Single-Cell RNA-Sequencing Analysis of Colonic Lamina Propria Immune Cells Reveals the Key Immune Cell-Related Genes of Ulcerative Colitis.

Background: Ulcerative colitis (UC) is a severe threat to humans worldwide. Single-cell RNA sequencing (scRNA-seq) can be used to screen gene expression patterns of each cell in the intestine, provide new insights into the potential mechanism of UC, and analyze the development of immune cell changes. These findings can provide new ideas for the diagnosis and treatment of intestinal diseases. In this study, bioinformatics analysis combined with experiments applied in dextran sulfate sodium (DSS)-induced colitis mice was used to explore new diagnostic genes for UC and their potential relationship with immune cells. Methods: We downloaded microarray datasets (GSE75214, GSE87473, GSE92415) from the Gene Expression Omnibus and used these datasets to screen differentially expressed genes (DEGs) and conduct Weighted Gene Co-expression Network Analysis (WGCNA) after quality control. The hub genes were screened, and ROC curves were drawn to verify the reliability of the results in both training set (GSE75214, GSE87473, GSE92415) and validation cohort (GSE87466). Also, we explored the relation of diagnostic genes and immune cells by CIBERSORT algorithm and single-cell analysis. Finally, the expression of hub genes and their relation with immune cells were verified in DSS-induced colitis mice. Results: Diagnostic genes (ANXA5, MMP7, NR1H4, CYP3A4, ABCG2) were identified. In addition, we found these five genes firmly related to immune infiltration. The DSS-induced colitis mice confirm that the expression of ANXA5 mainly increased in the intestinal macrophages and had a strong negative correlation with M2 macrophages, which indicated its possible influence on the polarization of macrophages in UC patients. Conclusion: We identified ANXA5, MMP7, NR1H4, CYP3A4, and ABCG2 as diagnostic genes of UC that are closely related to immune infiltration and ANXA5 maintains a negative correlation with M2 macrophages which indicated its possible influence on the polarization of macrophage in UC patients.

Construction of a Colorectal Cancer Prognostic Risk Model and Screening of Prognostic Risk Genes Using Machine-Learning Algorithms.

This study is aimed at constructing a prognostic risk model for colorectal cancer (CRC) using machine-learning algorithms to provide accurate staging and screening of credible prognostic risk genes. We extracted CRC data from GSE126092 and GSE156355 of the Gene Expression Omnibus (GEO) database and datasets from TCGA to analyze the differentially expressed genes (DEGs) using bioinformatics analysis. Among the 330 shared DEGs related to CRC prognosis, we divided the analysis period into different phases and applied univariate COX regression, LASSO, and multivariate COX regression analysis. GO analysis and KEGG analysis revealed that the functions of these DEGs were primarily focused on cell cycle, DNA replication, cell mitosis, and other related functions, and this confirmed our results from a biological perspective. Finally, a prognostic risk model for CRC based on the CHGA, CLU, PLK1, AXIN2, NR3C2, IL17RB, GCG, and AJUBA genes was constructed, and the risk score enabled us to predict the prognosis for CRC. To obtain a comprehensive and accurate model, we used both internal and external evaluations, and the model was able to correctly differentiate patients with CRC into a high-risk group with poor prognosis and a low-risk group with good prognosis. The AUC values of the 3-, 5-, and 10-year survival ROC curves were 0.715, 0.721, and 0.777, respectively, according to the internal evaluation, and the AUC values were 0.606, 0.698, and 0.608, respectively, for the external evaluation using GSE39582 from the GEO database. We determined that CLU, PLK1, and IL17RB could be considered to be independent prognostic factors for CRC with significantly different expression (P < 0.05). Using machine-learning methods, a prognostic risk model comprised of eight genes was constructed. Not only does this model provide improved treatment guidance, but it also provides a novel perspective for analyzing survival conditions at a deeper biological level.

CpMAX1a, a Cytochrome P450 Monooxygenase Gene of Chimonanthus praecox Regulates Shoot Branching in Arabidopsis.

