A functional gene module identification algorithm in gene expression data based on genetic algorithm and gene ontology.

Since genes do not function individually, the gene module is considered an important tool for interpreting gene expression profiles. In order to consider both functional similarity and expression similarity in module identification, GMIGAGO, a functional Gene Module Identification algorithm based on Genetic Algorithm and Gene Ontology, was proposed in this work. GMIGAGO is an overlapping gene module identification algorithm, which mainly includes two stages: In the first stage (initial identification of gene modules), Improved Partitioning Around Medoids Based on Genetic Algorithm (PAM-GA) is used for the initial clustering on gene expression profiling, and traditional gene co-expression modules can be obtained. Only similarity of expression levels is considered at this stage. In the second stage (optimization of functional similarity within gene modules), Genetic Algorithm for Functional Similarity Optimization (FSO-GA) is used to optimize gene modules based on gene ontology, and functional similarity within gene modules can be improved. Without loss of generality, we compared GMIGAGO with state-of-the-art gene module identification methods on six gene expression datasets, and GMIGAGO identified the gene modules with the highest functional similarity (much higher than state-of-the-art algorithms). GMIGAGO was applied in BRCA, THCA, HNSC, COVID-19, Stem, and Radiation datasets, and it identified some interesting modules which performed important biological functions. The hub genes in these modules could be used as potential targets for diseases or radiation protection. In summary, GMIGAGO has excellent performance in mining molecular mechanisms, and it can also identify potential biomarkers for individual precision therapy.

Early warning of red tides using bacterial and eukaryotic communities in nearshore waters.

Anthropogenic discharge activities have increased nutrient pollution in coastal areas, leading to algal blooms and microbial community changes. Particularly, microbial communities could easily be affected with variation in nutrient pollution, and thus offered a promising strategy to predict early red tides warning via microbial community-levels variation and their keystone taxa hysteretic responses to nutrient pollution. Herein high-throughput sequencing technology from 52 samples were used to explore the variation of microbial communities and find the significant tipping points with aggravating nutrient conditions in Xiaoping Island coastal area. Results indicated that bacterial and microeukaryote communities were generally spatial and seasonal heterogeneity and were influenced by the different nutrient conditions. Procrustes test results showed that the comprehensive index of organics polluting (OPI), total nitrogen (TN), inorganic nitrogen (DIN), and total phosphorus (TP) were significantly correlated with the composition of bacteria and microeukaryotes. A SEGMENTED analysis revealed that the threshold of TN, DIN, and NH4-N for bacterial community were 0.23 ± 0.091 mg/L, 0.21 ± 0.084 mg/L, 0.09 ± 0.057 mg/L, respectively. Tipping points for TN, DIN, and NH4-N agreed with the concentration during Ceratium tripos and Skeletonema costatum blooms. Co-occurrence network results found that Planktomarina, Acinetobacter, and Verrucomicrobiaceae were keystone and OPI-discriminatory taxa. The abundant changes of Planktomarina at station A1 were significantly correlated with the development of C. tripos blooms (r = 0.55, p < 0.05), and also significantly correlated with TN, DIN, and NO3-N (r≥|0.55|, p < 0.05). The abundant changes of Acinetobacter and Verrucomicrobiaceae at station C1 were significantly correlated with the development of C. tripos blooms (r ≥ 0.77, p < 0.05), and also significantly correlated with PO4-P (r ≥ 0.64, p < 0.05). The dynamic abundance of keystone taxa showed that the trend of rapid changes could be monitored 1.5 months before the occurrence of red tide. Therefore, this study provides an assessment method for early warning of red tide occurrence and factors that trigger red tide.

Identification of key genes in hepatocellular carcinoma associated with exposure to TCDD and α-endosulfan by WGCNA.

