Journal: Journal of Neurochemistry

Article Title: Mitochondrial and lysosomal biogenesis are activated following PINK 1/parkin‐mediated mitophagy

doi: 10.1111/jnc.13412

Figure Lengend Snippet: TFEB translocates to the nucleus and affects p62 expression following carbonyl cyanide m‐chlorophenylhydrazone ( CCCP ) treatment. (a) SH ‐ SY 5Y cells were treated with scrambled (scram) or TFEB si RNA for 72 h and TFEB protein expression measured by western blotting. ** p < 0.01 versus scram; n = 4. (b) During the last 24 h of TFEB knock‐down, cells were treated with vehicle or 10 μM CCCP for 24 h and RNA extracted. p62 m RNA levels were measured by q PCR and normalised to β‐actin m RNA levels. ** p < 0.01 versus scram CCCP ‐treated cells; n = 4. (c) p62 protein levels were also measured following 24 h CCCP treatment of SH ‐ SY 5Y cells treated with scram or TFEB and Nrf2 si RNA for previous 72 h. (d) Following 24 h CCCP treatment of SH ‐ SY 5Y cells, total cell lysates were prepared and subcellular fractionation performed to generate cytosolic and nuclear fractions. TFEB protein was detected by western blotting. Lamin A and β‐actin were also measured to assess purity of the nuclear and cytosolic fractions respectively. (e) SH ‐ SY 5Y cells were treated with CCCP for 24 h and endogenous TFEB measured in total cell lysates by western blotting. (f) SH ‐ SY 5Y cell lines expressing exogenous TFEB with a DDK tag (clones T4 and T5) were generated. TFEB protein expression in parental SH ‐ SY 5Y cell line and clones T4 and T5 was measured by western blotting with a TFEB antibody. Endogenous TFEB is shown by arrow. (g) TFEB ‐ DDK cells were treated with vehicle or CCCP for 24 h and TFEB detected by immunofluorescence with an antibody against DDK (green). Nuclei are stained blue with 4′,6‐diamidino‐2‐phenylindole. (h) Total cell lysates were prepared from SH ‐ SY 5Y cells ( SH ) and TFEB ‐ DDK cells and p62 protein levels measured by western blotting.

Article Snippet: Blots were probed with antibodies against Nrf2 (ab31163; Abcam, Cambridge, UK), p62 (610833; BD Biosciences, Oxford, UK), prohibitin 1 (2426; Cell Signaling Technology, Beverly, MA, USA), cytochrome oxidase (COX) subunit IV (ab14744; Abcam), LC3B (2775; Cell Signaling Technology), cathepsin D (ab6313; Abcam), TOM20 (FL‐145; Santa Cruz Biotechnology, Santa Cruz, CA, USA), TFEB (ab2636; Abcam), DDK (clone 4C5; Origene), lamin A (ab26300; Abcam), PINK1 (BC100‐494; Novus Biologicals, Cambridge, UK), PGC‐1α (NBP1‐04676; Novus Biologicals) or β‐actin (ab82618; Abcam).

Techniques: Expressing, Western Blot, Fractionation, Clone Assay, Generated, Immunofluorescence, Staining

Journal: Journal of Neurochemistry

Article Title: Mitochondrial and lysosomal biogenesis are activated following PINK 1/parkin‐mediated mitophagy

doi: 10.1111/jnc.13412

Figure Lengend Snippet: Lysosomal enzyme activity increased following carbonyl cyanide m‐chlorophenylhydrazone ( CCCP )‐induced mitophagy. (a) TFEB ‐ DDK cells were treated with vehicle (black) or 10 μM CCCP (white) for 24 h and the activities of GC ase (nmol/h/mg protein) and β‐hexosaminidase ( HEX ) (nmol/min/mg protein) were measured in cell lysates. * p < 0.05 versus vehicle; ** p < 0.01 versus vehicle; n = 4. (b) SH ‐ SY 5Y cells treated with scrambled (scram) or TFEB si RNA for 72 h. For the last 24 h cells were treated with vehicle or 10 μM CCCP and GC ase activity measured in cell lysates. * p < 0.05 versus vehicle; n = 4. (c) SH ‐ SY 5Y cells expressing scrambled (scram) sh RNA or PINK 1 sh RNA were treated with vehicle or CCCP for 24 h. GC ase and HEX enzyme activity was measured in cell lysates. * p < 0.05 versus vehicle; n = 5. (d) SH ‐ SY 5Y cells or TFEB ‐ DDK cells were treated with vehicle or CCCP for 24 h and cathepsin D protein levels measured by western blotting.

