Electronic Journal of Biotechnology最新文献

Background

Gliomas are common malignant intracranial tumors. Efficacious targeted therapy against gliomas is lacking.

Results

GANT61 combined with the chemotherapy drug doxorubicin for treatment of glioma (LN-229) cells, and the effect of their combination, was tested. The molecular mechanism was explored by target prediction, along with functional analysis using the Gene Ontology (GO) database, enrichment analysis using the Kyoto Encyclopedia of Genes and Genomes (KEGG) database, construction of protein–protein interaction (PPI) networks, and protein expression. Combination of GANT61 plus doxorubicin could inhibit the growth of LN-229 cells effectively. Wound-healing data and expression of migration proteins related to epithelial-to-mesenchymal transition showed that this combination could inhibit the migration of LN-229 cells. Sixty-one targets of drug and disease intersected. Functional analysis revealed negative regulation of apoptosis, positive regulation of cell proliferation, and other biological processes related to apoptosis and proliferation. Pathway-enrichment analysis showed drug combination to be related to the cyclic adenosine monophosphate signaling pathway, pathways in cancer, and Hedgehog signaling pathway. Measurement of expression of several proteins related to these pathways revealed expression of BIRC5, GLi1 and GLi2, MMP3 and MMP9 proteins to decrease, and expression of MDM2 and P53 proteins to decrease and increase, respectively.

Conclusions

This study provides a: (a) new direction for targeted therapy of gliomas; (b) theoretical basis for drug research and molecular-mechanism research on gliomas.

How to cite: Chen J, Zhang Q, Zhang G et al. Molecular mechanism of GANT61 combined with doxorubicin in the treatment of gliomas based on network pharmacology. Electron J Biotechnol 2022;55. https://doi.org/10.1016/j.ejbt.2021.11.001.

Background

Biopolymer based edible films have emerged as potential alternatives for conventional plastics in food packaging industry. The properties such as thickness, water vapour transmission rate (WVTR) and transparency of these films would be significantly influenced by the solution components and concentration and process conditions (pH, temperature and relative humidity of drying).

Results

Control and glycerol blended pectin films were developed as per 2³ (two-level three-factor) factorial design of experiments by varying glycerol fraction (25% and 40% w/w) and solution concentration (3% and 5% w/v). The films made from 5% solution showed good moisture barrier properties. Glycerol addition reduced the moisture barrier capability of the films compared to control pectin films. Statistical analysis suggests that, the solution pH and drying temperature considerably affect film properties while the effect of relative humidity of drying is not evident enough. However, the interaction effect of relative humidity (H) with the pH and temperature appeared significant. Regression models were fitted to the data by considering the main and interaction effects, which were significantly affecting a particular property.

Conclusions

Detailed analysis reveals that for obtaining pectin based films with less thickness, low WVTR and high transparency, the optimal conditions preferred are low pH = 3, high T = 48°C and low to medium humidity of drying (H = 40–50%). The fitted regression models were statistically significant at 90% confidence level, pass Lack-of-fit analysis and are adequate to describe the effects of different factors on the targeted film properties.

How to cite: Mehraj S, Sistla YS. Optimization of process conditions for the development of pectin and glycerol based edible films: statistical design of experiments. Electron J Biotechnol 2022;55. https://doi.org/10.1016/j.ejbt.2021.11.004

Background

Engineering thermal adaptations of enzymes is a popular field of study. Enzymes active at low temperature have been used in many industries; however, reports seldom describe improvements in enzyme activity at low temperatures using protein engineering.

Results

Multiple amino acid sequence alignment of glycoside hydrolase (GH) family 32 showed an unconserved region located in the catalytic pocket. The exo-inulinase InuAGN25 showed the highest frequency of charged amino acid residues (47.4%) in this region among these GH 32 members. Notably, five consecutive charged amino acid residues (¹³⁷EEDRK¹⁴¹) were modeled as a loop fragment in this region of InuAGN25. Deletion of the loop fragment broke two salt bridges, one cation–π interaction, and the α-helix–loop–310-helix structure at the N-terminal tail. The mutant exo-inulinase RfsMutE137Δ5 without the loop fragment was expressed in Escherichia coli, digested using human rhinovirus 3C protease for removal of the fused sequence at the N-terminus, and purified using immobilized metal affinity chromatography. Compared to the wild-type enzyme, the optimum temperature and t_1/2 at 50°C of purified RfsMutE137Δ5 decreased by 10°C and 31.7 min, respectively, and the activities at 20°C and 30°C increased by 11% and 18%, respectively.

