Sunday. Gapjunctions I (525-530)
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Localization of Condensin Subunit XCAP-E in Interphase Nucleus, Nucleoid and Nuclear
1 Localization of condensin subunit XCAP-E in interphase nucleus, nucleoid and nuclear matrix of XL2 cells. Elmira Timirbulatova, Igor Kireev, Vladimir Ju. Polyakov, and Rustem Uzbekov* Division of Electron Microscopy, A.N.Belozersky Institute of Physico-Chemical Biology, Moscow State University, 119899, Moscow, Russia. *Author for correspondence: telephone. 007-095-939-55-28; FAX 007-095-939-31-81 e-mail: [email protected] Key words: XCAP-E; nucleolus; condensin; nuclear matrix; Xenopus. Abbreviations: DAPI , 4’, 6 diamidino-2-phenylindole; DNP, deoxyribonucleoprotein; DRB, 5,6-dichloro-1b-d-ribofuranosylbenzimidazole; SMC, structural maintenance of chromosomes; XCAP-E, Xenopus chromosome associated protein E. 2 Abstract The Xenopus XCAP-E protein is a component of condensin complex In the present work we investigate its localization in interphase XL2 cells and nucleoids. We shown, that XCAP-E is localizes in granular and in dense fibrillar component of nucleolus and also in small karyoplasmic structures (termed “SMC bodies”). Extraction by 2M NaCl does not influence XCAP-E distribution in nucleolus and “SMC bodies”. DNAse I treatment of interphase cells permeabilized by Triton X-100 or nucleoids resulted in partial decrease of labeling intensity in the nucleus, whereas RNAse A treatment resulted in practically complete loss of labeling of nucleolus and “SMC bodies” labeling. In mitotic cells, however, 2M NaCl extraction results in an intense staining of the chromosome region although the labeling was visible along the whole length of sister chromatids, with a stronger staining in centromore region. The data are discussed in view of a hypothesis about participation of XCAP-E in processing of ribosomal RNA. -
Role of Excess Inorganic Pyrophosphate in Primer-Extension Genotyping Assays
Methods Role of Excess Inorganic Pyrophosphate in Primer-Extension Genotyping Assays Ming Xiao,1 Angie Phong,1 Kristen L. Lum,1 Richard A. Greene,2 Philip R. Buzby,2,3 and Pui-Yan Kwok1,4,5 1Cardiovascular Research Institute, University of California, San Francisco, San Francisco, California 94143-0130, USA; 2PerkinElmer Life and Analytical Sciences, Inc., Boston, Massachusetts 02118-2512, USA We have developed and genotyped >15,000 SNP assays by using a primer extension genotyping assay with fluorescence polarization (FP) detection. Although the 80% success rate of this assay is similar to those of other SNP genotyping assays, we wanted to determine the reasons for the failures and find ways to improve the assay. We observed that the failed assays fell into three general patterns: PCR failure, excess of heterozygous genotypes, and loss of FP signal for one of the dye labels. After analyzing several hundred failed assays, we concluded that 5% of the assays had PCR failure and had to be redesigned. We also discovered that the other two categories of failures were due to misincorporation of one of the dye-terminators during the primer extension reaction as a result of primer shortening with a reverse reaction involving inorganic pyrophosphate, and to the quenching of R110-terminator after its incorporation onto the SNP primer. The relatively slow incorporation of R110 acycloterminators by AcycloPol compounds the problem with the R110 label. In this report, we describe the source of the problems and simple ways to correct these problems by adding pyrophosphatase, using quenching as part of the analysis, and replacing R110 by Texas red as one of the dye labels. -
Neuropeptidergic Signaling Partitions Arousal Behaviors in Zebrafish
3142 • The Journal of Neuroscience, February 26, 2014 • 34(9):3142–3160 Behavioral/Cognitive Neuropeptidergic Signaling Partitions Arousal Behaviors in Zebrafish Ian G. Woods,1,2 David Schoppik,2 Veronica J. Shi,2 Steven Zimmerman,2 Haley A. Coleman,1 Joel Greenwood,3 Edward R. Soucy,3 and Alexander F. Schier2,3 1Department of Biology, Ithaca College, Ithaca, New York 14850, and 2Department of Molecular and Cellular Biology and 3Center for Brain Science, Harvard University, Cambridge, Massachusetts 02138 Animals modulate their arousal state to ensure that their sensory responsiveness and locomotor activity match environmental demands. Neuropeptides can regulate arousal, but studies of their roles in vertebrates have been constrained by the vast array of neuropeptides and their pleiotropic effects. To