Screening of the key volatile organic compounds of Tuber melanosporum fermentation by aroma sensory evaluation combination with principle component analysis

Volatile Organic Compounds of Anchote Tuber and Leaf Extracted Using Simultaneous Steam Distillation and Solvent Extraction

Anchote (Coccinia abyssinica (Lam.) (Cogn)) is an endemic and potentially valuable crop of Ethiopia principally categorized under root and tuber crops, and its newly growing leaves along with the tendrils are also used as nutritious vegetable served after being cooked. Leaf and tuber powders were extracted for the first time to identify volatile organic compounds by simultaneous steam distillation and solvent extraction (SDE) and characterized using gas chromatography mass spectrometry (GC-MS). VOCs having an area percentage above 0.5% were used for identification analysis. From the results, thirty volatile flavor compounds from leaves and fifteen from tubers were identified with the total fraction yield of 770.57 mg/kg and 4536.91 mg/kg, respectively, and from the 30 compounds identified from leaf 16 were distinguished in each of the tested accessions. Ethyl acetate 90.47% (697.13 mg/kg) was detected in a higher amount exhibiting >1% peak area. The rest 6.03% (46.46 mg/kg) were minor quantities (<1%) of the total (770.57 mg/kg) volatile flavor fraction. Among the 15 identified compounds in the tuber, ethyl acetate was the only major compound that accounted together for 99.15% (4498.33 mg/kg) of the total volatile flavor fraction and 0.85% (38.58 mg/kg) being reported in minor quantities (<1%). The SDE extraction and GC-MS analysis of anchote leaves and tubers successfully identified various volatile flavor compounds, which indicates that anchote was found to be a potential source of volatile flavor compounds that can be used as a food flavoring agent and in folk medicines. Thus, this study confirms that anchote leaf and tuber can be used for more specific and valuable applications in food and medicine industries.

Headspace Solid-Phase Microextraction Followed by Gas Chromatography-Mass Spectrometry as a Powerful Analytical Tool for the Discrimination of Truffle Species According to Their Volatiles

This study provides the first assessment of the volatile metabolome map of Tuber Aestivum and Tuber Borchii originating from Greece using headspace solid-phase micro-extraction (HS-SPME) coupled to gas chromatography-mass spectrometry (GC-MS). For the extraction of the volatile fraction, the SPME protocol was optimized after examining the effects of sample mass, extraction temperature, and extraction time using the one-variable at-a-time approach (OVAT). The optimum parameters involved the extraction of 100 mg of homogenized truffle for 45 min at 50°C. Overall, 19 truffle samples were analyzed, and the acquired data were normalized and further processed with chemometrics. Agglomerative hierarchical clustering (HCA) was used to identify the groups of the two species. Partial least squares-discriminant analysis (PLS-DA) was employed to develop a chemometric model that could discriminate the truffles according to the species and reveal characteristic volatile markers for Tuber Aestivum and Tuber Borchii grown in Greece.

Transcriptome Analyses Reveal Systematic Molecular Pathology After Optic Nerve Crush

The function of glial cells in axonal regeneration after injury has been the subject of controversy in recent years. Thus, deeper insight into glial cells is urgently needed. Many studies on glial cells have elucidated the mechanisms of a certain gene or cell type in axon regeneration. However, studies that manipulate a single variable may overlook other changes. Here, we performed a series of comprehensive transcriptome analyses of the optic nerve head over a period of 90 days after optic nerve crush (ONC), showing systematic molecular changes in the optic nerve head (ONH). Furthermore, using weighted gene coexpression network analysis (WGCNA), we established gene module programs corresponding to various pathological events at different times post-ONC and found hub genes that may be potential therapeutic targets. In addition, we analyzed the changes in different glial cells based on their subtype markers. We revealed that the transition trend of different glial cells depended on the time course, which provides clues for modulating glial function in further research.