2,3,7,8-tet-rachlorodibenzo-p-dioxin (TCDD) and α-endosulfan are two typical persistent organic pollutants (POPs), both of which accumulate in the liver and have potential carcinogenic hepatic effects. The underlying molecular mechanisms of pathogenesis of hepatocellular carcinoma (HCC) remain elusive when exposure to POPs. The aim of this study is to explore the key genes involved in HCC when exposure to TCDD and α-endosulfan by weighted gene co-expression network analysis (WGCNA). First, we performed co-expressed analysis on HCC and normal condition, based on WGCNA. In results, seven co-expressed modules were identified from 56 human liver samples, and the brown module correlated with five stages of HCC. Subsequently, we predicted that human five liver diseases were associated with exposure to TCDD and/or α-endosulfan by Nextbio analysis. Functional enrichment analysis showed that the brown module enriched in oxidation-reduction process, DNA replication, oxidoreductase activity and aging, which were the same as the results when exposure to the mixture of TCDD and α-endosulfan. Lastly, based on the protein-protein interaction network, we identified three novel genes including HK2, EXO1 and PFKP as key genes in HCC associated with exposure to TCDD and α-endosulfan mixture. In addition, survival analysis of key genes in Kaplan-Meier plotter demonstrated that aberrant expression levels of all the three key genes were associated with poor prognosis of HCC. Finally, Western blot analysis confirmed that protein expression levels of PFKP and HK2 in the three exposed groups were significantly elevated, while EXO1 were significantly upregulated when exposure to TCDD and α-endosulfan mixture in HepaRG cells. This study provides a new perspective to the understanding of the genetic mechanism of HCC when exposure to POPs.

Modeling of ionizing radiation-induced chromosome aberration and tumor prevalence based on two classes of DNA double-strand breaks clustering in chromatin domains.

There has been some controversy over the use of radiobiological models when modeling the dose-response curves of ionizing radiation (IR)-induced chromosome aberration and tumor prevalence, as those curves usually show obvious non-targeted effects (NTEs) at low doses of high linear energy transfer (LET) radiation. The lack of understanding the contribution of NTEs to IR-induced carcinogenesis can lead to distinct deviations of relative biological effectiveness (RBE) estimations of carcinogenic potential, which are widely used in radiation risk assessment and radiation protection. In this work, based on the initial pattern of two classes of IR-induced DNA double-strand breaks (DSBs) clustering in chromatin domains and the subsequent incorrect repair processes, we proposed a novel radiobiological model to describe the dose-response curves of two carcinogenic-related endpoints within the same theoretical framework. The representative experimental data was used to verify the consistency and validity of the present model. The fitting results indicated that, compared with targeted effect (TE) and NTE models, the current model has better fitting ability when dealing with the experimental data of chromosome aberration and tumor prevalence induced by multiple types of IR with different LETs. Notably, the present model without introducing an NTE term was adequate to describe the dose-response curves of IR-induced chromosome aberration and tumor prevalence with NTEs in low-dose regions. Based on the fitting parameters, the LET-dependent RBE values were calculated for three given low doses. Our results showed that the RBE values predicted by the current model gradually decrease with the increase of doses for the endpoints of chromosome aberration and tumor prevalence. In addition, the calculated RBE was also compared with those evaluated from other models. These analyses show that the proposed model can be used as an alternative tool to well describe dose-response curves of multiple carcinogenic-related endpoints and effectively estimate RBE in low-dose regions.

Unraveling the skatole biodegradation process in an enrichment consortium using integrated omics and culture-dependent strategies.

