Journal: Journal of Biological Chemistry

Article Title: Expression Profiles of Arabidopsis thaliana in Mineral Deficiencies Reveal Novel Transporters Involved in Metal Homeostasis

doi: 10.1074/jbc.m309338200

Figure Lengend Snippet: FIG. 6. Functional characterization of AtOPT3. A, hybridization of an 600-bp AtOPT3 cDNA probe, corresponding to the 3-terminal exon, to RNA extracted from Arabidopsis roots of plants grown in control conditions (Ctl), copper (-Cu), manganese (-Mn), zinc (-Zn), and iron (-Fe) deficiency. The ethidium bromide-stained RNA gel is shown for quantification. B, growth of ctr1 expressing AtOPT3 on YPG-Ura plates supplemented with 10 M CuSO4 compared with the mutant transformed with the vector alone. C, growth of smf1 expressing AtOPT3 on manganese-limited medium, with and without 1 mM EGTA compared with the growth of the mutant transformed with the vector alone.

Article Snippet: Genome-wide Analysis Provides Insight into Metal Transport—We have used Affymetrix Arabidopsis DNA chips containing 8,300 genes (which cover about one-third of the ge- FIG. 7.

Techniques: Functional Assay, Hybridization, Control, Staining, Expressing, Mutagenesis, Transformation Assay, Plasmid Preparation

Journal: Nutrients

Article Title: Long-Term Consumption of a Sugar-Sweetened Soft Drink in Combination with a Western-Type Diet Is Associated with Morphological and Molecular Changes of Taste Markers Independent of Body Weight Development in Mice

doi: 10.3390/nu14030594

Figure Lengend Snippet: Transcriptome analysis of 59 selected genes associated with oral chemosensation, displayed as a heatmap showing mean fold changes in gene expression of the SSB-fed diet groups in relation to the respective water-fed group (=1) in the form of a color code. The gene expression was analyzed using one customized cDNA microarray per group from pooled RNA samples of the CV from mice that received either a standard diet (chow, n = 10–11) or Western-type diet (WD, n = 7–8) with water (Water) or a sugar-sweetened beverage (SSB) as a drink for 24 weeks.

Article Snippet: The isolated RNA samples per mouse were reverse transcribed to cDNA using the LunaScript RT Supermix Kit (New England Biolabs GmbH, Frankfurt am Main, Germany).

Techniques: Expressing, Microarray, Western Blot

Journal: Cell reports

Article Title: Redox regulation of age-associated defects in generation and maintenance of T cell self-tolerance and immunity to foreign antigens

doi: 10.1016/j.celrep.2022.110363

Figure Lengend Snippet:

Article Snippet: CellsDirect one-Step RT-PCR kit (Invitrogen, Catalog number 11753–100) was used for reverse transcription and specific target amplification (RT-PCR) for each single-cell and universal mouse total RNA of 200 pg.

Techniques: Recombinant, Expressing, Microarray, Software

Journal: NPJ Vaccines

Article Title: Epitope-specific immunity against Staphylococcus aureus coproporphyrinogen III oxidase

doi: 10.1038/s41541-020-00268-2

Figure Lengend Snippet: a S. aureus CgoX structure was modulated from B. subtillis (3I6D.pdb). The linear epitope of mAb D3 (red) was identified by microarray technology using overlapping 13mer CgoX peptides (Supplementary Fig. ). Protein structure was visualised by EzMol2.1. b Alanine scan of epitope peptides for binding analysis of anti-CgoX mAb D3. Single amino acid positions of the D3 epitope were consecutively replaced by alanine (red in right panel). Immobilised peptides were stained by anti-CgoX mAb D3 detected with anti-mIgG-HRP. Data are presented as mean ± s.d. ( n = 2 technical replicates). c Allele frequencies of anti-CgoX mAb D3 epitope. Genome sequences of S. aureus clinical isolates were analysed for epitope aa sequence using the RidomSeqsphere core genome multi locus sequence typing (cgMLST) database. Amino acids interacting with paratope of anti-CgoX mAb D3 according to alanine scan are marked in red. Amino acid differences from identified epitope peptide sequence are marked in blue. Frequencies of alleles with non-restricted binding of anti-CgoX mAb D3 are marked in green. d Uniqueness of the CgoX D3 epitope in S. aureus . Sequence alignment of CgoX from S. aureus with PPOX from H. sapiens and M. musculus . CgoX D3 epitope is depicted in yellow. e Competition analysis of CgoX mAb. Binding of DyLight-649-conjugated anti-CgoX mAb D3 to rCgoX was competed for with different concentrations of unconjugated, indicated mAbs and analysed by ELISA. Binding was determined by fluorescence measurement (Ex 646/Em 674). Data are presented as mean ± s.d. ( n = 2). f Saturation binding curve was generated by plotting absorbance signals (OD 450nm ) of increasing amounts of anti-CgoX huMAb D3 to rCgoX coated on ELISA MaxiSorp plate using the GraphPadPrism 8.4 software. Kd was calculated by non-linear fitting and the equation for one-site binding model [Y = Bmax*X/(Kd + X)].

Article Snippet: Upon washing with TBST (3 × 15 min), HRP conjugated secondary goat anti-mouse IgG (Sigma-Aldrich, Germany, cat. No. A3673) or goat anti-human IgG antibody (Bio-Rad, Germany, cat. No. 172-1050) were diluted 1:3,000 and applied for 1 h at room temperature, respectively.

Techniques: Microarray, Binding Assay, Staining, Sequencing, Enzyme-linked Immunosorbent Assay, Fluorescence, Generated, Software

Journal: NPJ Vaccines

Article Title: Epitope-specific immunity against Staphylococcus aureus coproporphyrinogen III oxidase

doi: 10.1038/s41541-020-00268-2

Figure Lengend Snippet: a Competition ELISA. Binding of anti-CgoX mAb D3 to rCgoX coated on ELISA MaxiSorp plate was competed for with CgoX-D3-BSA conjugate. Binding was detected with anti-mIgG-HRP and compared to control sample (BSA). b Anti-CgoX-BSA IgG titer. Sera of two CgoX-D3-BSA immunised mice were collected at day 68 and analysed together with preimmune serum for anti-CgoX IgGs by ELISA. c Survival of mice challenged with S. aureus upon immunisation with CgoX-D3 epitope peptide conjugated with BSA. BALB/c mice ( n = 11) immunised with CgoX-D3-BSA or the carrier protein BSA (black) as control group ( n = 10), were infected i.p. with 3.3 × 10 7 cfu S. aureus USA300 mixed with 5% mucin from porcine stomach. Significance was calculated by Log-rank (Mantel-Cox) test.

Article Snippet: Upon washing with TBST (3 × 15 min), HRP conjugated secondary goat anti-mouse IgG (Sigma-Aldrich, Germany, cat. No. A3673) or goat anti-human IgG antibody (Bio-Rad, Germany, cat. No. 172-1050) were diluted 1:3,000 and applied for 1 h at room temperature, respectively.

Techniques: Enzyme-linked Immunosorbent Assay, Binding Assay, Control, Infection