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Objective: As the world's food safety and environmental safety problems become increasingly severe, the agricultural sectors of various countries are also paying closer attention to the use of biofertilizers and biocontrol agents. Rhizosphere bacteria are a significant source of commonly used biofertilizers and biocontrol agents. This study aims to describe the genome and genomic traits of a biocontrol agent in the genus Bacillus.Results: In this paper, a strain of Bacillus amyloliquefaciens IBFCBF-5 was isolated and identified to have an inhibitory effect on several common oomycete and fungal pathogens Phytophthora capsica, Sclerotinia sclerotiorum, Colletotrichum gloeosporioides, and Fusarium oxysporum f.sp. cucumerinum. The genome of strain IBFCB-5 was sequenced, and the assembled genome was 4,338,658bp, with a G+C content of 46.05%. The IBFCBF-5 genome contains abundant GH, GT, CE, PL, AA, and CBM gene families, potentially degrading cellulose and hemicellulose, chitin, starch, xylan, peptidoglycan, etc. In addition, 14 lipopeptide and polypeptide antibiotic gene clusters were found in IBFCBF-5, including those coding for the synthesis of several known antifungal and antibacterial compounds Fengycin, Bacilysin, Bacillibactin, and plantazolicin.Conclusion: Our results show that Bacillus amyloliquefaciens IBFCBF-5 has a broad-spectrum antifungal ability and that its genome contains many genes coding for antimicrobial metabolites.

l -cysteine (L-cys) modified ZnS (LZS) quantum dots (QDs) were synthesized by a two-step way. The effects of LZS QDs on the phenotype, biomass, morphology and extracellular protein content of Aspergillus oryzae (A. oryzae) were studied in detail for the first time. The results illustrated that both uncoated and coated QDs had a cubic blend ZnS structure, and the particle size was about 4.0 and 4.3 nm, respectively. It was found that LZS QDs acted as an activator to stimulate the growth of A. oryzae in both solid and liquid media, and the biomass with 50 μg/mL (25 μg/mL) QDs in solid (liquid) medium was the highest and was about 1.65 (3.74) times higher than that in control medium (without QDs). The data of ultraviolet–visible (UV–Vis) revealed that the protein concentration of A. oryzae was 824.904 and 467.748 μg/mL relating to liquid medium with and without QDs, respectively. This work can provide a new way to increase the production of A. oryzae or microorganisms.

Andrographis paniculata (Burm. f.) Wall. ex Nees, a renowned herb medicine in China, is broadly utilized in traditional Chinese medicine (TCM) for the treatment of cold and fever, sore throat, sore tongue, snake bite with its excellent functions of clearing heat and toxin, cooling blood and detumescence from times immemorial. Modern pharmacological research corroborates that andrographolide, the major ingredient in this traditional herb, is the fundamental material basis for its efficacy. As the main component of Andrographis paniculata (Burm. f.) Wall. ex Nees, andrographolide reveals numerous therapeutic actions, such as antiinflammatory, antioxidant, anticancer, antimicrobial, antihyperglycemic and so on. However, there are scarcely systematic summaries on the specific mechanism of disease treatment and pharmacokinetics. Moreover, it is also found that it possesses easily ignored security issues in clinical application, such as nephrotoxicity and reproductive toxicity. Thereby it should be kept a lookout over in clinical. Besides, the relationship between the efficacy and security issues of andrographolide should be investigated and evaluated scientifically. In this review, special emphasis is given to andrographolide, a multifunctional natural terpenoids, including its pharmacology, pharmacokinetics, toxicity and pharmaceutical researches. A brief overview of its clinical trials is also presented. This review intends to systematically and comprehensively summarize the current researches of andrographolide, which is of great significance for the development of andrographolide clinical products. Noteworthy, those un-cracked issues such as specific pharmacological mechanisms, security issues, as well as the bottleneck in clinical transformation, which detailed exploration and excavation are still not to be ignored before achieving integration into clinical practice. In addition, given that current extensive clinical data do not have sufficient rigor and documented details, more high-quality investigations in this field are needed to validate the efficacy and/or safety of many herbal products.

Mitophagy, a form of autophagy, plays a role in cancer development, progression and recurrence. Cancer stem cells (CSCs) also play a key role in these processes, although it not known whether mitophagy can regulate the stemness of CSCs. Here, we employed the A549‐SD human non‐small cell lung adenocarcinoma CSC model that we have developed and characterized to investigate the effect of mitophagy on the stemness of CSCs. We observed a positive relationship between mitophagic activity and the stemness of lung CSCs. At the mechanistic level, our results suggest that augmentation of mitophagy in lung CSCs can be induced by FIS1 through mitochondrial fission. In addition, we assessed the clinical relevance of FIS1 in lung adenocarcinoma using The Cancer Genome Atlas database. An elevation in FIS1, when observed together with other prognostic markers for lung cancer progression, was found to correlate with shorter overall survival., In the human non‐small cell lung adenocarcinoma cancer stem cell model A549‐SD, inhibiting the expression of FIS1 can inhibit mitochondrial division, thereby inhibiting mitophagy and consequently inhibiting the stemness of cancer stem cells.

Somatic variations are a major source of genetic diversification in asexual plants, and underpin clonal evolution and the breeding of asexual crops. Sweet orange is a model species for studying somatic variation because it reproduces asexually through apomixis and is propagated asexually through grafting. To dissect the genomic basis of somatic variation, we de novo assembled a reference genome of sweet orange with an average of three gaps per chromosome and a N50 contig of 24.2 Mb, as well as six diploid genomes of somatic mutants of sweet oranges. We then sequenced 114 somatic mutants with an average genome coverage of 41×. Categorization of the somatic variations yielded insights into the single-nucleotide somatic mutations, structural variations and transposable element (TE) transpositions. We detected 877 TE insertions, and found TE insertions in the transporter or its regulatory genes associated with variation in fruit acidity. Comparative genomic analysis of sweet oranges from three diversity centres supported a dispersal from South China to the Mediterranean region and to the Americas. This study provides a global view on the somatic variations, the diversification and dispersal history of sweet orange and a set of candidate genes that will be useful for improving fruit taste and flavour.

The impact of volatile organic compounds (VOCs) and odor on indoor environment and people has attracted much attention. To reduce this problem of odorous compounds contained in wood panel, this study focused on identifying odorant compounds and exploring the influence of moisture content factors on VOCs and odor emissions. Paper mulberry (Broussonetia papyrifera (L.)Vent.) was investigated using the technology of gas chromatography-mass spectrometry/olfactory (GC–MS/O). Total volatile organic compounds (TVOC) and characteristic odor-active compounds were studied, and the emission of heartwood and sapwood of paper mulberry was compared at the same time. It was found that the main components from heartwood and sapwood were aromatics, alkanes, alkenes, aldehydes ketones, alcohols and esters. Totally, 23 kinds of odor-active compounds were identified from heartwood and sapwood of paper mulberry, among which, aromatics and aldehydes ketones were the main odorant compounds. Seven kinds of key odorant compounds were identified in this process. With the decrease in moisture content, the TVOC and total odor intensity of heartwood and sapwood generally decreased. The moisture content had a great effect on VOC release when the moisture content decreased from 70 to 50% and reduced from fiber saturation point (30%) to air saturation point (10%). The main odor impressions of paper mulberry were aromatic, fresh fruit fragrance, sweet scent and special pungent. In the whole process of moisture content decrease, the TVOC, concentration of odorant and odor intensity of sapwood were higher than that of heartwood.

