DOCSLIB.ORG

Supporting Information for Proteomics DOI 10.1002/Pmic.200600983

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Supporting Information for Proteomics DOI 10.1002/Pmic.200600983 Supporting Information for Proteomics DOI 10.1002/pmic.200600983 Julia Strathmann, Krisztina Paal, Carina Ittrich, Eberhard Krause, Klaus E. Appel, Howard P. Glauert, Albrecht Buchmann and Michael Schwarz Proteome analysis of chemically induced mouse liver tumors with different genotype ª 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim www.proteomics-journal.com A. 2DE pictures Normal liver GS negative GS positive MW pI 3 10 B. Zoomed regions 1. Expression of GS 2. Expression of GST M2 3. A. Expression of MUP 8/11 3. B. Expression of MUP 2 4. Expression of Annexin A2 5. Expression of regucalcin: identified in 3 different spots % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 650.0393 672.0223 666.0108 Acetyl 707.2025 776.1843 842.5089 877.0358 905.6765 967.9841 1066.0697 1150.0699 1143.0863 1281.6 - 1224.1243 CoA acetyltransferase 1307.7966 1335.1716 1404.7513 1531.8387 1621.8403 1684.9310 4700 ReflectorSpec#1[BP=1753.9,424] 1753.9518 1796.9624 1964.2 1875.0048 Q8CAY6 1938.9302 1934.9824 1964.9377 2043.1290 Mass (m/z) 2142.0527 2211.1064 2233.1333 2226.1382 2292.2849 2284.1768 2322.2368 2338.2627 2384.2915 2453.2107 2447.2783 2646.8 2576.3389 2654.2969 2667.3318 2745.3074 2866.4612 , cytosolic 3329.4 3244.7070 , 4012.0 424.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 628.0881 644.0302 666.0172 701.4904 815.4185 842.5089 881.2626 877.0427 870.5422 976.4503 Actin Cytoplasmic 1045.5627 1066.0701 1106.5577 1132.5288 1281.6 1198.7013 1361.8008 1516.7139 P60710, Score152 1629.8191 1688.8756 4700 ReflectorSpec#1[BP=842.5,689] 1794.8589 1790.8900 1964.2 1853.8925 1954.0649 1986.0228 Mass (m/z) 2226.1201 2211.1040 2285.1621 2382.1338 1( 2646.8 2539.1863 beta actin 3329.4 ), 4012.0 688.8 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 656.0695 679.5138 795.4752 856.5247 842.5089 945.5387 Actin Cytoplasmic 976.4440 1045.5591 1106.5510 1132.5244 1164.7384 1281.6 1198.6996 1231.6733 1354.6144 1461.7360 1516.7034 P60710, Score400 1547.7396 1629.8165 4700 ReflectorSpec#1[BP=1198.7,1496] 1746.8453 1790.8829 1838.7776 1964.2 1954.0613 1976.0229 2084.0659 Mass (m/z) 2216.0757 2211.1038 2284.1619 2343.1553 1( 2475.1460 2646.8 2550.1672 beta actin 2750.2891 3137.5925 3199.6357 3329.4 3338.7297 ), 4012.0 1496.5 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 644.3745 758.8766 842.5090 976.4437 Actin Cytoplasmic 1045.5402 1111.6035 1132.5186 1281.8 1171.5673 1198.6964 1236.5779 1354.6180 1499.6642 1516.7151 P60710, Score470 1592.8094 4700 ReflectorSpec#1[BP=1790.9,2808] 1746.8669 1790.8763 1822.7810 1964.6 1915.9297 1960.8990 1954.0522 1993.9595 Mass (m/z) 2211.1038 2215.0554 2284.1641 2343.1519 1( 2647.4 2550.1470 beta actin 2730.3281 2807.3477 3183.5964 3330.2 3251.4219 3338.7551 3413.6157 ), 3491.6208 3555.6621 4013.0 2808.2 Actin Cytoplasmic 1 (beta actin), P60710, Score 393 4700 Reflector Spec #1[BP = 1790.9, 921] 100 1790.8904 921.0 90 80 70 1198.7015 60 50 % Intensity 40 1954.0656 30 20 842.5090 2211.1062 1132.5289 10 1516.7206 666.0146 978.0363 1629.8209 2285.1748 2550.1917 893.0243 1977.0419 1036.6520 795.4677 1812.8555 1221.7039 3199.6316 1744.8641 2384.0688 1315.5662 0 599.0 1281.6 1964.2 2646.8 3329.4 4012.0 Mass (m/z) % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 679.5235 795.4698 842.5089 870.5468 4- 976.4493 mitochondrial precursor 1045.5627 1106.5598 aminobutyrate aminotransferase 1132.5289 1281.8 1187.5555 1198.7042 1231.6796 1282.5927 1354.6279 1475.7566 1461.7422 1516.7252 1547.7468 1623.8331 4700 ReflectorSpec#1[BP=1790.9,1042] 1707.8058 1790.8885 1822.8090 1964.6 1954.0664 1976.9465 2099.0430 Mass (m/z) 2225.1252 2211.1035 2284.1775 2359.1765 2647.4 2567.2017 2628.2463 2870.4541 , P61922 3138.5989 3199.6423 3330.2 3723.9290 4013.0 1041.5 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 679.5110 662.3986 795.4604 842.5090 856.5297 870.5416 Alpha-1- 963.5132 1045.5637 1070.5369 1108.5952 1104.6084 1281.6 1179.5991 1257.6239 1320.5909 1420.7356 1516.7264 1585.7773 antitrypsin 1652.7773 4700 ReflectorSpec#1[BP=1070.5,3904] 1730.9104 1790.8865 1964.2 1851.9172 1940.9385 Q00897 2000.0323 2003.9980 2041.9832 2083.0164 Mass (m/z) 2221.1211 2211.1042 2284.1719 2367.0718 2432.2224 1-4 2646.8 2549.1531 2634.3521 2705.1321 2808.2993 precursor 2914.5293 3028.6248 3090.6089 3329.4 3252.7480 3347.6755 3499.7815 , 3742.4299 4012.0 3904.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 650.0491 666.0205 727.4628 815.5123 877.0413 948.5746 1035.5275 1111.5500 1281.6 1277.7108 1343.8066 1432.6624 1421.6912 Annexin 1470.2003 1491.8658 1560.7603 1542.8427 1628.9364 1650.9790 4700 ReflectorSpec#1[BP=1542.8,4467] 1688.9087 1747.9241 1779.8154 1848.9506 1964.2 1908.8827 1993.9749 2105.0137 A2,P07356 Mass (m/z) 2211.1042 2288.1689 2284.1729 2367.2612 2480.2307 2646.8 2664.3662 2780.9927 2838.4138 2923.3550 2938.3787 2999.3989 3095.6091 3329.4 3339.7539 3635.9451 4012.0 4467.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 660.0098 650.0457 681.9913 666.0161 727.4576 787.4554 881.2709871.0233 Fumarate hydratase 971.2996 1031.5612 1116.60791106.5530 1281.6 1234.6249 1332.6622 1426.8475 1442.8418 1498.8510 1560.7795 precursor 1644.8098 4700 ReflectorSpec#1[BP=1763.9,1423] 1724.8716 1763.9237 1794.7975 1964.2 1853.9353 1927.0150 1988.0818 2070.0591 Mass (m/z) 2141.0850 2225.1213 2211.1040 2284.1694 , P97807 2307.1650 2300.1794 2376.1792 2467.2119 , 2483.2375 mitochondrial 2646.8 2557.2766 2663.3074 2781.4595 2914.5171 3121.5525 3182.5649 3329.4 3286.5994 3347.5845 3496.7319 4012.0 1423.3 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 628.0757 644.0302 666.0161 695.1690 679.5115 771.4939 849.0469 833.0671 871.0224855.0512 907.2377917.2798 996.6064 1082.0454 1106.5570 1150.5891 1281.6 1271.0764 1364.6718 Annexin 1458.7570 1528.7466 1623.7616 4700 ReflectorSpec#1[BP=2212.1,2565] 1704.8688 1794.8191 1964.2 1873.9042 1868.8792 1940.9457 2025.9644 A3,O35639 Mass (m/z) 2137.0820 2211.1040 2239.1331 2225.1233 2284.1772 2314.1941 2300.1794 2402.2681 2480.2939 2646.8 2541.2512 2663.3640 2721.2578 2781.4697 2914.4990 3096.6270 3329.4 3338.7268 4012.0 2564.7 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 666.0195 688.0060 774.8920 842.5090 900.4556 975.4771 1001.5952 1014.5106 1076.0389 1106.5778 1155.5638 1281.6 1234.6713 1268.5865 1290.6289 1432.7452 Annexin 1531.7677 1548.7688 1659.8832 4700 ReflectorSpec#1[BP=1799.9,1055] 1703.8787 1749.8678 1799.8915 1821.8617 1836.9589 1964.2 1942.8949 2005.5322 2022.9894 2109.1582 A5,P48036 Mass (m/z) 2151.0847 2211.1038 2284.1436 2646.8 2915.2512 3329.4 3883.7710 4012.0 1055.4 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 666.0172 