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Biomay Inc plasmid encoding mrna egfp
Ion-pair reverse-phase polishing of <t>mRNA</t> on CIMmultus SDVB with linear gradient removes dsRNA and truncated RNA (A) A mass of 0.5 mg of Oligo dT pre-purified mRNA <t>(eGFP)</t> was loaded onto 1 mL CIMmultus SDVB column at room temperature and eluted in linear gradient from 7.5% to 18% ACN over 95 CV at 1 CV/min. (B) Fragment Analyzer electropherograms of selected fractions show lower molecular weight (MW) impurities eluting in fractions 1 and 2, with higher MW impurities observable in fractions 5–7 and significant in fraction 11. LM: Low molecular weight marker. (C) Elution fractions were analyzed on J2 dot blot, which confirmed the presence of dsRNA sub-populations in fractions 1, 2, 12, and strip.
Plasmid Encoding Mrna Egfp, supplied by Biomay Inc, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/construct+encoding+egfp/plasmid+encoding+for+egfp+mrna+constructs/pmc11957593-189-5-15
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plasmid encoding mrna egfp - by Bioz Stars, 2026-10
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Article Title: Reverse-phase chromatography removes double-stranded RNA, fragments, and residual template to decrease immunogenicity and increase cell potency of mRNA and saRNA

Journal: Molecular Therapy. Nucleic Acids

doi: 10.1016/j.omtn.2025.102491

Ion-pair reverse-phase polishing of mRNA on CIMmultus SDVB with linear gradient removes dsRNA and truncated RNA (A) A mass of 0.5 mg of Oligo dT pre-purified mRNA (eGFP) was loaded onto 1 mL CIMmultus SDVB column at room temperature and eluted in linear gradient from 7.5% to 18% ACN over 95 CV at 1 CV/min. (B) Fragment Analyzer electropherograms of selected fractions show lower molecular weight (MW) impurities eluting in fractions 1 and 2, with higher MW impurities observable in fractions 5–7 and significant in fraction 11. LM: Low molecular weight marker. (C) Elution fractions were analyzed on J2 dot blot, which confirmed the presence of dsRNA sub-populations in fractions 1, 2, 12, and strip.
Figure Legend Snippet: Ion-pair reverse-phase polishing of mRNA on CIMmultus SDVB with linear gradient removes dsRNA and truncated RNA (A) A mass of 0.5 mg of Oligo dT pre-purified mRNA (eGFP) was loaded onto 1 mL CIMmultus SDVB column at room temperature and eluted in linear gradient from 7.5% to 18% ACN over 95 CV at 1 CV/min. (B) Fragment Analyzer electropherograms of selected fractions show lower molecular weight (MW) impurities eluting in fractions 1 and 2, with higher MW impurities observable in fractions 5–7 and significant in fraction 11. LM: Low molecular weight marker. (C) Elution fractions were analyzed on J2 dot blot, which confirmed the presence of dsRNA sub-populations in fractions 1, 2, 12, and strip.

Techniques Used: Purification, Molecular Weight, Marker, Dot Blot, Stripping Membranes

Analytical characterization of RNA fractions collected from SDVB linear gradient purification A mass of 0.5 mg of ARCA-capped mRNA eGFP, pre-purified with CIM Oligo dT, was loaded onto CIM SDVB column at room temperature and eluted in a linear gradient (from 7.5% to 18% ACN over 95 CV) at 1 CV/min. The first 10 mL of elution peak was collected in 20 fractions (1-20), and the remaining 30 mL was collected as one fraction (21). (A) Fragment Analyzer results show RNA size distribution in fractionated elution peak. LM: molecular weight marker. (B) Capping efficiency analysis of selected elution fractions. (C) CIMac Oligo dT chromatographic analysis indicates % polyadenylation of elution fractions. Relative amounts of unbound, non-specifically bound, and bound RNA are presented in the bar chart, from integration of CIMac Oligo dT flow-through (FT), wash (W), and elution (E) peaks, respectively.
Figure Legend Snippet: Analytical characterization of RNA fractions collected from SDVB linear gradient purification A mass of 0.5 mg of ARCA-capped mRNA eGFP, pre-purified with CIM Oligo dT, was loaded onto CIM SDVB column at room temperature and eluted in a linear gradient (from 7.5% to 18% ACN over 95 CV) at 1 CV/min. The first 10 mL of elution peak was collected in 20 fractions (1-20), and the remaining 30 mL was collected as one fraction (21). (A) Fragment Analyzer results show RNA size distribution in fractionated elution peak. LM: molecular weight marker. (B) Capping efficiency analysis of selected elution fractions. (C) CIMac Oligo dT chromatographic analysis indicates % polyadenylation of elution fractions. Relative amounts of unbound, non-specifically bound, and bound RNA are presented in the bar chart, from integration of CIMac Oligo dT flow-through (FT), wash (W), and elution (E) peaks, respectively.

