Journal: Nature chemical biology

Article Title: Membrane editing with proximity labeling reveals regulators of lipid homeostasis

doi: 10.1038/s41589-025-02104-x

Figure Lengend Snippet: a , b , Quantification of miRFP-Nir2 (T59A mutant with lipid transfer activity disabled) co-localization with PA-fed membranes. Black horizontal bars indicate means and vertical error bars indicate standard deviations. Statistical significance was determined using two-sided Student’s t-test ( n = 10–16 cells with exact numbers provided in the Source Data, p = 8.6E-06 and 8.9E-07). c , Confocal images of HEK 293T cells stably expressing V5-tagged Nir2 (PITPNM1), PDZD8, ORP1L (OSBPL1A), full-length SCP2 (SCP-x), or the mature form of SCP2 (mSCP2). Cells were co-stained with α-LAMP1 and α-Calnexin antibodies as lysosome and ER markers. Shown are representative images from two independent experiments. d , e , Zoomed-in images of cells expressing V5-SCP-x ( d ) or V5-mSCP2 ( e ). V5-mSCP2 shows more cytosolic localization. Scale bars, 20 μm. f , Scheme of IMPACT labeling to quantify superPLD activity in live cells. g , h , Flow cytometry results of cells co-expressing superPLD targeted to the plasma membrane (PM; g ) or lysosomes (Lyso; h ) and the indicated lipid-transfer protein. mCherry signal (readout of superPLD expression level) and BODIPY signal (readout of PLD activity) are plotted. Wild-type cells expressing deadPLD were included as a negative control. Shown are representative plots from two independent experiments.

Article Snippet: Antibody and dilutions used for validation experiments ( – ) were the following: anti-LPIN1 polyclonal antibody (Proteintech, 27026–1-AP; 1:1,000), anti-LPIN2 monoclonal antibody (Santa Cruz Biotechnology, sc-514353; 1:100), anti-Nir2 polyclonal antibody (Proteintech, 26983–1-AP; 1:1,000), anti-PDZD8 polyclonal antibody (Proteintech, 25512–1-AP; 1:1,000), anti-SCP-x polyclonal antibody (Proteintech, 14397–1-AP; 1:1,000), anti-SCP-2 polyclonal antibody (Proteintech, 23006–1-AP; 1:1,000), anti-DGKD polyclonal antibody (Abcepta, AP8126b; 1:1,000), anti-DGKH polyclonal antibody (Proteintech, 13873–1-AP; 1:1,000) and anti-β-tubulin monoclonal antibody (Cell Signaling Technology, 86298).

Techniques: Mutagenesis, Activity Assay, Stable Transfection, Expressing, Staining, Labeling, Flow Cytometry, Clinical Proteomics, Membrane, Negative Control

Journal: Nature chemical biology

Article Title: Membrane editing with proximity labeling reveals regulators of lipid homeostasis

doi: 10.1038/s41589-025-02104-x

Figure Lengend Snippet: a , Western blot of LOVPLD-expressing HEK 293T cells treated with DsiRNA to deplete Nir2, SCP-x/SCP2, or PDZD8. DsiRNA #1 (colored red) was used in the subsequent experiments. , Quantification of ( a ), with relative levels compared to the control shown in parentheses. Plots are representative of two independent experiments. c , d , Expression levels of LOVPLD ( c ) and the PA probe GFP-PASS ( d ) in HEK 293T cells depleted with Nir2 (siNir2), SCP2 (siSCP2), or PDZD8 (siPDZD8), co-expressing PA probe and LOVPLD targeted to either plasma membrane (PM) or lysosomes (Lyso). Plots are representative of two independent experiments. e , f , Quantification of colocalization between LOVPLD and GFP-PASS shown in , . Black horizontal bars indicate means and vertical error bars indicate standard deviations. Statistical analysis was performed using one-way ANOVA followed by post-hoc Tukey-HSD test ( n = 14–19 cells with exact numbers provided in the Source Data, p = 0.01 and 0.6 for ( e ) and 0.03 and 0.9 for ( f ) for Control vs. siRNA samples). g , Western blot of p-S6K to measure mTOR activity in LTP-depleted cells expressing LOVPLD, with quantification presented in . LOVPLD was localized to plasma membrane (PM), lysosomes (Lyso), or endoplasmic reticulum (ER), and 30-min incubation with intermittent blue light illumination (470 nm, 500 ms per 5 s) was used to activate PA production by LOVPLD. β-actin was used as a loading control. h , Similar experiment as ( g ) but in LTP-depleted HEK 293T cells without LOVPLD activation. i , Quantification of ( h ). n = 4 (except for siPDZD8, where n = 2) biological replicates. Statistical analysis was performed using one-way ANOVA followed by post-hoc Tukey-HSD test ( p = 0.004, 0.01, and 0.07 for Control vs. siRNA samples). Black horizontal bars indicate means and vertical error bars indicate standard deviations.

