LucidDraw: Efficiently visualizing complex biochemical networks within MATLAB

<p>Abstract</p> <p>Background</p> <p>Biochemical networks play an essential role in systems biology. Rapidly growing network data and versatile research activities call for convenient visualization tools to aid intuitively perceiving abstract structures of networks and gaining insights into the functional implications of networks. There are various kinds of network visualization software, but they are usually not adequate for visual analysis of complex biological networks mainly because of the two reasons: 1) most existing drawing methods suitable for biochemical networks have high computation loads and can hardly achieve near real-time visualization; 2) available network visualization tools are designed for working in certain network modeling platforms, so they are not convenient for general analyses due to lack of broader range of readily accessible numerical utilities.</p> <p>Results</p> <p>We present LucidDraw as a visual analysis tool, which features (a) speed: typical biological networks with several hundreds of nodes can be drawn in a few seconds through a new layout algorithm; (b) ease of use: working within MATLAB makes it convenient to manipulate and analyze the network data using a broad spectrum of sophisticated numerical functions; (c) flexibility: layout styles and incorporation of other available information about functional modules can be controlled by users with little effort, and the output drawings are interactively modifiable.</p> <p>Conclusions</p> <p>Equipped with a new grid layout algorithm proposed here, LucidDraw serves as an auxiliary network analysis tool capable of visualizing complex biological networks in near real-time with controllable layout styles and drawing details. The framework of the algorithm enables easy incorporation of extra biological information, if available, to influence the output layouts with predefined node grouping features.</p

N-terminal lid swapping contributes to the substrate specificity and activity of thermophilic lipase TrLipE

TrLipE is a thermophilic lipase that has potential commercial applications because of its catalytic ability under extreme conditions. Consistent with most lipases, the lid of TrLipE is located over the catalytic pocket, controls the substrate channel to the active center, and regulates the substrate specificity, activity, and stability of the enzyme through conformational changes. TrLipE from Thermomicrobium roseum has potential industrial applications, which is hindered by its weak enzymatic activity. Here, 18 chimeras (TrL1-TrL18) were reconstructed by N-terminal lid swapping between TrLipE and structurally similar enzymes. The results showed that the chimeras had a similar pH range and optimum pH as wild TrLipE but a narrower temperature range of 40–80°C, and TrL17 and the other chimeras showed lower optimum temperatures of 70°C and 60°C, respectively. In addition, the half-lives of the chimeras were lower than those of TrLipE under optimum temperature conditions. Molecular dynamics simulations indicated that chimeras had high RMSD, RMSF, and B-factor values. When p-nitrophenol esters with different chains were used as substrates, compared with TrLipE, most of the chimeras had a low Km and high kcat value. The chimeras TrL2, TrL3, TrL17, and TrL18 could specifically catalyze the substrate 4-nitrophenyl benzoate, with TrL17 showing the highest kcat/Km value of 363.88 ± 15.83 L⋅min–1⋅mmol–1. Mutants were then designed by investigating the binding free energies of TrL17 and 4-nitrophenyl benzoate. The results indicated that single, double, and triple substitution variants (M89W and I206N; E33W/I206M and M89W/I206M; and M89W/I206M/L21I and M89W/I206N/L21I, respectively) presented approximately 2- to 3-fold faster catalysis of 4-nitrophenyl benzoate than the wild TrL17. Our observations will facilitate the development of the properties and industrial applications of TrLipE

Reconstruction and Analysis of a Genome-Scale Metabolic Model of Ganoderma lucidum for Improved Extracellular Polysaccharide Production

In this study, we reconstructed for the first time a genome-scale metabolic model (GSMM) of Ganoderma lucidum strain CGMCC5.26, termed model iZBM1060, containing 1060 genes, 1202 metabolites, and 1404 reactions. Important findings based on model iZBM1060 and its predictions are as follows: (i) The extracellular polysaccharide (EPS) biosynthetic pathway was elucidated completely. (ii) A new fermentation strategy is proposed: addition of phenylalanine increased EPS production by 32.80% in simulations and by 38.00% in experiments. (iii) Eight genes for key enzymes were proposed for EPS overproduction. Model iZBM1060 provides a useful platform for regulating EPS production in terms of system metabolic engineering for G. lucidum, as well as a guide for future metabolic pathway construction of other high value-added edible/ medicinal mushroom species

