[Exploration of cystathionine β-synthase and cystathionine γ-lyase gene expression poor prognostic predictive value with the application of bioinformatics data mining in liver cancer]

Objective: To study the relationship between cystathionine β-synthase (CBS) and cystathionine γ-lyase (CTH) genes-related signaling pathways in liver cancer cells. Methods: We conducted a correlation analysis between the clinical features of CBS and CTH gene expression by mining the GEO (Gene Expression Omnibus) and TCGA (The Cancer Genome Atlas) databases of liver cancer. Additionally, liver cancer cell lines were verified by immunoblotting. Results: CBS and CTH expressions were significantly lower in tumors than in non-tumors (P < 0.05). COX regression result showed that CBS was an independent risk factor for the poor prognosis of liver cancer cells (HR=0.65, P = 0.02). A univariate logistic regression analysis was performed on the different tumor stages focusing on the CBS gene, which showed that TNM stage II verses I (P = 0.01, OR=0.50), stage III verses I (P = 0.03, OR=0.56), T stage T2 verses T1 (P < 0.01, OR=0.43), and T3 stage verses T1 (P = 0.02, OR=0.54) were significantly lower in liver cancer. TNM stage III verses I (P = 0.01, OR=0.50), Edmondson stage II verses I (P = 0.03, OR=0.48), stage III verses stage I (P < 0.01, OR=0.30), stage IV verses I (P = 0.03, OR=0.22), and T stage T3 verses T1(P = 0.03, OR=0.22) of the CTH gene expressions were significantly lower in liver cancer. GSEA enrichment analysis result revealed that the signaling pathway most correlated with the expression of CTH and CBS genes in liver cancer cells was cytochrome P450 (CYP450) (FDR Q < 0.01, FWER P < 0.01). Western blot results showed that the expression of the CTH downstream protein CSE was reduced in HCC cell lines such as HLE and Hep3B cells compared with the human immortalized liver cell line HL-7702. Conclusion: CBS and CTH gene expressions are lower in tumor tissue than in normal tissue groups. The CBS gene is an independent risk factor for poor prognosis in stem cell carcinoma. The cytochrome P450 is the signaling pathway most closely related to the CBS and CTH genes.

[Phenotypic and genotypic characteristics of Escherichia coli causing bloodstream and abdominal co-infection]

Objective: To analyze the phenotypic and genotypic characteristics of Escherichia coli causing bloodstream and abdominal co-infection (CoECO), and provide clues for empirical antibiotics treatment. Methods: The strains of Escherichia coli isolated from blood and abdominal samples in the Department of Laboratory Medicine of the First Medical Center of the PLA General Hospital from 2010 to 2020 were retrospectively analyzed. Mass spectrometer was used to identify all of the strains and the minimum inhibitory concentration (MIC) were detected by VITEK 2 Compact. All isolates were sequenced by 2×150 bp double terminal sequencing strategy on the HiSeq X Ten sequencer (Illumina). After the genome sequence was spliced, the single nucleotide polymorphism (SNP) analysis of the strain sequence was performed using kSNP3 software to clarify the homologous relationship between strains. If the strains isolated from two different parts had high homology, they were regarded as the same strain and the case was with CoECO infection. Meanwhile, the multilocus sequence type (MLST) was determined using PubMLST website and resistant genes were screened by CARD website. Results: A total of 70 cases of CoECO infection were screened, including 45 males and 25 females, and aged (59.2±16.3) years old. The 70 CoECO isolates belonged to 35 sequence types (STs). The most prevalent STs included ST38 (n=6), ST 405 (n=6), ST 1193 (n=6) and ST131 (n=5), and other ST types contained less than 5 strains. The homologous relationship among strains was relatively scattered, presenting a sporadic trend as a whole, and only a few strains had a small-scale outbreak. The CoECO isolates showed significantly resistance to ampicillin (91.4%, 64/70), ampicillin/sulbactam (74.3%, 5 2/70), ceftriaxone (72.9%, 51/70), ciprofloxacin (71.4%, 50/70) and levofloxacin (71.4%, 50/70), and high-sensitivity to piperacillin/tazobactam, carbapenems and amikacin. The most prevalent resistant gene was tet (A/B) (70%, 49/70), followed by bla_TEM (58.6%, 41/70), sul1 (55.7%, 40/70), sul2 (54.3%, 38/70), bla_CTX-M-14(25.7%, 18/70), bla_CTX-M-15(17.1%, 13/70), bla_CTX-M-55(15.7%, 11/70), bla_CTX-M-64/65(5.7%, 4/70), bla_CTX-M-27(4.3%, 3/70), mcr-1 (4.3%, 3/70), bla_NDM-5(2.9%, 2/70). Conclusions: CoECO is distributed dispersedly and has no obvious advantage clone. No genotype with obvious advantages was found. Although the strain has a high resistance rate to some antibacterial drugs, the proportion of carrying resistant genes is low, and it has a high sensitivity to some first-line antibacterial drugs.

