Journal: Molecular cell

Article Title: Rad52 Restrains Resection at DNA Double-Strand Break Ends in Yeast

doi: 10.1016/j.molcel.2019.08.017

Figure Lengend Snippet: KEY RESOURCES TABLE

Article Snippet: Images were captured by the Azure c400 Imaging System (Azure Biosystems). table ft1 table-wrap mode="anchored" t5 caption a7 REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Monoclonal ANTI-FLAG M2-Peroxidase (HRP) antibody produced in mouse Sigma-Aldrich A8592–1MG; RRID:AB_439702 Monoclonal Anti-HA antibody produced in mouse Sigma-Aldrich H3663–100UL; RRID:AB_262051 Goat Anti-Mouse Goat anti-mouse IgG-HRP Polyclonal, Hrp Conjugated antibody Santa Cruz Biotechnology sc-2005; RRID:AB_631736 PGK1 antibody [22C5D8] abcam ab113687; RRID:AB_10861977 Monoclonal ANTI-FLAG M2 antibody produced in mouse Sigma-Aldrich F3165–1MG; RRID:AB_259529 Monoclonal Anti-c-Myc antibody produced in mouse Sigma-Aldrich M4439–100UL; RRID:AB_439694 Chemicals, Peptides, and Recombinant Proteins Anhydrotetracycline hydrochloride (ahTET) Acros Organics AC23313–1000 cOmplete, Mini Protease Inhibitor Cocktail Roche 4693124001 Protein G-Agarose Roche 11243233001 Ribonuclease A from bovine pancreas Sigma-Aldrich R6513–250MG Easytides dATP, [α- 32 P] PerkinElmer BLU512H250UC Hydroxyurea (HU) Sigma-Aldrich H8627–100G Camptothecin (CPT) Sigma-Aldrich C9911–250MG Phleomycin InvivoGen ant-ph-5 Methyl methanesulfonate (MMS) Sigma-Aldrich M4016–1G Doxycycline hyclate Sigma-Aldrich D9891–5G SNAP-Surface Alexa Fluor 546 NEB S9129S Chitin resin NEB S6651L cOmplete His-tag resin Roche 5893682001 SP Sepharose GE Healthcare 28950513 anti-FLAG-M2 resin Sigma A1205 PD10 desalting column GE Healthcare 17085101 DOPC Avanti Polar Lipids 850375C biotinylated-PE Avanti Polar Lipids 860562C mPEG 2OOO-DOPE Avanti Polar Lipids 880130C quartz slides Finkenbeiner N/A Polymethylmethacrylate 25 kDa Polymer Source P9790-MMA 3% PMMA 495 kDa MICROCHEM N/A AquaSave Mitsubishi Rayon Co., Ltd N/A λ-dsDNA NEB N3011S M13mp18 ssDNA NEB N4040S TLC plates Millipore HX71732079 Critical Commercial Assays amfiSure ONE PCR Master Mix (2×) GenDEPOT P7000–010 In-Fusion HD Cloning Plus TaKaRa Bio 638909 Ex Taq DNA Polymerase TaKaRa Bio RR001A NucleoSpin Gel and PCR clean-up MACHEREY-NAGEL 740609.250 RadPrime DNA Labeling System Invitrogen 18428–011 PowerUp SYBR Green Master Mix Applied Biosystems A25742 Amersham ECL Prime Western Blotting Detection Reagent GE Healthcare RPN2232 Deposited Data Unprocessed autoradiographs, western blot images and fluorescence microscopy images of this study This study https://doi.org/10.17632/g566xfgd96.1 Experimental Models: Organisms/Strains Fission and budding yeast strains used in this study are listed in Table S1 and Table S2 .