Arginase 757.3782 893.0151 948.5461 1010.0403 1082.0381 arginase 1152.5870 1161.6438 1281.6 1285.6378 1357.6819 -1 (TypeI 1456.7607 1460.7017 1444.7058 1635.8414 4700 ReflectorSpec#1[BP=1910.0,3137] 1693.7960 1764.4441 , Q61176,Score588 1822.9733 1964.2 1857.9951 1896.9578 1909.9738 1969.9567 2018.0718 2042.5602 2093.0479 Mass (m/z) 2130.9941 2203.0708 2225.0974 arginase 2284.1897 2502.2231 2646.8 2567.2808 2706.1631 2782.4546 ) livertype 3113.5737 3329.4 3269.7227 3339.7168 3397.8086 3525.8887 4012.0 3136.9 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 628.0848 644.0328 666.0200 697.9635 681.9938 771.4896 842.5089 877.0427 902.9794 948.5489 1009.5405 Arginase 1082.0433 1157.5959 1143.0886 1281.6 1332.6711 1398.6594 1444.7135 1509.6848 1603.8058 1670.8756 4700 ReflectorSpec#1[BP=1911.0,1619] 1693.8060 -1, Q61176,Score158 1812.9609 1964.2 1857.9966 1873.9972 1914.9839 1909.9738 2003.0503 2018.0724 2093.0532 Mass (m/z) 2158.0608 2211.1038 2240.13602225.1221 2284.1716 2314.1970 2299.1892 2403.2839 2463.2268 2646.8 2663.3516 2722.2380 2780.9580 2914.4883 3096.6008 3329.4 3269.7510 3338.7449 3812.6619 4012.0 1618.7 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 639.4114 666.0236 743.4389 831.4809 893.0197 989.5396 1004.5209 Argininsuccinate lyase 1088.5040 1157.5931 1281.6 1253.6364 1265.6147 1315.6487 1373.7021 1445.7462 1481.7059 1549.7283 1620.8109 4700 ReflectorSpec#1[BP=1934.1,1012] 1692.8912 1676.8923 1776.8433 1964.2 1851.9309 1916.0519 1933.0768 2002.0015 2023.0021 2040.0249 2089.1655 Mass (m/z) 2211.1030 2322.0920 2401.2759 2466.1870 2646.8 2534.3523 2622.2751 2705.1702 2780.3923 , Q91YI0 2875.3098 3329.4 3338.7627 3771.9731 4012.0 1012.0 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 672.0247 666.0132 ATP 779.4278 842.5090 877.0328 960.0540 1045.5618 synthasebetachain 1106.5563 1088.6304 1281.6 1168.0807 1262.6412 1314.6086 1391.6755 1401.7020 1406.6768 1435.7455 1475.8306 1555.7953 precursor 1601.8090 1633.8062 1617.8019 4700 ReflectorSpec#1[BP=1989.0,1097] 1762.9443 1780.9612 1842.8795 1964.2 1874.8694 1858.8761 1919.0919 1942.0385 1988.0421 2015.0421 2010.0959 2077.0168 Mass (m/z) 2211.1045 2234.1028 2298.0840 , P56480 2646.8 2563.2476 , 2691.3960 mitochondrial 2836.4041 3042.5957 3329.4 3713.8579 3845.0930 4012.0 1096.6 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 644.0295 666.0146 717.4493 703.9759 787.4315 855.0472 870.5423 881.2572 917.2670 Carbohydrate kinaselikeprotein 1033.5331 1113.5402 1106.5465 1281.6 1236.6642 1270.1685 1368.6932 1400.6836 1552.8191 1645.8466 1625.8618 4700 ReflectorSpec#1[BP=2212.1,778] 1756.9755 1794.8038 1964.2 1891.0143 Q9D5J6 2050.0471 2065.0532 Mass (m/z) 2140.9192 2156.1602 2204.2209 2211.1055 2300.1746 2284.1809 2402.2478 2477.3723 2646.8 2538.3433 2628.4019 2749.3279 3023.6658 3104.6924 3329.4 3326.7659 , 4012.0 778.2 % Intensity 100 10 20 30 40 50 60 70 80 90 599.0 0 666.0200 679.5151 741.4979 Carbonic anhydrase 842.5089 856.5272 870.5426 903.4647 938.6435 1026.9664 1042.5194 1106.5472
Load more

Recommended publications
  • The Rise and Fall of the Bovine Corpus Luteum
