Labelling of the surface of intact roots of seedlings indicated that LM13 bound very weakly whereas LM14 bound strongly to the surface of root hairs (Fig.?8e and f). was homogenized to a fine powder in liquid nitrogen. The homogenate was incubated with 20?ml 50?mM 1,2-Diaminocyclohexanetetraacetic acid (CDTA; pH?7.5) for 3?h at 18C and centrifuged for 20?min at 4,400?rpm. The supernatant was collected and dialyzed extensively against deionized water (dH2O) in dialysis tubing (6C8,000?kDa molecular weight cut off) to remove low molecular weight molecules and freeze dried. The material was dissolved in phosphate-buffered saline (PBS) to generate the immunogen. Rats were used for antibody production so as to make subsequent comparisons with existing mAbs, most of which were produced in rats, as valid as possible. The immunization of rats, hybridoma preparation and cloning procedures were as described previously . Briefly, two male Wistar rats were each injected subcutaneously with SCA14 250?l of an emulsion of the isolated cell wall material at 1?mg/ml in PBS with an equal volume Freunds complete adjuvant on day?0. On days?40 and 79 the injections were repeated using incomplete adjuvant. Tail bleeds were taken 10?days after injections to assess the immune response. On day?198 a pre-fusion boost was given to the selected rat and 3?days later, the spleen was removed and lymphocytes were isolated and fused with rat myeloma cell line IR983F  using standard polyethylene glycol fusion of lymphocytes and myeloma cells. Hybridoma lines were EVP-6124 (Encenicline) initially screened by ELISA with the immunogen coated onto microtitre plates (MaxiSorp, Nunc, Roskilde, Denmark) at 50?g/ml. Previously described monoclonal antibodies Arrays were probed with 23 mAbs with previously described specificities and details of these are provided in Table?1. All were rat antibodies except mAbs CCRC-M1, BS-400-02, BS-400-03, and BS-400-04 which were produced in mice and PAM1 which was produced by phage display. Table?1 Previously characterized monoclonal antibodies used to probe glycan arrays. HG, homogalacturonan organs listed in Table?2 using CDTA and 4?M NaOH. Fifty milligrams (fresh weight) of each organ collected from at least four separate plants were homogenized to a fine powder prior to adding 300?l of 50?mM CDTA (pH?7.5). After incubating with rotation for 4?h at 20C, the extracts were centrifuged at 4,400?rpm for 10?min and the supernatants (CDTA extracts) removed. Pellets were resuspended in 300?l of 4?M NaOH and EVP-6124 (Encenicline) samples were incubated with rotation for 4?h at 20C prior to centrifugation at 4,400?rpm for 10?min. Supernatants were NaOH extracts. Table?2 Samples included on the glycan arrays flowers)D7CDTA extract (siliques)E7CDTA extract (stem top)F7CDTA extract (stem middle)G7CDTA extract (stem base)H7CDTA extract (leaves)A8CDTA extract (roots)B8NaOH extract (flowers)C8NaOH extract (siliques)D8NaOH extract (stem top)E8NaOH extract (stem middle)F8NaOH extract (stem base)G8NaOH extract (leaves)H8NaOH extract (roots) Open in a separate window Alphanumerical codes refer to the position of samples on arrays. Source EVP-6124 (Encenicline) organisms are in parentheses Rhamnogalcturonan I; rhamnogalacturonan II; modified hairy region; arabinogalactan-protein Post-printing modification of glycans Glycan samples on selected arrays were modified after printing by enzymatic digestion. For the data in EVP-6124 (Encenicline) Fig.?6 selected arrays were digested with endo-indicate that enzyme digestion had no effect on mAb binding, whereas spots that lie below the dotted line indicate where enzyme digestion reduced mAb binding. e The binding of LM13 to oligoarabinosides was tested by competitive inhibition ELISA, in which arabinan was the immobilized polymer. Oligoarabinosides with degrees of polymerization less than five failed to inhibit LM13 binding, even when used at 1?mg/ml. Both arabino-material was printed as extracted and as a five fold dilution, also in duplicate. Printing was performed using a microarray robot (Microgrid II, Genomic Solutions, Ann Arbor, MI, USA) equipped with split pins (MicroSpot 2500, Genomic Solutions). Pins were washed twice in EVP-6124 (Encenicline) dH2O after deposition of each sample. Probing of arrays Arrays were blocked by incubation for 1?h in PBS (140?mM NaCl, 2.7?mM KCl,10?mM Na2HPO4, 1.7?mM KH2PO4, pH?7.5) containing 5% low fat milk powder (5%MPBS). Arrays were then probed for 2?h with antibodies.