Techniques: Produced, Recombinant, Protease Inhibitor, Polymer, Clone Assay, DNA Labeling, SYBR Green Assay, Western Blot, Fluorescence, Microscopy, Software, Real-time Polymerase Chain Reaction, Imaging, Hybridization, Membrane

Journal: Cell Death & Disease

Article Title: Cross organelle stress response disruption promotes gentamicin-induced proteotoxicity

doi: 10.1038/s41419-020-2382-7

Figure Lengend Snippet: a Misfolded protein load in gentamicin (GENTA), tunicamycin (TUNICA), and/or GGA-exposed cells assessed by Thioflavin T staining. Red = Thioflavin T; blue = Hoechst stained nuclei; bars = 50 µm. b Thioflavin T puncta quantified in gentamicin or tunicamycin vs. GGA-exposed renal cells. c Gentamicin increased oxidative stress evidenced by increased steady-state 4HNE content. d GGA significantly reduced 4HNE content in gentamicin-exposed cells. e Content of ROS in renal cells after variable duration exposure to gentamicin assessed by fluorescent whole-cell oxidative stress assay. f GGA significantly reduced whole-cell ROS content in gentamicin-exposed cells; bars = 50 µm; NS = nonsignificant; * P < 0.05.

Article Snippet: Thioflavin T puncta was measured by automated image cytometry via the Celigo Image Cytometer (Nexcelom; Lawrence, MA).

Techniques: Staining

Journal: Neuron

Article Title: Full field-of-view virtual reality goggles for mice.

doi: 10.1016/j.neuron.2023.11.019

Figure Lengend Snippet: Figure 5. Two-photon calcium imaging during iMRSIV spatial behaviors (A) iMRSIV+2P. Example two-photon imaging field of CA1 neurons labeled with jGCaMP8m and regions of interest (ROIs). Imaging during familiar linear track navigation using iMRSIV.

Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Bacterial and virus strains AAV9-syn-jGCaMP8m-WPRE Addgene RRID: Addgene_162375 Deposited data Processed behavior and 2p imaging data This paper Zenodo: https://doi.org/10.5281/zenodo.8393062 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory RRID: IMSR_JAX:000664 BALB/C Charles River RRID: IMSR_CRL:028 Software and algorithms Unity 2021.2.9f1 Unity Technologies https://unity.com MATLAB R2022b MathWorks https://www.mathworks.com OpticStudio 23.1.1 Zemax, LLC https://www.zemax.com Blender 3.5 The Blender Foundation https://www.blender.org Custom Unity scripts and VR environments This paper github.com/DombeckLab/IMRSIV and Zenodo: https://doi.org/10.5281/zenodo.10127394 Other Lens design in Zemax This paper github.com/DombeckLab/IMRSIV STL files for custom-printed parts This paper github.com/DombeckLab/IMRSIV

Techniques: Imaging, Labeling

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Mitogen‐activated protein kinase 4 (MAPK4) expression during the development of non‐small cell lung cancer (NSCLC). (a) Schematic diagram showing subcutaneous injection of Lewis lung carcinoma (LLC) cells (5 × 10 5 ) into the right flanks of wild‐type (WT) mice. (b) Tumor volume. (c) Tumor weight. (d) Tumor pathology was analyzed by hematoxylin‐eosin (H&E) staining. (e) The expression levels of MAPK4 in tumors was analyzed by immunofluorescence and (f) quantified. (g) The colocalization of CD34 and MAPK4 in tumors were analyzed by immunofluorescence. (h) Colocation coefficient between CD34 and MAPK4 expression were quantified by ImageJ. Representative data from three independent experiments were shown. * p < 0.05, ** p < 0.01. NS, no significance.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Expressing, Injection, Staining, Immunofluorescence

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Mitogen‐activated protein kinase 4 (MAPK4) silencing inhibits the proliferarion of endothelial cells (ECs) in vitro. Human umbilical vein ECs (HUVECs) were transiently transfected with MAPK4 small interfering RNA (siRNA) (50 nM) in 24‐well plates via Lipofectamine 3000 reagent in vitro, 48 h later. (a) The expression of MAPK4 was analyzed by real‐time polymerase chain reaction (PCR). (b) Western blot analysis and (c) immunofluorescence staining were used to detect and quantitatively analyze MAPK4 expression in the two groups. (d, e) Cell counting kit‐8 (CCK‐8) assay was used to evaluate the proliferation of HUVECs 24, 48, and 72 h after transfection of MAPK4‐RNA interference (RNAi). (f) Colony formation assay was used to evaluate the colony‐forming ability of HUVECs and the colonies were counted. (g) The tube‐forming ability of HUVECs was evaluated by tube formation assay. (h) The cell cycle distribution was evaluated by fluorescence‐activated cell sorting. (i) The expression levels of CDKs in HUVECs were determined by real‐time PCR. (j) Western blot analysis was used to evaluate the expression of Cyclin A, Cyclin B1, and cyclin‐dependent kinase inhibitor 1A (p21) in HUVECs. Representative data from three independent experiments were shown. * p < 0.05, ** p < 0.01. NS, no significance.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: In Vitro, Transfection, Small Interfering RNA, Expressing, Real-time Polymerase Chain Reaction, Western Blot, Immunofluorescence, Staining, Cell Counting, CCK-8 Assay, Colony Assay, Tube Formation Assay, Fluorescence, FACS

