Journal: BMC Research Notes

Article Title: Multiplex preamplification of specific cDNA targets prior to gene expression analysis by TaqMan Arrays

doi: 10.1186/1756-0500-1-21

Figure Lengend Snippet: Mean CT and mean AE for the 46 bladder cancer related genes and the endogenous control GUSB obtained before and after cDNA preamplification.

Article Snippet: ANLN , Hs00218803_m1 , 17 , 20 , 28,50 , 1,58 , 23,97 , 1,64 , 4,53 , 0,966 , 1,807 , 0,06 , 1,834 , 0,09.

Techniques: Control

Journal: OncoTargets and Therapy

Article Title:

Overexpression of Progerin Results in Impaired Proliferation and Invasion of Non-Small Cell Lung Cancer Cells

doi: 10.2147/ott.s237016

Figure Lengend Snippet: Figure 6 Progerin significantly impaired the migration and invasion abilities of A549 cells. (A and B) The migration ability of A549 cells was evaluated by wound migration experiments. (C and D) Transwell assay of A549 cells. (E and F) Progerin impaired the invasive ability in A549-PG. (G and H) Representative Western blot analysis of relevant proteins showing that progerin decreased ANLN, MMP7 and MMP9 levels in A549-PG cells. *p<0.05, and **p<0.01.

Article Snippet: The PVDF membranes were then incubated with rabbit anti-p53 polyclonal antibody (#9284, Cell Signaling, USA), rabbit anti-ATM monoclonal antibody (#2873, Cell Signaling, USA), rabbit anti-ATR monoclonal antibody (#13934, Cell Signaling, USA), mouse anti-DNA-PKcs monoclonal antibody (#12311, Cell Signaling, USA), rabbit anti-Phospho-p53 polyclonal antibody (#9284, Cell Signaling, USA), mouse anti-FLAG monoclonal antibody (#TA180144, OriGene, USA), rabbit anti-γ-H2AX monoclonal antibody (#2577, Cell Signaling, USA), mouse anti-Lamin A/C monoclonal antibody (sc376248, Santa Cruz Biotechnology, USA), rabbit antiH2AX monoclonal antibody (#7631, Cell Signaling, USA), rabbit anti-GAPDH monoclonal antibody (#5174, Cell Signaling, USA), rabbit anti-CDK4 monoclonal antibody (ab108357, Abcam, USA), rabbit anti-cyclin D1 monoclonal antibody (#2978, Cell Signaling, USA), mouse anti-cyclin E1 monoclonal antibody (#4129, Cell Signaling, USA), mouse anti-pRB (#9308, Cell Signaling, USA) polyclonal antibody, mouse anti-ANLN monoclonal antibody (sc271814, Santa Cruz Biotechnology, USA), rabbit anti-MMP7 monoclonal antibody (ab205525, Abcam, USA) and rabbit anti-MMP9 monoclonal antibody (ab137867, Abcam, USA).

Techniques: Migration, Transwell Assay, Western Blot

Journal: eLife

Article Title: Anillin facilitates septin assembly to prevent pathological outfoldings of central nervous system myelin

doi: 10.7554/eLife.43888

Figure Lengend Snippet: ( A ) Immunoblotting of myelin purified from the brains of wild type mice at P75 compared to brain lysates indicates that anillin (ANLN) is enriched in myelin similar to septin 8 variant 1 (SEPT8_v1). The same amount of protein was loaded. The myelin marker MOG and the axonal marker TUJ1 served as controls. Blot shows n = 2 mice per genotype representative of n = 3 mice per genotype. ( B–C ) Immunofluorescent signal of ANLN (green in B ) and SEPT7 (green in C ) extends longitudinally along axons identified by neurofilament-labelling (red in B–C ). Additional ANLN-immunopositive puncta (asterisks in B ) were not evidently associated with filamentous structures (arrowheads in B,C ). The panels show maximal projections of confocal stacks and 3-dimensional reconstructions of longitudinally sectioned spinal cord of P75 WT mice. Images representative of three mice. ( D ) Immunoblotting of myelin purified from the brains of wild-type mice at P15, P18, P21 and P24 indicates that the abundance of ANLN in myelin increases with maturation. Myelin septins (SEPT2, SEPT4, SEPT7, SEPT8) and MAG served as control. Blot shows n = 1 mouse per timepoint. ( E ) Immunolabelling of longitudinally sectioned WT optic nerves detects ANLN (red) in proximity to SEPT8 (green); co-labeled structures (arrowheads) were seen occasionally at P21 and frequently at P28 but not at P15. TUJ1 served as axonal marker. Images representative of three experiments.

