PCR-Based Seamless Genome Editing with High Efficiency and Fidelity in <i>Escherichia coli</i>

Efficiency and fidelity are the key obstacles for genome editing toolboxes. In the present study, a PCR-based tandem repeat assisted genome editing (TRAGE) method with high efficiency and fidelity was developed. The design of TRAGE is based on the mechanism of repair of spontaneous double-strand breakage (DSB) via replication fork reactivation. First, cat-sacB cassette flanked by tandem repeat sequence was integrated into target site in chromosome assisted by Red enzymes. Then, for the excision of the cat-sacB cassette, only subculturing is needed. The developed method was successfully applied for seamlessly deleting, substituting and inserting targeted genes using PCR products. The effects of different manipulations including sucrose addition time, subculture times in LB with sucrose and stages of inoculation on the efficiency were investigated. With our recommended procedure, seamless excision of cat-sacB cassette can be realized in 48 h efficiently. We believe that the developed method has great potential for seamless genome editing in E. coli

YTHDF1 Regulates Tumorigenicity and Cancer Stem Cell-Like Activity in Human Colorectal Carcinoma

YTH N6-methyladenosine (m6A) RNA binding protein 1 (YTHDF1) is a core factor in RNA methylation modification. Recent studies have shown that m6A is closely related to multiple tumors, thus YTHDF1 may also play a role in tumorigenesis. This study, aimed to explore the role of YTHDF1 in the colorectal cancer (CRC). In this study, we identified YTHDF1 as being highly expressed at the mRNA and protein levels in TCGA, GEO CRC and primary CRC. Furthermore, the YTHDF1 gene copy number was positively correlated with YTHDF1 mRNA expression in CRC. Knocking down the expression of YTHDF1 significantly inhibited the CRC cell's tumorigenicity in vitro and murine xenograft tumor growth in vivo. Furthermore, silencing of YTHDF1 inhibited the colonosphere formation ability in vitro. Mechanistically, we found that silencing YTHDF1 significantly inhibited Wnt/β-catenin pathway activity in CRC cells. Together, YTHDF1 is overexpressed in CRC and plays a vital oncogenic role in CRC, and this novel finding may provide a potential therapeutic target for CRC

Bioresour. Technol.

In this study, pinewood and corn stover pretreated with the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride (AmimCl) were used as a feedstock for succinic acid production. Results reveal that 5% (v/v) AmimCl inhibited bacterial growth, whereas 0.01% (v/v) AmimCl inhibited succinic acid production. AmimCl was effective in extracting cellulose from pinewood and in degrading pinewood into a uniform pulp, as revealed by scanning electron microscopy (SEM). The rate of enzymatic hydrolysis of pinewood extract reached 72.16%. The combinations of AmimCl pretreatment with steam explosion or with hot compressed water were effective in treating corn stover, whereas AmimCl treatment alone did not result in a significant improvement. Pinewood extract produced 20.7 g/L succinic acid with an average yield of 0.37 g per gram of biomass. Workflow calculations indicated pine wood pretreated with IL has a theoretical yield of succinic acid of 57.1%. IL pretreatment led to increase in succinic acid yields. (C) 2014 Elsevier Ltd. All rights reserved.In this study, pinewood and corn stover pretreated with the ionic liquid (IL) 1-allyl-3-methylimidazolium chloride (AmimCl) were used as a feedstock for succinic acid production. Results reveal that 5% (v/v) AmimCl inhibited bacterial growth, whereas 0.01% (v/v) AmimCl inhibited succinic acid production. AmimCl was effective in extracting cellulose from pinewood and in degrading pinewood into a uniform pulp, as revealed by scanning electron microscopy (SEM). The rate of enzymatic hydrolysis of pinewood extract reached 72.16%. The combinations of AmimCl pretreatment with steam explosion or with hot compressed water were effective in treating corn stover, whereas AmimCl treatment alone did not result in a significant improvement. Pinewood extract produced 20.7 g/L succinic acid with an average yield of 0.37 g per gram of biomass. Workflow calculations indicated pine wood pretreated with IL has a theoretical yield of succinic acid of 57.1%. IL pretreatment led to increase in succinic acid yields. (C) 2014 Elsevier Ltd. All rights reserved

