Journal: BMC Evolutionary Biology

Article Title: Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

doi: 10.1186/1471-2148-11-47

Figure Lengend Snippet: Summary of evidence for evolutionary origins of Arabidopsis thaliana lineage-specific genes . The number of LSGs that fit each evolutionary scenario tested, plus the number of LSGs without elucidated origins. Support for gene model expression provided by an EST or cDNA consistent with the of gene model (as listed by TAIR). Support of expression at the locus provided by EST, cDNA or microarray probeset (TAIR and Ath1 affymetrix microarray).

Article Snippet: Different accessions from three Arabidopsis sp. were used; Arabidopsis thaliana accessions- N22614 (CVI-0), N22621 (CS22491), N22630 (Ag-0), N22633 (Bay-0), N22639 (Kas-1), N22643 (NOK-3), N22647 (TS-1), N22658 (OY-0), CS1642 (Ler-1), Got-7 (CS22283) and CS1028 (Bur-0) (obtained from Nottingham Arabidopsis Stock Centre); Arabidopsis lyrata petreae accessions- NT12b (8-3), Tannenberg T1a (15-1), random T14 (17-7), random T25 (13-4) and random spiterstulen (11-2) and Arabidopsis cebennensis (obtained from Prof. Karl Schmid, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Germany).

Techniques: Expressing, Microarray

Journal: BMC Evolutionary Biology

Article Title: Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

doi: 10.1186/1471-2148-11-47

Figure Lengend Snippet: Distribution of percentage coverage for LSG CDS vs. Arabidopsis lyrata intergenic region alignments . Where percentage coverage is greater than 100% indicates a gap in the alignment in the LSG, indicating an indel in the LSG in Arabidopsis thaliana .

Article Snippet: Different accessions from three Arabidopsis sp. were used; Arabidopsis thaliana accessions- N22614 (CVI-0), N22621 (CS22491), N22630 (Ag-0), N22633 (Bay-0), N22639 (Kas-1), N22643 (NOK-3), N22647 (TS-1), N22658 (OY-0), CS1642 (Ler-1), Got-7 (CS22283) and CS1028 (Bur-0) (obtained from Nottingham Arabidopsis Stock Centre); Arabidopsis lyrata petreae accessions- NT12b (8-3), Tannenberg T1a (15-1), random T14 (17-7), random T25 (13-4) and random spiterstulen (11-2) and Arabidopsis cebennensis (obtained from Prof. Karl Schmid, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Germany).

Techniques:

Journal: BMC Evolutionary Biology

Article Title: Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

doi: 10.1186/1471-2148-11-47

Figure Lengend Snippet: Polymorphic LSGs resulting in interruption of the open reading frame.

Article Snippet: Different accessions from three Arabidopsis sp. were used; Arabidopsis thaliana accessions- N22614 (CVI-0), N22621 (CS22491), N22630 (Ag-0), N22633 (Bay-0), N22639 (Kas-1), N22643 (NOK-3), N22647 (TS-1), N22658 (OY-0), CS1642 (Ler-1), Got-7 (CS22283) and CS1028 (Bur-0) (obtained from Nottingham Arabidopsis Stock Centre); Arabidopsis lyrata petreae accessions- NT12b (8-3), Tannenberg T1a (15-1), random T14 (17-7), random T25 (13-4) and random spiterstulen (11-2) and Arabidopsis cebennensis (obtained from Prof. Karl Schmid, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Germany).

Techniques:

Journal: BMC Evolutionary Biology

Article Title: Evolutionary origins of Brassicaceae specific genes in Arabidopsis thaliana

doi: 10.1186/1471-2148-11-47

Figure Lengend Snippet: Distribution of SNPs causing interruptions to the ORFs of LSGs in various Arabidopsis thaliana accessions . Predicted SNPs predicted by Perlegen re-sequencing data sets that cause the interruption of an LSG ORF. Left hand axis: lists the gene model and the SNP name. Left hand column: Lists the reference nucleotide found in the Columbia accession (Col-0). Main body of table: SNPs causing a missing of a start codon (MSC) are coloured orange. SNPs causing an internal stop codon (ISC) are coloured green. Missing data (i.e. when the nucleotide is undetermined at that position) coloured gray. Only SNPs causing ISC or MSC are annotated. Bottom axis: lists the accessions tested, they are divided by broad geographical distinctions; i.e. red = Northern Europe, blue = Central Europe, purple = Mediterranean, orange = British Isles, yellow = Central Asia, brown = Japan, pink = North America and gray = Cape Verde Islands. Right hand columns: First column represents the SNP data at the position for the intergenic alignment between the LSGs and intergenic regions in Arabidopsis lyrata . SNP types marked the same as the main table with the addition of an "X" representing those instances were no alignment was identified in Arabidopsis lyrata . The second column represent the total number of ISC and indels found in the aligned Arabidopsis lyrata sequence. The final column represents the proportion of the LSG that is covered by the Arabidopsis lyrata alignment.