Article Snippet: Antibody and dilutions used for validation experiments ( – ) were the following: anti-LPIN1 polyclonal antibody (Proteintech, 27026–1-AP; 1:1,000), anti-LPIN2 monoclonal antibody (Santa Cruz Biotechnology, sc-514353; 1:100), anti-Nir2 polyclonal antibody (Proteintech, 26983–1-AP; 1:1,000), anti-PDZD8 polyclonal antibody (Proteintech, 25512–1-AP; 1:1,000), anti-SCP-x polyclonal antibody (Proteintech, 14397–1-AP; 1:1,000), anti-SCP-2 polyclonal antibody (Proteintech, 23006–1-AP; 1:1,000), anti-DGKD polyclonal antibody (Abcepta, AP8126b; 1:1,000), anti-DGKH polyclonal antibody (Proteintech, 13873–1-AP; 1:1,000) and anti-β-tubulin monoclonal antibody (Cell Signaling Technology, 86298).

Techniques: Western Blot, Expressing, Control, Clinical Proteomics, Membrane, Activity Assay, Incubation, Activation Assay

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function

doi: 10.1073/pnas.1603544113

Figure Lengend Snippet: Yeast strains used in this study

Article Snippet: Ret2LD2α T158K ( BY4743 Spore ) MAT a his3 ∆ 1 leu2 ∆ 0 met15 ∆ 0 ura3 ∆ 0; YFR051c::kanMX4; p415 ret2LD2 α T158K This study Open in a separate window Yeast strains used in this study table ft1 table-wrap mode="anchored" t5 Table S2. caption a7 No. Plasmids Addgene ID Database ID Source 1. p415 CHI 1 73863 Z1280 This study 2. p415 CHI 2 73864 Z1281 This study 3. p415 CHI 3 73865 Z1283 This study 4. p415 CHI 4 73866 Z1284 This study 5. p415 CHI 5 73867 Z1285 This study 6. p415 CHI 6 73868 Z1286 This study 7. p415 CHI 7 73869 Z1287 This study 8. p415 CHI 8 73870 Z1288 This study 9. pRS303 Bt δCOP 73871 AE1540 This study 10. p415 Ret2 73872 AE1541 This study 11. p415 Ret2LD2α 73873 AE1518 This study 12. p415 δCLD2α 73874 AE1519 This study 13. p415 Ret2LD 73875 AE1520 This study 14. p415 δCLD 73876 AE1521 This study 15. p415 Ret2LD+δC2α 73877 AE1516 This study 16. p415 δCLD+Ret2-2α 73878 AE1523 This study 17. p415 CHI 9 73879 AF1551 This study 18. p415 CHI 10 73880 AF1553 This study 19. p415 CHI 12 73881 AF1557 This study 20. p415 CHI 13 73882 AH1658 This study 21. p415 CHI 14 73883 AH1660 This study 22. p415 CHI 15 73884 AH1662 This study 23. p415 Ret2 I145A 73885 AI1732 This study 24. p415 Ret2 I148A 73886 AI1733 This study 25. p415 Ret2 I149A 73887 AI1734 This study 26. p415 Ret2 I155A 73888 AI1735 This study 27. pGEX6P1- Mst7-Erp1CT 73920 This study 28. pGEX6P1-GCN4cc-Erp1CT 73921 This study 29. pGEX6P1- Mst7-Erp2CT 73922 This study 30. pGEX6P1-GCN4cc-Erp2CT 73923 This study 31. p415 Ret2LD2α Q146F 75259 This study 32. p415 Ret2LD2α N152T 75260 This study 33. p415 Ret2LD2α K153Q 75261 This study 34. p415 Ret2LD2α T158K 75262 This study 35. p416 PMP2-YFP-LRKRS — M650 14 36. p416 PMP2-YFP-KKXX — N654 14 37. p416 PMP2-YFP-NVRNRRK — R890 14 38. p416 PMP2-YFP-KKK — M643 14 39. p416 PMP2-YFP-AAXX — N655 14 40. p416 PMP2-YFP-Task3C44T — S901 27 41. pGEX6P1-MST27-LRKRS — F291 14 42. pGEX6P1-MST27-KKXX — O732 14 Open in a separate window Plasmids used in this study Secretion Assay.

