Image_8_Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources.tif

IntroductionIn marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.MethodsUnder laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.ResultsThe results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.DiscussionThe above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.</p

Image_2_Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources.tif

IntroductionIn marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.MethodsUnder laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.ResultsThe results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.DiscussionThe above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.</p

Image_3_Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources.tif

IntroductionIn marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.MethodsUnder laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.ResultsThe results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.DiscussionThe above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.</p

Image_1_Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources.tif

IntroductionIn marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.MethodsUnder laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.ResultsThe results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.DiscussionThe above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.</p

Image_5_Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources.tif

IntroductionIn marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.MethodsUnder laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.ResultsThe results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.DiscussionThe above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.</p

DataSheet_3_Single-Cell Transcriptome Analysis Reveals RGS1 as a New Marker and Promoting Factor for T-Cell Exhaustion in Multiple Cancers.xlsx

T-cell exhaustion is one of the main reasons of tumor immune escape. Using single-cell transcriptome data of CD8+ T cells in multiple cancers, we identified different cell types, in which Pre_exhaust and exhausted T cells participated in negative regulation of immune system process. By analyzing the coexpression network patterns and differentially expressed genes of Pre_exhaust, exhausted, and effector T cells, we identified 35 genes related to T-cell exhaustion, whose high GSVA scores were associated with significantly poor prognosis in various cancers. In the differentially expressed genes, RGS1 showed the greatest fold change in Pre_exhaust and exhausted cells of three cancers compared with effector T cells, and high expression of RGS1 was also associated with poor prognosis in various cancers. Additionally, RGS1 protein was upregulated significantly in tumor tissues in the immunohistochemistry verification. Furthermore, RGS1 displayed positive correlation with the 35 genes, especially highly correlated with PDCD1, CTLA4, HAVCR2, and TNFRSF9 in CD8+ T cells and cancer tissues, indicating the important roles of RGS1 in CD8+ T-cell exhaustion. Considering the GTP-hydrolysis activity of RGS1 and significantly high mRNA and protein expression in cancer tissues, we speculated that RGS1 potentially mediate the T-cell retention to lead to the persistent antigen stimulation, resulting in T-cell exhaustion. In conclusion, our findings suggest that RGS1 is a new marker and promoting factor for CD8+ T-cell exhaustion and provide theoretical basis for research and immunotherapy of exhausted cells.</p

Image_7_Response of bacterial communities (Marivita, Marinobacter, and Oceanicaulis) in the phycosphere to the growth of Phaeodactylum tricornutum in different inorganic nitrogen sources.tif

IntroductionIn marine ecosystems, microbial communities are important drivers of material circulation and energy flow. The complex interactions between phytoplankton and bacterial communities constitute one of the most crucial ecological relationships in the marine environment. Inorganic nitrogen can affect the type of relationship between algae and bacteria. However, the quantitative relationship between the bacterial communities, inorganic nitrogen, and phytoplankton remains unclear.MethodsUnder laboratory conditions, we altered the forms (nitrate and ammonium) and amounts of nitrogen sources to study the dynamics of bacterial biomass, diversity, and community structure in the phycosphere of the marine model species Phaeodactylum tricornutum. The bacterial community structure during P. tricornutum growth was analyzed using Illumina HiSeq sequencing of 16S rDNA amplicons.ResultsThe results indicated that inorganic nitrogen concentration was the main factor promoting P. tricornutum biomass growth. The change in the algal biomass would significantly increase the phycosphere bacterial biomass. The bacterial biomass in the algal-bacteria co-culture system was 1.5 ~ 5 times that of the conditional control groups without microalgae under the same culture conditions. The variation of P. tricornutum biomass also affected the bacterial communities in the phycosphere. When P. tricornutum was in the exponential phase (96 ~ 192 h), the bacterial community structure differed between the high- and low-concentration groups. The difference in the bacterial communities over time in the high-concentration groups was more prominent than in the low-concentration groups. Under high-concentration groups (HA and HN), the relative abundance of Marivita and Marinobacter, engaged in the transformation of aquatic inorganic nitrogen, gradually decreased with time. However, the relative abundance of Oceanicaulis, closely related to algal growth, gradually increased with time.DiscussionThe above phenomena might be related to the change in P. tricornutum biomass. Our results explain when and how the phycosphere bacterial communities responded to algal biomass variations. The study provides a foundation for the quantitative relationship among nutrients, microalgae, and bacteria in this system.</p

