Computational Modelling of Genome-Side Transcription Assembly Networks Using a Fluidics Analogy

Understanding how a myriad of transcription regulators work to modulate mRNA output at thousands of genes remains a fundamental challenge in molecular biology. Here we develop a computational tool to aid in assessing the plausibility of gene regulatory models derived from genome-wide expression profiling of cells mutant for transcription regulators. mRNA output is modelled as fluid flow in a pipe lattice, with assembly of the transcription machinery represented by the effect of valves. Transcriptional regulators are represented as external pressure heads that determine flow rate. Modelling mutations in regulatory proteins is achieved by adjusting valves' on/off settings. The topology of the lattice is designed by the experimentalist to resemble the expected interconnection between the modelled agents and their influence on mRNA expression. Users can compare multiple lattice configurations so as to find the one that minimizes the error with experimental data. This computational model provides a means to test the plausibility of transcription regulation models derived from large genomic data sets

Global patient outcomes after elective surgery: prospective cohort study in 27 low-, middle- and high-income countries.

BACKGROUND: As global initiatives increase patient access to surgical treatments, there remains a need to understand the adverse effects of surgery and define appropriate levels of perioperative care. METHODS: We designed a prospective international 7-day cohort study of outcomes following elective adult inpatient surgery in 27 countries. The primary outcome was in-hospital complications. Secondary outcomes were death following a complication (failure to rescue) and death in hospital. Process measures were admission to critical care immediately after surgery or to treat a complication and duration of hospital stay. A single definition of critical care was used for all countries. RESULTS: A total of 474 hospitals in 19 high-, 7 middle- and 1 low-income country were included in the primary analysis. Data included 44 814 patients with a median hospital stay of 4 (range 2-7) days. A total of 7508 patients (16.8%) developed one or more postoperative complication and 207 died (0.5%). The overall mortality among patients who developed complications was 2.8%. Mortality following complications ranged from 2.4% for pulmonary embolism to 43.9% for cardiac arrest. A total of 4360 (9.7%) patients were admitted to a critical care unit as routine immediately after surgery, of whom 2198 (50.4%) developed a complication, with 105 (2.4%) deaths. A total of 1233 patients (16.4%) were admitted to a critical care unit to treat complications, with 119 (9.7%) deaths. Despite lower baseline risk, outcomes were similar in low- and middle-income compared with high-income countries. CONCLUSIONS: Poor patient outcomes are common after inpatient surgery. Global initiatives to increase access to surgical treatments should also address the need for safe perioperative care. STUDY REGISTRATION: ISRCTN5181700

Microbial reclamation of squid pens and shrimp shells

[[abstract]]Byproducts generated in high levels by marine processes have been recognized for their value as recyclable or reclaimable waste. Among marine byproducts, shrimp shells, crab shells, and squid pens have the highest chitin content. The chemical treatments of these chitin-containing byproducts for preparing chitin and chitosan create waste disposal problems because neutralization and detoxification of the discharged wastewater are necessary. Therefore, the cost of chitin and chitosan preparations was far higher than those of their raw materials, marine chitin-containing byproducts. Chitin and chitosan have been widely used as the major carbon source of bacteria for producing chitinolytic enzymes. In 1997, the bifunctional chitinase/lysozymes from Pseudomonas aeruginosa K-187 using shrimp and crab shells as the sole carbon/nitrogen (C/N) source was first reported. Thereafter, the use of squid pens as the only C/N source for producing enzymes and bioactive materials had also been studied. The use of shellfish chitin waste as the sole C/N source not only solves environmental problems, it decreases the production costs for microbial conversion. This review summarizes our recent research of microbial reclamation of these marine byproducts for producing enzymes and bioactive materials; the characterization and applications of these products were also studied.[[notice]]補正完