    University of Nebraska Medical Center DigitalCommons@UNMC Theses & Dissertations Graduate Studies Spring 5-6-2017 The Rise and Fall of the Bovine Corpus Luteum Heather Talbott University of Nebraska Medical Center Follow this and additional works at: https://digitalcommons.unmc.edu/etd Part of the Biochemistry Commons, Molecular Biology Commons, and the Obstetrics and Gynecology Commons Recommended Citation Talbott, Heather, "The Rise and Fall of the Bovine Corpus Luteum" (2017). Theses & Dissertations. 207. https://digitalcommons.unmc.edu/etd/207 This Dissertation is brought to you for free and open access by the Graduate Studies at DigitalCommons@UNMC. It has been accepted for inclusion in Theses & Dissertations by an authorized administrator of DigitalCommons@UNMC. For more information, please contact [email protected]. THE RISE AND FALL OF THE BOVINE CORPUS LUTEUM by Heather Talbott A DISSERTATION Presented to the Faculty of the University of Nebraska Graduate College in Partial Fulfillment of the Requirements for the Degree of Doctor of Philosophy Biochemistry and Molecular Biology Graduate Program Under the Supervision of Professor John S. Davis University of Nebraska Medical Center Omaha, Nebraska May, 2017 Supervisory Committee: Carol A. Casey, Ph.D. Andrea S. Cupp, Ph.D. Parmender P. Mehta, Ph.D. Justin L. Mott, Ph.D. i ACKNOWLEDGEMENTS This dissertation was supported by the Agriculture and Food Research Initiative from the USDA National Institute of Food and Agriculture (NIFA) Pre-doctoral award; University of Nebraska Medical Center Graduate Student Assistantship; University of Nebraska Medical Center Exceptional Incoming Graduate Student Award; the VA Nebraska-Western Iowa Health Care System Department of Veterans Affairs; and The Olson Center for Women’s Health, Department of Obstetrics and Gynecology, Nebraska Medical Center.
    [Show full text]
  • Annexin A2 Flop-Out Mediates the Non-Vesicular Release of Damps/Alarmins from C6 Glioma Cells Induced by Serum-Free Conditions
    cells Article Annexin A2 Flop-Out Mediates the Non-Vesicular Release of DAMPs/Alarmins from C6 Glioma Cells Induced by Serum-Free Conditions Hayato Matsunaga 1,2,† , Sebok Kumar Halder 1,3,† and Hiroshi Ueda 1,4,* 1 Pharmacology and Therapeutic Innovation, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8521, Japan; [email protected] (H.M.); [email protected] (S.K.H.) 2 Department of Medical Pharmacology, Graduate School of Biomedical Sciences, Nagasaki University, Nagasaki 852-8523, Japan 3 San Diego Biomedical Research Institute, San Diego, CA 92121, USA 4 Department of Molecular Pharmacology, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan * Correspondence: [email protected]; Tel.: +81-75-753-4536 † These authors contributed equally to this work. Abstract: Prothymosin alpha (ProTα) and S100A13 are released from C6 glioma cells under serum- free conditions via membrane tethering mediated by Ca2+-dependent interactions between S100A13 and p40 synaptotagmin-1 (Syt-1), which is further associated with plasma membrane syntaxin-1 (Stx-1). The present study revealed that S100A13 interacted with annexin A2 (ANXA2) and this interaction was enhanced by Ca2+ and p40 Syt-1. Amlexanox (Amx) inhibited the association between S100A13 and ANXA2 in C6 glioma cells cultured under serum-free conditions in the in situ proximity ligation assay. In the absence of Amx, however, the serum-free stress results in a flop-out of ANXA2 Citation: Matsunaga, H.; Halder, through the membrane, without the extracellular release. The intracellular delivery of anti-ANXA2 S.K.; Ueda, H. Annexin A2 Flop-Out antibody blocked the serum-free stress-induced cellular loss of ProTα, S100A13, and Syt-1.
