The Hypothesis That Helicobacter Pylori Predisposes to Alzheimer's
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Gene Symbol Gene Description ACVR1B Activin a Receptor, Type IB
Table S1. Kinase clones included in human kinase cDNA library for yeast two-hybrid screening Gene Symbol Gene Description ACVR1B activin A receptor, type IB ADCK2 aarF domain containing kinase 2 ADCK4 aarF domain containing kinase 4 AGK multiple substrate lipid kinase;MULK AK1 adenylate kinase 1 AK3 adenylate kinase 3 like 1 AK3L1 adenylate kinase 3 ALDH18A1 aldehyde dehydrogenase 18 family, member A1;ALDH18A1 ALK anaplastic lymphoma kinase (Ki-1) ALPK1 alpha-kinase 1 ALPK2 alpha-kinase 2 AMHR2 anti-Mullerian hormone receptor, type II ARAF v-raf murine sarcoma 3611 viral oncogene homolog 1 ARSG arylsulfatase G;ARSG AURKB aurora kinase B AURKC aurora kinase C BCKDK branched chain alpha-ketoacid dehydrogenase kinase BMPR1A bone morphogenetic protein receptor, type IA BMPR2 bone morphogenetic protein receptor, type II (serine/threonine kinase) BRAF v-raf murine sarcoma viral oncogene homolog B1 BRD3 bromodomain containing 3 BRD4 bromodomain containing 4 BTK Bruton agammaglobulinemia tyrosine kinase BUB1 BUB1 budding uninhibited by benzimidazoles 1 homolog (yeast) BUB1B BUB1 budding uninhibited by benzimidazoles 1 homolog beta (yeast) C9orf98 chromosome 9 open reading frame 98;C9orf98 CABC1 chaperone, ABC1 activity of bc1 complex like (S. pombe) CALM1 calmodulin 1 (phosphorylase kinase, delta) CALM2 calmodulin 2 (phosphorylase kinase, delta) CALM3 calmodulin 3 (phosphorylase kinase, delta) CAMK1 calcium/calmodulin-dependent protein kinase I CAMK2A calcium/calmodulin-dependent protein kinase (CaM kinase) II alpha CAMK2B calcium/calmodulin-dependent -
Defective Lymphocyte Chemotaxis in Я-Arrestin2- and GRK6-Deficient Mice
Defective lymphocyte chemotaxis in -arrestin2- and GRK6-deficient mice Alan M. Fong*, Richard T. Premont*, Ricardo M. Richardson*, Yen-Rei A. Yu†, Robert J. Lefkowitz*‡§, and Dhavalkumar D. Patel*†¶ Departments of *Medicine, ‡Biochemistry, and †Immunology, and §Howard Hughes Medical Institute, Duke University Medical Center, Durham, NC 27710 Contributed by Robert J. Lefkowitz, April 4, 2002 Lymphocyte chemotaxis is a complex process by which cells move kinase, extracellular receptor kinase, and c-jun terminal kinase within tissues and across barriers such as vascular endothelium and activation (9–12), they might also act as positive regulators of is usually stimulated by chemokines such as stromal cell-derived chemotaxis. To evaluate the role of the GRK-arrestin pathway factor-1 (CXCL12) acting via G protein-coupled receptors. Because in chemotaxis, we studied the chemotactic responses of lym- members of this receptor family are regulated (‘‘desensitized’’) by phocytes from -arrestin- and GRK-deficient mice toward G protein-coupled receptor kinase (GRK)-mediated receptor phos- gradients of stromal cell-derived factor 1 (CXCL12), a well  phorylation and -arrestin binding, we examined signaling and characterized chemokine whose receptor is CXCR4, a core- chemotactic responses in splenocytes derived from knockout mice ceptor for HIV. deficient in various -arrestins and GRKs, with the expectation that these responses might be enhanced. Knockouts of -arrestin2, Materials and Methods GRK5, and GRK6 were examined because all three proteins are :expressed at high levels in purified mouse CD3؉ T and B220؉ B Mice. The following mouse strains were used in this study splenocytes. CXCL12 stimulation of membrane GTPase activity was -arrestin2-deficient (back-crossed for six generations onto the unaffected in splenocytes derived from GRK5-deficient mice but C57͞BL6 background; ref. -
Core Lab Brochure
