p9310  (New England Biolabs)

Journal: The Journal of Biological Chemistry

Article Title: Heparan sulfate antagonism alters bone morphogenetic protein signaling and receptor dynamics, suggesting a mechanism in hereditary multiple exostoses

doi: 10.1074/jbc.RA117.000264

Figure Lengend Snippet: Surfen promotes recruitment of BMPRII population to lipid raft domains. Vehicle-treated ( A and B ) and surfen-treated Ad-293 cells ( C and D ) expressing SNAP-BMPRII or SNAP-BMPRIa were homogenized and fractionated by sucrose gradient ultracentrifugation. Fractions were blotted with anti-SNAP or anti-caveolin 1 antibodies. A , in vehicle-treated cells, the BMPRII population is distributed in both lipid raft and nonlipid raft domains. C , in surfen-treated cells, there is a robust shift in BMPRII population to lipid raft domains, depicted in particular in fraction 1. B , in vehicle-treated cells, the BMPRIa population is mostly in the lipid raft domains. D , in surfen-treated cells, the majority of the BMPRIa population is seen in lipid raft domains, but there are a significant amount of receptors in the nonlipid raft domains compared with the control cells. E and F , quantification of receptor population in either DRM or non-DRM (*, p

Article Snippet: Membranes were blocked in TBST and incubated overnight at 4 °C with anti-SNAP-tag (1:1000; New England Biolabs) and caveolin-1 (1:1000; Cell Signaling).

Techniques: Expressing

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

Article Title: SEK1 deficiency reveals mitogen-activated protein kinase cascade crossregulation and leads to abnormal hepatogenesis

doi:

Figure Lengend Snippet: Characterization of SEK1 −/− embryos. ( a ) ( Top ) Wild-type (WT) and SEK1 −/− (−/−) embryos at E12.5. ( Bottom ) Histological analysis with hematoxylin and eosin staining. Wild-type and SEK1 −/− liver at E11.5 (×10 and ×25) and E12.5 (×25). ( b ) ( Top ) Immunohistochemical analysis of wild type (WT) and SEK1 −/− (−/−) embryos at E11.5 with mAb to cytokeratin (Dako) (×63). The red color indicates specific staining. The numbers of cytokeratin-expressing cells per high power field are 476 ± 34, 318 ± 63, 350 ± 44, and 318 ± 17 for livers from wild-type E12.5, SEK1 −/− E12.5, wild-type E11.5, and SEK1 −/− E11.5 embryos, respectively. ( Bottom ) ApopTag staining of sections from wild-type (WT) and SEK1 −/− (−/−) embryos at E12.5 (×63). The brown color indicates specific staining. The number of apoptotic cells per high power field was 34 ± 1 and 66 ± 13 for wild-type and SEK1 −/− embryos, respectively. ( c ) In situ hybridization studies for transthyretin mRNA expression at day 11.5 and 12.5. ( Right ) Hematoxylin and eosin staining of corresponding sections. ( d ) Immunohistochemical analysis of wild-type (WT) and SEK1 −/− (−/−) embryos at E11.5 with polyclonal antisera to Factor VIII (Dako) (×63). ( Top ) Liver. The small arrow delineates megakaryocytes. The large arrow shows the endothelial cells. ( Bottom ) Control section on other regions of the embryo. ( e ) Representative Southern blot analysis of tissues from a highly chimeric mouse. SEK1 −/− cells fail to contribute to the liver. Five Chimeras were analyzed. Lanes: 1, marker; 2, phage DNA containing the SEK1 gene; B, bladder; LI, large intestine; Lv, liver; Lg, lung; SG, salivary gland; SK, skin; SI, small intestine; ST, stomach; MS, muscle. ( f ) Histopathology of liver derived from a highly chimeric adult mouse. Stained with hematoxylin and eosin. (a) Normal liver (×40). (b) SEK1 −/− chimera (×40). Note the nuclear fragmentation and abnormal hepatocyte lobule structure.

Article Snippet: Immunoblot analysis of cell lysates was performed by probing with polyclonal antibodies to SAPK/JNK, phosphorylated SAPK/JNK (Thr 183/Tyr 185) (New England Biolabs), p38 and phosphorylated p38 (New England Biolabs), MKK3 [Santa Cruz Biotechnology, MEK-3 (C-19)] and phosphorylated MKK3/MKK6 (Ser189/207) (New England Biolabs), and SEK1 (Santa Cruz Biotechnology).

