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Aberrant RNA splicing is recognized to contribute to cancer pathogenesis, but the underlying mechanisms remain mainly obscure. Here, we report that the splicing factor SRSF2 is upregulated frequently in human hepatocellular carcinoma (HCC), where this event is associated with poor prognosis in patients. RNA-seq and other molecular analyses were used to identify SRSF2-regulated alternative splicing events. SRSF2 binding within an alternative exon was associated with its inclusion in the RNA, whereas SRSF2 binding in a flanking constitutive exon was associated with exclusion of the alternative exon. Notably, cancer-associated splice variants upregulated by SRSF2 in clinical specimens of HCC were found to be crucial for pathogenesis and progression in hepatoma cells, where SRSF2 expression increased cell proliferation and tumorigenic potential by controlling expression of these variants. Our findings identify SRSF2 as a key regulator of RNA splicing dysregulation in cancer, with possible clinical implications as a candidate prognostic factor in patients with HCC. Cancer Res; 77(5); 1168–78. ©2017 AACR.

Supplementary Fig S1. SRSF2 increases colony-forming efficiencies of hepatocarcinoma cells. Supplementary Fig S2. Exogenous expression of SRSF2 in KD cells restores WT splicing patterns of SRSF2-targeted transcripts. Supplementary Fig S3. Knockdown of SRSF10 and hnRNPK has no obvious effects on the SRSF2-regulated splicing events. Supplementary Fig S4. HCC-related splice variants are examined for their functions in SK-Hep-1 and Huh7 cells. Supplementary Fig S5. Both GCH-L and STK39-L variants are required for cell growth in vitro. Supplementary Fig S6. Overexpression of GCH1-L or STK39-L slightly increases colony-forming efficiencies of SRSF2-depleted cells. Supplementary Table S1: Relationship between expression of SRSF2 in HCC and clinical and pathological features of the individuals. Supplementary Table S2: Summary of RNA-seq data mapping results. Supplementary Table S3: Relationship between ratios of GCH1-E6(IN/EX) in HCC and clinical and pathological features of the individuals from TCGA database. Supplementary Table S4: Relationship between expression of SRSF2 in HCC and clinical and pathological features of the individuals from TCGA database.

Microplastics are readily accumulated in coastal sediments, where active sulfur (S) cycling takes place. However, the effects of microplastics on S cycling in coastal sediments and their underlying mechanisms remain poorly understood. In this study, the transformation patterns of different S species in mangrove sediments amended with different microplastics and their associated microbial communities were investigated using stable isotopic analysis and metagenomic sequencing. Biodegradable poly(lactic acid) (PLA) microplastics treatment increased sulfate (SO

Rhizoremediation is a potential technique for PAH remediation; however, the catabolic pathways of in situ rhizosphere PAH degraders and the main factors driving PAH rhizoremediation remain unclear. To address these issues, stable-isotope-probing coupled with metagenomics and molecular ecological network analyses were firstly used to investigate the phenanthrene rhizoremediation by three different prairie grasses in this study. All rhizospheres exhibited a significant increase in phenanthrene removal and markedly modified the diversity of phenanthrene degraders by increasing their populations and interactions with other microbes. Of all the active phenanthrene degraders, Marinobacter and Enterobacteriaceae dominated in the bare and switchgrass rhizosphere, respectively; Achromobacter was markedly enriched in ryegrass and tall fescue rhizospheres. Metagenomes of 13 C-DNA illustrated several complete pathways of phenanthrene degradation for each rhizosphere, which clearly explained their unique rhizoremediation mechanisms. Additionally, propanoate and inositol phosphate of carbohydrates were identified as the dominant factors that drove PAH rhizoremediation by strengthening the ecological networks of soil microbial communities. This was verified by the results of rhizospheric and non-rhizospheric treatments supplemented with these two substances, further confirming their key roles in PAH removal and in situ PAH rhizoremediation. Our study offers novel insights into the mechanisms of in situ rhizoremediation at PAH-contaminated sites. This article is protected by copyright. All rights reserved.