3-Methylindole (skatole) is regarded as one of the most offensive compounds in odor emission. Biodegradation is feasible for skatole removal but the functional species and genes responsible for skatole degradation remain enigmatic. In this study, an efficient aerobic skatole-degrading consortium was obtained. Rhodococcus and Pseudomonas were identified as the two major and active populations by integrated metagenomic and metatranscriptomic analyses. Bioinformatic analyses indicated that the skatole downstream degradation was mainly via the catechol pathway, and upstream degradation was likely catalyzed by the aromatic ring-hydroxylating oxygenase and flavin monooxygenase. Genome binning and gene analyses indicated that Pseudomonas, Pseudoclavibacter, and Raineyella should cooperate with Rhodococcus for the skatole degradation process. Moreover, a pure strain Rhodococcus sp. DMU1 was successfully obtained which could utilize skatole as the sole carbon source. Complete genome sequencing showed that strain DMU1 was the predominant population in the consortium. Further crude enzyme and RT-qPCR assays indicated that strain DMU1 degraded skatole through the catechol ortho-cleavage pathway. Collectively, our results suggested that synergistic degradation of skatole in the consortium should be performed by diverse bacteria with Rhodococcus as the primary degrader, and the degradation mainly proceeded via the catechol pathway.

The Memory of Rice Response to Spaceflight Stress: From the Perspective of Metabolomics and Proteomics.

The stress response of plants to spaceflight has been confirmed in contemporary plants, and plants retained the memory of spaceflight through methylation reaction. However, how the progeny plants adapt to this cross-generational stress memory was rarely reported. Here, we used the ShiJian-10 retractable satellite carrying Dongnong416 rice seeds for a 12.5-day on-orbit flight and planted the F2 generation after returning to the ground. We evaluated the agronomic traits of the F2 generation plants and found that the F2 generation plants had no significant differences in plant height and number of tillers. Next, the redox state in F2 plants was evaluated, and it was found that the spaceflight broke the redox state of the F2 generation rice. In order to further illustrate the stress response caused by this redox state imbalance, we conducted proteomics and metabolomics analysis. Proteomics results showed that the redox process in F2 rice interacts with signal transduction, stress response, and other pathways, causing genome instability in the plant, leading to transcription, post-transcriptional modification, protein synthesis, protein modification, and degradation processes were suppressed. The metabolomics results showed that the metabolism of the F2 generation plants was reshaped. These metabolic pathways mainly included amino acid metabolism, sugar metabolism, cofactor and vitamin metabolism, purine metabolism, phenylpropane biosynthesis, and flavonoid metabolism. These metabolic pathways constituted a new metabolic network. This study confirmed that spaceflight affected the metabolic changes in offspring rice, which would help better understand the adaptation mechanism of plants to the space environment.

Endosulfan promotes cell proliferation and extracellular matrix accumulation through TGF-ß/Smad signaling pathway in HRMCs.

Endosulfan is an organochlorine pesticide, which poses a potential danger to human health and safety. It is known that dysfunction of glomerular mesangial cells causes glomerular sclerosis, associated with chronic kidney diseases. In the present study, we investigated the effects of endosulfan on cell proliferation and extracellular matrix accumulation (ECM) in human renal mesangial cells (HRMCs). Cells were treated with endosulfan, endosulfan (10 µM) plus specific inhibitor of TGF-ß signaling (LY2109761) or antioxidant (NAC). The results showed that endosulfan significantly promoted cell proliferation, accompanied with the decrease of p27 mRNA expression and the increase in the mRNA expression levels of p21 and inflammatory factors IL-6/IL-8. qRT-PCR results showed that matrix metalloproteinase-2 (MMP2) and tissue metalloproteinase-3 (TIMP3) were down-regulated whereas laminin was up-regulated when exposure to endosulfan. Western blot results showed that p-Smad2/3 was up-regulated, while Smad7 was down-regulated when exposure to endosulfan, which were reversed in the presence of LY2109761. Endosulfan significantly decreased the activity of SOD and increased the MDA level and CAT activity, which were reversed in the presence of NAC. These findings suggest that endosulfan can cause excessive proliferation and massive accumulation of ECM through TGF-ß/Smad signaling pathway, and also induced oxidative stress and inflammation in HRMCs.

Assessment bioaccumulation factor (BAF) of methyl siloxanes in crucian carp (Carassius auratus) around a siloxane production factory.