Effect of optimized thrombus aspiration on myocardial perfusion and prognosis in acute ST-segment elevation myocardial infarction patients with primary percutaneous coronary intervention

ObjectiveTo investigate the impact of optimized thrombus aspiration on myocardial perfusion, prognosis, and safety in patients with acute ST-segment elevation myocardial infarction (STEMI) undergoing primary percutaneous coronary intervention(primary PCI).MethodsA total of 129 patients with STEMI were randomly allocated into control group (Subgroup A and B) and experimental group(Subgroup C and D). Control group received percutaneous transluminal coronary angioplasty (PTCA),thrombus aspiration and primary PCI. Experimental group received optimized thrombus aspiration and primary PCI. The number of thrombus aspiration was less than 4 times in Subgroup A and C. The number of thrombus aspiration was performed more than 4 times in Subgroups B and D. The classification of thrombi extracted, the TIMI flow grade, the incidence of no-reflow and slow flow, cTFC, TPI and CK-MB at 12 h and 24 h after stenting, ST segment resolution of ECG after stenting, NT-proBNP, LVEFat 24 h, 30 days and 180 days after stenting were compared between groups. The incidence of intraoperative and postoperative bleeding complications, stroke events and major cardiovascular events (MACE) were recorded and compared between groups.ResultsThe classification of thrombi extracted in the experimental group was higher than that in the control group. The TIMI flow grade of the experimental group was better than the control group after thrombus aspiration. After stenting, the advantage still existed, but the difference was not statistically significant. On cTFC, the experimental group was lower than the control group, but the difference was not statistically significant; After stenting the experimental group was significantly lower than the control group. The CK-MB at 12 h and 24 h of the experimental group was lower than the control group. After thrombus aspiration the incidence of no-reflow in the experimental group was significantly lower than that in the control group; after stenting the incidence of no-reflow in the experimental group was still lower than the control group, but no statistically difference. After thrombus aspiration and stenting the incidence of slow flow in the experimental group were lower than that in the control group. After stenting, NT-proBNP at 24 h was lower in the experimental group than that in the control group, However, there was no statistical difference; after stenting, The NT-proBNP in the experimental group was lower than that in the control group at 30 days and 180 days. After stenting, LVEF of the experimental group was significantly higher than the control group at 24 h and 30 days; superiority remained after 180 days but no statistical difference. There was no statistical difference between two groups for intraoperative and postoperative bleeding complications, stroke events, and MACE events. In Subgroup analysis,there was no significant difference in the classification of thrombi extracted, TIMI flow grade, cTFC, CK-MB,NT-proBNP and LVEF between group C and D, but group A was better than group B. Analysis of variance showed that the optimal number of suction was 4–5 times.ConclusionsOptimized thrombus aspiration can significantly improve myocardial perfusion and short-term and medium-term prognosis of STEMI patients after PCI, and reduce the incidence of slow flow and no-reflow. The optimal suction times were 4–5 times. Traditional aspiration method with more aspiration times is harmful to cardiac prognosis. Thrombus aspiration does not increase the incidence of stroke events and is safe.Clinical Trial Registration: identifier, ChiCTR2300073410

Robust estimation of bacterial cell count from optical density

Optical density (OD) is widely used to estimate the density of cells in liquid culture, but cannot be compared between instruments without a standardized calibration protocol and is challenging to relate to actual cell count. We address this with an interlaboratory study comparing three simple, low-cost, and highly accessible OD calibration protocols across 244 laboratories, applied to eight strains of constitutive GFP-expressing E. coli. Based on our results, we recommend calibrating OD to estimated cell count using serial dilution of silica microspheres, which produces highly precise calibration (95.5% of residuals &lt;1.2-fold), is easily assessed for quality control, also assesses instrument effective linear range, and can be combined with fluorescence calibration to obtain units of Molecules of Equivalent Fluorescein (MEFL) per cell, allowing direct comparison and data fusion with flow cytometry measurements: in our study, fluorescence per cell measurements showed only a 1.07-fold mean difference between plate reader and flow cytometry data