The function and change of global soil carbon (C) reserves in natural ecosystems are key regulators of future carbon-climate coupling. Microbes play a critical role in soil carbon cycling and yet there is poor understanding of their roles and C metabolism flexibility in many ecosystems. We wanted to determine whether vegetation type and climate zone influence soil microbial community composition (fungi and bacteria) and carbon resource preference. We used a biomarker (phospholipid fatty acids, PLFAs), natural abundance 13C and 14C probing approach to measure soil microbial composition and C resource use, along a 1900–4167-m elevation gradient on Mount Gongga (7556 m asl), China. Mount Gongga has a vertical mean annual temperature gradient of 1.2–10.1°C and a diversity of typical vegetation zones in the Tibetan Plateau. Soils were sampled at 10 locations along the gradient capturing distinct vegetation types and climate zones from lowland subtropical-forest to alpine-meadow. PLFA results showed that microbial communities were composed of 2.1–51.7% bacteria and 2.0–23.2% fungi across the elevation gradient. Microbial biomass was higher and the ratio of soil fungi to bacteria (F/B) was lower in forest soils compared to meadow soils. δ13C varied between −33‰ to −17‰ with C3 plant carbon sources dominant across the gradient. Soil organic carbon (SOC) turnover did not vary among three soils we measured from three forest types (i.e., evergreen broadleaved subtropical, mixed temperate, coniferous alpine) and dissolved organic carbon (DOC) turnover decreased with soil elevation. Forest soil microbial PLFA 14C and δ13C measurements showed that forest type and climate were related to different microbial C use. The 14C values of microbial PLFAs i15, a15, 16:1, br17 decreased with elevation while those of C16:0, cyC17, and cyC19 did not show much difference among three forest ecosystems. Bacteria and bacillus represented by C16:1 and brC17 showed considerable microbial C metabolism flexibility and tended to use ancient carbon at higher altitudes. Anaerobes represented by cyC17 and cyC19 showed stronger C metabolism selectivity. Our findings reveal specific C source differences between and within soil microbial groups along elevation gradients.

Organophosphate flame retardants (OPFRs), as a replacement for polybrominated diphenyl ethers (PBDEs), are of increasing concern due to their high production over the years. Soil is the major environmental reservoir and interchange for OPFRs. OPFRs in soil could be transferred to the food chain, and pose potential ecological and human health risks. This review focused on the environmental fate and effects of typical OPFRs in the soil-plant system. We concluded that the sorption and transformation behaviors of OPFRs due to their crucial impact on bioavailability. The root uptake and translocation of OPFRs by plants were summarized with analyses of their potential affecting factors. The in planta transformation and potential ecological effects of OPFRs were also briefly discussed. Finally, we highlighted several research gaps and provided suggestions for future research, including the development of simulative/computative methods to evaluate the bioavail-ability of OPFRs, the effects of root exudates and rhizosphere microorganisms on the bioavailability and plant uptake of OPFRs, and the development of green and sustainable technologies for in situ remediation of OPFRs-contaminated soil.

Plant uptake and translocation of perfluorooctane sulfonate (PFOS) are critical for food safety and raise major concerns. However, those processes are associated with many undisclosed mechanisms, especially when PFOS coexist with heavy metals. In this study, we investigated the effect of copper (Cu) on PFOS distribution in maize tissues by assessing the PFOS concentration and enantioselectivity. The presence of100 μmol/L Cu exerted a limited effect on PFOS bioaccumulation, while100 μmol/L Cu damaged the root cell membrane and increased root permeability, resulting in a higher PFOS concentration in roots. The suppression of acropetal translocation might be attributed to Cu inhibition of carrier proteins. The enantiomer fraction (EF) of 1m-PFOS at100 μmol/L Cu was higher than that in a commercial product (0.5). Racemic PFOS was detected at100 μmol/L Cu in roots and the EF variation changed from positive to negative in shoots. These EF results evidenced the existence of a protein-mediated uptake pathway. Besides, this study indicated the challenge of chiral signature application in PFOS source identification, given the effects of heavy metals and plants on PFOS enantioselectivity. The findings provide insight into PFOS bioaccumulation in plants cocontaminated with Cu and will facilitate environmental risk assessment.

