miR-4687-5p Affects Intracellular Survival of Mycobacterium tuberculosis through Its Regulation of NRAMP1 Expression in A549 Cells.

Tuberculosis (TB), as one of the leading causes of death, poses a serious predicament to the world. MicroRNAs (miRNAs) play a role in the post-transcriptional regulation of gene expression. It has been reported that the expression of miRNAs changes upon mycobacterial infection; the screening and identification of miRNAs regulating the expression of genes could benefit our understanding of TB pathogenesis and generate effective strategies for its control and prevention. In this study, luciferase assays showed that miR-4687-5p is bound to the 3'-untranslated region of natural resistance-associated macrophage protein 1 (NRAMP1). Additionally, we found a significant increase in miR-4687-5p expression in Mycobacterium tuberculosis (Mtb)-infected A549 cells. Concomitantly, we detected a reduced level of NRAMP1 expression, suggesting that NRAMP1 is one of the targets of miR-4687-5p. Infection experiments evidenced that the transfection of miR-4687-5p induced a decrease in NRAMP1 expression and increased intracellular Mtb loads post-infection, indicating that miR-4687-5p promotes the intracellular survival of Mtb through its downregulation of the NRAMP1 protein level. We also found that the transfection of miR-4687-5p induced increased apoptosis and decreased cell proliferation post-infection with Mtb. The results presented in our study suggest that miR-4687-5p may be indicative of the susceptibility of Mtb infection to humans and could act as a potential therapeutic target for tuberculosis treatment.

The expression of Nramp1 modulates the uptake of Mycobacterium tuberculosis by macrophages through alternating inflammatory responses.

Natural-resistance-associated macrophage protein-1 (NRAMP1) is a transmembrane protein of the mammalian SLC11 gene family. Previously, genome-wide association study (GWAS) have shown that the single nucleotide polymorphisms (SNPs) of NRAMP1 are associated with human susceptibility to tuberculosis (TB), and the detection of clinical samples have demonstrated that the expression levels of NRAMP1 are concomitant with the susceptibility to TB in humans and cows, but underlying mechanism is unknown. In this study, we completed a series of experiments to investigate how the expression of Nramp1 affects the infection of macrophages with Mycobacterium tuberculosis (Mtb). We found that the increase of Nramp1 expression induced the decrease of Mtb infection efficiency and the higher-level expression of pro-inflammatory cytokines and chemokines, However, the knockdown of Nramp1 promoted the efficiency of bacilli infection to macrophages and induced lower-levels of expression of pro-inflammatory cytokines and chemokines. Collectively, the results in this study demonstrated that the levels of Nramp1 expression affect Mtb infection of macrophage and regulate pro-inflammatory responses of macrophages to Mtb infection, indicating the population with the low-expression level of NRAMP1 predispose to Mtb infection and TB development, and suggesting SNPs in NRAMP1 modulate the host susceptibility to TB through its regulation of NRAMP1 expression.

Loss of Dip2b leads to abnormal neural differentiation from mESCs.

BACKGROUND: Disco-interacting protein 2 homolog B is a member of the Dip2 family encoded by the Dip2b gene. Dip2b is widely expressed in neuro-related tissues and is essential in axonal outgrowth during embryogenesis. METHODS: Dip2b knockout mouse embryonic stem cell line was established by CRISPR/Cas9 gene-editing technology. The commercial kits were utilized to detect cell cycle and growth rate. Flow cytometry, qRT-PCR, immunofluorescence, and RNA-seq were employed for phenotype and molecular mechanism assessment. RESULTS: Our results suggested that Dip2b is dispensable for the pluripotency maintenance of mESCs. Dip2b knockout could not alter the cell cycle and proliferation of mECSs, or the ability to differentiate into three germ layers in vitro. Furthermore, genes associated with axon guidance, channel activity, and synaptic membrane were significantly downregulated during neural differentiation upon Dip2b knockout. CONCLUSIONS: Our results suggest that Dip2b plays an important role in neural differentiation, which will provide a valuable model for studying the exact mechanisms of Dip2b during neural differentiation.

