Weighted gene co-expression network analysis of hub genes in lung adenocarcinoma.

Lung adenocarcinoma (LUAD) is a tumor with high incidence. This study aimed to identify the central genes of LUAD. LUAD were analyzed by weighted gene co-expression network (WGCNA), and differentially expressed genes (DEGs) were identified. Samples were obtained from The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression (GTEx) databases and included 515 LUAD samples and 347 normal samples. The WGCNA algorithm generated a total of 10 modules. The top 2 modules (MEturquoise and MEblue) with the highest correlation to LUAD were selected. Ten Hub genes (IL6, CDH1, PECAM1, SPP1, THBS1, HGF, SNCA, CDH5, CAV1, and DLC1) were screened in the intersecting genes of DEGs and WGCNA (MEturquoise and MEblue). Only SPP1 was correlated with LUAD poor survival, indicating that SPP1 may be a key Hub gene for LUAD. The competing endogenous RNA (ceRNA) network was constructed to analyze the regulatory relationship of Hub genes, and SPP1 may be directly regulated by 4 microRNAs (miRNAs) and indirectly regulated by 49 long noncoding RNAs (lncRNAs).

Continuous changes in biological levels of complete blood count in a high altitude area of China.

OBJECTIVES: We aimed to establish a new reference interval of blood cell parameters by classifying and counting blood Cells of 16- to 85-year-old healthy volunteers and observing continuous changes with age. METHODS: We analyzed the blood cell parameters of 42,678 cases (men, 24,406; women, 18,272), and compared the blood cell parameters of men and women in different age groups using an independent samples t-test. Using limits of 2.5%-97.5%, a 90% confidence interval was used to develop new reference intervals. RESULTS: Counts of blood cell parameters, including white blood Cells, neutrophils, lymphocytes, monocytes, eosinophils, basophils, red blood Cells, hemoglobin, hematocrit, distribution width of red blood Cells and platelets, were found to differ between men and women in different age groups. These parameters were used to establish a new reference interval of blood Cells. CONCLUSION: The blood cell parameters of both men and women changed with increasing age. The reference interval that we established will provide more accurate basic evidence for clinical diagnosis and treatment of diseases.

Age-related trends in lipid levels: a large-scale cross-sectional study of the general Chinese population.

OBJECTIVES: This study aimed to investigate the dynamic trends in total cholesterol (TC), triglyceride (TG), high-density lipoprotein cholesterol (HDL-C) and low-density lipoprotein cholesterol (LDL-C) levels with ageing. DESIGN: A Chinese population-based cross-sectional study. SETTING: A physical examination centre of a general hospital. PARTICIPANTS: Adult subjects (178 167: 103 461 men and 74 706 women) without a known medical history or treatments that affect lipid metabolism. MAIN OUTCOME MEASURES: Dynamic trends in the above-mentioned lipid parameters with ageing were explored; turning points of age were established using age stratification and validated by fitted multivariate linear regression modelling. RESULTS: Age was found to be an independent factor extensively associated with lipid levels in both sexes when adjusted for serum glucose, body mass index, lifestyle, drinking and smoking. Age was positively associated with TC, logarithm-transformed TG (LnTG) and LDL-C levels in men ≤40, ≤40 and ≤60 years old (yo) and in women ≤60, ≤70 and ≤60 yo, respectively. Conversely, age correlated negatively with TC, LnTG and LDL-C levels in men ≥61, ≥41 and ≥61 yo and in women ≥61, ≥71 and ≥61 yo, respectively. TC, TG and LDL-C levels in women were initially lower than those in men but surpassed those in men in 51-55, 61-65 and 51-55 yo age groups. The trends in HDL-C levels with age were relatively irregular, although HDL-C levels in women were higher than in men for all age groups. CONCLUSIONS: The definition of dyslipidaemia, the atherosclerotic cardiovascular disease risk assessment and the initiation/goals of statin therapy should fully consider age-related trends in lipid levels and sex differences.

Correlation between Prognostic Nutritional Index, Glasgow Prognostic Score, Systemic Inflammatory Response, and TNM Staging in Colorectal Cancer Patients.

