{"id":8746,"date":"2025-05-05T08:54:39","date_gmt":"2025-05-04T23:54:39","guid":{"rendered":"http:\/\/dna.brc.riken.jp\/en\/?page_id=8746"},"modified":"2025-06-16T17:59:10","modified_gmt":"2025-06-16T08:59:10","slug":"bioengmiscen","status":"publish","type":"page","link":"http:\/\/dna.brc.riken.jp\/en\/researchen\/bioengmiscen","title":{"rendered":"Bioengineering misc"},"content":{"rendered":"<p><!-- js calling begin --><code><script type=\"text\/javascript\" src=\"\/en\/wp-content\/uploads\/js\/functions_list.js\"><\/script><\/code><!-- js calling end --><\/p>\n<h2>Bioengineering misc<\/h2>\n<h3>Antibiotics<\/h3>\n<h4>Blasticidin S deaminase<\/h4>\n<ul style=\"line-height: 1.5em;\">\n<li>Cloning of the blasticidin S deaminase gene (BSD) from Aspergillus terreus and its use as a selectable marker for Schizosaccharomyces pombe and Pyricularia oryzae.<br \/>\nKimura M, Kamakura T, Tao QZ, Kaneko I, Yamaguchi I.<br \/>\nMol. Gen. Genet. 242 (2): 121-129 (1994). PMID 8159161.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB19904<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19904\">pBSA712<\/a><\/td>\n<td>Expression vector of lacZ:BSD (blasticidin-S deaminase) fusion in E. coli.<\/td>\n<\/tr>\n<tr>\n<td>RDB19905<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19905\">pBF101<\/a><\/td>\n<td>Expression vector of BSD (blasticidin-S deaminase) in a filamentous fungus, such as Pyricularia oryzae.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h4>Hygromicin resistance gene<\/h4>\n<ul style=\"line-height: 1.5em;\">\n<li>Loss of function and reduced levels of sphingolipid desaturase DEGS1 variants are both relevant in disease mechanism.<br \/>\nDei Cas, M., Montavoci, L., Pasini, C., Caretti, A., Penati, S., Martinelli, C., Gianelli, U., Casati, S., Nardecchia, F., Torella, A., Brunetti-Pierri, N., Trinchera, M. J. Lipid Res. 65 (3): 100517 (2024). PubMed PMID 38342436 [<a href=\"https:\/\/pubmed.ncbi.nlm.nih.gov\/38342436\/\" target=\"_blank\">PubMed<\/a>] [<a href=\"https:\/\/doi.org\/10.1016\/j.jlr.2024.100517\" target=\"_blank\">Article<\/a>] [<a href=\"https:\/\/rrc.nbrp.jp\/references\/83326\" target=\"_blank\">RRC of NBRP<\/a>]<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/strong><\/th>\n<th>Name of resource<\/strong><\/th>\n<th>Short Description<\/strong><\/th>\n<\/tr>\n<tr>\n<td>RDB20899<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB20899\">pCDNA3-HygR<\/a><\/td>\n<td>Mammalian expression vector of hygromicin resistance gene, coding Streptomyces hygroscopicus phosphotransferase.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h4>Thermostable kanamycin for microbial gene disruption<\/h4>\n<ul style=\"line-height: 1.5em;\">\n<li>Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus.<br \/>\nHoseki, J., Yano, T., Koyama, Y., Kuramitsu, S., Kagamiyama, H.<br \/>\nJ. Biochem. 126 (5): 951-956 (1999). <a href=\"https:\/\/www.ncbi.nlm.nih.gov\/pubmed\/10544290\">PubMed PMID 10544290<\/a>.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB03436<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB03436\">pUC18-HTK (with promoter)<\/a><\/td>\n<td>Expression vector of Thermus highly thermostable kanamycin nucleotidyltransferase (HTK) gene<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<hr \/>\n<h3>Nanoparticle<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>Multiplexed <sup>129<\/sup>Xe HyperCEST MRI Detection of Genetically Reconstituted Bacterial Protein Nanoparticles in Human Cancer Cells.<br \/>\nMizushima R, Inoue K, Fujiwara H, Iwane AH, Watanabe TM, Kimura A.<br \/>\nContrast Media Mol. Imaging 2020: 5425934 (2020). PMID 32256252.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB16904<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB16904\">pT2b_mT_gvpC16-T2A-EGFP_pP_rm<\/a><\/td>\n<td>Tol2 transposon expression vector of Planktothrix rubescens gvpC16 and EGFP marker (C).<\/td>\n<\/tr>\n<tr>\n<td>RDB16905<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB16905\">pT2b_mT_gvpC20-T2A-mKO2_pP_rm<\/a><\/td>\n<td>Tol2 transposon expression vector of Planktothrix rubescens gvpC20 and mKO2 marker (C).<\/td>\n<\/tr>\n<tr>\n<td>RDB16906<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB16906\">pT2b_mT_gvpC28-T2A-EGFP_pP_rm<\/a><\/td>\n<td>Tol2 transposon expression vector of Planktothrix agardhii gvpC28 and EGFP marker (C).<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h3>Streptavidin<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>Streptavidin-aequorin fusion protein for bioluminescent immunoassay.