Business in practice: valuable takeaways from an immersive business simulation

Business in Practice was definitely one of my most unforgettable memories of the summer, and although it was only three weeks, I really enjoyed myself. Not only did I make a lot of new friends, but I also learned a lot of valuable content and gained very precious experience that I can use in the future during the lectures and the simulatio

Comparison of Regional Urban Water Pollutants Emission Standards and Determination of Factors Influencing Their Integration—A Case Study of the Biopharmaceutical Industry in the Yangtze River Delta Urban Agglomeration

Urban pharmaceutical industries are responsible for high intensity emissions of water pollutants. The regional water pollutant emission standards vary greatly throughout the Yangtze River Delta Urban Agglomeration (YRDUA) in China, which, to some extent, results in increased risks and hidden dangers to regional water environment safety, especially water quality. Under the national strategy of Yangtze River Delta ecological and green integration development, a unified standard of water pollutant emissions should be integrated into the integration development process, but differences between characteristic items, concentration limits, and conditions among four local standards of water pollutant emission have become a key influencing factor in their integration in industry and in green transformation. When comparing the water pollutant emission standards of the biopharmaceutical industry in three provinces and one municipality of the YRDUA, the factors influencing integration were determined and caused by the main differences in local water pollutant emission standards, namely, the race to the bottom of the biopharmaceutical industry, the inconsistency of environmental protection regulation law, and transboundary water pollution risks. From the perspective of urban water quality safety, we propose the following strategies for promoting the integration of water pollutant emission standards in the YRDUA: (1) increasing government funding for local water pollution governance and encouraging industries to adopt the third-party governance model for pollution control in the YRDUA; (2) unifying water pollutant emission standards and environmental law enforcement standards in the YRDUA with a mechanism involving shared economic responsibility; and (3) establishing a platform for sharing data and governance performance for the emission of water pollutants in the YRDUA

Comparison of Regional Urban Water Pollutants Emission Standards and Determination of Factors Influencing Their Integration—A Case Study of the Biopharmaceutical Industry in the Yangtze River Delta Urban Agglomeration

Urban pharmaceutical industries are responsible for high intensity emissions of water pollutants. The regional water pollutant emission standards vary greatly throughout the Yangtze River Delta Urban Agglomeration (YRDUA) in China, which, to some extent, results in increased risks and hidden dangers to regional water environment safety, especially water quality. Under the national strategy of Yangtze River Delta ecological and green integration development, a unified standard of water pollutant emissions should be integrated into the integration development process, but differences between characteristic items, concentration limits, and conditions among four local standards of water pollutant emission have become a key influencing factor in their integration in industry and in green transformation. When comparing the water pollutant emission standards of the biopharmaceutical industry in three provinces and one municipality of the YRDUA, the factors influencing integration were determined and caused by the main differences in local water pollutant emission standards, namely, the race to the bottom of the biopharmaceutical industry, the inconsistency of environmental protection regulation law, and transboundary water pollution risks. From the perspective of urban water quality safety, we propose the following strategies for promoting the integration of water pollutant emission standards in the YRDUA: (1) increasing government funding for local water pollution governance and encouraging industries to adopt the third-party governance model for pollution control in the YRDUA; (2) unifying water pollutant emission standards and environmental law enforcement standards in the YRDUA with a mechanism involving shared economic responsibility; and (3) establishing a platform for sharing data and governance performance for the emission of water pollutants in the YRDUA

Integrative genomic and transcriptomic analyses of a bud sport mutant ‘Jinzao Wuhe’ with the phenotype of large berries in grapevines

Background Bud sport mutation occurs frequently in fruit plants and acts as an important approach for grapevine improvement and breeding. ‘Jinzao Wuhe’ is a bud sport of the elite cultivar ‘Himord Seedless’ with obviously enlarged organs and berries. To date, the molecular mechanisms underlying berry enlargement caused by bud sport in grapevines remain unclear. Methods Whole genome resequencing (WGRS) was performed for two pairs of bud sports and their maternal plants with similar phenotype to identify SNPs, InDels and structural variations (SVs) as well as related genes. Furthermore, transcriptomic sequencing at different developmental stages and weighted gene co-expression network analysis (WGCNA) for ‘Jinzao Wuhe’ and its maternal plant ‘Himord Seedless’ were carried out to identify the differentially expressed genes (DEGs), which were subsequently analyzed for Gene Ontology (GO) and function annotation. Results In two pairs of enlarged berry bud sports, a total of 1,334 SNPs, 272 InDels and 74 SVs, corresponding to 1,022 target genes related to symbiotic microorganisms, cell death and other processes were identified. Meanwhile, 1,149 DEGs associated with cell wall modification, stress-response and cell killing might be responsible for the phenotypic variation were also determined. As a result, 42 DEGs between ‘Himord Seedless’ and ‘Jinzao Wuhe’ harboring genetic variations were further investigated, including pectin esterase, cellulase A, cytochromes P450 (CYP), UDP-glycosyltransferase (UGT), zinc finger protein, auxin response factor (ARF), NAC transcription factor (TF), protein kinase, etc. These candidate genes offer important clues for a better understanding of developmental regulations of berry enlargement in grapevine. Conclusion Our results provide candidate genes and valuable information for dissecting the underlying mechanisms of berry development and contribute to future improvement of grapevine cultivars

