Objective
To explore the gene expression during induction and formation of starvation state of Candida albicans (C.albicans) .
Methods
C.albicans American Type Culture Collection (ATCC) 10231 was cultured and induced into starvation phase. After induction for 0, 12, 24, and 48 h, the fungal cells were collected. Total RNA was extracted and microarrays were used to identify the gene expression changes under starvation conditions. T-test was used to statistically analyze the data of different time points.
Results
Statistical analysis demonstrated that 14.45% to 29.13% of gene expression has changed during the induction into starvation conditions (P<0.05) , these genes are related with many biologic pathways including amino acid metabolism, carbohydrate metabolism, lipid metabolism, nucleic acid metabolism and cell cycles. Especially, the differentially expressed genes included the down-regulation of alanine metabolism related genes, ATP synthesis related gene SDH4, mitosis related gene PRE1, and exopolymeric matrix production gene GCA1, and up-regulation of PXA2 and VPS34.
Conclusions
During the induction into starvation conditions, the genes related with metabolic and proliferative activities were down-regulated, while the genes related with environment and drug resistance were up-regulated. These changes may be contributed to maintain the survival and pathogenic capabilities of C.albicans under starvation conditions.
Key words:
Candida albicans; Starvation condition; Microarray
To investigate the expression of wingless-type MMTV integration site family, member 3 (Wnt3) in rat dental follicles and its protein level in dental follicle cells (DFC) undergoing osteogenic induction and to discuss the effects of Wnt3 on the differentiation of DFC.Rats at postnatal days 1, 3, 5, 7, 9, 11 and 13 were executed, then the mandibles were immediately removed and immunohistochemistry was performed to detect the expression of Wnt3 in dental follicles of postnatal rats. The expression and distribution of Wnt3 in DFC were determined by immunofluorescence. Alizarin red-S staining was performed to assess the mineralization of DFC. Western blotting was used to evaluate Wnt3 and β-catenin protein levels after stimulated by osteogenic medium for 1, 2 and 3 weeks, respectively.Immunohistochemistry revealed that the expression of Wnt3 in rat dental follicles began at day 5 and sustained to day 13. On day 1 and 3, the expression of Wnt3 in dental follicles was negative.Wnt3 was expressed in the cytoplasm of DFC. Alizarin red-S staining indicated that the osteogenic medium stimulated the differentiation of DFC into osteoblastic lineage.Western blotting demonstrated that the Wnt3 protein levels were significantly up-regulated after stimulated with osteogenic medium for 1 weeks compared with the control (2.60 ± 0.04 vs.1.00 ± 0.00, P < 0.05). Then the levels of Wnt3 protein were declined, and at the 3rd week, no significant difference was observed between osteo-induced group and the control (1.00 ± 0.05 vs.1.00 ± 0.00, P > 0.05). The levels of β-catenin were increased in osteo-induced groups compared with the control (1.95 ± 0.05 vs.1.00 ± 0.00, P < 0.05; 9.77 ± 0.65 vs.1.00 ± 0.00, P < 0.05;1.75 ± 0.21 vs.1.00 ± 0.00, P < 0.05). Furthermore, the expression of β-catenin reached to a peak on the 2nd week (9.77 ± 0.65), and then declined.Wnt3 was expressed in the rat dental follicles both in vivo and in vitro and up-regulated during early phase of osteoblast differentiation in DFC.Wnt3 may be involved in early phase of osteoblast differentiation.
A high prevalence of Enterococcus faecalis (E. faecalis) is observed in teeth with root canal treatment failures. Clustered regularly interspaced short palindromic repeats (CRISPR) are widely distributed in prokaryotes that have adaptive immune systems against mobile elements, including pathogenic genes. The present study investigated the relevance of the CRISPR in E. faecalis strains isolated from retreated root canals on biofilms, periapical lesions and drug resistance. A total of 20 E. faecalis strains were extracted from the root canals of teeth referred for root canal retreatment. CRISPR-Cas loci were identified by two pairs of relevant primers and polymerase chain reaction. The susceptibility of the 20 isolated strains to intracanal irrigants was evaluated by 1- and 5-minute challenges with a mixture of a tetracycline isomer, an acid and a detergent (MTAD), 2% chlorhexidine (CHX) and 5.25% sodium hypochlorite (NaOCl). The microtiter plate assay and crystal violet staining were used to compare the biofilm formation of the E. faecalis isolate strains. Out of the 20 E. faecalis isolate strains, 5 strains that lacked CRISPR-cas determinants exhibited significant periapical lesions. Among the 15 strains containing CRISPR-cas determinants, 8 were isolated from root canals with inadequate fillings and 7 were isolated from root canals without any fillings. The five strains lacking CRISPR-cas loci were observed to be more resistant to MTAD and 2% CHX than the 15 strains that had CRISPR-cas loci. All of the strains exhibited the same susceptibility to 5.25% NaOCl. Furthermore, the 5 strains lacking CRISPR-cas determinants generated more biofilm than the other 15 strains. Thus, the results of the present study suggested that E. faecalis root canal isolates lacking CRISPR-cas exhibit higher resistance to intracanal irrigants, stronger biofilm formation and generate significant periapical lesions.
