Incubation:Article Title: Abolishing PorB-induced mitophagy enhances gonococcal outer membrane vesicle vaccine efficacy
Article Snippet: For co-localization analysis between mitochondria and LC3 or lysosomes, mature DCs (1 × 106 cells per group) were stimulated for 4 h with 20 μg of OMV-PorB WT or OMV-PorB K117Q/K171Q or with a PBS-only Mock control and subsequently fixed with 4% paraformaldehyde (Biosharp). .. Fixed cells were blocked and permeabilized with QuickBlock buffer (Beyotime), transferred onto poly-lysine-coated slides (Solarbio), and incubated overnight at 4 °C with mouse anti-HSP60 (Santa Cruz, #sc-13115), rabbit anti-LC3B (Huabio, #ET1701-65), rabbit anti-LAMP1 (Huabio, #HA722302) or mouse anti-TOM20 (Huabio, # HA601454 ). .. Subsequently, slides were incubated for 1 h at room temperature with Alexa Fluor 488 goat anti-mouse (Proteintech, #RGAM002) or Alexa Fluor 594 goat anti-rabbit (Lablead, #Y1007) and nuclei were counterstained with 10 μg/mL DAPI (Solarbio).
Lysis:Article Title: Apolipoprotein D neofunctionalization couples lipid allocation to wing evolution.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Bombyx mori Zhejiang University N/A Spodoptera frugiperda Zhejiang University N/A Antibodies Rabbit anti-p-AMPKα (Ser473) Cell Signaling Technology Cat# 2535 Rabbit anti-AMPKα Abcam Cat# ab80039 Rabbit anti-Lkb1 HuaBio Cat# HA500143 Rabbit anti-ATG8 Lu et al, 2023 N/A Rabbit anti-Beclin-1 Proteintech Cat# 11306-1- AP Reagent/resource Reference or source Identifier or catalog number Rabbit anti-p62/SQSTM1 ABclonal Cat# A18679 Rabbit anti-ULK1 ABclonal Cat# A8529 Rabbit anti-Tubulin Wang et al, 2009 N/A HRP Goat Anti-Rabbit IgG DINGGUO CHANGSHENG Cat# IH-0011 Chemicals, enzymes and other reagents RIPA lysis buffer Verde Bio (Fryd Bio) Cat# FD009 PMSF Shanghai Biotech Cat# A610425 Dichloromethane Thermo Fisher Cat# A454-4 Methanol Thermo Fisher Cat# A998-4 Isopropanol Sinopharm Chemical Analytical grade Acetonitrile Thermo Fisher N/A n-Hexane Sinopharm Chemical Analytical grade Ammonium formate Honeywell Fluka Cat# 17843- 250 G Formic acid DIMKA Cat# 50144- 50mL BSA Merck Cat# 9048- 46-8 PBS Biosharp Cat# BL601A DMSO Biosharp Cat# BS087 Trizol (RNAiso Plus) Takara Cat# 9109 Acridine Orange (AO) Merck Cat# 65-61-2 Propidium Iodide (PI) Merck Cat# P4170 PVDF membrane Merck Millipore Cat# IPVH00010 ECL chemiluminescent substrate Fdbio Science Biotech Cat# FD8020 Software DIAMOND v2.0.11 https://github.com/bbuchfink/ diamond N/A MAFFT v6.861 https://mafft.cbrc.jp/ alignment/software/ N/A TrimAl v1.4.1 https://vicfero.github.io/ trimal/ N/A IQ-TREE v1.5.5 http://www.iqtree.org/ N/A iTOL v6.4.3 https://itol.embl.de/ N/A SOAPnuke v1.4.0 https://github.com/BGIflexlab/SOAPnuke N/A Figure 5. scRNA-seq analysis of wild-type and ApoD2−/− mutant wings at the cell cluster level. (A) Uniform manifold approximation and projection (UMAP) clustering identified 18 overlapping clusters. (B) Proportion of cells in each cluster for WT (blue) and ApoD2−/− mutant (red) across the four wing cell types. (C) Pathway enrichment analysis of clusters PM2–PM5 and PH2. (D) Violin plots showing cluster-specific changes in gene expression for the Notch signaling pathway. (E) Violin plots depicting cluster-specific changes in gene expression for cell development-related genes. (F) Violin plots illustrating cluster-specific changes in gene expression for lipid-related pathways. (G) Violin plots displaying cluster-specific changes in gene expression for autophagy-related pathways. ..
