Phosphodiesterase 1B Knock-Out Mice Exhibit Exaggerated Locomotor Hyperactivity and DARPP-32 Phosphorylation in Response to Dopa
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Endogenous Reverse Transcriptase and Rnase H-Mediated Antiviral Mechanism in Embryonic Stem Cells
www.nature.com/cr www.cell-research.com ARTICLE Endogenous reverse transcriptase and RNase H-mediated antiviral mechanism in embryonic stem cells Junyu Wu1, Chunyan Wu1, Fan Xing1, Liu Cao1, Weijie Zeng1, Liping Guo1, Ping Li1, Yongheng Zhong1, Hualian Jiang1, Manhui Luo1, Guang Shi2, Lang Bu1, Yanxi Ji1, Panpan Hou1, Hong Peng1, Junjiu Huang2, Chunmei Li1 and Deyin Guo 1 Nucleic acid-based systems play important roles in antiviral defense, including CRISPR/Cas that adopts RNA-guided DNA cleavage to prevent DNA phage infection and RNA interference (RNAi) that employs RNA-guided RNA cleavage to defend against RNA virus infection. Here, we report a novel type of nucleic acid-based antiviral system that exists in mouse embryonic stem cells (mESCs), which suppresses RNA virus infection by DNA-mediated RNA cleavage. We found that the viral RNA of encephalomyocarditis virus can be reverse transcribed into complementary DNA (vcDNA) by the reverse transcriptase (RTase) encoded by endogenous retrovirus-like elements in mESCs. The vcDNA is negative-sense single-stranded and forms DNA/RNA hybrid with viral RNA. The viral RNA in the heteroduplex is subsequently destroyed by cellular RNase H1, leading to robust suppression of viral growth. Furthermore, either inhibition of the RTase activity or depletion of endogenous RNase H1 results in the promotion of virus proliferation. Altogether, our results provide intriguing insights into the antiviral mechanism of mESCs and the antiviral function of endogenized retroviruses and cellular RNase H. Such a natural nucleic acid-based antiviral mechanism in mESCs is referred to as ERASE (endogenous RTase/RNase H-mediated antiviral system), which is an addition to the previously known nucleic acid-based antiviral mechanisms including CRISPR/Cas in bacteria and RNAi in plants and invertebrates. -
Restriction Endonucleases
Molecular Biology Problem Solver: A Laboratory Guide. Edited by Alan S. Gerstein Copyright © 2001 by Wiley-Liss, Inc. ISBNs: 0-471-37972-7 (Paper); 0-471-22390-5 (Electronic) 9 Restriction Endonucleases Derek Robinson, Paul R. Walsh, and Joseph A. Bonventre Background Information . 226 Which Restriction Enzymes Are Commercially Available? . 226 Why Are Some Enzymes More Expensive Than Others? . 227 What Can You Do to Reduce the Cost of Working with Restriction Enzymes? . 228 If You Could Select among Several Restriction Enzymes for Your Application, What Criteria Should You Consider to Make the Most Appropriate Choice? . 229 What Are the General Properties of Restriction Endonucleases? . 232 What Insight Is Provided by a Restriction Enzyme’s Quality Control Data? . 233 How Stable Are Restriction Enzymes? . 236 How Stable Are Diluted Restriction Enzymes? . 236 Simple Digests . 236 How Should You Set up a Simple Restriction Digest? . 236 Is It Wise to Modify the Suggested Reaction Conditions? . 237 Complex Restriction Digestions . 239 How Can a Substrate Affect the Restriction Digest? . 239 Should You Alter the Reaction Volume and DNA Concentration? . 241 Double Digests: Simultaneous or Sequential? . 242 225 Genomic Digests . 244 When Preparing Genomic DNA for Southern Blotting, How Can You Determine If Complete Digestion Has Been Obtained? . 244 What Are Your Options If You Must Create Additional Rare or Unique Restriction Sites? . 247 Troubleshooting . 255 What Can Cause a Simple Restriction Digest to Fail? . 255 The Volume of Enzyme in the Vial Appears Very Low. Did Leakage Occur during Shipment? . 259 The Enzyme Shipment Sat on the Shipping Dock for Two Days. -