Conclusions

In this study, we engineered the loop to obtain the mutant exo-inulinase that showed an improved performance at low temperatures. These findings suggest that the loop may be a useful target in formulating rational designs for engineering thermal adaptations of GH 32 exo-inulinases.

How to cite: He L, Zhang R, Shen J. et al. Improving the low-temperature properties of an exo-inulinase via the deletion of a loop fragment located in its catalytic pocket. Electron J Biotechnol 2022;55. https://doi.org/10.1016/j.ejbt.2021.09.004

Background

Hepatocellular carcinoma (HCC) is a malignant tumor with complex pathogenesis. In HCC, the possible roles of transcriptional factor WD repeat and HMG-box DNA binding protein 1 (WDHD1) remain unclear. Hence, our study is aimed at verifying the prognosis prediction ability and potential biological mechanisms of WDHD1 in HCC.

Results

In this study, a total of 7171 clinical samples were obtained to quantitatively analyze the protein and mRNA expression levels of WDHD1 by using immunohistochemistry, gene microarrays, and high-throughput sequencing technologies. The result of in-house immunohistochemistry assay indicated that WDHD1 protein was remarkably overexpressed in HCC tissues compared with the non-HCC tissues (AUC > 0.99, the single Standardized Mean Difference [SMD] = 4.46). The overexpression trend of WDHD1 was validated by the comprehensive analysis based on a total of 4004 HCC tissues and 3167 controls (SMD = 1.333; AUC = 0.91). Moreover, the higher WDHD1 expression resulted in the poorer prognosis of HCC, as assessed by overall survival and relapse-free survival analyses (pooled hazard ratios > 1). WDHD1-coexpressed genes were screened out for enrichment analyses to enquire the prospective signaling pathways of WDHD1 in HCC and to probe the potential transcriptional targets of WDHD1. The WDHD1-coexpressed genes were mainly involved in the division process of chromosome and cell nucleus in HCC. UBA52 was identified as a crucial target of WDHD1.

Conclusions

WDHD1 may act as an oncogene in HCC and it has the potential to become a novel marker for predicting the prognosis of HCC patients, which may benefit from the early intervention of HCC.

How to cite: He R-Q, Li J-D, He W-Y, et al. Prognosis prediction ability and prospective biological mechanisms of WDHD1 in hepatocellular carcinoma tissues. Electron J Biotechnol 2022;55. https://doi.org/10.1016/j.ejbt.2021.12.001

Background

Hydroxycinnamic acids and some of their derivatives are molecules with interesting biological activities; for instance, hydroxylated hydroxycinnamic esters have proved to have antifungal properties, and thus the generation of these molecules is of industrial importance. In this study, the direct esterification capacity of the pure recombinant type B feruloyl esterase from Aspergillus terreus (AtFAE B) was evaluated by its ability to catalyze the synthesis of isobutyl o-coumarate, an interesting antifungal molecule. A ternary solvent system (isooctane/isobutanol/water) was employed to improve the synthesis of isobutyl o-coumarate, assessing different substrate concentrations, enzyme load, water percentages and pH and temperature values.

Results

AtFAE B showed the highest initial rate at 18% (v/v) isobutanol and 50 mM o-coumaric acid, 0.04 mg/ml of enzyme, 4% (v/v) water without buffer and 40°C. AtFAE B half-lives at 30°C, 40°C and 50°C were 16.5 h, 1.75 h and 3.5 min, respectively. Thus, we decided to evaluate the bioconversion yield at 30°C, where the enzyme showed the highest operational stability. At this temperature, we obtained a yield of ~80% after only 8 h of reaction, using a 78:18:4 isooctane:isobutanol:water ternary solvent system, with 50 mM of o-coumaric acid.

