MicroRNA and transcription factor co-regulatory networks and subtype classification of seminoma and non-seminoma in testicular germ cell tumors

Recent studies have revealed that feed-forward loops (FFLs) as regulatory motifs have synergistic roles in cellular systems and their disruption may cause diseases including cancer. FFLs may include two regulators such as transcription factors (TFs) and microRNAs (miRNAs). In this study, we extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types of testicular germ cell tumors (TGCT): seminoma (SE) and non-seminoma (NSE). Specifically, we identified differentially expressed mRNA genes and miRNAs in 103 tumors using the transcriptomic data from The Cancer Genome Atlas. Next, we determined significantly correlated TF-gene/miRNA and miRNA-gene/TF pairs with regulation direction. Subsequently, we determined 288 and 664 dysregulated TF-miRNA-gene FFLs in SE and NSE, respectively. By constructing dysregulated FFL networks, we found that many hub nodes (12 out of 30 for SE and 8 out of 32 for NSE) in the top ranked FFLs could predict subtype-classification (Random Forest classifier, average accuracy ≥90%). These hub molecules were validated by an independent dataset. Our network analysis pinpointed several SE-specific dysregulated miRNAs (miR-200c-3p, miR-25-3p, and miR-302a-3p) and genes (EPHA2, JUN, KLF4, PLXDC2, RND3, SPI1, and TIMP3) and NSE-specific dysregulated miRNAs (miR-367-3p, miR-519d-3p, and miR-96-5p) and genes (NR2F1 and NR2F2). This study is the first systematic investigation of TF and miRNA regulation and their co-regulation in two major TGCT subtypes

Evaluation of positioning error-induced pixel shifts on satellite linear push-broom imagery

Georeferencing is one of the major tasks of satellite-borne remote sensing. Compared to traditional indirect methods, direct georeferencing through a Global Positioning System/inertial navigation system requires fewer and simpler steps to obtain exterior orientation parameters of remotely sensed images. However, the pixel shift caused by geographic positioning error, which is generally derived from boresight angle as well as terrain topography variation, can have a great impact on the precision of georeferencing. The distribution of pixel shifts introduced by the positioning error on a satellite linear push-broom image is quantitatively analyzed. We use the variation of the object space coordinate to simulate different kinds of positioning errors and terrain topography. Then a total differential method was applied to establish a rigorous sensor model in order to mathematically obtain the relationship between pixel shift and positioning error. Finally, two simulation experiments are conducted using the imaging parameters of Chang’ E-1 satellite to evaluate two different kinds of positioning errors. The experimental results have shown that with the experimental parameters, the maximum pixel shift could reach 1.74 pixels. The proposed approach can be extended to a generic application for imaging error modeling in remote sensing with terrain variation

The alkaline pectate lyase PEL168 of Bacillus subtilis heterologously expressed in Pichia pastoris is more stable and efficient for degumming ramie fiber

BACKGROUND: The conventional degumming process of ramie with alkaline treatment at high temperature causes severe environmental pollution. Pectate lyases can be used to remove pectin from ramie in a degumming process with reduced environmental pollution and energy consumption. Pectate lyase PEL168 from Bacillus subtilis has been previously characterized and the protein structure was resolved. However, Bacillus is not a suitable host for pectate lyases during the degumming process since most Bacillus produce cellulases endogenously with a detrimental effect to the fiber. Pichia pastoris, which does not express endogenous cellulases and has high secretion capability, will be an ideal host for the expression. No previous work was reported concerning the heterologous expression of pectate lyase PEL168 in P. pastoris with an aim for industrial application in ramie bio-degumming. RESULTS: The gene pel168 was expressed in P. pastoris in this study. The recombinant protein PEL168 in P. pastoris (PEL168P) showed two bands of 48.6 kDa and 51.4 kDa on SDS-PAGE whereas the enzyme expressed in E. coli (PEL168E) was the same as predicted with a band of 46 kDa. Deglycosylation digestion suggested that PEL168P was glycosylated. The optimum reaction temperature of the two PEL168s was 50°C, and the optimum pH 9.5. After preincubation at 60°C for 20 min, PEL168E completely lost its activity, whereas PEL168P kept 26% of the residual activity. PEL168P had a specific activity of 1320 U/mg with a K(m) of 0.09 mg/ml and a V(max) of 18.13 μmol/min. K(+), Li(+), Ni(2+) and Sr(2+) showed little or no inhibitory effect on PEL168P activity, and Ca(2+) enhanced enzyme activity by 38%. PEL168P can remove the pectin from ramie effectively in a degumming process. A 1.5 fold increase of PEL168 enzyme expression in P. pastoris was achieved by further codon optimization. CONCLUSIONS: Pectate lyase PEL168 with an available protein structure can be heterologously expressed in P. pastoris. The characterized recombinant PEL168P can be used to remove pectin from ramie efficiently and the expression level of PEL168 in P. pastoris was increased markedly by codon optimization. Therefore, PEL168 is an ideal candidate for further optimization and engineering for bio-degumming