Structure-Based Redesigning of Pentoxifylline Analogs Against
www.nature.com/scientificreports OPEN Structure‑based redesigning of pentoxifylline analogs against selective phosphodiesterases to modulate sperm functional competence for assisted reproductive technologies Mutyala Satish1,5, Sandhya Kumari2,5, Waghela Deeksha1, Suman Abhishek1, Kulhar Nitin1, Satish Kumar Adiga2, Padmaraj Hegde3, Jagadeesh Prasad Dasappa4, Guruprasad Kalthur2* & Eerappa Rajakumara1* Phosphodiesterase (PDE) inhibitors, such as pentoxifylline (PTX), are used as pharmacological agents to enhance sperm motility in assisted reproductive technology (ART), mainly to aid the selection of viable sperm in asthenozoospermic ejaculates and testicular spermatozoa, prior to intracytoplasmic sperm injection (ICSI). However, PTX is reported to induce premature acrosome reaction (AR) and, exert toxic efects on oocyte function and early embryo development. Additionally, in vitro binding studies as well as computational binding free energy (ΔGbind) suggest that PTX exhibits weak binding to sperm PDEs, indicating room for improvement. Aiming to reduce the adverse efects and to enhance the sperm motility, we designed and studied PTX analogues. Using structure‑guided in silico approach and by considering the physico‑chemical properties of the binding pocket of the PDEs, designed analogues of PTX. In silico assessments indicated that PTX analogues bind more tightly to PDEs and form stable complexes. Particularly, ex vivo evaluation of sperm treated with one of the PTX analogues (PTXm‑1), showed comparable benefcial efect at much lower concentration—slower -
Targets and Mechanisms Validated Trials on the Horizon Targets And
TargetsTargets and and Mechanisms Mechanisms Validated Validated TrialsTrials on on the the Horizon Horizon Research Investors Report 2011 TABLE OF CONTENTS Huntington’s Disease Research in 2011: Targets and Mechanisms Validated; Trials on the Horizon FINDING AND VALIDATING TARGETS 4 DRP1 4 Ku705 5 A CLOSER LOOK AT THE HD PROTEIN 6 HR Protein aggregates visualized 6 Form of the HD protein associated with neurodegeneration identified 7 DISCOVERING/DEVELOPING NEW DRUGS AND UNDERSTANDING THEIR MECHANISMS 10 Dantrolene appears to be neuroprotective 10 Melatonin delays onset and prolongs survival in the R6/2 Mouse 11 KMO Inhibitor developed 12 New Caspase Inhibitors identified and Optimized 14 Quinazoline derivative looks promising 15 Phosphodiesterase-10 inhibitors 16 Novel benzoxazine compounds may be neuroprotective 18 Dimethylfumarate is helpful to the YAC128 Mouse 18 IPSC Consortium creates stem cell lines 19 FINDING AND VALIDATING BIOMARKERS 21 H2AFY 21 Protein Aggregates 22 TRACK-HD 22 UNDERSTANDING THE DISEASE COURSE AND IMPROVING CLINICAL MEASURES 25 Progression of HD and MRI imaging 25 Enroll-HD 25 POTENTIAL TREATMENTS MOVING CLOSE TO CLINICAL TRIALS 27 RNAi Primate Study 27 ASOs can be made allele specific 27 Mesenchymal stem cells with BDNF 28 CLINICAL TRIALS 30 Lessons from Dimebon 30 Neurosearch -- Huntexil (ACR-16) 31 Prana Biotech Copper Chelator 31 Siena Biotech Sirt1 Inhibitor 32 THE OTHER MEMBERS OF THE RESEARCH TEAM - THE PARTICIPANTS 33 FINAL THOUGHTS 35 HD DRUG DEVELOPMENT PIPELINE CHART 36 HDSA COALITION FOR THE CURE 37 HDSA CENTERS OF EXCELLENCE 38 Cover Photo: Polarizing optical microscopy image of huntingtin peptide aggregates stained with Congo Red. Courtesy of Dr. -
N-Glycan Trimming in the ER and Calnexin/Calreticulin Cycle