Abstract Background Circular RNAs (circRNAs) are newly discovered noncoding RNAs (ncRNAs) that play key roles in various biological functions, such as the regulation of gene expression and alternative splicing. CircRNAs have been identified in some species, including western honeybees. However, the understanding of honeybee circRNA is still very limited, and to date, no study on eastern honeybee circRNA has been conducted. Here, the circRNAs in the midguts of Apis cerana cerana workers were identified and validated, and the regulatory networks were constructed. Differentially expressed circRNAs (DEcircRNAs) and the corresponding competitively endogenous RNA (ceRNA) networks in the development of the worker’s midgut were further investigated. Results Here, 7- and 10-day-old A. c. cerana workers’ midguts (Ac1 and Ac2) were sequenced using RNA-seq, and a total of 9589 circRNAs were predicted using bioinformatics. These circRNAs were approximately 201-800 nt in length and could be classified into six types; the annotated exonic circRNAs were the most abundant. Additionally, five novel A. c. cerana circRNAs were confirmed by PCR amplification and Sanger sequencing, indicating the authenticity of A. c. cerana circRNAs. Interestingly, novel_circ_003723, novel_circ_002714, novel_circ_002451 and novel_circ_001980 were the most highly expressed circRNAs in both Ac1 and Ac2, which is indicative of their key roles in the development of the midgut. Moreover, 55 DEcircRNAs were identified in the Ac1 vs Ac2 comparison group, including 34 upregulated and 21 downregulated circRNAs. Further investigation showed that the source genes of circRNAs were classified into 34 GO terms and were involved in 141 KEGG pathways. In addition, the source genes of DEcircRNAs were categorized into 10 GO terms and 15 KEGG pathways, which demonstrated that the corresponding DEcircRNAs may affect the growth, development, and material and energy metabolisms of the worker’s midgut by regulating the expression of the related source genes. Additionally, the circRNA-miRNA regulatory networks were constructed and analyzed, and the results demonstrated that 1060 circRNAs can bind to 74 miRNAs and that 71.51% of circRNAs can be linked to only one miRNA. Furthermore, the DEcircRNA-miRNA-mRNA networks were constructed and explored, and the results indicate that the 13 downregulated circRNAs can bind to eight miRNAs and to 29 target genes. In addition, the results indicate that the 16 upregulated circRNAs can bind to 9 miRNAs and to 29 target genes, demonstrating that DEcircRNAs are likely involved in the regulation of midgut development via ceRNA mechanisms. Moreover, the regulatory networks of miR-6001-y-targeted DEcircRNAs were analyzed, and the results showed that eight DEcircRNAs may affect the development of A. c. cerana workers’ midguts by targeting miR-6001-y. Finally, four randomly selected DEcircRNAs were verified via RT-qPCR, confirming the reliability of our sequencing data. Conclusion This is the first systematic investigation of circRNAs and their corresponding regulatory networks in eastern honeybees. The identified circRNAs from the A. c. cerana worker’s midgut will enrich the known reservoir of honeybee ncRNAs. DEcircRNAs may play a comprehensive role during the development of the worker’s midgut via the regulation of source genes and the interaction with miRNAs by acting as ceRNAs. The eight DEcircRNAs that targeted miR-6001-y were likely to be vital for the development of the worker’s midgut. Our results provide a valuable resource for the future studies of A. c. cerana circRNA and lay a foundation to reveal the molecular mechanisms underlying the regulatory networks of circRNAs responsible for the worker’s midgut development; in addition, these findings facilitate a functional study on the key circRNAs involved in the developmental process. Graphical Abstract
Abstract Objectives Topographic cues can modulate morphology and differentiation of mesenchymal stem cells. This study aimed to determine how topographic cues of a novel bilayered poly (lactic‐co‐glycolic acid) (PLGA) scaffold affect osteogenic/odontogenic differentiation of dental pulp stem cells (DPSCs). Methods The surface morphology of the scaffolds was visualized by scanning electron microscope, and the surface roughness was measured by profilometry. DPSCs were cultured on each side of the scaffolds. Cell morphology, expression of Yes‐associated protein (YAP) and osteogenic/odontogenic differentiation were analysed by immunohistochemistry, real‐time polymerase chain reaction, and Alizarin Red S staining. In addition, cytochalasin D (CytoD), an F‐actin disruptor, was used to examine the effects of F‐actin on intracellular YAP localisation. Verteporfin, a YAP transcriptional inhibitor, was used to explore the effects of YAP signalling on osteogenic/odontogenic differentiation of DPSCs. Results The closed side of our scaffold showed smaller pores and less roughness than the open side. On the closed side, DPSCs exhibited enhanced F‐actin stress fibre alignment, larger spreading area, more elongated appearance, predominant nuclear YAP localization and spontaneous osteogenic differentiation. Inhibition of F‐actin alignments was correlated with nuclear YAP exclusion of DPSCs. Verteporfin restricted YAP localisation to the cytoplasm, down‐regulated expression of early osteogenic/odontogenic markers and inhibited mineralization of DPSCs cultures. Conclusions The surface topographic cues changed F‐actin alignment and morphology of DPSCs, which in turn regulated YAP signalling to control osteogenic/odontogenic differentiation.
