Presentation_2_Analysis of Genetic Structure of Wild and Cultured Giant Freshwater Prawn (Macrobrachium rosenbergii) Using Newly Developed Microsatellite.pptx

The giant freshwater prawn (GFP) is one of the most critical crustacean species cultured in Southeast Asia. Investigation of the genetic structure of current commercial stocks allows GFP breeding programs to better manage crosses and germplasm banks as well as to promote the rational use of GFP. The objective of the study was to characterize genetic diversity in diverse prawn populations with emphasis on those cultured in China. Seventeen microsatellite loci, including 12 novel loci derived from GFP transcriptome data, were screened to assess genetic diversity in one wild (Myanmar) and six cultured populations (i.e., four Chinese (Zhejiang, Guangxi, and Guangdong A and B), one Malaysian, and one Thai population). The results showed that the number of alleles per locus ranged from 3 to 18. The mean observed heterozygosity (0.363 ± 0.048) was less than the expected heterozygosity (0.637 ± 0.048). The mean values of polymorphism information content among the seven populations were >0.5 (ranging from 0.110 to 0.915). These cultured populations exhibited reduced genetic diversity when compared with that of the wild population. Pair-wise genetic differentiation ranged from 0.006 to 0.131 within the seven populations. The dendrogram of the genetic distance shows that the six cultured populations were distributed on the same major branch, suggesting that they have are genetically close, whereas the wild population was distributed on an independent branch. The results provide a basic assessment of genetic diversity in some available stocks and lay a foundation for future research efforts toward genetic monitoring and selective breeding.</p

Data_Sheet_1_Analysis of Genetic Structure of Wild and Cultured Giant Freshwater Prawn (Macrobrachium rosenbergii) Using Newly Developed Microsatellite.docx

The giant freshwater prawn (GFP) is one of the most critical crustacean species cultured in Southeast Asia. Investigation of the genetic structure of current commercial stocks allows GFP breeding programs to better manage crosses and germplasm banks as well as to promote the rational use of GFP. The objective of the study was to characterize genetic diversity in diverse prawn populations with emphasis on those cultured in China. Seventeen microsatellite loci, including 12 novel loci derived from GFP transcriptome data, were screened to assess genetic diversity in one wild (Myanmar) and six cultured populations (i.e., four Chinese (Zhejiang, Guangxi, and Guangdong A and B), one Malaysian, and one Thai population). The results showed that the number of alleles per locus ranged from 3 to 18. The mean observed heterozygosity (0.363 ± 0.048) was less than the expected heterozygosity (0.637 ± 0.048). The mean values of polymorphism information content among the seven populations were >0.5 (ranging from 0.110 to 0.915). These cultured populations exhibited reduced genetic diversity when compared with that of the wild population. Pair-wise genetic differentiation ranged from 0.006 to 0.131 within the seven populations. The dendrogram of the genetic distance shows that the six cultured populations were distributed on the same major branch, suggesting that they have are genetically close, whereas the wild population was distributed on an independent branch. The results provide a basic assessment of genetic diversity in some available stocks and lay a foundation for future research efforts toward genetic monitoring and selective breeding.</p

Table1_Identification of the core genes in Randall’s plaque of kidney stone and immune infiltration with WGCNA network.XLSX

Background: Randall’s plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease.Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein–protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518.Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518.Conclusion: Randall’s plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.</p

Additional file 4 of Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history

Supplementary table: Table 1–1 and Tables 1 and 2 presents related molecule for indentification in TARTs

Additional file 2 of Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history

Supplementary Fig. 2: The pigmented skin in lower limbs and abdomen. Supplementary Fig. 3: (A) Fibrous tissues separate tumor into multi-nodular masses.(B)(C)(D)Images display several molecule results in IHC staining.Method: Olympus BX53 and Axiocam 305 color were used to capture the microscopy images, the horizontal and vertical dpi are 300 in 4 images. We add scale bar to these images by Zen 2.6 (blue edition) without enhancement and merge them int

