Selection of reference genes in liproxstatin-1-treated K562 Leukemia cells via RT-qPCR and RNA sequencing.

BACKGROUND: Reverse transcription quantitative polymerase chain reaction (RT-qPCR) can accurately detect relative gene expression levels in biological samples. However, widely used reference genes exhibit unstable expression under certain conditions. METHODS AND RESULTS: Here, we compared the expression stability of eight reference genes (RPLP0, RPS18, RPL13, EEF1A1, ß-actin, GAPDH, HPRT1, and TUBB) commonly used in liproxstatin-1 (Lip-1)-treated K562 cells using RNA-sequencing and RT-qPCR. The expression of EEF1A1, ACTB, GAPDH, HPRT1, and TUBB was considerably lower in cells treated with 20 µM Lip-1 than in the control, and GAPDH also showed significant downregulation in the 10 µM Lip-1 group. Meanwhile, when we used geNorm, NormFinder, and BestKeeper to compare expression stability, we found that GAPDH and HPRT1 were the most unstable reference genes among all those tested. Stability analysis yielded very similar results when geNorm or BestKeeper was used but not when NormFinder was used. Specifically, geNorm and BestKeeper identified RPL13 and RPLP0 as the most stable genes under 20 µM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable under 10 µM Lip-1 treatment. TUBB and EEF1A1 were the most stable genes in both treatment groups according to the results obtained using NormFinder. An assumed most stable gene was incorporated into each software to validate the accuracy. The results suggest that NormFinder is not an appropriate algorithm for this study. CONCLUSIONS: Stable reference genes were recognized using geNorm and BestKeeper but not NormFinder. Overall, RPL13 and RPLP0 were the most stable reference genes under 20 µM Lip-1 treatment, whereas RPL13, EEF1A1, and TUBB were the most stable genes under 10 µM Lip-1 treatment.

Hyb-Seq provides new insights into the phylogeny and evolution of the Chrysanthemum zawadskii species complex in China.

A species complex is an assemblage of closely related species with blurred boundaries, and from which species could arise from different speciation processes and/or a speciation continuum. Such a complex can provide an opportunity to investigate evolutionary mechanisms acting on speciation. The Chrysanthemum zawadskii species complex in China, a monophyletic group of Chrysanthemum, consists of seven species with considerable morphological variation, diverse habitats and different distribution patterns. Here, we used Hyb-Seq data to construct a well-resolved phylogeny of the C. zawadskii complex. Then, we performed comparative analyses of variation patterns in morphology, ecology and distribution to investigate the roles of geography and ecology in this complex's diversification. Lastly, we implemented divergence time estimation, species distribution modelling and ancestral area reconstruction to trace the evolutionary history of this complex. We concluded that the C. zawadskii complex originated in the Qinling-Daba mountains during the early Pliocene and then spread west and northward along the mountain ranges to northern China. During this process, geographical and ecological factors imposing different influences resulted in the current diversification and distribution patterns of this species complex, which is composed of both well-diverged species and diverging lineages on the path of speciation.

GSTT1 and GSTM1 polymorphisms predict treatment outcome for breast cancer: a systematic review and meta-analysis.

Observational studies have reported controversial results on the association between GSTT1 and GSTM1 genotypes and treatment outcome of breast cancer. The purpose of this study is to evaluate the association between GSTT1 and GSTM1 and treatment outcome in breast cancer patients. Eligible studies were searched in PubMed, EMBASE, Cochrane Library, and China National Knowledge Infrastructure databases. A random-effect model or fixed-effect model was used to calculate the overall combined risk estimates. Twenty-one studies with a total of 4990 patients were included in this meta-analysis. The GSTM1 null genotype (odds ratio (OR) = 1.33, 95 % confidence interval (CI) 1.01-1.75, P = 0.046) and GSTT1/GSTM1 double null genotype (OR = 2.22, 95 % CI 1.02-4.84, P = 0.045) were significantly associated with an increased tumor response. A reduced overall survival (hazard ratio (HR) = 0.84, 95 % CI 0.72-0.98, P = 0.024) was observed in GSTM1 null genotype, especially in mixed descent (HR = 0.77, 95 % CI 0.61-0.96, P = 0.018) and large sample size (HR = 0.85, 95 % CI 0.72-0.99, P = 0.033). Evidence of publication bias was observed in GSTM1 genotype rather than in GSTT1 genotype. This meta-analysis suggests that GSTM1 null and GSTT1/GSTM1 double null polymorphisms might be significantly associated with an increased tumor response. However, the GSTM1 null genotype might be significantly associated with a reduced overall survival. Future studies are warranted to confirm these findings.