Membrane:Article Title: Apolipoprotein D neofunctionalization couples lipid allocation to wing evolution.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Bombyx mori Zhejiang University N/A Spodoptera frugiperda Zhejiang University N/A Antibodies Rabbit anti-p-AMPKα (Ser473) Cell Signaling Technology Cat# 2535 Rabbit anti-AMPKα Abcam Cat# ab80039 Rabbit anti-Lkb1 HuaBio Cat# HA500143 Rabbit anti-ATG8 Lu et al, 2023 N/A Rabbit anti-Beclin-1 Proteintech Cat# 11306-1- AP Reagent/resource Reference or source Identifier or catalog number Rabbit anti-p62/SQSTM1 ABclonal Cat# A18679 Rabbit anti-ULK1 ABclonal Cat# A8529 Rabbit anti-Tubulin Wang et al, 2009 N/A HRP Goat Anti-Rabbit IgG DINGGUO CHANGSHENG Cat# IH-0011 Chemicals, enzymes and other reagents RIPA lysis buffer Verde Bio (Fryd Bio) Cat# FD009 PMSF Shanghai Biotech Cat# A610425 Dichloromethane Thermo Fisher Cat# A454-4 Methanol Thermo Fisher Cat# A998-4 Isopropanol Sinopharm Chemical Analytical grade Acetonitrile Thermo Fisher N/A n-Hexane Sinopharm Chemical Analytical grade Ammonium formate Honeywell Fluka Cat# 17843- 250 G Formic acid DIMKA Cat# 50144- 50mL BSA Merck Cat# 9048- 46-8 PBS Biosharp Cat# BL601A DMSO Biosharp Cat# BS087 Trizol (RNAiso Plus) Takara Cat# 9109 Acridine Orange (AO) Merck Cat# 65-61-2 Propidium Iodide (PI) Merck Cat# P4170 PVDF membrane Merck Millipore Cat# IPVH00010 ECL chemiluminescent substrate Fdbio Science Biotech Cat# FD8020 Software DIAMOND v2.0.11 https://github.com/bbuchfink/ diamond N/A MAFFT v6.861 https://mafft.cbrc.jp/ alignment/software/ N/A TrimAl v1.4.1 https://vicfero.github.io/ trimal/ N/A IQ-TREE v1.5.5 http://www.iqtree.org/ N/A iTOL v6.4.3 https://itol.embl.de/ N/A SOAPnuke v1.4.0 https://github.com/BGIflexlab/SOAPnuke N/A Figure 5. scRNA-seq analysis of wild-type and ApoD2−/− mutant wings at the cell cluster level. (A) Uniform manifold approximation and projection (UMAP) clustering identified 18 overlapping clusters. (B) Proportion of cells in each cluster for WT (blue) and ApoD2−/− mutant (red) across the four wing cell types. (C) Pathway enrichment analysis of clusters PM2–PM5 and PH2. (D) Violin plots showing cluster-specific changes in gene expression for the Notch signaling pathway. (E) Violin plots depicting cluster-specific changes in gene expression for cell development-related genes. (F) Violin plots illustrating cluster-specific changes in gene expression for lipid-related pathways. (G) Violin plots displaying cluster-specific changes in gene expression for autophagy-related pathways. ..