Background: Various biomarkers have been shown to assess and diagnose colorectal cancer in some researchers. Three indicators including PNI, SIR, GPS were used to predict the outcome for a variety of cancers in existing studies. However, few studies have analyzed the relationship between these biomarkers and different TNM staging. The aim of this study was to investigate the relationship between biomarkers and TNM staging and metastasis of CRC.Patients and methods: Three hundred fifty-five eligible patients were included who were diagnosed with CRC from October 2012 to October 2018 in People's Hospital of Yuxi City. Firstly, we separately calculated PNI, SIR markers and GPS in these patients. Next, the relationship between PNI and GPS with clinical factors were evaluated. Finally, the relationship between TNM staging and tumor metastasis was analyzed.Results: Our results demonstrate that there were statistical differences between PNI and TNM staging, distance metastasis, NLR, PLR, LMR, GPS, CEA, CA199, ALB, L, N, M, PLT, Hb, CRP. GPS with age, TNM staging, distance metastasis, NLR, CA199, ALB, N, CRP have statistical differences. PNI is associated with SIR in patients with CRC, and in which PNI is negatively proportional to NLR and PLR, but positively proportional to LMR.Conclusion: We attempt to combine PNI, SIR, GPS with TNM staging, and the results showed that the three indicators were closely related to TNM staging. Therefore, they can assist in the diagnosis of CRC and are closely related to TNM staging. Detection of three indicators is of important clinical value in the evaluation of TNM staging and metastasis prediction.

Identification of novel variants in MYO15A, OTOF, and RDX with hearing loss by next-generation sequencing.

BACKGROUND: Nonsyndromic hearing loss (NSHL) is the most common sensorineural disorder and one of the most common human defects. Autosomal recessive inheritance accounts for a huge percentage of familial cases. Next-generation sequencing (NGS) is a powerful molecular diagnostic strategy for NSHL. The combination of a microarray gene chip and NGS can better delineate the etiology and genetic cause of deafness in many cases. METHODS: One hundred and thirty-one unrelated students with NSHL who attend a special education school in Yunnan Province were recruited. Firstly, four common deafness-related genes (GJB2, GJB3, SLC26A4, and mtDNA 12S rRNA) were evaluated for mutations using a microarray kit. Furthermore, 227 known human deafness genes were sequenced to identify the responsible genetic variant of the proband in three Chinese families with autosomal recessive hearing loss. The mutational status of family members of the probands was validated by Sanger sequencing. RESULTS: Five novel variants were found in three families using NGS. In family 1, we identified compound heterozygosity at the MYO15A (OMIM, #600316), including an duplication variant c.3866dupC, p.His1290Alafs*25 and a 3-bp deletion (c.10251_10253del, p.Phe3420del), resulting in protein length changes and premature protein truncation, respectively. In family 2, two affected siblings from a consanguineous Chinese Dai family harbored an c.1274G>C, p.Arg425Pro missense variant in the OTOF (OMIM, #601071). In family 3, we identified compound heterozygosity for c.129_130del, p.His43Glnfs*28 and c.76_79del, p.Lys26* in the RDX gene (OMIM, #611022). CONCLUSION: Five novel variants were found in three families with NSHL. Our findings extend the mutational spectrum in deafness-related genes and will help physicians in better understanding the etiology of hearing loss.

Effect of adjuvant therapy with electroacupuncture on bone turnover markers and interleukin 17 in patients with rheumatoid arthritis.

OBJECTIVE: To evaluate the effect of electroacupuncture as an adjuvant treatment with first-line medications on bone metabolism biomarkers and interleukin-17 (IL-17) in the peripheral blood of patients with rheumatoid arthritis (RA). METHODS: Sixty RA patients were randomized into three groups. The control group was treated with methotrexate plus leflunomide (MTX+LEF), the acupuncture group was treated with simple needling plus MTX + LEF, and the patients in the electroacupuncture (EA) group were treated with EA plus MTX + LEF. EA or acupuncture was applied every other day for a total of 10 times over a treatment period of 8 weeks. RESULTS: In all three treatment groups, serum levels of the bone metabolism markers PICP, N-MID, and B-ALP were elevated and the concentrations of the inflammatory markers ß-CTx, IL-17, CRP, and TRACP-5b were reduced after treatment. These differences were significant for the EA group but not the other groups (P < 0.05). CONCLUSION: EA could effectively reduce the suffering and improve the quality of life of RA patients. It is a promising adjuvant therapy for enhancing the effectiveness of clinical therapeutics.