Plasma-derived exosomal let-7c-5p, miR-335-3p, and miR-652-3p as potential diagnostic biomarkers for stable coronary artery disease.

Objectives: Circulating exosomal microRNAs (miRNAs) have been identified as promising biomarkers for diagnosis of cardiovascular diseases. Nevertheless, the diagnostic potential of miRNAs in circulating exosomes for stable coronary artery disease (SCAD) remains unclear. We aim here to analyze the exosomal differentially expressed miRNAs (DEmiRNAs) in plasma of SCAD patients and investigate their diagnostic potential as SCAD biomarkers. Methods: Plasma was collected from SCAD patients and healthy controls, and exosomes were isolated by ultracentrifugation. Exosomal DEmiRNAs were analyzed by small RNA sequencing and were further validated by quantitative real-time PCR (qRT-PCR) in a larger set of plasma samples. Relationships between plasma exosomal let-7c-5p, miR-335-3p, miR-652-3p, genders and Gensini Scores in patients with SCAD were analyzed using correlation analyses. Moreover, we conducted receiver operating characteristic (ROC) curves for these DEmiRNAs and analyzed their possible functions and signaling pathways. Results: Vesicles isolated from plasma displayed all characteristics of exosomes. In the small RNA sequencing study, a total of 12 DEmiRNAs were identified, among which seven were verified to be statistically significant by qRT-PCR. The areas under the ROC curves of exosomal let-7c-5p, miR-335-3p, and miR-652-3p were 0.8472, 0.8029, and 0.8009, respectively. Exosomal miR-335-3p levels were positively correlated with Gensini scores of patients with SCAD. Bioinformatics analysis revealed that these DEmiRNAs may be involved in the pathogenesis of SCAD. Conclusion: Our findings indicated that plasma exosomal let-7c-5p, miR-335-3p, and miR-652-3p can be used as promising biomarkers for diagnosis of SCAD. In addition, plasma exosomal miR-335-3p levels coordinated with severity of SCAD.

Genetic diversity, distribution, and evolution of chicken anemia virus: A comparative genomic and phylogenetic analysis.

Chicken infectious anemia (CIA) is an immunosuppressive poultry disease that causes aplastic anemia, immunosuppression, growth retardation and lymphoid tissue atrophy in young chickens and is responsible for huge economic losses to the poultry industry worldwide. The disease is caused by the chicken anemia virus (CAV), which belongs to the genus Gyrovirus, family Anelloviridae. Herein, we analyzed the full-length genomes of 243 available CAV strains isolated during 1991-2020 and classified them into two major clades, GI and GII, divided into three and four sub-clades, GI a-c, and GII a-d, respectively. Moreover, the phylogeographic analysis revealed that the CAVs spread from Japan to China, China to Egypt and subsequently to other countries, following multiple mutational steps. In addition, we identified eleven recombination events within the coding and non-coding regions of CAV genomes, where the strains isolated in China were the most active and involved in ten of these events. Furthermore, the amino acids variability analysis indicated that the variability coefficient exceeded the estimation limit of 1.00 in VP1, VP2, and VP3 proteins coding regions, demonstrating substantial amino acid drift with the rise of new strains. The current study offers robust insights into the phylogenetic, phylogeographic and genetic diversity characteristics of CAV genomes that may provide valuable data to map the evolutionary history and facilitate preventive measures of CAVs.

Component analysis of Xylaria sp. L1 sporocarps after solid-state fermentation by okara and its safety evaluation in mice and rats.

To explore the chemical components and nutrient components of Xylaria sp. L1 sporocarps, component analysis was characterized using UHPLC-LTQ-Orbitrap-MS/MS. Then, the acute toxicity and the subacute toxicity were conducted, respectively. A total of 38 compounds were detected and quantified. Meanwhile, Xylaria sp. L1 sporocarps had higher quantities of macronutrients, primarily Zn, which was remarkably higher than the human recommended daily values (p < 0.001). Importantly, no evidence of toxicity was observed in the mice after acute exposure to Xylaria sp. L1 sporocarps. In subacute toxicity studies, there were no significant differences in the body and organ weights. In the blood chemistry analysis, no significant changes occurred. Pathologically, neither histopathological changes nor gross abnormalities were observed. Thus, our study highlights the potential for using Xylaria sp. L1 sporocarps as novel food with Zn supplementation for humans.