To identify odorous substances of solid wood, the emission from two types of wood species, namely Phoebe neurantha (Hemsl.) Gamble and Osmanthus fragrans (Thunb.) Lour. was sampled by micro-chamber extractor, combined with the Tenax TA tube and multi-bed tube (carbopack C, carbopack B and carboxen 1000). The odor-active compounds were identified by gas chromatography-mass spectrometry/olfactometry (GC–MS/O), which combine instrumental and sensory analyses. The results showed that, for Phoebe neurantha and Osmanthus fragrans, 12 and 20 kinds of odor-active compounds were identified. The main odor contributors of Phoebe neurantha were “D-limonene, 2-hexanol, 1-heptanol and 2-hexanone”, with the dominant odor impressions of fragrant, irritant, special and fruity. The main odor contributors of Osmanthus fragrans were “camphene, heptanal and pentanal”, while the key odor impressions were spicy, fruity and fatty. VOC concentration and odorous concentration of Phoebe neurantha were higher than Osmanthus fragrans. The proportion of the odorant concentration to the TVOC concentration of Phoebe neurantha and Osmanthus fragrans was 77.39 and 58.68 percent, respectively. The multi-bed tube, which showed excellent adsorption performance for alcohols and compounds with low molecular weight in this study, is able to capture some of the key odor-active compounds that Tenax TA tube cannot collect. Identification of the composition of these two wood species will expand the solid wood odorous substance database and help to establish a method to investigate the odorants with low molecular weight from wood. Through this study, a better understanding of the characteristic odor from wooden materials used in daily life could be obtained.

Objective The aim of this study is to evaluate the efficacy of the strain Paenibacillus polymyxa HX-140, isolated from the rhizosphere soil of rape, to control Fusarium wilt of cucumber seedlings caused by Fusarium oxysporum f. sp. cucumerinum. Results Strain HX-140 was able to produce protease, cellulase, β-1,3-glucanase and antifungal volatile organic compounds. An in vitro dual culture test showed that strain HX-140 exhibited broad spectrum antifungal activity against soil-borne plant pathogenic fungi. Strain HX-140 also reduced the infection of Fusarium wilt of cucumber seedlings by 55.6% in a greenhouse pot experiment. A field plot experiment confirmed the biocontrol effects and further revealed that antifungal activity was positively correlated with inoculum size by the root-irrigation method. Here, inoculums at 106 107 and 108 cfu/mL of HX-140 bacterial suspension reduced the incidence of Fusarium wilt of cucumber seedling by 19.5, 41.1, and 50.9%, respectively. Conclusions Taken together, our results suggest that P. polymyxa HX-140 has significant potential in the control of Fusarium wilt and possibly other fungal diseases of cucumber.

Epstein-Barr virus (EBV)-associated gastric cancer (EBVaGC) is a common malignant tumor associated with EBV infection. The molecular classification of gastric carcinoma indicates that EBVaGC is a distinct subtype in terms of oncogenesis and molecular features. Viral proteins, Bam-HI-A rightward transcripts (BART) miRNAs, and Bam-HI A rightward frame 1 (BARF1) promote oncogenesis after EBV infection via the induction of methylation, regulation of host gene expression, and malignant transformation. Together with abnormal mutations and amplification of the host genome as driving factors, interactions between the EBV genome and host genome accelerate carcinogenesis. The molecular profile of EBVaGC is that of EBV driving DNA hypermethylation, frequent phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha (PIK3CA) mutations, and the overexpression of Janus kinase 2 (JAK2), programmed death ligand-1 (PD-L1), and PD-L2. Clinically, the frequency of lymph node metastasis is lower, and the prognosis is better for EBVaGC than EBV-negative gastric cancer (EBVnGC). Pathologically, EBVaGC is a gastric adenocarcinoma with lymphoid stroma. This review interprets how the EBV genome is involved in the oncogenesis of gastric cancer and describes the molecular and clinicopathological features of EBVaGC.

Obese individuals are more susceptible to comorbidities than individuals of healthy weight, including cardiovascular disease and metabolic disorders. MicroRNAs are a class of small and noncoding RNAs that are implicated in the regulation of chronic human diseases. We previously reported that miR-125b plays a critical role in adipogenesis in vitro. However, the involvement of miR-125b-2 in fat metabolism in vivo remains unknown. In the present study, miR-125b-2 knockout mice were generated using CRISPR/CAS9 technology, resulting in mice with a 7 bp deletion in the seed sequence of miR-125b-2. MiR-125b-2 knockout increased the weight of liver tissue, epididymal white fat and inguinal white fat. MiR-125b-2 knockout also increased adipocyte volume in HFD-induced obese mice, while there were no significant differences in body weight and feed intake versus mice fed a normal diet. Additionally, qRT-PCR and western blot analysis revealed that the expression of the miR-125b-2 target gene SCD-1 and fat synthesis-associated genes, such as PPARγ and C/EBPα, were significantly up-regulated in miR-125b-2KO mice (P

Aims This study aimed to investigate the antimicrobial resistance (AMR) profiles and genotypes of Streptococcus suis from Jiangxi Province, China. Methods and results A total of 314 nasal swab samples were collected from clinically healthy pigs, with a positive isolation rate of S. suis of 34·08%. Antimicrobial susceptibility testing showed that more than 80% of the isolates were susceptible to vancomycin, penicillin, minocycline and chloramphenicol. A high frequency of resistance to clindamycin, tetracycline, clarithromycin and erythromycin was observed. All of the isolates were resistant to three or more categories of antimicrobials. The erm(B) and tet(O) served as the most frequent genotypes that contributed to lincosamide, macrolide and tetracycline resistances. A part of macrolide-resistant genotypes could not exhibit specific phenotypes. Finally, integrative and conjugative elements (ICEs) were identified in 28·97% of the isolates. Conclusions The multidrug resistance of S. suis has widely emerged in Jiangxi Province. The most prevalent resistance genes and genotypes were similar to those in other regions or countries. The presence of ICEs is increasing the risk of horizontal transfer of AMR genes. Significance and impact of the study The findings could provide guidance for the rational use of antimicrobial drugs and be helpful for monitoring the AMR information of S. suis in China.

Metastasis is the main cause of failure of cancer treatment. Metastatic colonization is regarded the most rate-limiting step of metastasis and is subjected to regulation by a plethora of biological factors and processes. On one hand, regulation of metastatic colonization by autophagy appears to be stage- and context-dependent, whereas mechanistic characterization remains elusive. On the other hand, interactions between the tumor cells and their microenvironment in metastasis have long been appreciated, whether the secretome of tumor cells can effectively reshape the tumor microenvironment has not been elucidated mechanistically. In the present study, we have identified “SEC23A-S1008-BECLIN1-autophagy axis” in the autophagic regulation of metastatic colonization step, a mechanism that tumor cells can exploit autophagy to exert self-restrain for clonogenic proliferation before the favorable tumor microenvironment is established. Specifically, we employed a paired lung-derived oligometastatic cell line (OL) and the homologous polymetastatic cell line (POL) from human melanoma cell line M14 that differ in colonization efficiency. We show that S100A8 transported by SEC23A inhibits metastatic colonization via autocrine activation of autophagy. Furthermore, we verified the clinical relevance of our experimental findings by bioinformatics analysis of the expression of Sec23a and S100A8 and the clinical-pathological associations. We demonstrate that higher Sec23a and Atg5 expression levels appear to be protective factors and favorable diagnostic (TNM staging) and prognostic (overall survival) markers for skin cutaneous melanoma (SKCM) and colon adenocarcinoma (COAD) patients. And we confirm the bioinformatics analysis results with SKCM biopsy samples.

Breast milk is the most important nutrient source for newborn mammals. Studies have reported that milk contains microRNAs (miRNAs), which are potential regulatory components. Currently, existing functional and nutritional two competing hypotheses in milk field though little date have been provided for nutritional hypothesis. In this study, we used the qRT-PCR method to evaluated whether milk miRNAs can be absorbed by newborn piglets by feeding them porcine or bovine milk. The result showed that miRNA levels (miR-2284×, 2291, 7134, 1343, 500, 223) were significantly different between bovine and porcine milk. Four miRNAs (miR-2284×, 2291, 7134, 1343) were significantly different in piglet serum after feeding porcine or bovine milk. After separated milk exosomes by ultracentrifugation, the results showed the selected milk miRNAs (miR-2284×, 2291, 7134, 1343) were present in both exosomes and supernatants, and the miRNAs showed the coincidental expression in IPEC-J2 cells. All our founding suggested that the milk miRNAs can be absorbed both in vivo and in vitro, which will building the foundation for understanding whether these sort of miRNAs exert physiological functions after being absorbed and provided additional evidence for the nutritional hypotheses.