Overexpression of Porcine Beta-Defensin 2 Enhances Resistance to Actinobacillus pleuropneumoniae Infection in Pigs.

To reduce the need for antibiotics in animal production, alternative approaches are needed to control infection. We hypothesized that overexpression of native defensin genes will provide food animals with enhanced resistance to bacterial infections. In this study, recombinant porcine beta-defensin 2 (PBD-2) was overexpressed in stably transfected PK-15 porcine kidney cells. PBD-2 antibacterial activities against Actinobacillus pleuropneumoniae, an important respiratory pathogen causing porcine contagious pleuropneumonia, were evaluated on agar plates. Transgenic pigs constitutively overexpressing PBD-2 were produced by a somatic cell cloning method, and their resistance to bacterial infection was evaluated by direct or cohabitation infection with A. pleuropneumoniae. Recombinant PBD-2 peptide that was overexpressed in the PK-15 cells showed antibacterial activity against A. pleuropneumoniae. PBD-2 was overexpressed in the heart, liver, spleen, lungs, kidneys, and jejunum of the transgenic pigs, which showed significantly lower bacterial loads in the lungs and reduced lung lesions after direct or cohabitation infection with A. pleuropneumoniae. The results demonstrate that transgenic overexpression of PBD-2 in pigs confers enhanced resistance against A. pleuropneumoniae infection.

Incorporating eco-evolutionary information into species distribution models provides comprehensive predictions of species range shifts under climate change.

As climate changes increasingly influence species distributions, ecosystem functions, and biodiversity, the urgency to understand how species' ranges shift under those changes is great. Species distribution models (SDMs) are vital approaches that can predict species distributions under changing climates. However, SDMs based on the species' current occurrences may underestimate the species' climatic tolerances. Integrating species' realized niches at different periods, also known as multi-temporal calibration, can provide an estimation closer to its fundamental niche. Based on this, we further proposed an integrated framework that combines eco-evolutionary data and SDMs (phylogenetically-informed SDMs) to provide comprehensive predictions of species range shifts under climate change. To evaluate our approach's performance, we applied it to a group of related species, the Chrysanthemum zawadskii species complex (Anthemidae, Asteracee). First, we investigated the niche differentiation between species and intraspecific lineages of the complex and estimated their rates of niche evolution. Next, using both standard SDMs and our phylogenetically-informed SDMs, we generated predictions of suitability areas for all species and lineages and compared the results. Finally, we reconstructed the historical range dynamics for the species of this complex. Our results showed that the species and intraspecific lineages of the complex had varying degrees of niche differentiation and different rates of niche evolution. Lineage-level SDMs can provide more realistic predictions for species with intraspecific differentiation than species-level models can. The phylogenetically-informed SDMs provided more complete environmental envelopes and predicted broader potential distributions for all species than the standard SDMs did. Range dynamics varied among the species that have different rates of niche evolution. Our framework integrating eco-evolutionary data and SDMs contributes to a better understanding of the species' responses to climate change and can help to make more targeted conservation efforts for the target species under climate change, particularly for rare species.

Prognostic value of the cervical lymph node necrosis ratio in nasopharyngeal carcinoma.

PURPOSE: Whether cervical lymph node necrosis (CNN) is an independent adverse prognostic factor in nasopharyngeal carcinoma (NPC) has not been determined. In this study, the CNN ratio was graded quantitatively to explore the prognostic value in NPC. PARTICIPANTS AND METHODS: We retrospectively reviewed a total of 648 pathologically confirmed as NPC. We outlined metastatic lymph nodes and necrotic area of lymph nodes slice by slice on the magneticresonanceimages (MRI) cross section, and calculated the corresponding CNN ratio. RESULTS: The median CNN ratio (17.37 %) was taken as the cut-off point, 256 (39.51 %) patients were divided into CNN1 group (<17.37 %, n = 128) and CNN2 group (≥17.37 %, n = 128), 392 (60.49 %) patients without lymph nodes necrosis were CNN0. Among the CNN0, CNN1 and CNN2 groups, five-year overall survival (OS) was 82.4 %, 76.6 % and 71.1 %, locoregional recurrence-free survival (LRRFS) was 91.3 %, 91.1 % and 90.5 %, distant metastasis-free survival (DMFS) was 83.7 %, 78.5 % and 68.7 %, progression-free survival (PFS) was 78.3 %, 71.7 % and 61.6 % respectively. By multivariate analysis, CNN was an independent prognostic factor for OS (P = 0.003), DMFS (P = 0.019) and PFS (P = 0.007). More than 3 cycles of chemotherapy significantly increased OS (P = 0.024) and DMFS (P = 0.015) in the CNN1 group. CONCLUSIONS: This study indicated that CNN is one of the factors with the negative prognosis of NPC. The CNN ratio might be used as one of the reference factors in the formulation of individualized treatment plan.

