Identification of key genes and construction of CircRNA–miRNA–mRNA regulatory networks in osteoarthritis

BackgroundOsteoarthritis (OA) is one of the most frequent degenerative joint diseases with high rate of disability, but its mode of action remains largely unclear. The current study was aimed at identifying key genes and molecular mechanism in OA. Gene expression datasets (GSE1919, GSE55235, GSE55457) were downloaded from Gene Expression Omnibus for integrated bioinformatics analysis. Differentially expressed genes (DEGs) in OA synovial tissues were identified using GeoDiver and GEO2R. Gene ontology enrichment analyses were undertaken via FunRich and Metascape. Also, Gene Set Enrichment Analysis was performed using miRWalk3.0. Subsequently, pathways interrelation analysis of hub genes was carried out using plug-in ClueGO v2.3.3. Additionally, circRNA–miRNA–mRNA regulatory networks were visualized using Cytoscape.ResultsA total of 508 DEGs were obtained from three GSE datasets, of these five intersection DEGs (TNFAIP3, VEGFA, GADD45B, SIK1, KLF9) were shared by three GSE datasets. Intersection DEGs were significantly enriched in LKB1 signaling events, signaling events mediated by focal adhesion kinase, and PDGFR-beta signaling pathway. Enrichment analysis for all the DEGs showed that they mainly enriched in inflammatory response, cytokine production, blood vessel development, stress response, osteoclast differentiation, and MAPK signaling pathway. A total of 39 genes were regarded as hub genes and pathways interrelation analysis indicated that hub genes mainly enriched in TNF signaling pathway, IL-17 signaling pathway, and NF-kappa B signaling pathway.ConclusionsThe current study revealed the potential key genes, pathways, and circRNA–miRNA–mRNA regulatory networks in OA, which may contribute to a more comprehensive understanding of OA pathogenesis.How to cite: Li HZ, Xu XH, Lu HD. Identification of key genes and construction of CircRNA–miRNA–mRNA regulatory networks in osteoarthritis. Electron J Biotechnol 2019;37. https://doi.org/10.1016/j.ejbt.2018.11.004.     

Optimization of callus cultures at Echinacea purpurea L. for the amount of caffeic acid derivatives

BackgroundIn order to produce an effective callus in Echinacea purpurea L.; determination of the explant type and growth regulators that best respond to callus induction and the optimization of the culture conditions to increase the amount of caffeic acid derivatives (CADs) in the obtained callus. CADs contents of callus cultures of E. purpurea were evaluated by establishing an effective callus induction system in vitro.ResultsVarious medium containing different growth regulators were tested using leaf, petiole, cotyledon and root as the explants. The best callus development was achieved in MS medium with 1.0 mg l⁻¹ 2,4-D + 2.0 mg l⁻¹ BAP in leaf, 1.0 mg l⁻¹ NAA + 0.5 mg l⁻¹ TDZ in petiole, 2.0 mg l⁻¹ NAA + 1.0 mg l⁻¹ TDZ in cotyledon and 0.5 mg l⁻¹ NAA + 0.5 mg l⁻¹ BAP in roots. Upon optimisation of callus growth, each type of explant was cultured for 4, 6, 8 and 10 weeks in medium for the analyses of caftaric acid, chlorogenic acid, caffeic acid and chicoric acid contents. The highest amounts of caftaric acid (4.11 mg/g) and chicoric acid (57.89 mg/g) were found from petiole explants and chlorogenic acid (8.83 mg/g) from root explants at the end of the 10-week culture time.ConclusionsAs a result of the present study, the production of caffeic acid derivatives was performed by providing the optimization of E. purpurea L. callus cultures. Effective and repeatable protocols established in this study may offer help for further studies investigating the production of caffeic acid derivatives in vitro.How to cite: Tanur Erkoyuncu M, Yorgancilar M. Optimization of callus cultures at Echinacea purpurea L. for the amount of caffeic acid derivatives. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.02.003.     