Methyl siloxanes are identified as emerging persistent toxic compounds and the ecological environment risks of these compounds have been caused of great concern worldwide. In this study, the concentrations of methyl siloxanes were reported in dissolved water and crucian carp around a methyl siloxane production factory located in Liaoning Province, Northeast China. D4, D5, D6, D7, L4, L5 and L6 were detectable both in dissolved water and crucian carp. The total concentrations of 7 methyl siloxanes (Σ7MS) were 14 ± 6.3 ng/L in dissolved water and 43 ± 22 ng/g ww in crucian carp, respectively. D5 has the highest concentration both in dissolved water (5.5 ± 3.5 ng/L) and crucian carp (17 ± 11 ng/g ww). Based on the monitoring values, bioaccumulation factor (BAF) of these compounds were calculated. Significant bioaccumulation potential was observed for D4 (BAF = 5900 ± 3500 L/kg) based on the bioaccumulation criteria suggested by USEPA and EU (BAF > 5000 L/kg). To our understanding, this is the first report of BAF values of methyl siloxane in field study, which will provide important support for further assessment of bioaccumulation of these compounds.

iso-µmGene: an isothermal amplification-based portable microfluidic system for simple, reliable and flexibly multiplexed genetic identification and quantification.

Simple, reliable and flexibly multiplexed genetic identification and quantification of microbial pathogens is in urgent need for early disease diagnosis and timely treatment. This study presented an isothermal amplification-based portable microfluidic system (iso-µmGene) with features of multi-well chips for convenient filling and reliable sealing, flexible detection throughput, and a stand-alone and well-performing point of care (POC) genetic testing device. Using disposable chips with two kinds of reaction wells (eighteen and ten wells) and a device prototype with independent four chip holders, the iso-µmGene enables on-demand analysis of different target genes in one sample per chip and one to four samples (chips) per run, requiring only a single pipetting step for dispensing per chip with dehydrated primers. To completely seal the loop-mediated isothermal amplification (LAMP) reaction system to minimize the risk of amplicon escape, a dedicated plastic shell is used to assemble the array-type chip and reliably close its openings. Meanwhile, to enhance the precision for flexibly multiplexed detection and decrease the size and cost of the device, we designed a thermoelectric cooler (TEC)-based temperature-control module including two separate units and a CCD-based fluorescence imaging module containing a linear translation stage for real-time LAMP assay. This work demonstrated applications for the parallel detection of 2-2000 CFU (colony forming units) per reaction well with good intra- and inter-chip reproducibility using the crude lysates of two aquaculture pathogens Edwardsiella tarda and Vibrio harveyi. Overall, the iso-µmGene presented here possesses both a sophisticated instrument's functionality and performance and POC device's portability and cost.

Biodegradation of skatole by Burkholderia sp. IDO3 and its successful bioaugmentation in activated sludge systems.

Skatole is the key malodorous compound in livestock and poultry waste and wastewater with a low odor threshold. It not only causes serious nuisance to residents and workers, but also poses threat to the environment and human health due to its biotoxicity and recalcitrant nature. Biological treatment is an eco-friendly and cost-effective approach for skatole removal, while the bacterial resources are scarce. Herein, the Burkholderia strain was reported to efficiently degrade skatole for the first time. Results showed that strain IDO3 maintained high skatole-degrading performance under the conditions of pH 4.0-9.0, rotate speed 0-250 rpm, and temperature 30-35 °C. RNA-seq analysis indicated that skatole activated the oxidative phosphorylation and ATP production levels in strain IDO3. The oxidoreductase activity item which contained 373 differently expressed genes was significantly impacted by Gene Ontology analysis. Furthermore, the bioaugmentation experiment demonstrated that strain IDO3 could notably increase the removal of skatole in activated sludge systems. High-throughput 16S rRNA gene sequencing data indicated that the alpha-diversity and bacterial community tended to be stable in the bioaugmented group after 8 days operation. PICRUSt analysis indicated that xenobiotics biodegradation and metabolism, and membrane transport categories significantly increased, consistent with the improved skatole removal performance in the bioaugmented group. Burkholderia was survived and colonized to be the predominant population during the whole operation process (34.19-64.00%), confirming the feasibility of Burkholderia sp. IDO3 as the bioaugmentation agent in complex systems.