In vitro anti-Helicobacter pylori activity and the underlining mechanism of an empirical herbal formula – Hezi Qingyou

BackgroundHelicobacter pylori (H. pylori) is thought to primarily colonize the human stomach and lead to various gastrointestinal disorders, such as gastritis and gastric cancer. Currently, main eradication treatment is triple or quadruple therapy centered on antibiotics. Due to antibiotic resistance, the eradication rate of H. pylori is decreasing gradually. Therefore, searching for anti-H. pylori drugs from herbal sources has become a strategy for the treatment. Our team proposed a Hezi Qingyou Formula (HZQYF), composed of Chebulae Fructus, Ficus hirta Vahl and Cloves, and studied its anti-H. pylori activity and mechanism.MethodsChemical components of HZQYF were studied using UHPLC–MS/MS and HPLC. Broth microdilution method and agar dilution method were used to evaluate HZQYF’s antibacterial activity. The effects of HZQYF on expression of adhesion genes (alpA, alpB, babA), urease genes (ureE, ureF), and flagellar genes (flaA, flaB) were explored using Reverse Transcription-quantitative Polymerase Chain Reaction (RT-qPCR) technology. Effects on morphology and permeability of the extracellular membrane were studied using scanning electron microscopy (SEM) and N-phenylnaphthalen-1-amine (NPN) uptake. Effect on urease activity was studied using a urease kinetics analysis in vitro. Immunofluorescence staining method was used to examine the effect on adhesion. Western blot was used to examine the effect on cagA protein.ResultsMinimum inhibitory concentration (MIC) values of the formula against H. pylori clinical strains and standard strains were 80–160 μg/mL, and minimum bactericidal concentration (MBC) values were 160–320 μg/mL. The formula could down-regulate the expression of adhesion genes (alpA, alpB, babA), urease genes (ureE, ureF) and flagellar genes (flaA, flaB), change the morphology of H. pylori, increase its extracellular membrane permeability, and decrease its urease activity.ConclusionPresent studies confirmed that HZQYF had promising in vitro anti-H. pylori activities and demonstrated its possible mechanism of action by down-regulating the bacterial adhesion, urease, and flagellar gene expression, which provided scientific bases for further clinical investigations

Modeling image motion in airborne Three-Line-Array (TLA) push-broom cameras

This paper presents an image motion model for airborne three-line-array (TLA) push-broom cameras. Both aircraft velocity and attitude instability are taken into account in modeling image motion. Effects of aircraft pitch, roll, and yaw on image motion are analyzed based on geometric relations in designated coordinate systems. The image motion is mathematically modeled by image motion velocity multiplied by exposure time. Quantitative analysis to image motion velocity is then conducted in simulation experiments. The results have shown that image motion caused by aircraft velocity is space invariant while image motion caused by aircraft attitude instability is more complicated. Pitch,roll and yaw all contribute to image motion to different extents. Pitch dominates the along-track image motion and both roll and yaw greatly contribute to the cross-track image motion. These results provide a valuable base for image motion compensation to ensure high accuracy imagery in aerial photogrammetry