Techniques Used: Purification, Molecular Weight, Marker

Ion-pair reverse-phase polishing of mRNA with CIMmultus SDVB operated with step elution removes dsRNA, truncated RNA, and residual pDNA template at least to 80-mL column scale Purification of (A.i) 0.6 mg and (B.i) 4.8 mg of Oligo dT-prepurified mRNA eGFP on 1 mL and 8 mL CIMmultus SDVB column, respectively, at room temperature and at 1 CV/min. Step elutions of 8.5% ACN, 11.7% ACN, and 18% ACN were applied. (A.ii and B.ii) Fragment Analyzer results of corresponding fractions. (A.iii and B.iii) J2 dot blot confirmed clearance of truncated sequences and dsRNA species in main mRNA fractions (“2”). (C.i) Scale-up preparative chromatogram of Oligo dT-prepurified mRNA (48 mg) on 80 mL CIMmultus SDVB column at room temperature and at 2 CV/min operated with Hipersep Flowdrive Pilot HPLC chromatography system. Step elutions were fractionated in five fractions (1–4 and strip). (C.ii) Fragment Analyzer and (C.iii) J2 dot blot analytics of collected fractions. (C.iv) AGE residual DNA template analysis and (C.v) CIMac pDNA quantification of residual DNA template in collected fractions.
Figure Legend Snippet: Ion-pair reverse-phase polishing of mRNA with CIMmultus SDVB operated with step elution removes dsRNA, truncated RNA, and residual pDNA template at least to 80-mL column scale Purification of (A.i) 0.6 mg and (B.i) 4.8 mg of Oligo dT-prepurified mRNA eGFP on 1 mL and 8 mL CIMmultus SDVB column, respectively, at room temperature and at 1 CV/min. Step elutions of 8.5% ACN, 11.7% ACN, and 18% ACN were applied. (A.ii and B.ii) Fragment Analyzer results of corresponding fractions. (A.iii and B.iii) J2 dot blot confirmed clearance of truncated sequences and dsRNA species in main mRNA fractions (“2”). (C.i) Scale-up preparative chromatogram of Oligo dT-prepurified mRNA (48 mg) on 80 mL CIMmultus SDVB column at room temperature and at 2 CV/min operated with Hipersep Flowdrive Pilot HPLC chromatography system. Step elutions were fractionated in five fractions (1–4 and strip). (C.ii) Fragment Analyzer and (C.iii) J2 dot blot analytics of collected fractions. (C.iv) AGE residual DNA template analysis and (C.v) CIMac pDNA quantification of residual DNA template in collected fractions.

Techniques Used: Purification, Dot Blot, Chromatography, Stripping Membranes

mRNA polishing to remove dsRNA performed with CIM SDVB spin (0.1 mL) column in a benchtop centrifuge (A) A mass of 95 μg of Oligo dT-prepurified mRNA eGFP was diluted 10 times in loading buffer containing 7.5% ACN and applied onto a CIM SDVB spin (0.1 mL) column. Wash with 8.5% ACN eluted truncated species (fraction 1), elution with 11.7% ACN yielded full-length RNA (fraction 2) and strip with 18% ACN eluted dsRNA (strip). Recovery of mRNA in fraction 2 was 77%. (B) Fragment Analyzer of load, fractions 1, 2, and strip. (C) J2 dot blot of collected fractions.
Figure Legend Snippet: mRNA polishing to remove dsRNA performed with CIM SDVB spin (0.1 mL) column in a benchtop centrifuge (A) A mass of 95 μg of Oligo dT-prepurified mRNA eGFP was diluted 10 times in loading buffer containing 7.5% ACN and applied onto a CIM SDVB spin (0.1 mL) column. Wash with 8.5% ACN eluted truncated species (fraction 1), elution with 11.7% ACN yielded full-length RNA (fraction 2) and strip with 18% ACN eluted dsRNA (strip). Recovery of mRNA in fraction 2 was 77%. (B) Fragment Analyzer of load, fractions 1, 2, and strip. (C) J2 dot blot of collected fractions.