overcome these limitations, we systematically dissected the neuropeptidergic modulation of arousal in larval zebrafish. We quantified spontaneous locomotor activity and responsiveness to sensory stimuli after genetically induced expression of seven evolutionarily conserved neuropeptides, including adenylate cyclase activating polypeptide 1b (adcyap1b), cocaine-related and amphetamine-related transcript (cart), cholecystokinin (cck), calcitonin gene-related peptide (cgrp), galanin, hypocretin, and nocicep- tin. Our study reveals that arousal behaviors are dissociable: neuropeptide expression uncoupled spontaneous activity from sensory responsiveness, and uncovered modality-specific effects upon sensory responsiveness. Principal components analysis and phenotypic clustering revealed both shared and divergent features of neuropeptidergic functions: hypocretin and cgrp stimulated spontaneous locomotor activity, whereas galanin and nociceptin attenuated these behaviors. In contrast, cart and adcyap1b enhanced sensory respon- siveness yet had minimal impacts on spontaneous activity, and cck expression induced the opposite effects. Furthermore, hypocretin and nociceptin induced modality-specific differences in responsiveness to changes in illumination. -
Figure S1. HAEC ROS Production and ML090 NOX5-Inhibition
Figure S1. HAEC ROS production and ML090 NOX5-inhibition. (a) Extracellular H2O2 production in HAEC treated with ML090 at different concentrations and 24 h after being infected with GFP and NOX5-β adenoviruses (MOI 100). **p< 0.01, and ****p< 0.0001 vs control NOX5-β-infected cells (ML090, 0 nM). Results expressed as mean ± SEM. Fold increase vs GFP-infected cells with 0 nM of ML090. n= 6. (b) NOX5-β overexpression and DHE oxidation in HAEC. Representative images from three experiments are shown. Intracellular superoxide anion production of HAEC 24 h after infection with GFP and NOX5-β adenoviruses at different MOIs treated or not with ML090 (10 nM). MOI: Multiplicity of infection. Figure S2. Ontology analysis of HAEC infected with NOX5-β. Ontology analysis shows that the response to unfolded protein is the most relevant. Figure S3. UPR mRNA expression in heart of infarcted transgenic mice. n= 12-13. Results expressed as mean ± SEM. Table S1: Altered gene expression due to NOX5-β expression at 12 h (bold, highlighted in yellow). N12hvsG12h N18hvsG18h N24hvsG24h GeneName GeneDescription TranscriptID logFC p-value logFC p-value logFC p-value family with sequence similarity NM_052966 1.45 1.20E-17 2.44 3.27E-19 2.96 6.24E-21 FAM129A 129. member A DnaJ (Hsp40) homolog. NM_001130182 2.19 9.83E-20 2.94 2.90E-19 3.01 1.68E-19 DNAJA4 subfamily A. member 4 phorbol-12-myristate-13-acetate- NM_021127 0.93 1.84E-12 2.41 1.32E-17 2.69 1.43E-18 PMAIP1 induced protein 1 E2F7 E2F transcription factor 7 NM_203394 0.71 8.35E-11 2.20 2.21E-17 2.48 1.84E-18 DnaJ (Hsp40) homolog. -
Gemin4 Is an Essential Gene in Mice, and Its Overexpression in Human Cells Causes Relocalization of the SMN Complex to the Nucleoplasm Ingo D
© 2018. Published by The Company of Biologists Ltd | Biology Open (2018) 7, bio032409. doi:10.1242/bio.032409 RESEARCH ARTICLE Gemin4 is an essential gene in mice, and its overexpression in human cells causes relocalization of the SMN complex to the nucleoplasm Ingo D. Meier1,*,§, Michael P. Walker1,2,‡,§ and A. Gregory Matera¶ ABSTRACT nuclear ribonucleoproteins (snRNPs). Each of these snRNPs Gemin4 is a member of the Survival Motor Neuron (SMN) protein contains a common set of seven RNA binding factors, called Sm complex, which is responsible for the assembly and maturation of Sm- proteins, that forms a heptameric ring around the snRNA, known as class small nuclear ribonucleoproteins (snRNPs). In metazoa, Sm the Sm core. Biogenesis of the Sm core is carried out by another snRNPs are assembled in the cytoplasm and subsequently imported macromolecular assemblage called the Survival Motor Neuron into the nucleus. We previously showed that the SMN complex is (SMN) complex, consisting of at least nine proteins (Gemins 2-8, required for snRNP import in vitro, although it remains unclear which unrip and SMN) (reviewed in Battle et al., 2006a; Matera et al., specific components direct this process. Here, we report that Gemin4 2007; Matera and Wang, 2014). overexpression drives SMN and the other Gemin proteins from the Following RNA polymerase II-mediated transcription in the cytoplasm into the nucleus. Moreover, it disrupts the subnuclear nucleus, pre-snRNAs are exported to the cytoplasm for assembly localization of the Cajal body marker protein, coilin, in a dose- into stable RNP particles (Jarmolowski et al., 1994; Ohno et al., dependent manner. -