Effect of chitosan and gum Arabic with natamycin on the aroma profile and bacterial community of Australian grown black Périgord truffles (Tuber melansoporum) during storage

This study aimed to assess the effect of chitosan or gum Arabic edible coatings, with natamycin (200, 300, 400 mg/L) on the aroma profiles of Western Australian grown truffles at five storage intervals: 0, 7, 14, 21, and 28 days using solid-phase microextraction (SPME)-followed by gas chromatography-mass spectrometry (GC-MS). The population structure of the bacterial community of both untreated and chitosan-natamycin (400 mg/L) coated truffles were assessed using metagenomic sequencing analysis alongside GC-MS. The results demonstrated that all the coating treatments were able to have a positive impact in halting or delaying the changes of truffle aroma throughout the storage period, with chitosan-natamycin (400 mg/L) coating having the best preservation results compared to the other coatings. Only 9 volatile organic compounds (VOCs) were found to have significant changes in chitosan-natamycin (400 mg/L) coated truffles throughout the storage period compared to 11 VOCs in untreated controls. The result also demonstrated the gradual change of fresh truffle's bacteria communities over the storage period. Over 4 weeks of storage, the dominant bacterial classes of the truffles (α-Proteobacteria, Bacteroidia or Actinobacteria classes) were replaced by Bacteroidia, Actinobacteria, Deltaprotobacteria and γ-Proteobacteria classes. The preliminary results from this study show that edible coatings can affect the VOC and bacterial communities of the truffles which may have implications for future research into truffle preservation techniques.

Construction and Comprehensive Analysis of a ceRNA Network to Reveal Potential Novel Biomarkers for Triple-Negative Breast Cancer

Background

Triple-negative breast cancer (TNBC) is the most common and aggressive type of breast cancer with an unfavourable outcome worldwide. Novel therapeutic targets are urgently required to explore this malignancy. This study explored the ceRNA network and the important genes for predicting the therapeutic targets.

Methods

It identified the differentially expressed genes of mRNAs, lncRNAs and miRNAs between TNBC and non-TNBC samples in four cohorts (TCGA, GSE38959, GSE45827 and GSE65194) to explore the novel therapeutic targets for TNBC. Downstream analyses, including functional enrichment analysis, ceRNA network, protein–protein interaction and survival analysis, were then conducted by bioinformatics analysis. Finally, the potential core protein of the ceRNA network in TNBC was validated by immunohistochemistry.

Results

A total of 1,045 lncRNAs and 28 miRNAs were differentially expressed in the TCGA TNBC samples, and the intersections of 282 mRNAs (176 upregulations and 106 downregulations) between the GEO and TCGA databases were identified. A ceRNA network composed of 7 lncRNAs, 62 mRNAs, 12 miRNAs and 244 edges specific to TNBC was established. The functional assay showed dysregulated genes, and GO, DO and KEGG enrichment analysis were performed. Survival analysis showed that mRNA LIFR and lncRNA AC124312.3 were significantly correlated with the overall survival of patients with TNBC in the TCGA databases (P < 0.05). Finally, the LIFR protein was validated, and immunohistochemical results showed the upregulated expression of LIFR in TNBC tissues.

Conclusion

Thus, our study presents an enhanced understanding of the ceRNA network in TNBC, where the key gene LIFR may be a new promising potential therapeutic target for patients with TNBC.

Potentials of truffles in nutritional and medicinal applications: a review

Truffles, the symbiotic hypogeous edible fungi, have been worldwide regarded as a great delicacy because of their unique flavor and high nutritional value. By identifying their bioactive components such as phenolics, terpenoids, polysaccharides, anandamide, fatty acids, and ergosterols, researchers have paid attention to their biological activities including antitumor, antioxidant, antibacterial, anti-inflammatory, and hepatoprotective activities. In addition, numerous factors have been investigating that can affect the quality and productivity of truffles to overcome their difficulty in culturing and preserving. To provide the information for their potential applications in medicine as well as in functional food, this review summarizes the relevant literature about the biochemical composition, aromatic and nutritional benefits, and biological properties of truffles. Besides, various factors affecting their productivity and quality as well as the preservation methods are also highlighted.