Article Snippet: Antibodies were specific for ANLN (Acris AP16165PU-N; 1:200), SEPT7 (IBL18991; 1:1000), SEPT8 (ProteinTech Group 11769–1-AP; 1:500), TUJ1 (Covance MMS-435P; 1:1000), neurofilament (Covance SMI-31; 1:1500), myelin-associated glycoprotein (MAG clone 513; Chemicon MAB1567; 1:50), voltage-gated sodium channel Na v 1,6 (alomonelabs ASC-009; 1:500) or contactin-associated protein (CASPR; Neuromabs 75–001; 1:500).

Techniques: Western Blot, Purification, Variant Assay, Marker, Control, Labeling

Journal: eLife

Article Title: Anillin facilitates septin assembly to prevent pathological outfoldings of central nervous system myelin

doi: 10.7554/eLife.43888

Figure Lengend Snippet: ( A–B ) Immunolabelling of coronal brain sections of WT mice at P75 detects ANLN (red) and SEPT8 (green) filaments (arrowheads) in the indicated white matter tracts. ( A–A’ ) shows labelling in the fimbria. ( A’ ), enlargement of the dashed square in ( A ). ( B ) shows labelling in the corpus callosum. MAG or neurofilaments (NF) were co-labelled as control. Images representative of three experiments.

Article Snippet: Antibodies were specific for ANLN (Acris AP16165PU-N; 1:200), SEPT7 (IBL18991; 1:1000), SEPT8 (ProteinTech Group 11769–1-AP; 1:500), TUJ1 (Covance MMS-435P; 1:1000), neurofilament (Covance SMI-31; 1:1500), myelin-associated glycoprotein (MAG clone 513; Chemicon MAB1567; 1:50), voltage-gated sodium channel Na v 1,6 (alomonelabs ASC-009; 1:500) or contactin-associated protein (CASPR; Neuromabs 75–001; 1:500).

Techniques: Control

Journal: eLife

Article Title: Anillin facilitates septin assembly to prevent pathological outfoldings of central nervous system myelin

doi: 10.7554/eLife.43888

Figure Lengend Snippet: ( A ) Scheme of the wild type (WT) Anln gene and the engineered Anln allele before and after recombination. Exon 4 of the Anln flox -allele is flanked by loxP-sites (floxed) for Cre-mediated recombination. Positions of PCR primers ( P1, P2, P3 ) are indicated. ( B ) Genotyping PCR of DNA isolated from mouse tail tips identifies the indicated alleles. Gel shows n = 2 mice per genotype. ( C ) Immunoblot analysis of brain lysates and myelin purified from P75 control ( Anln fl/fl ) and Anln fl/fl ;Cnp Cre/WT ( Anln cKO) mice. Note that ANLN is only detectable in myelin purified from the brains of control mice. Note that the abundance of SEPT8 is reduced in myelin purified from Anln cKO compared to control mice. MOG and TUJ1 were detected as controls. Blot shows n = 2 mice per genotype. ( D ) Electron micrographs of optic nerves at eight mo indicates unaltered myelin periodicity and compaction in Anln cKO mice. Representative of three mice per genotype.

Article Snippet: Antibodies were specific for ANLN (Acris AP16165PU-N; 1:200), SEPT7 (IBL18991; 1:1000), SEPT8 (ProteinTech Group 11769–1-AP; 1:500), TUJ1 (Covance MMS-435P; 1:1000), neurofilament (Covance SMI-31; 1:1500), myelin-associated glycoprotein (MAG clone 513; Chemicon MAB1567; 1:50), voltage-gated sodium channel Na v 1,6 (alomonelabs ASC-009; 1:500) or contactin-associated protein (CASPR; Neuromabs 75–001; 1:500).