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Mitogen‐activated protein kinase 4 (MAPK4) silencing inhibits the proliferation of endothelial cells (ECs) by regulating the Raf/MEK/ERK1/2 signaling pathway. Human umbilical vein ECs (HUVECs) were transiently transfected with MAPK4 small interfering RNA (siRNA) (50 nM) in 24‐well plates via Lipofectamine 3000 reagent in vitro. (a) Volcano plot showing genes with differential expression in MAPK4‐silenced HUVECs (MAPK4 HUVECs) compared with NC HUVECs, as determined by RNA sequencing (RNA‐seq). n = 3 per group. (b, c) Gene set enrichment analysis plots (left) and heat maps (right) of the RNA‐seq data for NC HUVECs and MAPK4 HUVECs. (d) Western blot analysis was used to evaluate the levels of protein kinase B (AKT), phosphorylated AKT (p‐AKT), c‐Jun n‐terminal kinase (JNK), phosphorylated JNK (p‐JNK), nuclear factor κB (NF‐κB), phosphorylated NF‐κB (p‐NF‐κB), (e) ERK1/2, phosphorylated ERK1/2 (p‐ERK1/2), (f) rat sarcoma (Ras), Raf, p‐Raf, MEK, and phosphorylated MEK (p‐MEK) in HUVECs. (g) 24 h after transfection, transfected cells were treated with the p‐ERK1/2 inhibitor and cultured for another 24 h. (h) Immunofluorescence was used to evaluate and quantitatively analyze the p‐ERK1/2 level in HUVECs. Representative data from three independent experiments are shown. ** p < 0.01. ERK1/2, extracellular regulated protein kinases 1/2; MEK, mitogen‐activated extracellular signal‐regulated kinase; Raf, rapidly accelerated fibrosarcoma.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Transfection, Small Interfering RNA, In Vitro, Expressing, RNA Sequencing Assay, Western Blot, Cell Culture, Immunofluorescence

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Mitogen‐activated protein kinase 4 (MAPK4) silencing inhibits endothelial cell (EC) growth. Human umbilical vein ECs (HUVECs) were cultured in the supernatant of human non‐small cell lung cancer (NSCLC) cells and transiently transfected with MAPK4 small interfering RNA (siRNA) (50 nM) in 24‐well plates via Lipofectamine 3000 reagent in vitro. (a) The expression of MAPK4 in HUVECs was detected by immunofluorescence. (b) The number of cells was determined by cell counting. (c) Cell counting kit‐8 (CCK‐8) assay was used to evaluate the proliferation ability of HUVECs. (d) The tube‐forming ability of HUVECs was evaluated by tube formation assay. (e) The expression of ki‐67 in HUVECS was detected by fluorescence‐activated cell sorting. (f, g) Extracellular regulated protein kinases 1/2 (ERK1/2) and phosphorylated ERK1/2 (p‐ERK1/2) in HUVECs was detected by western blot analysis. (h, i) The expression of p‐ERK1/2 in HUVECs was detected by immunofluorescence analysis and calculated. Representative data from three independent experiments are shown. ** p < 0.01, NS, no significance.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Cell Culture, Transfection, Small Interfering RNA, In Vitro, Expressing, Immunofluorescence, Cell Counting, CCK-8 Assay, Tube Formation Assay, Fluorescence, FACS, Western Blot