Differential analysis of disease risk assessment using binary logistic regression with different analysis strategies.

Objective To investigate the importance of controlling confounding factors during binary logistic regression analysis. Methods Male coronary heart disease (CHD) patients (n = 664) and healthy control subjects (n = 400) were enrolled. Fourteen indexes were collected: age, uric acid, cholesterol, triglyceride, high density lipoprotein cholesterol, low density lipoprotein cholesterol, apolipoprotein A1, apolipoprotein B100, lipoprotein a, homocysteine, total bilirubin, direct bilirubin, indirect bilirubin, and γ-glutamyl transferase. Associations between these indexes and CHD were assessed by logistic regression, and results were compared by using different analysis strategies. Results 1) Without controlling for confounding factors, 14 indexes were directly inputted in the analysis process, and 11 indexes were finally retained. A model was obtained with conflicting results. 2) According to the application conditions for logistic regression analysis, all 14 indexes were weighed according to their variances and the results of correlation analysis. Seven indexes were finally included in the model. The model was verified by receiver operating characteristic curve, with an area under the curve of 0.927. Conclusions When binary logistic regression analysis is used to evaluate the complex relationships between risk factors and CHD, strict control of confounding factors can improve the reliability and validity of the analysis.

Higher HbA1c and/or glucose levels alter the association patterns between glycated hemoglobin and fasting glucose levels.

AIMS: To verify the correlations between HbA1c and fasting glucose levels. METHODS: A cross-sectional study with 14,249 Chinese subjects. Objective was evaluated in pooled, age-stratified, HbA1c and fasting glucose-stratified populations. RESULTS: In pooled populations, the Pearson correlation coefficients (PCCs) of males and females were 0.684 (P < 0.001) and 0.800 (P < 0.001), respectively. HbA1c and fasting glucose maintained significant correlations within the group with HbA1c < 6.5% and glucose <7.0 mmol/L and the group with HbA1c ≥ 6.5% and glucose ≥7.0 mmol/L in both males (PCC: 0.342, P < 0.001; and PCC: 0.765, P < 0.001, respectively) and females (PCC: 0.318, P < 0.001 and PCC: 0.788, P < 0.001, respectively). The slopes increased from the group with HbA1c < 6.5% and glucose <7.0 mmol/L to the group with HbA1c ≥ 6.5% and glucose ≥7.0 mmol/L in both males (0.26-0.44) and females (0.31-0.46). Linear regression analysis showed that fasting glucose and age were two common factors positively associated with HbA1C, and red blood cell count and red cell distribution width were two common factors negatively associated with HbA1c in both males and females with HbA1c < 6.5% and glucose <7.0 mmol/L. The correlations changed dramatically in the groups with HbA1c ≥ 6.5% and glucose <7.0 mmol/L and HbA1c < 6.5% and glucose ≥7.0 mmol/L. CONCLUSIONS: High HbA1c and fasting glucose levels greatly altered the associations between HbA1c, glucose and age.

Combination of susceptibility gene and traditional risk factors might enhance the performance of coronary heart disease screening strategy.

Coronary heart disease (CHD) associated risk factors and susceptibility genes were studied in parallel for decades, however, the combination of the classic CHD risk factors and genetic risk factors has been rarely studied. Previously; we reported that a single nucleotide polymorphism (SNP) in the stromal cell-derived factor 1 (SDF-1) gene was associated with CHD risk; in addition, we also established a CHD screening strategy using traditional CHD risk factors as independent variables. To explore how to combine genetic factors and traditional risk factors in CHD screening strategy, the CHD probabilities were tested in 218 males and 121 females according to their stromal cell-derived factor 1 (SDF-1) genotypes using CHD screening equations we reported previously. The genotypes had not altered the distribution characteristics of age, high-density lipoprotein cholesterol (HDL-C), triglyceride (TG), lipoprotein(a) (LP(a)), homocysteine (HCY) and total bilirubin (TBil) in males and age, HDL-C, HCY and γ-glutamyl transpeptidase (GGT) in females among genotypes. However, the mean CHD probability of subjects with G/G genotype was significantly higher than that of subjects with A/A genotype (0.51 ± 0.35 vs. 0.31 ± 0.31, P = 0.035). The mean CHD probability of subjects with G homozygous and G heterozygote was 0.48 ± 0.34 which displayed a difference trend to that of subjects with A homozygous (0.31 ± 0.31, P = 0.059). Our data suggested that genetic risk factors might be used as a classification standard to improve current CHD screening strategies.