TBC1D8B Mutations Implicate RAB11-Dependent Vesicular Trafficking in the Pathogenesis of Nephrotic Syndrome
BASIC RESEARCH www.jasn.org TBC1D8B Mutations Implicate RAB11-Dependent Vesicular Trafficking in the Pathogenesis of Nephrotic Syndrome Lina L. Kampf,1 Ronen Schneider,2 Lea Gerstner,1 Roland Thünauer,3,4 Mengmeng Chen,1 Martin Helmstädter,1 Ali Amar,2 Ana C. Onuchic-Whitford,2,5 Reyner Loza Munarriz,6 Afig Berdeli,7 Dominik Müller,8 Eva Schrezenmeier,9 Klemens Budde,9 Shrikant Mane,10 Kristen M. Laricchia,11 Heidi L. Rehm ,11 Daniel G. MacArthur,11 Richard P. Lifton,10,12 Gerd Walz,1 Winfried Römer,3 Carsten Bergmann,13,14,15 Friedhelm Hildebrandt,2 and Tobias Hermle 1 Due to the number of contributing authors, the affiliations are listed at the end of this article. ABSTRACT Background Mutations in about 50 genes have been identified as monogenic causes of nephrotic syndrome, a frequent cause of CKD. These genes delineated the pathogenetic pathways and rendered significant insight into podocyte biology. Methods We used whole-exome sequencing to identify novel monogenic causes of steroid-resistant nephrotic syndrome (SRNS). We analyzed the functional significance of an SRNS-associated gene in vitro and in podocyte-like Drosophila nephrocytes. Results We identified hemizygous missense mutations in the gene TBC1D8B in five families with nephrotic syndrome. Coimmunoprecipitation assays indicated interactions between TBC1D8B and active forms of RAB11. Silencing TBC1D8B in HEK293T cells increased basal autophagy and exocytosis, two cellular functions that are independently regulated by RAB11. This suggests that TBC1D8B plays a regulatory role by inhibiting endogenous RAB11. Coimmunoprecipitation assays showed TBC1D8B also interacts with the slit diaphragm protein nephrin, and colocalizes with it in immortalized cell lines. -
Small Gtpase Ran and Ran-Binding Proteins
BioMol Concepts, Vol. 3 (2012), pp. 307–318 • Copyright © by Walter de Gruyter • Berlin • Boston. DOI 10.1515/bmc-2011-0068 Review Small GTPase Ran and Ran-binding proteins Masahiro Nagai 1 and Yoshihiro Yoneda 1 – 3, * highly abundant and strongly conserved GTPase encoding ∼ 1 Biomolecular Dynamics Laboratory , Department a 25 kDa protein primarily located in the nucleus (2) . On of Frontier Biosciences, Graduate School of Frontier the one hand, as revealed by a substantial body of work, Biosciences, Osaka University, 1-3 Yamada-oka, Suita, Ran has been found to have widespread functions since Osaka 565-0871 , Japan its initial discovery. Like other small GTPases, Ran func- 2 Department of Biochemistry , Graduate School of Medicine, tions as a molecular switch by binding to either GTP or Osaka University, 2-2 Yamada-oka, Suita, Osaka 565-0871 , GDP. However, Ran possesses only weak GTPase activ- Japan ity, and several well-known ‘ Ran-binding proteins ’ aid in 3 Japan Science and Technology Agency , Core Research for the regulation of the GTPase cycle. Among such partner Evolutional Science and Technology, Osaka University, 1-3 molecules, RCC1 was originally identifi ed as a regulator of Yamada-oka, Suita, Osaka 565-0871 , Japan mitosis in tsBN2, a temperature-sensitive hamster cell line (3) ; RCC1 mediates the conversion of RanGDP to RanGTP * Corresponding author in the nucleus and is mainly associated with chromatin (4) e-mail: [email protected] through its interactions with histones H2A and H2B (5) . On the other hand, the GTP hydrolysis of Ran is stimulated by the Ran GTPase-activating protein (RanGAP) (6) , in con- Abstract junction with Ran-binding protein 1 (RanBP1) and/or the large nucleoporin Ran-binding protein 2 (RanBP2, also Like many other small GTPases, Ran functions in eukaryotic known as Nup358). -
Genome-Wide Discovery of G-Quadruplexes in Barley