[Progress in research of etiology of childhood obesity based on interaction between genes and environment]

Childhood obesity is a global public health problem, which can not only endangers children's health, but also might be an important cause of chronic diseases in adulthood. In recent years, with the in-depth development of precision medicine research, more and more research evidences have shown that there are interactions between environmental factors, such as early intrauterine environment, children's diet, physical activity and children's gene factor on the incidence of childhood obesity, which can result in or inhibit the incidence and development of childhood obesity. This paper summarizes the progress in research in this field to reveal the effects and potential mechanisms of genetic factors and environmental factors on the incidence of childhood obesity in order to provide reference for the precise prevention and control of childhood obesity under different genetic backgrounds.

[The study of mitochondrial disorder pedigree associated with FASTKD2 variants and uniparental disomy]

Objective: To analyse the genetic cause of a proband with mitochondrial disease caused by FASTKD2 gene variation and uniparental disomy. Methods: Detailed medical history of a child suspected "mitochondrial disease" were inquired in Peking University First Hospital on November 23, 2017. c.810_820dup homozygous variation in FASTKD2 gene was found by high-throughput sequencing, and her mother had heterozygous variation, but her father didn't have such variation, which didn't conform to the genetic law of variation. Further clinical examinations and molecular genetic tests were carried out. The venous blood of the child and her parents was drawn, and genomic DNA was extracted. Sanger sequencing, polymerase chain reaction (PCR) testing, short tandem repeat (STR) analysis, chromosome microarray analysis and loss of heterozygosity (LOH) genetic relationship analysis were performed on the proband and the parents to determine the variation. Results: The clinical manifestations, physical examination and laboratory examination of the child supported the diagnosis of mitochondrial disease. c.810_820dup(p.Ser274Phefs*8) homozygous variant in FASTKD2 gene was identified. Sanger sequencing indicated that the mother was a heterozygote of the variant, while the father had no such variation, which did not conform to the genetic law. PCR testing and Sanger sequencing review to eliminate sampling errors, PCR amplification and sequencing errors. Non-biological father was excluded by STR analysis. Three large segmental LOH of FASTKD2 gene were found by chromosome microarray analysis, then the LOH relative analysis verified the child was a mixed maternal uniparental disomy of chromosome 2. The child was diagnosed as mitochondrial disease caused by oxidative phosphorylation coupling defect of type 44. Conclusions: In this study, an autosomal recessive mitochondrial disease which does not conform to the genetic law was found, and it was confirmed that this mitochondrial disease family had both pathogenic variation and uniparental disomy phenomenon. It was diagnosed as mitochondrial disease caused by type 44 oxidative phosphorylation coupling defect.

[Progress in application of deep learning in orthodontic diagnosis and treatment]

In recent years, the application of artificial intelligence technology in the field of orthodontics has gradually increased, and deep learning, as a hot direction, has also been rapidly applied in the detection, evaluation, diagnosis, prediction and effect evaluation. At present, deep learning research has the advantages of high efficiency and accuracy, but it also has limitations such as weak interpretability and insufficient data volume. This paper reviewed the proposal and development of deep learning, the application in orthodontic diagnosis and treatment, as well as the limitations and countermeasures of the popularization, and prospect of the future research.

Nomogram Model for Predicting the Risk of Multidrug-Resistant Bacteria Infection in Diabetic Foot Patients

Objective

This study established an individualized nomogram for predicting the risk of multidrug-resistant bacterial (MDRB) infection in patients with the diabetic foot (DF), and providing a reference for clinical prevention and treatment.

Methods

A total of 199 DF patients admitted to the hospital from July 2015 to December 2018 were included in this study. The pathogenic bacteria at the site of infection were detected and the factors affecting the occurrence of MDRB infection in DF patients summarized. The R software was used to draw the nomogram, and the Bootstrap Method used to internally verify the model. The calibration curve and the Harrell’s Concordance Index (C-index) were used to evaluate the predictive effect of the nomogram model.

Results

Logistic regression analysis showed that age, course of diabetes, previous use of antibacterial drugs, types of antibacterial drugs, and osteoporosis were risk factors for multidrug-resistant infections in DF (P<0.05). The area under the receiver operating characteristic curve (AUC, Area Under Curve) of the nomogram model after internal verification was 0.773 (95% CI: 0.704–0.830). The mean absolute error between the predicted probability of infection in the nomogram and the actual occurrence of MDRB was 0.032, indicating that the nomogram model had good forecasting efficiency and stability.