    [Show full text]
  • Supplemental Table 3 - Male Genes Differentially Expressed > 1.5-Fold Among Strains in E11.5 XY Gonads
    Supplemental Table 3 - Male genes differentially expressed > 1.5-fold among strains in E11.5 XY gonads. Male genes differentially expressed between C57BL/6J and 129S1/SvImJ. Note: Positive fold values reflect male genes that are up regulated in C57BL/6J relative to 129S1/SvImJ. Fold Diff Gene symbol Genbank acc Description 10.77 Gcnt1 NM_173442 Mus musculus glucosaminyl (N-acetyl) transferase 1, core 2 (Gcnt1), mRNA [NM_173442] 5.50 Afp NM_007423 Mus musculus alpha fetoprotein (Afp), mRNA [NM_007423] 4.95 Hnf4a NM_008261 Mus musculus hepatic nuclear factor 4, alpha (Hnf4a), mRNA [NM_008261] 4.71 Ppp1r14c AK082372 Mus musculus 0 day neonate cerebellum cDNA, RIKEN full-length enriched library, clone:C230042N14 product:hypothetical protein, full insert sequence. [AK082372] 4.41 Gorasp2 AK020521 Mus musculus 12 days embryo embryonic body between diaphragm region and neck cDNA, RIKEN full-length enriched library, clone:9430094F20 product:inferred: golgi reassembly stacking protein 2, full insert sequence. [AK020521] 3.69 Tmc7 NM_172476 Mus musculus transmembrane channel-like gene family 7 (Tmc7), mRNA [NM_172476] 2.97 Mt2 NM_008630 Mus musculus metallothionein 2 (Mt2), mRNA [NM_008630] 2.62 Gstm6 NM_008184 Mus musculus glutathione S-transferase, mu 6 (Gstm6), mRNA [NM_008184] 2.43 Adhfe1 NM_175236 Mus musculus alcohol dehydrogenase, iron containing, 1 (Adhfe1), mRNA [NM_175236] 2.38 Txndc2 NM_153519 Mus musculus thioredoxin domain containing 2 (spermatozoa) (Txndc2), mRNA [NM_153519] 2.30 C030038J10Rik AK173336 Mus musculus mRNA for mKIAA2027
    [Show full text]
  • Annexin A1 Is a New Functional Linker Between Actin Filaments and Phagosomes During Phagocytosis
    578 Research Article Annexin A1 is a new functional linker between actin filaments and phagosomes during phagocytosis Devang M. Patel1, Syed Furquan Ahmad1, Dieter G. Weiss1, Volker Gerke2 and Sergei A. Kuznetsov1,* 1Institute of Biological Sciences, Cell Biology and Biosystems Technology, University of Rostock, Albert-Einstein Straße 3, Rostock 18059, Germany 2Institute of Medical Biochemistry, Centre for Molecular Biology of Inflammation, University of Münster, Von-Esmarch-Straße 56, Münster 48149, Germany *Author for correspondence ([email protected]) Accepted 19 October 2010 Journal of Cell Science 124, 578-588 © 2011. Published by The Company of Biologists Ltd doi:10.1242/jcs.076208 Summary Remodelling of the actin cytoskeleton plays a key role in particle internalisation and the phagosome maturation processes. Actin- binding proteins (ABPs) are the main players in actin remodelling but the precise role of these proteins in phagocytosis needs to be clarified. Annexins, a group of ABPs, are known to be present on phagosomes. Here, we identified annexin A1 as a factor that binds to isolated latex bead phagosomes (LBPs) in the presence of Ca2+ and facilitates the F-actin–LBP interaction in vitro. In macrophages the association of endogenous annexin A1 with LBP membranes was strongly correlated with the spatial and temporal accumulation of F-actin at the LBP. Annexin A1 was found on phagocytic cups and around early phagosomes, where the F-actin was prominently concentrated. After uptake was completed, annexin A1, along with F-actin, dissociated from the nascent LBP surface. At later stages of phagocytosis annexin A1 transiently concentrated only around those LBPs that showed transient F-actin accumulation (‘actin flashing’).
    [Show full text]
  • Journal of Proteomics 151 (2017) 131–144
    Journal of Proteomics 151 (2017) 131–144 Contents lists available at ScienceDirect Journal of Proteomics journal homepage: www.elsevier.com/locate/jprot Profiling the proteomics in honeybee worker brains submitted to the proboscis extension reflex Anally Ribeiro da Silva Menegasso a,MarcelPratavieiraa, Juliana de Saldanha da Gama Fischer b, Paulo Costa Carvalho b, Thaisa Cristina Roat a, Osmar Malaspina a, Mario Sergio Palma a,⁎ a Center of the Study of Social Insects, Department of Biology, Institute of Biosciences of Rio Claro, São Paulo State University (UNESP), Rio Claro, SP 13500, Brazil b Laboratory for Proteomics and Protein Engineering, Carlos Chagas Institute, Fiocruz, Paraná, Brazil article info abstract Article history: The proboscis extension reflex (PER) is an unconditioned stimulus (US) widely used to access the ability of hon- Received 13 January 2016 eybees to correlate it with a conditioned stimulus (CS) during learning and memory acquisition. However, little is Received in revised form 20 May 2016 known about the biochemical/genetic changes in worker honeybee brains induced by the PER alone. The present Accepted 25 May 2016 investigation profiled the proteomic complement associated with the PER to further the understanding of the Available online 31 May 2016 major molecular transformations in the honeybee brain during the execution of a US. In the present study, a quantitative shotgun proteomic approach was employed to assign the proteomic complement of the honeybee Keywords: Neuroproteomics brain. The results were analyzed under the view of protein networking for different processes involved in PER be- Shotgun havior. In the brains of PER-stimulated individuals, the metabolism of cyclic/heterocyclic/aromatic compounds Label-free quantitation was activated in parallel with the metabolism of nitrogenated compounds, followed by the up-regulation of car- Honeybee bohydrate metabolism, the proteins involved with the anatomic and cytoskeleton; the down-regulation of the Memory anatomic development and cell differentiation in other neurons also occurred.