Polymorphisms in the ASAP1 and SP110 Genes and Its Association with the Susceptibility to Pulmonary Tuberculosis in a Mongolian Population.

Tuberculosis (TB) remains one of the deadliest infectious diseases in the world. Previous genome-wide association studies suggested that single-nucleotide polymorphisms (SNPs) in some genes could indicate the susceptibility to TB in some populations. Herein, we studied the association of SNPs in the immunity-related genes, i.e., ASAP1 and SP110 genes with the susceptibility to TB in a Mongolian population in China. A case-control study was performed with 197 TB patients and 217 healthy controls. Six SNPs in ASAP1 and six SNPs in SP110 were selected for genotyping test by second-generation sequencing technique. A SNP in SP110 gene (rs722555) was identified to be associated with susceptibility to TB in the Mongolian population (p < 0.05). The T allele of rs722555 in SP110 gene was associated with a 36% increase of risk at TB (OR 1.36, 95% CI 1.03-1.81), and the CT+TT genotype of rs722555 was associated with a 74% increase of risk at TB (OR 1.74, 95% CI 1.16-2.60) in the dominant genetic model. None of SNPs in ASAP1 gene tested in this study were significantly associated with TB susceptibility, while some individuals with SNPs (rs10956514, rs4733781, rs2033059, rs12680942, rs1017281, rs1469288, and rs17285138) in the ASAP1 gene tended to have a reduced risk at TB. In conclusion, this study suggested that the rs722555 SNP in SP110 gene might be a risk factor for TB in a Mongolian population.

Preparation of the Carbonized Zif-8@PAN Nanofiber Membrane for Cadmium Ion Adsorption.

The zeolitic imidazolate framework (ZIF-8)@polyacrylonitrile (PAN) nanofiber membrane was prepared and carbonized for heavy metal cadmium ion (Cd2+) adsorption in aqueous medium. Zinc oxide (ZnO) was first sputtered onto the surface of the PAN electrospun nanofiber membrane to provide a metal ion source. Then, the ZIF-8@PAN nanofiber membrane was prepared via in situ solvothermal reaction and carbonized in a tube furnace at 900 °C under a N2 atmosphere to enhance adsorption performance. The synthesized ZIF-8 particles with polyhedral structure were uniformly immobilized on the surface of the PAN electrospun nanofiber membrane. After being heated at 900 °C, the polygonal ZIF-8 shrank, and the carbonized ZIF-8@PAN nanofiber membrane was obtained. Compared with the nanofiber membrane without being carbonized, the adsorption capacity of the carbonized ZIF-8@PAN nanofiber membrane reached 102 mg L-1, and its Cd2+ adsorption efficiency could be more than 90% under the adsorption temperature of 35 °C and solution of pH = 7.5 conditions. According to the adsorption thermodynamics analysis, the Cd2+ adsorption process of the carbonized ZIF-8@PAN nanofiber membrane was spontaneous. The whole Cd2+ adsorption process was more suitably described by the pseudo second-order adsorption kinetics model, indicating that there exists a chemical adsorption mechanism besides physical adsorption.

Isothermal and Non-Isothermal Crystallization Kinetics of Poly(ethylene chlorotrifluoroethylene).