Neurotransmitter receptorsGABA and A postsynapticreceptor activation signal transmission Ligand-gated ion channel transport GABAGABA Areceptor receptor alpha-5 alpha-1/beta-1/gamma-2 subunit GABA A receptor alpha-2/beta-2/gamma-2GABA receptor alpha-4 subunit GABAGABA receptor A receptor beta-3 subunitalpha-6/beta-2/gamma-2 GABA-AGABA receptor; A receptor alpha-1/beta-2/gamma-2GABA receptoralpha-3/beta-2/gamma-2 alpha-3 subunit GABA-A GABAreceptor; receptor benzodiazepine alpha-6 subunit site GABA-AGABA-A receptor; receptor; GABA-A anion site channel (alpha1/beta2 interface) GABA-A receptor;GABA alpha-6/beta-3/gamma-2 receptor beta-2 subunit GABAGABA receptorGABA-A receptor alpha-2receptor; alpha-1 subunit agonist subunit GABA site Serotonin 3a (5-HT3a) receptor GABA receptorGABA-C rho-1 subunitreceptor GlycineSerotonin receptor subunit3 (5-HT3) alpha-1 receptor GABA receptor rho-2 subunit GlycineGlycine receptor receptor subunit subunit alpha-2 alpha-3 Ca2+ activated K+ channels Metabolism of ingested SeMet, Sec, MeSec into H2Se SmallIntermediateSmall conductance conductance conductance calcium-activated calcium-activated calcium-activated potassium potassium potassiumchannel channel protein channel protein 2 protein 1 4 Small conductance calcium-activatedCalcium-activated potassium potassium channel alpha/beta channel 1 protein 3 Calcium-activated potassiumHistamine channel subunit alpha-1 N-methyltransferase Neuraminidase Pyrimidine biosynthesis Nicotinamide N-methyltransferase Adenosylhomocysteinase PolymerasePolymeraseHistidine basic -
Regulation of Calmodulin-Stimulated Cyclic Nucleotide Phosphodiesterase (PDE1): Review
95-105 5/6/06 13:44 Page 95 INTERNATIONAL JOURNAL OF MOLECULAR MEDICINE 18: 95-105, 2006 95 Regulation of calmodulin-stimulated cyclic nucleotide phosphodiesterase (PDE1): Review RAJENDRA K. SHARMA, SHANKAR B. DAS, ASHAKUMARY LAKSHMIKUTTYAMMA, PONNIAH SELVAKUMAR and ANURAAG SHRIVASTAV Department of Pathology and Laboratory Medicine, College of Medicine, University of Saskatchewan, Cancer Research Division, Saskatchewan Cancer Agency, 20 Campus Drive, Saskatoon SK S7N 4H4, Canada Received January 16, 2006; Accepted March 13, 2006 Abstract. The response of living cells to change in cell 6. Differential inhibition of PDE1 isozymes and its environment depends on the action of second messenger therapeutic applications molecules. The two second messenger molecules cAMP and 7. Role of proteolysis in regulating PDE1A2 Ca2+ regulate a large number of eukaryotic cellular events. 8. Role of PDE1A1 in ischemic-reperfused heart Calmodulin-stimulated cyclic nucleotide phosphodiesterase 9. Conclusion (PDE1) is one of the key enzymes involved in the complex interaction between cAMP and Ca2+ second messenger systems. Some PDE1 isozymes have similar kinetic and 1. Introduction immunological properties but are differentially regulated by Ca2+ and calmodulin. Accumulating evidence suggests that the A variety of cellular activities are regulated through mech- activity of PDE1 is selectively regulated by cross-talk between anisms controlling the level of cyclic nucleotides. These Ca2+ and cAMP signalling pathways. These isozymes are mechanisms include synthesis, degradation, efflux and seque- also further distinguished by various pharmacological agents. stration of cyclic adenosine 3':5'-monophosphate (cAMP) and We have demonstrated a potentially novel regulation of PDE1 cyclic guanosine 3':5'- monophosphate (cGMP) within the by calpain. -
Analyses of PDE-Regulated Phosphoproteomes Reveal Unique and Specific Camp-Signaling Modules in T Cells