Conclusions

Under these improved conditions, the productivity was 1.06 g isobutyl o-coumarate/L*h with a biocatalyst yield of 209.6 kg isobutyl o-coumarate/kg free AtFAE B, demonstrating the promising potential of AtFAE B to accept the non-canonical o-coumaric acid as the substrate and to achieve the synthesis of isobutyl o-coumarate.

How to cite: Vega-Rodríguez AD, Armendáriz-Ruiz MA, Grajales-Hernández DA, et al. Improved synthesis of the antifungal isobutyl o-coumarate catalyzed by the Aspergillus terreus type B feruloyl esterase. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.08.001

Background

Synthesis of selenium nanoparticles from selenite by Shewanella sp. HN-41 demonstrated that particle size depended on the reaction time and biomass of cells. The slow reaction and low biomass tended to form small particles. In this study, Shewanella sp. HN-41 was introduced into the anode of a nonexternal circuit bioelectrochemical system (nec_BES) to convert chemical energy from lactate to low electron current to the cathode, where selenite was reduced.

Results

Our experiment with two systems, one bioelectrochemical system with a cathode flushed with nitrogen and the other with a no-nitrogen-flushing cathode, showed that the former could not produce Se nanoparticles after 21 d, but the latter formed them with an average size of 37.7 nm. The SEM and TEM images demonstrated that the particle size of 10 nm occupied over 10% and most of the particles were in the range of 30–60 nm. The XRD result and SAED image demonstrated no clear peaks of crystal and proved that the Se nanoparticles are amorphous.

Conclusions

The clean Se nanoparticles were synthesized and completely separated from bacterial cells in the bioelectrochemical system. This study opened a new approach for the biological synthesis of metal nanoparticles. Finally, the Se products in the range of 30–60 nm can be tested for antimicrobial activities in medical applications.

How to cite: Ho CT, Nguyen T-H, Lam T-T, et al. Biogenic synthesis of selenium nanoparticles by Shewanella sp. HN-41 using a modified bioelectrochemical system. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.07.004

Background

Qaidam cattle are local breeds that habitats in northwest China. It has many excellent characteristics, such as high cold and roughage tolerance, low oxygen adaptability, and tender meat quality. Copy number variation (CNV) can induce phenotypic changes in animals by a variety of effects, and thus affects the biological functions of the animals. To explore the molecular mechanism of its adaptation to extreme cold weather and muscle fat development, the CNV variations in the genome of three Qaidam cattle were detected by whole-genome sequencing, in this study.

Results

A total of 16,743 CNVs and 9498 copy number variable regions (CNVRs) were obtained after the screening, which accounts for 2.18% of the bovine genome. The CNVR length detected ranged from 0.3 KB to 10.77 KB, with a total length of 58.17 MB and an average length of 6.12 KB/ CNVR. Through functional enrichment of CNVR related genes, LDHB, and ME1 genes were screened as the key genes for Qaidam cattle to adapt to the cold and low oxygen environments, whereas KIT and FGF18 genes might be related to the coat color and growth. In the CNVR overlapped with QTLs, variation in CAPN1 and CAST genes might be closely related to the tender meat quality of Qaidam cattle.

Conclusions

Therefore, this study provides new genetic insights on the environmental adaptability and important economic traits of Qaidam cattle.

How to cite: Guo S, Wu X, Pei J, et al. Genome-wide CNV analysis reveals variants associated with high-altitude adaptation and meat traits in Qaidam cattle. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.07.006

Background

The heterologous expression of parasitic proteins is challenging because the sequence composition often differs significantly from host preferences. However, the production of such proteins is important because they are potential drug targets and can be screened for interactions with new lead compounds. Here we compared two expression systems for the production of an active recombinant aldehyde dehydrogenase (SmALDH_312) from Schistosoma mansoni, which causes the neglected tropical disease schistosomiasis.

