Journal: Science Advances

Article Title: Shifting IRES versus Cap-initiated translation during homeostatic stem cell differentiation and stress

doi: 10.1126/sciadv.adz7896

Figure Lengend Snippet: ( A ) Representative gating strategy for sorting low, mid, and high IRES/Cap SLAM-LKS. ( B and C ) Colony formation (B) and size (C, mm 2 ) of Translator SLAM-LKS sorted on the basis of IRES/Cap ( n = 6). ( D and E ) Colony formation (D) and size (E, mm 2 ) of Translator GMP sorted on the basis of IRES/Cap ( n = 9). ( F ) Total protein synthesis rates of Translator GMP based on IRES/Cap measured by AF647-OPP MFI ( n = 3). ( G ) Colony formation of EMCV-IRES reporter-transduced CD34+CD90+EPCR+CD45RA− human cord blood sorted on the basis of IRES/Cap ( n = 3). ( H and I ) Colony formation of SLAM-LKS (H) and GMPs (I) based on RUNX1-IRES/Cap sorted from transplant recipients ( n = 3 and 2, respectively). ( J ) Primary competitive transplant schema. Twenty CD45.2 SLAM-LKS sorted on the basis of IRES/Cap versus 200,000 CD45.1 whole BM cells in lethally irradiated CD45.1 recipients. Peripheral blood chimerism analyzed every four weeks through week 16. Created in BioRender. Li, D. (2026) https://BioRender.com/d7k2abt . ( K ) Total chimerism Translator SLAM-LKS based on IRES/Cap in primary recipients evaluated through week 16 ( n = 12). ( L ) Secondary competitive transplant schema. One million total BM cells were collected from primary recipients (16 weeks posttransplantation) and transplanted to lethally irradiated CD45.1 recipients. Created in BioRender. Li, D. (2026) https://BioRender.com/d7k2abt . ( M ) Total chimerism Translator SLAM-LKS based on IRES/Cap in secondary recipients through week 16 ( n = 12). ( N and O ) Representative image of the culture of a single low (N) or high (O) IRES/Cap SLAM-LKS after 5 days of culture. ( P and Q ) Pie charts depicting the percentage of wells with megakaryocytes (MK) after 5 days of culturing a single low (P) or high (Q) IRES/Cap Translator SLAM-LKS ( n = 20). Data show individual replicates and means ± SEM. * P ≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001; **** P ≤ 0.0001. Significance was assessed using a two-way ANOVA with Dunnett’s one-way ANOVA (B to I) or an ANOVA with Tukey’s multiple comparisons test (K and M).

Article Snippet: WT CD45.2 C57BL/6J (strain #000664), CD45.1 (B6.SJL- Ptprc a Pepc b /BoyJ; strain #002014), KH2/iCas9 [B6;129S4- Gt(ROSA)26Sor tm1(rtTA*M2)Jae Col1a1 tm1(tetO-cas9)Sho /J; strain #029415], Rpl24 Bst (C57BLKS-Rpl24 Bst /J; strain #000516), and NSG mice (NOD.Cg-PrkdcscidIl2rgtm1Wjl/SzJ; strain #005557) were purchased from the Jackson Laboratory.

Techniques: Irradiation

Journal: Nature Communications

Article Title: TGFβR signalling controls CD103 + CD11b + dendritic cell development in the intestine

doi: 10.1038/s41467-017-00658-6

Figure Lengend Snippet: T-cell-dependent inflammatory disease in CD11c-Cre. Tgfbr1 fl/fl mice. a Body weights of CD11c - Cre. Tgfbr1 fl/fl (Cre + ) mice and Tgfbr1 fl/fl (Cre − ) mice littermate controls presented as a percentage of original bodyweight at 9 weeks of age. The results are the means ± 1 SD of five (Cre + ) or six (Cre − ) mice per group and are representative of two experiments (** p < 0.01 and *** p < 0.001—Student’s t -test followed by Holm–Sidak correction). († indicates the loss of animal from group). b Representative colonic pathology as assessed by epithelial cell turnover (Ki67 staining— left panels ) and goblet cell density (PAS staining— right panels ) in Cre − ( upper panels ) and Cre + mice ( lower panels ). Arrows indicate loss of goblet cells. Scale bar , 1 mm. c Experimental scheme for the transfer of splenic T cells from Cre − or Cre + mice into congenic WT recipients. d Survival of WT recipients given T cells from Cre − ro Cre + mice. Data are pooled from two experiments with a total of seven (Cre − ) or eight (Cre + ) mice per group. e Frequency of CD45.2 + donor T cells among total blood T cells ( left ) and the frequency of donor cells within the CD4 + and CD8 + T-cell compartments ( centre and right ) at 1, 2 and 3 weeks post transfer in the mice from c , d above. Data are from one of two independent experiments each with 3 (Cre + ) or 4 (Cre − ) mice per group. f Expression of mRNA transcripts for Gzmb , Ifng , Tnfa and Nos2 in the stomach of recipients of splenic T cells from Cre − or Cre + mice in d above. In e , f , bars represent the mean + SD of three mice per group and mRNA expression is relative to expression of Gapdh . * p < 0.05, ** p < 0.01, *** p < 0.001 and **** p < 0.0005 determined by two-tailed Student’s t -test