Regulation of crucial enzymes and transcription factors on 2-phenylethanol biosynthesis via Ehrlich pathway in Saccharomyces cerevisiae.

2-Phenylethanol (2-PE) is widely used in food, perfume and pharmaceutical industry, but lower production in microbes and less known regulatory mechanisms of 2-PE make further study necessary. In this study, crucial genes like ARO8 and ARO10 of Ehrlich pathway for 2-PE synthesis and key transcription factor ARO80 in Saccharomyces cerevisiae were re-regulated using constitutive promoter; in the meantime, the effect of nitrogen source in synthetic complete (SC) medium with L-phenylalanine (L-Phe) on Aro8/Aro9 and Aro10 was investigated. The results showed that aromatic aminotransferase activities of ARO8 over-expressing strains were seriously inhibited by ammonia sulfate in SC + Phe medium. Flask fermentation test demonstrated that over-expressing ARO8 or ARO10 led to about 42 % increase in 2-PE production when compared with the control strain. Furthermore, influence of transcription factors Cat8 and Mig1 on 2-PE biosynthesis was explored. CAT8 over-expression or MIG1 deletion increased in the transcription of ARO9 and ARO10. 2-PE production of CAT8 over-expressing strain was 62 % higher than that of control strain. Deletion of MIG1 also led to 2-PE biosynthesis enhancement. The strain of CAT8 over-expression and MIG1 deletion was most effective in regulating expression of ARO9 and ARO10. Analysis of mRNA levels and enzyme activities indicates that transaminase in Ehrlich pathway is the crucial target of Nitrogen Catabolize Repression (NCR). Among the engineering strains, the higher 3.73 g/L 2-PE production in CAT8 over-expressing strain without in situ product recovery suggests that the robust strain has potentiality for commercial exploitation.

Scarless gene deletion in methylotrophic Hansenula polymorpha by using mazF as counter-selectable marker.

With increasing application of Hansenula polymorpha in fundamental research and biotechnology, many more genetic manipulations are required. However, these have been restricted for the finiteness of selectable markers. Here, MazF, a toxin protein from Escherichia coli, was investigated as a counter-selectable marker in H. polymorpha. The lethal effect of MazF on yeast cells suggested that it is a candidate for counter-selection in H. polymorpha. Markerless or scarless gene deletion in H. polymorpha was conducted based on selectable markers cassette mazF-zeoR, in which the zeocin resistance cassette and mazF expression cassette were used as positive and counter-selectable markers, respectively. For markerless deletion, the target region can be replaced by CYC1TT via two-step homologous recombination. For scarless deletion, the innate upstream region (5'UP) of target genes rather than CYC1TT mediates homologous recombination to excise both selectable markers and 5' sequence of target genes. Moreover, scarless deletion can be accomplished by using short homologous arms for the effectiveness of mazF as a counter-selectable marker. The applicability of the strategies in markerless or scarless deletion of PEP4, LEU2, and TRP1 indicates that this study provides easy, time-efficient, and host-independent protocols for single or multiple genetic manipulations in H. polymorpha.

Speciation of chromium in chromium yeast.

High-performance liquid chromatography was used to separate Cr(III) and Cr(VI) in samples with detection by inductively coupled plasma mass spectrometry(ICP-MS). The separation was achieved on a weak anion exchange column. The mobile phase was pH 7.0 ammonium nitrate solution. The redox reaction between Cr(III) and Cr(VI) was avoided during separation and determination. This separation method could be used to separate the samples with large concentration differences between Cr(III) and Cr(VI). The alkaline digestion was used to extract chromium in solid sample, which had no effect on the retention time and the peak area of the Cr(VI). However, the conversion of Cr(VI) from Cr(III) was observed during alkaline digestion, which displayed positive relation with the ratio of Cr(III) and Cr(VI) in samples. Both Cr(III) and Cr(VI) contents of chromium yeasts cultured in media with different chromium additions were determined. The spike recoveries of Cr(VI) for chromium yeasts were in the range of 95-108 %.