Article Snippet: Blots were probed with antibodies against Nrf2 (ab31163; Abcam, Cambridge, UK), p62 (610833; BD Biosciences, Oxford, UK), prohibitin 1 (2426; Cell Signaling Technology, Beverly, MA, USA), cytochrome oxidase (COX) subunit IV (ab14744; Abcam), LC3B (2775; Cell Signaling Technology), cathepsin D (ab6313; Abcam), TOM20 (FL‐145; Santa Cruz Biotechnology, Santa Cruz, CA, USA), TFEB (ab2636; Abcam), DDK (clone 4C5; Origene), lamin A (ab26300; Abcam), PINK1 (BC100‐494; Novus Biologicals, Cambridge, UK), PGC‐1α (NBP1‐04676; Novus Biologicals) or β‐actin (ab82618; Abcam).

Techniques: Activity Assay, Expressing, Western Blot

Journal: Journal of Neurochemistry

Article Title: Mitochondrial and lysosomal biogenesis are activated following PINK 1/parkin‐mediated mitophagy

doi: 10.1111/jnc.13412

Figure Lengend Snippet: Mitochondrial content and PGC ‐1α levels are increased in cells with greater TFEB protein expression. (a) Mitochondrial content was measured in SH ‐ SY 5Y cells and TFEB ‐ DDK cells under basal conditions by assaying citrate synthase ( CS ) activity. ** p < 0.01 versus SH ‐ SY 5Y; n = 6. (b) Western blotting for the mitochondrial proteins prohibitin 1 and cytochrome oxidase (COX) subunit IV also indicated that mitochondrial content was increased in TFEB ‐ DDK cells. (c) PGC ‐1α m RNA levels were measured in SH ‐ SY 5Y cells and TFEB ‐ DDK cells under basal conditions by q PCR . Data normalised against β‐actin m RNA levels. ** p < 0.01 versus SH ‐ SY 5Y cells; n = 3. (d) SH ‐ SY 5Y cells were treated with scrambled (scram) or TFEB si RNA for 72 h and PGC ‐1α m RNA levels measured. * p < 0.05 versus scram; n = 4. (e) PGC ‐1α protein levels were detected by western blotting in total cell lysates of SH ‐ SY 5Y cells, TFEB ‐ DDK cells and a SH ‐ SY 5Y cell line over‐expressing human PGC ‐1α. The fold increase in PGC ‐1α protein density for this blot and PGC ‐1α m RNA levels of the respective cell lines are reported underneath the blot. (f) TFEB ‐ DDK cells were treated with 10 μM carbonyl cyanide m‐chlorophenylhydrazone ( CCCP ) for 18 h and cytosolic and nuclear fractions prepared. PGC ‐1α protein was detected in cytosolic (3.5% of total volume) and nuclear fractions (35% of total volume) by western blotting. The purity of the nuclear and cytosolic fractions was assessed by western blotting using lamin A and β‐actin antibodies respectively.

Article Snippet: Blots were probed with antibodies against Nrf2 (ab31163; Abcam, Cambridge, UK), p62 (610833; BD Biosciences, Oxford, UK), prohibitin 1 (2426; Cell Signaling Technology, Beverly, MA, USA), cytochrome oxidase (COX) subunit IV (ab14744; Abcam), LC3B (2775; Cell Signaling Technology), cathepsin D (ab6313; Abcam), TOM20 (FL‐145; Santa Cruz Biotechnology, Santa Cruz, CA, USA), TFEB (ab2636; Abcam), DDK (clone 4C5; Origene), lamin A (ab26300; Abcam), PINK1 (BC100‐494; Novus Biologicals, Cambridge, UK), PGC‐1α (NBP1‐04676; Novus Biologicals) or β‐actin (ab82618; Abcam).

Techniques: Expressing, Activity Assay, Western Blot

Journal: International Journal of Clinical and Experimental Pathology

Article Title: Isolated Langerhans cell histiocytosis of the stomach: a case report and literature review

doi:

Figure Lengend Snippet: Reported cases of adult LCH

Article Snippet: We used the the following primary antibodies: Vimentin (clone V9, OriGene), S100 (clone poly, OriGene), CD1a (clone O10, OriGene), langerin (clone343828, OriGene), Pan-cytokeratin (clone AE1, OriGene), CD68 (clone PG-M1, OriGene), CD163 (clone 10D6, OriGene), CD21 (clone 2G9, OriGene), CD35 (clone E11, OriGene), CD117 (clone poly, OriGene), CD34 (clone QBEnd-10, OriGene), DOG-1 (clone SP31, OriGene), cyclinD1 (clone DCS-6, OriGene), MLH1 (clone ES05, OriGene), MSH2 (clone 25D12, OriGene), MSH6 (clone EP49, OriGene), PMS2 (clone EP51, OriGene), HP, P53 (clone DO7, OriGene), Ki-67 (clone UMAB107, Ori-Gene).