Article Snippet: WT C57BL/6 (CD45.2 + ) mice were obtained from Harlan Olac (Bicester, UK), whereas C57BL/6.SJL (CD45.1 + ) mice, C57BL/6.SJL × C57Bl/6 (CD45.1 + × CD45.2 + ) and OTII OVA-specific TcR transgenic mice on the CD45.1 + background were bred in house.

Techniques: Staining, Expressing, Two Tailed Test

Journal: Nature Communications

Article Title: TGFβR signalling controls CD103 + CD11b + dendritic cell development in the intestine

doi: 10.1038/s41467-017-00658-6

Figure Lengend Snippet: TGFβR1-mediated control of DC homeostasis is cell intrinsic. a Experimental scheme for generation of mixed BM chimeric mice by reconstitution of irradiated CD45.1 + × CD45.2 + mice with a 1 : 1 mixture of BM from CD45.1 + WT and Rag1 − / − Cre − or Rag1 − / − Cre + CD45.2 + donors. b CD45.2 + Tgfbr1 fl/fl -derived chimerism among DC subsets from WT: Rag1 − / − Cre − or WT: Rag1 − / − Cre + mixed BM chimeras 8–12 weeks post reconstitution. Data are pooled from two independent experiments with a total of 10 mice per group and dotted line represents input chimerism. **** p < 0.0001 determined by Student’s t -test followed by Holm–Sidak correction. c , d Representative expression of CD103 and CD11b by CD45.1 + (WT-derived) or CD45.2 + ( Tgfbr1 fl/fl -derived) CD11c + MHCII + CD64 − cells from the SILP c or MLN d of WT: Rag1 − / − Cre − or WT: Rag1 − / − Cre + mixed BM chimeras 8–12 weeks post reconstitution. Scatter plots show the frequency of each DC subset of the total DC pool derived from each BM source. Data are pooled from two independent experiments with 10 mice per group. Each symbol represents an individual animal and the horizontal bar represents the mean. *** p < 0.001 and **** p < 0.0001 using one-way ANOVA followed by Bonferroni’s multiple comparisons test

Article Snippet: WT C57BL/6 (CD45.2 + ) mice were obtained from Harlan Olac (Bicester, UK), whereas C57BL/6.SJL (CD45.1 + ) mice, C57BL/6.SJL × C57Bl/6 (CD45.1 + × CD45.2 + ) and OTII OVA-specific TcR transgenic mice on the CD45.1 + background were bred in house.

Techniques: Control, Irradiation, Derivative Assay, Expressing

Journal: Nature Communications

Article Title: TGFβR signalling controls CD103 + CD11b + dendritic cell development in the intestine

doi: 10.1038/s41467-017-00658-6

Figure Lengend Snippet: CD101 and TREM1 are surrogate markers for intestinal CD103 + CD11b + DC. a Representative expression of TREM1 and CD101 by DC subsets and CD64 + MHCII + macrophages from SILP of Rag1 − / − Cre − mice. b Representative expression of CD103, SiglecF, TREM1 and CD101 by total CD11b + DC from the SILP of Rag1 − / − Cre − or Rag1 − / − Cre + mice. c Representative expression of CD103 and CD101 by total CD11c + MHCII + CD64 − DC ( left ) and the frequency and absolute numbers of CD101 + DC in the SILP of Rag1 − / − Cre − or Rag1 − / − Cre + mice. Data are pooled from two independent experiments with seven mice per group. d Proportion of CD45.2 + Tgfbr1 fl/fl -derived cells among CD101 + DC from WT: Rag1 − / − Cre − or WT: Rag1 − / − Cre + mixed BM chimeras 8–12 weeks post reconstitution. Data are from one of two independent experiments with five mice per group

Article Snippet: WT C57BL/6 (CD45.2 + ) mice were obtained from Harlan Olac (Bicester, UK), whereas C57BL/6.SJL (CD45.1 + ) mice, C57BL/6.SJL × C57Bl/6 (CD45.1 + × CD45.2 + ) and OTII OVA-specific TcR transgenic mice on the CD45.1 + background were bred in house.