DataSheet_1_Single-Cell Transcriptome Analysis Reveals RGS1 as a New Marker and Promoting Factor for T-Cell Exhaustion in Multiple Cancers.xlsx

T-cell exhaustion is one of the main reasons of tumor immune escape. Using single-cell transcriptome data of CD8+ T cells in multiple cancers, we identified different cell types, in which Pre_exhaust and exhausted T cells participated in negative regulation of immune system process. By analyzing the coexpression network patterns and differentially expressed genes of Pre_exhaust, exhausted, and effector T cells, we identified 35 genes related to T-cell exhaustion, whose high GSVA scores were associated with significantly poor prognosis in various cancers. In the differentially expressed genes, RGS1 showed the greatest fold change in Pre_exhaust and exhausted cells of three cancers compared with effector T cells, and high expression of RGS1 was also associated with poor prognosis in various cancers. Additionally, RGS1 protein was upregulated significantly in tumor tissues in the immunohistochemistry verification. Furthermore, RGS1 displayed positive correlation with the 35 genes, especially highly correlated with PDCD1, CTLA4, HAVCR2, and TNFRSF9 in CD8+ T cells and cancer tissues, indicating the important roles of RGS1 in CD8+ T-cell exhaustion. Considering the GTP-hydrolysis activity of RGS1 and significantly high mRNA and protein expression in cancer tissues, we speculated that RGS1 potentially mediate the T-cell retention to lead to the persistent antigen stimulation, resulting in T-cell exhaustion. In conclusion, our findings suggest that RGS1 is a new marker and promoting factor for CD8+ T-cell exhaustion and provide theoretical basis for research and immunotherapy of exhausted cells.</p

DataSheet_2_Single-Cell Transcriptome Analysis Reveals RGS1 as a New Marker and Promoting Factor for T-Cell Exhaustion in Multiple Cancers.xlsx

T-cell exhaustion is one of the main reasons of tumor immune escape. Using single-cell transcriptome data of CD8+ T cells in multiple cancers, we identified different cell types, in which Pre_exhaust and exhausted T cells participated in negative regulation of immune system process. By analyzing the coexpression network patterns and differentially expressed genes of Pre_exhaust, exhausted, and effector T cells, we identified 35 genes related to T-cell exhaustion, whose high GSVA scores were associated with significantly poor prognosis in various cancers. In the differentially expressed genes, RGS1 showed the greatest fold change in Pre_exhaust and exhausted cells of three cancers compared with effector T cells, and high expression of RGS1 was also associated with poor prognosis in various cancers. Additionally, RGS1 protein was upregulated significantly in tumor tissues in the immunohistochemistry verification. Furthermore, RGS1 displayed positive correlation with the 35 genes, especially highly correlated with PDCD1, CTLA4, HAVCR2, and TNFRSF9 in CD8+ T cells and cancer tissues, indicating the important roles of RGS1 in CD8+ T-cell exhaustion. Considering the GTP-hydrolysis activity of RGS1 and significantly high mRNA and protein expression in cancer tissues, we speculated that RGS1 potentially mediate the T-cell retention to lead to the persistent antigen stimulation, resulting in T-cell exhaustion. In conclusion, our findings suggest that RGS1 is a new marker and promoting factor for CD8+ T-cell exhaustion and provide theoretical basis for research and immunotherapy of exhausted cells.</p

Table2_Towards an accurate and robust analysis pipeline for somatic mutation calling.XLSX

Accurate and robust somatic mutation detection is essential for cancer treatment, diagnostics and research. Various analysis pipelines give different results and thus should be systematically evaluated. In this study, we benchmarked 5 commonly-used somatic mutation calling pipelines (VarScan, VarDictJava, Mutect2, Strelka2 and FANSe) for their precision, recall and speed, using standard benchmarking datasets based on a series of real-world whole-exome sequencing datasets. All the 5 pipelines showed very high precision in all cases, and high recall rate in mutation rates higher than 10%. However, for the low frequency mutations, these pipelines showed large difference. FANSe showed the highest accuracy (especially the sensitivity) in all cases, and VarScan and VarDictJava outperformed Mutect2 and Strelka2 in low frequency mutations at all sequencing depths. The flaws in filter was the major cause of the low sensitivity of the four pipelines other than FANSe. Concerning the speed, FANSe pipeline was 8.8∼19x faster than the other pipelines. Our benchmarking results demonstrated performance of the somatic calling pipelines and provided a reference for a proper choice of such pipelines in cancer applications.</p