Electronic Journal of Biotechnology最新文献

Background

Millenary fermented beverages are a source of industrially important microorganisms. Aguamiel and pulque are traditional Mexican beverages of pre-Hispanic origin, with a microbial diversity that contributes to the different fermentations (lactic, alcoholic and acetic). The aim of this research was to characterize the Bacillus mojavensis (BF2A1) strain isolated from aguamiel and determine its probiotic potential. The strain was identified through Mass Spectrometry (MS), molecular techniques, as well as morphological and biochemical profiling. The probiotic activity of the BF2A1 strain and its response during the gastric simulation was determined.

Results

The strain BF2A1 is a Gram-positive, spore-forming bacillus, positive for catalase, gamma-hemolysis, citrate, ornithine, grows at 7.5% NaCl, and acetoin, but negative for motility, indole, and methyl red. Its taxonomic identity was determined as B. mojavensis both by MALDI-TOF MS and sequencing of 16S rDNA. Its probiotic potential was demonstrated as BF2A1 was tolerant to pH 2 (OD_620nm 0.289 ± 0.012), 0.3% bile salts (OD_620nm 0.103 ± 0.089), 8% NaCl (OD_620nm 0.254 ± 0.096), and 1% lysozyme (OD_620nm 1.342 ± 0.078) compared to the probiotic strain Lactobacillus leichmannii ATCC 7830TM (Laclei). The antagonistic effect of BF2A1 against Escherichia coli (ATCC25922), Staphylococcus aureus (ATCC25923), and Candida albicans (ATCC60193) showed 25.5%, 8% and, 65% inhibitory growing effect, respectively. BF2A1 in the gastric simulation showed only a reduction of 1–2 log CFU/mL and showed after the intestinal phase a survival rate of 84.4% as compared to the control strains.

Conclusions

This study shows that BF2A1 isolated from aguamiel is a bacterium with probiotic properties that can be used in different areas of Biotechnology.

How to cite: Martínez-Ortiz V, Trujillo-López MA, El-Kassis EG, et al. Bacillus mojavensis isolated from aguamiel and its potential as a probiotic bacterium. Electron J Biotechnol 2024;67. https://doi.org/10.1016/j.ejbt.2023.11.002.

Background

This research probed the relevant mechanism of miR-379-3p by regulating suppressor of cytokine signaling1 (SOCS1) in the processes of inflammation, oxidative stress, and angiogenesis in fat grafting. An increasing body of research indicates the involvement of miRNA/mRNA pathways in the process of fat transplantation, yet the underlying molecular mechanisms remain to be fully elucidated.

Results

miR-379-3p knockdown improved the survival rate of adipocytes, promoted adipose tissue angiogenesis, and reduced inflammation and oxidative stress levels. miR-379-3p targeted SOCS1. SOCS1 upregulation improved adipose tissue survival and angiogenesis and reduced inflammation. miR-379-3p affected adipose tissue survival, angiogenesis, and inflammation by targeting SOCS1 expression.

Conclusions

miR-379-3p inhibits fat grafting survival and angiogenesis by targeting SOCS1 to mediate adipose inflammation, suffering a novel way to improve fat grafting technique development.

How to cite: Zhu J, Zhao F, Han X, et al. miR-379-3p inhibits fat grafting survival and angiogenesis by targeting SOCS1-mediated adipose inflammation. Electron J Biotechnol 2024:67. https://doi.org/10.1016/j.ejbt.2023.11.001.

Background

Glaucoma is marked by retinal neuron death in the ganglion cell layer, leading to irreversible vision loss. Aberrant long non-coding RNA (lncRNA) expression is associated with glaucoma. The study was to explore the latent molecular mechanism of lncRNA KCNQ1 opposite strand/antisense transcript 1 (KCNQ1OT1) in N-methyl-D-aspartate (NMDA)-stimulated glaucoma.

Results

The data demonstrated that KCNQ1OT1 expression was elevated in glaucoma patients, serving as a diagnostic biomarker of glaucoma. Rats injected with NMDA developed visual loss and retinopathy and expressed high KCNQ1OT1. After treating retinal ganglion cells (RGCs) with NMDA, cell proliferation was suppressed and apoptosis was augmented. Silenced KCNQ1OT1 or HOXB3 or elevated miR-93-5p alleviated NMDA-induced suppression of RGC growth. KCNQ1OT1 mediated miR-93-5p expression by targeting homeobox box 3 (HOXB3). The protection of silenced KCNQ1OT1 in NMDA-treated RGCs was turned around by elevated HOXB3.

Conclusions

Overall, KCNQ1OT1 accelerates glaucoma progression via miR-93-5p/HOXB3 axis.

How to cite: Xie ZL, Wang H, Liu LL, et al. Long non-coding RNA KCNQ1 opposite strand/antisense transcript 1, a potential biomarker for glaucoma, accelerates glaucoma progression via microRNA-93-5p/Homeobox box 3 axis. Electron J Biotechnol 2024;67 . https://doi.org/10.1016/j.ejbt.2023.10.002.

Background

This study investigates the link between SARS-CoV-2-associated long non-coding RNAs (lncRNAs) and lung adenocarcinoma (LUAD). LUAD is a prevalent and aggressive lung cancer type. The study aims to identify prognostic lncRNAs and construct a predictive model while shedding light on potential therapeutic targets during the COVID-19 era.

Results

Eight SARS-CoV-2-associated lncRNAs with significant prognostic value in LUAD were identified, forming a robust prognostic risk model. The model exhibited strong predictive performance, with high area under the ROC curve (AUC) values at one, three, and five years. Furthermore, the risk score was an independent prognostic factor, correlating with the cancer stage. Notably, differences in immune function, drug sensitivity, and immune checkpoint expression were observed between high- and low-risk groups.

Conclusions

This study unveils eight SARS-CoV-2-associated lncRNAs as valuable prognostic markers in LUAD, yielding a reliable prognostic risk model. Additionally, the model's ability to predict patient outcomes and its correlation with cancer stage underscores its clinical utility. The observed variances in immune function, drug sensitivity, and immune checkpoint expression suggest potential avenues for personalized LUAD treatment strategies. Clinicians can utilize the prognostic risk model to predict LUAD patient outcomes, informing treatment decisions. The insights into immune function, drug sensitivity, and immune checkpoints offer opportunities for tailored therapies, potentially enhancing patient outcomes. This study underscores the importance of considering the interplay between SARS-CoV-2-associated factors and cancer biology, especially in the context of the COVID-19 pandemic.

How to cite: Zhou Q, Yuan T, Xie Z, et al. Unraveling SARS-CoV-2-associated lncRNAs' prognostic significance in lung adenocarcinoma-survival, immunity, and chemotherapy responses. Electron J Biotechnol 2024;67. https://doi.org/10.1016/j.ejbt.2023.10.001.

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.