CHOOSE THE MOST TRUSTED LONG-READ TECHNOLOGY FOR YOUR CORE Sequence with Confidence The Sequel® II and IIe Systems are powered by Single Molecule, Real-Time (SMRT®) Sequencing, a technology proven to produce highly accurate long reads, known as HiFi reads, for sequencing data you and your customers can trust. SMRT SEQUENCING IS SMART BUSINESS HiFi Reads: PacBio is the only sequencing technology to offer highly accurate long reads. Because HiFi reads are extremely accurate, downstream analysis is simplified and streamlined, requiring less compute time than the error-prone long reads of other technologies. High Throughput: The Sequel II and IIe Systems have high data yields on robust, highly automated platforms to increase productivity and reduce project costs. Efficient and Easy-To-Use Workflows: Our end-to-end solutions feature library preparation in <3 hours and many push- button analysis workflows, so you can run projects quickly and easily. Support: All of our products are backed by a global team of scientists, bioinformaticians, and engineers who stand ready to provide you with outstanding service. OUTSTANDING PERFORMANCE AND RELIABILITY 99% of runs on the Sequel II System completed successfully Sequel II Systems provide reliable performance with the total bases produced by the PacBio fleet steadily increasing, and 99% of runs completed successfully. “In our experience, the Sequel II System was essentially production-ready right out of the box. We have used it for a range of applications and sample types — from human genome sequencing to metagenome and microbiome profiling to non-model plant and animal genomes — and results have been very good.” — Luke Tallon, Director of the Genomics Resource Center at Maryland Genomics pacb.com/Sequel SMRT SEQUENCING APPLICATIONS – EFFICIENT AND COST EFFECTIVE The Sequel II and IIe Systems support a wide range of applications, each adding unique value to a sequencing study. -
Combined Integrin Phosphoproteomic Analyses and Small Interfering RNA–Based Functional Screening Identify Key Regulators for Cancer Cell Adhesion and Migration
Published OnlineFirst April 7, 2009; DOI: 10.1158/0008-5472.CAN-08-2515 Published Online First on April 7, 2009 as 10.1158/0008-5472.CAN-08-2515 Research Article Combined Integrin Phosphoproteomic Analyses and Small Interfering RNA–Based Functional Screening Identify Key Regulators for Cancer Cell Adhesion and Migration Yanling Chen,1 Bingwen Lu,2 Qingkai Yang,1 Colleen Fearns,3 John R. Yates III,2 and Jiing-Dwan Lee1 Departments of 1Immunology, 2Chemical Physiology, and 3Chemistry, The Scripps Research Institute, La Jolla, California Abstract cytoskeletal components (2, 7) and regulation of cell survival, Integrins interact with extracellular matrix (ECM) and deliver proliferation, differentiation, cell cycle, and migration (8, 9). Understanding the mechanism by which integrins modulate these intracellular signaling for cell proliferation, survival, and motility. During tumor metastasis, integrin-mediated cell cellular activities is of significant biological importance. adhesion to and migration on the ECM proteins are required The most common cancers in human include breast cancer, for cancer cell survival and adaptation to the new microen- prostate cancer, lung cancer, colon cancer, and ovarian cancer (10, 11), and their metastasis is the leading cause of mortality in vironment. Using stable isotope labeling by amino acids in cell cancer patients, causing 90% of deaths from solid tumors (11, 12). culture–mass spectrometry, we profiled the phosphoproteo- During the process of metastasis, tumor cells leave the primary mic changes induced by the interactions of cell integrins with site, travel via blood and/or lymphatic circulatory systems, attach type I collagen, the most common ECM substratum. Integrin- to the substratum of ECM at a distant site, and establish a ECM interactions modulate phosphorylation of 517 serine, secondary tumor, accompanied by angiogenesis of the newly threonine, or tyrosine residues in 513 peptides, corresponding formed neoplasm (12). -