Strigolactones (SLs) are a class of important hormones in the regulation of plant branching. In the model plant Arabidopsis, AtMAX1 encodes a cytochrome P450 protein and is a crucial gene in the strigolactone synthesis pathway. Yet, the regulatory mechanism of MAX1 in the shoot branching of wintersweet (Chimonanthus praecox) remains unclear. Here we identified and isolated three MAX1 homologous genes, namely CpMAX1a, CpMAX1b, and CpMAX1c. Quantitative real-time PCR (qRT-PCR) revealed the expression of CpMAX1a in all tissues, being highest in leaves, whereas CpMAX1b was only expressed in stems, while CpMAX1c was expressed in both roots and stem tips. However, CpMAX1a's expression decreased significantly after decapitation; hence, we verified its gene function. CpMAX1a was located in Arabidopsis chloroplasts. Overexpressing CpMAX1a restored the phenotype of the branching mutant max1−3, and reduced the rosette branch number, but resulted in no significant phenotypic differences from the wild type. Additionally, expression of AtBRC1 was significantly upregulated in transgenic lines, indicating that the CpMAX1a gene has a function similar to the homologous gene of Arabidopsis. In conclusion, our study shows that CpMAX1a plays a conserved role in regulating the branch development of wintersweet. This work provides a molecular and theoretical basis for better understanding the branch development of wintersweet.

Soft machining-induced surface and edge chipping damage in pre-crystalized lithium silicate glass ceramics.

Soft machining is a key procedure in fabrication of high-strength lithium-based silicate glass ceramic (LS) restorations. This paper reports on the diamond machining-induced surface and edge chipping damage in two pre-crystalized LS materials: pre-crystallized lithium metasilicate/orthophosphate glass ceramic (Pre-LS, IPS e.max CAD) and pre-crystallized zirconia-containing lithium metasilicate glass ceramic (Pre-ZLS, Vita Suprinity). Indentation techniques were used to measure the material mechanical properties. Soft machining was conducted using a robotic controlled apparatus mimicking dental CAD/CAM machining processes at different removal rates and enabling in-process force measurement. Machined surface roughness was assessed using 3D confocal optical profilometry in terms of the average and maximum surface heights. Scanning electron microscopy was used to assess diamond tool and machined surface and edge morphology. Soft machining of both materials was dominated by brittle fracture mixed with localized ductile flow. However, the higher brittleness index of Pre-ZLS than Pre-LS yielded higher degrees of machining-induced conchoidal fractures in Pre-ZLS in comparison with irregular fractures in Pre-LS. Thus, much larger surface roughness and deeper edge chipping damage were produced in Pre-ZLS than Pre-LS. Machining forces for Pre-ZLS were significantly smaller than Pre-LS, due to the lower machinability index associated with a complex relation of the mechanical properties as well as less debris adhesion for Pre-ZLS than Pre-LS. Further, increased material removal rates resulted in significantly increased machining forces, maximum surface roughness and fracture, and edge chipping damage in both Pre-ZLS and Pre-LS materials. Therefore, optimization of soft machining processes needs to be practiced to achieve accepted surface and edge quality at balanced removal rates.

CpBBX19, a B-Box Transcription Factor Gene of Chimonanthus praecox, Improves Salt and Drought Tolerance in Arabidopsis.