Defensin γ-thionin from Capsicum chinense improves butyrate cytotoxicity on human colon adenocarcinoma cell line Caco-2

BackgroundButyrate is a histone deacetylase inhibitor that induces apoptosis and inhibits cell proliferation of colorectal cancer cells. To improve its anticancer activity, butyrate has been evaluated mixed with drugs and different molecules. Plant antimicrobial peptides are attractive anticancer alternative molecules because they show selective cytotoxic activity against different cancer cell lines. In this work, we explore if the plant defensin γ-thionin (Capsicum chinense) can improve butyrate activity on Caco-2 cell line and we also determined the mechanism of death activated.ResultsThe combined treatment of γ-thionin (3.5 µM) and butyrate (50 mM) showed higher cytotoxicity on Caco-2 cells with respect to single treatments. Also, the combined treatment reduced cell proliferation and exhibited a higher rate of apoptosis than single treatments. Combined treatment induced caspases 8 and 9 activation to an extent comparable with that of butyrate while γ-thionin did not activate caspases. Additionally, reactive oxygen species generation preceded the onset of apoptosis, and superoxide anion production was higher in cells treated with the combined treatment.ConclusionsThe γ-thionin from Habanero chili pepper improved the butyrate cytotoxicity on Caco-2 cells. This effect occurred through apoptosis induction associated with reactive oxygen species production. Therefore, the combination of butyrate with cytotoxic antimicrobial peptides could be an attractive strategy for cancer therapy.How to cite: Velázquez-Hernández ME, Ochoa-Zarzosa A, López-Meza JE, Defensin γ-thionin from Capsicum chinense improves butyrate cytotoxicity on human colon adenocarcinoma cell line Caco-2. Electron J Biotechnol 2021;52. https://doi.org/10.1016/j.ejbt.2021.04.009     

Alpha-hederin induces the apoptosis of oral cancer SCC-25 cells by regulating PI3K/Akt/mTOR signaling pathway

BackgroundOral cancer is one of the common malignant tumors of the head and neck. However, current treatments have numerous side effects, and drugs from natural sources may have better therapeutic potential. This research investigated the induction of apoptosis by α-hederin (α-HN), a constituent of Pulsatilla chinensis (Bunge) Regel, in the oral cancer cell line SCC-25 and its underlying mechanism.ResultsSCC-25 cells were treated with 50, 100, and 200 μmol/L α-HN. Cell proliferation; extent of apoptosis; activities of caspases-3, 8, and 9; and the expression of Bcl-2, Bax, phosphorylated (p)-phosphoinositide 3-kinase (PI3K), p-Akt, and p-mammalian target of rapamycin (mTOR) proteins were determined using the 3-(4,5)-2-thiazole-(2,5)-diphenyl tetrazolium bromide, flow cytometry, caspase activity detection kits, and western blot assays, respectively. The results showed that the proliferation of SCC-25 cells in the α-HN-treated groups decreased significantly, and the inhibitory effect was time and concentration dependent. Compared with cells in the control group, the extent of apoptosis increased significantly, caspase-3 and -9 activities were significantly enhanced, and the Bcl-2 level was lowered and the Bax level was elevated significantly in SCC-25 cells treated with α-HN for 48 h (P < 0.05). The expression of p-PI3K, p-Akt, and p-mTOR was also significantly lower in SCC-25 cells treated with α-HN than that in the control group (P < 0.05).ConclusionThese results indicate that α-HN can inhibit proliferation and induce apoptosis of SCC-25 cells and may exert these effects by inhibiting the PI3K/Akt/mTOR signaling pathway.How to cite: Wang H, Wu B, Wang H. Alpha-hederin induces the apoptosis of oral cancer SCC-25 cells by regulating PI3K/Akt/mTOR signaling pathway. Electron J Biotechnol 2019;38. https://doi.org/10.1016/j.ejbt.2018.12.005     

Metabolic engineering strategies for caffeic acid production in Escherichia coli

Caffeic acid (CA; 3,4-dihydroxycinnamic acid) is an aromatic compound obtained by the phenylpropanoid pathway. This natural product has antioxidant, antitumor, antiviral, and anti-inflammatory activities. It is also a precursor of CA phenethyl ester (CAPE), a compound with potential as an antidiabetic and liver-protective agent. CA can be found at low concentrations in plant tissues, and hence, its purification is difficult and expensive. Knowledge regarding the pathways, enzymes, and genes involved in CA biosynthesis has paved the way for enabling the design and construction of microbial strains with the capacity of synthesizing this metabolite. In this review, metabolic engineering strategies for the generation of Escherichia coli strains for the biotechnological production of CA are presented and discussed.How to cite: Hernández-Chávez G, Martinez A, Gosset G. Metabolic engineering strategies for caffeic acid production in Escherichia coli. Electron J Biotechnol 2019;38. https://doi.org/10.1016/j.ejbt.2018.12.004.     