Article Snippet: Different accessions from three Arabidopsis sp. were used; Arabidopsis thaliana accessions- N22614 (CVI-0), N22621 (CS22491), N22630 (Ag-0), N22633 (Bay-0), N22639 (Kas-1), N22643 (NOK-3), N22647 (TS-1), N22658 (OY-0), CS1642 (Ler-1), Got-7 (CS22283) and CS1028 (Bur-0) (obtained from Nottingham Arabidopsis Stock Centre); Arabidopsis lyrata petreae accessions- NT12b (8-3), Tannenberg T1a (15-1), random T14 (17-7), random T25 (13-4) and random spiterstulen (11-2) and Arabidopsis cebennensis (obtained from Prof. Karl Schmid, Institute of Plant Breeding, Seed Science and Population Genetics, University of Hohenheim, Germany).

Techniques: Sequencing, Northern Blot

Journal: PLoS ONE

Article Title: Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants

doi: 10.1371/journal.pone.0190526

Figure Lengend Snippet: (A-F) Scheme of the cloning procedure. (A) Amplification of expression cassette from template plasmid using primers with appropriate 5’ and 3’ extensions to add A0 and AR homology regions. (B) Expression cassette assembly in Hin dIII restricted pL0A_0-R Level 0 vector by NEBuilder HiFi assembly method. (C) Release of expression cassette with flanking homology regions A0 and AR from Level 0 vector by Pme I digestion. (D) Assembly of expression cassette with flanking homology regions A0 and AR into Pac I digested pL1A-hc / pL1A-lc (A0/AR) Level 1 vector by TAR or NEBuilder HiFi. (E) Release of expression cassette flanked by URA3 yeast selection marker and homology regions A0 and B0 from Level 1 vector by I- Sce I digestion. (F) Assembly of expression cassette flanked by URA3 yeast selection marker and homology regions A0 and B0 into Plant X-tender expression vectors by SLiCE or NEBuilder HiFi. (G-I) Images of agroinfiltrated N . benthamiana leaves obtained by laser scanning confocal microscopy. Leaves were agroinfiltrated with agrobacteria containing pCAMBIA_ASX_cassette, pK7WG_ASX_cassette, pH7WG_ASX_cassette, pB7WG_ASX_cassette or empty agrobacteria (top to bottom). (G) Nuclear localisation of RFP. Fluorescence is represented as maximum projections of z-stacks. (H) Bright field. (I) Overlay of G with H. Scale bars are 100 μm. p35S: cauliflower mosaic virus CaMV 35S promoter, H2BRFP: histon sequence fused to red fluorescence protein (mRFP1), tNOS: nopaline synthase terminator, A0, AR, B0: homology regions, Rp: selection marker conferring resistance in plants (hygromycin in the case of pCAMBIA_ASX and pH7WG_ASX, kanamycin in the case of pK7WG_ASX, glufosinate-ammonium in the case of pB7WG_ASX), Re: selection marker conferring resistance in E . coli and A . tumefaciens (kanamycin in the case of pCAMBIA_ASX, spectinomycinin in the case of pK7WG_ASX, pH7WG_ASX and pB7WG_ASX), Amp: selection marker conferring ampicillin resistance in E . coli and A . tumefaciens , Kan: selection marker conferring kanamycin resistance in E . coli and A . tumefaciens , LB: left border of T-DNA, RB: right border of T-DNA, Hin dIII, I- Sce I, Pac I, Pme I: restriction enzyme recognition sites, URA3 : yeast selection marker, ccd B: bacterial suicide gene, SLiCE: Seamless ligation cloning extract cloning method, HiFi: NEBuilder HiFi DNA assembly method, Gibson: Gibson DNA assembly method, TAR: cloning based on transformation-associated recombination, PCR: Polymerase chain reaction, ASX: Plant X-tender expression vector.

Article Snippet: N . benthamiana seeds (obtained from prof. Van der Vlugt, Wageningen University and Research Centre) were soaked in gibberellic acid overnight to induce germination.