Zinc-finger proteins are important transcription factors in plants, responding to adversity and regulating the growth and development of plants. However, the roles of the BBX gene family of zinc-finger proteins in wintersweet (Chimonanthus praecox) have yet to be elucidated. In this study, a group IV subfamily BBX gene, CpBBX19, was identified and isolated from wintersweet. Quantitative real-time PCR (qRT-PCR) analyses revealed that CpBBX19 was expressed in all tissues and that expression was highest in cotyledons and inner petals. CpBBX19 was also expressed in all flower development stages, with the highest expression detected in early initiating bloom, followed by late initiating bloom and bloom. In addition, the expression of CpBBX19 was induced by different abiotic stress (cold, heat, NaCl, and drought) and hormone (ABA and MeJA) treatments. Heterologous expression of CpBBX19 in Arabidopsis thaliana (Arabidopsis) enhanced the tolerance of this plant to salt and drought stress as electrolyte leakage and malondialdehyde (MDA) concentrations in transgenic Arabidopsis after stress treatments were significantly lower than those in wild-type (WT) plants. In conclusion, this research demonstrated that CpBBX19 plays a role in the abiotic stress tolerance of wintersweet. These findings lay a foundation for future studies on the BBX gene family of wintersweet and enrich understanding of the molecular mechanism of stress resistance in wintersweet.

Prostate stromal tumor with prostatic cysts after transurethral resection of the prostate: A case report.

BACKGROUND: A prostatic stromal tumor is deemed to be a rare oncology condition. Based on the retrospective analysis of clinical data and scientific literature review, a case of prostatic stromal tumor was reported in this article to explore the diagnosis, treatment and prognosis of this rare disease. CASE SUMMARY: The present case involved an older male patient who was admitted to our department for a medical consultation of dysuria. Serum prostate-specific antigen was 8.30 ng/mL, Ultrasound and magnetic resonance imaging suggested evident enlargement of the prostate and multiple cystic developments internally. Considering that the patient was an elderly male with a poor health status, transurethral resection of the prostate was performed to improve the symptoms of urinary tract obstruction. Furthermore, based on histopathologic examination and immunohistochemical staining, the patient was pathologically diagnosed with prostatic stromal tumor. The patient did not receive any further adjuvant therapy following surgery leading to a clinical recommendation that the patient should be followed up on a long-term basis. However, during the recent follow-up assessment, the patient demonstrated recurrence of lower urinary tract symptoms and gross hematuria. CONCLUSION: Referring to scientific literature review, we believe that the management of these lesions requires a thorough assessment of the patient. Furthermore, the treatment of prostate stromal tumors should be based on the imaging examination and pathological classification. Active surgical treatment is of great significance to the prognosis of patients, and subsequent surveillance after the treatment is warranted.

Identification of CDK1 as a candidate marker in cutaneous squamous cell carcinoma by integrated bioinformatics analysis.

BACKGROUND: Cutaneous squamous cell carcinoma (cSCC) is a relatively common cancer that accounts for nearly 50% of non-melanoma skin cancer cases. However, the genotypes that are linked with poor prognosis and/or high relapse rates and pathogenic mechanisms of cSCC are not fully understood. To address these points, three gene expression datasets were analyzed to identify candidate biomarker genes in cSCC. METHODS: The GSE117247, GSE32979, and GSE98767 datasets comprising a total of 32 cSCC samples and 31 normal skin tissue samples were obtained from the National Center for Biotechnology Information Gene Expression Omnibus database. Differentially expressed genes (DEGs) were identified and underwent pathway enrichment analyses with the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes (KEGG). A putative DEG protein-protein interaction (PPI) network was also established that included hub genes. The expression of CDK1, MAD2L1, BUB1 ans CDC20 were examined in the study. RESULTS: A total of 335 genes were identified, encompassing 219 found to be upregulated and 116 genes that were downregulated in cSCC, compared to normal tissue. Enriched functions of these DEGs were associated with Ephrin receptor signaling and cell division; cytosol, membrane, and extracellular exosomes; ATP-, poly(A) RNA-, and identical protein binding. We also established a PPI network comprising 332 nodes and identified KIF2C, CDC42, AURKA, MAD2L1, MYC, CDK1, FEN1, H2AFZ, BUB1, BUB1B, CKS2, CDC20, CCT2, ACTR2, ACTB, MAPK14, and HDAC1 as candidate hub genes. The expression of CDK1 are significantly higher in the cSCC tissues than that in normal skin. CONCLUSIONS: The DEGs identified in this study are potential therapeutic targets and biomarkers for cSCC. CDK1 is a gene closely related to the occurrence and development of cSCC, which may play an important role. Bioinformatics analysis shows that it is involved in the important pathway of the pathogenesis of cSCC, and may be recognized and applied as a new biomarker in the future diagnosis and treatment of cSCC.