Vibrio sp. ArtGut-C1, a polyhydroxybutyrate producer isolated from the gut of the aquaculture live diet Artemia (Crustacea)

BackgroundVibrio species display variable and plastic fitness strategies to survive and interact with multiple hosts, including marine aquaculture species that are severely affected by pathogenic Vibrios. The culturable Vibrio sp. strain ArtGut-C1, the focus of this study, provides new evidence of such phenotypic plasticity as it accumulates polyhydroxybutyrate (PHB), a biodegradable polymer with anti-pathogen activity, particularly in the marine larviculture phase. The strain was isolated from the gut of laboratory-reared Artemia individuals, the live diet and PHB carrier used in larviculture. Its main phenotypic properties, taxonomic status and genomic properties are reported based on the whole-genome sequencing.ResultsVibrio sp. ArtGut-C1 yielded 72.6% PHB of cells’ dry weight at 25°C. The genomic average nucleotide identity (ANI) shows it is closely related to V. diabolicus (ANI: 88.6%). Its genome contains 5,236,997-bp with 44.8% GC content, 3,710 protein-coding sequences, 96 RNA, 9 PHB genes functionally related to PHB metabolic pathways, and several genes linked to competing and colonizing abilities.ConclusionsThis culturable PHB-accumulating Vibrio strain shows high genomic and phenotypic variability. It may be used as a natural pathogen biocontrol in the marine hatchery and as a potential cell factory for PHB production.How to cite: Yévenes M, Quiroz M, Maruyama F, et al. Vibrio sp. ArtGut-C1, a polyhydroxybutyrate producer isolated from the gut of the aquaculture live diet Artemia (Crustacea). Electron J Biotechnol 2021;49. https://doi.org/10.1016/j.ejbt.2020.10.003     

Polyphenolic extracts of walnut (Juglans regia) green husk containing juglone inhibit the growth of HL-60 cells and induce apoptosis

BackgroundJuglone is a naphthoquinone currently obtained by chemical synthesis with biological activities including antitumor activity. Additionally, juglone is present in the green husk of walnut, which suggests evaluating the effect of GH extracts on carcinogenic cell lines.ResultsWalnut green husk ethanolic extract was obtained as 169.1 mg _juglone/100 g _{Green Husk} and antioxidant activity (ORAC) of 44,920 μmol Trolox Equivalent/100 g DW _{Green Husk}. At 1 μM juglone in HL-60 cell culture, green husk extract showed an antiproliferative effect, but pure juglone did not; under these conditions, normal fibroblast cells were not affected. A dose-dependent effect on mitochondrial membrane potential loss was observed. Apoptosis of HL-60 was detected at 10 μM juglone. Despite high ORAC values, neither purified juglone nor the extract showed protective effects on HL-60 cells under oxidative conditions.ConclusionsGreen husk extract generates an antiproliferative effect in HL-60 cells, which is related to an induction of the early stages of apoptosis and a loss of mitochondrial membrane potential. The normal cells were not affected when juglone is present at concentrations of 1 μM, while at higher concentrations, there is loss of viability of both cancerous and healthy cells.How to cite: Soto-Maldonado C, Vergara-Castro M, Jara-Quezada J, et al. Polyphenolic extracts of walnut (Juglans regia) green husk containing juglone inhibit the growth of HL-60 cells and induce apoptosis. Electron J Biotechnol 2019;39. https://doi.org/10.1016/j.ejbt.2019.02.001.     