Conclusion

The risk factors for multidrug-resistant infections in DF are age, course of diabetes, previous use of antibacterial drugs, types of antibacterial drugs used, and osteoporosis. The nomogram model drawn on these risk factors has good predictive accuracy and can assist medical staff in formulating targeted infection prevention strategies for patients.

[The diagnostic value of chromosome microarray analysis technique in the genetic causes of children with intellectual disability or global developmental delay]

Objective: To study the value of chromosome microarray analysis (CMA) application in children with developmental delay (DD), intellectual disability (ID), autistic spectrum disorder (ASD) and multiple congenital anomalies (MCA). Methods: Genomic DNA was extracted from peripheral blood samples. Array-based comparative genomic hybridization (array-CGH) analysis and single nucleotide polymorphism array (SNP-array) were performed in 1 320 children with DD/ID, ASD, with or without epilepsy and MCA who were admitted to Peking University First Hospital from 2014 to 2019. The results of genetic etiology test of CMA in children with mental retardation or global DD was summarized. Results: Of 1 320 samples, there were 10 cases of aneuploid abnormality, 6 cases of uniparental disomy and one case of mosaicism, respectively. Pathogenic copy number variations (CNVs) were found in 320 cases and pathogenic CNVs were detected in 23 cases, with a combined detection rate of 26% (343/1 320). CNVs of uncertain clinical significance occurred in 107 cases, accounting for 8.1% (107/1 320). There were 25 cases of possible benign CNVs, accounting for 2% (25/1 320), while benign CNVs were reported in 20 cases, accounting for 1.5% (20/1 320). The detection rate of MCA with DD/ID was 39.8% (130/327). Conclusions: CMA has the advantages of high resolution and covering the whole genome. It can detect the chromosomal abnormalities, microdeletions and duplications seen under the microscope, thus the genetic etiology of children with mental retardation or global DD can be diagnosed.

The relevance of MTHFR C677T, A1298C, and MTRR A66G polymorphisms with response to male infertility in Asians: A meta-analysis

Although published studies have reported the association between MTHFR C677T (rs 1801133), A1298C (rs 1801131), and MTRR A66G (rs1801394) polymorphisms and male infertility in Asian populations, the results are conflicting. In order to accurately evaluate the relevance, a meta-analysis was performed.We searched for potential studies in 4 databases, containing PubMed, ScienceDirect, China National Knowledge Infrastructure (CNKI), and Wanfang database until May 31, 2018. The summarized odds ratio (OR) with 95% confidence intervals (95% CI) were calculated to evaluate the relevance in 5 genetic models. The heterogeneity test, sensitivity analysis, and publication bias test was performed by Review Manager 5.3 software.Overall, 22 case-control studies with 5049 cases and 4157 controls were included in this meta-analysis, which contained 20 studies of MTHFR C677T polymorphism, 12 studies of MTHFR A1298C polymorphism and 4 studies of MTRR A66G polymorphism. The results indicated that MTHFR C677T, A1298C, and MTRR A66G polymorphisms were significantly associated with male infertility in Asian populations (Dominant model: MTHFR CC + CT vs TT: OR = 0.60, 95% CI (0.53, 0.67), P <.00001; MTHFR AA + AC vs CC: OR = 0.62, 95% CI (0.49, 0.79), P = .0001; MTRR AA + AG vs GG: OR = 0.60, 95% CI (0.45, 0.81), P = .001. Recessive model: MTHFR CC vs CT + TT: OR = 0.67, 95% CI (0.61, 0.74), P <.00001; MTHFR AA vs AC + CC: OR = 0.79, 95% CI (0.70, 0.88), P <.0001; MTRR AA vs AG + GG: OR = 0.70, 95% CI (0.56, 0.88), P = .002. Heterozygote model: MTHFR CC vs CT: OR = 0.74, 95% CI (0.67, 0.82), P <.00001; MTHFR AA vs AC: OR = 0.83, 95% CI (0.73, 0.93), P = .002; MTRR AA vs AG: OR = 0.76, 95% CI (0.60, 0.92), P = .02. Homozygote model: MTHFR CC vs TT: OR = 0.48, 95% CI (0.41, 0.56), P <.00001; MTHFR AA vs CC: OR = 0.61, 95% CI (0.39, 0.93), P = .02; MTRR AA vs GG: OR = 0.51, 95% CI (0.36, 0.72), P = .0001. Allele model: MTHFR C vs T: OR = 0.70, 95% CI (0.66, 0.75), P <.00001; MTHFR A vsC: OR = 0.82, 95% CI (0.71, 0.95), P = .01; MTRR A vs G: OR = 0.76, 95% CI (0.66, 0.88), P = .00003). Stratified analyses by geographical location and source of controls showed the same results. Sensitivity analyses indicated that the final consequences of this meta-analysis were stable, and the publication biases test had not found obvious asymmetry.This meta-analysis indicates that MTHFR C677T, A1298C, and MTRR A66G polymorphisms are the risk factors with susceptibility to male infertility in Asians.