    [Show full text]
  • 2812 Matrix Vesicles: Structure, Composition, Formation and Function in Ca
    [Frontiers in Bioscience 16, 2812-2902, June 1, 2011] Matrix vesicles: structure, composition, formation and function in calcification Roy E. Wuthier Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208 TABLE OF CONTENTS 1. Abstract 2. Introduction 3. Morphology of matrix vesicles (MVs) 3.1. Conventional transmission electron microscopy 3.2. Cryofixation, freeze-substitution electron microscopy 3.3. Freeze-fracture studies 4. Isolation of MVs 4.1. Crude collagenase digestion methods 4.2. Non-collagenase dependent methods 4.3. Cell culture methods 4.4. Modified collagenase digestion methods 4.5. Other isolation methods 5. MV proteins 5.1. Early SDS-PAGE studies 5.2. Isolation and identification of major MV proteins 5.3. Sequential extraction, separation and characterization of major MV proteins 5.4. Proteomic characterization of MV proteins 6. MV-associated extracellular matrix proteins 6.1. Type VI collagen 6.2. Type X collagen 6.3. Proteoglycan link protein and aggrecan core protein 6.4. Fibrillin-1 and fibrillin-2 7. MV annexins – acidic phospholipid-dependent ca2+-binding proteins 7.1. Annexin A5 7.2. Annexin A6 7.3. Annexin A2 7.4. Annexin A1 7.5. Annexin A11 and Annexin A4 8. MV enzymes 8.1. Tissue-nonspecific alkaline phosphatase(TNAP) 8.1.1. Molecular structure 8.1.2. Amino acid sequence 8.1.3. 3-D structure 8.1.4. Disposition in the MV membrane 8.1.5. Catalytic properties 8.1.6. Collagen-binding properties 8.2. Nucleotide pyrophosphate phosphodiesterase (NPP1, PC1) 8.3. PHOSPHO-1 (Phosphoethanolamine/Phosphocholine phosphatase 8.4. Acid phosphatase 8.5.
    [Show full text]
  • Changes in the Cytosolic Proteome of Aedes Malpighian Tubules
    329 The Journal of Experimental Biology 212, 329-340 Published by The Company of Biologists 2009 doi:10.1242/jeb.024646 Research article Signaling to the apical membrane and to the paracellular pathway: changes in the cytosolic proteome of Aedes Malpighian tubules Klaus W. Beyenbach1,*, Sabine Baumgart2, Kenneth Lau1, Peter M. Piermarini1 and Sheng Zhang2 1Department of Biomedical Sciences, VRT 8004, Cornell University, Ithaca, NY 14853, USA and 2Proteomics and Mass Spectrometry Core Facility, 143 Biotechnology Building, Cornell University, Ithaca, NY 14853, USA *Author for correspondence (e-mail: [email protected]) Accepted 6 November 2008 Summary Using a proteomics approach, we examined the post-translational changes in cytosolic proteins when isolated Malpighian tubules of Aedes aegypti were stimulated for 1 min with the diuretic peptide aedeskinin-III (AK-III, 10–7 mol l–1). The cytosols of control (C) and aedeskinin-treated (T) tubules were extracted from several thousand Malpighian tubules, subjected to 2-D electrophoresis and stained for total proteins and phosphoproteins. The comparison of C and T gels was performed by gel image analysis for the change of normalized spot volumes. Spots with volumes equal to or exceeding C/T ratios of ±1.5 were robotically picked for in- gel digestion with trypsin and submitted for protein identification by nanoLC/MS/MS analysis. Identified proteins covered a wide range of biological activity. As kinin peptides are known to rapidly stimulate transepithelial secretion of electrolytes and water by Malpighian tubules, we focused on those proteins that might mediate the increase in transepithelial secretion. We found that AK- III reduces the cytosolic presence of subunits A and B of the V-type H+ ATPase, endoplasmin, calreticulin, annexin, type II regulatory subunit of protein kinase A (PKA) and rab GDP dissociation inhibitor and increases the cytosolic presence of adducin, actin, Ca2+-binding protein regucalcin/SMP30 and actin-depolymerizing factor.