CRISPR/Cas9-mediated MSTN gene editing induced mitochondrial alterations in C2C12 myoblast cells

BackgroundMyostatin (MSTN) negatively regulates muscle mass and is a potent regulator of energy metabolism. However, MSTN knockout have affect mitochondrial function. This research assessed the mitochondrial energy metabolism of Mstn −/+ KO cells, and wondered whether the mitochondria biogenesis are affected.ResultsIn this study, we successfully achieved Mstn knockout in skeletal muscle C2C12 cells using a CRISPR/Cas9 system and measured proliferation and differentiation using the Cell-Counting Kit-8 assay and qPCR, respectively. We found that MSTN dysfunction could promote proliferation and differentiation compared with the behaviour of wild-type cells. Moreover, Mstn KO induced an increase in KIF5B expression. The mitochondrial content was significantly increased in Mstn KO C2C12 cells, apparently associated with the increases in PGC-1α, Cox1, Cox2, ND1 and ND2 expression. However, no differences were observed in glucose consumption and lactate production. Interestingly, Mstn KO C2C12 cells showed an increase in IL6 and a decrease in TNF-1α levels.ConclusionThese findings indicate that MSTN regulates mitochondrial biogenesis and metabolism. This gene-editing cells provided favourable evidence for animal breeding and metabolic diseases.How to cite: Wang L, Ding Q, Ma S, et al. CRISPR/Cas9-mediated MSTN gene editing Induced Mitochondrial Alterations in C2C12 myoblast Cells. Electron J Biotechnol 2019;40. https://doi.org/10.1016/j.ejbt.2019.03.009     

Effects of exogenous γ-Aminobutyric acid on the regulation of respiration and protein expression in germinating seeds of mungbean (Vigna radiata) under salt conditions

Backgroundγ-Aminobutyric acid (GABA) bypasses the TCA cycle via GABA shunt, suggesting a relationship with respiration. However, little is known about its role in seed germination under salt conditions.ResultsIn this study, exogenous GABA was shown to have almost no influence on mungbean seed germination, except 0.1 mM at 10 h, while it completely alleviated the inhibition of germination by salt treatment. Seed respiration was significantly inhibited by 0.1 and 0.5 mM GABA, but was evidently enhanced under salt treatment, whereas both were promoted by 1 mM GABA alone or with salt treatment. Mitochondrial respiration also showed a similar trend at 0.1 mM GABA. Moreover, proteomic analysis further showed that 43 annotated proteins were affected by exogenous GABA, even 0.1 mM under salt treatment, including complexes of the mitochondrial respiratory chain.ConclusionsOur study provides new evidence that GABA may act as a signal molecule in regulating respiration of mungbean seed germination in response to salt stress.How to citeJi J, Shi S, Chen W, et al. Effects of exogenous γ-Aminobutyric acid on the regulation of respiration and protein expression in germinating seeds of mungbean (Vigna radiata) under salt conditions. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.05.005     

Fructosan form Paenibacillus kribbensis PS04 enhance disease resistance against Rhizoctonia solani and tobacco mosaic virus

BackgroundRice sheath blight (caused by Rhizoctonia solani) and tobacco mosaic virus are very important plant diseases, causing a huge loss in global crop production. Paenibacillus kribbensis PS04 is a broad-spectrum biocontrol agent, used for controlling these diseases. Previously, extracellular polysaccharides (EPS) from P. kribbensis PS04 had been purified and their structure was inferred to be fructosan. This study aimed to evaluate the effects of exogenous EPS treatment on plant–pathogen interactions.ResultsPlant defense genes such as phenylalanine ammonia-lyase, catalase, chitinase, allene oxide synthase, and PR1a proteins were significantly induced by exogenous EPS treatment. Moreover, subsequent challenge of EPS-pretreated plants with the pathogens (R. solani or tobacco mosaic virus) resulted in higher expression of defense-associated genes. Increased activities of defense-associated enzymes, total phenols, and flavonoids were also observed in EPS pretreated plants. The contents of malondialdehyde in plants, which act as indicator of lipid peroxidation, were reduced by EPS treatment.ConclusionsThis study comprehensively showed that EPS produced from P. kribbensis PS04 enhances disease resistance in plants by the activation of defense-associated genes as well as through the enhancement of activities of defense-related enzymes.How to citeCanwei S, Xiaoyun H, Ahmed N, et al. Fructosan form Paenibacillus kribbensis PS04 enhance disease resistance against Rhizoctonia solani and tobacco mosaic virus. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.07.002     

Next generation sequencing and microbiome's taxonomical characterization of frozen soil of north western Himalayas of Jammu and Kashmir,India

