Electronic Journal of Biotechnology最新文献

Background

Although SNORD3A has been implicated in cancer progression, its specific roles and underlying mechanisms in gastric cancer (GC) remain poorly understood. We analysed SNORD3A expression using TCGA data and evaluated patient survival via Kaplan‒Meier curves. Additionally, we conducted GO-KEGG enrichment analysis to identify relevant biological processes and signaling pathways, while ssGSEA was used to assess the correlation between SNORD3A and cancer immune infiltrates. Furthermore, we explored the relationship between SNORD3A and immunotherapy response through TIDE. We verified SNORD3A expression using real-time qPCR and assessed cell proliferation, migration, and invasion via CCK8 and Transwell migration and invasion assays.

Results

Our results revealed that SNORD3A was significantly upregulated in GC, with high expression correlating with poor survival. SNORD3A and related genes were primarily enriched in the insulin/insulin-related growth factor signaling pathway. We also observed negative associations between SNORD3A expression and several immune cells, including activated dendritic cells, CD56bright natural killer cells, central memory CD8 T cells, effector memory CD8 T cells, effector memory CD4 T cells, eosinophils, immature dendritic cells, macrophages, mast cells, MDSCs, memory B cells, monocytes, neutrophil cells, plasmacytoid dendritic cells, regulatory T cells, and T follicular helper cells. High SNORD3A expression also correlated with a poorer response to immunotherapy. Finally, inhibition of SNORD3A suppressed cell proliferation, migration, and invasion.

Conclusions

Our findings suggest that SNORD3A plays a catalytic role in the proliferation, migration and invasiveness of GC and may have potential as a diagnostic biomarker and therapeutic target for GC.

How to cite: Wang Q, Li Y, Niu X, et al. SNORD3A acts as a potential prognostic and therapeutic biomarker in gastric cancer. Electron J Biotechnol 2023; 67. https://doi.org/10.1016/j.ejbt.2023.08.004.

Background

The aim of the present study was to investigate the effect of substrate conformational structure changes on the laccase-induced protein cross-linking. The effects of laccase amount, pH, and ferulic acid (FA) on the enzymatic cross-linking of substrate, Cyt C, were determined by sodium dodecyl sulfate–polyacrylamide gel electrophoresis. High-performance size exclusion chromatography, laser particle size analysis and isothermal titration calorimetry (ITC) were also applied to investigate the cross-linking product and enthalpy changes. Structural changes of Cyt C at different pH values were analyzed by ultraviolet–visible (UV–vis), fluorescence, and circular dichroism (CD) measurements.

Results

Complete cross-linking, partial cross-linking, minute cross-linking, and no cross-linking occurred at pH 2.0, 4.0, 6.0, and 8.0, respectively. ITC analysis demonstrated that the enzymatic cross-linking of Cyt C was an endothermic process. The UV–vis, fluorescence, and CD measurements exhibited that the tertiary structure of Cyt C was disrupted, and part of the α-helical polypeptide region unfolded at pH 2.0. The structural flexibilities decreased, and the tertiary structure of Cyt C became increasingly compact with the increase in pH values from 4.0 to 8.0. The gradual changes in the structure of Cyt C at different pH values were in accordance with the cross-linking results of Cyt C catalyzed by laccase.

Conclusions

The results demonstrated that minute structure changes of substrate had a remarkable effect on the laccase-induced cross-linking. The findings promote the understanding of the substrate requirement of laccase in protein cross-linking and are instructive for the modulation of laccase-induced protein cross-linking.

How to cite: Li D-X, Qi Z-Y, Liu J-Y, et al. Effect of pH on the conformational structure of cytochrome c and subsequent enzymatic cross-linking catalyzed by laccase. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.07.002.

Background

Palmitoleic acid is a fatty acid that possesses nutritional, health, and industrial applications. However, it accumulates in the seed oil of few plant species that often lack agronomic value. A bioinformatics approach was developed as a complementary tool to effort- and time-consuming traditional methods to identify palmitoleic acid-accumulating plant species. The approach involved identifying acyl-ACP desaturases with a sequence variation linked to a switch in the substrate preference from stearic to palmitic acid.