Analyses of PDE-regulated phosphoproteomes reveal unique and specific cAMP-signaling modules in T cells Michael-Claude G. Beltejara, Ho-Tak Laua, Martin G. Golkowskia, Shao-En Onga, and Joseph A. Beavoa,1 aDepartment of Pharmacology, University of Washington, Seattle, WA 98195 Contributed by Joseph A. Beavo, May 28, 2017 (sent for review March 10, 2017; reviewed by Paul M. Epstein, Donald H. Maurice, and Kjetil Tasken) Specific functions for different cyclic nucleotide phosphodiester- to bias T-helper polarization toward Th2, Treg, or Th17 pheno- ases (PDEs) have not yet been identified in most cell types. types (13, 14). In a few cases increased cAMP may even potentiate Conventional approaches to study PDE function typically rely on the T-cell activation signal (15), particularly at early stages of measurements of global cAMP, general increases in cAMP- activation. Recent MS-based proteomic studies have been useful dependent protein kinase (PKA), or the activity of exchange in characterizing changes in the phosphoproteome of T cells under protein activated by cAMP (EPAC). Although newer approaches various stimuli such as T-cell receptor stimulation (16), prosta- using subcellularly targeted FRET reporter sensors have helped glandin signaling (17), and oxidative stress (18), so much of the define more compartmentalized regulation of cAMP, PKA, and total Jurkat phosphoproteome is known. Until now, however, no EPAC, they have limited ability to link this regulation to down- information on the regulation of phosphopeptides by PDEs has stream effector molecules and biological functions. To address this been available in these cells. problem, we have begun to use an unbiased mass spectrometry- Inhibitors of cAMP PDEs are useful tools to study PKA/EPAC- based approach coupled with treatment using PDE isozyme- mediated signaling, and selective inhibitors for each of the 11 PDE – selective inhibitors to characterize the phosphoproteomes of the families have been developed (19 21). -
The Rational Search for PDE10A Inhibitors from Sophora Flavescens Roots Using Pharmacophore‑ and Docking‑Based Virtual Screening
388 MOLECULAR MEDICINE REPORTS 17: 388-393, 2018 The rational search for PDE10A inhibitors from Sophora flavescens roots using pharmacophore‑ and docking‑based virtual screening HAN-TIAN FAN1, JUN-FANG GUO1, YU-XIN ZHANG2, YU-XI GU1, ZHONG-QI NING1, YAN-JIANG QIAO2 and XING WANG1,3 1School of Traditional Chinese Medicine, Capital Medical University, Beijing 100069; 2Key Laboratory of TCM-Information Engineer of State Administration of TCM, School of Chinese Materia Medica, Beijing University of Chinese Medicine, Beijing 100102; 3Beijing Key Laboratory of Traditional Chinese Medicine (TCM) Collateral Disease Theory Research, Capital Medical University, Beijing 100069, P.R. China Received May 27, 2017; Accepted August 31, 2017 DOI: 10.3892/mmr.2017.7871 Abstract. Phosphodiesterase 10A (PDE10A) has been Introduction confirmed to be an important target for the treatment of central nervous system (CNS) disorders. The purpose of the Phosphodiesterases (PDEs) are a family of enzymes that are present study was to identify PDE10A inhibitors from herbs able to lyse phosphodiester bonds, are expressed widely, and used in traditional Chinese medicine. Pharmacophore and have demonstrable clinical significance (1,2). PDE10A has molecular docking techniques were used to virtually screen been demonstrated to be a potential target for the treatment the chemical molecule database of Sophora flavescens, a of central nervous system (CNS) disorders (3,4). Previous well-known Chinese herb that has been used for improving studies have confirmed that PDE10A inhibitors have impor- mental health and regulating the CNS. The pharmacophore tant biological activity in the treatment of psychosis (5-7). model generated recognized the common functional groups of Therefore, screening for PDE10A inhibitors is an effective known PDE10A inhibitors. -