BackgroundTraditionally, microbial genome sequencing has been restrained to the species grown in pure culture. The development of culture-independent techniques over the last decade allows scientists to sequence microbial communities directly from environmental samples. Metagenomics is the study of complex genome by the isolation of DNA of the whole community. Next generation sequencing (NGS) of metagenomic DNA gives information about the microbial and taxonomical characterization of a particular niche. The objective of the present research is to study the microbial and taxonomical characterization of the metagenomic DNA, isolated from the frozen soil sample of a glacier in the north western Himalayas through NGS.ResultsThe glacier community comprised of 16 phyla with the representation of members belonging to Proteobacteria and Acidobacteria. The number of genes annotated through the Kyoto Encyclopedia of Genes and Genomes (KEGG), GO, Pfam, Clusters of Orthologous Groups of proteins (COGs), and FIG databases were generated by COGNIZER. The annotation of genes assigned in each group from the metagenomics data through COG database and the number of genes annotated in different pathways through KEGG database were reported.ConclusionResults indicate that the glacier soil taken in the present study, harbors taxonomically and metabolically diverse communities. The major bacterial group present in the niche is Proteobacteria followed by Acidobacteria, and Actinobacteria, etc. Different genes were annotated through COG and KEGG databases that integrate genomic, chemical, and systemic functional information.How to cite: Gupta V, Singh I, Rasool S, et al. Next Generation sequencing and microbiome’s taxonomical characterization of frozen soil of North Western Himalayas of Jammu and Kashmir, India. Electron J Biotechnol 2020;45. https://doi.org/10.1016/j.ejbt.2020.03.003.     

Short-chain fatty acids production by Bifidobacterium species in the presence of salep

BackgroundSalep is obtained by grinding dried orchid tubers and used as a valuable ingredient in the food industry. Because of the glucomannan content of salep, it is thought to have prebiotic potential. However, there is little information in studies concerning the fermentation characteristics and potential prebiotic properties of salep. The objective of this study was to investigate the effect of salep on bifidobacterial growth by measuring the highest optical density (OD), calculating the specific growth rates, and determining the production of lactic acid and short-chain fatty acids (acetic, propionic, and butyric acid) as a result of bacterial fermentation.ResultThe OD and pH values obtained in this study showed that salep was utilized as a source of assimilable carbon and energy by the Bifidobacterium species (BS). All Bifidobacterium strains produced lactic, acetic, propionic, and butyric acid, indicating that salep is readily fermented by these bacteria. Salep at 1% (w/v) showed a similar effect on bifidobacterial growth as that promoted by 1% (w/v) glucose used as a traditional carbon source.ConclusionsBifidobacterium species can develop in media containing salep as well as in glucose and exhibit the potential to be used as new sources of prebiotics.How to cite: Usta-Gorgun B, Yilmaz-Ersan L. Short-chain fatty acid production by the Bifidobacterium species in the presence of salep. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.06.004.     

Prospective production of fructose and single cell protein from date palm waste

BackgroundFructose and single cell protein are important products for the food market. Abundant amounts of low-grade dates worldwide are annually wasted. In this study, highly concentrated fructose syrups and single cell protein were obtained through selective fermentation of date extracts by Saccharomyces cerevisiae.ResultsThe effect of air flow (0.1, 0.5, 0.75, 1, 1.25 and 1.5 vvm) and pH (4.5, 4.8, 5, 5.3 and 5.6) was investigated. Higher air flow led to lower fructose yield. The optimum cell mass production of 10 g/L was achieved at air flow of 1.25 vvm with the fructose yield of 91%. Similar cell mass production was obtained in the range pH of 5.0–5.6, while less cell mass was obtained at pH less than 5. Controlling the pH at 4.5, 5.0 and 5.3 failed to improve the production of cell mass which were 5.6, 5.9 and 5.4 g/L respectively; however, better fructose yield was obtained.ConclusionsExtension of the modified Gompertz enabled excellent predictions of the cell mass, fructose production and fructose fraction. The proposed model was also successfully validated against data from literatures. Thus, the model will be useful for wide application of biological processes.How to cite: Putra MD, Abasaeed AE, Al-Zahrani SM. Prospective production of fructose and single cell protein from date palm waste. Electron J Biotechnol 2020;48. https://doi.org/10.1016/j.ejbt.2020.09.007.