Techniques Used: Stripping Membranes, Dot Blot

Purification of mRNA and saRNA with CIM SDVB does not compromise functionality in immuno-incompetent BHK-21 cells (A) A mass of 100 ng mRNA purified with Oligo dT (“w/o SDVB”) or Oligo dT + SDVB with linear gradient elution strategy (“linear-SDVB”) or Oligo dT + SDVB with step elution strategy (“step-SDVB”) was transfected into BHK-21 cells. After 24 h, GFP expression was measured by flow cytometry. The mean fluorescence intensity was multiplied with the percentage of GFP expressing cells to receive the total GFP expression levels. (B) Relative viability of cells was assessed by measuring viability after 48 h and normalized to the mock control. (C) BHK-21 cells were lipofected with the indicated doses of either Swiper (“w/o SDVB”) or Swiper and SDVB-purified saRNA (“+SDVB”). Luciferase expression was measured 6, 24, 48, and 72 h after transfection. Area under the curve (AUC) was calculated to determine the total luciferase expression. (D) Viability was measured 48 h after transfection and normalized to the mock control. Mean and standard error of the mean (SEM) of three independent experiments, each performed in technical triplicates, are shown.
Figure Legend Snippet: Purification of mRNA and saRNA with CIM SDVB does not compromise functionality in immuno-incompetent BHK-21 cells (A) A mass of 100 ng mRNA purified with Oligo dT (“w/o SDVB”) or Oligo dT + SDVB with linear gradient elution strategy (“linear-SDVB”) or Oligo dT + SDVB with step elution strategy (“step-SDVB”) was transfected into BHK-21 cells. After 24 h, GFP expression was measured by flow cytometry. The mean fluorescence intensity was multiplied with the percentage of GFP expressing cells to receive the total GFP expression levels. (B) Relative viability of cells was assessed by measuring viability after 48 h and normalized to the mock control. (C) BHK-21 cells were lipofected with the indicated doses of either Swiper (“w/o SDVB”) or Swiper and SDVB-purified saRNA (“+SDVB”). Luciferase expression was measured 6, 24, 48, and 72 h after transfection. Area under the curve (AUC) was calculated to determine the total luciferase expression. (D) Viability was measured 48 h after transfection and normalized to the mock control. Mean and standard error of the mean (SEM) of three independent experiments, each performed in technical triplicates, are shown.

Techniques Used: Purification, W/O, Transfection, Expressing, Flow Cytometry, Fluorescence, Control, Luciferase

