Effect of miR-125b on dermal papilla cells of goat secondary hair follicle

BackgroundMicroRNAs (miRNAs) are endogenous noncoding RNAs that regulate various biological processes. miR-125b is a miRNA that has been reported to be critical for hair follicle (HF) morphogenesis and development. We identified that the expression of miR-125b varies during an individual hair cycle (anagen, catagen, and telogen) in the skin of cashmere goats. We constructed a gain model (by overexpressing miR-125b) and a loss model (by inhibiting endogenous miR-125b) based on dermal papilla cells (DPCs) to further investigate the role of miR-125b in HF cycle. In addition, we used a dual-luciferase system to highlight the predicated target genes of miR-125b.ResultsWe found that miR-125b affects the expression of FGF5, IGF-1, SHH, TNF-α, MSX2, LEF-1, FGF7, NOGGIN, BMP2, BMP4, TGF-β1, and β-catenin. The dual-luciferase assay further validated a direct interaction between miR-125b and FGF5 and TNF-α.ConclusionmiR-125b affects the expression levels of genes related to hair cycle and may also play a critical role in regulating the periodic development of HF.     

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.     

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     

Simple synthesis of photoluminescent carbon dots from a marine polysaccharide found in shark cartilage

BackgroundFor more than a decade, water-soluble, eco-friendly, biocompatible, and low-toxicity fluorescent nanomaterials have received considerable attention for their numerous in vivo and in vitro applications in biomedical imaging, disease diagnostics, and environmental monitoring. Owing to their tunable photoluminescence properties, carbon-based luminescent nanomaterials have shown great potential in bioimaging, photocatalysis, and biosensing among other applications.ResultsMarine environments provide excellent resources for the fabrication of these nanomaterials, because many marine organisms contain interesting trigger organic compounds that can be used as precursors. Herein, we synthesize multi-color emissive carbon dots (CDs) with an intrinsic photoluminescence quantum yield of 20.46%. These nanostructures were achieved through the one-step hydrothermal treatment of marine polysaccharide chondroitin sulfate, obtained from shark cartilage, in aqueous solution.ConclusionsWe successfully demonstrate the low toxicity of our marine resource-derived CDs in zebrafish, and provide an initial assessment of their possible use as a bioimaging agent. Notably, the newly synthesized CDs localize in the intestines of zebrafish larvae, thereby indicating their biocompatibility and potential use as in vivo dyes.How to cite: Kim KW, Choi TY, Kwon YM, et al. Simple synthesis of photoluminescent carbon dots from a marine polysaccharide found in shark cartilage. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.07.003.     

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.     

Expression of Pinellia ternata leaf agglutinin under rolC promoter confers resistance against a phytophagous sap sucking aphid,Myzus persicae

BackgroundPiercing/sucking insect pests in the order Hemiptera causes substantial crop losses by removing photoassimilates and transmitting viruses to their host plants. Cloning and heterologous expression of plant-derived insect resistance genes is a promising approach to control aphids and other sap-sucking insect pests. While expression from the constitutive 35S promoter provides broad protection, the phloem-specific rolC promoter provides better defense against sap sucking insects. The selection of plant-derived insect resistance genes for expression in crop species will minimize bio-safety concerns.ResultsPinellia ternata leaf agglutinin gene (pta), encodes an insecticidal lectin, was isolated and cloned under the 35S and rolC promoters in the pGA482 plant transformation vector for Agrobacterium-mediated tobacco transformation. Integration and expression of the transgene was validated by Southern blotting and qRT-PCR, respectively. Insect bioassays data of transgenic tobacco plants showed that expression of pta under rolC promoter caused 100% aphid mortality and reduced aphid fecundity up to 70% in transgenic tobacco line LRP-9. These results highlight the better effectivity of pta under rolC promoter to control phloem feeders, aphids.ConclusionsThese findings suggested the potential of PTA against aphids and other sap sucking insect pests. Evaluation of gene in tobacco under two different promoters; 35S constitutive promoter and rolC phloem-specific promoter could be successfully use for other crop plants particularly in cotton. Development of transgenic cotton plants using plant-derived insecticidal, PTA, would be key step towards commercialization of environmentally safe insect-resistant crops.How to citeUmer N, Naqvi RZ, Rauf I, et al. Expression of Pinellia ternata leaf agglutinin under rolC promoter confers resistance against a phytophagous sap sucking aphid, Myzus persicae. Electron J Biotechnol 2020;47. https://doi.org/10.1016/j.ejbt.2020.07.004.     

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     

Bovine TMEM95 gene: Polymorphisms detecting in five Chinese indigenous cattle breeds and their association with growth traits

BackgroundTransmembrane protein 95 (TMEM95) plays a role in male fertility. Previous studies showed that genes with a significant impact on reproductive traits can also affect the growth traits of livestock. Thus, we speculated that the genetic variation of TMEM95 gene may have effects on growth traits of cattle.ResultsTwo SNPs were genotyped. The rs136174626 and rs41904693 were in the intron 4 and 3′-untranslated region, respectively. The linkage disequilibrium analysis illustrated that these two loci were not linked. The rs136174626 was associated with six growth traits of Nanyang cattle, four traits of Luxi cattle, and three traits of Ji’an cattle. For rs41904693 locus, the GG individuals had greater body height and abdominal girth in Ji’ an cattle than TT and TG individuals. In Jinnan cattle, GG and TT individuals had greater body height, height at hip cross, body length, and heart girth than TG individuals. The potential splice site prediction results suggest that the rs136174626 may influence the splicing efficiency of TMEM95, and the miRNA binding site prediction results showed that the rs41904693 may influence the expression of TMEM95 by affecting the binding efficiency of Bta-miR-1584 and TMEM95 3′-UTR.ConclusionsThe findings of the study suggested that the two SNPs in TMEM95 could be a reliable basis for molecular breeding in cattle.How to cite: Guo X, Zhang S, Yang H, et al. Bovine TMEM95 gene: Polymorphisms detecting in five Chinese indigenous cattle breeds and their association with growth traits. Electron J Biotechnol 2021;51. https://doi.org/10.1016/j.ejbt.2021.03.004     

