Journal: TAG. Theoretical and Applied Genetics. Theoretische Und Angewandte Genetik

Article Title: Exome sequencing of bulked segregants identified a novel TaMKK3 - A allele linked to the wheat ERA8 ABA-hypersensitive germination phenotype

doi: 10.1007/s00122-019-03503-0

Figure Lengend Snippet: The BSA-exome-seq method. a Genetics. The BC 3 F 2:3 population was developed by crossing Zak WT (+/+) and BC 2 F 3 Zak ERA8 ( ERA8/ERA8 ). BC 3 F 2:3 genomic DNA was used for exome-seq. The phenotype was BC 3 F 2:3 grain germination on ABA. b Selection of bulked lines. Compared to the parental ERA8 (purple arrow) and WT (green arrow) germination on ABA, 17 ERA8 -like and 15 WT-like lines were chosen for bulked segregant analysis. c The number of 125 bp paired-end Illumina HiSeq 2000 reads generated for each parent, WT bulk (WT_b), and ERA8 bulk ( ERA8 _b) are shown. d Alignment of parental reads to the Chinese Spring IWGSC reference sequence (v 1.0), where varietal differences from Chinese Spring were shared by the Zak WT and ERA8 parents, and mutagen-induced (C/G to T/A) were ERA8 -specific. e Unlinked SNPs showed random variation in WT_b versus ERA8_b, whereas ERA8 -linked SNPs did not. An example of an exon alignment and bulk frequency ratios is shown. f KASP markers were designed to score SNPs. SNP_17 is shown (color figure online)

Article Snippet: A standard 10 μL KASP reaction volume contained 15 ng/μL gDNA, 1x KASP Master Mix (LGC Genomics; V4.0 2x Mastermix 96/384; Low Rox), 0.42 μM reverse primer, and 0.168 μM each of allele 1 and 2 forward primers (Smith and Maughan ).

Techniques: Selection, Generated, Sequencing

Journal: Nutrients

Article Title: The Gut Microbiome in Early Life Stress: A Systematic Review

doi: 10.3390/nu15112566

Figure Lengend Snippet: Characteristics and results of prenatal stress studies.

Article Snippet: Grant-Beurmann et al., 2022 [ ] , N total = 272 mother–infant pairs N (HIV/HUU) = 131 N(HIV+/HEU) = 141 , - Pregnant women with or without HIV infection Ages: 26–33 yrs (HUU) 31–37 yrs (HEU) - Babies born to these women: • Children HEU • Children HUU Study during first 18 mths of life - Country: Nigeria , Prospective cohort study of mother–infant pairs 2015–2018 Aim: to assess potential differences in the gut microbiota in infants born to HIV-positive and -negative mothers during the first 18 mths of life , Mother samples: - Vaginal swabs and stool (at 12 gwk and at birth) - Breast milk samples (at 6 wks and 6 mths postpartum) - Fecal sample (at enrollment and after birth) Infant fecal samples (meconium, 6 wks and 6, 9, 15 and 18 mths postpartum) Analysis of fecal and vaginal samples: - DNA extraction (DNeasy Power Soil Kit, Qiagen) - 16S rRNA gene sequencing (Illumina HiSeq 2500 modified for the V3–V4 region 16S rDNA) Analysis of metabolites in breast milk: UHPLC/MS/MS and library-based , Clinical assessment: Standardized questionnaires (medication and comorbidity history), general physical examination, anthropometric assessment , Maternal vaginal and infant fecal microbiota showed increased the diversity over time. Breastfeeding was associated with differences in gut microbiota of infants (HEU and HUU). The relative abundance association was: - Positively: Bifidobacterium and Collinsella ; - Negatively: Faecalibacterium and Streptococcus . Bifidobacterium, significantly more abundant in the breastfeeding HUU infants than in breastfeeding HEU infants at 6 mths postpartum Low Bifidobacterium abundance associated with low weight Breast milk composition differed by time point and HIV infection status - 106 metabolites in the breast milk of mothers with or without HIV at 6 wks and 6 mths postpartum significantly differed between the two groups and time points; - Kynurenine and antiretroviral therapy more abundant in the breast milk of mothers with HIV; - Lower tiglyl carnitine (C5) and acylcarnitine concentrations in breast milk in mothers without HIV; - Nevirapine (antiretroviral therapy), high concentrations correlated with lower relative abundance of Bifidobacterium longum in cohort of 17 HEU infants..

Techniques: Extraction, Sequencing, Infection, DNA Extraction, Modification, Microarray, Concentration Assay, Bacteria