The isothermal (IT) and non-isothermal (NIT) crystallization kinetics, morphology, and structure of poly(ethylene chlorotrifluoroethylene) (ECTFE) were investigated via differential scanning calorimetry (DSC), polarized optical microscopy (POM), and wide-angle X-ray diffraction (XRD). The Avrami equation could well describe the overall IT crystallization process of ECTFE, and, furthermore, the overall crystallization rate decreased at higher crystallization temperatures (Tc). The equilibrium melting point for ECTFE was found to be 238.66 °C. The activation energies for IT and NIT crystallization were determined as -137.68 and -120.54 kJ/mol, respectively. The Jeziorny model fitted well with the initial stages of NIT melt crystallization, while deviations from linearity in the later stages of the process were due to the collisions of spherulites. Spherulites of ECTFE organized in a hexagonal crystal system were found. The relative crystalline degree of ECTFE under NIT conditions was about 54.55%, and this decreased with the increase in cooling rate. Moreover, the Ozawa and Mo models were suitable for modeling the overall NIT crystallization process of ECTFE.

Isolation and characterization of the novel bacteriophage vB_SmaS_BUCT626 against Stenotrophomonas maltophilia.

Stenotrophomonas maltophilia has been recognized as an emerging global opportunistic pathogen, and it is intrinsically resistant to most antibiotics, which makes the limited choice for treating S. maltophilia infections. Bacteriophage with the proper characterization is considered as a promising alternative treatment option to control S. maltophilia infections. In this study, we isolated a novel Siphoviridae bacteriophage vB_SmaS_BUCT626 with lytic activity against S. maltophilia. Phage vB_SmaS_BUCT626 can lysis 10 of 20 S. maltophilia and was relatively stable at a wide range of temperatures (4-70 °C) and pH values (3.0-13.0) and exhibited good tolerance to chloroform. The genome of phage vB_SmaS_BUCT626 was a 61,662-bp linear double-stranded DNA molecule with a GC content of 56.2%, and contained 100 open-reading frames. It carried no antibiotic resistance, toxin, virulence-related genes, or lysogen-formation gene clusters. Together, these characteristics make phage vB_SmaS_BUCT626, a viable candidate as a biocontrol agent against S. maltophilia infection.

Knockout of Dip2c in murine ES cell line IBMSe001-B-1 by CRISPR/Cas9 genome editing technology.

DIP2 protein contains three members: DIP2A, DIP2B and DIP2C, and are broadly expressed in the nervous system from Drosophila to human during embryonic development. Dip2c gene-associated mutations have been reported in tumors and neuronal diseases. However, the role ofDip2cin the context of mouse embryonic stem (mES) cells has not been explored.To investigate the biological function of Dip2c during early embryo development, we generated Dip2c-/- mES line using a CRISPR/Cas9 system. This cell line has contributed to further investigation of molecular mechanism of Dip2c during cell differentiation, as well as a cell model for screening for neurogenic drug and cancer clinical cure.

Association of polymorphisms of innate immunity-related genes and tuberculosis susceptibility in Mongolian population.

BACKGROUNDS: Genetic polymorphism of the toll-like receptor 2, 4 (TLR2, TLR4) and natural resistance-associated macrophage protein 1 (NRAMP1) genes may affect host immune response to Mycobacterium tuberculosis (Mtb) and lead to the variation of susceptibility to tuberculosis (TB) in humans. However, the association of single nucleotide polymorphisms (SNP) in these genes and the susceptibility to TB in Mongolian population has not been investigated. METHODS: We conducted a genetic association study including 197 Mongolian TB patients and 217 Mongolian healthy controls in Inner Mongolia, China. DNA of blood samples was extracted and genotyped for 5 SNPs in TLR4, 4 SNPs in TLR2 and 5 SNPs in NRAMP1 by next-generation sequencing. A logistic regression was performed and odds ratios (OR) with 95% confidence intervals (CI) were calculated to estimate the risk at TB by each SNP. RESULTS: The most significant locus associated with the susceptibility to TB was TLR4 rs11536889. The frequency for allele C of TLR4 rs11536889 was 16.0% in TB patients and 23.5% in healthy controls, respectively. Rs11536889 C/C genotype of TLR4 was significantly associated with the low susceptibility against TB compared to G/G genotype in the dominant model (OR 0.62, 95% CI 0.41-0.94). CONCLUSIONS: The TLR4 rs11536889 polymorphisms might be an indicative of the low susceptibility to TB in Mongolian population, which provides valuable information for the generation of effective strategy or measurement against TB in Mongolian population.