Techniques: Staining, Immunohistochemistry, Expressing, In Situ Hybridization, Southern Blot, Marker, Mass Spectrometry, Histopathology, Derivative Assay

Journal: PLoS Genetics

Article Title: Reversible Oxidation of a Conserved Methionine in the Nuclear Export Sequence Determines Subcellular Distribution and Activity of the Fungal Nitrate Regulator NirA

doi: 10.1371/journal.pgen.1005297

Figure Lengend Snippet: Interaction of KapK with the NirA-NES is sensitive to methionine oxidation. (A) Western blot using S-tag antibody shows in vitro interaction of KapK with synthetic NES peptide variants containing wild type or mutated amino acid sequences. M ox , NES peptide carrying methionine 169 sulfoxide; M, NES peptide carrying reduced methionine 169; M169A, NES peptide carrying a M169A substitution, L172A_L174A, NES peptide carrying a double L172A, L174A mutation. Signal densities reflect the interaction strengths between biotinylated NES peptides, immobilized on streptavidin sepharose, and KapK-Stag in non-induced cell-free extracts. (B) Western blot of co-IP experiments showing that in vivo NirA-KapK interaction is sensitive to the thiol redox status and to the presence of the C-terminal activation domain. Co-immunoprecipitation of cell-free extracts prepared from a strain co-expressing FLAG-NirA and KapK-S-tag. Extracts were prepared from cells grown under non-induced conditions (NI, 3 mM arginine) or induced conditions (IND, 10 mM NO 3 - ). The extracts were prepared either in the presence (+), or absence (-) of 5 mM DTT. Input of pre-cleared cell-free extracts of all strains is shown in the upper panel. Elutions after the Co-IPs were separated on SDS-PAGE and equal loading of the co-IP resin with the S-tag capture Ab was verified by probing with the secondary Ab against the IgG heavy chain (~52 kDa) of the anti-S-tag antibody. A 70 kDa band of a proteolytically processed form of FLAG-NirA lacking around 30 kDa at the C-terminus is present.

Article Snippet: Co-immunoprecipitation (Co-IP) 5 μl of the “capture” anti-S-tag antibody (Ab) was first bound to 40 μl protein G agarose beads (PGAB, New England Biolabs) in TSA buffer (10 mM Tris-HCl, pH 8.0; 150 mM NaCl) in a final volume of 800 μl.

Techniques: Western Blot, In Vitro, Mutagenesis, Co-Immunoprecipitation Assay, In Vivo, Activation Assay, Immunoprecipitation, Expressing, SDS Page

Journal: The Journal of Cell Biology

Article Title: Retargeting of macroH2A following mitosis to cytogenetic-scale heterochromatic domains

doi: 10.1083/jcb.201811109

Figure Lengend Snippet: Nucleosomal organization of macroH2A. (A) Mononucleosomes (red box) were purified using high-density sucrose gradient ultracentrifugation of samples synchronized as in Fig. 1 A . (B) Western blotting before and after immunoprecipitation of pure mononucleosomes using anti-SNAP antibody or rabbit IgG as a negative control. Input samples (and 1:10 dilutions) were loaded in the four lanes on the left. The lower Western blot shows that histone H3 is present in the isolated mononucleosomes and that the loading of the pairs of samples before (pre-S) or after S phase (post-S) lanes is balanced. In the upper blot, there is no evidence for nucleosomes containing SNAP-macroH2A also containing detectable levels of endogenous macroH2A, as the signal intensities in the anti-SNAP lanes do not exceed those of the nonspecific IgG lanes. (C) The brightness of individual nucleosomes containing Oregon Green–labeled SNAP-macroH2A measured by FCS was indistinguishable from individual beads with single molecules of SNAP–Oregon Green, demonstrating that individual nucleosomes contain only single molecules of SNAP-macroH2A. The graph shows means and standard deviations from three independent experiments.

Article Snippet: The purified mononucleosome fraction was incubated with 5 µl of anti-SNAP antibody (New England Biolabs) or rabbit IgG for 2 h at 4°C.

Techniques: Purification, Western Blot, Immunoprecipitation, Negative Control, Isolation, Labeling