SDVB purification of mRNA and saRNA improves transgene expression in A549 cells, where IFNβ response limits expression (A) A549 cells were lipofected with 100 ng of mRNA purified with Oligo dT (“w/o SDVB”) or Oligo dT plus SDVB with linear gradient elution strategy (“linear-SDVB”) or Oligo dT plus step elution strategy (“step-SDVB”). Twenty-four hours after transfection, GFP expression was detected by flow cytometry. (B) Viability of cells was detected 48 h after lipofection and normalized to untreated cells. (C) IFNβ release into the supernatant was quantified by ELISA 6 and 24 h after transfection. (D) 10, 40, or 160 ng of saRNA without (“w/o SDVB”) or with (“+ SDVB”) SDVB purification was transfected into A549 cells. Luciferase expression was measured at 6, 24, 48, and 72 h after transfection and area under the curve was calculated to assess total transgene expression. (E) After 48 h, ATP levels were quantified and normalized to the levels of untreated cells to determine relative viability. (F) 6 and 24 h after lipofection, IFNβ levels in the supernatant were quantified by ELISA. Mean and standard error of the mean of three independent experiments, each done in technical triplicates, are shown. Statistical differences were calculated using two-sided unpaired t tests with p values lower than 0.05 considered as significant and classified into ∗: p < 0.05; ∗∗: p < 0.01; ∗∗∗: p < 0.001; ∗∗∗∗: p < 0.0001.
Figure Legend Snippet: SDVB purification of mRNA and saRNA improves transgene expression in A549 cells, where IFNβ response limits expression (A) A549 cells were lipofected with 100 ng of mRNA purified with Oligo dT (“w/o SDVB”) or Oligo dT plus SDVB with linear gradient elution strategy (“linear-SDVB”) or Oligo dT plus step elution strategy (“step-SDVB”). Twenty-four hours after transfection, GFP expression was detected by flow cytometry. (B) Viability of cells was detected 48 h after lipofection and normalized to untreated cells. (C) IFNβ release into the supernatant was quantified by ELISA 6 and 24 h after transfection. (D) 10, 40, or 160 ng of saRNA without (“w/o SDVB”) or with (“+ SDVB”) SDVB purification was transfected into A549 cells. Luciferase expression was measured at 6, 24, 48, and 72 h after transfection and area under the curve was calculated to assess total transgene expression. (E) After 48 h, ATP levels were quantified and normalized to the levels of untreated cells to determine relative viability. (F) 6 and 24 h after lipofection, IFNβ levels in the supernatant were quantified by ELISA. Mean and standard error of the mean of three independent experiments, each done in technical triplicates, are shown. Statistical differences were calculated using two-sided unpaired t tests with p values lower than 0.05 considered as significant and classified into ∗: p < 0.05; ∗∗: p < 0.01; ∗∗∗: p < 0.001; ∗∗∗∗: p < 0.0001.

Techniques Used: Purification, Expressing, W/O, Transfection, Flow Cytometry, Enzyme-linked Immunosorbent Assay, Luciferase

Related Articles

other:

Article Title: Reverse-phase chromatography removes double-stranded RNA, fragments, and residual template to decrease immunogenicity and increase cell potency of mRNA and saRNA
Article Snippet: All media (Eagle’s minimum essential medium, F-12K Nutrient Mixture-Kaighn’s RPMI Modification medium) as well as non-essential amino acids and sodium pyruvate were from HiMedia, fetal calf serum from Bio&Sell, plasma-derived human serum from OneLambda.

Article Title: High Recovery Chromatographic Purification of mRNA at Room Temperature and Neutral pH.
Article Snippet: We gratefully acknowledge BioMay AG for providing the plasmid-encoding eGFP mRNA, and Mario Perković and Tim Beissert from TRON for kindly providing the saRNA construct (10,000 nt) used in the study.

Plasmid Preparation:

Article Title: Gram‐Scale mRNA Production Using a 250‐mL Single‐Use Bioreactor
Article Snippet: The COVID-19 pandemic triggered an unprecedented surge in development of mRNA-based vaccines.. Despite the need to increase process productivity and thus decrease the cost of mRNA vaccines, limited scientific literature is available on strategies to increase the yield of in vitro transcription (IVT) reaction, the unit operation with highest cost of goods, which has traditionally been performed as a batch reaction.. Single-use bioreactors are traditionally used for cell-based production of biopharmaceuticals, but some core functionalities, such as controlled and automated feed addition, are potentially useful for cell-free mRNA processes.

Article Title: Quality by design approach to improve quality and decrease cost of in vitro transcription of mRNA using design of experiments.
Article Snippet: .. Authors would like to thank Biomay AG for providing plasmid encoding for eGFP mRNA constructs, Prof. Tomaž Bratkovič (Faculty of Pharmacy, University of Ljubljana) and Lennart Eriksson (Sartorius SSDA) for constructive feedback during manuscript preparation. ..

Purification:

Article Title: Gram‐Scale mRNA Production Using a 250‐mL Single‐Use Bioreactor
Article Snippet: The COVID-19 pandemic triggered an unprecedented surge in development of mRNA-based vaccines.. Despite the need to increase process productivity and thus decrease the cost of mRNA vaccines, limited scientific literature is available on strategies to increase the yield of in vitro transcription (IVT) reaction, the unit operation with highest cost of goods, which has traditionally been performed as a batch reaction.. Single-use bioreactors are traditionally used for cell-based production of biopharmaceuticals, but some core functionalities, such as controlled and automated feed addition, are potentially useful for cell-free mRNA processes.