Taste buds are not derived from neural crest in mouse, chicken, and zebrafish.

Our lineage tracing studies using multiple Cre mouse lines showed a concurrent labeling of abundant taste bud cells and the underlying connective tissue with a neural crest (NC) origin, warranting a further examination on the issue of whether there is an NC derivation of taste bud cells. In this study, we mapped NC cell lineages in three different models, Sox10-iCreERT2/tdT mouse, GFP+ neural fold transplantation to GFP- chickens, and Sox10-Cre/GFP-RFP zebrafish model. We found that in mice, Sox10-iCreERT2 specifically labels NC cell lineages with a single dose of tamoxifen at E7.5 and that the labeled cells were widely distributed in the connective tissue of the tongue. No labeled cells were found in taste buds or the surrounding epithelium in the postnatal mice. In the GFP+/GFP- chicken chimera model, GFP+ cells migrated extensively to the cranial region of chicken embryos ipsilateral to the surgery side but were absent in taste buds in the base of oral cavity and palate. In zebrafish, Sox10-Cre/GFP-RFP faithfully labeled known NC-derived tissues but did not label taste buds in lower jaw or the barbel. Our data, together with previous findings in axolotl, indicate that taste buds are not derived from NC cells in rodents, birds, amphibians or teleost fish.

Comprehensive MicroRNA Expression Profile of the Mammary Gland in Lactating Dairy Cows With Extremely Different Milk Protein and Fat Percentages.

A total of 31 differentially expressed genes in the mammary glands were identified in our previous study using RNA sequencing (RNA-Seq), for lactating cows with extremely high and low milk protein and fat percentages. To determine the regulation of milk composition traits, we herein investigated the expression profiles of microRNA (miRNA) using small RNA sequencing based on the same samples as in the previous RNA-Seq experiment. A total of 497 known miRNAs (miRBase, release 22.1) and 49 novel miRNAs among the reads were identified. Among these miRNAs, 71 were found differentially expressed between the high and low groups (p < 0.05, q < 0.05). Furthermore, 21 of the differentially expressed genes reported in our previous RNA-Seq study were predicted as target genes for some of the 71 miRNAs. Gene ontology and KEGG pathway analyses showed that these targets were enriched for functions such as metabolism of protein and fat, and development of mammary gland, which indicating the critical role of these miRNAs in regulating the formation of milk protein and fat. With dual luciferase report assay, we further validated the regulatory role of 7 differentially expressed miRNAs through interaction with the specific sequences in 3'UTR of the targets. In conclusion, the current study investigated the complexity of the mammary gland transcriptome in dairy cattle using small RNA-seq. Comprehensive analysis of differential miRNAs expression and the data from previous study RNA-seq provided the opportunity to identify the key candidate genes for milk composition traits.

Generation of Dip2a homozygous knockout murine ES cell line IBMSe001-A-1 via CRISPR/Cas9 technology.

DIP2A mutation is associated with abnormal brain development and diseases including dyslexia, autism and Alzheimer's disease. However, the role and the involved mechanisms remain unknown. To study the biological function of DIP2A during mESCs neural differentiation in early neural development, we generated a Dip2a homozygous knockout 46C ESC cell line using CRISPR/Cas9 genome editing technology. The eighth exon of Dip2a gene was replaced with PGK-Puro-P2A-mCherry. This 46C-Dip2a KO cell line offers a useful resource to investigate the molecular mechanisms of DIP2A in the process of cell fate determination, as well as a potential source of building disease mouse model.

Dysregulated NF-κB signal promotes the hub gene PCLAF expression to facilitate nasopharyngeal carcinoma proliferation and metastasis.

