Journal: Bone Reports

Article Title: Voluntary exercise in mice triggers an anti-osteogenic and pro-tenogenic response in the ankle joint without affecting long bones

doi: 10.1016/j.bonr.2024.101810

Figure Lengend Snippet: Regulation of bone markers in response to exercise and comparison between joint and long bone samples. (A–B) After RNA extraction from tissue samples, relative gene expression was measured by RT-qPCR for the mechanosensors Sclerostin ( Sost ) and Periostin ( Postn ) (A) and for the bone formation markers Osterix ( Osx ), Runx2 , Dentin matrix acidic phosphoprotein ( Dmp1 ), and Tissue non-specific alkaline phosphatase ( Alpl ) (B). Data were obtained from n = 14 to n = 17 mice and represented as the mean with 95 % confidence interval (CI). (C–D) Immunolocalization of SOST expression by IHC (representative picture of n = 3 per group). (C) Positive staining of osteocytes in bone structures of control samples either surrounding the enthesis or in tibia cortical zone, (D) Focus on the enthesis, where chondrocyte-like cells at the Achilles tendon insertion site in the calcaneus were also positive (dotted circle), and comparison between the exercise and the control groups. (E) Immunolocalization of ALPL expression by IHC, focus on the enthesis (dotted circle), where few chondrocyte-like cells were positive (arrowheads).

Article Snippet: Sections were then incubated with the primary antibody overnight at 4 °C (Goat anti SOST, R&D Systems, #AF1589; Rabbit anti ALPL, Novus Biologicals, #NBP2-67295; Rabbit anti TNMD, Fisher Scientific, #17238803; Mouse anti pro-BMP2, Novus Biologicals, #MAB2260), and with a secondary antibody conjugated with polymerase-HRP (Vector Laboratories) for 45 min at room temperature.

Techniques: Comparison, RNA Extraction, Gene Expression, Quantitative RT-PCR, Expressing, Staining, Control

Journal: Cell reports

Article Title: Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin

doi: 10.1016/j.celrep.2018.07.106

Figure Lengend Snippet: (A) Htt mRNA (green) detected in cells of non-neuronal origin (HeLa, Hm, and Mm primary fibroblasts) and In cells of neuronal origin (Mm Neuro2a, Mm cortical primary neurons, and Mm brain section) by dual-color FISH. Nuclei are labeled with Hoechst (blue). Representative images of maximum Z projections of optical sections through the nucleus are spaced 0.5 μm apart. 100× oil objective is shown (scale bars, 5 μm). (B) Scatterplot representing the absolute quantification of Htt transcript in each cell line. Each dot represents the number of nuclear and cytoplasmic foci for one cell (n = 20–30 cells). Linear regression is shown for each transcript. (C) Percentage of nuclear and cytoplasmic localization of Htt mRNA in different cell lines (n ~20 cells; mean ± SEM; ****p < 0.0001; one-way ANOVA-Bonferroni’s multiple comparisons test). See also Figure S2.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-HTT Sapp et al., 2012 Ab1; RRID: N/A rabbit polyclonal anti-RPB1 Cell Signaling Cat#2629; RRID: AB_2167468 mouse monoclonal anti-GAPDH Sigma Cat#MAB374; RRID: AB_21G7445 chicken monoclonal anti-NeuN Millipore Cat#MAB377B; RRID: AB_177621 chicken polyclonal anti-GFAP Millipore Cat#AB5541; RRID: AB_177521 Chemicals, Peptides, and Recombinant Proteins AlamarBlue Life Technologies Cat#DAL1G25 Critical Commercial Assays See Table S1 for the list and cat# of RNAscope probes ACDBio N/A RNAscope Fluorescent Multiplex Assay ACDBio Cat#32G85G QuantiGene 2.0 Assay Affymetrix Cat#QSGG11 QuantiGene 2.0 Htt probe Affymetrix Cat#SB-1415G QuantiGene 2.0 Ppib probe Affymetrix Cat#SB-1GGG2 Experimental Models: Cell Lines Mouse: Neuro2a ATCC Cat#CCL-131 Mouse: embryonic day 16 cortical primary neurons N/A N/A Mouse: primary fibroblasts N/A N/A Human: HeLa ATCC Cat#CCL-2 Human: primary fibroblasts Coriell Cat#GMG8399 Experimental Models: Organisms/Strains Mouse: wild-type FVB/NJ (female) The Jackson Laboratory Cat#GG18GG Oligonucleotides Chol-siRNAHTT Alterman et al., 2015 hsiRNA HTT1G15G Chol-siRNANTC Alterman et al., 2015 hsiRNA NTC DHA-siRNAHTT Nikan et al., 2016 DHA-hsiRNAHTT DHA-siRNANTC Nikan et al., 2016 DHA-hsiRNANTC ASOhtt Hung and Leeds, 2007 ; Exiqon ASO-32G9 (IONIS) ASOntc Exiqon ASO-ContA Oligonucleotides This paper Table S2 Software and Algorithms ImageJ NIH https://imagei.nih.gov/ii/ GraphPad Prism GraphPad Software Inc. https://www.graphpad.com/scientifc-software/prism/ R The R Foundation https://www.r-proiect.org/ Other RNaseq Blair et al., 2017 N/A RNaseq Zhang et al., 2014 https://web.stanford.edu/group/barres_lab/brain_rnaseq.html Open in a separate window KEY RESOURCES TABLE