Mass Rapid Transit (MRT) systems, i.e. subway systems, all over the world, are experiencing an increase in ridership. This also means that in case of an unplanned MRT service disruption, the number of affected passengers is larger, requiring a fast and comprehensive response. In this paper, we thus study the disruption management of MRT systems. We develop an optimization model to identify the optimal bridging plan in response to an MRT disruption, so that the negative effects of a disruption could be minimized. Our approach supports deployment of multiple types of bridging buses, reflecting the diversity of vehicle types in a typical public transportation provider’s vehicle fleet. The optimization objective of our approach is to decrease the travel delay of passengers and increase the number of passengers who can be served. We demonstrate the effectiveness of our approach on a hypothetical case study in the central business district of Singapore. Moreover, we validate our analytical results with microscopic simulation, showing that our simplified analytical optimization approach can be used for disruption response planning. Some deviations indicate, however, that a combined simulation and optimization approach yields better results to obtain an effective bridging plan.

Co-contamination of heavy metals and organic pollutants is widespread in the environment. Metal-tolerant/hyperaccumulating plants have the advantage of enhancing co-operation between plants and rhizospheric microbes under heavy metal stress, but the underlying mechanism remains unclear. In the present study, the effects of Elsholtzia splendens and Lolium perenne on the rhizospheric microbial community and degraders of phenanthrene (PHE) and polychlorinated biphenyls (PCBs) were investigated. The results showed E. splendens could tolerate high Cu concentrations, while L. perenne was sensitive to Cu toxicity. Although Cu played the most important role in microbial community construction, both E. splendens and L. perenne caused shifts in the rhizospheric microbial community. For PHE and PCB degradation, L. perenne was more efficient under low Cu concentrations, whereas E. splendens performed better under high Cu concentrations. This difference can be attributed to shifts in the degrader community and key degradation genes identified by stable isotope probing. Moreover, higher abundances of various genes for organic pollutant degradation were observed in the rhizosphere of E. splendens than L. perenne based on gene prediction under high Cu stress. Our study reveals underlying mechanism of the advantages of heavy metal-tolerant plants for organic pollutant removal in soils co-contaminated with heavy metals.

Biochar has been widely used for the remediation of polycyclic aromatic hydrocarbon (PAH)-contaminated soil, but its mechanism of influencing PAH biodegradation remains unclear. Here, DNA-stable isotope probing coupled with high-throughput sequencing was employed to assess its influence on phenanthrene (PHE) degradation, the active PHE-degrading microbial community and PAH-degradation genes (PAH-RHD

In this paper, we propose a new concept of almost second-degree stochastic dominance (ASSD), which we term almost risk-averse stochastic dominance (ARSD). Compared with existing ASSD conditions, ARSD can exclude extremely risk-averse utility functions. Hence, ARSD is able to reveal clear preferences of most risk-averse decision makers in practice, which are otherwise unable to be revealed. The simple closed-form of ARSD not only makes it easy to use in practice but also provides a clear insight into the preferences of decision makers and the difference in expected values and stochastic dominance violations. Moreover, we show that ARSD can be inferred based on mean and variance alone, and thus it is applicable even when distribution information is incomplete.

In this paper, we propose the concept of maximum excess dominance (MED) and illustrate how it can be used to compare solutions in linear optimization problems with interval objective coefficients. When a solution dominates another solution with MED, the expected outcome of the former is guaranteed to be better than that of the latter across a wide range of probability distributions. Hence, MED can be used to eliminate dominated solutions from consideration. Furthermore, we provide an efficient way to check if a solution is dominated by another feasible solution in binary optimization problems and illustrate how dominated solutions can be pruned away by introducing MED constraints to the original binary optimization formulation. We also propose an algorithm to find the best non-dominated solution and conduct computational experiments to evaluate its performance.