A chord error conforming tool path B-spline fitting method for NC machining based on energy minimization and LSPIA

Piecewise linear (G01-based) tool paths generated by CAM systems lack G1 and G2 continuity. The discontinuity causes vibration and unnecessary hesitation during machining. To ensure efficient high-speed machining, a method to improve the continuity of the tool paths is required, such as B-spline fitting that approximates G01 paths with B-spline curves. Conventional B-spline fitting approaches cannot be directly used for tool path B-spline fitting, because they have shortages such as numerical instability, lack of chord error constraint, and lack of assurance of a usable result. Progressive and Iterative Approximation for Least Squares (LSPIA) is an efficient method for data fitting that solves the numerical instability problem. However, it does not consider chord errors and needs more work to ensure ironclad results for commercial applications. In this paper, we use LSPIA method incorporating Energy term (ELSPIA) to avoid the numerical instability, and lower chord errors by using stretching energy term. We implement several algorithm improvements, including (1) an improved technique for initial control point determination over Dominant Point Method, (2) an algorithm that updates foot point parameters as needed, (3) analysis of the degrees of freedom of control points to insert new control points only when needed, (4) chord error refinement using a similar ELSPIA method with the above enhancements. The proposed approach can generate a shape-preserving B-spline curve. Experiments with data analysis and machining tests are presented for verification of quality and efficiency. Comparisons with other known solutions are included to evaluate the worthiness of the proposed solution

Simultaneous Removal of Thiophene and Dibenzothiophene by Immobilized Pseudomonas delafieldii R-8 cells

Biodesulfurization (BDS) is a promising technology for deep desulfurization. In this work, Pseudomonas delafieldii R-8 cells are immobilized in calcium alginate beads and used for BDS of transportation fuels. It is found that thiophene and dibenzothiophene (DBT) can be simultaneously metabolized by immobilized R-8 cells. The initial sulfur content in the model oil is 300 mg·kg ?1 (thiophene: UDBT1:U1). After 10 h of treatment, the thiophene concentration is reduced by 40%, while DBT is reduced by 25%. The utilization rate of thiophene is faster than that of DBT. Moreover, the oi

Clarification of succinic acid fermentation broth by ultrafiltration in succinic acid biorefinery

BACKGROUND: Succinic acid is an important precursor chemical for the synthesis of high value-added products. In this work, ultrafiltration was first investigated to clarify succinic acid fermentation broth by integrating fermentation and separation and removal processes of the product in situ. Four different ultrafiltration membranes (PES 100 kDa, PES 30 kDa, PES 10 kDa and RC 10 kDa) were used in this work. RESULTS: Results indicate that ultrafiltration is feasible for clarifying succinic acid fermentation broth. Almost all the microorganism cells (99.6%) were removed from the fermentation broth. Proteins were also removed effectively by all the membranes studied. The removal rate was 79.86% for PES 100 kDa, 86.43% for PES 30 kDa, 86.83% for PES 10 kDa, and 80.06% for the RC 10 kDa. After ultrafiltration, a clearer permeate was obtained compared with that from centrifugation. CONCLUSION: Membranes operating at high flux are always susceptible to rapid fouling. Compared with molecular weight cut-offs (MWCO), membrane material has a significant influence on the flux. Membrane flux measured in this study shows industrial potential of this technology in treatment of succinic acid fermentation broth. (c) 2012 Society of Chemical Industr

Heterotrophic nitrification and aerobic denitrification by a novel Halomonas campisalis

A novel halophilic strain that could carry out heterotrophic nitrification and aerobic denitrification was isolated and named as Halomonas campisalis ha3. It removed inorganic nitrogen compounds (e.g. NO3 (-), NO2 (-) and NH4 (+)) simultaneously, and grew well in the medium containing up to 20 % (w/v) NaCl. PCR revealed four genes in the genome of ha3 related to aerobic denitrification: napA, nirS, norB and nosZ. The optimal conditions for aerobic denitrification were pH 9.0, at 37 A degrees C, with 4 % (w/v) NaCl and sodium succinate as carbon source. The nitrogen removal rate was 87.5 mg NO3 (-)-N l(-1) h(-1). Therefore, this strain is a potential aerobic denitrifier for the treatment of saline wastewater