Techniques: Labeling, Quantitative Proteomics

Journal: Cell reports

Article Title: Nuclear Localization of Huntingtin mRNA Is Specific to Cells of Neuronal Origin

doi: 10.1016/j.celrep.2018.07.106

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies rabbit polyclonal anti-HTT Sapp et al., 2012 Ab1; RRID: N/A rabbit polyclonal anti-RPB1 Cell Signaling Cat#2629; RRID: AB_2167468 mouse monoclonal anti-GAPDH Sigma Cat#MAB374; RRID: AB_21G7445 chicken monoclonal anti-NeuN Millipore Cat#MAB377B; RRID: AB_177621 chicken polyclonal anti-GFAP Millipore Cat#AB5541; RRID: AB_177521 Chemicals, Peptides, and Recombinant Proteins AlamarBlue Life Technologies Cat#DAL1G25 Critical Commercial Assays See Table S1 for the list and cat# of RNAscope probes ACDBio N/A RNAscope Fluorescent Multiplex Assay ACDBio Cat#32G85G QuantiGene 2.0 Assay Affymetrix Cat#QSGG11 QuantiGene 2.0 Htt probe Affymetrix Cat#SB-1415G QuantiGene 2.0 Ppib probe Affymetrix Cat#SB-1GGG2 Experimental Models: Cell Lines Mouse: Neuro2a ATCC Cat#CCL-131 Mouse: embryonic day 16 cortical primary neurons N/A N/A Mouse: primary fibroblasts N/A N/A Human: HeLa ATCC Cat#CCL-2 Human: primary fibroblasts Coriell Cat#GMG8399 Experimental Models: Organisms/Strains Mouse: wild-type FVB/NJ (female) The Jackson Laboratory Cat#GG18GG Oligonucleotides Chol-siRNAHTT Alterman et al., 2015 hsiRNA HTT1G15G Chol-siRNANTC Alterman et al., 2015 hsiRNA NTC DHA-siRNAHTT Nikan et al., 2016 DHA-hsiRNAHTT DHA-siRNANTC Nikan et al., 2016 DHA-hsiRNANTC ASOhtt Hung and Leeds, 2007 ; Exiqon ASO-32G9 (IONIS) ASOntc Exiqon ASO-ContA Oligonucleotides This paper Table S2 Software and Algorithms ImageJ NIH https://imagei.nih.gov/ii/ GraphPad Prism GraphPad Software Inc. https://www.graphpad.com/scientifc-software/prism/ R The R Foundation https://www.r-proiect.org/ Other RNaseq Blair et al., 2017 N/A RNaseq Zhang et al., 2014 https://web.stanford.edu/group/barres_lab/brain_rnaseq.html Open in a separate window KEY RESOURCES TABLE

