomic study illustrated that cysteine biosynthesis pathway was down-regulated while cysteine catabolism was up-regulated with cysteine supplementation. Mutants for genes involved in cysteine metabolism were constructed, and metabolites in cysteine metabolic pathway including methionine, glutathione, NaHS, glutamate, and pyruvate were supplemented into media. Cysteine supplementation boosted glutathione synthesis or H2S release effectively in Z. mobilis leading to the reduced accumulation of reactive oxygen species (ROS) induced by furfural, while pyruvate and glutamate produced in the H2S generation pathway promoted cell growth by serving as the carbon or nitrogen source. Finally, cysteine supplementation was confirmed to enhance Z. mobilis tolerance against ethanol, acetate, and corncob hydrolysate with an enhanced ethanol productivity from 0.38 to 0.55 g-1∙L-1∙h-1.

Effects of the Chinese Herb Medicine Formula "She-Xiang-Yu-Hong" Ointment on Wound Healing Promotion in Diabetic Mice.

Wound healing in diabetic patients is a difficult problem to be solved at present. In addition, patients with diabetes have an increased risk of postoperative wound complications. "She-Xiang-Yu-Hong" (SXYH) ointment is a type of traditional Chinese medicine (TCM) compound used to treat wounds. Over the past few years, SXYH has been applied in the Affiliated Hospital of Chengdu University of TCM (Chengdu, China) for the treatment of diabetic foot infections and bedsores, whereas there has been rare research on the effect of SXYH ointment on wound healing. In this study, SXYH ointment was first applied to streptozotocin (STZ)-triggered diabetic ICR mice (4-6 weeks, 20 ± 2 g) to observe the accelerated wound healing and the shortened wound healing period. As indicated by the histology and biochemistry analyses of skin biopsies, the wounds treated using SXYH ointment showed an increase in the granulation tissue. Moreover, SXYH also modulated the inflammation response by regulating affinity proinflammatory cytokines release (e.g., IL-6 and TNF-α). Furthermore, SXYH ointment obviously improved collagen fiber deposition and tissue on the wound surface. On the whole, this study indicated that SXYH ointment could accelerate wound healing, promote blood vessel formation, and suppress inflammations. Thus, the clinical potential of SXYH ointment was demonstrated in the treatment of diabetes and refractory wounds.

Curcumin: A review of experimental studies and mechanisms related to periodontitis treatment.

Curcumin is the main active ingredient of turmeric, which has a wide range of pharmacological effects, including antitumor, antibacterial, anti-inflammatory, anti-oxidation, immune regulation, and so on. Periodontitis is a prevalent oral inflammatory disease caused by a variety of factors. In recent years, many studies have shown that curcumin has a potential role on the treatment of periodontitis. Curcumin has been used in research related to the treatment of periodontitis in the form of solution, chip, gel, and capsule. Combined with other periodontitis treatment methods, such as scaling and root planing (SRP) and photodynamic therapy (PDT), can enhance curcumin's efficacy in treating periodontitis. In addition to natural curcumin, chemically modified curcumin, such as 4-phenylaminocarbonyl bis-demethoxy curcumin (CMC 2.24) and 4-methoxycarbonyl curcumin (CMC 2.5), have also been used in animal models of periodontitis. Here, this paper reviews the research progress of curcumin on the treatment of periodontitis and its related mechanisms.

The Magnesium Concentration in Yeast Extracts Is a Major Determinant Affecting Ethanol Fermentation Performance of Zymomonas mobilis.

Zymomonas mobilis is a model ethanologenic bacterium for diverse biochemical production. Rich medium (RM) is a complex medium that is routinely used to cultivate Z. mobilis, which contains carbon sources such as glucose, nitrogen sources such as yeast extract (YE), and KH2PO4. Glucose consumption and cell growth of Z. mobilis is usually coupled during ethanol fermentation. However, sometimes glucose was not consumed during the exponential growth phase, and it took extended time for cells to consume glucose and produce ethanol, which eventually reduced the ethanol productivity. In this study, the effects of different nitrogen sources, as well as the supplementation of an additional nitrogen source into RM and minimal medium (MM), on cell growth and glucose consumption of Z. mobilis were investigated to understand the uncoupled cell growth and glucose consumption. Our results indicated that nitrogen sources such as YE from different companies affected cell growth, glucose utilization, and ethanol production. We also quantified the concentrations of major ion elements in different nitrogen sources using the quantitative analytic approach of Inductively Coupled Plasma Optical Emission Spectroscopy (ICP-OES), and demonstrated that magnesium ion in the media affected cell growth, glucose consumption, and ethanol production. The effect of magnesium on gene expression was further investigated using RNA-Seq transcriptomics. Our results indicated that the lack of Mg2+ triggered stress responses, and the expression of genes involved in energy metabolism was reduced. Our work thus demonstrated that Mg2+concentration in nitrogen sources is essential for vigorous cell growth and ethanol fermentation, and the difference of Mg2+concentration in different YE is one of the major factors affecting the coupled cell growth, glucose consumption and ethanol fermentation in Z. mobilis. We also revealed that genes responsive for Mg2+ deficiency in the medium were majorly related to stress responses and energy conservation. The importance of magnesium on cell growth and ethanol fermentation suggests that metal ions should become one of the parameters for monitoring the quality of commercial nitrogen sources and optimizing microbial culture medium.

Origins and features of pectate lyases and their applications in industry.