Endosulfan promotes cell migration via PTP4A3-mediated signaling pathways in HUVECs.

Endosulfan is a persistent organic pollutant and can cause endothelial dysfunction, closely related to cardiovascular diseases. Endothelial cell migration plays a critical role in atherosclerosis and angiogenesis. This study was aimed to investigate the effect of environmentally relevant doses of endosulfan and underlying molecular mechanism on endothelial cell migration. Human umbilical vein endothelial cells (HUVECs) were treated with DMSO (control) or endosulfan (0.1, 1, 10 and 20 µM) in the presence or absence of inhibitors. Wound healing and Transwell assay were employed to explore the effect of endosulfan on endothelial cell migration. The expression of genes or proteins was assayed by real-time PCR or immunoblotting. The results showed that endosulfan at relative low concentration (0.1, 1, 10 and 20 µM) increased cell migration ability horizontally and vertically at 12 h after exposure. In line with this cellular effect, Protein-tyrosine Phosphatase 4A3 (PTP4A3) expression was significantly increased in endosulfan-exposed endothelial cells. Specific inhibitor of PTP4A3 significantly inhibited 20 µM endosulfan-induced cell migration, the expression and phosphorylation of Src and phosphorylation of focal adhesion kinase (FAK). Exposure to endosulfan resulted in activation of various signaling pathways including phosphoinositide 3-kinase (PI3K)/AKT, mitogen-activated protein kinase (MAPK) and nuclear factor kappa B (NF-κB), which were suppressed by PTP4A3 inhibitor or specific inhibitor for each signaling pathway. Exposure to endosulfan significantly reduced nitric oxide production and caused oxidative stress in HUVECs. These findings suggest that endosulfan promoted cell migration through PTP4A3-mediated various signaling pathways in endothelial cells.

Effect of dys-1 mutation on gene expression profile in space-flown Caenorhabditis elegans.

INTRODUCTION: Dystrophin-like dys-1 gene expression increases in the body wall muscles of Caenorhabditis elegans after spaceflight (SF). Here we used a dys-1(cx18) mutant to analyze the molecular adaptive responses of C. elegans to SF. METHODS: DNA microarrays were performed to identify differentially expressed genes between wild-type (WT) and dys-1 mutant worms after SF. We performed Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway analyses, predicted human diseases, and screened out key genes for human muscle diseases with NextBio. RESULTS: Gene expression was less affected by SF in the dys-1 mutant than in the WT worms. The dys-1 mutation influenced neuromuscular gene expression (neuropeptide genes, muscle-related genes, and dystrophin-related genes) under SF conditions, among which 15 genes were specifically regulated by dys-1. NextBio analysis predicted that cdka-1, lev-11, unc-27, and unc-94 genes might play critical roles in muscle atrophy. DISCUSSION: dys-1 Potentially regulates the neuromuscular system in space. Muscle Nerve, 2018.

The subsequent biological effects of simulated microgravity on endothelial cell growth in HUVECs.

