Data_Sheet_1_Comparative Analysis of Total and Size-Fractionated Chlorophyll a in the Yellow Sea and Western Pacific.docx

Measurements of different size-fractionated chlorophyll a concentrations (Chl a) of phytoplankton assemblages in situ are vital for advancing our understanding of the phytoplankton size structure and thus the marine biogeochemical cycle. In the present study, we thus made a comparative analysis of total and size-fractionated Chl a in the Yellow Sea (YS) and Western Pacific (WP). Our results suggest that the total Chl a was highly variable in the YS (averaging ~1.02 μg L−1) and was generally 3–4-fold more than that in the WP (averaging ~0.30 μg L−1). The pico-sized Chl a had a significant contribution to total Chl a in the WP (range 75–88%), while the average contributions of the nano-sized and pico-sized Chl a to total Chl a in the YS were 47 and 38%, respectively, suggesting that a majority of the total Chl a in the YS was associated with nano- and picophytoplankton. Moreover, we applied the generalized additive models (GAMs) to explore the relationships between the total Chl a and that contained in each of the three size classes. These GAMs relationships suggested a continuum from picophytoplankton dominated waters to large phytoplankton (cells> 2 μm) domination with increasing Chl a. Finally, we made a comparison of the total Chl a obtained with GF/F filters and that measured from size-fractionated filtration and revealed that their corresponding concentrations are in good agreement, indicating the size-fractionated filtration had no effect on total Chl a determination.</p

DataSheet_1_Exploring the key factors affecting the seasonal variation of phytoplankton in the coastal Yellow Sea.doc

Marine phytoplankton play crucial roles in the ocean’s biological pump and have great impacts on global biogeochemical cycles, yet the knowledge of environmental variables controlling their seasonal dynamics needs to be improved further, especially in the coastal ecosystems. In order to explore the determinants affecting the seasonal variation of phytoplankton, here we conducted three surveys during spring, summer and autumn along the coastal Yellow Sea. Among the phytoplankton community, 49 species of diatoms and 9 species of dinoflagellates were observed in spring, 63 species of diatoms and 10 species of dinoflagellates in summer, and 62 species of diatoms and 11 species of dinoflagellates in autumn. These results thus suggested that there were obvious differences in the number of species across the three seasons, of which diatoms were the most diverse group, followed by dinoflagellates. Additionally, diatoms were the most dominant species of the phytoplankton community and varied largely during different seasons. According to the redundancy analysis, the abundance of phytoplankton community was mainly related to water temperature and dissolved inorganic nitrogen (DIN) during the three seasons, indicating that water temperature and DIN could be the key factors controlling the seasonal variability of phytoplankton community along the coastal Yellow Sea. Also, significant correlations were observed between phytoplankton abundance and heavy metals Zn, As, and Hg during the three seasons, suggesting that these metals also had potential influences on the seasonal dynamics of phytoplankton community in the coastal Yellow Sea.</p

Image3_Identification of potential target genes of breast cancer in response to Chidamide treatment.TIFF

Chidamide, a new chemically structured HDACi-like drug, has been shown to inhibit breast cancer, but its specific mechanism has not been fully elucidated. In this paper, we selected ER-positive breast cancer MCF-7 cells and used RNA-seq technique to analyze the gene expression differences of Chidamide-treated breast cancer cells to identify the drug targets of Chidamide’s anti-breast cancer effect and to lay the foundation for the development of new drugs for breast cancer treatment. The results showed that the MCF-7 CHID group expressed 320 up-regulated genes and 222 down-regulated genes compared to the control group; Gene Ontology functional enrichment analysis showed that most genes were enriched to biological processes. Subsequently, 10 hub genes for Chidamide treatment of breast cancer were identified based on high scores using CytoHubba, a plug-in for Cytoscape: TP53, JUN, CAD, ACLY, IL-6, peroxisome proliferator-activated receptor gamma, THBS1, CXCL8, IMPDH2, and YARS. Finally, a combination of the Gene Expression Profiling Interactive Analysis database and Kaplan Meier mapper to compare the expression and survival analysis of these 10 hub genes, TP53, ACLY, PPARG, and JUN were found to be potential candidate genes significantly associated with Chidamide for breast cancer treatment. Among them, TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. Therefore, we identified four genes central to the treatment of breast cancer with Chidamide by bioinformatics analysis, and clarified that TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. This study lays a solid experimental and theoretical foundation for the treatment of breast cancer at the molecular level with Chidamide and for the combination of Chidamide.</p

Image2_Identification of potential target genes of breast cancer in response to Chidamide treatment.TIF