    [Show full text]
  • Transcriptomic and Proteomic Profiling Provides Insight Into
    BASIC RESEARCH www.jasn.org Transcriptomic and Proteomic Profiling Provides Insight into Mesangial Cell Function in IgA Nephropathy † † ‡ Peidi Liu,* Emelie Lassén,* Viji Nair, Celine C. Berthier, Miyuki Suguro, Carina Sihlbom,§ † | † Matthias Kretzler, Christer Betsholtz, ¶ Börje Haraldsson,* Wenjun Ju, Kerstin Ebefors,* and Jenny Nyström* *Department of Physiology, Institute of Neuroscience and Physiology, §Proteomics Core Facility at University of Gothenburg, University of Gothenburg, Gothenburg, Sweden; †Division of Nephrology, Department of Internal Medicine and Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, Michigan; ‡Division of Molecular Medicine, Aichi Cancer Center Research Institute, Nagoya, Japan; |Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden; and ¶Integrated Cardio Metabolic Centre, Karolinska Institutet Novum, Huddinge, Sweden ABSTRACT IgA nephropathy (IgAN), the most common GN worldwide, is characterized by circulating galactose-deficient IgA (gd-IgA) that forms immune complexes. The immune complexes are deposited in the glomerular mesangium, leading to inflammation and loss of renal function, but the complete pathophysiology of the disease is not understood. Using an integrated global transcriptomic and proteomic profiling approach, we investigated the role of the mesangium in the onset and progression of IgAN. Global gene expression was investigated by microarray analysis of the glomerular compartment of renal biopsy specimens from patients with IgAN (n=19) and controls (n=22). Using curated glomerular cell type–specific genes from the published literature, we found differential expression of a much higher percentage of mesangial cell–positive standard genes than podocyte-positive standard genes in IgAN. Principal coordinate analysis of expression data revealed clear separation of patient and control samples on the basis of mesangial but not podocyte cell–positive standard genes.
    [Show full text]
  • Calcium-Binding Proteins Annexin A2 and S100A6 Are Sensors of Tubular Injury and Recovery in Acute Renal Failure
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Elsevier - Publisher Connector Kidney International, Vol. 68 (2005), pp. 2694–2703 Calcium-binding proteins annexin A2 and S100A6 are sensors of tubular injury and recovery in acute renal failure CHAO-WEN CHENG,ABDALLA RIFAI,SHUK-MAN KA,HAO-AI SHUI,YUH-FENG LIN,WEI-HWA LEE, and ANN CHEN Graduate Institute of Life Sciences, Graduate Institute of Medical Sciences, Department of Internal Medicine, Department of Pathology, Tri-Service General Hospital, National Defense Medical Center, Taiwan, Republic of China; and Department of Pathology, Rhode Island Hospital, Rhode Island Calcium-binding proteins annexin A2 and S100A6 are sensors Acute tubular necrosis is the most common pathologic of tubular injury and recovery in acute renal failure. entity responsible for the clinical state of acute renal fail- Background. Rise in cellular calcium is associated with acute ure (ARF) [1, 2]. The two main causes of acute tubu- tubular necrosis, the most common cause of acute renal failure (ARF). The mechanisms that calcium signaling induce in the lar necrosis are ischemic and toxic injuries [3]. In the quiescent tubular cells to proliferate and differentiate during latter type, a variety of renal environmental substances acute tubular necrosis have not been elucidated. that include heavy metals such as mercury, lead, and ura- Methods. Acute tubular necrosis induced in mice by sin- nium are known to cause ARF.Nephrotoxic acute tubular gle intravenous injection of uranyl nitrate and examined af- necrosis is histologically evident as epithelial cell necrosis, ter 1, 3, 7, and 14 days.