Organophosphate esters (OPEs) are normally used as flame retardants, plasticizers and lubricants, but have become environmental pollutants. Because OPEs are normally present alongside heavy metals in soils, the effects of interactions between OPEs and heavy metals on plant uptake of OPEs need to be determined. In this study, we investigated the effects of OPEs chemical structure, plant cultivar and copper (Cu) on the uptake and translocation of OPEs by plants. The bioaccumulation of OPEs varied among plant cultivars. They were preferentially enriched in carrot, with the lowest concentrations observed in maize. OPEs with electron-ring substituents (ER-OPEs) exhibited a higher potential for root uptake than did OPEs with open-chain substituents (OC-OPEs), which could be attributed to the higher sorption of ER-OPEs onto root charged surfaces. This was explained by the stronger noncovalent interactions with the electron-rich structure of ER-OPEs. The presence of Cu slightly reduced the distinct difference in the ability of roots to take up OC-OPEs and ER-OPEs. This was explained by the interactions of Cu ions with the electron-rich structure of ER-OPEs, which suppressed the sorption of ER-OPEs on the root surface. A negative relationship between the logarithms of the translocation factor and octanol-water partition coefficient (Kow) was observed in treatments with either OPEs only or OPEs + Cu, implying the significant role of hydrophobicity in the OPEs acropetal translocation. The results will improve our understanding of the uptake and translocation of OPEs by plant cultivars as well as how the process is affected by the chemical structure of OPEs and Cu, leading to improvements in the ecological risk assessment of OPEs in the food chain.

The combination of microbial reductive dechlorination and aerobic oxidation (RD-AO) process was proposed to be a promising strategy for extensive bioremediation of highly chlorinated polychlorinated biphenyls (PCBs). Nonetheless, experimental evidence on the impact of the RD on subsequent AO in anaerobic-aerobic two-stage treatment remains scarce. The present study applied stable-isotope probing (SIP) to explore the RD-AO mediated degradation of PCBs in an e-waste-contaminated soil. The RD-AO treatment resulted in 37.1 % and 48.2 % degradation of PCB180 and PCB9, respectively, while the PCB9 degradation efficiency decreased compared to the sole AO (81.2 %). The inhibition of PCB aerobic degradation might be caused by the alteration of aerobic bacterial community, which was proved by a higher abundance of anaerobic bacteria and a lower abundance of aerobic bacteria being observed in the aerobic stage of RD-AO. Further evidence was obtained using DNA-SIP that the anaerobic stage altered the PCB degraders' community structures and changed three of the five degraders. There were four lineages (Arenimonas, Steroidobacter, Sulfurifustis, and Thermoanaerobacterales) identified as PCB degraders for the first time. Interestingly, three of them were found in RD-AO microcosm, suggesting that anaerobic-aerobic two-stage treatment can recruit novel bacteria involved in PCBs aerobic degradation. The present study provided novel insight into the synergistic integration of anaerobic and aerobic processes for extensive degradation of highly chlorinated PCBs.

Background: Cyanobacterial bloom challenges the aquatic ecosystem and ecological restoration is an effective approach for cyanobacterial bloom control, but the change of aquatic community after ecological restoration is still unclear. Dianchi Lake is a eutrophic lake with frequent cyanobacterial blooms in China, and recent ecological restoration projects in Caohai (north part) have a satisfactory performance. In this study, we collected 249 water samples at 23 sites from Dianchi Lake to explore the relationships between water physiochemical variables and aquatic microbial communities.Results: Water physicochemical variables in Waihai (south part) intensively changed along time, whereas those in Caohai did not. Photoautotrophic communities were significantly divergent between Caohai and Waihai. Waihai had a lower diversity of photoautotrophic community, containing higher abundance of Cyanophyceae (89.9%) than Caohai (42.7%). Nutrient level and Cyanophyceae only exhibited strong correlations in Wahai (p90% for photoautotrophs), and particularly in Caohai.Conclusions: Our results unraveled that the structure and assembly of bacterial and photoautotrophic communities significantly changed after ecological restoration, offering valuable suggestions that photosynthetic diversity should be focused for other ecological restoration projects.