Construct:

Article Title: Quality by design approach to improve quality and decrease cost of in vitro transcription of mRNA using design of experiments.
Article Snippet: .. Authors would like to thank Biomay AG for providing plasmid encoding for eGFP mRNA constructs, Prof. Tomaž Bratkovič (Faculty of Pharmacy, University of Ljubljana) and Lennart Eriksson (Sartorius SSDA) for constructive feedback during manuscript preparation. ..



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Synbio Technologies LLC plasmids encoding the gluc constructs pcdna5-to-frt-egfp-p2a-gluc2-m2
A) Schematic of the experimental strategy. eGFP-nanos3’UTR containing mRNA was injected into 1-cell stage zebrafish embryos from which two different experimental approaches were used to investigate the ratio of maternal and somatic ribosomes in PGCs and to test which ribosomes are bound to PGC-localized mRNAs. B) Brightfield and eGFP images of 1 day post-fertilization embryos, previously injected with only water, eGFP-nanos3’UTR mRNA, or biotinylated <t>eGFP-nanos3-3’UTR</t> mRNA. Scale bars indicate 500 μm. C) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S rRNA in FACS-isolated eGFP-positive (PGCs) and eGFP-negative (somatic) cells analyzed by RT-qPCR. D) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S variants associated with biotinylated eGFP-nanos3-3’UTR mRNAs isolated by RIP (RNA immunoprecipitation). Non-biotinylated eGFP-nanos3-3’UTR mRNA served as control. Non-specific (background) amplification was determined using IPs from wild-type (uninjected) lysate and was set to zero. In (C) and (D), three biological replicates from independent natural crosses were used, and significance was calculated by t-test (if not indicated, p-value > 0.05).
Plasmids Encoding The Gluc Constructs Pcdna5 To Frt Egfp P2a Gluc2 M2, supplied by Synbio Technologies LLC, used in various techniques. Bioz Stars score: 90/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/construct+encoding+egfp/plasmids+encoding+the+gluc+constructs+pcdna5+to+frt+egfp+p2a+gluc2+m2/pm38992438-167-11-8
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96
TaKaRa retroviral constructs encoding egfp
A) Schematic of the experimental strategy. eGFP-nanos3’UTR containing mRNA was injected into 1-cell stage zebrafish embryos from which two different experimental approaches were used to investigate the ratio of maternal and somatic ribosomes in PGCs and to test which ribosomes are bound to PGC-localized mRNAs. B) Brightfield and eGFP images of 1 day post-fertilization embryos, previously injected with only water, eGFP-nanos3’UTR mRNA, or biotinylated <t>eGFP-nanos3-3’UTR</t> mRNA. Scale bars indicate 500 μm. C) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S rRNA in FACS-isolated eGFP-positive (PGCs) and eGFP-negative (somatic) cells analyzed by RT-qPCR. D) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S variants associated with biotinylated eGFP-nanos3-3’UTR mRNAs isolated by RIP (RNA immunoprecipitation). Non-biotinylated eGFP-nanos3-3’UTR mRNA served as control. Non-specific (background) amplification was determined using IPs from wild-type (uninjected) lysate and was set to zero. In (C) and (D), three biological replicates from independent natural crosses were used, and significance was calculated by t-test (if not indicated, p-value > 0.05).
Retroviral Constructs Encoding Egfp, supplied by TaKaRa, used in various techniques. Bioz Stars score: 96/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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Average 96 stars, based on 1 article reviews
retroviral constructs encoding egfp - by Bioz Stars, 2026-10
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94
Addgene inc construct encoding mpiezo1 ires egfp
A) Schematic of the experimental strategy. eGFP-nanos3’UTR containing mRNA was injected into 1-cell stage zebrafish embryos from which two different experimental approaches were used to investigate the ratio of maternal and somatic ribosomes in PGCs and to test which ribosomes are bound to PGC-localized mRNAs. B) Brightfield and eGFP images of 1 day post-fertilization embryos, previously injected with only water, eGFP-nanos3’UTR mRNA, or biotinylated <t>eGFP-nanos3-3’UTR</t> mRNA. Scale bars indicate 500 μm. C) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S rRNA in FACS-isolated eGFP-positive (PGCs) and eGFP-negative (somatic) cells analyzed by RT-qPCR. D) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S variants associated with biotinylated eGFP-nanos3-3’UTR mRNAs isolated by RIP (RNA immunoprecipitation). Non-biotinylated eGFP-nanos3-3’UTR mRNA served as control. Non-specific (background) amplification was determined using IPs from wild-type (uninjected) lysate and was set to zero. In (C) and (D), three biological replicates from independent natural crosses were used, and significance was calculated by t-test (if not indicated, p-value > 0.05).
Construct Encoding Mpiezo1 Ires Egfp, supplied by Addgene inc, used in various techniques. Bioz Stars score: 94/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/construct+encoding+egfp/mPiezo1-IRES-eGFP+(Plasmid+%2380925)/pm36610555-46-1-10
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Image Search Results