[Mechanism of apoptosis in human leukemia NB4 cells induced by total astragalosides].

OBJECTIVE: To investigate the effect of total astragalosides (TA) on proliferation and apoptosis in human leukemia NB4 cells in vitro. METHODS: The NB4 cells were treated with TA at different concentrations for 48 h in culture. Growth inhibition rates were measured by CCK-8 method. Flow cytometry was used to explore the cell apoptosis and the activity of NF-κB and Akt during apoptosis. RESULTS: TA at different concentrations (200, 400, 600, 800 mg/L) inhibited proliferation of NB4 cells in a dose-dependent manner (P < 0.05), and the inhibitory rates of TA on NB4 cells were (14.54 ± 3.20)%, (24.79 ± 3.98)%, (57.28 ± 4.71)% and (88.28 ± 4.65)%, respectively. In terms of the induction of apoptosis, there was a significant difference between the TA group and blank control [(1.80 ± 1.24)%, P < 0.05]. At TA doses of 200, 400 and 600 mg/L, the apoptotic rates of NB4 cells were (10.03 ± 3.31)%, (14.87 ± 3.65)%, (23.45 ± 1.90)%, respectively. Besides, TA induced apoptosis of NB4 cells in a dose-dependent manner in the groups of 200 mg/L, 400 mg/L, 600 mg/L (P < 0.05). But there was no significant difference in apoptotic rates between the groups of 800 mg/L and 600 mg/L [(23.45 ± 1.90)%, P > 0.05]. In the group of 800 mg/L, the necrotic cells increased highly and the necrotic rate reached (45.65 ± 3.16)%. After TA treatment of NB4 cells at different concentrations (200, 400, 600 mg/L), the expression of NF-κB protein was significantly decreased compared with that of the blank control (9.79 ± 0.95, P < 0.05), while Akt protein was not significantly decreased (P > 0.05). CONCLUSION: TA can inhibit the growth of NB4 cells and induce apoptosis in NB4 cells through an Akt-independent NF-κB signaling pathway.

[Distribution and Ecological Risk Assessment of Antibiotics in the Songhua River Basin of the Harbin Section and Ashe River].

Solid phase extraction (SPE) and high-performance liquid chromatography-mass spectrometry (HPLC-MS) were used to detect and analyze the distribution of 10 antibiotics including sulfonamides, fluoroquinolones, and macrolides in the Harbin section of Songhua River basin and Ashe River, a tributary of Songhua River. The correlation between the antibiotic concentration and water quality indexes was analyzed and the ecological risks were evaluated. The results showed that only six antibiotics were detected in the entry section of Harbin city on the Songhua River and the concentration was relatively low. However, nine antibiotics were detected in the exit section and only sulfamethazine (SM1) was not detected. The concentrations of macrolide antibiotics increased most significantly, followed by those of sulfonamides and fluoroquinolones. The inflow of three tributaries in Harbin city was the direct cause of the increase in antibiotic concentration in the Songhua River. Only sulfapyridine (SMPD) was not detected in the upper section of Ashe River. Ten antibiotics were detected in the section where the Ashe River enters the Songhua River. The other nine antibiotics were the highest except norfloxacin (NOR). Wastewater discharged from four sewage treatment plants along Ashe River is an important factor affecting the concentration of antibiotics in the Ashe River. Correlation analysis shows that three kinds of antibiotics in the Songhua River have certain positive correlations with ammonia nitrogen, total phosphorus, and total organic carbon. There is a significant positive correlation between the three kinds of antibiotics and ammonia nitrogen and total phosphorus in the Ashe River system, indicating that the water quality indexes of the Harbin section of Songhua River and Ashe River are closely related to their antibiotic concentrations. The results of ecological risk assessment showed that macrolide antibiotics in the Harbin section of Songhua and Ashe Rivers had certain ecological risks.

Transformation and apoptosis of NIH/3T3 cells treated with nickel-smelting fumes.