BACKGROUND: Nasopharyngeal carcinoma (NPC) is common in Southern China. The molecular mechanism underlying NPC genesis and progression has been comprehensively investigated, but the key gene (s) or pathway (s) pertaining to NPC are unidentified. METHODS: We explored some key genes and pathways involved in NPC through using meta-analysis of deposited expression of microarray data of NPC. The expression of proliferating cell nuclear antigen clamp associated factor (PCLAF) was determined by real-time PCR and western blots. CCK-8 assay, colony formation assay, transwell migration assay, cell wound healing assay, cell cycle analysis and cell apoptosis were carried out to assess biological behaviors caused by downregulation and overexpression of PCLAF in vitro. CHIP was utilized to determine the direct upstream regulatory transcription factors of PCLAF. RESULTS: PCLAF was the key gene of NPC, which was significantly up-regulated in NPC cell line compared to the normal nasopharyngeal cell line. Additionally, in vitro assay has demonstrated the down-regulation and overexpression of PCLAF, resulted in significantly suppressed and enhanced NPC proliferation, metastasis and invasion respectively. Furthermore, the up-regulation of PCLAF in NPC is induced by direct binding of dysregulated NF-κB p50/RelB complex to the promoter of PCLAF. CONCLUSION: Our results offer a strategy for re-using the deposited data to find the key genes and pathways involved in pathogenesis of cancer. Our study has provided evidence of supporting the role of PCLAF in NPC genesis and progression.

Early taste buds are from Shh+ epithelial cells of tongue primordium in distinction from mature taste bud cells which arise from surrounding tissue compartments.

Mammalian taste buds emerge perinatally and most become mature 3-4 weeks after birth. Mature taste bud cells in rodents are known to be renewed by the surrounding K14+ basal epithelial cells and potentially other progenitor source(s), but the dynamics between initially developed taste buds and surrounding tissue compartments are unclear. Using the K14-Cre and Dermo1-Cre mouse lines to trace epithelial and mesenchymal cell lineages, we found that early taste buds in E18.5 and newborn mouse tongues are not derived from either lineage. At E11.5 when the tongue primordia (i.e., lingual swellings) emerge, the relatively homogeneous sonic hedgehog-expressing (Shh+) epithelial cells express Keratin (K) 8, a marker that is widely used to label taste buds. Mapping lineage of E11.0 Shh+ epithelium of the tongue rudiment with Shh-CreERT2/RFP mice demonstrated that both the early taste buds and the surrounding lingual epithelium are from the same population of progenitors - Shh+ epithelial cells of the tongue primordium. In combination with previous reports, we propose that Shh+K8+ cells in the homogeneous epithelium of tongue primordium at early embryonic stages are programmed to become taste papilla and taste bud cells. Switching off Shh and K8 expression in the Shh+ epithelial cells of the tongue primordium transforms the cells to non-gustatory cells surrounding papillae, including K14+ basal epithelial cells which will eventually contribute to the cell renewal of mature taste buds.

RNA-Seq analysis on chicken taste sensory organs: An ideal system to study organogenesis.

RNA-Seq is a powerful tool in transcriptomic profiling of cells and tissues. We recently identified many more taste buds than previously appreciated in chickens using molecular markers to stain oral epithelial sheets of the palate, base of oral cavity, and posterior tongue. In this study, RNA-Seq was performed to understand the transcriptomic architecture of chicken gustatory tissues. Interestingly, taste sensation related genes and many more differentially expressed genes (DEGs) were found between the epithelium and mesenchyme in the base of oral cavity as compared to the palate and posterior tongue. Further RNA-Seq using specifically defined tissues of the base of oral cavity demonstrated that DEGs between gustatory (GE) and non-gustatory epithelium (NGE), and between GE and the underlying mesenchyme (GM) were enriched in multiple GO terms and KEGG pathways, including many biological processes. Well-known genes for taste sensation were highly expressed in the GE. Moreover, genes of signaling components important in organogenesis (Wnt, TGFß/ BMP, FGF, Notch, SHH, Erbb) were differentially expressed between GE and GM. Combined with other features of chicken taste buds, e.g., uniquely patterned array and short turnover cycle, our data suggest that chicken gustatory tissue provides an ideal system for multidisciplinary studies, including organogenesis and regenerative medicine.