Software:Article Title: Apolipoprotein D neofunctionalization couples lipid allocation to wing evolution.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Bombyx mori Zhejiang University N/A Spodoptera frugiperda Zhejiang University N/A Antibodies Rabbit anti-p-AMPKα (Ser473) Cell Signaling Technology Cat# 2535 Rabbit anti-AMPKα Abcam Cat# ab80039 Rabbit anti-Lkb1 HuaBio Cat# HA500143 Rabbit anti-ATG8 Lu et al, 2023 N/A Rabbit anti-Beclin-1 Proteintech Cat# 11306-1- AP Reagent/resource Reference or source Identifier or catalog number Rabbit anti-p62/SQSTM1 ABclonal Cat# A18679 Rabbit anti-ULK1 ABclonal Cat# A8529 Rabbit anti-Tubulin Wang et al, 2009 N/A HRP Goat Anti-Rabbit IgG DINGGUO CHANGSHENG Cat# IH-0011 Chemicals, enzymes and other reagents RIPA lysis buffer Verde Bio (Fryd Bio) Cat# FD009 PMSF Shanghai Biotech Cat# A610425 Dichloromethane Thermo Fisher Cat# A454-4 Methanol Thermo Fisher Cat# A998-4 Isopropanol Sinopharm Chemical Analytical grade Acetonitrile Thermo Fisher N/A n-Hexane Sinopharm Chemical Analytical grade Ammonium formate Honeywell Fluka Cat# 17843- 250 G Formic acid DIMKA Cat# 50144- 50mL BSA Merck Cat# 9048- 46-8 PBS Biosharp Cat# BL601A DMSO Biosharp Cat# BS087 Trizol (RNAiso Plus) Takara Cat# 9109 Acridine Orange (AO) Merck Cat# 65-61-2 Propidium Iodide (PI) Merck Cat# P4170 PVDF membrane Merck Millipore Cat# IPVH00010 ECL chemiluminescent substrate Fdbio Science Biotech Cat# FD8020 Software DIAMOND v2.0.11 https://github.com/bbuchfink/ diamond N/A MAFFT v6.861 https://mafft.cbrc.jp/ alignment/software/ N/A TrimAl v1.4.1 https://vicfero.github.io/ trimal/ N/A IQ-TREE v1.5.5 http://www.iqtree.org/ N/A iTOL v6.4.3 https://itol.embl.de/ N/A SOAPnuke v1.4.0 https://github.com/BGIflexlab/SOAPnuke N/A Figure 5. scRNA-seq analysis of wild-type and ApoD2−/− mutant wings at the cell cluster level. (A) Uniform manifold approximation and projection (UMAP) clustering identified 18 overlapping clusters. (B) Proportion of cells in each cluster for WT (blue) and ApoD2−/− mutant (red) across the four wing cell types. (C) Pathway enrichment analysis of clusters PM2–PM5 and PH2. (D) Violin plots showing cluster-specific changes in gene expression for the Notch signaling pathway. (E) Violin plots depicting cluster-specific changes in gene expression for cell development-related genes. (F) Violin plots illustrating cluster-specific changes in gene expression for lipid-related pathways. (G) Violin plots displaying cluster-specific changes in gene expression for autophagy-related pathways. ..
Mutagenesis:Article Title: Apolipoprotein D neofunctionalization couples lipid allocation to wing evolution.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Bombyx mori Zhejiang University N/A Spodoptera frugiperda Zhejiang University N/A Antibodies Rabbit anti-p-AMPKα (Ser473) Cell Signaling Technology Cat# 2535 Rabbit anti-AMPKα Abcam Cat# ab80039 Rabbit anti-Lkb1 HuaBio Cat# HA500143 Rabbit anti-ATG8 Lu et al, 2023 N/A Rabbit anti-Beclin-1 Proteintech Cat# 11306-1- AP Reagent/resource Reference or source Identifier or catalog number Rabbit anti-p62/SQSTM1 ABclonal Cat# A18679 Rabbit anti-ULK1 ABclonal Cat# A8529 Rabbit anti-Tubulin Wang et al, 2009 N/A HRP Goat Anti-Rabbit IgG DINGGUO CHANGSHENG Cat# IH-0011 Chemicals, enzymes and other reagents RIPA lysis buffer Verde Bio (Fryd Bio) Cat# FD009 PMSF Shanghai Biotech Cat# A610425 Dichloromethane Thermo Fisher Cat# A454-4 Methanol Thermo Fisher Cat# A998-4 Isopropanol Sinopharm Chemical Analytical grade Acetonitrile Thermo Fisher N/A n-Hexane Sinopharm Chemical Analytical grade Ammonium formate Honeywell Fluka Cat# 17843- 250 G Formic acid DIMKA Cat# 50144- 50mL BSA Merck Cat# 9048- 46-8 PBS Biosharp Cat# BL601A DMSO Biosharp Cat# BS087 Trizol (RNAiso Plus) Takara Cat# 9109 Acridine Orange (AO) Merck Cat# 65-61-2 Propidium Iodide (PI) Merck Cat# P4170 PVDF membrane Merck Millipore Cat# IPVH00010 ECL chemiluminescent substrate Fdbio Science Biotech Cat# FD8020 Software DIAMOND v2.0.11 https://github.com/bbuchfink/ diamond N/A MAFFT v6.861 https://mafft.cbrc.jp/ alignment/software/ N/A TrimAl v1.4.1 https://vicfero.github.io/ trimal/ N/A IQ-TREE v1.5.5 http://www.iqtree.org/ N/A iTOL v6.4.3 https://itol.embl.de/ N/A SOAPnuke v1.4.0 https://github.com/BGIflexlab/SOAPnuke N/A Figure 5. scRNA-seq analysis of wild-type and ApoD2−/− mutant wings at the cell cluster level. (A) Uniform manifold approximation and projection (UMAP) clustering identified 18 overlapping clusters. (B) Proportion of cells in each cluster for WT (blue) and ApoD2−/− mutant (red) across the four wing cell types. (C) Pathway enrichment analysis of clusters PM2–PM5 and PH2. (D) Violin plots showing cluster-specific changes in gene expression for the Notch signaling pathway. (E) Violin plots depicting cluster-specific changes in gene expression for cell development-related genes. (F) Violin plots illustrating cluster-specific changes in gene expression for lipid-related pathways. (G) Violin plots displaying cluster-specific changes in gene expression for autophagy-related pathways. ..