Characterization of the Key Aroma Compounds in Three Truffle Varieties from China by Flavoromics Approach

The volatile compounds of three different fresh-picked truffle varieties (Tuber sinensis, T1, Tuber sinoalbidum, T2 and Tuber sinoexcavatum, T3) were extracted by headspace solid-phase microextraction (HS-SPME). Separation and identification of volatile components and sulfur compounds were investigated by gas chromatography-olfactometry (GC-O), gas chromatography-mass spectrometry (GC-MS) and gas chromatography with flame photometric detection (GC-FPD). The results showed that 44, 43 and 44 volatile compounds were detected in T1, T2 and T3 samples, respectively. In addition, 9, 10 and 9 sulfur compounds were identified in three samples by GC-FPD, respectively. Combining physicochemical and sensory properties, T1 presented fatty, green and rotten cabbage odor; T2 exhibited mushroom, sulfuric and musty odor notes; T3 had nutty, floral and roasted potato odor. Dimethyl sulfide, 3-methylbutanal, dimethyl disulfide, 3-octanone, bis(methylthio) methane, octanal, 1-octen-3-one, 1-octen-3-ol and benzeneacetaldehyde played indispensable roles in the overall aroma of three truffles. Finally, based on quantitative concentration in T1, odorous compounds (OAV) > 1 were mixed to recombine aroma, demonstrating that these key aroma compounds based on OAV can successfully recombine pretty similar aroma of each variety.

Transcriptomic and functional network features of lung squamous cell carcinoma through integrative analysis of GEO and TCGA data

Lung squamous cell carcinoma (LUSC) is associated with poor clinical prognosis and lacks available targeted therapy. Novel molecules are urgently required for the diagnosis and prognosis of LUSC. Here, we conducted our data mining analysis for LUSC by integrating the differentially expressed genes acquired from Gene Expression Omnibus (GEO) database by comparing tumor tissues versus normal tissues (GSE8569, GSE21933, GSE33479, GSE33532, GSE40275, GSE62113, GSE74706) into The Cancer Genome Atlas (TCGA) database which includes 502 tumors and 49 adjacent non-tumor lung tissues. We identified intersections of 129 genes (91 up-regulated and 38 down-regulated) between GEO data and TCGA data. Based on these genes, we conducted our downstream analysis including functional enrichment analysis, protein-protein interaction, competing endogenous RNA (ceRNA) network and survival analysis. This study may provide more insight into the transcriptomic and functional features of LUSC through integrative analysis of GEO and TCGA data and suggests therapeutic targets and biomarkers for LUSC.

Tuber indicum shapes the microbial communities of ectomycorhizosphere soil and ectomycorrhizae of an indigenous tree (Pinus armandii)

The aim of this study was to investigate the effect of an ectomycorrhizal fungus (Tuber indicum) on the diversity of microbial communities associated with an indigenous tree, Pinus armandii, and the microbial communities in the surrounding ectomycorhizosphere soil. High-throughput sequencing was used to analyze the richness of microbial communities in the roots or rhizosphere of treatments with or without ectomycorrhizae. The results indicated that the bacterial diversity of ectomycorhizosphere soil was significantly lower compared with the control soil. Presumably, the dominance of truffle mycelia in ectomycorhizosphere soil (80.91%) and ectomycorrhizae (97.64%) was the main factor that resulted in lower diversity and abundance of endophytic pathogenic fungi, including Fusarium, Monographella, Ustilago and Rhizopus and other competitive mycorrhizal fungi, such as Amanita, Lactarius and Boletus. Bacterial genera Reyranena, Rhizomicrobium, Nordella, Pseudomonas and fungal genera, Cuphophyllus, Leucangium, Histoplasma were significantly more abundant in ectomycorrhizosphere soil and ectomycorrhizae. Hierarchical cluster analysis of the similarities between rhizosphere and ectomycorrhizosphere soil based on the soil properties differed significantly, indicating the mycorrhizal synthesis may have a feedback effect on soil properties. Meanwhile, some soil properties were significantly correlated with bacterial and fungal diversity in the rhizosphere or root tips. Overall, this work illustrates the interactive network that exists among ectomycorrhizal fungi, soil properties and microbial communities associated with the host plant and furthers our understanding of the ecology and cultivation of T. indicum.