ELIHKSIR Web Server: Evolutionary Links Inferred for Histidine Kinase Sensors Interacting with Response Regulators.

Two-component systems (TCS) are signaling machinery that consist of a histidine kinases (HK) and response regulator (RR). When an environmental change is detected, the HK phosphorylates its cognate response regulator (RR). While cognate interactions were considered orthogonal, experimental evidence shows the prevalence of crosstalk interactions between non-cognate HK-RR pairs. Currently, crosstalk interactions have been demonstrated for TCS proteins in a limited number of organisms. By providing specificity predictions across entire TCS networks for a large variety of organisms, the ELIHKSIR web server assists users in identifying interactions for TCS proteins and their mutants. To generate specificity scores, a global probabilistic model was used to identify interfacial couplings and local fields from sequence information. These couplings and local fields were then used to construct Hamiltonian scores for positions with encoded specificity, resulting in the specificity score. These methods were applied to 6676 organisms available on the ELIHKSIR web server. Due to the ability to mutate proteins and display the resulting network changes, there are nearly endless combinations of TCS networks to analyze using ELIHKSIR. The functionality of ELIHKSIR allows users to perform a variety of TCS network analyses and visualizations to support TCS research efforts.

Optimal Timing of Simethicone Addition for Bowel Preparation Using Polyethylene Glycol Plus Ascorbic Acid.

BACKGROUND: Colonic bubbles obscure the colonic mucosa during colonoscopy following bowel preparation with polyethylene glycol plus ascorbic acid (PEG-Asc). Simethicone is used to enhance visualization during colonoscopy. We aimed to determine the optimal timing of simethicone addition to improve bowel preparation using PEG-Asc. METHODS: This prospective, randomized study enrolled patients undergoing elective colonoscopy from April 2017 to January 2018. They were randomly assigned to one of the following three groups: PEG-Asc only (control) or simethicone addition in the morning on the day of colonoscopy (PEG-S1) or in the evening of the day prior to colonoscopy (PEG-S2). The primary outcome was the quality of colon cleansing, and the secondary outcomes were the adenoma detection rate (ADR), polyp detection rate (PDR), and diminutive (≤ 5 mm) ADR. RESULTS: In total, 240 patients were randomly allocated to the three groups; six patients were withdrawn. Of the 234 patients evaluated, 78, 79, and 77 were allocated to the control, PEG-S1, and PEG-S2 groups, respectively. The bubble scores of all colonic segments were lowest in the PEG-S2 group. There was no significant difference in ADR or PDR among the three groups. However, the diminutive ADR was significantly higher in the PEG-S2 group compared to the other two groups (control 5.1% vs. PEG-S1 8.9% vs. PEG-S2 20.8%; P = 0.009). CONCLUSION: Addition of simethicone to PEG-Asc at the optimal time prevents the formation of air bubbles and so improves the quality of bowel preparation, especially enhancing diminutive ADR.

[An experience of cyberknife treatment in patients with advanced pancreaticobilliary malignancy].

BACKGROUND/AIMS: CyberKnifeTM stereotactic body radiotherapy (SBRT) has been thought as a promising treatment modality for inoperable or recurred pancreaticobiliary malignancies. But, clinical course of CyberKnifeTM treatment have not been established yet, so we report the experience of CyberKnifeTM treatment in 19 patients with recurred or advanced pancreaticobilliary malignancies. METHODS: Between July 2008 and May 2009, 19 patients (gallbladder cancer 4, common bile duct cancer 5, and pancreatic cancer 10) with recurred (12) and advanced pancreaticobiliary cancer (7) underwent CyberKnifeTM treatment in Soonchunhyang University Hospital. Tumor size was evaluated at 1, 3, 6, 8 and every 3 months after SBRT. RESULTS: The mean age was 60.2 years, and the mean size of target lesions was 28.1±1.30 mm. After CyberKnifeTM treatment, the average size of target lesions was decreased; 2.53±4.18 mm from months 0-1 in 19 patients, 2.47±4.7 mm from months 1-3 in 15 patients, 0.08±5.11 mm from months 3-6 in 12 patients. However, the average size of target lesions was increased 3.67±8.98 mm from months 6-8 in 6 patients. There were 2 cases of massive duodenal ulcer bleeding after CyberKnifeTM treatment, one of them expired due to ulcer bleeding. Also, other minor complications appeared such as 1 case of abdominal pain and 1 case of diarrhea. CONCLUSIONS: CyberKnifeTM treatment seems to be effective in local control of pancreaticobiliary cancer, but we experienced serious complications. Further prospective studies will be needed for the proper evaluation of role of CyberknifeTM treatment in patients with advanced pancreaticobiliary malignancies.

Raceway cultivation of Spirulina platensis using underground water.

The semi-outdoor cultivation of Spirulina platensis was attempted using an underground-water-based medium. Occurrence of contaminant organisms such as Chlorella sp. and Chlamydomonas sp. was not found from a microscopic observation and bacteria were not detected from denaturing gradient gel electrophoresis (DGGE) analysis of PCR-amplified 16S rDNA during the cultivation, owing to pH control and the high quality of the underground water. The mean productivity was high at 10.5 g/m2/d with a range of 4.2-12.3 g/m2/d despite the unfavorable weather conditions of the rainy season. The cultivated S. platensis included a normal protein content of 58.9%. Consequently, the underground water improved the biomass productivity and the biomass quality because of an abundant supplementation of natural minerals and through a contaminant-free culture.

Factors indicating culture status during cultivation of Spirulina (Arthrospira) platensis.

Factors indicating culture status of two Spirulina platensis strains were monitored in a batch mode cultivation for 36 days. Changing mode in all factors showed a common turning point, indicating shift of cell or culture status. Mean biomass productivity was highly sustained until day 22, chlorophyll a concentration peaked on day 22, pH value was >12 on day 22, coil number was abruptly shortened on day 22, and floating activity was sustained at greater than 79% after day 22, indicating that day 22 is a criterion reflecting phase-transfer in cell physiology in a batch culture system. Many of these changes may have been caused by increased pH, suggesting that pH control is essential for mass production of S. platensis. Fluctuations in floating activity were likely induced by the number of cellular gas vacuoles. Consequently, coil number per trichome and floating activity of S. platensis could readily act as simple indicators for determination of culture status or harvesting time of cells.