Techniques:

Journal: Proceedings of the National Academy of Sciences of the United States of America

Article Title: δ-COP contains a helix C-terminal to its longin domain key to COPI dynamics and function

doi: 10.1073/pnas.1603544113

Figure Lengend Snippet: Plasmids used in this study

Article Snippet: Ret2LD2α T158K ( BY4743 Spore ) MAT a his3 ∆ 1 leu2 ∆ 0 met15 ∆ 0 ura3 ∆ 0; YFR051c::kanMX4; p415 ret2LD2 α T158K This study Open in a separate window Yeast strains used in this study table ft1 table-wrap mode="anchored" t5 Table S2. caption a7 No. Plasmids Addgene ID Database ID Source 1. p415 CHI 1 73863 Z1280 This study 2. p415 CHI 2 73864 Z1281 This study 3. p415 CHI 3 73865 Z1283 This study 4. p415 CHI 4 73866 Z1284 This study 5. p415 CHI 5 73867 Z1285 This study 6. p415 CHI 6 73868 Z1286 This study 7. p415 CHI 7 73869 Z1287 This study 8. p415 CHI 8 73870 Z1288 This study 9. pRS303 Bt δCOP 73871 AE1540 This study 10. p415 Ret2 73872 AE1541 This study 11. p415 Ret2LD2α 73873 AE1518 This study 12. p415 δCLD2α 73874 AE1519 This study 13. p415 Ret2LD 73875 AE1520 This study 14. p415 δCLD 73876 AE1521 This study 15. p415 Ret2LD+δC2α 73877 AE1516 This study 16. p415 δCLD+Ret2-2α 73878 AE1523 This study 17. p415 CHI 9 73879 AF1551 This study 18. p415 CHI 10 73880 AF1553 This study 19. p415 CHI 12 73881 AF1557 This study 20. p415 CHI 13 73882 AH1658 This study 21. p415 CHI 14 73883 AH1660 This study 22. p415 CHI 15 73884 AH1662 This study 23. p415 Ret2 I145A 73885 AI1732 This study 24. p415 Ret2 I148A 73886 AI1733 This study 25. p415 Ret2 I149A 73887 AI1734 This study 26. p415 Ret2 I155A 73888 AI1735 This study 27. pGEX6P1- Mst7-Erp1CT 73920 This study 28. pGEX6P1-GCN4cc-Erp1CT 73921 This study 29. pGEX6P1- Mst7-Erp2CT 73922 This study 30. pGEX6P1-GCN4cc-Erp2CT 73923 This study 31. p415 Ret2LD2α Q146F 75259 This study 32. p415 Ret2LD2α N152T 75260 This study 33. p415 Ret2LD2α K153Q 75261 This study 34. p415 Ret2LD2α T158K 75262 This study 35. p416 PMP2-YFP-LRKRS — M650 14 36. p416 PMP2-YFP-KKXX — N654 14 37. p416 PMP2-YFP-NVRNRRK — R890 14 38. p416 PMP2-YFP-KKK — M643 14 39. p416 PMP2-YFP-AAXX — N655 14 40. p416 PMP2-YFP-Task3C44T — S901 27 41. pGEX6P1-MST27-LRKRS — F291 14 42. pGEX6P1-MST27-KKXX — O732 14 Open in a separate window Plasmids used in this study Secretion Assay.