( a ) U2OS wildtype (WT), VPS13C-KO1, VPS13C-KO2 or PI4K2A-KO cells were fed 3 μm polystyrene microbeads, treated with LLOMe (1 mM, 10 min) as indicated, immunostained for LAMP1 ( red ) and VAPA ( green ), and imaged by DeltaVision microscopy. Scale bar, 10 µm. ( b ) Time-lapse images of U2OS wildtype (WT), VPS13C-KO1, VPS13C-KO2 or PI4K2A-KO cells containing 3 µm pHrodo-labeled microbeads ( magenta ), expressing GFP-tagged OSBP ( green ) and treated with 1 mM LLOMe for the indicated time. Cells were imaged by spinning disk microscopy. Scale bar, 10 µm. ( c ) Time-lapse images of U2OS wildtype (WT), VPS13C-KO1 or PI4K2A-KO cells containing 3 µm pHrodo-labeled microbeads ( magenta ), expressing GFP-tagged PI4P sensor P4MX1 ( green ) and treated with 1 mM LLOMe for the indicated time. Cells were imaged by spinning disk microscopy. Scale bar, 10 µm. ( d ) Phase contrast (Phaco) and fluorescence images of polystyrene microbead-containing untreated or LLOMe-treated (1 mM, 10 min) U2OS wildtype (WT), VPS13C-KO1 or PI4K2A-KO cells immunostained for OSBP ( magenta ) and ALIX ( green ) or ORP9 ( magenta ) and hIST1 ( green ) and counterstained with DAPI ( blue ). Cells were imaged by spinning disk microscopy. Scale bar, 10 µm. ( e ) Percentage of microbead-containing lysosomes with positive immunostaining for OSBP or ORP9 in cells treated as in (d). Data are means ± SD of three independent experiments.

Journal: bioRxiv

Article Title: VPS13C/PARK23 initiates lipid transfer and membrane remodeling for efficient lysosomal repair

doi: 10.1101/2025.10.23.684214

Figure Lengend Snippet: ( a ) U2OS wildtype (WT), VPS13C-KO1, VPS13C-KO2 or PI4K2A-KO cells were fed 3 μm polystyrene microbeads, treated with LLOMe (1 mM, 10 min) as indicated, immunostained for LAMP1 ( red ) and VAPA ( green ), and imaged by DeltaVision microscopy. Scale bar, 10 µm. ( b ) Time-lapse images of U2OS wildtype (WT), VPS13C-KO1, VPS13C-KO2 or PI4K2A-KO cells containing 3 µm pHrodo-labeled microbeads ( magenta ), expressing GFP-tagged OSBP ( green ) and treated with 1 mM LLOMe for the indicated time. Cells were imaged by spinning disk microscopy. Scale bar, 10 µm. ( c ) Time-lapse images of U2OS wildtype (WT), VPS13C-KO1 or PI4K2A-KO cells containing 3 µm pHrodo-labeled microbeads ( magenta ), expressing GFP-tagged PI4P sensor P4MX1 ( green ) and treated with 1 mM LLOMe for the indicated time. Cells were imaged by spinning disk microscopy. Scale bar, 10 µm. ( d ) Phase contrast (Phaco) and fluorescence images of polystyrene microbead-containing untreated or LLOMe-treated (1 mM, 10 min) U2OS wildtype (WT), VPS13C-KO1 or PI4K2A-KO cells immunostained for OSBP ( magenta ) and ALIX ( green ) or ORP9 ( magenta ) and hIST1 ( green ) and counterstained with DAPI ( blue ). Cells were imaged by spinning disk microscopy. Scale bar, 10 µm. ( e ) Percentage of microbead-containing lysosomes with positive immunostaining for OSBP or ORP9 in cells treated as in (d). Data are means ± SD of three independent experiments.