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: The expression of mitogen‐activated protein kinase 4 (MAPK4) in the tumor tissue of patients with clinical non‐small cell lung cancer (NSCLC). (a) The microarray of NSCLC tissues obtained from relevant patients was analyzed by multiplex immunofluorescence staining of CD34 and MAPK4. MAPK4 staining is shown in red, CD34 staining is shown in green, and 4′,6‐diamidino‐2‐phenylindole (DAPI) staining is shown in blue. Carcinoma tissues (1, 3, 5…17): 92 samples; paracarcinoma tissues (2, 4, 6…18): 88 samples. (b) The expression of MAPK4 in carcinoma and paracarcinoma clinical samples from patients with NSCLC were analyzed, and the H‐scores were calculated. (c) Comparison of MAPK4 expression in CD34‐positive cells between cancer and adjacent tissues. (d) The 5‐year overall survival rate in the four groups was determined through Kaplan–Meier analysis.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Expressing, Microarray, Multiplex Assay, Immunofluorescence, Staining, Comparison

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Correlations of MAPK4 expression with clinical characteristics of patients with NSCLC.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Expressing

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Targeted intervention of the expression of mitogen‐activated protein kinase 4 (MAPK4) could inhibit the growth of non‐small cell lung cancer (NSCLC) tumor in vivo. Lewis lung carcinoma (LLC) cells (5 × 10 5 ) were subcutaneously injected into the right flanks of wild‐type (WT) C57BL/6 mice. Tumors were collected on day 21. (a) Schematic diagram showing subcutaneously injection of LLC cells (5 × 10 5 ) into the right flanks of WT mice. Seven days later, the constructed PGL3.0 basic‐CD34 promoter‐MAPK4 RNA interference (RNAi) eukaryotic expression vectors (termed as p‐siMAPK4) or p‐cont given by subcutaneous injection into the left flank of murine NSCLC tumor model three times every 3 days. Tumor growth was monitored every 2 days to generate the growth curve, and tumors were collected on day 14. (b) Tumor size. (c) Tumor volume and (d) tumor weight. (e) Tumor pathology was analyzed by hematoxylin‐eosin (H&E) staining. The arrows indicate neovascularization. (f–h) The expression of MAPK4 and CD34 in tumors was analyzed by immunofluorescence and quantitated. (i, j) Cell proliferation nuclear antigen (Ki67) expression in tumors was analyzed by immunofluorescence and quantitated. Representative data from three independent experiments were shown. * p < 0.05, ** p < 0.01.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Expressing, In Vivo, Injection, Construct, Staining, Immunofluorescence

Journal: Cancer Innovation

Article Title: MAPK4 facilitates angiogenesis by inhibiting the ERK pathway in non‐small cell lung cancer

doi: 10.1002/cai2.117

Figure Lengend Snippet: Schematic diagram of mitogen‐activated protein kinase 4 (MAPK4) role in tumor angiogenesis and progression of non‐small cell lung cancer (NSCLC). (a) MAPK4 facilitates tumor angiogenesis and progression in NSCLC by promoting the growth of endothelial cell (CD34 + EC), which is related to altered transduction of Raf/MEK/ERK1/2 signaling pathway. (b) Targeted intervention the expression of MAPK4 in CD34 + ECs can repress tumor angiogenesis and progression of NSCLC. ERK1/2, extracellular regulated protein kinases 1/2; MEK, mitogen‐activated extracellular signal‐regulated kinase; Raf, rapidly accelerated fibrosarcoma.

Article Snippet: After deparaffinization and rehydration, the slides were incubated with the corresponding primary antibodies (anti‐MAPK4: Proteintech, 26102‐1‐AP; anti‐phosphorylated ERK1/2 [p‐ERK1/2]: Abcam, ab201015; anti‐CD34: Abcam, ab8158; anti‐cell proliferation nuclear antigen [Ki67; Abcam, 92742]) and secondary antibodies (Alexa Fluor 647: Cell Signaling, 4414S; Alexa Fluor 488: Abcam, ab150077; anti‐MAPK6: Absin, abs133606; anti‐NLK: Abcam, ab26050; anti‐MAPK15: Thermo Fisher, PA5‐105740).

Techniques: Transduction, Expressing