Techniques: Isolation, Western Blot, Purification, Control

Journal: eLife

Article Title: Anillin facilitates septin assembly to prevent pathological outfoldings of central nervous system myelin

doi: 10.7554/eLife.43888

Figure Lengend Snippet: ( A ) Differential myelin proteome analysis indicates that ANLN is readily identified in myelin purified from the brains of control mice at P75 but undetectable in Anln fl/fl ;Cnp Cre/WT ( Anln cKO)-myelin. Mean +/SEM; n = 3 mice per genotype. ( B ) Differential myelin proteome analysis reveals that the abundance of myelin septins (SEPT2, SEPT4, SEPT7, SEPT8) is diminished in myelin purified from Anln cKO-mice at P75 compared to Anln fl/fl mice. The abundance of the putative septin-associated proteins RHOB and CDC42 is also significantly reduced in Anln cKO-myelin, although to a lesser degree. The horizontal black dashed line marks a threshold indicating halved abundance of a protein in myelin. Mean +/SEM; n = 3 mice per genotype; For q-values as calculated by R data analysis (see Materials and Methods for details) see . ( C ) Differential myelin proteome analysis indicates that the abundance of classical myelin proteins is unaltered in Anln cKO-myelin. Mean +/SEM. n = 3 mice per genotype; not significant according to q-value calculation using R (see Materials and Methods for details); for exact q-values see . ( D ) By differential myelin proteome analysis, the abundance of cytoskeletal proteins is unaltered in Anln cKO-myelin, except for myelin septins and septin-associated proteins as highlighted in ( B ). Mean +/SEM. n = 3 mice per genotype; not significant according to q-value calculation using R; for exact q-values see . ( E ) qRT-PCR to determine the abundance of mRNAs encoding putative septin-associated proteins RHOB and CDC42 in the white matter (corpus callosum) of control ( Anln fl/fl ) versus Anln cKO-mice. Note that Rhob and Cdc42 mRNAs were unaltered in abundance. Mean +/SEM. n = 6 mice per genotype; two-way ANOVA; RhoB p>0.9999, Cdc42 p>0.9999.

Article Snippet: Antibodies were specific for ANLN (Acris AP16165PU-N; 1:200), SEPT7 (IBL18991; 1:1000), SEPT8 (ProteinTech Group 11769–1-AP; 1:500), TUJ1 (Covance MMS-435P; 1:1000), neurofilament (Covance SMI-31; 1:1500), myelin-associated glycoprotein (MAG clone 513; Chemicon MAB1567; 1:50), voltage-gated sodium channel Na v 1,6 (alomonelabs ASC-009; 1:500) or contactin-associated protein (CASPR; Neuromabs 75–001; 1:500).

Techniques: Purification, Control, Quantitative RT-PCR

Journal: eLife

Article Title: Anillin facilitates septin assembly to prevent pathological outfoldings of central nervous system myelin