The indigenous microorganisms with the ability of metabolising di-(2-ethylhexyl) phthalate (DEHP) in agricultural soils and their interactions with non-degrading microbes were revealed by DNA-based stable isotope probing coupled with molecular ecological network. Aside from the previously reported DEHP degraders (family Planococcaceae and genus Sphingobacterium), five OTUs representing bacteria affiliated with genus Brevundimona, class Spartobacteria, genus Singulisphaera, genus Dyella and class Ktedonobacteria were linked with DEHP biodegradation. The analysis of the constructed ecological network based on soil microbial communities demonstrated the negative relationships between DEHP degraders and the dominant family Oxalobacteraceae in soils. Additionally, two cultivable bacteria isolated from the same soils, Rhizobium-1 and Ensifer-1, had strong capabilities in degrading DEHP but their involvement in in situ DEHP degradation was questioned, as their DNA was not labelled with 13C from DEHP. These findings provide deeper understanding on the indigenous DEHP-degrading communities and will benefit the remediation of phthalate esters contaminated soils.

Atrazine (2-chloro-4-ethylamino-6-isopropylamino-1,3,5-triazine) is a triazine herbicide intensively used in agricultural production and is often detected in different environmental matrices at concentrations above the permitted limit. This study investigated the influence of two earthworm species (epigeic Eisenia foetida and endogeic Amynthas robustus) on atrazine speciation and the degradation pathway. Our results revealed that both earthworms significantly accelerated atrazine degradation in a 28-day vermiremediation, and the residual atrazine declined from 4.23 ± 0.21 mg/kg in bulk soils to 0.51 ± 0.29 mg/kg (E. foetida) and 0.43 ± 0.19 mg/kg (A. robustus). By consuming organic matter (from 40.37 ± 1.14 to 36.31 ± 1.55 and 34.59 ± 1.13 g/kg for E. foetida and A. robustus) and neutralizing the soil pH (from 5.37 ± 0.27 to 6.36 ± 0.11 and 6.61 ± 0.30 for E. foetida and A. robustus), both earthworms reduced humus-fixed atrazine and increased the available atrazine. The percentage of available atrazine increased from 8.80 ± 0.21% in bulk soil to 10.30 ± 0.29% and 16.42 ± 0.18% in the vermiremediation treatments. Both earthworms promoted the hydroxyatrazine pathway by consuming soil organic matter and encouraged the deethylatrazine/deisopropylatrazine pathway by neutralizing the soil pH. Our findings unravel a new mechanism of vermiremediation by improving the soil physical-chemical properties and altering the atrazine degradation pathway, providing new insights into the influential factors on atrazine bioremediation in red soil.

Root exudates can stimulate microbial degradation within the rhizosphere, but their exact roles are embedded within the complicated rhizospheric effects. In the present study, we applied both 12C- and 13C-phenanthrene to distinguish the effects of root exudates within ryegrass rhizosphere on phenanthrene degradation via DNA stable isotope probing (DNA-SIP). A significant increase of phenanthrene biodegradation efficiency (10.7%) was found in ryegrass rhizosphere compared to bulk soils, but not in soils supplemented with ryegrass root exudates. Results from high-throughput sequencing and computational analyses suggested that treatments with both ryegrass rhizosphere and root exudates markedly increased total bacterial populations and shaped the composition of the active phenanthrene-degrader community. Of all the phenanthrene-degraders belonging to eight bacterial classes revealed by DNA-SIP, only Alphaproteobacteria and Nitrososphaeria were shared between bulk soils, ryegrass rhizosphere and soils supplemented with ryegrass root exudates. Sphingobacteriia and Actinobacteria were active phenanthrene-degraders within both ryegrass rhizosphere and soils supplemented with ryegrass root exudates, whereas others were observed only in bulk soils or soils supplemented with ryegrass root exudates. Most of the degraders were linked to phenanthrene degradation for the first time based on their incorporation of 13C-phenanthrene. In 13C-phenanthrene microcosms, the relative abundance of PAH-RHDα genes and active phenanthrene-degraders was strongly correlated with phenanthrene degradation efficiency. Compared to the rhizosphere, root exudates provided a minor contribution to the abundance of PAH-RHDα gene. This study helps in better understanding the roles of root exudates supplement in the phenanthrene biodegradation process within the rhizosphere and provides theoretical insights into the mechanisms of enhanced phenanthrene degradation via phytoremediation at PAH-contaminated sites.