Ran Activation Assay Kit
Product Manual Ran Activation Assay Kit Catalog Number STA-409 20 assays FOR RESEARCH USE ONLY Not for use in diagnostic procedures Introduction Small GTP-binding proteins (or GTPases) are a family of proteins that serve as molecular regulators in signaling transduction pathways. Ran, a 25 kDa protein of the Ras superfamily, regulates a variety of biological response pathways that include DNA synthesis, cell cycle progression, and translocation of RNA/proteins through the nuclear pore complex. Like other small GTPases, Ran regulates molecular events by cycling between an inactive GDP-bound form and an active GTP-bound form. In its active (GTP-bound) state, Ran binds specifically to RanBP1 to control downstream signaling cascades. Cell Biolabs’ Ran Activation Assay Kit utilizes RanBP1 Agarose beads to selectively isolate and pull- down the active form of Ran from purified samples or endogenous lysates. Subsequently, the precipitated GTP-Ran is detected by western blot analysis using an anti-Ran antibody. Cell Biolabs’ Ran Activation Assay Kit provides a simple and fast tool to monitor the activation of Ran. The kit includes easily identifiable RanBP1 Agarose beads (see Figure 1), pink in color, and a GTPase Immunoblot Positive Control for quick Ran identification. Each kit provides sufficient quantities to perform 20 assays. Figure 1: RanBP1 Agarose beads, in color, are easy to visualize, minimizing potential loss during washes and aspirations. 2 Assay Principle Related Products 1. STA-400: Pan-Ras Activation Assay Kit 2. STA-400-H: H-Ras Activation Assay Kit 3. STA-400-K: K-Ras Activation Assay Kit 4. STA-400-N: N-Ras Activation Assay Kit 5. -
The Drug Sensitivity and Resistance Testing (DSRT) Approach
A phenotypic screening and machine learning platform eciently identifies triple negative breast cancer-selective and readily druggable targets Prson Gautam 1 Alok Jaiswal 1 Tero Aittokallio 1, 2 Hassan Al Ali 3 Krister Wennerberg 1,4 Identifying eective oncogenic targets is challenged by the complexity of genetic alterations in 1Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Finland cancer and their poorly understood relation to cell function and survival. There is a need for meth- Current kinome coverage of kinase inhibitors in TNBC exhibit diverse kinase dependencies MFM-223 is selectively addicted to FGFR2 2Department of Mathematics and Statistics, University of Turku, Finland 3The Miami Project to Cure Paralysis, Peggy and Harold Katz Family Drug Discovery Center, A A Sylvester Comprehensive Cancer Center, and Department of Neurological Surgery and Medicine ods that rapidly and accurately identify “pharmacologically eective” targets without the require- clinical evaluation TN Kinases MFM-223 CAL-120 MDA-MB-231 TNBC TNBC TNBC TNBC TNBC TNBC HER2+ 100 University of Miami Miller School of Medicine, Miami, FL 33136, USA. non- HER2+ FGFR1 0.97 0.00 0.00 MFM-223 BL1 BL2 M MSL IM LAR ER+, PR+ 50 ment for priori knowledge of complex signaling networks. We developed an approach that uses ma- cancerous FGFR2 56.46 0.00 0.00 CAL-120 25 4 MDA-MB-231 Biotech Research & Innovation Centre (BRIC) and Novo Nordisk Foundation Center HCC1937 CAL-85-1 CAL-120 MDA-MB-231 DU4475 CAL-148 MCF-10A SK-BR-3 BT-474 FGFR3 25.10 0.00 0.00 0 chine learning to relate results from unbiased phenotypic screening of kinase inhibitors to their bio- for Stem Cell Biology (DanStem), University of Copenhagen, Denmark HCC1599 HDQ-P1 BT-549 MDA-MB-436 MFM-223 FGFR4 0.00 0.00 0.00 MAXIS*Bk Clinical status MDA-MB-468 CAL-51 Hs578T MDA-MB-453 score chemical activity data. -