The purpose of this study was to investigate the transformation and apoptosis of NIH/3T3 cells treated with nickel (Ni) smelting fumes. Cytotoxicity of NIH/3T3 cells was detected with a methyl thiazolyl tetrazolium (MTT) colorimetric assay. The cell translation model was established by cell focus translation using two types of Ni-smelting fumes from a Ni smelting plant in China. The transformed focus was determined by soft agar culture assay. The apoptotic characteristics of NIH/3T3 cells treated with Ni-smelting fumes were detected by flow cytometry using Annexin V-FITC and PI as markers. The DNA fragment of apoptosis in NIH/3T3 cells treated with nickel smelting fumes was detected by observing agarose electrophoresis and morphological characteristics of cells under electron microscopy. With increase in exposure time, growth of NIH/3T3 cells was inhibited. The NIH/3T3 cell transformation model was established successfully using two Ni-smelting fumes, and the transformed cells grow in soft agar. No apoptosis peak was detected by flow cytometry. Apoptotic cells characterized by necrosis were observed using electron microscopy. There was no apparent "ladder" observed by DNA fragment analysis. Data indicated that Ni-smelting fumes produced cytotoxicity by mechanisms associated with necrosis but not apoptosis.

Diffusion-weighted MR imaging in prediction of response to neoadjuvant chemotherapy in patients with breast cancer.

This study aims to evaluate the potential of apparent diffusion coefficient (ADC) derived from diffusion-weighted MR imaging for predicting the treatment response to neoadjuvant chemotherapy (NACT) in patients with breast cancer. Magnetic resonance imaging was performed prior to NACT and after two cycles of NACT. The correlation between mean ADCpre values, mean ADCpost values, changes in ADC values and changes in tumor diameters after NACT was examined using Spearman rank correlation. A total of 164 breast cancers were enrolled in this study. Mean ADCpre values of responders ([0.85 ± 0.16] × 10-3 mm2/s) and non-responders ([0.84 ± 0.21] × 10-3 mm2/s) had no significant difference (P = 0.759). While mean ADCpost value of responders was significantly higher than that of non-responders ([1.17 ± 0.37] × 10-3 mm2/s vs. [1.01 ± 0.28] × 10-3 mm2/s; P = 0.002). Both mean ADCpost values (r = 0.288, P = 0.000) and changes in mean ADC values (r = 0.222, P = 0.004) were positively correlated to changes in tumor diameter after NACT, except for mean ADCpre values (r = 0.031, P = 0.695). Our results indicated that mean ADCpost values and changes in ADC values after NACT might be a biological marker for assessing the efficacy of chemotherapy.

Genetic polymorphisms -137 (rs187238) and -607 (rs1946518) in the interleukin-18 promoter may not be associated with development of hepatocellular carcinoma.

This study meta-analyzed the literature on possible association of polymorphisms -137 (rs187238) and -607 (rs1946518) in the interleukin-18 (IL-18) promoter with risk of hepatocellular carcinoma (HCC). The analysis included 8 case-control studies on the -137 polymorphism (1,318 cases, 2,254 controls) and 7 case-control studies on the -607 polymorphism (1,262 cases, 1,696 controls). None of the five genetic models suggested a significant association between the -137 polymorphism and HCC risk: allelic model, OR 0.99, 95% CI 0.74-1.34, P = 0.97; recessive model, OR 0.98, 95% CI 0.65-1.46, P = 0.91; dominant model, OR 1.35, 95% CI 0.73-2.52, P = 0.34; homozygous model, OR 0.99, 95% CI 0.65-1.49, P = 0.95; heterozygous model, OR 0.99, 95% CI 0.66-1.48, P = 0.94. Similar results were obtained in subgroup analyses of Asian patients, Chinese patients, or patients with hepatitis B virus (HBV)-related HCC. Similar results were also obtained for the -607 polymorphism across the entire study population as well as in the three subgroups. The available evidence suggests no significant association of the -137 or -607 polymorphisms with risk of HCC in general or specifically of HBV-related HCC. These conclusions should be verified in large, well-designed studies.

Nickel-smelting fumes increased the expression of HIF-1α through PI3K/ERK pathway in NIH/3T3 cells.