Techniques: Mutagenesis

Journal: BMC Cancer

Article Title: High Beclin-1 and ARID1A expression corelates with poor survival and high recurrence in intrahepatic cholangiocarcinoma: a histopathological retrospective study

doi: 10.1186/s12885-019-5429-3

Figure Lengend Snippet: Distribution of staining intensities of Beclin-1, ARID1A, CA9 and IDH1 in patients with intrahepatic cholangiocarcinoma ( n = 113)

Article Snippet: Primary antibodies used in this study included the following: for Beclin-1, sc-11,427 H300 (1:100, Santa-Cruz Biotechnology, Santa-Cruz, CA, USA), for ARIDIA, sc-32,761 PSG3 (1:200, Santa-Cruz Biotechnology), for IDH1, Clone OTI24A2 (1:150, Origene Technologies, Rockville, MD, USA) and for CA9, Clone OTI1G7 (1:150, Origene Technologies).

Techniques: Staining

Journal: BMC Cancer

Article Title: High Beclin-1 and ARID1A expression corelates with poor survival and high recurrence in intrahepatic cholangiocarcinoma: a histopathological retrospective study

doi: 10.1186/s12885-019-5429-3

Figure Lengend Snippet: The risk of death in ICC patients according to the expression of Beclin-1, ARID1A, IDH1 and CA9

Article Snippet: Primary antibodies used in this study included the following: for Beclin-1, sc-11,427 H300 (1:100, Santa-Cruz Biotechnology, Santa-Cruz, CA, USA), for ARIDIA, sc-32,761 PSG3 (1:200, Santa-Cruz Biotechnology), for IDH1, Clone OTI24A2 (1:150, Origene Technologies, Rockville, MD, USA) and for CA9, Clone OTI1G7 (1:150, Origene Technologies).

Techniques: Expressing

Journal: BMC Cancer

Article Title: High Beclin-1 and ARID1A expression corelates with poor survival and high recurrence in intrahepatic cholangiocarcinoma: a histopathological retrospective study

doi: 10.1186/s12885-019-5429-3

Figure Lengend Snippet: The risk of recurrence in ICC patients according to the expression of Beclin-1, ARID1A, IDH1 and CA9

Article Snippet: Primary antibodies used in this study included the following: for Beclin-1, sc-11,427 H300 (1:100, Santa-Cruz Biotechnology, Santa-Cruz, CA, USA), for ARIDIA, sc-32,761 PSG3 (1:200, Santa-Cruz Biotechnology), for IDH1, Clone OTI24A2 (1:150, Origene Technologies, Rockville, MD, USA) and for CA9, Clone OTI1G7 (1:150, Origene Technologies).

Techniques: Expressing

Journal: European Journal of Histochemistry : EJH

Article Title: The anti-inflammatory effects of exercise training promote atherosclerotic plaque stabilization in apolipoprotein E knockout mice with diabetic atherosclerosis

doi: 10.4081/ejh.2013.e3

Figure Lengend Snippet: Effects of exercise training on IL-6, MMP-2, MMP-3, MMP-8 and TIMP-2 content of the atherosclerotic lesions. CO, control group; SED, sedentary group; EX, exercise group. Results are expressed as mean ± standard deviation.*P<0.05, EX compared to CO group; #P<0.05, EX compared to SED group.

Article Snippet: Consecutive sections were also stained with polyclonal antibodies against MMP-2 and MMP-3 (MBL International Corporation, Woburn, MA, USA), MMP-8 (Chemicon International Inc., Temecula, CA, USA), TIMP-2 (Acris Antibodies GmbH, Herford, Germany) or rat monoclonal anti-mouse IL-6 (Biolegends, San Diego, CA, USA).

Techniques: Standard Deviation

Journal: PLoS ONE

Article Title: α2,3-Sialyltransferase ST3Gal III Modulates Pancreatic Cancer Cell Motility and Adhesion In Vitro and Enhances Its Metastatic Potential In Vivo

doi: 10.1371/journal.pone.0012524

Figure Lengend Snippet: Capan-1 variant cells ( Figure 3A ) and MDAPanc-28 variant cells ( Figure 3B ), previously incubated with PBS-1% BSA (light bars) or anti-SLe x MAb (dark bars), were added to 96-well microplates coated with rh E-selectin or PBS-1% BSA (negative control). Adherent cells were estimated with a MTT-based colorimetric assay. Results are expressed as the Specific binding to E-selectin (O.D. 570 nm of cells bounded to E-selectin – O.D. 570 nm of cells bonded to PBS-1% BSA) versus cells previously incubated or not with anti-SLe x MAb. Data represents the mean ± SD of 3 separate experiments, each in five replicates (n = 15). * Significantly different ( P<0.001 ).

Article Snippet: 2 µg/mL anti-murine CD62 E (E-selectin) MAb (Acris Antibodies GmbH, Herford, Germany) was added to HSE 30 minutes before tumour cell addition.

Techniques: Variant Assay, Incubation, Negative Control, Colorimetric Assay, Binding Assay