Three-dimensional spheroid culture of adipose stromal vascular cells for studying adipogenesis in beef cattle

Protocols designed for the adipogenic differentiation of human and mouse cells are commonly used for inducing the adipogenesis of bovine stromal vascular cells. However, likely due to metabolic differences between ruminant and non-ruminant animals, these methods result in only few cells undergoing complete adipogenesis with minimal lipid droplet accumulation. Here, we discuss the development of an adipogenic differentiation protocol for bovine primary cells through a three-dimensional spheroid culture. Stromal vascular cells derived from bovine intramuscular fat were isolated and stored in liquid nitrogen before culturing. Cells were cultured in hanging drops for 3 days to allow for the formation of spherical structures. The spheroids were then transferred to cell culture plates with endothelial basal medium-2 for 3 days and in Dulbecco's Modified Eagle's Medium (DMEM) supplemented with a standard adipogenic cocktail for 3 additional days, which were then allowed to fully differentiate for 3 days in DMEM supplemented with insulin. Compared with conventional two-dimensional culture, cells in a three-dimensional spheroid culture system had higher adipogenic gene expression and consequently contained more adipocytes with larger lipid droplets. In addition, endothelial induction of spheroids prior to adipogenic differentiation is essential for efficient induction of adipogenesis of bovine stromal vascular cells, mimicking in vivo adipose development. In summary, the newly developed three-dimensional spheroid culture method is an efficient way to induce adipogenic differentiation and study adipose development of cells derived from ruminant animals, which also can be used for studying the role of angiogenesis in adipose development.

Population genetic structure and its implication in the conservation of Schizopygopsis pylzovi in Yellow River as inferred from mitochondrial DNA sequence analysis

To assess the genetic diversity, structure, and population dynamics of Schizopygopsis pylzovi, we examined the changes in mitochondrial DNA sequences (the mtDNA control region and the Cyt b gene; 1835 bp) in 304 individuals from nine populations. The samples were segregated into 112 haplotypes, with high haplotype diversity and low nucleotide diversity. The haplotype diversity was highest in the Minhe (HS) range of Huangshui River and lowest in the Weiyuan (WY) range of Weihe River. Analysis of molecular variance showed that 69.64% of the total genetic variance was contributed by within-the-group variation and 30.36% was contributed by among-the-group variation. Pairwise F_ST revealed significant divergence between the populations. The F_ST between the MT and WY was highest, and that between the YZ and YJ was lowest. The neighbor-joining phylogenetic tree demonstrated that all geographic populations were not monophyletic, but overlapped each other, indicating that the duration of geographical isolation was not long enough or the populations had not yet reached significant genetic isolation or differentiation at the monophyletic level. Tajima's D and Fu's Fs were negative and statistically significant, indicating that S. pylzovi had experienced certain population expansion events, which is consistent with the hypothesis that the headwater area of the Yellow River was dramatically affected by the geological and climatic upheaval during the Quaternary ice age. Our analysis indicated that the management units corresponding to the WY population should be managed and conserved first. In situ conservation is first recommended to protect the original habitat from further destruction.

[Relationship between ER-α36 and Akt in PC12 cells exposed to glucose deprivation]