Chidamide, a new chemically structured HDACi-like drug, has been shown to inhibit breast cancer, but its specific mechanism has not been fully elucidated. In this paper, we selected ER-positive breast cancer MCF-7 cells and used RNA-seq technique to analyze the gene expression differences of Chidamide-treated breast cancer cells to identify the drug targets of Chidamide’s anti-breast cancer effect and to lay the foundation for the development of new drugs for breast cancer treatment. The results showed that the MCF-7 CHID group expressed 320 up-regulated genes and 222 down-regulated genes compared to the control group; Gene Ontology functional enrichment analysis showed that most genes were enriched to biological processes. Subsequently, 10 hub genes for Chidamide treatment of breast cancer were identified based on high scores using CytoHubba, a plug-in for Cytoscape: TP53, JUN, CAD, ACLY, IL-6, peroxisome proliferator-activated receptor gamma, THBS1, CXCL8, IMPDH2, and YARS. Finally, a combination of the Gene Expression Profiling Interactive Analysis database and Kaplan Meier mapper to compare the expression and survival analysis of these 10 hub genes, TP53, ACLY, PPARG, and JUN were found to be potential candidate genes significantly associated with Chidamide for breast cancer treatment. Among them, TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. Therefore, we identified four genes central to the treatment of breast cancer with Chidamide by bioinformatics analysis, and clarified that TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. This study lays a solid experimental and theoretical foundation for the treatment of breast cancer at the molecular level with Chidamide and for the combination of Chidamide.</p

Image1_Identification of potential target genes of breast cancer in response to Chidamide treatment.TIF

Chidamide, a new chemically structured HDACi-like drug, has been shown to inhibit breast cancer, but its specific mechanism has not been fully elucidated. In this paper, we selected ER-positive breast cancer MCF-7 cells and used RNA-seq technique to analyze the gene expression differences of Chidamide-treated breast cancer cells to identify the drug targets of Chidamide’s anti-breast cancer effect and to lay the foundation for the development of new drugs for breast cancer treatment. The results showed that the MCF-7 CHID group expressed 320 up-regulated genes and 222 down-regulated genes compared to the control group; Gene Ontology functional enrichment analysis showed that most genes were enriched to biological processes. Subsequently, 10 hub genes for Chidamide treatment of breast cancer were identified based on high scores using CytoHubba, a plug-in for Cytoscape: TP53, JUN, CAD, ACLY, IL-6, peroxisome proliferator-activated receptor gamma, THBS1, CXCL8, IMPDH2, and YARS. Finally, a combination of the Gene Expression Profiling Interactive Analysis database and Kaplan Meier mapper to compare the expression and survival analysis of these 10 hub genes, TP53, ACLY, PPARG, and JUN were found to be potential candidate genes significantly associated with Chidamide for breast cancer treatment. Among them, TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. Therefore, we identified four genes central to the treatment of breast cancer with Chidamide by bioinformatics analysis, and clarified that TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. This study lays a solid experimental and theoretical foundation for the treatment of breast cancer at the molecular level with Chidamide and for the combination of Chidamide.</p

Image4_Identification of potential target genes of breast cancer in response to Chidamide treatment.TIF

Chidamide, a new chemically structured HDACi-like drug, has been shown to inhibit breast cancer, but its specific mechanism has not been fully elucidated. In this paper, we selected ER-positive breast cancer MCF-7 cells and used RNA-seq technique to analyze the gene expression differences of Chidamide-treated breast cancer cells to identify the drug targets of Chidamide’s anti-breast cancer effect and to lay the foundation for the development of new drugs for breast cancer treatment. The results showed that the MCF-7 CHID group expressed 320 up-regulated genes and 222 down-regulated genes compared to the control group; Gene Ontology functional enrichment analysis showed that most genes were enriched to biological processes. Subsequently, 10 hub genes for Chidamide treatment of breast cancer were identified based on high scores using CytoHubba, a plug-in for Cytoscape: TP53, JUN, CAD, ACLY, IL-6, peroxisome proliferator-activated receptor gamma, THBS1, CXCL8, IMPDH2, and YARS. Finally, a combination of the Gene Expression Profiling Interactive Analysis database and Kaplan Meier mapper to compare the expression and survival analysis of these 10 hub genes, TP53, ACLY, PPARG, and JUN were found to be potential candidate genes significantly associated with Chidamide for breast cancer treatment. Among them, TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. Therefore, we identified four genes central to the treatment of breast cancer with Chidamide by bioinformatics analysis, and clarified that TP53 may be a potential target gene for Chidamide to overcome multi-drug resistance in breast cancer. This study lays a solid experimental and theoretical foundation for the treatment of breast cancer at the molecular level with Chidamide and for the combination of Chidamide.</p

Image_1_Comparative investigation on heterotrophic denitrification driven by different biodegradable polymers for nitrate removal in mariculture wastewater: Organic carbon release, denitrification performance, and microbial community.TIF