doi: 10.7554/eLife.43888

Figure Lengend Snippet: ( A ) Volcano plot summarizing genotype-dependent quantitative myelin proteome analysis. Data points represent quantified proteins in myelin purified at P75 from the brains of Anln cKO compared to Anln fl/fl mice (n = 3 mice per genotype). Data points are plotted as log2-transformed fold-change (FC) on the x-axis against the −log10-transformed q-value on the y-axis. The horizontal red dashed line indicates a q-value of q = 0.01; the vertical black dashed lines mark the ±1 log2 fold-change threshold indicating a halved or doubled abundance of a protein in myelin, respectively. Data points representing myelin septin monomers (SEPT2, SEPT4, SEPT7, SEPT8) are highlighted in light red color with protein names given; note that their abundance is strongly reduced in Anln cKO compared to Anln fl/fl myelin. Also note that ANLN is not represented because it was not detected in Anln cKO myelin. For bar graphs showing genotype-dependent comparison of the abundance of individual proteins in myelin see . For the original dataset and exact q-values see . ( B ) Immunoblotting validates the lack of anillin (ANLN) and the strong reduction of septins (SEPT2, SEPT4, SEPT7, SEPT8) in myelin purified from the brains of Anln cKO-mice. ATPase Na+/K + transporting subunit alpha 3 (ATP1A3) was detected as control. Blot shows n = 3 mice per genotype. ( C ) Immunoblotting indicates that the abundance of classical myelin proteins (PLP/DM20, SIRT2, CD9, CA2) is unaltered in myelin purified from the brains of Anln cKO-mice. ATP1A1 served as control. Blot shows n = 3 mice per genotype. ( D ) Genotype-dependent quantitative assessment of PtdIns(4,5)P 2 (PIP 2 )–levels in myelin purified from the brains of Anln cKO-mice compared to controls ( Anln fl/fl ) at P75. Mean +/SEM. n = 6 mice per genotype; two-tailed unpaired t-test; PtdIns(4,5)P 2 p=0.0435. ( E ) qRT-PCR to determine the abundance of mRNAs encoding anillin and myelin septins in the white matter (corpus callosum) of control ( Anln fl/fl ) versus Anln cKO-mice. Note that Anln mRNA was virtually undetectable in Anln cKO-mice while the abundances of Sept2 , Sept4 , Sept7 and Sept8 mRNAs were unaltered. Mean +/SEM. n = 6 mice per genotype; two-way ANOVA; Anln p<0.0001, Sept2 p>0.9999, Sept4 p>0.9999, Sept7 p>0.9999, Sept8 p>0.9999. 10.7554/eLife.43888.010 Figure 3—source data 1. Label-free quantification of proteins in myelin purified from the brains of Anln cKO and control mice Tryptic peptides derived from two technical replicates (replicate digestion) per biological replicate (n = 3 mice per genotype) were analyzed by LC-MS (12 runs in total). Proteins (FDR < 1%; two peptides/protein) and peptides (FDR < 1%;≥6 amino acids) were identified by database search against the UniprotKB/SwissProt mouse database using PLGS. Data were post-processed with the software package ISOQuant to calculate absolute in-sample amounts for each detected protein based on the TOP3 approach. Reported abundance values are defined as the relative amount of each protein in respect to the sum over all detected proteins (ppm: parts per million (w/w) of total protein). The typical contaminant proteins trypsin and keratins were filtered. One technical replicate of a control sample was identified as outlier based on its low correlation coefficient of ≤0.76 (all other runs ≥ 0.95) and thus excluded from analysis.

Article Snippet: Antibodies were specific for ANLN (Acris AP16165PU-N; 1:200), SEPT7 (IBL18991; 1:1000), SEPT8 (ProteinTech Group 11769–1-AP; 1:500), TUJ1 (Covance MMS-435P; 1:1000), neurofilament (Covance SMI-31; 1:1500), myelin-associated glycoprotein (MAG clone 513; Chemicon MAB1567; 1:50), voltage-gated sodium channel Na v 1,6 (alomonelabs ASC-009; 1:500) or contactin-associated protein (CASPR; Neuromabs 75–001; 1:500).

Techniques: Purification, Transformation Assay, Comparison, Western Blot, Control, Two Tailed Test, Quantitative RT-PCR, Quantitative Proteomics, Derivative Assay, Liquid Chromatography with Mass Spectroscopy, Software

Journal: Scientific Reports

Article Title: Murine bone-derived mesenchymal stem cells undergo molecular changes after a single passage in culture

doi: 10.1038/s41598-024-63009-8

Figure Lengend Snippet: Gene ontology enrichment analysis and RT-qPCR validation of the upregulated genes in cultured MSCs compared to primary MSCs. ( A ) Gene ontology (GO) analysis of biological processes enriched in the 952 genes upregulated in cultured MSCs. The top 20 significantly enriched biological processes are displayed (based on q-value ≤ 0.05). ( B ) GO analysis of cellular components enriched in the 952 genes upregulated in cultured MSCs. The top 20 significantly enriched cellular components are displayed. ( C ) Upregulation of Ccna2 and Anln genes as validated by RT-qPCR analysis. All datapoints are presented as biological replicates (n = 7 for primary MSCs and n = 4 for cultured MSCs). Data presented as mean ± SEM relative to primary MSCs. ****p ≤ 0.0001.

Article Snippet: To perform quantitative reverse transcription polymerase chain reaction (RT-qPCR), cDNA was prepared in a reaction mix of Taqman fast advanced master mix and the following TaqMan gene expression assays: Ccna2 ( Mm00438063_m1), Anln (Mm00503748_m1), Myoc (Mm00447900_m1), Igf1 (Mm00439560_m1), Tmem119 (Mm00525305_m1), Cfh (Mm01299248_m1), Enpp2 (Mm00516572_m1), Col14a1 (Mm00805269_m1), Thbs3 (Mm00449802_m1), Mmp2 (Mm00439498_m) and Hprt (Mm03024075_m1).