PURPOSE: Microgravity is known to cause endothelium dysfunction in astronauts returning from spaceflight. We aimed to reveal the regulatory mechanism in alterations of human endothelial cells after simulated microgravity (SMG). METHODS: We utilized the rotary cell culture system (RCCS-1) to explore the subsequent effects of SMG on human umbilical vein endothelial cells (HUVECs). RESULTS: SMG-treated HUVECs appeared obvious growth inhibition after return to normal gravity, which might be attributed to a set of responses including alteration of cytoskeleton, decreased cell adhesion capacity and increased apoptosis. Expression levels of mTOR and its downstream Apaf-1 were increased during subsequent culturing after SMG. miR-22 was up-regulated and its target genes SRF and LAMC1 were down-regulated at mRNA levels. LAMC1 siRNAs reduced cell adhesion rate and inhibited stress fiber formation while SRF siRNAs caused apoptosis. CONCLUSION: SMG has the subsequent biological effects on HUVECs, resulting in growth inhibition through mTOR signaling and miR-22-mediated mechanism.

A novel multitarget model of radiation-induced cell killing based on the Gaussian distribution.

The multitarget version of the traditional target theory based on the Poisson distribution is still used to describe the dose-survival curves of cells after ionizing radiation in radiobiology and radiotherapy. However, noting that the usual ionizing radiation damage is the result of two sequential stochastic processes, the probability distribution of the damage number per cell should follow a compound Poisson distribution, like e.g. Neyman's distribution of type A (N. A.). In consideration of that the Gaussian distribution can be considered as the approximation of the N. A. in the case of high flux, a multitarget model based on the Gaussian distribution is proposed to describe the cell inactivation effects in low linear energy transfer (LET) radiation with high dose-rate. Theoretical analysis and experimental data fitting indicate that the present theory is superior to the traditional multitarget model and similar to the Linear - Quadratic (LQ) model in describing the biological effects of low-LET radiation with high dose-rate, and the parameter ratio in the present model can be used as an alternative indicator to reflect the radiation damage and radiosensitivity of the cells.

Protective effects of melatonin on bovine sperm characteristics and subsequent in vitro embryo development.

We aimed to investigate the effect of melatonin on bovine frozen-thawed semen and its impact on fertilization outcome. Plasma membrane integrity, mitochondrial activity, acrosome integrity, and levels of intracellular reactive oxygen species (ROS) were measured in spermatozoa treated with different concentrations of melatonin. Melatonin-treated spermatozoa were then used for in vitro fertilization, followed by analysis of subsequent embryo development and the expression of apoptosis- and antioxidant-related genes. The results revealed that 10-5 and 10-3 M melatonin led to higher plasma membrane integrity, mitochondrial activity, and acrosome integrity, and significantly decreased intracellular ROS levels (P < 0.05). The blastocyst development rate of in vitro-produced bovine embryos originating from 10-3 M melatonin-treated spermatozoa was significantly higher, while the incidence of apoptotic nuclei in blastocysts was markedly lower than for embryos from any other group (P < 0.05). CASP3 and BAX mRNA abundance were significantly reduced whereas BCL2, XIAP, and CAT transcript abundance were significantly increased in embryos produced from spermatozoa treated with 10-3 M melatonin; GPX4 expression, however, was comparable in all treatment groups. Thus, 10-3 M melatonin can improve the quality of bovine frozen-thawed semen. These beneficial effects appear to influence preimplantation embryos, given the correlation with its anti-apoptotic and anti-oxidative properties. Mol. Reprod. Dev. 83: 993-1002, 2016 © 2016 Wiley Periodicals, Inc.

Melatonin inhibits paraquat-induced cell death in bovine preimplantation embryos.