Results

We produced SmALDH_312 successfully in the bacterium Escherichia coli and in the baculovirus expression vector system (BEVS). Both versions of the recombinant protein were found to be active in vitro, but the BEVS-derived enzyme showed 3.7-fold higher specific activity and was selected for further characterization. We investigated the influence of Mg²⁺, Ca²⁺ and Mn²⁺, and found out that the specific activity of the enzyme increased 1.5-fold in the presence of 0.5 mM Mg²⁺. Finally, we characterized the kinetic properties of the enzyme using a design-of-experiment approach, revealing optimal activity at pH 7.6 and 41°C.

Conclusions

Although, E. coli has many advantages, such as rapid expression, high yields and low costs, this system was outperformed by BEVS for the production of a schistosome ALDH. BEVS therefore provides an opportunity for the expression and subsequent evaluation of schistosome enzymes as drug targets.

How to cite: Harnischfeger J, Beutler M, Salzig D, et al. Biochemical characterization of the recombinant schistosome tegumental protein SmALDH_312 produced in E. coli and baculovirus expression vector system. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.08.002

Background

Plant tissue culture involves the use of explants obtained from plants to induce organogenesis with the help of plant growth regulators (PGRs). Micropropagation techniques provide a faster and economical solution to the limitations associated with traditional methods of plant cultivation. The present study focuses on the multiple shoot induction and proliferation of Ficus carica var. Black Jack. Factors that influence the growth of in vitro multiple shoots on the apical buds, which include growth media and PGRs, were investigated in this study. Different concentrations of cytokinins like 6-benzylaminopurine (BAP), Thidiazuron (TDZ), and Kinetin (Kin) were used on woody plant medium (WPM) for the optimization of media for multiple shoot induction and proliferation.

Results

Apical buds of Ficus carica var. Black Jack growing in WPM supplemented with BAP produced the healthiest plantlets, with the highest number of multiple shoots. The most efficient medium composition which produced the highest number of multiple shoots (37.8) per growing explant was WPM supplemented with 20 µM BAP. Proliferated multiple shoots were efficiently rooted using WPM + 20 µM BAP + 8 µM indole-3-acetic acid (IAA). This optimized medium composition significantly enhanced the production of multiple, disease-free plantlets using single apical bud explants of Ficus carica var. Black Jack.

Conclusions

In the present study the observations indicate that WPM supplemented with 20 µM BAP is the best-suited medium for organogenesis and multiple shoot culture of Ficus carica var. Black Jack, and this technique can be potentially applied for commercialization of the plant.

How to cite: Parab AR, Chew BL, Yeow LC, et al. Organogenesis on apical buds in common fig (Ficus carica) var. Black Jack. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2020.01.010

Background

Profilin proteins (PRFs) are small (12–15 kD) actin-binding protein, which play a significant role in cytoskeleton dynamics and plant development via regulating actin polymerization. Profilins have been well documented in Arabidopsis, Zea mays L. as well as Phaseolus vulgaris, however no such fully characterization of rice (Oryza sativa L.) profilin gene family has been reported thus far.

Result

In the present study, a comprehensive genome-wide analysis of rice PRF genes was completed and three members were identified. OsPRF1 and OsPRF2 shared 98.5% similarity (6 nucleotide divergence), but the deduced amino acid sequences of OsPRF1 and OsPRF2 are fully identical. In contrast, the OsPRF3 presents relatively lower similarity with OsPRF1 and OsPRF2. Phylogenetic analysis also support that OsPRF1 has a closer relationship with OsPRF2. Expression pattern analysis revealed the differential expression of OsPRFs in tissues of mature plant, which suggested the potential spatial functional specificity for rice profilin genes. Subcellular localization analysis revealed the OsPRFs were localized in cytoplasm and nucleus and all of them could bind actin monomers. Furthermore, abiotic stresses and hormones treatments assay indicated that the three OsPRF genes could be differentially regulated, suggesting that OsPRF genes might participate in different stress processes in rice.

Conclusions

Taken together, our study provides a comprehensive analysis of the OsPRF gene family and will provide a basis for further studies on their roles in rice development and in response to abiotic stresses.

How to cite: Zhang Y, Dong G, Wu L, et al. Identification and characterization of profilin gene family in rice. Electron J Biotechnol 2021;54. https://doi.org/10.1016/j.ejbt.2021.08.004.