This paper studies the resilient performance of urban rail transit systems by extending a linear programming optimization model, which can provide optimized commuter flows with contingency routing under multiple disruptions. The rail transit systems in Singapore and Chongqing (China) are selected as case studies, and the system resilience and the effectiveness of providing bus-bridging services are comparatively studied. Intuitively, failures of the interchange stations would inevitably lead to a significant loss of resilience due to deteriorated network connectivity. However, the Singapore case shows that attacking those interchange stations does not always result in an extensive resilience loss. Comparing with the Chongqing case, it is discernible that the position of interchange stations would affect the system resilience. The numerical simulations reveal that the positive effect of providing bus-bridging strategy, in terms of improving the system resilience, is heterogeneous in different systems, which varies from 14% to 30% on average. As demonstrated in the sensitivity on travel demands, this positive effect is robust, yet dynamic, indicating that there is no one-size-fits-all solution for designing transfer-based recovery strategies in disruption management of rail transit systems. The managerial implications for decision makers are also provided and discussed in terms of infrastructure planning.

Per- and polyfluoroalkyl substances (PFASs) are ubiquitous in the environment but pose potential risks to ecosystems and human health. The soil–plant system plays an important role in the bioaccumulation of PFASs. Because most PFASs in the natural environment are anionic and amphiphilic (both lipophilic and hydrophilic), their sorption and accumulation behaviors differ from those of neutral organic and common ionic compounds. In this review, we discuss processes affecting the availability of PFASs in soil after analyzing the potential mechanisms underlying the sorption and uptake of PFASs in the soil–plant system. We also summarize the current knowledge on root uptake and translocation of PFASs in plants. We found that the root concentration factor of PFASs for plants grown in soil was not significantly correlated with hydrophobicity, whereas the translocation factor was significantly and negatively correlated with PFAS hydrophobicity regardless of whether plants were grown hydroponically or in soil. Further research on the cationic, neutral, and zwitterionic forms of diverse PFASs is urgently needed to comprehensively understand the environmental fates of PFASs in the soil–plant system. Additional research directions are suggested, including the development of more accurate models and techniques to evaluate the bioavailability of PFASs, the effects of root exudates and rhizosphere microbiota on the bioavailability and plant uptake of PFASs, and the roles of different plant organelles, lipids, and proteins in the accumulation of PFASs by plants.

This study provides new knowledge on the mobility, behavior, and partitioning of 17 perfluoroalkyl substances (PFASs) in the water-sediment-plant system along the Dongzhulong and Xiaoqing Rivers. The fate of PFASs in these rivers is also discussed. The study area is affected by the industrial production of perfluorooctanoic acid (PFOA). The ∑PFASs in water and sediments close to the industrial discharge were 84,000 ± 2000 ng/L and 2300 ± 200 ng/g dw, respectively, with the concentrations decreasing along the river due to dilution. PFOA was the dominant compound (74–97% of the ∑PFASs), although other PFASs were identified close to urban areas. Principal component analysis and solid-liquid distribution coefficients revealed that long-chain PFASs accumulated in the sediment whereas short-chain PFASs remained in the water all along the river. PFASs were taken up by plants and remobilized to different plant compartments according to shoot concentration factors (SCFs), root concentration factors (RCF), and transfer factors (TFs). Among the four plant species studied, floating plants absorbed high levels of PFASs, while rooted species translocated short-chain PFASs from the roots to the shoots. Therefore, floating species, due to their high uptake capacity and large proliferation rate, could eventually be used for phytoremediation., Pere Colomer Vidal acknowledges the funding from the European Union Europe Aid ‘SEW-REAP’ project [ECRIP ICI+/2014/348–010]. The Spanish Ministry of Science and Innovation under the grant PID2019–105732GB-C21 and the Local Innovative and Research Teams Project of the Guangdong Pearl River Talents Program (2017BT01Z134) provided financial support. Dr. Chunling Luo would like to thank the support from the Ten Thousand Talent Program of the Organization Department of the Central Committee of the CPC. This work was carried out at the facilities of the Guangzhou Institute of Geochemistry.