Preimplantation embryos are sensitive to oxidative stress-induced damage that can be caused by reactive oxygen species (ROS) originating from normal embryonic metabolism and/or the external surroundings. Paraquat (PQ), a commonly used pesticide and potent ROS generator, can induce embryotoxicity. The present study aimed to investigate the effects of melatonin on PQ-induced damage during embryonic development in bovine preimplantation embryos. PQ treatment significantly reduced the ability of bovine embryos to develop to the blastocyst stage, and the addition of melatonin markedly reversed the developmental failure caused by PQ (20.9% versus 14.3%). Apoptotic assay showed that melatonin pretreatment did not change the total cell number in blastocysts, but the incidence of apoptotic nuclei and the release of cytochrome c were significantly decreased. Using real-time quantitative polymerase chain reaction analysis, we found that melatonin pre-incubation significantly altered the expression levels of genes associated with redox signaling, particularly by attenuating the transcript level of Txnip and reinforcing the expression of Trx. Furthermore, melatonin pretreatment significantly reduced the expression of the pro-apoptotic caspase-3 and Bax, while the expression of the anti-apoptotic Bcl-2 and XIAP was unaffected. Western blot analysis showed that melatonin protected bovine embryos from PQ-induced damage in a p38-dependent manner, but extracellular signal-regulated kinase (ERK) and c-JUN N-terminal kinase (JNK) did not appear to be involved. Together, these results identify an underlying mechanism by which melatonin enhances the developmental potential of bovine preimplantation embryos under oxidative stress conditions.

Polycyclic aromatic hydrocarbons (PAHs) and alkylated PAHs in the coastal seawater, surface sediment and oyster from Dalian, Northeast China.

A total of 46 polycyclic aromatic hydrocarbons (PAHs, 21 parent and 25 alkylated) were determined in seawater, surface sediment and oyster from coastal area of Dalian, North China. The concentration of Σ46PAHs in seawater, sediment, and oyster were 136-621 ng/L, 172-4700 ng/g dry weight (dw) and 60.0-129 ng/g wet weight (ww) in winter, and 65.0-1130 ng/L, 71.1-1090 ng/g dw and 72.8-216 ng/g ww in summer, respectively. High PAH levels were found in industrial area both in winter and summer. Selected PAH levels in sediments were compared with Sediments Quality Guidelines (ERM-ERL, TEL-PEL indexes) for evaluation probable toxic effects on marine organism and the results indicate that surface sediment from all sampling sites have a low to medium ecotoxicological risk. Daily intake of PAHs via oyster as seafood by humans were estimated and the results indicated that oyster intake would not pose a health risk to humans even 30 days after a oil spill accident near by. Water-sediment exchange analysis showed that, both in winter and summer, the fluxes for most high molecular weight PAHs were from seawater to sediment, while for low molecular weight PAHs, an equilibrium was reached between seawater and sediment.

Inhibition of cell growth and induction of inflammation by endosulfan in HUVEC-C cells.

Endosulfan is one of the organochlorine pesticides. It has been associated with a wide range of adverse health effects. However, it is unknown whether endosulfan causes endothelial dysfunction. In the present study, we investigated the effects of endosulfan on human vascular endothelial cells. We exposed human umbilical vein endothelial cells (HUVEC-C) to varying concentrations of endosulfan for 48 h. The results showed that endosulfan lowered cell viability and inhibited cell proliferation in a dose-dependent manner. Flow cytometric analysis showed that endosulfan at 60 µM induced G1 cell cycle arrest, a response attributed to down-regulation of CDK6 and pRb dephosphorylation. We observed that endosulfan at 40 and 60 µM induced a considerable percentage of cells to undergo apoptosis, as detected by Annexin-V binding assays. Endosulfan reduced mitochondrial transmembrane potential, leading to the release of cytochrome c into the cytoplasm; meanwhile, endosulfan also inhibited the mRNA expression level of survivin, which resulted in the activation of caspase-3. These results indicated that the intrinsic mitochondria-mediated pathway was involved in apoptotic process. Exposure to endosulfan increased the secretion and mRNA expression levels of inflammation factors interleukin (IL)-6 and IL-8, suggesting that endosulfan could cause inflammation. Overall, these findings suggested that endosulfan is toxic to HUVEC-C cells, resulting in endothelial dysfunction. © 2015 Wiley Periodicals, Inc. Environ Toxicol 31: 1785-1795, 2016.

TGIF1 Gene Silencing in Tendon-Derived Stem Cells Improves the Tendon-to-Bone Insertion Site Regeneration.

