Journal: bioRxiv

Article Title: NaP-TRAP: A versatile and accessible workflow to dissect principles of translational regulation and mRNA stability

doi: 10.64898/2026.04.12.718002

Figure Lengend Snippet: Overview of the NaP-TRAP workflow and examples of use cases. ( A ) NaP-TRAP can be performed using either complex reporter libraries or individual reporters, delivered in vivo by zebrafish embryo microinjection or in vitro by mammalian cell transfection, followed by pulldown, RNA purification, and either sequencing- or qPCR-based readout. ( B ) Principle of NaP-TRAP: FLAG-tagged nascent peptides on actively translating ribosomes are immunocaptured to enrich ribosome-associated reporter mRNAs (Pulldown). Reporter abundance is measured in the Input, and translation output is quantified as Pulldown/Input (NaP-TRAP TE). ( C ) Robust delivery and readout across a 100-fold range of injected reporter amounts in zebrafish embryos, with consistent NaP-TRAP TE across all doses. ( D ) Comparable reporter trends across mammalian cell types illustrated by differential translation of control versus oORF-containing reporters in HEK293T, H9, and MCF7 cells. ( E ) NaP-TRAP supports interrogation of diverse regulatory features across the reporter mRNA, including mRNA cap types, 5′-UTR elements (e.g., uORFs/oORFs), coding sequence codon optimality, 3′-UTR elements (e.g., miR-430 sites), and poly(A) tail length in zebrafish embryos. Cartoon diagrams were created individually in BioRender (Smith, J. (2025). BioRender.com/c248457 ).

Article Snippet: Cultured cell lines We have used NaP-TRAP on HEK293T (RRID: CVCL_0063, ATCC Cat. No. CRL-3216) but successfully performed it in various other cell lines including MCF7 (RRID: CVCL_0031, ATCC Cat. No. HTB-22) and H9 (RRID:CVCL_1240, ATCC Cat. No. HTB-176) .

Techniques: In Vivo, Microinjection, In Vitro, Transfection, Purification, Sequencing, Injection, Control

Journal: bioRxiv

Article Title: NaP-TRAP: A versatile and accessible workflow to dissect principles of translational regulation and mRNA stability

doi: 10.64898/2026.04.12.718002

Figure Lengend Snippet: Expected results from NaP-TRAP MPRA analysis pipeline. ( A ) Example histogram of per-insert read counts for one Input replicate with 7,839,828 reads. ( B ) Representative replicate-to-replicate correlations of NaP-TRAP translation efficiency (TE; Pulldown/Input) at 2 hpf and 6 hpf ( R values are Pearson correlations). ( C ) Hierarchical clustering heatmap of Pearson correlations showing TE similarity across replicates and conditions (zebrafish 2 hpf, zebrafish 6 hpf, and HEK293T). ( D ) Distribution of NaP-TRAP TE values at 2 hpf, with the top and bottom 10% of reporters highlighted as activated (blue) and repressed (orange), respectively. ( E ) Example k-mer enrichment analysis for activated and repressed reporter sets at 2 hpf. ( F ) Scatter plot comparing reporter NaP-TRAP TE at 2 versus 6 hpf, highlighting four reporter sets: reporters activated (blue) and repressed (orange) at both stages, reporters with higher TE at 2 hpf than at 6 hpf (2 hpf activated; green), and reporters with high TE at 6 hpf than at 2 hpf (6 hpf activated; pink). ( G ) k-mer enrichment analyses for each of the four reporter sets defined in (F): 2 hpf activated (green), 6 hpf activated (pink), globally repressed (orange) and globally activated (blue).

Article Snippet: Cultured cell lines We have used NaP-TRAP on HEK293T (RRID: CVCL_0063, ATCC Cat. No. CRL-3216) but successfully performed it in various other cell lines including MCF7 (RRID: CVCL_0031, ATCC Cat. No. HTB-22) and H9 (RRID:CVCL_1240, ATCC Cat. No. HTB-176) .