Additional file 3 of Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history

Supplementary Fig. 3 by Adobe Illustrator CC 2017

Table3_Identification of the core genes in Randall’s plaque of kidney stone and immune infiltration with WGCNA network.XLSX

Background: Randall’s plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease.Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein–protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518.Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518.Conclusion: Randall’s plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.</p

Image1_Identification of the core genes in Randall’s plaque of kidney stone and immune infiltration with WGCNA network.TIF

Background: Randall’s plaque is regarded as the precursor lesion of lithiasis. However, traditional bioinformatic analysis is limited and ignores the relationship with immune response. To investigate the underlying calculi formation mechanism, we introduced innovative algorithms to expand our understanding of kidney stone disease.Methods: We downloaded the GSE73680 series matrix from the Gene Expression Omnibus (GEO) related to CaOx formation and excluded one patient, GSE116860. In the RStudio (R version 4.1.1) platform, the differentially expressed genes (DEGs) were identified with the limma package for GO/KEGG/GSEA analysis in the clusterProfiler package. Furthermore, high-correlated gene co-expression modules were confirmed by the WGCNA package to establish a protein–protein interaction (PPI) network. Finally, the CaOx samples were processed by the CIBERSORT algorithm to anchor the key immune cells group and verified in the validation series matrix GSE117518.Results: The study identified 840 upregulated and 1065 downregulated genes. The GO/KEGG results revealed fiber-related or adhesion-related terms and several pathways in addition to various diseases identified from the DO analysis. Moreover, WGCNA selected highly correlated modules to construct a PPI network. Finally, 16 types of immune cells are thought to participate in urolithiasis pathology and are related to hub genes in the PPI network that are proven significant in the validation series matrix GSE117518.Conclusion: Randall’s plaque may relate to genes DCN, LUM, and P4HA2 and M2 macrophages and resting mast immune cells. These findings could serve as potential biomarkers and provide new research directions.</p

Additional file 1 of Case Report:clinical experience of bilateral giant pediatric Testicular adrenal rest tumors with 3 Beta-Hydroxysteroid Dehydrogenase-2 family history

Supplementary Fig. 1: Gene analysis showed there were two mutations in siblings’s chrosome 1. c.674T > A occurs at chr1:119,964,900 and c.776 C > T occurs at chr1:119,964,798

Presentation_1_Analysis of Genetic Structure of Wild and Cultured Giant Freshwater Prawn (Macrobrachium rosenbergii) Using Newly Developed Microsatellite.pptx

The giant freshwater prawn (GFP) is one of the most critical crustacean species cultured in Southeast Asia. Investigation of the genetic structure of current commercial stocks allows GFP breeding programs to better manage crosses and germplasm banks as well as to promote the rational use of GFP. The objective of the study was to characterize genetic diversity in diverse prawn populations with emphasis on those cultured in China. Seventeen microsatellite loci, including 12 novel loci derived from GFP transcriptome data, were screened to assess genetic diversity in one wild (Myanmar) and six cultured populations (i.e., four Chinese (Zhejiang, Guangxi, and Guangdong A and B), one Malaysian, and one Thai population). The results showed that the number of alleles per locus ranged from 3 to 18. The mean observed heterozygosity (0.363 ± 0.048) was less than the expected heterozygosity (0.637 ± 0.048). The mean values of polymorphism information content among the seven populations were >0.5 (ranging from 0.110 to 0.915). These cultured populations exhibited reduced genetic diversity when compared with that of the wild population. Pair-wise genetic differentiation ranged from 0.006 to 0.131 within the seven populations. The dendrogram of the genetic distance shows that the six cultured populations were distributed on the same major branch, suggesting that they have are genetically close, whereas the wild population was distributed on an independent branch. The results provide a basic assessment of genetic diversity in some available stocks and lay a foundation for future research efforts toward genetic monitoring and selective breeding.</p