<br \/>\nInouye S, Sato J, Sasaki S, Sahara Y.<br \/>\nBiosci. Biotechnol. Biochem. 75 (3): 568-571 (2011). PMID 21389603.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td><script>newImage(2023,5,2)<\/script>RDB19843<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19843\">pSTA51<\/a><\/td>\n<td>Expression vector of S. avidinii Streptavidin.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h3>ZZ domain of Staphylococcal Protein A<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>Soluble protein expression in E. coli cells using IgG-binding domain of protein A as a solubilizing partner in the cold induced system.<br \/>\nInouye S, Sahara Y.<br \/>\nBiochem. Biophys. Res. Commun. 376 (3): 448-453 (2008). PMID 18789309.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td><script>newImage(2023,5,2)<\/script>RDB19844<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19844\">pJN-ZZ<\/a><\/td>\n<td>Expression vector of ZZ domain (Synthetic IgG-binding domain from Staphylococcal Protein A).<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h3>Artificial enzymatic RNA editing system<script>newImage(2022,03,20)<\/script><\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>RNA editing of BFP, a point mutant of GFP, using artificial APOBEC1 deaminase to restore the genetic code.<br \/>\nBhakta S, Sakari M, Tsukahara T.<br \/>\nSci. Rep. 10 (1): 17304 (2020). PMID 33057101.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB19359<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19359\">Target BFP gene expression plasmid<\/a><\/td>\n<td>Expression vector of target BFP gene, a point mutant (T199C) of GFP for artificial enzymatic RNA editing system.<\/td>\n<\/tr>\n<tr>\n<td>RDB19360<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19360\">pCS2+MT-MS2HB-APOBEC1<\/a><\/td>\n<td>Expression vector of the catalytic domain of human APOBEC1 tagged with MS2HB at N-terminus for artificial enzymatic RNA editing system.<\/td>\n<\/tr>\n<tr>\n<td>RDB19361<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19361\">MS2-guideRNA21bp<\/a><\/td>\n<td>Expression vector of guideRNA, a 21 ntd sequence complementary to the target BFP mRNA tagged with MS2 stem loop at C-terminus for artificial enzymatic RNA editing system.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<h3>Biotin ligase<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>Proximity-dependent biotin labeling in testicular germ cells identified TESMIN-associated proteins.<br \/>\nOura, S., Ninomiya, A., Sugihara, F., Matzuk, M.M., Ikawa, M.<br \/>\nSci. Rep. 12 (1): 22198 (2022). PubMed PMID 36564444.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB19660<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19660\">pCAG-MCS-TurboID-3xFLAG<\/a><\/td>\n<td>CAG promoter-driven expression of TurboID-3xFLAG-fused protein (C terminus).<\/td>\n<\/tr>\n<tr>\n<td>RDB19659<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19659\">pCAG-MCS-BioID2-3xFLAG<\/a><\/td>\n<td>CAG promoter-driven expression of BioID2-3xFLAG-fused protein (C terminus).<\/td>\n<\/tr>\n<tr>\n<td>RDB19658<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19658\">pCAG-3xFLAG-TurboID-MCS<\/a><\/td>\n<td>CAG promoter-driven expression of 3xFLAG-TurboID-fused protein (N terminus).<\/td>\n<\/tr>\n<tr>\n<td>RDB19657<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB19657\">pCAG-3xFLAG-BioID2-MCS<\/a><\/td>\n<td>CAG promoter-driven expression of 3xFLAG-BioID2-fused protein (N terminus).<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<li>ChIP-seq analysis of genomic binding regions of five major transcription factors highlights a central role for ZIC2 in the mouse epiblast stem cell gene regulatory network.<br \/>\nMatsuda, K., Mikami, T., Oki, S., Iida, H., Andrabi, M., Boss, J.M., Yamaguchi, K., Shigenobu, S., Kondoh, H.<br \/>\nDevelopment 144 (11): 1948-1958 (2017). PubMed PMID 28455373.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB15774<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB15774\">pCAGGS-BLRP-BirA<\/a><\/td>\n<td>Expression vector to perform ChIP-seq analysis using biotinylated proteins.<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<p>ChIP-seq is a powerful method of comprehensive analysis of transcription factor (TF) binding sites. However, the bottle neck of ChIP-seq analysis is the quality of antibody, and thus many researchers have been given up. To overcome, authors constructed the vector expressing &#8220;biotinylated-tag&#8221; transcription factors. With this vector, you can get acceptable level of TF-DNA complex for ChIP-seq analysis by streptavidin-beads for any kinds of TF.