The mortality rate of lung cancer remains the highest amongst all cancers despite of new therapeutic developments. While cancer stem cells (CSCs) may play a pivotal role in cancer, mechanisms underlying CSCs self-renewal and their relevance to cancer progression have not been clearly elucidated due to the lack of reliable and stable CSC cellular models. In the present study, we unveiled the novel oncogene function of cadherin 1 (Cdh1) via bioinformatic analysis in a broad spectrum of human cancers including lung adenocarcinoma (LUAD), adding a new dimension to the widely reported tumor suppressor function of Cdh1. Experimentally, we show for the first time that Cdh1 promotes the self-renewal of lung CSCs, consistent with its function in embryonic and normal stem cells. Using the LLC-Symmetric Division (LLC-SD) model, we have revealed an intricate cross-talk between the oncogenic pathway and stem cell pathway in which Cdh1 functions as an oncogene by promoting lung CSC renewal via the activation of the Phosphoinositide 3-kinase (PI3K) and inhibition of Mitogen-activated protein kinase (MAPK) pathways, respectively. In summary, this study has provided evidence demonstrating effective utilization of the normal stem cell renewal mechanisms by CSCs to promote oncogenesis and progression.

The ZRT, IRT-like protein (ZIP) family exists in many species and plays an important role in many biological processes, but little is known about ZIP genes in Aspergillus oryzae. Here, 10 ZIP genes in A. oryzae were identified and these were classified into four groups based on phylogenetic analysis. The structures of these AoZip genes were determined, which indicated a great divergence of AoZip members from different groups. Synteny analysis revealed that AoZip7, AoZip8, and AoZip10 are conserved among Aspergillus species. We also found that the promoter regions of AoZip2, AoZip7, AoZip8, and AoZip10 contain multiple conserved response elements. Expression analysis revealed that AoZips exhibited different expression patterns in response to different metal treatments. Moreover, overexpression and RNA-interference (RNAi) of AoZip2 led to a decrease in mycelium growth diameter and inhibited conidia formation. AoZip2 overexpression and RNAi strains showed distinct sensitivity to severely Zn/Mn-depleted stress. In addition, kojic acid production was markedly lower in AoZip2 overexpression and RNAi strains than in the control strains, and the expression of kojA, kojR, and kojT was down-regulated in AoZip2 overexpression and RNAi strains. This study provides new insights into our understanding of ZIP genes and lays a foundation for further investigation of their roles in Aspergillus oryzae.

Extracellular vesicles are lipid bilayer-delimited particles carrying proteins, lipids, and small RNAs. Previous studies have demonstrated that they had regulatory functions both physiologically and pathologically. However, information remains inadequate on extracellular vesicles from the anterior pituitary, a key endocrine organ in animals and humans. In this study, we separated and identified extracellular vesicles from the anterior pituitary of the Duroc swine model. Total RNA was extracted and RNA-seq was performed, followed by a comprehensive analysis of miRNAs, lncRNAs, and circRNAs. Resultantly, we obtained 416 miRNAs, 16,232 lncRNAs, and 495 circRNAs. Furthermore, GO and KEGG enrichment analysis showed that the ncRNAs in extracellular vesicles may participate in regulating intracellular signal transduction, cellular component organization or biogenesis, small molecule binding, and transferase activity. The cross-talk between them also suggested that they may play an important role in the signaling process and biological regulation. This is the first report of ncRNA data in the anterior pituitary extracellular vesicles from the duroc swine breed, which is a fundamental resource for exploring detailed functions of extracellular vesicles from the anterior pituitary.

The Nramp (natural resistance-associated macrophage protein) family of genes has been identified and characterized widely in many species. However, the Nramp genes and their characterizations have not been reported for Aspergillus oryzae. Here, only one Nramp gene AoNramp1 in A. oryzae genome was identified. Phylogenetic analysis revealed that AoNramp1 is not clustered with Nramps from yeast genus. Expression analysis showed that the transcript level of AoNramp1 was strongly induced under both Zn/Mn-replete and -deplete conditions. The GUS-staining assay indicated that the expression of AoNramp1 was strongly induced by Zn/Mn. Moreover, the AoNramp1 deletion and overexpression strains were constructed by the CRISPR/Cas9 system and A. oryzae amyB promoter, respectively. Phenotypic analysis showed that overexpression and deletion of AoNramp1 caused growth defects under Zn/Mn-deplete and -replete conditions, including mycelium growth and conidia formation. Together, these findings provide valuable information for further study on the biological roles of AoNramp1 in A. oryzae.

Clinical data mining and bioinformatics analysis can be employed effectively to elucidate the function and underlying mechanisms of the gene of interest. Here, we have proposed a framework for the identification and validation of independent biomarkers in human cancer and for mechanistic profiling using gene sets enrichment analysis and pathway analysis. This is followed by validation within vitroexperiments. Using this framework to analyze the clinical relevance of SEC23A, we have discovered the prognostic potential of SEC23A in different cancers and identified SEC23A as an independent prognostic factor for poor prognosis in bladder cancer, which implicates SEC23A, for the first time, as an oncogene. Bioinformatic analyses have elucidated an association between SEC23A expression and the upregulation of the MAPK signaling pathway. Using the T24 human bladder cell line, we confirmed that knockdown of SEC23A expression could effectively impact the MAPK signaling pathway. Further, through PCR verification, we showed that MEF2A, one of the key genes of the MAPK signaling pathway, might be a downstream factor of the SEC23A gene.

S-phase kinase-associated protein 1 ( Skp1 ) is a component of the SKP1-Cullin1-F-box (SCF) complex, which facilitates ubiquitin-mediated protein degradation in eukaryotes. SLF interacting Skp1-like 1 ( SSK1 ), which is located outside the S-site, is a newly discovered type of self-incompatibility-related pollen-specific gene whose product interacts with pollen determinants. In this study, we identified 18 members of the Prunus dulcis Skp1 (PsdSkp1) family that were unevenly distributed across six chromosomes of the almond genome. The phylogenetic tree revealed that the PsdSkp1 members could divided into four groups: I, II, III, and IV. The conserved motifs, conserved domains, and motif structures of the PsdSSK1 and PsdSkp1-12 proteins are similar. There were three pairs of fragment duplication genes and one pair of tandem repeat genes, and their functions were highly evolutionarily conserved. Transcriptome data showed that PsdSkp1 was expressed in almond flower tissues, that its expression was affected by freezing stress, and that its expression changed significantly in cross-pollination. Molecular experiments proved that PsdSSK1 and PsdSkp1-12 had the same protein sequence, and the genes were significantly highly expressed mainly in the pollen or throughout pollen cells, with subcellular localization in the cytoplasm. PsdSkp1-12 is an ssk1 gene in almond, and it may be involved in the SCF complex to regulate the almond pollen response via SI and cross-compatibility. In conclusion, our research lays a foundation for future functional research on PsdSkp1 members, especially for exploring the mechanism of almond SI.