BACKGROUND/AIMS: The slow healing process of tendon-to-bone junctions can be accelerated via implanted tendon-derived stem cells (TDSCs) with silenced transforming growth interacting factor 1 (TGIF1) gene. Tendon-to-bone insertion site is the special form of connective tissues derivatives of common connective progenitors, where TGF-ß plays bidirectional effects (chondrogenic or fibrogenic) through different signaling pathways at different stages. A recent study revealed that TGF-ß directly induces the chondrogenic gene Sox9. However, TGIF1 represses the expression of the cartilage master Sox9 gene and changes its expression rate against the fibrogenesis gene Scleraxis (Scx). METHODS: TGIF1 siRNA was transduced or TGIF1 was over-expressed in tendon-derived stem cells. Following suprapinatus tendon repair, rats were either treated with transduced TDSCs or nontransduced TDSCs. Histologic examination and Western blot were performed in both groups. RESULTS: In this study, the silencing of TGIF1 significantly upregulated the chondrogenic genes and markers. Similarly, TGIF1 inhibited TDSC differentiation into cartilage via interactions with TGF-ß-activated Smad2 and suppressed the phosphorylation of Smad2. The area of fibrocartilage at the tendon-bone interface was significantly increased in the TGIF1 (-) group compared with the control and TGIF1-overexpressing groups in the early stages of the animal model. The interface between the tendon and bone showed a increase of new bone and fibrocartilage in the TGIF1 (-) group at 4 weeks. Fibrovascular scar tissue was observed in the TGIF1-overexpressing group and the fibrin glue only group. Low levels of fibrocartilage and fibrovascular scar tissue were found in the TDSCs group. CONCLUSION: Collectively, this study shows that the tendon-derived stem cell modified with TGIF1 gene silencing has promising effects on tendon-to-bone healing which can be further explored as a therapeutic tool in regenerative medicine.

Trophic transfer of methyl siloxanes in the marine food web from coastal area of Northern China.

Methyl siloxanes, which belong to organic silicon compounds and have linear and cyclic structures, are of particular concern because of their potential characteristic of persistent, bioaccumulated, toxic, and ecological harm. This study investigated the trophic transfer of four cyclic methyl siloxanes (octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), dodecamethylcyclohexasiloxane (D6), and tetradecamethylcycloheptasiloxane (D7)) in a marine food web from coastal area of Northern China. Trophic magnification of D4, D5, D6, and D7 were assessed as the slope of lipid equivalent concentrations regressed against trophic levels of marine food web configurations. A significant positive correlation (R = 0.44, p < 0.0001) was found between lipid normalized D5 concentrations and trophic levels in organisms, showing the trophic magnification potential of this chemical in the marine food web. The trophic magnification factor (TMF) of D5 was estimated to be 1.77 (95% confidence interval (CI): 1.41-2.24, 99.8% probability of the observing TMF > 1). Such a significant link, however, was not found for D4 (R = 0.14 and p = 0.16), D6 (R = 0.01 and p = 0.92), and D7 (R = -0.15 and p = 0.12); and the estimated values of TMFs (95% CI, probability of the observing TMF > 1) were 1.16 (0.94-1.44, 94.7%), 1.01 (0.84-1.22, 66.9%) and 0.85 (0.69-1.04, 48.6%) for D4, D6, and D7, respectively. The TMF value for the legacy contaminant BDE-99 was also estimated as a benchmark, and a significant positive correlation (R = 0.65, p < 0.0001) was found between lipid normalized concentrations and trophic levels in organisms. The TMF value of BDE-99 was 3.27 (95% CI: 2.49-4.30, 99.7% probability of the observing TMF > 1), showing the strong magnification in marine food webs. To the best of our knowledge, this is the first report on the trophic magnification of methyl siloxanes in China, which provided important information for trophic transformation of these compounds in marine food webs.