Techniques: Cloning, Amplification, Expressing, Plasmid Preparation, Selection, Marker, Confocal Microscopy, Fluorescence, Virus, Sequencing, Ligation, Transformation Assay, Polymerase Chain Reaction

Journal: PLoS ONE

Article Title: Plant X-tender: An extension of the AssemblX system for the assembly and expression of multigene constructs in plants

doi: 10.1371/journal.pone.0190526

Figure Lengend Snippet: Two expression cassettes were cloned into pCAMBIA_ASX and introduced into N . benthamiana . (A-F) Scheme of cloning procedure. (A) Amplification of expression cassette from template plasmid using primers with appropriate 5’ and 3’ extension homologies in the case of p35S::H2BRFP_tNOS expression cassette. PCR amplification of subunits (pNOS, ECFP, t35S) using custom-designed primers with appropriate 5’ extensions to add overlaps between the individual subunits and chosen Level 0 plasmid in the case of pNOS::ECFP_t35S expression cassette. (B) Assembly of subunits into Hin dIII digested Level 0 vectors by NEBuilder HiFi assembly method. Only the restriction of Level 0 vector with A0/A1 homology regions is shown. (C) Assembled cassettes flanked by homology regions were released from the backbone using Pme I. (D) Assembly of expression cassettes into Pac I digested Level 1 vector by TAR or NEBuilder HiFi. (E) Release of the multigene construct from Level 1 vector using I- Sce I homing endonuclease, cutting outside the homology regions A0 and B0. (F) Assembly of two expression cassettes and yeast selection marker ( URA3 ) into Hin dIII digested Plant X-tender expression vectors with SLiCE of NEBuilder HiFi. (G–J) Images of agroinfiltrated N . benthamiana leaves obtained by laser scanning confocal microscopy. Leaves were agroinfiltrated with agrobacteria containing pCAMBIA_ASX_multigene (upper panel) or with empty A . tumefaciens (bottom panel). (G) Nuclear localisation of RFP. Fluorescence is represented as a maximum projection of z-stacks. (H) ECFP is localised in the cytoplasm. Fluorescence is represented as maximum projections of z-stacks. (I) Bright field. (J) Overlay of G, H and I. Scale bars are 100 μm. p35S: cauliflower mosaic virus CaMV 35S promoter, H2BRFP: histon sequence fused to red fluorescence protein (mRFP1), tNOS: nopaline synthase terminator, pNOS: nopaline synthase promoter, ECFP: cyan fluorescent protein, t35S: cauliflower mosaic virus CaMV 35S terminator, A0, A1 AR, B0: homology regions, Rp: selection marker conferring hygromycin resistance in plants, Re: selection marker conferring kanamycin resistance in E . coli and A . tumefaciens , Amp: selection marker conferring ampicillin resistance in E . coli and A . tumefaciens , Kan: selection marker conferring kanamycin resistance in E . coli and A . tumefaciens , LB: left border of T-DNA, RB: right border of T-DNA, Hin dIII, I- Sce I, Pac I, Asc I, Sbf I, Swa I, Fse I, Pme I: restriction enzyme recognition sites, URA3 : yeast selection marker, ccd B: bacterial suicide gene, SLiCE: Seamless ligation cloning extract cloning method, HiFi: NEBuilder HiFi DNA assembly method, Gibson: Gibson DNA assembly method. TAR: cloning based on transformation-associated recombination, PCR: Polymerase chain reaction, ASX: Plant X-tender expression vector.

Article Snippet: N . benthamiana seeds (obtained from prof. Van der Vlugt, Wageningen University and Research Centre) were soaked in gibberellic acid overnight to induce germination.

Techniques: Expressing, Clone Assay, Cloning, Amplification, Plasmid Preparation, Construct, Selection, Marker, Confocal Microscopy, Fluorescence, Virus, Sequencing, Ligation, Transformation Assay, Polymerase Chain Reaction

Journal: Nanomedicine (London, England)

Article Title: Large extracellular vesicles from induced pluripotent stem cell-marrow stem cells enhance limb angiogenesis via ERK/MAPK.

doi: 10.1080/17435889.2024.2363743

Figure Lengend Snippet: Figure 5. Proteomics analysis of iMSC-lEVs. (A) Venn diag r am showing the overlapping and unique proteins in iMSC-lEVs with Vesiclepedia. (B) Gene ontology biological process analysis showed the proteins enriched in iMSC-lEVs. (C) Gene ontology cellular componen t analy sis show ed the pr ot eins enriched in iMSC-lEVs. (D) Gene ont ology molecular function analysis sho w ed the pr oteins enriched in iMSC-lEVs. (E) IPA showed canonical pathway analysis of iMSC-lEVs proteins. (F & G) Western blot analysis showed p-ERK and ERK expression in HMEC-1 cells under different treatments (n = 3/group). iMSC-lEVs: Large extracellular vesicles from induced pluripotent stem cell-derived mesenchymal stem cells; lEVs: Large extracellular vesicles.

Article Snippet: Prote omic anal ysis The iMSCs-lEVs prot eomic analy sis proc ess was carried out by the Shanghai Applied Protein Technology Company (Shanghai, China).

Techniques: Western Blot, Expressing, Derivative Assay