J. Chromatogr. A

Microbial production of fatty acids and fatty alcohols has attracted increasing concerns because of energy crisis and environmental impact of fossil fuels. Therefore, simple and efficient methods for the extraction and quantification of these compounds become necessary. In this study, a high-performance liquid chromatography-refractive index detection (HPLC-RID) method was developed for the simultaneous quantification of fatty acids and fatty alcohols in these samples. The optimum chromatographic conditions are C18 column eluted with methanol:water:acetic acid (90:9.9:0.1, v/v/v); column temperature, 26 C; flow rate, 1.0 mL/min. Calibration curves of all selected analytes showed good linearity (r(2) &gt;= 0.9989). The intra-day and inter-day relative standard deviations (RSDs) of the 10 compounds were less than 4.46% and 5.38%, respectively, which indicated that the method had good repeatability and precision. Besides, a method for simultaneous extraction of fatty acids and fatty alcohols from fermentation broth was optimized by orthogonal design. The optimal extraction conditions were as follows: solvent, ethyl acetate; solvent to sample ratio, 0.5:1; rotation speed, 2 min at 260 rpm; extraction temperature, 10 degrees C. This study provides simple and fast methods to simultaneously extract and quantify fatty acids and fatty alcohols for the first time. It will be useful for the study of microbial production of these products. (C) 2013 Elsevier B.V. All rights reserved.Microbial production of fatty acids and fatty alcohols has attracted increasing concerns because of energy crisis and environmental impact of fossil fuels. Therefore, simple and efficient methods for the extraction and quantification of these compounds become necessary. In this study, a high-performance liquid chromatography-refractive index detection (HPLC-RID) method was developed for the simultaneous quantification of fatty acids and fatty alcohols in these samples. The optimum chromatographic conditions are C18 column eluted with methanol:water:acetic acid (90:9.9:0.1, v/v/v); column temperature, 26 C; flow rate, 1.0 mL/min. Calibration curves of all selected analytes showed good linearity (r(2) >= 0.9989). The intra-day and inter-day relative standard deviations (RSDs) of the 10 compounds were less than 4.46% and 5.38%, respectively, which indicated that the method had good repeatability and precision. Besides, a method for simultaneous extraction of fatty acids and fatty alcohols from fermentation broth was optimized by orthogonal design. The optimal extraction conditions were as follows: solvent, ethyl acetate; solvent to sample ratio, 0.5:1; rotation speed, 2 min at 260 rpm; extraction temperature, 10 degrees C. This study provides simple and fast methods to simultaneously extract and quantify fatty acids and fatty alcohols for the first time. It will be useful for the study of microbial production of these products. (C) 2013 Elsevier B.V. All rights reserved

Bioresour. Technol.

Succinic acid was produced in a novel membrane-based fermentation and separation integrated system. With this integrated system, product inhibition was alleviated by removing acids and replenishing fresh broth. High cell density maintain for a longer time from 75 to 130 h and succinic acid concentration increased from 53 to 73 g/L. In the developed separation process, succinic acid was crystallized at a recovery of 85-90%. The purity of the obtained succinic acid crystals reached 99.4% as found by HPLC and H-1 NMR analysis. A crystallization experiment indicated that among by-products glucose had a negative effect on succinic acid crystallization. Poly (butylene succinate) (PBS) was synthesized using the purified succinic acid and H-1 NMR analysis confirmed that the composition of the synthesized PBS is in agreement with that from petro-based succinic acid. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved.Succinic acid was produced in a novel membrane-based fermentation and separation integrated system. With this integrated system, product inhibition was alleviated by removing acids and replenishing fresh broth. High cell density maintain for a longer time from 75 to 130 h and succinic acid concentration increased from 53 to 73 g/L. In the developed separation process, succinic acid was crystallized at a recovery of 85-90%. The purity of the obtained succinic acid crystals reached 99.4% as found by HPLC and H-1 NMR analysis. A crystallization experiment indicated that among by-products glucose had a negative effect on succinic acid crystallization. Poly (butylene succinate) (PBS) was synthesized using the purified succinic acid and H-1 NMR analysis confirmed that the composition of the synthesized PBS is in agreement with that from petro-based succinic acid. Crown Copyright (C) 2013 Published by Elsevier Ltd. All rights reserved