Techniques: Recombinant, RNAscope, Multiplex Assay, Software

Journal: Clinical Cancer Research

Article Title: Darolutamide Potentiates the Antitumor Efficacy of a PSMA-targeted Thorium-227 Conjugate by a Dual Mode of Action in Prostate Cancer Models

doi: 10.1158/1078-0432.CCR-21-0342

Figure Lengend Snippet: Darolutamide and PSMA-TTC combination shows synergistic antitumor efficacy in vitro . Isobolograms for the in vitro combination effect of PSMA-TTC and darolutamide on the proliferation of VCaP ( A ) and LNCaP ( B ) prostate cancer cells. PSMA ( FOLH1 ) expression in VCaP ( C ) and LNCaP ( D ) cells treated with 5 kBq/mL PSMA-TTC and/or 2 μmol/L darolutamide as determined by qRT-PCR 48 hours after treatment ( n = 2). The expression is presented as fold change compared with untreated cells. Cell surface PSMA expression as determined by flow cytometry in darolutamide or enzalutamide-treated VCaP ( E ) and LNCaP ( F ) cells. DMSO served as a baseline control and is depicted with a dashed line. CI, combination index; DMSO, dimethyl sulfoxide.

Article Snippet: Gene expression analysis was performed using the TaqMan Fast Advanced Master Mix (Applied Biosystems) and the following TaqMan probes: PSMA ( FOLH1 ; Hs00379515_m1), CDKN1A (Hs00355782_m1), and GAPDH (Hs02758991_g1), all from Applied Biosystems.

Techniques: In Vitro, Expressing, Quantitative RT-PCR, Flow Cytometry, Control

Journal: Viruses

Article Title: Transkingdom Analysis of the Female Reproductive Tract Reveals Bacteriophages form Communities

doi: 10.3390/v14020430

Figure Lengend Snippet: Bacteriome profiling by community group of self-collected vaginal swabs from South African women. ( A ) Relative abundance of the 16 most frequently identified bacterial taxa (y-axis) by sample (x-axis), grouped by community group (CG), bacterial vaginosis (BV) Status, visit number, highly active antiretroviral therapy (HAART) status, and human immunodeficiency virus (HIV) status (color key shown). Percent abundance is indicated by gradient key. Using Ward’s linkage hierarchical clustering, samples clustered into five distinct bacterial community profiles termed CG. ( B ) Bacterial composition (color key shown) for each of the five CGs (x-axis) expressed as relative abundance (y-axis). ( C ) Bar plot showing the relative abundance of 16S rRNA copies per 10 ng total DNA (y-axis) of L. iners (blue), L. crispatus (purple), L. gasseri (pink), and L. jensenii (green) bacterial species as determined by qPCR of FRT samples (x-axis) that clustered into CG1.

Article Snippet: To serve as positive controls, generate standard curves, and measure the detection limit of species-specific 16S rRNA gene qPCR assays, Lactobacillus iners (ATCC 55195), Lactobacillus crispatus (ATCC 33820), Lactobacillus gasseri (ATCC 33323), and Lactobacillus jensenii (ATCC25258) genomic DNA was extracted using isopropanol precipitation.

Techniques: Virus

Journal: Applied and Environmental Microbiology

Article Title: Regulator LdhR and d -Lactate Dehydrogenase LdhA of Burkholderia multivorans Play Roles in Carbon Overflow and in Planktonic Cellular Aggregate Formation