Article Snippet: The expression construct encoding eGFP-tagged P4Mx1 (Addgene, 108121) was described in Zewe et al. .

Techniques: Microscopy, Labeling, Expressing, Fluorescence, Immunostaining

(a) Representative images of day 6 neurons after Lysotracker treatment. Lysotracker is shown in magenta, and DAPI in blue. Scale bar = 20 μm. (b) Quantification of Lysotracker signal in day 6 neurons. The relative Lysotracker intensity of CLCN4 -variant neurons compared to the WT was presented. Each dot represents one biological replicate. (n=3-4, mean ± SEM, one-way ANOVA with Dunnett’s multiple comparisons test * p =0.039 for variant A; *** p =0.0007 for variant B; ** p =0.0092 for variant C) The magenta dashed line indicates the value for WT. (c) Relative acidity in acidic subcellular organelles. Each dot represents one biological replicate. (n=3, mean ± SEM, unpaired Student’s t-test; p =0.2894) (d-g) Dynamics of endo-lysosomal vesicles. RAB5, RAB7, RAB11 and LAMP1 indicates early endosome, late endosome, recycling endosome and lysosome markers, respectively. (RAB5, n=6; RAB7, n=3; RAB11, n=4; and LAMP1, n=3 or 4; mean ± SEM, unpaired Student’s t-test) (d) Representative images of a neuron with GFP-labeled vesicular organelles. TUJ1 and DAPI are shown in red and blue, respectively. Scale bar = 10 μm. (e) Relative GFP intensity expressed in vesicular organelles (* p =0.0265 for RAB5, * p =0.0158 for RAB7, * p =0.0475 for RAB11, and ** p =0.0067 for LAMP1) (f) Number of GFP-expressing vesicles in neurons. (* p =0.0186 for RAB5, * *p =0.0066 for RAB7, and p =0.9031 for LAMP1) (g) Average distance of GFP-expressing vesicles from the center of nucleus, representing the mean linear distance of puncta from the center of the nucleus in each cell. (** p =0.0011 for RAB5, * p =0.0463 for RAB7, and * p =0.0103 for LAMP1) (h) Scheme of autophagic flux analysis using tandem fluorescent protein fused to LC3. (i) Representative images of day 6 neurons expressing tandem fluorescent-tagged LC3. Red: RFP, green: GFP, white: TUJ1. Scale bar = 5 μm. (j) Quantification of the GFP-/RFP+ puncta. (n=5, mean ± SEM, unpaired Student’s t-test; * p =0.0164)

Journal: bioRxiv

Article Title: MEG3 Enhances Survival of Developing Human Neurons with CLCN4 -Linked Autophagy Impairment

doi: 10.1101/2025.07.16.665078

Figure Lengend Snippet: (a) Representative images of day 6 neurons after Lysotracker treatment. Lysotracker is shown in magenta, and DAPI in blue. Scale bar = 20 μm. (b) Quantification of Lysotracker signal in day 6 neurons. The relative Lysotracker intensity of CLCN4 -variant neurons compared to the WT was presented. Each dot represents one biological replicate. (n=3-4, mean ± SEM, one-way ANOVA with Dunnett’s multiple comparisons test * p =0.039 for variant A; *** p =0.0007 for variant B; ** p =0.0092 for variant C) The magenta dashed line indicates the value for WT. (c) Relative acidity in acidic subcellular organelles. Each dot represents one biological replicate. (n=3, mean ± SEM, unpaired Student’s t-test; p =0.2894) (d-g) Dynamics of endo-lysosomal vesicles. RAB5, RAB7, RAB11 and LAMP1 indicates early endosome, late endosome, recycling endosome and lysosome markers, respectively. (RAB5, n=6; RAB7, n=3; RAB11, n=4; and LAMP1, n=3 or 4; mean ± SEM, unpaired Student’s t-test) (d) Representative images of a neuron with GFP-labeled vesicular organelles. TUJ1 and DAPI are shown in red and blue, respectively. Scale bar = 10 μm. (e) Relative GFP intensity expressed in vesicular organelles (* p =0.0265 for RAB5, * p =0.0158 for RAB7, * p =0.0475 for RAB11, and ** p =0.0067 for LAMP1) (f) Number of GFP-expressing vesicles in neurons. (* p =0.0186 for RAB5, * *p =0.0066 for RAB7, and p =0.9031 for LAMP1) (g) Average distance of GFP-expressing vesicles from the center of nucleus, representing the mean linear distance of puncta from the center of the nucleus in each cell. (** p =0.0011 for RAB5, * p =0.0463 for RAB7, and * p =0.0103 for LAMP1) (h) Scheme of autophagic flux analysis using tandem fluorescent protein fused to LC3. (i) Representative images of day 6 neurons expressing tandem fluorescent-tagged LC3. Red: RFP, green: GFP, white: TUJ1. Scale bar = 5 μm. (j) Quantification of the GFP-/RFP+ puncta. (n=5, mean ± SEM, unpaired Student’s t-test; * p =0.0164)