ER-α36 is a novel 36-kDa variant of ER-α. A large of evidence demonstrated that ER-α36 responded to membrane-initiated estrogen signaling pathways which were involved in the physiological and pathological process in many kinds of cells. In this study, knock-down of ER-α36 expression in pheochromocytoma (PC12) cells (named as PC12-36L cells) by using the shRNA method was used to evaluate the relationship between ER-α36 and Akt in neurons under glucose deprivation. The effect of ER-α36 on outgrowth of PC12 cells, as well as the neuroprotective effect of ER-α36 on injured PC12 cells exposed to glucose deprivation was observed by using MTT assay, Western blot and Annexin V/PI staining et al. The results showed that, (1) Glucose deprivation induced by MEM treatment for 6 h reduced survival rate and increased apoptotic rate in PC12 cells significantly compared to control group (P < 0.01); and it produced a decrease in the expression of Glut-4 protein (P < 0.01); (2) The expression level of ER-α36 was decreased significantly at 3 h of glucose deprivation, and then increased, while phosphorylation of Akt participated in the glucose deprivation was increased at first and then reduced; LY294002 (PI3K inhibitor) contributed to decreased expression of ER-α36, and suppressed the activation of Akt; (3) The rate of apoptosis was significantly increased in PC12-36L cells after glucose deprivation compared with that in wild type PC12 cells (P < 0.01). Furthermore, phosphorylation of Akt was decreased and Caspase-3 was increased by glucose deprivation in PC12-36L cells compared with those in wild type PC12 cells. The study reveals that phosphorylation of Akt is associated with ER-α36 in PC12 cells exposed to glucose deprivation, and both are involved in the regulation of stress responses.

[Diverse expression of ER-α36, a novel variant of ER-α, in hippocampus and cortex of neonatal and adult rats]

ER-α36, a novel variant of ER-α, is expressed in breast, uterus, digestive tract, respiratory tract etc. The aim of the present study was to investigate the distribution and expression of ER-α36 in the central nervous system (CNS). Here, we comparatively analyzed the expression pattern of ER-α36 in the hippocampus and cortex of neonatal (1-day-old) and adult (12-week-old) Sprague-Dawley (SD) rats by using immunohistochemistry/immunocytochemistry analysis and Western blot. The results showed that ER-α36 was expressed both in hippocampus and cortex of adult rats, but mainly distributed in pyramidal neurons. ER-α36 was mainly located on the cytomembrane of hippocampal and cortical neurons from neonatal rats. Compared with the cortical neurons, the hippocampal neurons showed lower ER-α36 protein expression in the neonatal rats, but exhibited higher level of ER-α36 in the adult rats. Furthermore, the adult rats showed higher levels of ER-α36 expression in both hippocampus and cortex compared with the neonatal rats. These results suggest that ER-α36 might be involved in the regulation of membrane-initiated estrogen signaling throughout the postnatal development of diverse brain regions, and thus will be a potential target for the treatment of degenerative diseases in nervous system.

[Knock-down of ERα36 impacts the expression of differentiation protein in PC12 cells]

ERα36 is a novel subtype of estrogen receptor alpha (ERα) known to play an important role in breast cancer development and widely expressed in normal tissues and cells including nerve cells. However, the expression and function of ERα36 in nerve cells have not been well elucidated. To examine whether ERα36 is involved in differentiation of nerve cells, the differentiated and undifferentiated PC12 (PC12D and PC12unD) cells were used. Transfection of ERα36-shRNA plasmid into PC12 cells was performed to establish the ERα36 gene knock-down cells model. Immunocytofluorescence and Western blot were used to analyze the expression of Nestin, β-tubulinIII and Neu-N in the PC12 cells. The results showed that ERα36 was expressed in both cell types. Compared with PC12D cells, PC12unD cells showed higher expression of Nestin and lower expression of β-tubulinIII. ERα36-shRNA-mediated knock-down of ERα36 expression enhanced the expression of β-tubulinIII and Neu-N, but attenuated Nestin expressions in PC12unD cells; ERα36 knock-down in PC12D cells mediated Nestin, β-tubulinIII and Neu-N in a contrary manner. These results indicate that ERα36 knock-down appear to be associated with inhibiting differentiation in differentiated cells and promoting differentiation in undifferentiated cells, suggesting that ERα36 is a dual regulator in nerve differentiation.

Highly active carbonaceous nanofibers: a versatile scaffold for constructing multifunctional free-standing membranes

Translating the unique characteristics of individual nanoscale components into macroscopic materials such as membranes or sheets still remains a challenge, as the engineering of these structures often compromises their intrinsic properties. Here, we demonstrate that the highly active carbonaceous nanofibers (CNFs), which are prepared through a template-directed hydrothermal carbonization process, can be used as a versatile nanoscale scaffold for constructing macroscopic multifunctional membranes. In order to demonstrate the broad applicability of the CNF scaffold, we fabricate a variety of CNF-based composite nanofibers, including CNFs-Fe(3)O(4), CNFs-TiO(2), CNFs-Ag, and CNFs-Au through various chemical routes. Importantly, all of them inherit unique dimensionality (high aspect ratio) and mechanical properties (flexibility) of the original CNF scaffolds and thus can be assembled into macroscopic free-standing membranes through a simple casting process. We also demonstrate the wide application potentials of these multifunctional composite membranes in magnetic actuation, antibiofouling filtration, and continuous-flow catalysis.