Filamentous fungi are a group of economically important fungi used in the production of fermented foods, industrial enzymes, and secondary metabolites. Glycosphingolipids (GSLs) as constituents of lipid rafts are involved in growth, differentiation, and response to environment stress in filamentous fungi. In addition to these key roles, GSLs are also important in the barrier function of skin to retain moisture as a moisturizing ingredient in cosmetics or health products for their strong biological activity as a functional component. GSLs found in filamentous fungi are divided in two major classes: neutral GSLs (glycosylceramides), glucosylceramides (GlcCers), and/or galactosylceramides (GalCers) and acidic GSLs, mannosylinositol phosphorylceramide (MIPC) and mannosyldiinositol phosphorylceramide [M(IP)2C]. Glycosylceramides are one of the abundant GSLs in Aspergillus and known to improve skin-barrier function and prevent intestinal impairment as a prebiotic. Some filamentous fungi of Aspergillus spp., synthesizing both GlcCer and GalCer, would be an amenable source to exploit glycosylceramides that wildly adding in cosmetics as moisturizing ingredients or health food as dietary supplements. In this minireview, the types, structures, and biosynthetic pathways of GSLs in filamentous fungi, and the relevance of GSLs in fungal growth, spore formation, and environmental stress response are explained. Furthermore, the advantage, potential development, and application of GlcCer and GalCer from filamentous fungi Aspergillus spp. are also investigate based on the use of plant GlcCer in health foods and cosmetics.

The CRISPR/Cas9 system has become a great tool for target gene knock-out in filamentous fungi. It is laborious and time-consuming that identification mutants from a large number of transformants through PCR or enzyme-cut method. Here, we first developed a CRISPR/Cas9 system in Aspergillus oryzae using AMA1-based autonomously replicating plasmid and Cas9 under the control of the Aspergillus nidulans gpdA promoter. By the genome editing technique, we successfully obtained mutations within each target gene in Aspergillus oryzae. Then, we put the protospacer sequence of a target gene and its protospacer adjacent motif (PAM) behind the start codon "ATG" of DsRed, yielding the non‑functional DsRed (nDsRed) reporter gene, and the nDsRed reporter gene could be rescued after successful targeted editing. Moreover, this method was also applied by targeting the kojic acid synthesis gene kojA, and the transformants with DsRed activity were found to harbor targeted mutations in kojA. These results suggest that the nDsRed can be used as a powerful tool to facilitate the identification of mutants generated by CRISPR/Cas9 in Aspergillus oryzae.

Bone is a self-regenerative tissue that can repair small defects and fractures. In large defects, bone tissue is unable to provide nutrients and oxygen for repair, and autologous grafting is used as the gold standard. As an alternative method, the bone tissue regeneration approach uses osteoconductive biomaterials to overcome bone graft disadvantages. However, biomaterials are considered as foreign components that can stimulate host immune responses. Although traditional principles have been aimed to minimize immune reactions, the design of biomaterials has steadily shifted toward creating an immunomodulatory microenvironment to harness immune cells and responses to repair damaged tissue. Among immune cells, macrophages secrete various immunomodulatory mediators and crosstalk with bone-forming cells and play key roles in bone tissue engineering. Macrophage polarization toward M1 and M2 subtypes mediate pro-inflammatory and anti-inflammatory responses, respectively, which are crucial for bone repairing at different stages. This review provides an overview of the crosstalk between various immune cells and biomaterials, macrophage polarization, and the effect of physicochemical properties of biomaterials on the immune responses, especially macrophages, in bone tissue engineering.

Moringa oleifera has been considered as a potential functional feed or food, since it contains multiple components beneficial to animal and human. However, little is known about the effects of Moringa oleifera supplementation on productive performances in sows. In the current study, the results showed that dietary Moringa oleifera significantly decreased the farrowing length and the number of stillborn (p < .05), while had an increasing trend in the number of live-born (0.05 < p < .10). Furthermore, 8% Moringa oleifera supplementation significantly elevated protein levels in the colostrum (p < .05); 4% Moringa oleifera lowed serum urea nitrogen of sows after 90 days of gestation (p < .05) and significantly decreased serum glucose on 10 days of lactation (p < .05). Both groups showed significant elevation in serum T-AOC activity (p < .05). The serum malondialdehyde (MDA) of sows declined significantly in 4% Moringa oleifera addition group (p < .05). 8% Moringa oleifera meal significantly elevated serum CAT activity after 60 days of gestation (p < .05), while decreased the serum MDA level and increased the serum GSH-Px activity of sows at 10 days of lactation (p < .05). Of piglets, both two dosages of Moringa oleifera supplementation essentially reduced the serum urea nitrogen (p < .05), and 4% Moringa oleifera meal increased serum total protein (p < .05). In addition, piglets that received 8% Moringa oleifera had the highest serum CAT and SOD activities among all groups (p < .05). The present study indicated that Moringa oleifera supplementation could enhance the reproduction performances, elevate protein levels in the colostrum and improve the serum antioxidant indices in both sows and piglets.

Previous studies have demonstrated that bovine milk contains mRNA and microRNA that are largely encapsulated in milk-derived exosomes. However, little information is available about long noncoding RNAs (lncRNA) in bovine milk. Increasing evidence suggests that lncRNA are of particular interest given their key role in gene expression and development. We performed a comprehensive analysis of lncRNA in bovine milk exosomes by RNA sequencing. We used a validated human in vitro digestion model to investigate the stability of lncRNA encapsulated in bovine milk exosomes during the digestion process. We identified 3,475 novel lncRNA and 6 annotated lncRNA. The lncRNA shared characteristics with those of other mammals in terms of length, exon number, and open reading frames. However, lncRNA showed higher expression than mRNAs. We selected 12 lncRNA of high-expression abundance and identified them by PCR. Gene ontology (GO) enrichment and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses showed that lncRNA regulate immune function, osteoblastogenesis, neurodevelopment, reproduction, cell proliferation, and cell–cell communication. We also investigated the 12 lncRNA using quantitative real-time PCR to reveal their expression profiles in milk exosomes during different stages of lactation (colostrum 2 d, 30 d, 150 d, and 270 d); their resulting expression levels in milk exosomes showed variations across the stages. A digestion experiment showed that bovine milk exosome lncRNA was resistant to in vitro digestion with different digestive juices, including saliva, gastric juice, pancreatic juice, and bile juice. Taken together, these results show for the first time that cow milk contains lncRNA, and that their abundance varied at different stages of lactation. As expected, bovine milk exosomal lncRNA were stable during in vitro digestion. These findings provide a basis for further understanding of the physiological role of milk lncRNA.

Douchi has attracted people's attention because of its unique taste and rich health function. The microbes participated in the koji-making process contribute to taste compounds of Douchi. However, the majority of studies on Douchi focused on their functional components and the microbial community in single type of Douchi during koji-making so far. In the present study, the taste components of Mucor-type and Aspergillus-type Douchi were measured initially and the results showed that the amino acid and organic acid levels as well as the percentage of unsaturated fatty acids in Mucor-type Douchi were significantly higher than those in Aspergillus-type. The investigation of the microbial composition in two types of Douchi showed that Aspergillus, Candida, Meyerozyma and Lecanicillium were shared by >50% of samples during koji-making. Comparison of the microbial community between the two types of Douchi revealed that Meyerozyma and Lecanicillium were the main microbial community with significant difference during the initial stage of koji-making, while Candida was significantly different during the later stage of koji-making. When supplemented with Meyerozyma and Candida in Aspergillus-type Douchi, the level of all amino acid and organic acids as well as the percentage of unsaturated fatty acid was significant improved, which further validated the importance roles of the two microorganisms in enhancing the taste components of Douchi during koji-making. The results provide useful information on optimizing the microbial community structure of Douchi during the process of koji-making and improving the product quality.