Techniques: Expressing, Derivative Assay

Journal: Nature Communications

Article Title: TGFβR signalling controls CD103 + CD11b + dendritic cell development in the intestine

doi: 10.1038/s41467-017-00658-6

Figure Lengend Snippet: TGFβR1 signalling is required for induction of regulatory T cells by DC in vivo and in vitro. a Experimental scheme for induction of Tregs in vivo. b Representative expression of FoxP3 + by adoptively transferred OTII T cells (Vα2 + CD45.1 + CD45.2 + ) from MLN of Rag1 − / − Cre − → WT or Rag1 − / − Cre + → WT BM chimeric mice 4 days after oral administration of 50 mg OVA ( left panels ). Scatterplot shows the frequency of FoxP3 + T cells among all Vα2 + CD45.1 + CD45.2 + T cells ( right panel ). Each symbol represents an individual animal and the horizontal bar represents the mean. Data are pooled from two independent experiments with nine mice per group. c – e Frequency of IL17A + c , IFNγ + d and IL17A + IFNγ + e T cells among CD45.1 + (residual host) T cells from the SILP of Rag1 − / − Cre − → WT or Rag1 − / − Cre + → WT BM chimeric mice. Data are pooled from two independent experiments with nine mice per group c or from one experiment with three ( Rag1 − / − Cre − → WT) or 5 ( Rag1 − / − Cre + → WT) mice per group d , e . ** p < 0.01 and **** p < 0.0001 determined by Student’s t -test. CFSE profile f and expression of FoxP3 g of CD4 + OTII T cells after 3.5 days of co-culture with FACS-purified CD103 + CD11b − DC or CD101 + DC from SILP of Rag1 − / − Cre − or Rag1 − / − Cre + mice in the presence of 0.5 μg ml −1 OVA 323–339 peptide. Data are pooled from at least four individual experiments, with each symbol representing a biological replicate and the horizontal bar representing the mean. *** p < 0.001 determined by Student’s t -test

Article Snippet: WT C57BL/6 (CD45.2 + ) mice were obtained from Harlan Olac (Bicester, UK), whereas C57BL/6.SJL (CD45.1 + ) mice, C57BL/6.SJL × C57Bl/6 (CD45.1 + × CD45.2 + ) and OTII OVA-specific TcR transgenic mice on the CD45.1 + background were bred in house.

Techniques: In Vivo, In Vitro, Expressing, Co-Culture Assay, Purification

Journal: Science Advances

Article Title: Shifting IRES versus Cap-initiated translation during homeostatic stem cell differentiation and stress

doi: 10.1126/sciadv.adz7896

Figure Lengend Snippet: ( A ) Representative gating strategy for sorting low, mid, and high IRES/Cap SLAM-LKS. ( B and C ) Colony formation (B) and size (C, mm 2 ) of Translator SLAM-LKS sorted on the basis of IRES/Cap ( n = 6). ( D and E ) Colony formation (D) and size (E, mm 2 ) of Translator GMP sorted on the basis of IRES/Cap ( n = 9). ( F ) Total protein synthesis rates of Translator GMP based on IRES/Cap measured by AF647-OPP MFI ( n = 3). ( G ) Colony formation of EMCV-IRES reporter-transduced CD34+CD90+EPCR+CD45RA− human cord blood sorted on the basis of IRES/Cap ( n = 3). ( H and I ) Colony formation of SLAM-LKS (H) and GMPs (I) based on RUNX1-IRES/Cap sorted from transplant recipients ( n = 3 and 2, respectively). ( J ) Primary competitive transplant schema. Twenty CD45.2 SLAM-LKS sorted on the basis of IRES/Cap versus 200,000 CD45.1 whole BM cells in lethally irradiated CD45.1 recipients. Peripheral blood chimerism analyzed every four weeks through week 16. Created in BioRender. Li, D. (2026) https://BioRender.com/d7k2abt . ( K ) Total chimerism Translator SLAM-LKS based on IRES/Cap in primary recipients evaluated through week 16 ( n = 12). ( L ) Secondary competitive transplant schema. One million total BM cells were collected from primary recipients (16 weeks posttransplantation) and transplanted to lethally irradiated CD45.1 recipients. Created in BioRender. Li, D. (2026) https://BioRender.com/d7k2abt . ( M ) Total chimerism Translator SLAM-LKS based on IRES/Cap in secondary recipients through week 16 ( n = 12). ( N and O ) Representative image of the culture of a single low (N) or high (O) IRES/Cap SLAM-LKS after 5 days of culture. ( P and Q ) Pie charts depicting the percentage of wells with megakaryocytes (MK) after 5 days of culturing a single low (P) or high (Q) IRES/Cap Translator SLAM-LKS ( n = 20). Data show individual replicates and means ± SEM. * P ≤ 0.05; ** P ≤ 0.01; *** P ≤ 0.001; **** P ≤ 0.0001. Significance was assessed using a two-way ANOVA with Dunnett’s one-way ANOVA (B to I) or an ANOVA with Tukey’s multiple comparisons test (K and M).

Article Snippet: Heterozygous transgene positive founders were bred with WT CD45.2 C57BL/6J mice purchased from the Jackson Laboratory.

Techniques: Irradiation