Overexpression of Salicylic Acid Carboxyl Methyltransferase (Cssamt1) Enhances Tolerance to Huanglongbing Disease in Wanjincheng Orange (Citrus Sinensis (L.) Osbeck)
International Journal of Molecular Sciences Article Overexpression of Salicylic Acid Carboxyl Methyltransferase (CsSAMT1) Enhances Tolerance to Huanglongbing Disease in Wanjincheng Orange (Citrus sinensis (L.) Osbeck) Xiuping Zou * , Ke Zhao, Yunuo Liu, Meixia Du, Lin Zheng, Shuai Wang, Lanzhen Xu, Aihong Peng, Yongrui He, Qin Long and Shanchun Chen * Citrus Research Institute, Southwest University/Chinese Academy of Agricultural Sciences, Chongqing 400716, China; [email protected] (K.Z.); [email protected] (Y.L.); [email protected] (M.D.); [email protected] (L.Z.); [email protected] (S.W.); [email protected] (L.X.); [email protected] (A.P.); [email protected] (Y.H.); [email protected] (Q.L.) * Correspondence: [email protected] (X.Z.); [email protected] (S.C.) Abstract: Citrus Huanglongbing (HLB) disease or citrus greening is caused by Candidatus Liberibacter asiaticus (Las) and is the most devastating disease in the global citrus industry. Salicylic acid (SA) plays a central role in regulating plant defenses against pathogenic attack. SA methyltransferase (SAMT) modulates SA homeostasis by converting SA to methyl salicylate (MeSA). Here, we report on the functions of the citrus SAMT (CsSAMT1) gene from HLB-susceptible Wanjincheng orange Citation: Zou, X.; Zhao, K.; Liu, Y.; (Citrus sinensis (L.) Osbeck) in plant defenses against Las infection. The CsSAMT1 cDNA was Du, M.; Zheng, L.; Wang, S.; Xu, L.; expressed in yeast. Using in vitro enzyme assays, yeast expressing CsSAMT1 was confirmed to Peng, A.; He, Y.; Long, Q.; et al. specifically catalyze the formation of MeSA using SA as a substrate. Transgenic Wanjincheng orange Overexpression of Salicylic Acid plants overexpressing CsSAMT1 had significantly increased levels of SA and MeSA compared to Carboxyl Methyltransferase wild-type controls. -
Investigating the Role of Cdk11in Animal Cytokinesis
Investigating the Role of CDK11 in Animal Cytokinesis by Thomas Clifford Panagiotou A thesis submitted in conformity with the requirements for the degree of Master of Science Department of Molecular Genetics University of Toronto © Copyright by Thomas Clifford Panagiotou (2020) Investigating the Role of CDK11 in Animal Cytokinesis Thomas Clifford Panagiotou Master of Science Department of Molecular Genetics University of Toronto 2020 Abstract Finely tuned spatio-temporal regulation of cell division is required for genome stability. Cytokinesis constitutes the final stages of cell division, from chromosome segregation to the physical separation of cells, abscission. Abscission is tightly regulated to ensure it occurs after earlier cytokinetic events, like the maturation of the stem body, the regulatory platform for abscission. Active Aurora B kinase enforces the abscission checkpoint, which blocks abscission until chromosomes have been cleared from the cytokinetic machinery. Currently, it is unclear how this checkpoint is overcome. Here, I demonstrate that the cyclin-dependent kinase CDK11 is required for cytokinesis. Both inhibition and depletion of CDK11 block abscission. Furthermore, the mitosis-specific CDK11p58 kinase localizes to the stem body, where its kinase activity rescues the defects of CDK11 depletion and inhibition. These results suggest a model whereby CDK11p58 antagonizes Aurora B kinase to overcome the abscission checkpoint to allow for successful completion of cytokinesis. ii Acknowledgments I am very grateful for the support of my family and friends throughout my studies. I would also like to express my deep gratitude to Wilde Lab members, both past and present, for their advice and collaboration. In particular, I am very grateful to Matthew Renshaw, whose work comprises part of this thesis. -