Oxidative stress plays an important role in the progression of cardiac diseases, including acute myocardial infarction, ischemia/reperfusion (I/R) injury and heart failure. Growing evidence indicates that thyroid hormone has protective properties against cardiovascular diseases. However, little is known about its effect on oxidative stress in cardiomyocytes or the underlying mechanisms. This study showed that T3 pretreatment in vivo significantly reduced cardiac dysfunction by increasing the left ventricular ejection function and ameliorating the pathological changes induced by I/R-induced injury. In an in vitro experiment, T3 inhibited apoptosis in H2O2-treated cardiomyocytes, as evidenced by the decreased expression of Bax, cleaved caspase 3 and 9, and increased expression of Bcl-2. In addition, oxidative stress observed in hearts of mice with I/R injury was significantly alleviated by T3 pretreatment, intracellular ROS and mitochondrial ROS overproduction were effectively inhibited, and similar results were also detected in H2O2-treated cardiomyocytes in vitro. T3 significantly increased antioxidant protein (Nrf2 and HO-1) expression levels, and inhibited NOX2 and NOX4 protein expression levels in H2O2-treated cardiomyocytes. Moreover, T3 preserved mitochondrial functions upon H2O2-induced oxidative stress by increasing mitochondrial membrane potential and promoting the expression of mitochondrial biogenesis genes. Notably, the PI3K/AKT signaling was significantly activated by T3 pretreatment in H2O2-induced cardiomyocytes. Together, these findings revealed that T3 could be served as potential therapeutic target for protection against cardiac oxidative stress injury through its antioxidant and anti-apoptosis effects, which are mediated by the activation of the PI3K/AKT signaling pathway.

ATP-citrate lyase (ACL) plays a key role in the formation of acetyl-CoA, a crucial precursor for Monascus pigments biosynthesis. Whether ACL affects the pigments synthesis pathway in Monascus spp. is unknown. Here, we focus on acl1 and acl2 genes, encoding two subunits of ACL that were overexpressed in Monascus ruber CICC41233 to generate Monascus ruber ACL438469-4 and Monascus ruber ACL501969-11, respectively. Both acl overexpression strains significantly increased ACL activity, leading to elevate levels of acetyl-CoA. These strains completely degraded starch from rice powder after 4 days. Total Monascus pigments production was remarkably enhanced by 92.70% in M. ruber ACL438469-4 and 112.58% in M. ruber ACL501969-11 after 6 days. The red pigments in M. ruber ACL438469-4 and in M. ruber ACL501969-11 were more than that in parent strain. Transcriptome sequencing analysis of the acl overexpression strains vs the wild-type showed that differentially expressed genes were mainly involved in starch and glycolysis metabolism; valine, leucine, and isoleucine degradation; glycine, serine, and threonine metabolism; and Monascus pigment biosynthetic pathway. This implied metabolic flux for acetyl-CoA during pigment synthesis and NH3 for amination of red pigments. Thus, ACL modulated starch and amino acid metabolism to regulate Monascus pigments production in M. ruber.

Currently, the genetic modification of Aspergillus oryzae is mainly dependent on protoplastmediated transformation (PMT). In this study, we established a dual selection marker system in an industrial A. oryzae 3.042 strain by using Agrobacterium tumefaciens-mediated transformation (ATMT). We first constructed a uridine/uracil auxotrophic A. oryzae 3.042 strain and a pyrithiamine (PT)-resistance binary vector. Then, we established the ATMT system by using uridine/uracil auxotrophy and PT-resistance genes as selection markers. Finally, a dual selection marker ATMT system was developed. This study demonstrates a useful dual selection marker transformation system for genetic manipulations of A. oryzae 3.042.

Salt stress can trigger several physiological responses in microorganisms such as the increasing accumulation of unsaturated fatty acid, which was biosynthesized by delta-9 fatty acid desaturases (D9D) at the first step. In the present study, two D9D genes, designated AoD9D1 and AoD9D2, were isolated from Aspergillus oryzae. The expression analysis showed that AoD9D1 and AoD9D2 were upregulated under salt stress. To investigate the function of AoD9D, transgenic Saccharomyces cerevisiae strains that heterologously expressed AoD9D were exposed to salinity condition. These transgenic strains exhibited greater tolerance to salt stress than wild-type strains, and the heterologous expression of AoD9D increased the content in unsaturated fatty acids as compared to control cells. Moreover, AoD9D1 and AoD9D2 both contained fatty acid desaturase (FAD) and cytochrome b5-like Heme/Steroid-binding domains (Cyt-b5). S. cerevisiae separately transformed with the gene fragments coding for the FAD and Cyt-b5 domains in the AoD9D1 protein grew better and accumulated a higher concentration of unsaturated FAs than the control. Altogether, the heterologous expression of AoD9D enhanced the tolerance of transgenic S. cerevisiae to high salinity stress with increased accumulation of unsaturated fatty acid. The results provide some practical basis for the successful development of salt-tolerant fermentation microorganisms.

Moringa oleifera is a tropical plant with high nutritional and medicinal value. Recent studies have reported its remarkable effects in inflammatory, antioxidative, and anti‐diabetes modulations, but there was no significant report on its role in animal breeding. In this study, we investigated the effects of dietary Moringa oleifera leaf (MOL) on reproductive performances in mice. We studied the reproductive performance of mice for six consecutive gestations. Mice fed with 4% MOL diet showed improved litter size, litter birth weight, and litter survivals until weaning age compared to control mice fed with normal diet (p < 0.05). Mice fed with MOL diet did not change weight and organ coefficients. Serum malondialdehyde (MDA) concentrations in both male and female mice were significantly decreased by dietary MOL (p < 0.05), but glutathione peroxidase (GSH‐PX) and superoxide dismutase (SOD) were unchanged. For male, dietary MOL significantly reduced sperm abnormality rate (p < 0.05) and Bcl2‐associated X protein (Bax) expression in testis (p < 0.05), but did not affect serum testosterone and the expression levels of androgen receptor (AR), phosphoglycerate kinase 2 (Pgk2), protamine2 (Prm2), and B cell leukemia/lymphoma 2 (Bcl2) in testis. For female, dietary MOL did not change serum estradiol and the expressions of estrogen receptor beta (ERβ), Bcl2, Bax, and vascular endothelial growth factor receptor (VEGFR) in ovary. In summary, MOL increased litter size and antioxidant ability, reduced the rate of sperm abnormality and the expression of Bax. Therefore, MOL may serve as a functional feed addictive for improving animal reproductive performance.

Oxysterol-binding protein is an important non-vesicular trafficking protein involved in the transportation of lipids in eukaryotic cells. Oxysterol-binding protein is identified as oxysterol-binding protein-related proteins (ORPs) in mammals and oxysterol-binding protein homologue (Osh) in yeast. Research has described the function and structure of oxysterol-binding protein in mammals and yeast, but little information about the protein's structure and function in filamentous fungi has been reported. This article focuses on recent advances in the research of Osh proteins in yeast and filamentous fungi, such as Aspergillus oryzae, Aspergillus nidulans, and Candida albicans. Furthermore, we point out some problems in the field, summarizing the membrane contact sites (MCS) of Osh proteins in yeast, and consider the future of Osh protein development.

Skeletal muscle and adipose tissues are both involved in regulation of metabolism. In the skeletal muscle-adipose tissue crosstalk, exosomes may play an important role but the main components of exosomes are not clear. In this study, we found skeletal muscle-derived exosomes can inhibit adipogenesis of porcine preadipocytes. We identified microRNA expression profiles of muscle exosomes and adipose exosomes by high-throughput sequencing. There were 104 (both novel and known microRNAs) microRNAs differentially expressed (DE miRNAs) between M-EXO (muscle-derived exosomes) and A-EXO (adipose–derived exosomes) groups. A total of 2,137 target genes of DE miRNAs for M-EXO and 2,004 target genes of DE miRNAs for A-EXO were detected. Bioinformatic analyses revealed that some DE miRNAs of M-EXO (especially miR-221-5p) were mainly enriched in lipid-related metabolism processes. The findings may serve as a fundamental resource for understanding the detailed functions of exosomes between the skeletal muscle-adipose crosstalk and the potential relationship between skeletal muscle atrophy and obesity.