Molecular Characterization of a Novel Integrative Conjugative Element ICEHpa1 in Haemophilus parasuis.

ICEHpa1 was identified in the genome of a serovar 8 Haemophilus parasuis ST288 isolate YHP170504 from a case of swine lower respiratory tract infection. The aim of the present study was to characterize the integrative conjugative element ICEHpa1 and its multiresistance region. Susceptibility testing was determined by broth microdilution and the complete ICEHpa1 was identified by WGS analysis. The full sequence of ICEHpa1 was analyzed with bioinformatic tools. The presence of ICEHpa1, its circular intermediate and integration site were confirmed by PCR and sequence analysis. Transfer of ICEHpa1 was confirmed by conjugation. ICEHpa1 has a size of 68,922 bp with 37.42% GC content and harbors 81 genes responsible for replication and stabilization, transfer, integration, and accessory functions, as well as seven different resistance genes [bla Rob- 3, tet(B), aphA1, strA, strB, aac(6)'-Ie-aph(2')-Ia, and sul2]. Conjugation experiments showed that ICEHpa1 could be transferred to H. parasuis V43 with frequencies of 6.1 × 10-6. This is the first time a multidrug-resistance ICE has been reported in H. parasuis. Seven different resistance genes were located on a novel integrative conjugative element ICEHpa1, which suggests that the ICEHpa1 is capable of acquiring foreign genes and serving as a carrier for various resistance genes.

CpxR regulates the colistin susceptibility of Salmonella Typhimurium by a multitarget mechanism.

BACKGROUND: The two-component signalling systems PmrAB and PhoPQ of Salmonella have been extensively studied with regard to colistin resistance. We previously showed that overexpressed CpxR could significantly increase the colistin susceptibility (16-fold compared with the WT strain) of Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) through PmrAB and PhoPQ. OBJECTIVES: To identify the potential target genes of CpxR in PmrAB- and PhoPQ-related signalling pathways. METHODS: His6-CpxR was prokaryotically expressed and purified by Ni-NTA resin affinity chromatography. ß-Galactosidase activity assays were conducted to investigate whether CpxR could regulate the promoters of colistin resistance-related genes (CRRGs). Electrophoretic mobility shift assays (EMSAs) were used to further detect His6-CpxR complexes with promoters of CRRGs. RESULTS: We demonstrated for the first time (to the best of our knowledge) that CpxR and the AcrAB-TolC efflux pump have reciprocal effects on CRRG transcription. Additionally, CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by binding directly to the promoters of phoPQ, pmrC, pmrH and pmrD at the CpxR box-like sequences or indirectly through other regulators including pmrAB and mgrB. CONCLUSIONS: CpxR could regulate the colistin susceptibility of Salmonella Typhimurium by a multitarget mechanism.

Characterization of the IncHI2 plasmid pTW4 harboring tet(M) from an isolate of Escherichia coli ST162.

To investigate the genetic features and biological costs of the plasmid pTW4 harboring tet(M) in an isolate of Escherichia coli ST162 from a duck. The complete nucleotide sequence of plasmid pTW4 was determined. The characteristics of plasmid pTW4 in E. coli were investigated by stability and direct competition assays. pTW4 is an IncHI2-type plasmid that contained the resistant genes tet(M), floR, strAB, sul2, rmtB, and blaCMY-2. Tet(M) is located in the composite transposon Tn6539 within the multidrug resistant (MDR) region on this plasmid. Furthermore, the resistance gene rmtB and blaCMY-2 were found outside the MDR region. The plasmid pTW4 remained stable in the host strain E. coli J53 after passage under an antibiotic-free environment for 7 days. However, the strain E. coli J53/pTW4 showed a fitness disadvantage of 6% per ten generations in the process of growth competition with E. coli J53. In conclusion, the plasmid pTW4, a mobile MDR vehicle, may promote the dissemination of tet(M), floR, rmtB, strAB, sul2, and blaCMY-2 among bacteria and then, but it appears to confer growth disadvantage to the host.