Disruption of the Aldolase a Tetramer Into Catalytically Active Monomers PETER T
Proc. Natl. Acad. Sci. USA Vol. 93, pp. 5374-5379, May 1996 Biochemistry Disruption of the aldolase A tetramer into catalytically active monomers PETER T. BEERNINK* AND DEAN R. TOLANt Biology Department, Boston University, Boston, MA 02215 Communicated by Irwin A. Rose, Fox Chase Cancer Center, Philadelphia, PA, January 22, 1996 (received for review August 30, 1995) ABSTRACT The fructose-1,6-bisphosphate aldolase (EC interface loop of TIM resulted in a stable monomer with a 4.1.2.13) homotetramer has been destabilized by site-directed 103-fold reduction in kcat (11, 12). These studies have suggested mutagenesis at the two different subunit interfaces. A double that the quaternary structure is essential for proper catalytic mutant aldolase, Q125D/E224A, sediments as two distinct activity. species, characteristic of a slow equilibrium, with velocities Fructose-1,6-bisphosphate aldolase (Fru-1,6-P2; EC 4.1.2.13) is expected for the monomer and tetramer. The aldolase mono- an isologous homotetramer (Fig. 1A), each subunit ofwhich is an mer is shown to be catalytically active following isolation from eight-membered acq-barrel containing an active site near its sucrose density gradients. The isolated aldolase monomer had center (13). The two major subunit interfaces (A and B) are 72% of the specific activity of the wild-type enzyme and a distant (>20 A) from the Schiff base-forming Lys-229 (Fig. iB), slightly lower Michaelis constant, clearly indicating that the and aldolase does not exhibit cooperativity or allostery. Isolated quaternary structure is not required for catalysis. Cross- hybrids of isozymes indicated that subunits are catalytically linking of the isolated monomer confirmed that it does not independent; for example, A3B1 was indistinguishable from an rapidly reequilibrate with the tetramer following isolation. -
Directions for Use Shrimp Alkaline Phosphatase, Recombinant (Rsap)
Directions for Use Shrimp Alkaline Phosphatase, Recombinant (rSAP) Code Description Size 1B1633-1KU Shrimp Alkaline Phosphatase, Recombinant (rSAP) 1 vial, 1000 units (1 U/µL) 1B1633-5KU Shrimp Alkaline Phosphatase, Recombinant (rSAP) 5 vials, 1000 units each (1 U/µL) General Information Shrimp Alkaline Phosphatase, Recombinant (rSAP) is a heat-labile hydrolase enzyme produced in Pichia Pastoris that removes phosphate groups nonspecifically from 5’ ends of nucleic acid phosphomonoesters and proteins. This activity is most commonly utilized in molecular cloning to prevent self-ligation of linearized plasmid DNA and in 5’ end-labeling to facilitate the replacement of unlabeled phosphates with labeled phosphate groups. rSAP also prepares PCR products for DNA sequencing or SNP analysis, by dephosphorylating unincorporated dNTPs that would otherwise interfere with enzymatic reactions. VWR Life Science AMRESCO’s rSAP may be directly added to restriction enzyme digests and is conveniently inactivated 100% by heating at 65°C. This eliminates the need for vector purification, a step that is necessary when using alkaline phosphatases isolated from other sources, such as E. coli and calf intestine. rSAP works well in common buffers and does not require supplemental zinc or other additives. Removes 5’-phosphates from DNA, RNA, dNTPs and proteins Improves cloning efficiency by preventing vector recircularization 100% heat-inactivated at 65°C No vector purification necessary Removes unincorporated dNTPs in PCR products prior to DNA sequencing or SNP analysis Prepares templates for 5’-end labeling Dephosphorylates proteins Works in many different buffers without supplemental factors AMRESCO, LLC Corporate Headquarters, 28600 Fountain Parkway, Solon, OH 44139 Directions for Use Storage/Stability Stable at least 2 years when stored frozen (0 to -20°C). -