A Computational Approach for Defining a Signature of Β-Cell Golgi Stress in Diabetes Mellitus
Page 1 of 781 Diabetes A Computational Approach for Defining a Signature of β-Cell Golgi Stress in Diabetes Mellitus Robert N. Bone1,6,7, Olufunmilola Oyebamiji2, Sayali Talware2, Sharmila Selvaraj2, Preethi Krishnan3,6, Farooq Syed1,6,7, Huanmei Wu2, Carmella Evans-Molina 1,3,4,5,6,7,8* Departments of 1Pediatrics, 3Medicine, 4Anatomy, Cell Biology & Physiology, 5Biochemistry & Molecular Biology, the 6Center for Diabetes & Metabolic Diseases, and the 7Herman B. Wells Center for Pediatric Research, Indiana University School of Medicine, Indianapolis, IN 46202; 2Department of BioHealth Informatics, Indiana University-Purdue University Indianapolis, Indianapolis, IN, 46202; 8Roudebush VA Medical Center, Indianapolis, IN 46202. *Corresponding Author(s): Carmella Evans-Molina, MD, PhD ([email protected]) Indiana University School of Medicine, 635 Barnhill Drive, MS 2031A, Indianapolis, IN 46202, Telephone: (317) 274-4145, Fax (317) 274-4107 Running Title: Golgi Stress Response in Diabetes Word Count: 4358 Number of Figures: 6 Keywords: Golgi apparatus stress, Islets, β cell, Type 1 diabetes, Type 2 diabetes 1 Diabetes Publish Ahead of Print, published online August 20, 2020 Diabetes Page 2 of 781 ABSTRACT The Golgi apparatus (GA) is an important site of insulin processing and granule maturation, but whether GA organelle dysfunction and GA stress are present in the diabetic β-cell has not been tested. We utilized an informatics-based approach to develop a transcriptional signature of β-cell GA stress using existing RNA sequencing and microarray datasets generated using human islets from donors with diabetes and islets where type 1(T1D) and type 2 diabetes (T2D) had been modeled ex vivo. To narrow our results to GA-specific genes, we applied a filter set of 1,030 genes accepted as GA associated. -
Src Activation Plays an Important Key Role in Lymphomagenesis Induced by FGFR1 Fusion Kinases
Published OnlineFirst September 21, 2011; DOI: 10.1158/0008-5472.CAN-11-1109 Cancer Tumor and Stem Cell Biology Research Src Activation Plays an Important Key Role in Lymphomagenesis Induced by FGFR1 Fusion Kinases Mingqiang Ren, Haiyan Qin, Ruizhe Ren, Josephine Tidwell, and John K. Cowell Abstract Chromosomal translocations and activation of the fibroblast growth factor (FGF) receptor 1 (FGFR1) are a feature of stem cell leukemia–lymphoma syndrome (SCLL), an aggressive malignancy characterized by rapid transformation to acute myeloid leukemia and lymphoblastic lymphoma. It has been suggested that FGFR1 proteins lose their ability to recruit Src kinase, an important mediator of FGFR1 signaling, as a result of the translocations that delete the extended FGFR substrate-2 (FRS2) interacting domain that Src binds. In this study, we report evidence that refutes this hypothesis and reinforces the notion that Src is a critical mediator of signaling from the FGFR1 chimeric fusion genes generated by translocation in SCLL. Src was constitutively active in BaF3 cells expressing exogenous FGFR1 chimeric kinases cultured in vitro as well as in T-cell or B-cell lymphomas they induced in vivo. Residual components of the FRS2-binding site retained in chimeric kinases that were generated by translocation were sufficient to interact with FRS2 and activate Src. The Src kinase inhibitor dasatinib killed transformed BaF3 cells and other established murine leukemia cell lines expressing chimeric FGFR1 kinases, significantly extending the survival of mice with SCLL syndrome. Our results indicated that Src kinase is pathogenically activated in lymphomagenesis induced by FGFR1 fusion genes, implying that Src kinase inhibitors may offer a useful option to treatment of FGFR1-associated myeloproliferative/lymphoma disorders. -