Aspergillus oryzae usually suffers from oxidative stress during the process of aerobic fermentation. However, there is little information on what genes involve in oxidative stress of A. oryzae. Here, we found that the expression of a novel gene Aohps1 was induced during the growth and development of A. oryzae with and without oxidative stress. Sequence analysis revealed that Aohps1 has four transmembrane regions and is conserved in Aspergillus species. Overexpression and deletion of Aohpi1 caused the growth defects with and without oxidative stress, including mycelium growth, conidia formation and biomass. Meanwhile, the Aohpi1 overexpression strain exhibited more sensitivity to oxidative stress than the Aohpi1 disrupted mutant. Furthermore, overexpression and disruption of Aohps1 resulted in the inhibition of kojic acid production with and without oxidative stress, consistent with the reduced expression of kojA that directly contributed to the synthesis of kojic acid. Additionally, the yield of kojic acid is less in the Aohps1 overexpression strain than in the Aohps1 deletion mutant under oxidative stress. Collectively, the discovery of Aohps1 provides new insights into oxidative stress and kojic acid synthesis in A. oryzae.

The family of GRAS plant-specific transcription factor plays diverse roles in numerous biological processes. Despite the identification and characterization of GRAS genes family in dozens of plant species, until now, GRAS members in watermelon (Citrullus lanatus) have not been investigated comprehensively. In this study, using bioinformatic analysis, we identified 37 GRAS genes in the watermelon genome (ClGRAS). These genes are classified into 10 distinct subfamilies based on previous research, and unevenly distributed on 11 chromosomes. Furthermore, a complete analysis was conducted to characterize conserved motifs and gene structures, which revealed the members within same subfamily that have analogous conserved gene structure and motif composition. Additionally, the expression pattern of ClGRAS genes was characterized in fruit flesh and rind tissues during watermelon fruit development and under red light (RL) as well as root knot nematode infestation. Finally, for verification of the availability of public transcriptome data, we also evaluated the expression levels of randomly selected four ClGRAS genes under RL and nematode infection by using qRT-PCR. The qRT-PCR results indicated that several ClGRAS genes were differentially expressed, implying their vital role in RL induction of watermelon resistance against root-knot nematodes. The results obtained in this study could be useful in improving the quality of watermelon.

Bacteria of different shapes have adopted distinct mechanisms to faithfully coordinate morphogenesis and segregate their chromosomes prior to cell division. Despite recent focuses and advances, the mechanism of cell division in ovococci remains largely unknown. Streptococcus suis, a major zoonotic pathogen that causes problems in human health and in the global swine industry, is an elongated and ellipsoid bacterium that undergoes successive parallel splitting perpendicular to its long axis. Studies on cell cycle processes in this bacterium are limited. Here, we report that MsmK (multiple sugar metabolism protein K), an ATPase that contributes to the transport of multiple carbohydrates, has a novel role as a cell division protein in S. suis. MsmK can display ATPase and GTPase activities, interact with FtsZ via the N terminus of MsmK, and promote the bundling of FtsZ protofilaments in a GTP-dependent manner in vitro. Deletion of the C-terminal region or the Walker A or B motif affects the affinity between MsmK and FtsZ and decreases the ability of MsmK to promote FtsZ protofilament bundling. MsmK can form a complex with FtsZ in vivo, and its absence is not lethal but results in long chains and short, occasionally anuclear daughter cells. Superresolution microscopy revealed that the lack of MsmK in cells leads to normal septal peptidoglycan walls in mother cells but disturbed cell elongation and peripheral peptidoglycan synthesis. In summary, MsmK is a novel cell division protein that maintains cell shape and is involved in the synthesis of the peripheral cell wall. IMPORTANCE Bacterial cell division is a highly ordered process regulated in time and space and is a potential target for the development of antimicrobial drugs. Bacteria of distinct shapes depend on different cell division mechanisms, but the mechanisms used by ovococci remain largely unknown. Here, we focused on the zoonotic pathogen Streptococcus suis and identified a novel cell division protein named MsmK, which acts as an ATPase of the ATP-binding cassette-type carbohydrate transport system. MsmK has GTPase and ATPase activities. In vitro protein assays showed that MsmK interacts with FtsZ and promotes FtsZ protofilament bundling that relies on GTP. Superresolution microscopy revealed that MsmK maintains cell shape and is involved in peripheral peptidoglycan synthesis. Knowledge of the multiple functions of MsmK may broaden our understanding of known cell division processes. Further studies in this area will elucidate how bacteria can faithfully and continually multiply in a constantly changing environment.

Simple Summary As the irreplaceable nutrient source for young mammals, milk has a number of biological functions. Milk derived extracellular vesicles are a recently discovered component of milk and have potential regulatory effects on intestinal health and immunity. In this study, in vivo and in vitro experiments were performed to examine the effects of porcine milk small extracellular vesicles (PM-sEVs) on intestinal immunity. As a result, PM-sEVs promoted intestinal secretory immunoglobulin A (SIgA) levels, and increased the expression levels of the polymeric immunoglobulin receptor (pIgR) both in mice and piglet. We identified circ-XPO4 in PM-sEVs as a crucial circRNA, which promotes the expression of pIgR via the suppression of miR-221-5p in the intestinal cell. In conclusion, our research provides a new understanding of the nutritional physiology of porcine milk in intestinal immunity. Abstract Secretory immunoglobulin A (SIgA) plays an important role in gut acquired immunity and mucosal homeostasis. Breast milk is the irreplaceable nutritional source for mammals after birth. Current studies have shown the potential functional role of milk-derived small extracellular vesicles (sEVs) and their RNAs cargo in intestinal health and immune regulation. However, there is a lack of studies to demonstrate how milk-derived sEVs affect intestinal immunity in recipient. In this study, through in vivo experiments, we found that porcine milk small extracellular vesicles (PM-sEVs) promoted intestinal SIgA levels, and increased the expression levels of polymeric immunoglobulin receptor (pIgR) both in mice and piglet. We examined the mechanism of how PM-sEVs increased the expression level of pIgR in vitro by using a porcine small intestine epithelial cell line (IPEC-J2). Through bioinformatics analysis, dual-luciferase reporter assays, and overexpression or knockdown of the corresponding non-coding RNAs, we identified circ-XPO4 in PM-sEVs as a crucial circRNA, which leads to the expression of pIgR via the suppression of miR-221-5p in intestinal cells. Importantly, we also observed that oral administration of PM-sEVs increased the level of circ-XPO4 and decreased the level of miR-221-5p in small intestine of piglets, indicating that circRNAs in milk-derived sEVs act as sponge for miRNAs in recipients. This study, for the first time, reveals that PM-sEVs have a capacity to stimulate intestinal SIgA production by delivering circRNAs to receptors and sponging the recipient’s original miRNAs, and also provides valuable data for insight into the role and mechanism of animal milk sEVs in intestinal immunity.

Sanguinarine, a benzophenanthridine alkaloid, has been described to have an antiplatelet activity. However, its antithrombotic effect and the mechanism of platelet inhibition have not thoroughly been explored. The current study found that sanguinarine had an inhibitory effect on thrombus formation. This inhibitory effect was quite evident both in the flow-chamber assays as well as in a murine model of FeCl3-induced carotid artery thrombosis. Further investigations also revealed that sanguinarine inhibited the collagen-induced human platelet aggregation and granule release. At the same time, it also prevented platelet spreading and adhesion to immobilized fibrinogen. The molecular mechanisms of its antiplatelet activity were found to be as follows: 1. Reduced phosphorylation of the downstream signaling pathways in collagen specific receptor GPVI (Syk-PLCγ2 and PI3K-Akt-GSK3β), 2. Inhibition of collagen-induced increase in the intracellular Ca2+ concentration ([Ca2+]i), 3. Inhibition of integrin αIIbβ3 outside-in signaling via reducing β3 and Src (Tyr-416) phosphorylation. It can be concluded that sanguinarine inhibits collagen-induced platelet activation and reduces thrombus formation. This effect is mediated via inhibiting the phosphorylation of multiple components in the GPVI signaling pathway. Current data also indicate that sanguinarine can be of some clinical value to treat cardiovascular diseases involving an excess of platelet activation.