ABSTRACT Nosema ceranae is a widespread fungal parasite for adult honeybees, severely damaging bee health and sustainable development of apiculture. Circular RNAs (circRNAs) are a class of newly discovered noncoding RNAs (ncRNAs) that regulate a number of biological processes such as immune defense and development. In this current work, based on previously obtained whole transcriptome data, 8 199 and 8 711 circRNAs were predicted from the midguts of Apis mellifera ligustica workers at 7 days (AmT1) and 10 days (AmT2) post inoculation (dpi) with N. ceranae using bioinformatics. Additionally, in combination with transcriptome data from uninfected midguts (AmCK1 and AmCK2) (Xiong et al., 2018), 4 464 circRNAs were found to be shared by the aforementioned four groups, whereas the numbers of specifically transcribed circRNAs in each group were 1 389, 1 696, 1 019 and 1 871, respectively. Furthermore, 10 226 circRNAs were homologous to Apis cerana cerana circRNAs, while 20 circRNAs had homology with Homo sapiens circRNAs; in addition, 16 circRNAs were highly conserved in these three species. Differential expression analysis showed that 168 (306) differentially expressed circRNAs (DEcircRNAs) were identified in AmCK1 vs AmT1 (AmCK2 vs AmT2) comparison group, including 61 (143) upregulated circRNAs and 107 (163) downregulated circRNAs. Moreover, RT-qPCR results showed that the expression trend of eight DEcircRNAs was consistent with that of the transcriptome dataset. Based on GO database annotation, we observed that source genes of DEcircRNAs in AmCK1 vs AmT1 (AmCK2 vs AmT2) were engaged in 27 (35) functional terms, including two (two) cell renewal-associated terms, seven (seven) cell structure-associated terms, and one (one) immunity-associated terms. Additionally, DEcircRNA source genes in AmCK1 vs AmT1 were involved in two cell renewal-related pathways, Hippo and Wnt signaling pathways, and three carbohydrate metabolism-related pathways, galactose metabolism, starch and sucrose metabolism, fructose and mannose metabolism, only one energy metabolism-related pathway (oxidative phosphorylation pathway), three cellular immune-related pathways, endocytosis, phagosome, and lysosome, and a humoral immune-related pathway (FoxO signaling pathway). In AmCK2 vs AmT2 comparison group, more source genes of DEcircRNAs were associated with the abovementioned pathways relative to cell renewal, carbohydrate metabolism, and cellular and humoral immune pathways. In addition, 122 (234) DEcircRNAs in the host midgut at 7 dpi (10 dpi) with N. ceranae targeted 82 (106) miRNAs. Furthermore, 75 (103) miRNAs targeted by 86 (178) DEcircRNAs in AmCK1 vs AmT1 (AmCK2 vs AmT2) further bound to 215 (305) mRNAs. These targets could be annotated as an array of functional terms and pathways related to cellular renewal, cellular structure, carbohydrate and energy metabolism, and cellular and humoral immunity. In a word, we for the first time explored immune responses mediated by DEcircRNAs in the midguts of A. m. ligustica workers to N. ceranae infection. Our data provide a foundation for clarifying the molecular mechanism underlying immune response of western honeybee to N. ceranae invasion, but also a new insight into further understanding the host-pathogen interaction during bee microsporidiosis.
ABSTRACT Chalkbrood, a widespread fungal disease of bee larvae, is caused by the fungus Ascosphaera apis . In this article, mecylia and spores of A. apis were respectively collected followed by DNA isolation, bisulfite conversion, cDNA library construction and next-generation sequencing. Using whole genome bisulfite sequencing (WGBS), 69,844,360 and 60,570,990 raw reads were yielded from Aam and Aas, and after quality control, 9,982,386,951 and 8,825,601,434 clean reads were obtained, respectively. In addition, 67,685,866 and 58,886,072 clean reads were mapped to the reference genome of A. apis , including 37,643,592 and 31,568,442 unique mapped clean reads, and 49,686 and 13,348 multiple mapped clean reads. Furthermore, after bisulfite treatment, the conversion ratio of clean reads from Aam and Aas were 99.38% and 99.51%, respectively. The WGBS data ducumented here contributes to genome-wide identification of 5mC methylation sites in A. apis and comparison of methylomes between mycelium and spore. Value of the data This dataset can be used for genome-wide identification of 5mC methylation sites in A. apis . The accessible data could be used to systematically compare methylomes between mycelium and spore of A. apis . Current data provides a useful resource for further study on DNA methylation-mediated mechanism underlying mycelium growth, spore germination and sexual reproduction of mycelium with the opposite sex.
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