Techniques: Quantitative RT-PCR, Biomarker Discovery, Cell Culture

Journal: Journal of Cell Science

Article Title: Visualizing endogenous Rho activity with an improved localization-based, genetically encoded biosensor

doi: 10.1242/jcs.258823

Figure Lengend Snippet: The optimized dimericTomato-2xrGBD Rho sensor has the best location efficiency. (A) Spinning disk still images of a HeLa cells expressing the CMVdel-mNeonGreen-1xrGBD Rho sensor (upper panel) or CMVdel-dimericTomato-2xrGBD Rho sensor (lower panel) and H1R (not shown), which were stimulated with 100 μM histamine after 150 s and 10 μM pyrilamine after 350 s. The images match with the perturbation that is indicated for the plot in C. Times are min:s from the start of the recording. Scale bars: 25 µm. (B) Change in cytosolic intensity for CMV-mNeonGreen, CMV-eGFP-1xrGBD, CMVdel-3xmNeonGreen-1xrGBD, CMVdel-mNeonGreen-1xrGBD, -2xrGBD and -3xrGBD, and CMVdel-dimericTomato-1xrGBD and -2xrGBD (schematics on left) in HeLa cells expressing H1R, upon stimulation with 100 μM histamine. Each dot represents an individual cell. The median of the data is shown as a black circle and the 95% confidence interval for each median, determined by bootstrapping, is indicated by the bar. The gray dashed line indicates no change in cytosolic intensity. The data is from two biological replicates based on two independent transfections. The number of cells per condition is: 3xmNG-1xrGBD=27, dT-1xrGBD=32, dT-2xrGBD=33, eGFP-1xrGBD=40, mNG=39, mNG-1xrGBD=28, mNG-2xrGBD=34, mNG-3xrGBD=26. (C) Time traces of the change in cytosolic intensity for the displayed cells for the mNeonGreen-1xrGBD sensor in gray and for the dimericTomato-2xrGBD sensor in black. mNG, mNeonGreen; dT, dimericTomato; rGBD, rhotekin G protein binding domain.

Article Snippet: The following plasmids, generated in this study, are available on Addgene ( http://www.addgene.org/ ): 129625 , dTomato-2xrGBD (C1 vector); 176098 , dimericTomato-2xrGBD (pLV vector); 129624 , mNeongreen-2xrGBD; 176091 , mNeonGreen-3xrGBD; 129633 , mNeonGreen-aGBD (anillin); 129634 , mNeonGreen-pGBD (PKN1 codon optimized); 176094 , H2A-mTurquoise2-CDC42-G12V-ΔCaaX; 176095 , H2A-mTurquoise2-RAC1-G12V-ΔCaaX; and 176097 , H2A-mTurquoise2-RHOA-G14V-ΔCaaX.

Techniques: Expressing, Transfection, Protein Binding

Journal: PLoS ONE

Article Title: Transcriptional Events during the Recovery from MRSA Lung Infection: A Mouse Pneumonia Model

doi: 10.1371/journal.pone.0070176

Figure Lengend Snippet: Taqman gene expression assay ID numbers for the genes which were significantly regulated during the recovery after MRSA lung infection.

Article Snippet: anln , Mm01170327_m1.

Techniques: Gene Expression, Infection

Journal: PLoS ONE

Article Title: Transcriptional Events during the Recovery from MRSA Lung Infection: A Mouse Pneumonia Model

doi: 10.1371/journal.pone.0070176

Figure Lengend Snippet: The list of top 30 transcripts up-regulated during the recovery from MRSA lung infection.

Article Snippet: anln , Mm01170327_m1.

Techniques: Infection, Membrane, Binding Assay

Journal: PLoS ONE

Article Title: Transcriptional Events during the Recovery from MRSA Lung Infection: A Mouse Pneumonia Model

doi: 10.1371/journal.pone.0070176

Figure Lengend Snippet: The known functions of eight verified genes.

Article Snippet: anln , Mm01170327_m1.

Techniques: Binding Assay