8 research outputs found
Sequential MyD88-Independent and -Dependent Activation of Innate Immune Responses to Intracellular Bacterial Infection
Get PDFAbstractMicrobial infections induce chemokine and cytokine cascades that coordinate innate immune defenses. Infection with the intracellular bacterial pathogen Listeria monocytogenes induces CCR2-dependent monocyte recruitment and activation, an essential response for host survival. Herein we show that invasive L. monocytogenes, but not killed or noninvasive bacteria, induce secretion of MCP-1, the requisite chemokine for monocyte recruitment. Induction of MCP-1, but not TNF or IL-12, following L. monocytogenes infection is MyD88 independent. Consistent with these results, MyD88 deficiency does not impair monocyte recruitment to L. monocytogenes infected spleens, but prevents monocyte activation. Our results indicate that distinct microbial signals activate innate immune responses in an ordered, step-wise fashion, providing a mechanism to specify and modulate antimicrobial effector functions
Additional file 3: Figure S3. of Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
No full textScreening of ST12-specific DNA variation in the OsSPL14 promoter region through WGS data analysis. Note that the OsSPL14 gene lay on the opposite strand of the reference sequence. The reference genome sequence was shown at the bottom of the image. Screen-captured image of IGV software showed an ST12-specific SNP located at the Chr 8: 25282790 nucleotide position (IRGSP-1.0). (DOC 77 kb
Additional file 8: Table S4. of Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
No full textMarkers for Fluidigm SNP genotyping platform. (DOC 36 kb
Additional file 1: Figure S1. of Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
No full textScreening of DNA polymorphisms in the Gn1a gene using WGS data. Sequencing reads were aligned to the reference genome sequence (IRGSP-1.0). Note that the Gn1a gene lay on the opposite strand of the reference sequence. Screen-captured images of IGV software showed nucleotide variations that were used for marker development. (A) Three SNPs located in the Gn1a promoter region were shown with their genomic location on chromosome 1. Chr1: 5276405, Chr1: 5276521, and Chr1: 5276591 SNPs were used for Gn1a-17SNP/Gn1a-17SNP-FD, Gn1a-18SNP-FD, and Gn1a-19SNP-FD markers, respectively. (B) About a 70-bp deletion (red circles) near the 3’ UTR of Gn1a was found in varieties NSIC Rc158 and NSIC Rc238. This indel was used for designing the Gn1a-indel3 marker. (DOC 178 kb
Additional file 7: Table S3. of Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
No full textPrimers for preparation of PCR products and PCR product sequencing. (DOC 35 kb
Additional file 2: Figure S2. of Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.
No full textMarker designing schemes for SNP-type polymorphisms. (A) Schematic presentation of the tetra-primer PCR method for designing Gn1a-17SNP marker. The target SNPs, G and A, are highlighted in each genome and its surrounding sequences are represented with the allele-specific primers (pink, G allele-specific primer; green, A allele-specific primer). Actually, the SNP is determined by the last nucleotide (filled triangle) of the allele-specific primer. Proper annealing of the last nucleotide of the primer (the 3’ end) is very important for PCR amplification because Taq DNA polymerase start polymerization at that nucleotide through adding dNTP. For instance, the A allele-specific primer (green) can be annealed to the G allele genome but the efficiency of DNA polymerization will be very low because of no annealing of the 3’ end of the primer, resulting in no PCR band or a very weak band. To increase allele specificity, we gave an artificial mismatched nucleotide near the 3’ end (second or third nucleotide from the 3’ end) of the allele-specific primer (lowercase with underlined nucleotide in Figure). Primer combination of the Gn1a-17SNP marker, its predicted band size, and deduced gel image depending on genotypes were presented. (B) Schematic presentation of the separated allele-specific PCR method for designing the SPIKE-01SNP marker. To discriminate G/A SNP, the SPIKE-01SNP marker consisted of two PCRs (PCR #1, SPIKE-01SNP-GF/R; PCR #2, SPIKE-01SNP-AF/R). Between the G allele-specific primer (pink) and A allele-specific primer (green), only the last nucleotide of each allele-specific primer (filled triangle) is different. To increase allele specificity, the artificial mismatched nucleotide near the 3’ end was given in the allele-specific primer. PCRs were performed with each allele-specific primer and common reverse primer. Primer combinations of the SPIKE-01SNP marker, its predicted band size, and deduced gel image depending on genotypes were presented. (C) The effect of artificial mismatched nucleotide near the 3’ end of the allele-specific primer. As an example, the SPIKE-01SNP marker was designed without the artificial mismatched nucleotide in allele-specific primers that were shown on the gel image. Non-allele-specific PCR amplifications were obtained with these primers. Using artificial mismatch, we obtained allele-specific PCR amplifications (Fig. 6a). (DOC 240 kb