Genome-wide development of polymorphic microsatellite markers and their application in peanut breeding program

BackgroundCultivated peanut (Arachis hypogaea. L) represents one of the most important oil crops in the world. Although much effort has been expended to characterize microsatellites or Simple Sequence Repeats (SSRs) in peanut, the quantity and quality of the markers in breeding applications remain limited. Here, genome-wide SSR characterization and marker development were performed using the recently assembled genome of the cultivar Tifrunner.ResultsIn total, 512,900 microsatellites were identified from 2556.9-Mb genomic sequences. Based on the flanking sequences of the identified microsatellites, 7757 primer pairs (markers) were designed, and further evaluated in the assembled genomic sequences of the tetraploid Arachis cultivars, Tifrunner and Shitouqi, and the diploid ancestral species, A. duranensis and A. ipaensis. In silico PCR analysis showed that the SSR markers had high amplification efficiency and polymorphism in four Arachis genotypes. Notably, nearly 60% of these markers were single-locus SSRs in tetraploid Arachis species, indicating they are more specific in distinguishing the alleles of the A and B sub-genomes of peanut. In addition, two markers closely related with purple testa color and 27 markers near to FAD2 genes were identified, which could be used for breeding varieties with purple testa and high-oleic acid content, respectively. Moreover, the potential application of these SSR markers in tracking introgressions from Arachis wild relatives was discussed.ConclusionsThis study reported the development of genomic SSRs from assembled genomic sequences of the tetraploid Arachis Tifrunner, which will be useful for diversity analysis, genetic mapping and functional genomics studies in peanut.How to cite: Ma J, Zhao Y, Chen H, et al. Genome-wide development of polymorphic microsatellite markers and their application in peanut breeding program. Electron J Biotechnol 2020;44. https://doi.org/10.1016/j.ejbt.2020.01.004.     

In vitro screening for acetylcholinesterase and butyrylcholinesterase inhibition and antimicrobial activity of chia seeds (Salvia hispanica)

BackgroundChia seeds are gaining increasing interest among food producers and consumers because of their prohealth properties.ResultsThe aim of this work was to evaluate the potential of chia seeds to act as acetylcholinesterase (AChE) and butyrylcholinesterase (BChE) inhibitors. The highest inhibitory activity against AChE and BChE was observed for colored seed ethanol extracts. A positive correlation was found between the presence of quercetin and isoquercetin as well as protocatechuic, hydroxybenzoic, and coumaric acids and the activity of extracts as AChE and BChE inhibitors. It has also been shown that grain fragmentation affects the increase in the activity of seeds against cholinesterases (ChE). Furthermore, seeds have been shown to be a source of substances that inhibit microbial growth.ConclusionsIt was found that the chia seed extracts are rich in polyphenols and inhibit the activity of ChEs; therefore, their use can be considered in further research in the field of treatment and prevention of neurodegenerative diseases.How to cite: Kobus-Cisowska J, Szymanowska D, Maciejewska P, et al. In vitro screening for acetylcholinesterase and butyrylcholinoesterase inhibition and antimicrobial activity of chia seeds (Salvia hispanica). Electron J Biotechnol 2019;37. https://doi.org/10.1016/j.ejbt.2018.10.002     

Biosurfactant produced by Candida utilis UFPEDA1009 with potential application in cookie formulation

BackgroundBiosurfactants are biomolecules that have the potential to be applied in food formulations due to their low toxicity and ability to improve sensory parameters. Considering the ability of yeasts to produce biosurfactants with food-friendly properties, the aim of the present study was to apply a biosurfactant produced by Candida utilis in the formulation of cookies.ResultsThe biosurfactant was obtained with a yield of 24.22 ± 0.23 g/L. The characterization analysis revealed that the structure of a metabolized fatty acid with high oleic acid content (68.63 ± 0.61%), and the thermogravimetric analysis demonstrated good stability at temperatures lower than 200°C, potential for food applications. The biosurfactant also exhibited satisfactory antioxidant activity at concentrations evaluated, without cytotoxic potential for cell strains, L929 and RAW 264.7, according to the (3-(4,5-dimethylthiazol-2-yl)-2,5-diphenyltetrazolium bromide (MTT) assay. The incorporation of the surfactant into the dough of a standard cookie formulation to replace animal fat was carried out, achieving a softer, spongier product without significantly altering the physical and physicochemical properties or energy value.ConclusionThe thermal stability and antioxidant activity of the biosurfactant produced by C. utilis were verified, besides the positive contribution in the texture analysis of the cookies. Therefore, this biomolecule presents itself as a potential ingredient in flour-based sweet food formulations. How to cite: Ribeiro BG, de Veras BO, Aguiar JS, et al. Biosurfactant produced by Candida utilis UFPEDA1009 with potential application in cookie formulation. Electron J Biotechnol 2020;46. https://doi.org/10.1016/j.ejbt.2020.05.001.