doi: 10.1128/AEM.01343-17

Figure Lengend Snippet: Alternative pathways of gluconate-6P formation by dissimilation of glucose in Burkholderia. Glucose utilization can follow the direct oxidative pathway (orange arrows) or the phosphorylative pathway (blue arrows). Catabolism of other monomeric carbon sources (marked with brown boxes) is also indicated. Central metabolic pathways are glycolysis (G), Entner-Doudoroff pathway (ED), pentose-phosphate pathway (PPP), tricarboxylic acid (TCA) cycle, and gluconeogenesis (GN). Other abbreviations: 2KG, 2-ketogluconate; KGP, 2-ketogluconate-6P; KDPG, 2-keto-3-deoxy-gluconate-6P; gcd, glucose dehydrogenase; gad, gluconate dehydrogenase; gntK, gluconokinase; kgk, 2-ketogluconokinase; kgr, KGP reductase; zwf, glucose-6P dehydrogenase; glk, glucokinase; edd, glucose-6P dehydratase; eda, KDPG aldolase; tpi, triose isomerase; fba, fructose-1,6P aldolase; fbp, fructose-1,6P phosphatase; pgi, phosphoglucoisomerase; mdh_1, mannitol dehydrogenase; aceA, isocitrate lyase; frk, fructokinase; ldhA, d-lactate dehydrogenase; phbA, β-ketothiolase; phbB, acetoacetyl-coenzyme A reductase; phbC, poly-β-hydroxybutyrate synthase; gltA, citrate synthase; acn, aconitate hydratase; icdA, isocitrate dehydrogenase; suc, succinate-coenzyme A transferase; sdh, succinate dehydrogenase/fumarate reductase; fum, fumarate hydratase; mdh, malate dehydrogenase; gap, glyceraldehyde-3P dehydrogenase; pkg, phosphoglycerate kinase; pgm, phosphoglycerate mutase; eno, phosphopyruvate hydratase; pta, phosphate acetyltransferase; ack, acetate kinase; pps, phosphoenolpyruvate synthase; pyk, pyruvate kinase; PHB, poly-β-hydroxybutyrate; IM, inner membrane; and OM, outer membrane. This simplified catabolic pathway was based on reactions available for B. multivorans ATCC 17616 from the Kyoto Encyclopedia of Genes and Genomes (KEGG) database.

Article Snippet: Since the custom arrays used represent two different Burkholderia species ( 16 ), a digital mask was applied leaving only the 9,610 probe sets representing B. multivorans ATCC 17616 transcripts for analysis.

Techniques: Membrane

Journal: Applied and Environmental Microbiology

Article Title: Regulator LdhR and d -Lactate Dehydrogenase LdhA of Burkholderia multivorans Play Roles in Carbon Overflow and in Planktonic Cellular Aggregate Formation

doi: 10.1128/AEM.01343-17

Figure Lengend Snippet: LdhR regulator shows decreased expression in nonmucoid variants derived from mucoid Burkholderia strains and is cotranscribed with ldhA. (A) Expression by qRT-PCR of ldhR in nonmucoid variants compared with those in the respective mucoid parental strains of B. multivorans D2095, B. contaminans IST408, B. anthina FC0967, B. vietnamiensis PC259, and B. dolosa CEP0743. (B) In B. multivorans ATCC 17616, the genomic region containing ldhR and the flanking regions is located in chromosome 1 between the nucleotide positions indicated in the figure. The new NCBI locus tags for the indicated genes are BMUL_RS12975 (Bmul_2556), BMUL_RS12980 (Bmul_2557), BMUL_RS12985 (Bmul_2558), and BMUL_RS12990 (Bmul_2559). Nucleotide regions upstream of genes ldhR and scmR showing a lux box sequence (conserved residues in red) preceding the scmR gene of B. thailandensis E264, which is absent from the ldhR upstream region. Asterisks denote conserved nucleotides between the two regions. The putative start codons are underlined. (C) Reverse transcription-PCR showing the cotranscription of ldhR and ldhA in B. multivorans ATCC 17616 grown for 18 h in S medium with 2% d-mannitol. The image shows the amplification from genomic DNA (1), cDNA (2), or total RNA (3) of the 319-bp region comprising the end of ldhR and beginning of ldhA and amplification from genomic DNA (4), cDNA (5), or total RNA (6) of the 305-bp region comprising the end of ldhA and beginning of Bmul_2559. M, DNA marker; nt, nucleotides; aa, amino acids.

Article Snippet: Since the custom arrays used represent two different Burkholderia species ( 16 ), a digital mask was applied leaving only the 9,610 probe sets representing B. multivorans ATCC 17616 transcripts for analysis.

Techniques: Expressing, Derivative Assay, Quantitative RT-PCR, Sequencing, Reverse Transcription, Amplification, Marker