Results

A PHI-BLAST analysis identified Handroanthus impetiginosus as a candidate species with two acyl-ACP desaturases with the desired sequence variation. A substrate docking analysis showed that the presence of phenylalanine at the bottom of the active site plays a similar structural role to that of tryptophan present in the same position in the divergent desaturase of the palmitoleic acid accumulator Dolichandra unguis-cati. The analysis of the genome of H. impetiginosus allowed the identification of four putative ferredoxins, three of which are heterotrophic type and have been linked to an increase in the activity of unusual acyl-ACP desaturases. RT-PCR results showed that both studied H. impetiginosus desaturases are expressed in the pod but not in the seeds, while all 4 ferredoxins are expressed in both tissues. GC–MS analysis confirmed the presence of palmitoleic acid in seed oil.

Conclusions

These results suggest that the proposed bioinformatic approach can be a valuable compliment to traditional methods for the identification of plant species that accumulate palmitoleic acid. However, further improvements are needed, such as predicting seed expression of desaturases.

How to cite: Salazar Robles G, Hernández LR, Pedraza Pérez Y, et al. Bioinformatic approach for the identification of plant species that accumulate palmitoleic acid. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.008.

Background

A major portion of poultry feather waste is constituted by keratin, which is recalcitrant to degradation by common proteases. Feather waste contributes to a significant volume of biowaste load to the environment. Valorization of these wastes into various products has been attempted by many researchers. The present study aimed to produce peptides (molecular weight < 10 kDa) from feather waste by the action of keratinolytic bacteria or keratinase enzyme and to screen the peptides for pharmaceutical and therapeutic properties. The feathers were subjected to hydrolysis by using locally isolated keratinolytic microorganisms, namely Streptomyces tanashiensis-RCM-SSR-6, Bacillus sp. RCM-SSR-102, and purified keratinase enzyme KER-102.

Results

The feather keratin hydrolysate obtained by hydrolysis with different bacterial species/enzymes showed different protein profiles in SDS-PAGE. As indicated by Fourier Transform Infrared Spectroscopy (FTIR) analysis, a difference was observed in the composition of α-helix and β-sheet in the peptides produced by different microbial/enzymatic methods. The peptides were screened for antioxidant potential, antityrosinase property, and inhibitory activity against angiotensin-converting enzyme (ACE), lipoxygenase, and xanthine oxidase. The peptides showed promising results in all the assays, except peptide-102 that did not show ACE inhibitory activity. Interestingly, the crude peptide-6 (4.06 µg/mL) and peptide-102 (10.21 µg/mL) showed a lower EC₅₀ value than the standard Kojic acid (27.04 µg/mL) in antityrosinase assay.

Conclusions

Degradation of chicken feather waste with microbial or enzymatic method is an eco-friendly approach to yield diverse bioactive peptides. Hence, the present study established that feather keratin could be a potential source of many health-beneficial peptides.

How to cite: Kshetri P, Singh PL, Chanu SB, et al. Biological activity of peptides isolated from feather keratin waste through microbial and enzymatic hydrolysis. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.08.001.

Background

Ultrasonication was used to stimulate the growth and selenium (Se) biotransformation in Saccharomyces cerevisiae. An optimization study for maximal Se accumulation in S. cerevisiae was conducted using the Plackett–Burman screening method and response surface methodology (RSM) for optimization of conditions. The variables influencing Se biotransformation by yeast, including duration and power of ultrasound, inoculum treatment with ultrasound, duty cycle, growth phase, time, shaking rate, inorganic salt concentration (Se, Zn, Mg, and K), and nitrogen and carbon sources as well as their concentrations were screened using the Plackett–Burman design.

Results

The main variables were carbon and Se concentration as well as ultrasound power and duty cycle. The lack of fit was insignificant (P > 0.01). The optimum condition for Se accumulation was obtained at Se concentration of 60 µg/ml, carbon source brix of 15, ultrasound of 90 W/L, and duty cycle of 40%.

Conclusions

The results showed that optimization of parameters and application of ultrasonication lead to a successful enhancement (2.78-fold) in the accumulation of selenium by S. cerevisiae. Such enriched yeast can be utilized in bread for increasing consumption of Se in the diet of patients with Se deficiency.

How to cite: Alijan S, Hosseini M, Esmaeili S, et al. Impact of ultrasound and medium condition on production of selenium-enriched yeast. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.004.

Background

Hong Jiang (HC), a grafted chimera of sweet orange (Citrus sinensis (L.) Osbeck), is prone to variations in fruit shape, taste, and pulp mastication. We studied the transcriptomes and metabolomes pf pulps of HC and its two variants (CB: fruits with changed pulp mastication, taste, and color and JB: fruits with changed pulp color and taste) to explore the related pathways.

