DataSheet1_Analysis of RPGR gene mutations in 41 Chinese families affected by X-linked inherited retinal dystrophy.PDF

Background: This study analyzed the phenotypes and genotypes of 41 Chinese families with inherited retinal dystrophy (IRD) and RPGR gene mutations.Methods: This retrospective analysis evaluated a cohort of 41 patients who were subjected to a specific Hereditary Eye Disease Enrichment Panel (HEDEP) analysis. All (likely) pathogenic variants were determined by Sanger sequencing, and co-segregation analyses were performed on the available family members. All cases were subjected to Sanger sequencing for RPGR open reading frame 15 (ORF15) mutations.Results: A total of 41 probands from different families with a clinical diagnosis of retinitis pigmentosa (RP; 34 cases) and cone-rod dystrophy (CORD; 7 cases) were included in this cohort. According to clinical information, 2, 18, and 21 cases were first assigned as autosomal dominant (AD), sporadic, and X-linked (XL) inheritance, respectively. Several cases of affected females who presented with a male phenotype have been described, posing challenges at diagnosis related to the apparent family history of AD. Mutations were located in RPGR exons or introns 1–14 and in ORF15 of 12 of 41 (29.3%) and 29 of 41 (70.7%) subjects, respectively. Thirty-four (likely) pathogenic mutations were identified. Frameshifts were the most frequently observed variants, followed by nonsense, splice, and missense mutations. Herein, a detailed description of four RP patients carrying RPGR intronic mutations is reported, and in vitro splice assays were performed to confirm the pathogenicity of these intronic mutations.Conclusion: Our findings provide useful insights for the genetic and clinical counseling of patients with XL IRD, which will be useful for ongoing and future gene therapy trials.</p

Additional file 2 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 2: Table S2. The rumen microbiota and the presence of quorum sensing molecules

Additional file 9 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 9: Figure S4. The types of the CahR-type receptors. Numbers indicate the number of bacterial genomes in which the corresponding proteins were found. The MCPs and HKs were two dominant AI-2 receptor proteins in rumen bacteria

Additional file 10 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 10: Table S6. Expression of the identified AI-2 synthases and receptors in rumen metatranscriptome datasets

Additional file 14 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 14: Table S7. The network among the rumen bacterial taxa and AI-2

Additional file 8 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 8: Table S5. The diversity of predicted CahR-type receptors

Additional file 4 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 4: Table S4. The microbes and the presence of quorum sensing molecules in the pig gut (as the negative control group)

Additional file 11 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 11: Figure S5. Expression of the predicted AI-2 synthases and receptors within a rumen microbial metatranscriptome at the phylum level. (A) The number of bacterial genomes containing AI-2-related genes and the percentage of corresponding genomes that expressed these genes. (B) The number of bacterial genomes containing luxS synthases and the percentage of the corresponding genomes that expressed luxS genes at the phylum level. (C) The number of bacterial genomes containing lsrB receptors and the percentage of corresponding genomes that expressed lsrB genes at the phylum level. (D) The number of bacterial genomes containing CahR-type receptor genes and the percentage of the corresponding genomes that expressed these genes at the phylum level. Numbers indicate the numbers of bacterial genomes in which the corresponding functions were found at the phylum level. The phyla (> 0.6% of total microbial genomes) were selected. A total of 380 (68% of 558,) genomes expressed luxS synthases, which were mainly distributed in the phyla Bacteroidetes and Firmicutes; 26 (59% of the 44) genomes expressed known receptor lsrB genes; and 256 genomes (88% of 292) expressed CahR-type receptors, which were largely located in the phyla Firmicutes and Spirochaetes

Additional file 7 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 7: Figure S3. Occurrence of putative AI-2 synthase- and receptor-based QS in microbial genomes from different sources. (A) Putative LuxS synthases, LsrB, and CahR-type receptors in the rumen ecosystems including cattle, sheep, moose, deer, and bison (as the control group). (B) Putative LuxS synthases, LsrB, and CahR-type receptors in the pig gut (as the negative control group). Numbers indicate the numbers of bacterial genomes in which the corresponding proteins were found

Additional file 12 of Exploring AI-2-mediated interspecies communications within rumen microbial communities

Additional file 12: Figure S6. Widespread occurrence of rumen bacteria in the communication network. (A) The occurrence of rumen bacteria in the network. (B) The occurrence of bacteria that synthesize AI-2 at the phylum level. (C) The occurrence of bacteria that synthesize and sense AI-2 at the phylum level. (D) The occurrence of bacteria that sense AI-2 at the phylum level. Numbers indicate the numbers of bacterial genomes in which the corresponding functions were found at the phylum level. A total of 357 bacterial species were responsible for the synthesis of AI-2, which were mainly distributed in Actinobacteria, Bacteroidetes, and Firmicutes; 122 bacterial species sensed AI-2 to reprogram the expression of multiple genes, which were mainly distributed in Firmicutes; 201 bacterial species could not only produce AI-2 but also sense AI-2 in the environment, which primarily functioned in Firmicutes