Heterotrophic denitrification is widely studied to purify freshwater wastewater, but its application to seawater wastewater is rarely reported. In this study, two types of agricultural wastes and two types of synthetic polymers were selected as solid carbon sources in denitrification process to explore their effects on the purification capacity of low-C/N marine recirculating aquaculture wastewater (NO3−-N 30 mg/L, salinity 32‰). The surface properties of reed straw (RS), corn cob (CC), polycaprolactone (PCL) and poly3-hydroxybutyrate-hydroxypropionate (PHBV) were evaluated by Brunauer–Emmett–Teller, Scanning electron microscope and Fourier-transform infrared spectroscopy. Short-chain fatty acids, dissolved organic carbon (DOC), and chemical oxygen demand (COD) equivalents were used to analyze the carbon release capacity. Results showed that agricultural waste had higher carbon release capacity than PCL and PHBV. The cumulative DOC and COD of agricultural waste were 0.56–12.65 and 1.15–18.75 mg/g, respectively, while those for synthetic polymers were 0.07–1.473 and 0.045–1.425 mg/g, respectively. The removal efficiency of nitrate nitrogen (NO3−-N) was CC 70.80%, PCL 53.64%, RS 42.51%, and PHBV 41.35%. Microbial community analysis showed that Proteobacteria and Firmicutes were the most abundant phyla in agricultural wastes and biodegradable natural or synthetic polymers. Quantitative real-time PCR indicated the conversion from nitrate to nitrogen was achieved in all four carbon source systems, and all six genes had the highest copy number in CC. The contents of medium nitrate reductase, nitrite reductase and nitrous oxide reductase genes in agricultural wastes were higher than those in synthetic polymers. In summary, CC is an ideal carbon source for denitrification technology to purify low C/N recirculating mariculture wastewater.</p

Data_Sheet_1_Diversity, structure, and distribution of bacterioplankton and diazotroph communities in the Bay of Bengal during the winter monsoon.docx

The Bay of Bengal (BoB) is conventionally believed to be a low productive, oligotrophic marine ecosystem, where the diazotroph communities presumed to play a vital role in adding “new” nitrogen through the nitrogen fixation process. However, the diazotroph communities in the oceanic region of the BoB are still poorly understood though it represents most of the seawater volume. The present study investigated a detailed account of the bacterioplankton community structure and distribution in the oceanic BoB during the winter monsoon using high throughput sequencing targeting the 16S rRNA and nifH genes. Our study observed diverse groups of bacterioplankton communities in the BoB including both cyanobacterial and non-cyanobacterial phylotypes. Cyanobacteria (Prochlorococcus spp. and Synechococcus spp.) and Proteobacteria (mainly α-, γ-, and δ-Proteobacteria) were the most abundant groups within the bacterial communities, possessing differential vertical distribution patterns. Cyanobacteria were more abundant in the surface waters, whereas Proteobacteria dominated the deeper layers (75 m). However, within the diazotroph communities, Proteobacteria (mainly γ-Proteobacteria) were the most dominant groups than Cyanobacteria. Function prediction based on PICRUSt revealed that nitrogen fixation might more active to add fixed nitrogen in the surface waters, while nitrogen removal pathways (denitrification and anammox) might stronger in deeper layers. Canonical correspondence analysis (CCA) indicated that temperature, salinity, and silicate were major environmental factors driving the distribution of bacterial communities. Additionally, phosphate was also an important factor in regulating the diazotroph communities in the surface water. Overall, this study provided detailed information on bacterial communities and their vital role in the nitrogen cycles in oligotrophic ecosystems.</p

DataSheet_1_Effect of Mytilus coruscus selective filtration on phytoplankton assemblages.docx

The feeding selectivity of bivalves can play an important role in shaping the structure of phytoplankton communities of natural waters. This could be particularly true in waters with intensive bivalves farming, like Sungo Bay, Northern China. Understanding the role of bivalve feeding behavior is important for assessing how the dense cultivation of bivalves may affect phytoplankton community composition and food web structure in farm areas. In this study, we investigated the feeding selectivity of blue mussel Mytilus coruscus on natural phytoplankton assemblages in Sungo Bay using both optical microscopy and HPLC-pigment analysis. Results showed that cryptophytes dominated the phytoplankton community and made up 66.1% of the total phytoplankton abundance. A comparison of phytoplankton composition between natural and filtered seawater showed that M. coruscus preferred cryptophytes and dinoflagellates than Chaetoceros spp. and Skeletonema spp. Cryptophytes were not detected in gut contents by microscopic observation, while their marker pigment alloxanthin was present, suggesting they were also consumed by M. coruscus and can be readily digested. This highlights the shortcomings of microscopic methods and the significance of HPLC-pigment analysis in obtaining a comprehensive understanding of feeding selectivity of bivalves. The proportions of Chaetoceros spp. and Skeletonema spp. in gut contents were significantly lower than their proportions in the seawater, and contrastingly, the proportions of Cocconeis spp. and Pinnularia spp. showed opposite patterns. The marker pigments prasinoxanthin and zeaxanthin were detected in the gut of M. coruscus indicating that picophytoplankton (e.g., prasinophytes and Synechococcus) are also food sources for this bivalve. This information furthers our understanding of bivalve aquaculture and environment interactions.</p