Techniques:

Journal: International Journal of Molecular Sciences

Article Title: miR-24-3p and Body Mass Index as Type 2 Diabetes Risk Factors in Spanish Women 15 Years after Gestational Diabetes Mellitus Diagnosis

doi: 10.3390/ijms24021152

Figure Lengend Snippet: Boxplot diagram showing differential circulating miRNA expression profile in GDM women depending on their glycemic status after 15 years. ( a ) relative hsa-miR-1-3p expression, ( p = 0.385); ( b ) relative hsa-miR-24-3p expression ( p = 0.030); ( c ) relative hsa-miR-329-3p expression ( p = 0.596); ( d ) relative hsa-miR-543 expression ( p = 0.071). * p -value < 0.05 cel-miR-39-3p was used for miRNA expression normalization.

Article Snippet: hsa-miR-1-3p , 477820_mir , 5′-UGGAAUGUAAAGAAGUAUGUAU-3′.

Techniques: Expressing

Journal: Journal of Microbiology and Biotechnology

Article Title: Molecular Characterization of a Novel 1,3-α-3,6-Anhydro-L-Galactosidase, Ahg943, with Cold- and High-Salt-Tolerance from Gayadomonas joobiniege G7

doi: 10.4014/jmb.2008.08017

Figure Lengend Snippet: ( A ) Gene arrangement of Ahg943 compared to Ahg558 and Ahg786 in the G. joobiniege G7 genome and the distribution of the conserved domain. The nucleotide numbers of the chromosomal region used for gene arrangement are presented above both ends of each DNA fragment based on the genomic data of G. joobiniege G7. Each ORF is indicated by an arrow with a stop codon at the arrowhead. The NCBI accession number is marked in each arrow with the annotated function in the lower row. Similar to Ahg558 and Ahg786, Ahg943 (WP_017446943.1) has a long conserved domain (cd08992) of the GH117 family spanning between N-61 and D-389 with an e-value of 3.96 xe -164 . Three putative catalytic residues, D-88, H-292, and E-293, are represented by triangles. ( B ) Phylogenetic tree of α-neoagarooligosaccharide hydrolases, including Ahg943. A phylogenetic tree was constructed by comparing 11 α-neoagarooligosaccharide hydrolases, including Ahg943, identified so far through the neighbor-joining method in MEGA 6. The tree was constructed to have branch lengths in the same units as the evolutionary distances used to infer phylogenetic trees. Sequence ID of each protein is indicated in parentheses. ( C ) Comparison of secondary structure of Ahg943 with ZgAhgB. Two-dimensional structures of Ahg943 and ZgAhgB were constructed using the NetSurfP-2.0 program server ( http://www.cbs.dtu.dk/services/NetSurfP/ ) for comparison. Two proteins were aligned depending on their amino acid sequence using Clustal Omega ( https://www.ebi.ac.uk/Tools/msa/clustalo/ ). The secondary structure of the protein is indicated at the top of Ahg943 and the bottom of ZgAhgB. The alpha-helix structure is shown as a thick line, and the beta-strand is shown as an arrow. The conserved residues constituting the active site are depicted with boxes.

Article Snippet: G. joobiniege G7 (ATCC BAA-2321 = DSM25250 T = KCTC23721 T ) was used as a genomic source for ahg943 (NCBI reference sequence: WP_017446943) [ ].

Techniques: Construct, Sequencing, Comparison

Journal: eLife

Article Title: A conserved major facilitator superfamily member orchestrates a subset of O-glycosylation to aid macrophage tissue invasion

doi: 10.7554/eLife.41801

Figure Lengend Snippet:

Article Snippet: Anti-profilin (mouse monoclonal) , Developmental Studies Hybridoma Bank (DSHB), RRID: SCR_013527 , DSHB Cat# chi 1J, RRID: AB_528439 , (1:50).

Techniques: Amplification, Clone Assay, cDNA Library Assay, Expressing, Plasmid Preparation, Staining, Software

Journal: Antibiotics

Article Title: Antibacterial Activity of Biodegradable Films Incorporated with Biologically-Synthesized Silver Nanoparticles and the Evaluation of Their Migration to Chicken Meat

doi: 10.3390/antibiotics12010178

Figure Lengend Snippet: Maximum concentration of bacteria (CFU/cm 2 ) inhibited by bio-AgNP films.

Article Snippet: S . Typhimurium UK-1 ATCC 68169 , − , + , 10 5.

Techniques: Concentration Assay, Bacteria