www.nature.com/scientificreports OPEN Genome‑wide discovery of G‑quadruplexes in barley H. Busra Cagirici1, Hikmet Budak2,3 & Taner Z. Sen1* G‑quadruplexes (G4s) are four‑stranded nucleic acid structures with closely spaced guanine bases forming square planar G‑quartets. Aberrant formation of G4 structures has been associated with genomic instability. However, most plant species are lacking comprehensive studies of G4 motifs. In this study, genome‑wide identifcation of G4 motifs in barley was performed, followed by a comparison of genomic distribution and molecular functions to other monocot species, such as wheat, maize, and rice. Similar to the reports on human and some plants like wheat, G4 motifs peaked around the 5′ untranslated region (5′ UTR), the frst coding domain sequence, and the frst intron start sites on antisense strands. Our comparative analyses in human, Arabidopsis, maize, rice, and sorghum demonstrated that the peak points could be erroneously merged into a single peak when large window sizes are used. We also showed that the G4 distributions around genic regions are relatively similar in the species studied, except in the case of Arabidopsis. G4 containing genes in monocots showed conserved molecular functions for transcription initiation and hydrolase activity. Additionally, we provided examples of imperfect G4 motifs. DNA and RNA sequences ofen form functional secondary structures, such as loops, hairpins, duplexes, triplexes, and quadruplexes1,2. G-quadruplexes (G4) are four-stranded nucleic acid structures formed within guanine (G) rich sequences. Consecutive G bases form G-stems (also called G-islands3 or G-runs4), which make up one strand of a G4 structure. -
Structure of Inorganic Pyrophosphatase from Staphylococcus Aureus Reveals Conformational flexibility of the Active Site ⇑ ⇑ Chathurada S
Journal of Structural Biology 189 (2015) 81–86 Contents lists available at ScienceDirect Journal of Structural Biology journal homepage: www.elsevier.com/locate/yjsbi Structure of inorganic pyrophosphatase from Staphylococcus aureus reveals conformational flexibility of the active site ⇑ ⇑ Chathurada S. Gajadeera a, Xinyi Zhang b, Yinan Wei b, , Oleg V. Tsodikov a, a Department of Pharmaceutical Sciences, University of Kentucky, College of Pharmacy, 789 S. Limestone St., Lexington, KY 40536, United States b Department of Chemistry, University of Kentucky, 505 Rose St., Lexington, KY 40506, United States article info abstract Article history: Cytoplasmic inorganic pyrophosphatase (PPiase) is an enzyme essential for survival of organisms, from Received 17 November 2014 bacteria to human. PPiases are divided into two structurally distinct families: family I PPiases are Received in revised form 15 December 2014 Mg2+-dependent and present in most archaea, eukaryotes and prokaryotes, whereas the relatively less Accepted 16 December 2014 understood family II PPiases are Mn2+-dependent and present only in some archaea, bacteria and prim- Available online 7 January 2015 itive eukaryotes. Staphylococcus aureus (SA), a dangerous pathogen and a frequent cause of hospital infec- tions, contains a family II PPiase (PpaC), which is an attractive potential target for development of novel Keywords: antibacterial agents. We determined a crystal structure of SA PpaC in complex with catalytic Mn2+ at Pyrophosphorolysis 2.1 Å resolution. The active site contains two catalytic Mn2+ binding sites, each half-occupied, reconciling Hydrolase 2+ Phosphate metabolism the previously observed 1:1 Mn :enzyme stoichiometry with the presence of two divalent metal ion Novel drug target sites in the apo-enzyme. -
Covalent Modification of a Cysteine Residue in the XPB Subunit of The
Angewandte Chemie DOI: 10.1002/anie.201408817 Covalent Inhibitors Covalent Modification of a Cysteine Residue in the XPB Subunit of the General Transcription Factor TFIIH Through Single Epoxide Cleavage of the Transcription Inhibitor Triptolide** Qing-Li He, Denis V. Titov, Jing Li, Minjia Tan, Zhaohui Ye, Yingming Zhao, Daniel Romo, and Jun O. Liu* Abstract: Triptolide is a key component of the traditional Chinese medicinal plant Thunder God Vine and has potent anticancer and immunosuppressive activities. It is an irrever- sible inhibitor of eukaryotic transcription through covalent modification of XPB, a subunit of the general transcription factor TFIIH. Cys342 of XPB was identified as the residue that undergoes covalent modification by the 12,13-epoxide group of triptolide. Mutation of Cys342 of XPB to threonine conferred resistance to triptolide on the mutant protein. Replacement of the endogenous wild-type XPB with the Cys342Thr mutant in a HEK293T cell line rendered it completely resistant to Figure 1. Structures of triptolide and triptolide analogues under clinical triptolide, thus validating XPB as the physiologically relevant development. Potential sites of attack by a nucleophile from a protein target of triptolide. Together, these results deepen our under- are marked with red arrows. Sections for which the analogues differ in standing of the interaction between triptolide and XPB and structure from triptolide are highlighted in blue. have implications for the future development of new analogues of triptolide as leads for anticancer and immunosuppressive drugs. (XPB)/ERCC3 subunit of TFIIH as a new molecular target of triptolide.[4] We showed that triptolide forms a covalent Triptolide (1, TPL), a diterpene triepoxide (Figure 1), was complex with XPB and inhibits its DNA-dependent ATPase isolated from Trypterygium Wilfordii Hook F (Lei Gong Teng activity without affecting its DNA helicase activity. -
