diabetes 49 3 424 sv40 mef a rambold  (ATCC)

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: Phylogenetic tree highlighting the position of P. brasiliensis relative to the other species within the family Planctomycetaceae . The tree was inferred from 1,343 aligned characters of the 16S rRNA gene sequence under the maximum likelihood (ML) criterion as previously described . Rooting was done initially using the midpoint method and then checked for its agreement with the current classification (Table ). The branches are scaled in terms of the expected number of substitutions per site. Numbers above the branches are support values from 400 ML bootstrap replicates (left) and from 1,000 Maximum-Parsimony bootstrap replicates (right) if larger than 60% . Lineages with type strain genome sequencing projects registered in GOLD as unpublished are marked with one star, those listed as published (as well as the target organism) with two stars [ - ].

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques: Sequencing

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: Scanning-electron micrograph of P. brasiliensis DSM 5305 T highlighting stalks and crateriform structures on the cell surface.

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques:

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: Genomic G + C content of the Planctomycetaceae type strains, including Phycisphaera mikurensis as outgroup

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques: Sequencing

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: Venn diagram depicting the intersections of sets of homologous proteins of P. maris , P. brasiliensis , P. limnophilus and S. paludicola . Their cardinalities are given in parentheses; for the total number of proteins see Table and the resources listed in Table . The Venn diagram was calculated with the corresponding R package .

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques:

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: MaSH values calculated for the ML trees inferred in this study

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques:

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: Polyamines [ 96 ] and polar lipids [ 48 , 65 , 70 , 95 ] for several Planctomycetaceae as reported in the literature

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques:

Journal: Standards in Genomic Sciences

Article Title: Complete genome sequence of Planctomyces brasiliensis type strain (DSM 5305 T ), phylogenomic analysis and reclassification of Planctomycetes including the descriptions of Gimesia gen. nov., Planctopirus gen. nov. and Rubinisphaera gen. nov. and emended descriptions of the order Planctomycetales and the family Planctomycetaceae

doi: 10.1186/1944-3277-9-10

Figure Lengend Snippet: Classification and general features of P. brasiliensis DSM 5305 T in accordance with the MIGS recommendations [ 23 ] as published by the Genome Standards Consortium [ 24 ]

Article Snippet: Strain IFAM 1448 T (=DSM 5305 = ATCC 49424 = JCM 21570) is the type strain of Planctomyces brasiliensis .

Techniques: Staining, Isolation

Journal: Autophagy

Article Title: Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy

doi: 10.1080/15548627.2016.1252889

Figure Lengend Snippet: Mutation of the PY motif of MDM34 affects mitophagy but not nonselective bulk autophagy. (A and B). The MDM34-MYC OM45-GFP and mdm34[3PA]-MYC OM45-GFP strains were grown to early exponential growth phase in YNB with glycerol as the carbon source and supplemented with the appropriate amino acids. After one d in glycerol-containing medium, the cultures were split in 2: one half of the culture was left untreated for 3 d (A left part) and the other was washed 3 times with water and resuspended in SD-N medium and incubated for 2, 4 and 6 h (A, right panel and B). Protein extracts from atg1Δ, pep4Δ and a wild-type (WT) strain cultured to exponential growth phase in YPG were also prepared (B). Total protein extracts were prepared and analyzed by western immunobloting with antibodies against GFP (to detect full-length OM45-GFP and free GFP), MYC, Ape1 and Pgk1, as a loading control. MDM34-MYC and mdm34[3PA]-MYC strains, transformed with p GFP-ATG8 , were grown as in (B) and protein extracts were analyzed by western immunoblotting with anti-GFP and anti-Pgk1 antibodies. The percentage of Free GFP corresponds to the ratio free GFP: (free GFP + Om45-GFP) (A) or free GFP: (free GFP + GFP-Atg8) (C). The percentage of prApe1 corresponds to the ratio prApe1: prApe1+Ape1. *, nonspecific band.

Article Snippet: 504 , pGFP-ATG8 (416)/GFP-AUT7 (416) , GFP-ATG8, URA3 , CEN , Adgene/ .

Techniques: Mutagenesis, Incubation, Cell Culture, Western Blot, Transformation Assay

Journal: Autophagy

Article Title: Ubiquitination of ERMES components by the E3 ligase Rsp5 is involved in mitophagy

doi: 10.1080/15548627.2016.1252889

Figure Lengend Snippet: Plasmids.

Article Snippet: 504 , pGFP-ATG8 (416)/GFP-AUT7 (416) , GFP-ATG8, URA3 , CEN , Adgene/ .