<\/p><\/li>\n<li>Also refer <a href=\"https:\/\/dnaconda.riken.jp\/search\/KO\/K03\/K03524.html\">BirA family transcriptional regulator, biotin operon repressor \/ biotin&#8212;[acetyl-CoA-carboxylase] ligase [EC:6.3.4.15]<\/a>\n<\/li>\n<\/ul>\n<h3>Open-Sandwich Immunoassay (OS-IA)<\/h3>\n<ul style=\"line-height: 1.5em;\">\n<li>Homogeneous Noncompetitive Luminescent Immunodetection of Small Molecules by Ternary Protein Fragment Complementation.<br \/>\nOhmuro-Matsuyama, Y., Ueda, H.<br \/>\nAnal. Chem. 90 (5): 3001-3004 (2018). PubMed PMID 29446920.<\/p>\n<table>\n<tbody>\n<tr>\n<th>Catalog no.<\/td>\n<th>Name of resource<\/td>\n<th>Descriptiion<\/td>\n<\/tr>\n<tr>\n<td>RDB16003<\/td>\n<td><a href=\"https:\/\/brc.riken.jp\/dna\/RDB16003\">pET-LnBiT<\/a><\/td>\n<td>Bacterial expression vector of LnBiT, a comporntnt of the Open Sandwich Bioluminescent Immunoassay (OS-BLIA).<\/td>\n<\/tr>\n<\/tbody>\n<\/table>\n<\/li>\n<\/ul>\n<hr \/>\n<p style=\"text-align: left;\">2025.06.15 (T.M. GRP0084e)<\/p>\n","protected":false},"excerpt":{"rendered":"<p>Bioengineering misc Antibiotics Blasticidin S deaminase Cloning of the blasticidin S deaminase gene (BSD) from Aspergillus terreus and its use as a selectable marker for Schizosaccharomyces pombe and Pyricularia oryzae. Kimura M, Kamakura T, Tao QZ, Kaneko I, Yamaguchi I. Mol. Gen. Genet. 242 (2): 121-129 (1994). PMID 8159161. Catalog no. Name of resource Descriptiion RDB19904 pBSA712 Expression vector of lacZ:BSD (blasticidin-S deaminase) fusion in E. coli. RDB19905 pBF101 Expression vector of BSD (blasticidin-S deaminase) in a filamentous fungus, such as Pyricularia oryzae. Hygromicin resistance gene Loss of function and reduced levels of sphingolipid desaturase DEGS1 variants are both relevant in disease mechanism. Dei Cas, M., Montavoci, L., Pasini, C., Caretti, A., Penati, S., Martinelli, C., Gianelli, U., Casati, S., Nardecchia, F., Torella, A., Brunetti-Pierri, N., Trinchera, M. J. Lipid Res. 65 (3): 100517 (2024). PubMed PMID 38342436 [PubMed] [Article] [RRC of NBRP] Catalog no. Name of resource Short Description RDB20899 pCDNA3-HygR Mammalian expression vector of hygromicin resistance gene, coding Streptomyces hygroscopicus phosphotransferase. Thermostable kanamycin for microbial gene disruption Directed evolution of thermostable kanamycin-resistance gene: a convenient selection marker for Thermus thermophilus. Hoseki, J., Yano, T., Koyama, Y., Kuramitsu, S., Kagamiyama, H. J. Biochem. 126 (5): 951-956 (1999). PubMed PMID [&hellip;]<\/p>\n","protected":false},"author":13,"featured_media":0,"parent":8163,"menu_order":0,"comment_status":"closed","ping_status":"closed","template":"","meta":{"_seopress_titles_title":"","_seopress_titles_desc":"","_seopress_robots_index":"","_seopress_robots_follow":"","_seopress_robots_imageindex":"","_seopress_robots_snippet":"","_seopress_robots_primary_cat":"","_seopress_robots_breadcrumbs":"","_seopress_robots_freeze_modified_date":"","_seopress_robots_custom_modified_date":"","_seopress_robots_canonical":"","_seopress_social_fb_title":"","_seopress_social_fb_desc":"","_seopress_social_fb_img":"","_seopress_social_fb_img_attachment_id":0,"_seopress_social_fb_img_width":0,"_seopress_social_fb_img_height":0,"_seopress_social_twitter_title":"","_seopress_social_twitter_desc":"","_seopress_social_twitter_img":"","_seopress_social_twitter_img_attachment_id":0,"_seopress_social_twitter_img_width":0,"_seopress_social_twitter_img_height":0,"_seopress_redirections_value":"","_seopress_redirections_enabled":"","_seopress_redirections_enabled_regex":"","_seopress_redirections_logged_status":"both","_seopress_redirections_param":"","_seopress_redirections_type":301,"_seopress_analysis_target_kw":"","footnotes":"","_wp_rev_ctl_limit":""},"class_list":["post-8746","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8746","targetHints":{"allow":["GET"]}}],"collection":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/users\/13"}],"replies":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/comments?post=8746"}],"version-history":[{"count":5,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8746\/revisions"}],"predecessor-version":[{"id":9019,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8746\/revisions\/9019"}],"up":[{"embeddable":true,"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/pages\/8163"}],"wp:attachment":[{"href":"http:\/\/dna.brc.riken.jp\/en\/wp-json\/wp\/v2\/media?parent=8746"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}