Epigenetic Mechanisms Are Involved in the Oncogenic Properties of ZNF518B in Colorectal Cancer
Epigenetic mechanisms are involved in the oncogenic properties of ZNF518B in colorectal cancer Francisco Gimeno-Valiente, Ángela L. Riffo-Campos, Luis Torres, Noelia Tarazona, Valentina Gambardella, Andrés Cervantes, Gerardo López-Rodas, Luis Franco and Josefa Castillo SUPPLEMENTARY METHODS 1. Selection of genomic sequences for ChIP analysis To select the sequences for ChIP analysis in the five putative target genes, namely, PADI3, ZDHHC2, RGS4, EFNA5 and KAT2B, the genomic region corresponding to the gene was downloaded from Ensembl. Then, zoom was applied to see in detail the promoter, enhancers and regulatory sequences. The details for HCT116 cells were then recovered and the target sequences for factor binding examined. Obviously, there are not data for ZNF518B, but special attention was paid to the target sequences of other zinc-finger containing factors. Finally, the regions that may putatively bind ZNF518B were selected and primers defining amplicons spanning such sequences were searched out. Supplementary Figure S3 gives the location of the amplicons used in each gene. 2. Obtaining the raw data and generating the BAM files for in silico analysis of the effects of EHMT2 and EZH2 silencing The data of siEZH2 (SRR6384524), siG9a (SRR6384526) and siNon-target (SRR6384521) in HCT116 cell line, were downloaded from SRA (Bioproject PRJNA422822, https://www.ncbi. nlm.nih.gov/bioproject/), using SRA-tolkit (https://ncbi.github.io/sra-tools/). All data correspond to RNAseq single end. doBasics = TRUE doAll = FALSE $ fastq-dump -I --split-files SRR6384524 Data quality was checked using the software fastqc (https://www.bioinformatics.babraham. ac.uk /projects/fastqc/). The first low quality removing nucleotides were removed using FASTX- Toolkit (http://hannonlab.cshl.edu/fastxtoolkit/). -
<Abstract Centered> an ABSTRACT of the THESIS OF
AN ABSTRACT OF THE DISSERTATION OF Michael Austin Garland for the degree of Doctor of Philosophy in Toxicology presented on June 14, 2019. Title: Transcriptomic Approaches for Discovering Regenerative and Developmental Regulatory Networks in Zebrafish Abstract approved: _____________________________________________________________________ Robert L. Tanguay Zebrafish are capable of fully regenerating organs and tissue such as their caudal fin, which is similar to a human regrowing an arm or a leg. In contrast, most mammals including humans have a greatly reduced capacity for wound healing. The ability of zebrafish to undergo this regenerative process, called epimorphic regeneration, hinges on the capacity to form a blastema at the wound site. The blastema quickly recapitulates the developmental processes involved in complex tissue formation to restore lost or damaged tissue. One key mechanism for inducing blastema formation is global repression of genes involved in tissue differentiation and maintenance. Induction of repressive factors, such as microRNAs (miRNAs), are involved in reprogramming cells during epimorphic regeneration. The upstream mechanism by which zebrafish undergo epimorphic regeneration remains elusive. Furthermore, while focus is shifting toward regulatory RNAs such as miRNAs, the full complement of their repressive activities is unknown. We took a transcriptomics approach to investigating epimorphic regeneration and fin development. Parallel sequencing of total RNA and small RNA samples was performed on regenerating fin tissue at 1 day post-amputation (dpa). Most miRNAs had increased expression, consistent with global repression of genes involved in cell specialization during de-differentiation. We identified predicted interactions between miRNAs and genes involved in transcriptional regulation, chromatin modification, and developmental signaling. miR-146a and miR-146b are anti- inflammatory miRNAs that were predicted to target eya4, which is involved in chromatin remodeling and innate immunity.