    [Show full text]
  • Annexin A2 Complexes with S100 Proteins
    British Journal of DOI:10.1111/bph.12978 www.brjpharmacol.org BJP Pharmacology Themed Section: Annexins VII Programme Correspondence Dr Lodewijk V Dekker, School of Pharmacy, Centre for REVIEW Biomolecular Sciences, University of Nottingham, Nottingham NG7 2RD, UK. E-mail: Annexin A2 complexes [email protected] ---------------------------------------------------------------- Received with S100 proteins: 18 July 2014 Revised 16 September 2014 structure, function and Accepted 5 October 2014 pharmacological manipulation Yidong Liu, Helene K Myrvang and Lodewijk V Dekker School of Pharmacy, Centre for Biomolecular Sciences, University of Nottingham, Nottingham, UK Annexin A2 (AnxA2) was originally identified as a substrate of the pp60v-src oncoprotein in transformed chicken embryonic fibroblasts. It is an abundant protein that associates with biological membranes as well as the actin cytoskeleton, and has been implicated in intracellular vesicle fusion, the organization of membrane domains, lipid rafts and membrane-cytoskeleton contacts. In addition to an intracellular role, AnxA2 has been reported to participate in processes localized to the cell surface including extracellular protease regulation and cell-cell interactions. There are many reports showing that AnxA2 is differentially expressed between normal and malignant tissue and potentially involved in tumour progression. An important aspect of AnxA2 function relates to its interaction with small Ca2+-dependent adaptor proteins called S100 proteins, which is the topic of this review. The interaction between AnxA2 and S100A10 has been very well characterized historically; more recently, other S100 proteins have been shown to interact with AnxA2 as well. The biochemical evidence for the occurrence of these protein interactions will be discussed, as well as their function.
    [Show full text]
  • Structure – Function Studies of Annexin A2 & A5
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by University of Minnesota Digital Conservancy Structure – Function Studies of Annexin A2 & A5 Stephanie Schramel Swenson College of Science and Engineering University of Minnesota Duluth [email protected] Introduction: Within the cell, proteins exist to maintain the intracellular level of calcium ions (Ca2+), allowing calcium to act as a secondary messenger. Annexins are a group of these proteins located in muscle cells which bind calcium in order to bind to phospholipids in the plasma membrane. Although there are multiple forms of this protein found in humans, all contain a similar structural basis consisting of an amino-terminal head domain, a carboxyl terminal domain, and conserved structural repeats of around 70 residues. Both the calcium binding and membrane binding sites are located at the carboxyl domain. Annexins bind to negatively charged phospholipids at the cellular membranes, which differentiates them from other calcium binding proteins. Exocytosis/endocytosis, ion transport, and transport of vesicles are also processes orchestrated by these proteins.1 Specifically, annexin A2 (AnxA2) and A5 (AnxA5) are the proteins we studied. Figure 1 shows the 3-D structure of AnxA2 with calcium bound. The question we tried to understand is the mechanism for how AnxA2 and AnxA5 function at the membrane in terms of the redistribution of lipids and the effect on membrane permeability. In order to study the annexins, we grew E. coli cells that expressed our desired proteins. We then went through multiple week- long purification processes to obtain pure protein to be used for further studies.
    [Show full text]
  • Human Induced Pluripotent Stem Cell–Derived Podocytes Mature Into Vascularized Glomeruli Upon Experimental Transplantation
    BASIC RESEARCH www.jasn.org Human Induced Pluripotent Stem Cell–Derived Podocytes Mature into Vascularized Glomeruli upon Experimental Transplantation † Sazia Sharmin,* Atsuhiro Taguchi,* Yusuke Kaku,* Yasuhiro Yoshimura,* Tomoko Ohmori,* ‡ † ‡ Tetsushi Sakuma, Masashi Mukoyama, Takashi Yamamoto, Hidetake Kurihara,§ and | Ryuichi Nishinakamura* *Department of Kidney Development, Institute of Molecular Embryology and Genetics, and †Department of Nephrology, Faculty of Life Sciences, Kumamoto University, Kumamoto, Japan; ‡Department of Mathematical and Life Sciences, Graduate School of Science, Hiroshima University, Hiroshima, Japan; §Division of Anatomy, Juntendo University School of Medicine, Tokyo, Japan; and |Japan Science and Technology Agency, CREST, Kumamoto, Japan ABSTRACT Glomerular podocytes express proteins, such as nephrin, that constitute the slit diaphragm, thereby contributing to the filtration process in the kidney. Glomerular development has been analyzed mainly in mice, whereas analysis of human kidney development has been minimal because of limited access to embryonic kidneys. We previously reported the induction of three-dimensional primordial glomeruli from human induced pluripotent stem (iPS) cells. Here, using transcription activator–like effector nuclease-mediated homologous recombination, we generated human iPS cell lines that express green fluorescent protein (GFP) in the NPHS1 locus, which encodes nephrin, and we show that GFP expression facilitated accurate visualization of nephrin-positive podocyte formation in
    [Show full text]