New York esophageal squamous cell carcinoma 1 (NY-ESO-1) is a promising target for T-cell receptor-engineered T cell (TCR-T) therapy, and targeting the human leukocyte antigen (HLA)-A2 restricted NY-ESO-1157−165 epitope has yielded remarkable clinical benefits in the treatment of multiple advanced malignancies. Herein, we report the identification of two NY-ESO-1157−165 epitope-specific murine TCRs obtained from HLA-A*0201 transgenic mice. NY-ESO-1157−165 specific TCRs were isolated after vaccinating HLA-A2 transgenic mice with epitope peptides. HZ6 and HZ8 TCRs could specifically bind to NY-ESO-1157−165/HLA-A2 and were capable of cytokine secretion with engineered Jurkat T cells and primary T cells upon recognition with K562 target cells expressing the single-chain trimer (SCT) of NY-ESO-1157−165/HLA-A2. The reactivity profiles of the HZ6 and HZ8 TCRs were found to be distinct from one another when co-cultured with K562 target cells carrying alanine-substituted NY-ESO-1157−165 SCTs. The binding characterization revealed that the recognition pattern of the HZ6 TCR to NY-ESO-1157−165/HLA-A2 was substantially different from the widely used 1G4 TCR. These findings would broaden the understanding of immunogenicity of the NY-ESO-1157−165, and the two identified TCRs may serve as promising candidates for the future development of TCR-T therapy for tumors.

Exessive drinking is commonly associated with a wide spectrum of liver injuries. The term alcoholic liver disease (ALD) is generally used to refer to this spectrum of hepatic abnormalities, and the term hepatic steatosis denotes early lesions. Puerariae Lobatae Radix (PLR) is a common traditional Chinese medicine and has been widely used as an efficient treatment for alcohol-induced damage. Flavonoids are the principal components of PLR that could potentially be responsible for the activation of alcohol metabolism and lipid-lowering effects. However, little is known about the mechanisms underlying their activity against alcoholic injury. In this study, PLR flavonoids (PLF) were obtained by microwave extraction. A 2% ethanol solution was used to establish a model of alcoholic fatty liver disease by exposure of zebrafish larvae for 32 h, and then the zebrafish were administered PLF and puerarin. The results showed that PLF and puerarin significantly decreased lipid accumulation and the levels of total cholesterol and triglycerides in zebrafish larvae. Moreover, PLF and puerarin downregulated the expression of genes related to alcohol and lipid metabolism (CYP2y3, CYP3a65, ADH8a, ADH8b, HMGCRB, and FASN), endoplasmic reticulum stress, and DNA damage (CHOP, EDEM1, GADD45αa, and ATF6) and reduced levels of inflammatory factors (IL-1β, TNF-α) in zebrafish larvae. PLF and puerarin increased the phosphorylation of AMP-activated protein kinase-α (AMPKα) and decreased the total protein level of ACC1. The findings suggested that PLF and puerarin alleviated alcohol-induced hepatic steatosis in zebrafish larvae by regulating alcohol and lipid metabolism, which was closely related to the regulation of the AMPKα-ACC signaling pathway. In conclusion, the study provided a possible therapeutic drug for ALD treatment.

Long non-coding RNA (lncRNA) of plant species undergoes dynamic regulation and acts in developmental and stress regulation. Presently, there is little information regarding the identification of lncRNAs in jujube (Ziziphus jujubaMill.), and it is uncertain whether the lncRNAs could respond to heat stress (HS) or not. In our previous study, a cultivar (Hqing1-HR) ofZ.jujuba were treated by HS (45°C) for 0, 1, 3, 5 and 7 days, and it was found that HS globally changed the gene expression by RNA sequencing (RNA-seq) experiments and informatics analyses. In the current study, 8260 lncRNAs were identified successfully from the previous RNA-seq data, and it indicated that lncRNAs expression was also altered globally, suggesting that the lncRNAs might play vital roles in response to HS. Furthermore, bioinformatics analyses of potential target mRNAs of lncRNAs with cis-acting mechanism were performed, and it showed that multiple differentially expressed (DE) mRNAs co-located with DElncRNAs were highly enriched in pathways associated with response to stress and regulation of metabolic process. Taken together, these findings not only provide a comprehensive identification of lncRNAs but also useful clues for molecular mechanism response to HS in jujube.

It has been postulated that cancer stem cells (CSCs) are involved in all aspects of human cancer, although the mechanisms governing the regulation of CSC self-renewal in the cancer state remain poorly defined. In the literature, both the pro- and anti-oncogenic activities of autophagy have been demonstrated and are context-dependent. Mounting evidence has shown augmentation of CSC stemness by autophagy, yet mechanistic characterization and understanding are lacking. In the present study, by generating stable human lung CSC cell lines with the wild-type TP53 (A549), as well as cell lines in which TP53 was deleted (H1229), we show, for the first time, that autophagy augments the stemness of lung CSCs by degrading ubiquitinated p53. Furthermore, Zeb1 is required for TP53 regulation of CSC self-renewal. Moreover, TCGA data mining and analysis show that Atg5 and Zeb1 are poor prognostic markers of lung cancer. In summary, this study has elucidated a new CSC-based mechanism underlying the oncogenic activity of autophagy and the tumor suppressor activity of p53 in cancer, i.e., CSCs can exploit the autophagy-p53-Zeb1 axis for self-renewal, oncogenesis, and progression.

House mites, including D. pteronyssinus and D. farina, are common causes of allergic diseases, such as asthma, atopic dermatitis, eczema, conjunctivitis and perennial rhinitis in susceptible patients. Conventional acaricides, such as benzyl benzoate, bifenthrin, chlorpyrifos are effective chemicals in treating mites. However, they are usually with high drug resistance and high adverse effects on environment, human health, and non-target organisms. Recently, essential oils from different plants were found to be safe and effective alternatives for killing different types of mites. The present review summarized the essential oils from different plants. The crude essential oils from Melissa officinalis, S.lavandulifolia oil, cade oil, P. cattleianum, Patchouli oil, Horseradish oil, C. cassia, P. cablin, Manuka oil, Clove Bud oil, and the pure essential oils, such as eugenol, caryophyllene, and camphor might be good candidates for the dust mites. Further studies on biological mechanisms of the acaricidal effects of these active essential oils, and the structure-activity relationships are needed to make the functions of these drugs more clear.

Filamentous fungi possess the capacity to produce a wide array of secondary metabolites with diverse biological activities and structures, such as lovastatin and swainsonine. With the advent of the post-genomic era, increasing amounts of cryptic or uncharacterized secondary metabolite biosynthetic gene clusters are continually being discovered. However, owing to the longstanding lack of versatile, comparatively simple, and highly efficient genetic manipulation techniques, the broader exploration of industrially important secondary metabolites has been hampered thus far. With the emergence of CRISPR/Cas9-based genome editing technology, this dilemma may be alleviated, as this advanced technique has revolutionized genetic research and enabled the exploitation and discovery of new bioactive compounds from filamentous fungi. In this review, we introduce the CRISPR/Cas9 system in detail and summarize the latest applications of CRISPR/Cas9-mediated genome editing in filamentous fungi. We also briefly introduce the specific applications of the CRISPR/Cas9 system and CRISPRa in the improvement of secondary metabolite contents and discovery of novel biologically active compounds in filamentous fungi, with specific examples noted. Additionally, we highlight and discuss some of the challenges and deficiencies of using the CRISPR/Cas9-based genome editing technology in research on the biosynthesis of secondary metabolites as well as future application of CRISPR/Cas9 strategy in filamentous fungi are highlighted and discussed.