Secretion expression of SOD1 and its overlapping function with GSH in brewing yeast strain for better flavor and anti-aging ability.

Superoxide dismutase (SOD) is a significant antioxidant, but unlike glutathione (GSH), SOD cannot be secreted into beer by yeast cells during fermentation, this directly leads to the limited application of SOD in beer anti-aging. In this investigation, we constructed the SOD1 secretion cassette in which strong promoter PGK1p and the sequence of secreting signal factor from Saccharomyces cerevisiae were both harbored to the upstream of coding sequence of SOD1 gene, as a result, the obtained strains carrying this cassette successfully realized the secretion of SOD1. In order to overcome the limitation of previous genetic modification on yeast strains, one new comprehensive strategy was adopted targeting the suitable homologous sites by gene deletion and SOD1 + GSH1 co-overexpression, and the new strain ST31 (Δadh2::SOD1 + Δilv2::GSH1) was constructed. The results of the pilot-scale fermentation showed that the diacetyl content of ST31 was lower by 42 % than that of the host, and the acetaldehyde content decreased by 29 %, the GSH content in the fermenting liquor of ST31 increased by 29 % compared with the host. Both SOD activity test and the positive and negative staining assay after native PAGE indicated that the secreted active SOD in the fermenting liquor of ST31 was mainly a dimer with the size of 32,500 Da. The anti-aging indexes such as the thiobarbituric acid and the resistance staling value further proved that the flavor stability of the beer brewed with strain ST31 was not only better than that of the original strain, but also better than that of the previous engineering strains. The multi-modification and comprehensive improvement of the beer yeast strain would greatly enhance beer quality than ever, and the self-cloning strain would be attractive to the public due to its bio-safety.

Contribution of bovine lactoferrin inter-lobe region to iron binding stability and antimicrobial activity against Staphylococcus aureus.

The investigation of the recombinant bovine lactoferrin-derived antimicrobial protein (rBLfA) demonstrates that the inter-lobe region of bovine lactoferrin contributes to iron binding stability and antimicrobial activity against Staphylococcus aureus. rBLfA containing N-lobe (amino acid residues 1-333) and inter-lobe region (residues 334-344) was expressed in Pichia pastoris at shaking flask and fermentor level. The recombinant intact bovine lactoferrin (rBLf) and N-lobe (rBLfN) were expressed in the same system as control. The physical-chemical parameters of rBLfA, rBLfN and rBLf including amino acid residues, molecular weight, isoelectric point, net positive charge and instability index were computed and compared. The simulated tertiary structure and the calculated surface net charge showed that rBLfA maintained original structure and exhibited a higher cationic feature than rBLf and rBLfN. The three proteins showed different iron binding stability and antimicrobial activity. rBLfA released iron in the pH range of 7.0-3.5, whereas rBLfN lost its iron over the pH range of 7.0-4.0 and iron release from rBLf occurred in the pH range of 5.5-3.0. However, the minimum inhibition concentration of rBLfA against S. aureus ATCC25923 was 6.5 micromol/L, compared with 12.5 and 25 micromol/L that of rBLfN and rBLf, respectively. These results revealed that S. aureus was more sensitive to rBLfA than rBLfN and rBLf. It appeared that the strong cationic character of inter-lobe region related positively to the higher anti-S. aureus activity.

Enhancement of biodesulfurization in two-liquid systems by heterogeneous expression of vitreoscilla hemoglobin.

The vgb gene, encoding Vitreoscilla hemoglobin (VHb), was introduced into a specific desulfurization bacterium, Rhodococcus erythropolis LSSE8-1. The VHb-specific spectrum was observed for the recombinant. Compared to the wild type, the strain bearing vgb showed a higher biomass yield and desulfurizing activity.