Techniques: Plasmid Preparation

Journal: Aging (Albany NY)

Article Title: UBB +1 reduces amyloid-β cytotoxicity by activation of autophagy in yeast

doi: 10.18632/aging.203681

Figure Lengend Snippet: Low UBB +1 expression activates autophagy. ( A – B ) Western blot of GFP-Atg8p processing into free GFP. GAPDH was used as the loading control. ( C – D ) Translocation of GFP-Atg8p into yeast vacuole. Top panel: images from FLUO-GFP filter. Bottom panel: images from DIC filter. White arrow: GFP fluorescence inside vacuole. Scale bar = 5 μm. ( E ) The ratio of free GFP to total GFP (uncleaved GFP-ATG8 + free GFP) under wild type background was calculated and presented based on ( A ). Data is shown as average values ± SD from biological triplicates. ( F ) The percentage of cells with diffuse vacuolar GFP fluorescence was counted and represented based on ( C – D ). Above 200 cells were count per sample ( n = 3 ± SD). The asterisk ( * ) indicates a statistically significant p -value of < 0.05 from untreated control strain.

Article Snippet: The pRS416 GFP-ATG8 expression plasmid containing the GFP-Atg8 gene under the endogenous ATG8 promoter was donated by Prof. Daniel Klionsky, University of Michigan [ ] ( http://www.addgene.org/49425/ , RRID:Addgene 49425).

Techniques: Expressing, Western Blot, Translocation Assay, Fluorescence

Journal: The Journal of Biological Chemistry

Article Title: Potassium starvation induces autophagy in yeast

doi: 10.1074/jbc.RA120.014687

Figure Lengend Snippet: Potassium-dependent autophagy is mediated by autophagosomes. A, representative images of individual cell sections after 6 h of nitrogen limitation or potassium starvation. Vacuole (V), autophagosomes (*), lipid droplet (L), glycogen (G). B, distribution of the abundance (per cell) and size (area in µm2) of autophagosomes (n = 50). C, high magnification image (80,000×) showing an autophagosome (arrowhead) fused to the vacuolar membrane. D, representative single-cell images and distributions of GFP-Atg8 spots formed in response to 2 h of nitrogen limitation or potassium starvation (n = 85 cells).

Article Snippet: Plasmid pRS416-GFP-ATG8 (Addgene, 49425) was a gift from Daniel Klionsky ( 81 ), and the GFP- ATG8 construct was subsequently introduced into the pRS415 vector ( 82 ).

Techniques:

Journal: The Journal of Biological Chemistry

Article Title: Potassium starvation induces autophagy in yeast

doi: 10.1074/jbc.RA120.014687

Figure Lengend Snippet: Potassium-dependent autophagy requires autophagy-related kinases Atg1 and Atg5 and the PI 3-kinase complex. A, in pro-autophagy conditions, the GFP-Atg8 reporter is transported to the vacuole and enzymatically processed to release GFP. GFP-Atg8 processing was monitored in WT BY4741 cells after 0, 3, and 6 h of nitrogen limitation or potassium starvation. Protein bands were quantified using ImageLab and presented as the ratio of GFP and GFP-Atg8 (% of maximum). B, induction of autophagy results in activation of the Pho8Δ60 enzyme, which converts a fluorogenic substrate (α-naphthyl phosphate) into a fluorescent reporter (α-naphthol). Shown are data for Pho8Δ60 activity in the same conditions as (A). C, processing of mitophagy reporters Om45-GFP and Idh1-GFP in WT BY4741 after 6 h of nitrogen limitation or potassium starvation. Data are presented as the ratio of GFP and Om45-GFP/Idh1-GFP (% of maximum). D, processing of autophagy reporter GFP-Atg8 after 6 h of nitrogen limitation or potassium starvation in BY4741 cells lacking core components of the PI 3-kinase complex (Vps34 or Vps15) or the autophagy pathway (Atg1 or Atg5). E, processing of GFP-Atg8 after 6 h of nitrogen limitation or potassium starvation in BY4741 cells lacking regulatory components of the PI 3-kinase complex (Vps30, Vps38, or Atg14). All experiments were repeated three times and data are ± S.D. (error bars) for three or four biological replicates. Adjusted p-values were determined by one-way ANOVA relative to untreated cells (SCD).

Article Snippet: Plasmid pRS416-GFP-ATG8 (Addgene, 49425) was a gift from Daniel Klionsky ( 81 ), and the GFP- ATG8 construct was subsequently introduced into the pRS415 vector ( 82 ).

Techniques: Activation Assay, Activity Assay