Techniques:

Journal: Bone Reports

Article Title: Transferrin-dependent uptake and distribution of iron in osteoclast-like cells

doi: 10.1016/j.bonr.2026.101909

Figure Lengend Snippet: Modulation of gene expression by exogenous iron in cultures of osteoclast progenitor cells (OPC). OPC were grown with (black bars) or without (white bars) RANKL in media rendered iron deficient (+DFO) or control media (ØDFO) for the last 48 h of the culture. Gene expression was characterized after 5 d of culture by quantitative RT-PCR and normalized against levels of transcripts encoding ß-glucuronidase. Levels of transcripts encoding the pan-MΦ marker F4/80 were reduced in osteoclastogenic cultures and transcript levels for the OC marker TRAP were detected only in cells grown with RANKL. Levels of transcripts encoding TFRC were low in MΦ and and significantly elevated in OCL in control media, and were further increased when OCL were grown in conditions of iron deficiency. Similarly, levels of mRNA encoding DMT1 were increased during development of OCL as compared to MΦ, and were significantly elevated in OCL grown without iron. Levels of mRNA encoding FPN were lower in OCL as compared to MΦ. The data shown represent the mean of triplicates (±SD) of one out of 3–4 biological replicates; * p < 0.05.

Article Snippet: TRAP , Mm00475698_m1.

Techniques: Gene Expression, Control, Quantitative RT-PCR, Marker

Journal: Biomedical Microdevices

Article Title: Thermoplastic elastomer based microfluidic gradient generator for cell culture and drug testing

doi: 10.1007/s10544-026-00816-y

Figure Lengend Snippet: Quantification of live cell percentages at various positions across the chamber for PDMS ( n = 4) and TPE ( n = 3) microfluidic devices

Article Snippet: In addition to two-stage bubble traps integrated into the main flow channels on chip, a microfluidic bubble trap (Peek Bubble trap, Elveflow, France) was incorporated inline in the tubing prior to the device inlet to prevent bubble entering the cell chamber during cell culture.

Techniques:

Journal: Dose-Response

Article Title: Skeletal Stem Cells Rescue Radiation-Induced Osteogenic Precursor Cell Dysfunction via the Wnt/β-Catenin Signaling Pathway

doi: 10.1177/15593258261440983

Figure Lengend Snippet: SSCs alleviate the radiation-induced bone injury in mice. (A–G) Micro-CT analysis of bone microstructure. (A) Representative micro-CT images of femurs. Quantitative analysis of (B) bone mineral density (BMD), (C) bone volume fraction (BV/TV), (D) trabecular thickness (Tb.Th), (E) trabecular number (Tb.N), (F) connectivity density (Conn.D), and (G) trabecular separation (Tb.Sp) at 2- and 4-weeks post irradiation. (H–K) Histological analysis (Scale bar: 100 μm). (H) H&E staining showing steatosis (arrows) and (I) quantitative analysis of steatotic lesions per field. (J) TRAP staining showing osteoclasts (arrows) and (K) quantitative analysis of osteoclast number per field. (L–O) Immunohistochemical staining of osteogenic markers (Scale bar: 100 μm). (L) Osterix staining and (M) quantitative analysis of Osterix-positive area. (N) β-catenin staining and (O) quantitative analysis of β-catenin-positive area. All experiments were conducted in three groups: Control, irradiation (IR), and IR plus SSC (IR+SSC) at 2- and 4-weeks post-irradiation. All data are presented as mean ± SD, with statistical significance determined by unpaired two-tailed Student’s t-test (* p < 0.05; ** p < 0.01; *** p < 0.001)

Article Snippet: Paraffin sections of femurs were dewaxed to water, and TRAP staining was performed using a TRAP staining kit (Servicebio, Wuhan, China, G1050-50T) according to the manufacturer’s instructions.

Techniques: Micro-CT, Irradiation, Staining, Immunohistochemical staining, Control, Two Tailed Test