Graph-based and constraint-based heterologous metabolic pathway design methods and application / 生物工程学报

It is among the goals in metabolic engineering to construct microbial cell factories producing high-yield and high value-added target products, and an important solution is to design efficient synthetic pathway for the target products. However, due to the difference in metabolic capacity among microbial chassises, the available substrate and the yielded products are limited. Therefore, it is urgent to design related metabolic pathways to improve the production capacity. Existing metabolic engineering approaches to designing heterologous pathways are mainly based on biological experience, which are inefficient. Moreover, the yielded results are in no way comprehensive. However, systems biology provides new methods for heterologous pathway design, particularly the graph-based and constraint-based methods. Based on the databases containing rich metabolism information, they search for and uncover possible metabolic pathways with designated strategy (graph-based method) or algorithm (constraint-based method) and then screen out the optimal pathway to guide the modification of strains. In this paper, we reviewed the databases and algorithms for pathway design, and the applications in metabolic engineering and discussed the strengths and weaknesses of existing algorithms in practical application, hoping to provide a reference for the selection of optimal methods for the design of product synthesis pathway.

Randomized response surface pathway design with skewed starting point and stochastic dose window

Background:The aim was to introduce response surface pathway(RSP)-design with skewed starting value and stochastic dose-window to estimate optimal efficacy dose (OED) of BP-C2 after IL-1? stimulation in Atlantic salmon.Methods:54 healthy smolt of Atlantic salmon between 50 and 100g before habituated to saltwater were included. The study was conducted as a one-dimensional, randomized between-patient three-level RSP designed trial with one interventional-and one response variable and odd outcomes. The interventional variable was intraperitoneal injected BPC2 with skewed starting dose of 0.10 mg/100g related to the initial dose-window <0.02-0.5 mg/100g. The response variable was the Ct-value of mRNA IL-1? expression 24 hours after injection.Results:Skewed starting value of 0.10 mg/100g was chosen in the first design-level with a dose-window of <0.0-0.20].The three smolt obtained a reduction in Ct-value above 15%, and the dose-window adjusted with the lower boundary equals the previous dose. The five smolt at second esign-level received 0.16 mg/100g with a dose-window [0.10-0.22]. Four smolt obtained above 15% and one of 0.5% reduction in cycle threshold (Ct)-value. Six smolt in the third design-level received 0.21 mg/100g and one 0.16 mg/100g. The mean Ct-value was reduced from 30.0 in the nstimulated situation to 25.0, 24.8 and 26.4 after BP-C2 stimulation of 0.10, 0.16 and 0.21mg/100g, respectively. The OED of BP-C2 related to IL-1? was estimated to 0.14 mg/100g.Conclusions: Skewed starting value in the initial dose-window made the K-adjustment factor and dose-window stochastic. The RSP-procedure works in accordance to the expectation and estimated OED of BP-C2 sufficiently.

Progress in biological utilization of formic acid / 生物工程学报

The use of microbial cell factories to achieve efficient conversion of raw materials and synthesis of target substances is one of the important research directions of synthetic biology. Traditional industrial microorganisms have mainly used sugar-based raw materials as fermentation substrates. How to adopt cheaper carbon resources and realize their efficient use has been widely concerned. Formic acid is an important organic one-carbon source and widely used in industrial manufacturing of pesticides, leather, dyes, medicine and rubber. In recent years, due to the demand fluctuation in downstream industries, formic acid production is facing the dilemma of overcapacity, and therefore, requiring new conversion paths for expansion and extension of the related industrial chain. Biological route is one of the important options. However, natural formate-utilizing microorganisms generally grow slowly when metabolizing formic acid, and moreover, are difficult to be artificially modified by the absence of effective genetic tools. Construction of non-natural formate-utilizing microorganisms is another alternative strategy, but still in its infancy and has a huge space for further improvements. Here, we briefly summarize the recent research progress of biological utilization of formic acid, and also propose the future research focus and direction.

Randomized two dimensional between patient response surface pathway design with two interventional and one response variable in estimating minimum efficacy dose

Background:The aim of this paper is to introduce and evaluate the RSP design with two interventional and one response variable exemplified by estimating minimum efficacy dose (MED) of osteopathic manual therapy (OMT) in treatment of gastroesophageal reflux disease (GERD).Methods:15 GERD patients, divided in three design-level with three, five and seven patients. The study was performed as a randomized two-dimensional, between-patient RSP designed multicenter study with two interventional–and one response variable. The interventional variables “Number of OMT’s” and “Treatment Interval” with common response variable, formed two independent one-dimensional randomized between-patient RSP studies. The response variable was percent reduction in sum of the five GERD score from baseline. Three GERD patients were allocated on the first design level and given six OMT with five days’ interval. Based on results obtained in the first and second design level, five patients were included to the second design level and seven to the third.Results:The two-dimensional randomized between-patient RSP-design with the combined outcome procedure worked as expected. The percent reduction in GERD score increased with increasing number of OMT’s and time intervals. This increase leveled out after three to five OMT’s and three to four days between treatments. A clinical interaction between the two interventional variables was obtained. The estimated MED of OMT in treatment of GERD was three treatments with two days between treatments.Conclusions: The suggested two-dimensional, randomized between-patient RSP-design worked as expected and estimated MED of OMT in GERD patient sufficiently