Journal: BMC Plant Biology

Article Title: Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

doi: 10.1186/s12870-016-0745-0

Figure Lengend Snippet: Organization of pa1 genes on Medicago truncatula genome. Positions of genes are indicated on chromosomes (scale in Mbp). The Medicago truncatula physical scaffold map is that of the genome assembly version 3.5 (including chromosome size and assembly quality map). Genes and their relative positions (%) on the chromosomes are those of assembly 4.1; a fictitious chromosome, called “0”, harbors the unplaced genes. AC146565_12.1, AC146565_18.1, AC146565_34.1 and AJ574790.1 are from genome version 3.5 and are not present at 100 % match in assembly v4. The orphan EST “TA24778_3880” is also reported

Article Snippet: Medicago truncatula tissue gene expression data.

Techniques:

Journal: BMC Plant Biology

Article Title: Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

doi: 10.1186/s12870-016-0745-0

Figure Lengend Snippet: Phylogeny, CXC pattern and tissue EST expression of the Medicago truncatula PA1 paralogues. Unrooted Bayesian tree of Medicago truncatula PA1 family (53 sequences, 366 nucleic acid positions). The tree is presented according to rooted phylogeny shown on Fig. . Numbers at branch correspond respectively to posterior probabilities calculated with MrBayes, and to bootstrap values estimated by PhyML. The scale bar represents the average number of substitutions per site. Six strongly supported clusters were boxed and highlighted with colored backgrounds. The seven chemically and functionally synthetized sequences (AG41, EG41, GL44, AS40, AS37, DS37 and QT41) are indicated on the tree. Among them, AG41, EG41, AS40, and AS37 ( boxed in purple ), and showed toxicity against insect cells, whereas GL44, DS37 and QT41 ( boxed in light green ) did not show toxicity to insect cells. In the tissue expression part, the color-scale represent the expression value scales between 0 and >75 EST per cluster. Two internal sub-clusters were defined for running site model in cluster 3 and 6, and are named respectively 3a, 3b, and 6a, 6b (Table ). Red branches are those that were tested for positive selection (Table )

Article Snippet: Medicago truncatula tissue gene expression data.

Techniques: Expressing, Selection

Journal: BMC Plant Biology

Article Title: Genome-wide analysis identifies gain and loss/change of function within the small multigenic insecticidal Albumin 1 family of Medicago truncatula

doi: 10.1186/s12870-016-0745-0

Figure Lengend Snippet: Phylogeny of PA1 homologues identified in the complete genomes of Fabaceae species. Bayesian tree of PA1 homologues identified in Cajanus cajan (Phaseoleae), Glycine max (Phaseoleae), Phaseolus vulgaris (Phaseoleae), Pisum sativum (Fabeae), and Medicago truncatula (Trifolieae) (91 sequences, 327 nucleotide positions). No homologues were detected in Lotus corniculatus (Loteae) and Trifolium pratense ( Fabeae ) , and only one in Cicer arietinum (Fabeae), which was not included in this tree (see text and Additional file : Table S1). The tree was rooted with a sequence from Styphnolobium japonicum (Sophoreae), according to the current phylogeny of Papilionoideae [ , ]. Numbers at branch correspond to posterior probabilities calculated with MrBayes and bootstrap values estimated by PhyML. The scale bar represents the average number of substitutions per site. The six Medicago truncatula sequence clusters identified previously (Fig. ) are recovered and indicated with the same colors. Labels on the left identify sustained nodes in the phylogeny of legumes, and labels on the right identify the protein species with substantial experimental data (protein names, Uniprot identifiers & references therein, and PDB identifiers when available). Pea proteins are included as reference peptides ( P. sativum genome not available yet)

Article Snippet: Medicago truncatula tissue gene expression data.

Techniques: Sequencing

Journal: Nature Communications

Article Title: Desmoplakin and periplakin genetically and functionally contribute to eosinophilic esophagitis

doi: 10.1038/s41467-021-26939-9

Figure Lengend Snippet: a Immunoblots of lysates from DSP (non-variant or mutant p.Y895C)–transfected HEK293T cells with CAPN14 or enzymatically inactive CAPN14-C101A co-transfection for changes in DSP levels following the addition of exogenous Ca 2+ (left). Protein remaining after activation of CAPN14 was determined by the difference in band intensity between after and before activation [(after x 100)/before] (right). Statistics: DSP WT vs. DSP mutant, P = 0.0131. b Effect of DSP and PPL variants on protein degradation on activation of co-transfected CAPN14. Total protein remaining was determined for each mutation. Total protein (%) = (each protein remaining x 100)/average of non-variant cells. Statistics (versus non-variants): p.G46D, P = 0.8212; p.R808C, P = 0.0296; p.Y895C, P = 0.0352; p.1067_1068del, P = 0.0125; p.N1215S, P = 0.2675; p.R1340C, P = 0.2581; p.E1723Q, P = 0.6186; p.R108C, P = 0.0712; p.E632K, P = 0.0156; p.K1051V, P = 0.0946; p.L1154V, P = 0.0323; p.E1163K, P = 0.2167; p.V1377E, P = 0.9157. c Gene expression of CAPN14 in human normal tissues from the Human Protein Atlas ( https://www.proteinatlas.org/ ). d Calpain inhibition results in rescue of DSP and PPL levels by CAPN14-mediated degradation. Total protein (%) = (each protein remaining x 100)/average of cells without exogenous Ca 2+ and SNJ-1945. Statistics: DSP (without SNJ-1945 vs. with SNJ-1945, P = 0.0028); PPL (without SNJ-1945 vs. with SNJ-1945, P = 0.0188). For panels a , b , and d , data are representative of three experiments performed in duplicate and are presented as mean ± SEM, and two-tailed P -values were determined by the unpaired t -test ( a and d ) or one-way ANOVA test followed by a Dunnett’s multiple-comparison test ( b ). * P < 0.05 and ** P < 0.01. CAPN14 calpain-14, DSP desmoplakin, PPL periplakin, SEM standard error of the mean, WT wild-type.

Article Snippet: Statistics (versus non-variants): p.G46D, P = 0.8212; p.R808C, P = 0.0296; p.Y895C, P = 0.0352; p.1067_1068del, P = 0.0125; p.N1215S, P = 0.2675; p.R1340C, P = 0.2581; p.E1723Q, P = 0.6186; p.R108C, P = 0.0712; p.E632K, P = 0.0156; p.K1051V, P = 0.0946; p.L1154V, P = 0.0323; p.E1163K, P = 0.2167; p.V1377E, P = 0.9157. c Gene expression of CAPN14 in human normal tissues from the Human Protein Atlas ( https://www.proteinatlas.org/ ). d Calpain inhibition results in rescue of DSP and PPL levels by CAPN14-mediated degradation.

Techniques: Western Blot, Variant Assay, Mutagenesis, Transfection, Cotransfection, Activation Assay, Gene Expression, Inhibition, Two Tailed Test, Comparison