Results

JB accumulated higher organic acids as compared to HC and CB. Flavonoid content was highest in HC followed by JB and CB. The soluble sugar content was lower, while cellulose content was higher in both JB and CB as compared to HC. We found 5,156 and 1,673 DEGs and 283 and 94 DAMs in HC vs JB and HC vs CB, respectively. The differential regulation of starch and sucrose metabolism, galactose metabolism, glycolysis/gluconeogenesis, fructose and mannose metabolism, and citrate cycle pathways could be associated with changes in sugar contents and tastes in JB and CB. Cell-wall polymer-related DEGs/DAMs were associated with the inferior mastication quality of JB and CB. Carotenoid biosynthesis possibly imparts yellowish and reddish pulp color in HC. Additional to this pathway, the anthocyanin biosynthesis led to the changes in JB and CB pulp color.

Conclusions

This combined methodological approach proved to be useful in delineating the large-scale changes in the transcripts and metabolites of variant fruits in a chimeric citrus variety. This study provides advanced and large-scale data on citrus taste, mastication, and pulp color.

How to cite: Yang Z, Cao X, Zheng X, et al. Biochemical, transcriptome and metabolome analysis of the pulp of Citrus sinensis (L.) Osbeck ‘Hong Jiang’ and its two variants reveal pathways regulating pulp taste, mastication, and color. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.001.

Background

Geoffroea decorticans is a vulnerable native species inhabiting the Atacama Desert. Here, we describe the structure, gene composition and phylogeny of the complete chloroplast genome of this legume species.

Results

The chloroplast genome consisted of 158,399 bp, with typical quadripartite structures: a large single copy (88,081 bp), a small single copy (18,976 bp), and two inverted repeats (25,671 bp). Geoffroea decorticans chloroplast genome was similar in size and gene number to that of G. spinosa, but it was slightly different in structure. Complete chloroplast analysis of G. decorticans revealed 129 genes, including 83 protein-coding genes, 37 tRNA genes, 8 rRNA genes and 1 pseudogene (rpl22). In G. decorticans, the rps16 gene showed a deletion, which led to a premature stop codon, probably causing loss of functionality. Phylogenetic analysis of 20 complete chloroplast genomes confirmed the placement to G. decorticans within the Pterocarpus clade.

Conclusions

In this study, we report the complete chloroplast genome of Geoffroea decorticans for the first time, which can be used for phylogenetic studies and reconstruction of the biogeography history of the genus Geoffroea in South America.

How to cite: Contreras-Díaz R, Carevic FS, Huanca-Mamani W, et al. Chloroplast genome structure and phylogeny of Geoffroea decorticans, a native tree from Atacama Desert. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.005.

Background

Fungal nanofactories have been utilized to synthesize silver and gold nanoparticles. This study was designed to mycosynthesize and characterize silver and gold nanoparticles (AgNPs and AuNPs) and to study their effect on aflatoxin B₁ production by Aspergillus flavus.

Results

Silver and gold nanoparticles were synthesized by endophytic Aspergillus versicolor and then analyzed by UV–vis spectroscopy. The results revealed surface plasmon resonance peaks at 432 and 536 nm for Ag and Au nanoparticles, respectively. The obtained transmission electron microscopy results revealed the fashioning of spherical AgNPs and spherical and hexagonal AuNPs with a mean particle magnitude of 5–37 and 37–62 nm, respectively. X-ray diffraction showed the typical face-centered cubic structure of the mycosynthesized Ag and Au nanoparticles. An in vitro investigation showed that AgNPs, AuNPs, and their mixture at different concentrations (10000, 5000, 3000, 1000, 750, 500, 250, and 125 µg/mL) could inhibit or reduce the outgrowth and production of aflatoxin B₁ (AFB₁) by A. flavus. The concentration that showed no AFB₁ production was less than those for the inhibition of fungal growth. AgNPs, AuNPs, and their mixture also exhibited promising antiradical scavenging activity.

Conclusions

The use of fungi in the metallic nanoparticle’s fabrication and the utilization of mycosynthesized nanoparticles is promising as a substitute of chemicals to control antiaflatoxigenic fungi.

How to cite: Sheikh H, Awad MF. Biogenesis of nanoparticles with inhibitory effects on aflatoxin B1 production by Aspergillus flavus. Electron J Biotechnol 2022;60. https://doi.org/10.1016/j.ejbt.2022.09.003.