Supplementary Table 1
SI Table S1. Broad protein kinase selectivity for PF-2771. Kinase, PF-2771 % Inhibition at 10 μM Service Kinase, PF-2771 % Inhibition at 1 μM Service rat RPS6KA1 (RSK1) 39 Dundee AURKA (AURA) 24 Invitrogen IKBKB (IKKb) 26 Dundee CDK2 /CyclinA 21 Invitrogen mouse LCK 25 Dundee rabbit MAP2K1 (MEK1) 19 Dundee AKT1 (AKT) 21 Dundee IKBKB (IKKb) 16 Dundee CAMK1 (CaMK1a) 19 Dundee PKN2 (PRK2) 14 Dundee RPS6KA5 (MSK1) 18 Dundee MAPKAPK5 14 Dundee PRKD1 (PKD1) 13 Dundee PIM3 12 Dundee MKNK2 (MNK2) 12 Dundee PRKD1 (PKD1) 12 Dundee MARK3 10 Dundee NTRK1 (TRKA) 12 Invitrogen SRPK1 9 Dundee MAPK12 (p38g) 11 Dundee MAPKAPK5 9 Dundee MAPK8 (JNK1a) 11 Dundee MAPK13 (p38d) 8 Dundee rat PRKAA2 (AMPKa2) 11 Dundee AURKB (AURB) 5 Dundee NEK2 11 Invitrogen CSK 5 Dundee CHEK2 (CHK2) 11 Invitrogen EEF2K (EEF-2 kinase) 4 Dundee MAPK9 (JNK2) 9 Dundee PRKCA (PKCa) 4 Dundee rat RPS6KA1 (RSK1) 8 Dundee rat PRKAA2 (AMPKa2) 4 Dundee DYRK2 7 Dundee rat CSNK1D (CKId) 3 Dundee AKT1 (AKT) 7 Dundee LYN 3 BioPrint PIM2 7 Invitrogen CSNK2A1 (CKIIa) 3 Dundee MAPK15 (ERK7) 6 Dundee CAMKK2 (CAMKKB) 1 Dundee mouse LCK 5 Dundee PIM3 1 Dundee PDPK1 (PDK1) (directed 5 Invitrogen rat DYRK1A (MNB) 1 Dundee RPS6KB1 (p70S6K) 5 Dundee PBK 0 Dundee CSNK2A1 (CKIIa) 4 Dundee PIM1 -1 Dundee CAMKK2 (CAMKKB) 4 Dundee DYRK2 -2 Dundee SRC 4 Invitrogen MAPK12 (p38g) -2 Dundee MYLK2 (MLCK_sk) 3 Invitrogen NEK6 -3 Dundee MKNK2 (MNK2) 2 Dundee RPS6KB1 (p70S6K) -3 Dundee SRPK1 2 Dundee AKT2 -3 Dundee MKNK1 (MNK1) 2 Dundee RPS6KA3 (RSK2) -3 Dundee CHEK1 (CHK1) 2 Invitrogen rabbit MAP2K1 (MEK1) -4 Dundee -
FGF Signaling Network in the Gastrointestinal Tract (Review)
163-168 1/6/06 16:12 Page 163 INTERNATIONAL JOURNAL OF ONCOLOGY 29: 163-168, 2006 163 FGF signaling network in the gastrointestinal tract (Review) MASUKO KATOH1 and MASARU KATOH2 1M&M Medical BioInformatics, Hongo 113-0033; 2Genetics and Cell Biology Section, National Cancer Center Research Institute, Tokyo 104-0045, Japan Received March 29, 2006; Accepted May 2, 2006 Abstract. Fibroblast growth factor (FGF) signals are trans- Contents duced through FGF receptors (FGFRs) and FRS2/FRS3- SHP2 (PTPN11)-GRB2 docking protein complex to SOS- 1. Introduction RAS-RAF-MAPKK-MAPK signaling cascade and GAB1/ 2. FGF family GAB2-PI3K-PDK-AKT/aPKC signaling cascade. The RAS~ 3. Regulation of FGF signaling by WNT MAPK signaling cascade is implicated in cell growth and 4. FGF signaling network in the stomach differentiation, the PI3K~AKT signaling cascade in cell 5. FGF signaling network in the colon survival and cell fate determination, and the PI3K~aPKC 6. Clinical application of FGF signaling cascade in cell polarity control. FGF18, FGF20 and 7. Clinical application of FGF signaling inhibitors SPRY4 are potent targets of the canonical WNT signaling 8. Perspectives pathway in the gastrointestinal tract. SPRY4 is the FGF signaling inhibitor functioning as negative feedback apparatus for the WNT/FGF-dependent epithelial proliferation. 1. Introduction Recombinant FGF7 and FGF20 proteins are applicable for treatment of chemotherapy/radiation-induced mucosal injury, Fibroblast growth factor (FGF) family proteins play key roles while recombinant FGF2 protein and FGF4 expression vector in growth and survival of stem cells during embryogenesis, are applicable for therapeutic angiogenesis. Helicobacter tissues regeneration, and carcinogenesis (1-4).