Genomic and Transcriptomic Dissection of the Large-Effect Loci Controlling Drought-Responsive Agronomic Traits in Wheat

Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the genomes of two popular winter wheat cultivars, Lu-Mai 14 and Han-Xuan 10, using a whole-genome re-sequencing assay. There were 4972 loss-of-function mutations carried by protein-coding genes, such as CCA1/LHY, AGO1, ABI3/VP1, EIN3, TPP, and ARFs. We carried out a time-course abscisic acid (ABA)-treatment experiment and profiled 61,251 expressed genes in the roots using a strand-specific RNA sequencing approach. A large number of genes showed time-point specific and/or cultivar-preferential responsive expression patterns. Gene ontology enrichment analysis revealed that ABA-responsive genes were associated with stress-related functions. Among the 20 QTLs, we uncovered 306 expressed genes with high- and/or moderate-effect variations and 472 differentially expressed genes. Detailed analysis and verification of the homozygous genomic variations in the candidate genes encoding sulfotransferase, proteinase, kinase, nitrate transporter, and transcription factors suggested previously unexpected pathways associated with abiotic stress responses in wheat

Genomic and Transcriptomic Dissection of the Large-Effect Loci Controlling Drought-Responsive Agronomic Traits in Wheat

Drought tolerance is one of the most important targets for wheat breeding. Previous population genetics studies have uncovered 20 large-effect quantitative trait loci (QTLs) that contribute to stress-responsive agronomic traits. Here, we identified 19,035,814 single nucleotide polymorphisms and 719,049 insertion/deletion variations in the genomes of two popular winter wheat cultivars, Lu-Mai 14 and Han-Xuan 10, using a whole-genome re-sequencing assay. There were 4972 loss-of-function mutations carried by protein-coding genes, such as CCA1/LHY, AGO1, ABI3/VP1, EIN3, TPP, and ARFs. We carried out a time-course abscisic acid (ABA)-treatment experiment and profiled 61,251 expressed genes in the roots using a strand-specific RNA sequencing approach. A large number of genes showed time-point specific and/or cultivar-preferential responsive expression patterns. Gene ontology enrichment analysis revealed that ABA-responsive genes were associated with stress-related functions. Among the 20 QTLs, we uncovered 306 expressed genes with high- and/or moderate-effect variations and 472 differentially expressed genes. Detailed analysis and verification of the homozygous genomic variations in the candidate genes encoding sulfotransferase, proteinase, kinase, nitrate transporter, and transcription factors suggested previously unexpected pathways associated with abiotic stress responses in wheat

Table_6_Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.xlsx

Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.</p

Table_5_Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.xlsx

Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.</p

Table_7_Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.xlsx

Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.</p

Table_4_Comparative genomic analyses reveal genetic characteristics and pathogenic factors of Bacillus pumilus HM-7.xlsx

Bacillus pumilus plays an important role in industrial application and biocontrol activities, as well as causing humans and plants disease, leading to economic losses and biosafety concerns. However, until now, the pathogenesis and underlying mechanisms of B. pumilus strains remain unclear. In our previous study, one representative isolate of B. pumilus named HM-7 has been recovered and proved to be the causal agent of fruit rot on muskmelon (Cucumis melo). Herein, we present a complete and annotated genome sequence of HM-7 that contains 4,111 coding genes in a single 3,951,520 bp chromosome with 41.04% GC content. A total of 3,481 genes were functionally annotated with the GO, COG, and KEGG databases. Pan-core genome analysis of HM-7 and 20 representative B. pumilus strains, as well as six closely related Bacillus species, discovered 740 core genes and 15,205 genes in the pan-genome of 21 B. pumilus strains, in which 485 specific-genes were identified in HM-7 genome. The average nucleotide identity (ANI), and whole-genome-based phylogenetic analysis revealed that HM-7 was most closely related to the C4, GR8, MTCC-B6033, TUAT1 and SH-B11 strains, but evolutionarily distinct from other strains in B. pumilus. Collinearity analysis of the six similar B. pumilus strains showed high levels of synteny but also several divergent regions for each strains. In the HM-7 genome, we identified 484 genes in the carbohydrate-active enzymes (CAZyme) class, 650 genes encoding virulence factors, and 1,115 genes associated with pathogen-host interactions. Moreover, three HM-7-specific regions were determined, which contained 424 protein-coding genes. Further investigation of these genes showed that 19 pathogenesis-related genes were mainly associated with flagella formation and secretion of toxic products, which might be involved in the virulence of strain HM-7. Our results provided detailed genomic and taxonomic information for the HM-7 strain, and discovered its potential pathogenic mechanism, which lay a foundation for developing effective prevention and control strategies against this pathogen in the future.</p