CpxR overexpression increases the susceptibility of acrB and cpxR double-deleted Salmonella enterica serovar Typhimurium to colistin.

Background: Colistin has been used as the last therapeutic resort for treatment of MDR Gram-negative bacteria infections in humans. The two-component system CpxAR has been reported to contribute to the MDR of bacteria. There may be a more complex network mediated by CpxAR contributing to colistin susceptibility than previously understood. Methods: A series of AcrB or CpxR deletion mutants of a multidrug-susceptible standard strain of Salmonella enterica serovar Typhimurium (Salmonella Typhimurium) was constructed in our previous study. MICs of colistin were determined by the 2-fold serial broth microdilution method. Time-kill and survival assays were carried out with various concentrations of colistin. Growth curves and starvation survival were measured by OD600 or cfu count in LB and M9-glucose (0.2%) minimum media. Quantitative RT-PCR was used to determine the mRNA expression levels of target genes. Results: The results showed that the MIC of colistin for the CpxR-overexpressed strain JSΔacrBΔcpxR::kan/pcpxR was dramatically decreased (0.05 mg/L) by 16-fold compared with JS (0.8 mg/L) and JSΔacrBΔcpxR::kan (0.8 mg/L). Colistin time-kill and survival assays showed that JSΔacrBΔcpxR::kan/pcpxR was more susceptible to colistin (0.05 mg/L), but had a considerably higher survivability regarding prolonged starvation stress compared with JSΔacrBΔcpxR::kan. Furthermore, the expression levels of colistin resistance-related genes (phoP, phoQ, pmrB, pmrC, pmrH and pmrD) were found to be remarkably down-regulated and the negative regulatory protein mgrB was significantly up-regulated. Conclusions: This study demonstrated that CpxR may regulate the colistin susceptibility of Salmonella Typhimurium through the PmrAB and PhoPQ regulatory systems.

Identification and prevalence of RND family multidrug efflux pump oqxAB genes in Enterococci isolates from swine manure in China.

PURPOSE: The resistance/nodulation/cell division (RND) family multidrug efflux pump, OqxAB, has been identified as one of the leading mechanisms of plasmid-mediated quinolone resistance and has become increasingly prevalent among Enterobacteriaceae in recent years. However, oqxAB genes have not yet been reported in Enterococcus isolates. The aim of the present study was to identify the oqxAB genes and investigate their prevalence among Enterococcus from swine manure in China. METHODOLOGY: The oqxAB genes were screened in 87 Enterococcus isolates by PCR. The transferability of the oqxAB genes in Enterococcus was determined by conjugation experiments. The genetic environment of oqxAB genes was investigated by cloning experiments, PCR mapping and sequencing. RESULTS: A high prevalence (86.2 %) of olaquindox resistance was observed in Enterococcus and 98.9 % isolates exhibited multidrug-resistance phenotypes. The occurrence of oqxA and oqxB in Enterococcus was also high (79.3 and 65.5 %, respectively). Sequence analysis of the cloned fragment indicated that the oqxAB cassette was linked to an incomplete Tn5 transposon containing aph(3')-IIa and flanked by IS26 [IS26-oqxAB-IS26-aph(3')-IIa]. The oqxAB-aph(3')-IIa-positive transconjugant or transformant showed resistance or reduced susceptibility to enrofloxacin, ciprofloxacin, olaquindox, mequindox, florfenicol, neomycin and kanamycin. CONCLUSION: This is the first time that the oqxAB genes have been identified in Enterococcus faecalis from swine manure. The genetic linkage of oqxAB-aph(3')-IIa in Enterococcus has not been described before. The high prevalence of oqxAB genes in Enterococcus suggests that it may constitute a reservoir for oqxAB genes and pose a potential threat to public health.