GATA transcription factors (TFs) are involved in the regulation of growth processes and various environmental stresses. Although GATA TFs involved in abiotic stress in plants and some fungi have been analyzed, information regarding GATA TFs in Aspergillusoryzae is extremely poor. In this study, we identified and functionally characterized seven GATA proteins from A.oryzae 3.042 genome, including a novel AoSnf5 GATA TF with 20-residue between the Cys-X2-Cys motifs which was found in Aspergillus GATA TFs for the first time. Phylogenetic analysis indicated that these seven A. oryzae GATA TFs could be classified into six subgroups. Analysis of conserved motifs demonstrated that Aspergillus GATA TFs with similar motif compositions clustered in one subgroup, suggesting that they might possess similar genetic functions, further confirming the accuracy of the phylogenetic relationship. Furthermore, the expression patterns of seven A.oryzae GATA TFs under temperature and salt stresses indicated that A. oryzae GATA TFs were mainly responsive to high temperature and high salt stress. The protein–protein interaction network of A.oryzae GATA TFs revealed certain potentially interacting proteins. The comprehensive analysis of A. oryzae GATA TFs will be beneficial for understanding their biological function and evolutionary features and provide an important starting point to further understand the role of GATA TFs in the regulation of distinct environmental conditions in A.oryzae.

The problem of indoor odors can greatly affect a room’s occupants. To identify odorants and comprehensively evaluate emissions from wooden materials, emissions and odors from Choerospondias axillaris (Roxb.) Burtt et Hill with different moisture content percentages and lacquer treatments were investigated in this study. Thermal desorption–gas chromatography–mass spectroscopy/olfactometry was used to analyze the release characteristics. In total, 11 key odor-active compounds were identified as moisture content gradually decreased, concentrating between 15 and 33 min. Total volatile organic compounds, total very volatile organic compounds, and total odor intensity decreased as moisture content decreased. In addition, 35 odor-active compounds, including aromatics, alkenes, aldehydes, esters, and alcohols, were identified in the odor control list. Polyurethane (PU), ultraviolet (UV), and waterborne coatings had a good inhibitory effect on eight odor characteristics, but some scents arose after lacquer treatment. For equilibrium moisture content, the major characteristics of Choerospondias axillaris were fragrant (9.4) and mint-like (3.0) compared with the fragrant (8.2), fruity (7.8), and pleasant (5.8) characteristics of PU coating; the flowery (5.9), fragrant (5.0), glue-like (4.3), and pineapple-like (4.3) characteristics of UV coating; and the antiseptic solution (3.6), fragrant (2.9), cigarette-like (2.8), and fruity (2.5) characteristics of waterborne coating. Based on multicomponent evaluation, a Choerospondias axillaris board with waterborne coating was suggested for use indoors.

Purpose Duchenne muscular dystrophy (DMD) is currently the most commonly diagnosed form of muscular dystrophy due to mutations in the dystrophin gene. However, its pathological process remains unknown and there is a lack of specific molecular biomarkers. The aim of our study is to explore key regulatory connections underlying the progression of DMD. Materials and methods The gene expression profile dataset GSE38417 of DMD was obtained from the Gene Expression Omnibus (GEO) database. The differentially expressed genes (DEGs) between DMD patients and healthy controls were screened using geo2R, followed by Kyoto Encyclopedia of Genes and Genomes (KEGG) and Gene Ontology (GO) pathway enrichment analyses. Then a protein-protein interaction (PPI) network and sub-network of modules were constructed. To investigate the regulatory network underlying DMD, a global triple network including miRNAs, mRNAs and transcription factors (TFs) was constructed. Results A total of 1811 DEGs were found between the DMD and control groups, among which HERC5, SKP2 and FBXW5 were defined as hub genes with a degree of connectivity >35 in the PPI network. Furthermore, the five TFs ZNF362, ATAT1, SPI1, TCF12 and ABCF2, as well as the eight miRNAs miR-124a, miR-200b/200c/429, miR-19a/b, miR-23a/b, miR-182, miR-144, miR-498 and miR-18a/b were identified as playing crucial roles in the molecular pathogenesis of DMD. Conclusions This paper provides a comprehensive perspective on the miRNA-TF-mRNA co-regulatory network underlying DMD, although the bioinformatic findings need further validation in future studies.

RNA in milk exosomes can be absorbed in the mammalian intestinal tract and function in gene expression regulations. Our previous work demonstrated that porcine milk exosomes (PME) contain large amounts of miRNAs and mRNAs. Increasing evidence suggests that long non-coding RNAs (lncRNAs) and circular RNAs (circRNAs) are of particular interest, given their key role in diverse biological processes of animals. However, the expression profiles and the potential functions of lncRNAs and circRNAs in PME are still unknown. In the present study, we isolated PME by ultracentrifugation and performed a comprehensive analysis of lncRNA and circRNA in PME by using RNA sequencing. As a result, 2,466 novel lncRNAs, 809 annotated lncRNAs, and 61 circRNAs were identified in PME. The lncRNAs shared similar characteristics with other mammals in terms of length, exon number, and open reading frames. However, lncRNAs showed a higher level compared with mRNAs. Eight lncRNAs and five circRNAs in PME were selected for PCR identification. A functional enrichment analysis on the target genes of lncRNAs indicated that these genes were involved in cellular macromolecule metabolic, RNA metabolic, and immune processes. The circRNAs host genes were enriched in nucleic acid binding and adherence junction. We also evaluated the potential interaction targets between miRNAs and PME lncRNAs or circRNAs, and the results showed that the PME lncRNAs and the circRNAs have a high density of miRNA target sites. The top 20 highly expressed lncRNAs were found to interact with the proliferation-related miRNAs, and the circRNAs potentially targeted many miRNAs that are associated with the intestinal barrier. This study is the first to provide a resource for lncRNA and circRNA research of porcine milk. Moreover, the potential interaction between lncRNA/circRNA and miRNA is revealed. The present study expands our knowledge of non-coding RNAs in milk, and additional research is necessary to confirm their exactly physiological functions.

Extracellular vesicles (EVs) have diverse roles in the transport of proteins, lipids, and nucleic acids between cells, and they serve as mediators of intercellular communication. Noncoding RNAs (ncRNAs) that are present in EVs, including microRNAs, long noncoding RNAs, and circular RNAs, have been found to participate in complex networks of interactions and regulate a wide variety of genes in animals. Milk is an important source of nutrition for humans and other mammals. Evidence suggests that milk-derived EVs contain abundant ncRNAs, which are stable and can be transported to the offspring and other consumers. Current data suggest a strong link between milk EV ncRNAs and many biological processes, and these ncRNAs have been drawing increasing attention and might play an epigenetic regulatory role in recipients, though further research is still necessary to understand their precise roles. The present review introduces basic information about milk EV ncRNAs, summarizes their expression profiles, biological characteristics, and functions based on current knowledge, and discusses their biological roles, indeterminate issues, and perspectives. Our goal is to provide a deeper understanding of the physiological effects of milk EV ncRNAs on offspring and to provide a reference for future research in this field.

Glycerol dehydrogenase has been identified and characterized functionally in many species. However, little is known about glycerol dehydrogenase genes and their functions in Aspergillus oryzae. Here, a total of 45 glycerol dehydrogenase genes in Aspergillus oryzae were identified and renamed from AoGld1 to AoGld45 according to their chromosome distribution. They were classified into three groups based on phylogenetic analysis. Synteny analysis revealed that thirteen AoGld genes are conserved among Aspergillus species. Promoter analysis displayed that AoGld3 and AoGld13 harbored multiple binding elements of GATA-type transcription factors and zinc-finger protein msnA that were involved in nitrogen and kojic acid metabolism, respectively. Moreover, the AoGld3 deletion strain Δgld3 was generated by the CRISPR/Cas9 system, which had no visible growth defects compared with the control wild-type strain under the control and osmotic stress treatments. However, disruption of AoGld3 led to the inhibition of kojic acid production, and the expression of kojA, kojR was down-regulated in the Δgld3 strain. Furthermore, when kojA or kojR was overexpressed in the Δgld3 strain, the yield of kojic acid was restored, suggesting that AoGld3 is involved in kojic acid production through affecting the expression of kojR and kojA. Taken together, these findings provide new insights into our understanding of glycerol dehydrogenase and establish foundation for further study of their roles in Aspergillus oryzae.