Molecular signatures identified by integrating gene expression and methylation in non-seminoma and seminoma of testicular germ cell tumours

Testicular germ cell tumours (TGCTs) are the most common cancer in young male adults (aged 15 to 40). Unlike most other cancer types, identification of molecular signatures in TGCT has rarely reported. In this study, we developed a novel integrative analysis framework to identify co-methylated and co-expressed genes [mRNAs and microRNAs (miRNAs)] modules in two TGCT subtypes: non-seminoma (NSE) and seminoma (SE). We first integrated DNA methylation and mRNA/miRNA expression data and then used a statistical method, CoMEx (Combined score of DNA Methylation and Expression), to assess differentially expressed and methylated (DEM) genes/miRNAs. Next, we identified co-methylation and co-expression modules by applying WGCNA (Weighted Gene Correlation Network Analysis) tool to these DEM genes/miRNAs. The module with the highest average Pearson’s Correlation Coefficient (PCC) after considering all pair-wise molecules (genes/miRNAs) included 91 molecules. By integrating both transcription factor and miRNA regulations, we constructed subtype-specific regulatory networks for NSE and SE. We identified four hub miRNAs (miR-182-5p, miR-520b, miR-520c-3p, and miR-7-5p), two hub TFs (MYC and SP1), and two genes (RECK and TERT) in the NSE-specific regulatory network, and two hub miRNAs (miR-182-5p and miR-338-3p), five hub TFs (ETS1, HIF1A, HNF1A, MYC, and SP1), and three hub genes (CDH1, CXCR4, and SNAI1) in the SE-specific regulatory network. miRNA (miR-182-5p) and two TFs (MYC and SP1) were common hubs of NSE and SE. We further examined pathways enriched in these subtype-specific networks. Our study provides a comprehensive view of the molecular signatures and co-regulation in two TGCT subtypes

Investigation of Microscopic Structure and Ion Dynamics in Liquid Li(Na, K)EutecticCl Systems by Molecular Dynamics Simulation

Molten chloride salts are the main components in liquid metal batteries, high-temperature heat storage materials, heat transfer mediums, and metal electrolytes. In this paper, interest is centered on the influence of the LiCl component and temperature on the local structure and transport properties of the molten LiCl-NaCl-KCl system over the temperature range of 900 K to 1200 K. The liquid structure and properties have been studied across the full composition range by molecular dynamics (MD) simulation of a sufficient length to collect reliable values, such as the partial radial distribution function, angular distribution functions, coordination numbers distribution, density, self-diffusion coefficient, ionic conductivity, and shear viscosity. Densities obtained from simulations were underestimated by an average 5.7% of the experimental values. Shear viscosities and ionic conductivity were in good agreement with the experimental data. The association of all ion pairs (except for Li-Li and Cl-Cl) was weakened by an increasing LiCl concentration. Ion clusters were formed in liquids with increasing temperatures. The self-diffusion coefficients and ionic conductivity showed positive dependences on both LiCl concentration and temperature, however, the shear viscosity was the opposite. By analyzing the hydrodynamic radii of each ion and the coordination stability of cation-anion pairs, it was speculated that ion clusters could be the cation-anion coordinated structure and affected the macro properties

A flow-cytometry-based protocol for detection of mitochondrial ROS production under hypoxia

Summary: Hypoxia is known to stimulate mitochondrial reactive oxygen species (mROS) in cells. Here, we present a detailed protocol to detect mROS using MitoSOX staining in live cells under normoxia and hypoxia. Flow cytometry allows sensitive and reliable quantification of mROS by FlowJo software. We optimized several aspects of the procedure including hypoxic treatment, working concentrations of the staining buffer, and quantitative analyses. Here, we use HepG2 cells, but the protocol can be applied to other cell lines.For complete details on the use and execution of this protocol, please refer to Yang et al. (2020)