Article Snippet: For specific subcellular vesicle visualization, lentiviral constructs encoding GFP-tagged RAB5 (Addgene #134858), RAB7 (Addgene #133027), RAB11 (Addgene #134860), and LAMP1 (Addgene #134868) were utilized.

Techniques: Variant Assay, Labeling, Expressing

A) Schematic of the experimental strategy. eGFP-nanos3’UTR containing mRNA was injected into 1-cell stage zebrafish embryos from which two different experimental approaches were used to investigate the ratio of maternal and somatic ribosomes in PGCs and to test which ribosomes are bound to PGC-localized mRNAs. B) Brightfield and eGFP images of 1 day post-fertilization embryos, previously injected with only water, eGFP-nanos3’UTR mRNA, or biotinylated eGFP-nanos3-3’UTR mRNA. Scale bars indicate 500 μm. C) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S rRNA in FACS-isolated eGFP-positive (PGCs) and eGFP-negative (somatic) cells analyzed by RT-qPCR. D) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S variants associated with biotinylated eGFP-nanos3-3’UTR mRNAs isolated by RIP (RNA immunoprecipitation). Non-biotinylated eGFP-nanos3-3’UTR mRNA served as control. Non-specific (background) amplification was determined using IPs from wild-type (uninjected) lysate and was set to zero. In (C) and (D), three biological replicates from independent natural crosses were used, and significance was calculated by t-test (if not indicated, p-value > 0.05).

Journal: bioRxiv

Article Title: A dual ribosomal system in the zebrafish soma and germline

doi: 10.1101/2024.08.29.610041

Figure Lengend Snippet: A) Schematic of the experimental strategy. eGFP-nanos3’UTR containing mRNA was injected into 1-cell stage zebrafish embryos from which two different experimental approaches were used to investigate the ratio of maternal and somatic ribosomes in PGCs and to test which ribosomes are bound to PGC-localized mRNAs. B) Brightfield and eGFP images of 1 day post-fertilization embryos, previously injected with only water, eGFP-nanos3’UTR mRNA, or biotinylated eGFP-nanos3-3’UTR mRNA. Scale bars indicate 500 μm. C) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S rRNA in FACS-isolated eGFP-positive (PGCs) and eGFP-negative (somatic) cells analyzed by RT-qPCR. D) Ratio of maternal (yellow) versus somatic (blue) 18S and 28S variants associated with biotinylated eGFP-nanos3-3’UTR mRNAs isolated by RIP (RNA immunoprecipitation). Non-biotinylated eGFP-nanos3-3’UTR mRNA served as control. Non-specific (background) amplification was determined using IPs from wild-type (uninjected) lysate and was set to zero. In (C) and (D), three biological replicates from independent natural crosses were used, and significance was calculated by t-test (if not indicated, p-value > 0.05).

Article Snippet: To generate the RNA for microinjections, 2 μg of a construct encoding eGFP-nanos3’UTR was digested using NotI-HF (New England BioLabs, R3189S) for 1 h. The linearized product was purified according to manufacturer specifications via gel selection using NucleoSpin (Macherey-Nagel, 740588.50).

Techniques: Injection, Isolation, Quantitative RT-PCR, RNA Immunoprecipitation, Control, Amplification