OBJECTIVE: The purpose of this study was to investigate the effects of Nickel (Ni) -smelting fumes on oncogenic proteins in vivo and in vitro. METHODS: Ni fallout beside a Ni smelting furnace in a factory was sampled to study its toxic effect. The effects of Ni-smelting fumes on the regulation of PI3K and ERK signaling pathways and the important downstream hypoxia inducible factor, HIF-1α, were studied both in NIH/3T3 cells and in the lung tissue of rats. NIH/3T3 cell transformation induced by Ni-smelting fumes was also observed. RESULTS: Ni-smelting fumes activated PI3K, p-AKT, p70S6K1, and ERK proteins and increased HIF-1α expression in a time- and dose-dependent manner. However, activation was suppressed when NIH/3T3 cells were pretreated with PI3K/AKT or ERK inhibitors. Ni-smelting fumes caused malignant transformation of NIH/3T3 cells. CONCLUSIONS: Ni-smelting fumes increased the expression of HIF-1α through the PI3K/ERK pathway in NIH/3T3 cells and induced malignant transformation in these cells indicating that Ni-smelting fumes may be a potential carcinogen in mammalian cells.

Effects of nickel-smelting fumes on the regulation of NIH/3T3 cell viability, necrosis, and expression of hMLH1 and RASSF1A.

Nickel is widely used and distributed in various industries. This study investigated the effect of nickel-smelting fumes on the regulation of NIH/3T3 cell viability, apoptosis, and necrosis and the expression of the tumor suppressor genes hMLH1 and RASSF1A. Cell viability was determined using a methylthiazolyl tetrazolium colorimetric assay. NIH/3T3 cell viability was reduced after exposure to different concentrations of nickel-smelting fumes, but cell apoptosis and necrosis were induced. Moreover, cell morphology changed significantly after exposure to different concentrations of nickel-smelting fumes, as determined using an inverted microscope or transmission electron microscope. Real-time RT-PCR and Western blot analyses showed that exposure of cells to concentrations of ≥100 µg/mL of nickel-smelting fumes upregulated the expression of hMLH1 and RASSF1A compared to the negative controls. These data suggest that nickel-smelting fumes could be toxic to cells, upregulating the expression of hMLH1 and RASSF1A and in turn inducing cell apoptosis and necrosis.

[Role of BCL-2, caspase-3 and NF-κB in astragaloside inducing apoptosis of human NB4 cells].

This study was purposed to investigate the apoptosis-inducing effect of astragalosides on acute promyelocytic leukemia(APL) cell line NB4 and its mechanism. NB4 cells were treated with different concentrations (200, 300, 400 µg /ml) of astragalosides for 48 h. The cell proliferation was assayed by using CCK-8 method; the cell apoptosis was analyzed by flow cytometry with Annexin V-FITE/PI double staining. The mRNA expression of BCL-2 and the relative activity of BCL-2, NF-κB and caspase-3 were detected by RT-PCR and Western blot, respectively. The results showed that after treated with astragalosides for 48 h, astragalosides inhibited NB4 cell proliferation in concentration-dependent way, the apoptosis rate of NB4 cells gradually elevated from 4.69% to 40.85% with the increasing of astragalosides concentration. Simultaneously, the mRNA expression of BCL-2 was down-regulated, Western blot analysis showed that the protein expression levels of BCL-2 and NF-κB decreased after astragalosides treatment, while caspase-3 protein expression level increased. It is concluded that the molecular mechanism of the astragalosides-induced apoptosis in NB4 cells may be associated with down-regulation of the expression of BCL-2 and NF-κB, finally the relative activity of caspase-3 activated.

Tooth loss and risk of head and neck cancer: a meta-analysis.

BACKGROUND: Observational studies suggest an association between tooth loss and risk of head and neck cancer. However, whether tooth loss is an independent risk factor for head and neck cancer still remains controversial. The aim of this study is to assess the association between tooth loss and head and neck cancer risk. METHODS: Eligible studies were searched in PubMed and Embase databases from their inception to March 2013. A random-effects model or fixed-effects model was used to calculate the overall combined risk estimates. RESULTS: Eight case-control studies and one cross-sectional study involving 5,204 patients and 5,518 controls were included in the meta-analysis. The overall combined odds ratio for tooth loss and head and neck cancer was 2.00 (95% confidence interval, 1.28-3.14). Similar results yielded both in the moderate and severe tooth loss group. Sensitivity analysis based on various exclusion criteria maintained this significance with respect to head and neck cancer individually. Little evidence of publication bias was observed. CONCLUSION: This meta-analysis suggests that tooth loss is associated with increased risk of head and neck cancer. This increase is probably independent of conventional head and neck cancer risk factors.