Gene Expression:Article Title: Apolipoprotein D neofunctionalization couples lipid allocation to wing evolution.
Article Snippet: .. Reagents and tools table Reagent/resource Reference or source Identifier or catalog number Experimental models Bombyx mori Zhejiang University N/A Spodoptera frugiperda Zhejiang University N/A Antibodies Rabbit anti-p-AMPKα (Ser473) Cell Signaling Technology Cat# 2535 Rabbit anti-AMPKα Abcam Cat# ab80039 Rabbit anti-Lkb1 HuaBio Cat# HA500143 Rabbit anti-ATG8 Lu et al, 2023 N/A Rabbit anti-Beclin-1 Proteintech Cat# 11306-1- AP Reagent/resource Reference or source Identifier or catalog number Rabbit anti-p62/SQSTM1 ABclonal Cat# A18679 Rabbit anti-ULK1 ABclonal Cat# A8529 Rabbit anti-Tubulin Wang et al, 2009 N/A HRP Goat Anti-Rabbit IgG DINGGUO CHANGSHENG Cat# IH-0011 Chemicals, enzymes and other reagents RIPA lysis buffer Verde Bio (Fryd Bio) Cat# FD009 PMSF Shanghai Biotech Cat# A610425 Dichloromethane Thermo Fisher Cat# A454-4 Methanol Thermo Fisher Cat# A998-4 Isopropanol Sinopharm Chemical Analytical grade Acetonitrile Thermo Fisher N/A n-Hexane Sinopharm Chemical Analytical grade Ammonium formate Honeywell Fluka Cat# 17843- 250 G Formic acid DIMKA Cat# 50144- 50mL BSA Merck Cat# 9048- 46-8 PBS Biosharp Cat# BL601A DMSO Biosharp Cat# BS087 Trizol (RNAiso Plus) Takara Cat# 9109 Acridine Orange (AO) Merck Cat# 65-61-2 Propidium Iodide (PI) Merck Cat# P4170 PVDF membrane Merck Millipore Cat# IPVH00010 ECL chemiluminescent substrate Fdbio Science Biotech Cat# FD8020 Software DIAMOND v2.0.11 https://github.com/bbuchfink/ diamond N/A MAFFT v6.861 https://mafft.cbrc.jp/ alignment/software/ N/A TrimAl v1.4.1 https://vicfero.github.io/ trimal/ N/A IQ-TREE v1.5.5 http://www.iqtree.org/ N/A iTOL v6.4.3 https://itol.embl.de/ N/A SOAPnuke v1.4.0 https://github.com/BGIflexlab/SOAPnuke N/A Figure 5. scRNA-seq analysis of wild-type and ApoD2−/− mutant wings at the cell cluster level. (A) Uniform manifold approximation and projection (UMAP) clustering identified 18 overlapping clusters. (B) Proportion of cells in each cluster for WT (blue) and ApoD2−/− mutant (red) across the four wing cell types. (C) Pathway enrichment analysis of clusters PM2–PM5 and PH2. (D) Violin plots showing cluster-specific changes in gene expression for the Notch signaling pathway. (E) Violin plots depicting cluster-specific changes in gene expression for cell development-related genes. (F) Violin plots illustrating cluster-specific changes in gene expression for lipid-related pathways. (G) Violin plots displaying cluster-specific changes in gene expression for autophagy-related pathways. ..
Blocking Assay:
other:
|