Phosphodiesterase (PDE)
Phosphodiesterase (PDE) Phosphodiesterase (PDE) is any enzyme that breaks a phosphodiester bond. Usually, people speaking of phosphodiesterase are referring to cyclic nucleotide phosphodiesterases, which have great clinical significance and are described below. However, there are many other families of phosphodiesterases, including phospholipases C and D, autotaxin, sphingomyelin phosphodiesterase, DNases, RNases, and restriction endonucleases, as well as numerous less-well-characterized small-molecule phosphodiesterases. The cyclic nucleotide phosphodiesterases comprise a group of enzymes that degrade the phosphodiester bond in the second messenger molecules cAMP and cGMP. They regulate the localization, duration, and amplitude of cyclic nucleotide signaling within subcellular domains. PDEs are therefore important regulators ofsignal transduction mediated by these second messenger molecules. www.MedChemExpress.com 1 Phosphodiesterase (PDE) Inhibitors, Activators & Modulators (+)-Medioresinol Di-O-β-D-glucopyranoside (R)-(-)-Rolipram Cat. No.: HY-N8209 ((R)-Rolipram; (-)-Rolipram) Cat. No.: HY-16900A (+)-Medioresinol Di-O-β-D-glucopyranoside is a (R)-(-)-Rolipram is the R-enantiomer of Rolipram. lignan glucoside with strong inhibitory activity Rolipram is a selective inhibitor of of 3', 5'-cyclic monophosphate (cyclic AMP) phosphodiesterases PDE4 with IC50 of 3 nM, 130 nM phosphodiesterase. and 240 nM for PDE4A, PDE4B, and PDE4D, respectively. Purity: >98% Purity: 99.91% Clinical Data: No Development Reported Clinical Data: No Development Reported Size: 1 mg, 5 mg Size: 10 mM × 1 mL, 10 mg, 50 mg (R)-DNMDP (S)-(+)-Rolipram Cat. No.: HY-122751 ((+)-Rolipram; (S)-Rolipram) Cat. No.: HY-B0392 (R)-DNMDP is a potent and selective cancer cell (S)-(+)-Rolipram ((+)-Rolipram) is a cyclic cytotoxic agent. (R)-DNMDP, the R-form of DNMDP, AMP(cAMP)-specific phosphodiesterase (PDE) binds PDE3A directly. -
Rapid Alkaline Phosphatase
For life science research only. Not for use in diagnostic procedures. rAPid Alkaline Phosphatase Orthophosphoric-monoester phosphohydrolase (alkaline optimum), EC 3.1.3.1 Cat. No. 04 898 133 001 1000 units Cat. No. 04 898 141 001 5000 units y Version 03 Content version : May 2019 Store at Ϫ15 to Ϫ25°C 1. What this Product Does Enzyme Characteristics Number of Tests Parameter Description 1 kit is designed for Source Recombinant alkaline phosphatase from bovine intes- • 1000 dephosphorylation reactions (Cat. No. 04 898 133 001) tine (1) expressed in Pichia pastoris • 5000 dephosphorylation reactions (Cat. No. 04 898 141 001) Molecular 56 kD (by SDS-PAGE, monomer) with a final reaction volume of 20 l each. weight 2+ Pack Contents Subunits homodimer (Zn is essential for activity) Unit Definition One unit of rAPid Alkaline Phosphatase is the enzyme Label Contents / Function activity which hydrolyzes 1 mol of 4-nitrophenyl rAPid Alkaline Phos- 0.5 M Tris/HCl, 1mM EDTA, pH 8.5 (20°C) phosphatase in 1 min at 37°C under assay conditions. phatase Buffer, Volume 1 U/l 10ϫ conc. Activity rAPid Alkaline Phos- • 1000 U (Cat. No. 04 898 133 001) Specific Approx. 1U/g according to (2) and (3). phatase • 5000 U (Cat. No. 04 898 141 001) Activity See data label for lot-specific values. Storage and Stability Specificity Alkaline Phosphatase catalyzes the hydrolysis of numerous phosphate esters, such as esters of primary Ϫ Ϫ If stored at 15 to 25°C the product is stable through the expiration and secondary alcohols, saccharides, cyclic alcohols, date printed on the label.