Pectate lyase treatment can be an alternative strategy of the chemical processing, which causes severe environmental pollution, and has been broadly studied and applied for diverse industrial applications including textile industry, beverage industry, pulp processing, pectic wastewater pretreatment, and oil extraction. This review gave a brief description of the origins, enzymatic characterizations, structure, and applications of pectate lyases (Pels). Most of the reported pectate lyases are originated from microorganisms with a small number of them from plants and animals. Due to the diverse environments that these microorganisms exist, Pels present diversified features, especially for the range of optimal pH and temperature. The diversified biochemical properties of Pels define their applications in different industries, and the applications of alkaline Pels on cotton bioscouring and ramie degumming in textile industry were focused in this review. This review also discussed the perspectives of the development and applications of Pels. KEY POINTS: • The first review on pectate lyase focusing on biotechnological applications. • Origins, features, structures, applications of pectate lyases reviewed. • Applications of alkaline Pels in textile industry demonstrated. • Perspectives on future development and applications of Pels discussed.

Anti-inflammatory sesquiterpenoids from the leaves of Datura metel L.

Nine new (1-9) and three known (10-12) sesquiterpenoids were isolated from the ethanol-water (7:3, v/v) extract of the Datura metel L. leaves. The structures of 1-9 were elucidated by detailed spectroscopic analyses, including 1D and 2D NMR, HR-ESI-MS. All isolates (1-12) were evaluated for anti-inflammatory activity against the production of nitrogen oxide in lipopolysaccharide-induced RAW264.7 cells and compound 5 possessed the best inhibitory effect among them, with the IC50 value reaching 9.33-11.67 µM, which was lower than positive control, L-NMMA, with IC50 range from 13.64 to 17.02 µM.

Municipal wastewater treatment by forward osmosis using seawater concentrate as draw solution.

Forward osmosis (FO) has been used in the wastewater treatment due to its advantages including low energy consumption and low membrane fouling. In this study, real municipal wastewater was concentrated by FO process using seawater concentrate as draw solution (DS). The influences of operating conditions such as temperature, flow velocity and sewage pre-filtration on water flux were investigated. Chemical oxygen demand, total nitrogen, ammonia nitrogen and total phosphorus could not be enriched by 4 times while sewage was reduced to 1/4 volume. Excitation and emission matrix fluorescence spectrum showed that a fraction of dissolved organic compounds in sewage transported across membrane into DS. Membrane fouling was evaluated by scanning electronic microscope analysis that a dense cake layer was formed on the membrane surface after sewage filtration. However, water flux of the fouled membrane was highly recovered after 1 h of physical cleaning.

[Efficacy of ropivacaine injection at acupoints for labor analgesia and its effect on cortisol level in parturients].

OBJECTIVE: To evaluate the efficacy of ropivacaine injection at the acupoints Hegu and Sanyinjiao for labor analgesia and its effects on cortisol level in parturients. METHODS: A total of 120 ASA class I-II nulliparous women undergoing spontaneous term labor (37 to 41 weeks of gestation) with a live, singleton fetus in the occiput anterior position and requiring labor analgesia with acupuncture were enrolled in this study. These women were randomized into study group and control group and received injections of 1 mL of 0.2% ropivacaine and normal saline, respectively, at each of the acupoints of bilateral Sanyinjiao and Hegu in the first stage of labor. The Visual Analogue Scale (VAS) before and at 30, 60 and 120 min after analgesia, the time of labor, delivery outcome and cortisol levels were compared between the two groups. RESULTS: The VAS was significantly lower in the study group than in the control group (P<0.05). At 120 min after injections of ropivacaine or saline, serum cortisol level was significantly higher in the control group than in the study group (P<0.05). The rates of cesarean section and instrumental delivery and the time of labor were all similar between the two groups (P>0.05). CONCLUSION: Ropivacaine injection at Hegu and Sanyinjiao is effective for labor analgesia and does not prolong the process of labor or increase the rates of cesarean section or instrumental delivery.

Population behavior analysis of dspE and pelD regulation in Erwinia chrysanthemi 3937.

Erwinia chrysanthemi 3937 (Ech3937) is a phytopathogenic bacterium with a wide host range. The pectinolytic enzymes secreted by the bacterium and the type III secretion system (T3SS) are essential for full virulence. We used the green fluorescent protein gene as a reporter to investigate the expression of dspE (a putative T3SS effector) and pelD (a major pectin-degrading enzyme) in populations of Ech3937 under different conditions. Gene expression was analyzed by measuring the fluorescence intensity of individual cells with a fluorescence-activated cell sorter. Ech3937 dspE was induced in minimal medium (MM) with only a portion of Ech3937 cells (43.03%) expressing dspE after 12 h of culture. The nutrient-rich King's medium B did not fully eliminate the expression of dspE; a small percentage of Ech3937 cells (5.55%) was able to express dspE after 12 h of culture in this medium. In all, 68.95% of Ech3937 cells expressed pelD after 12 h of culture in MM supplemented with polygalacturonic acid (PGA). However, 96.34% of Echl31 cells (an hrpL deletion mutant of Ech3937) expressed pelD after 12 h of culture in MM supplemented with PGA. In potato tubers, 6.32% of the bacterial cells expressed dspE 2 h after inoculation, whereas only 0.25% of the cells expressed pelD. However, after 24 h, the percentage of cells expressing pelD (68.48%) was approximately 3.5 times that of cells expressing dspE (19.39%). In contrast to potato tubers, similar proportion of Ech3937 cells expressing dspE (39.34%) and pelD (40.30%) were observed in Chinese cabbage 24 h after inoculation. From promoter activity and real-time quantitative results, the expression of pelD in Ech3937 was demonstrated to be downregulated by HrpL in MM supplemented with PGA.