Niemann-Pick C1 functions in regulating lysosomal amine content.
AuthorsKaufmann AM, Krise JP,
JournalJ Biol Chem
PubMed ID18591242
'Mutations in the late endosomal/lysosomal membrane protein Niemann-Pick C1 (NPC1) are known to cause a generalized block in retrograde vesicle-mediated transport, resulting in the hyper-accumulation of multiple lysosomal cargos. An important, yet often overlooked, category of lysosomal cargo includes the vast array of small molecular weight amine-containing molecules that are ... More
Differential localization of the centromere-specific proteins in the major centromeric satellite of Arabidopsis thaliana.
AuthorsShibata F, Murata M
JournalJ Cell Sci
PubMed ID15161939
'The 180 bp family of tandem repetitive sequences, which constitutes the major centromeric satellite in Arabidopsis thaliana, is thought to play important roles in kinetochore assembly. To assess the centromere activities of the 180 bp repeats, we performed indirect fluorescence immunolabeling with antibodies against phosphorylated histone H3 at Ser10, HTR12 ... More
Viral nanoparticles as tools for intravital vascular imaging.
AuthorsLewis JD, Destito G, Zijlstra A, Gonzalez MJ, Quigley JP, Manchester M, Stuhlmann H
JournalNat Med
PubMed ID16501571
'A significant impediment to the widespread use of noninvasive in vivo vascular imaging techniques is the current lack of suitable intravital imaging probes. We describe here a new strategy to use viral nanoparticles as a platform for the multivalent display of fluorescent dyes to image tissues deep inside living organisms. ... More
Quantitative comparison of long-wavelength Alexa Fluor dyes to Cy dyes: fluorescence of the dyes and their bioconjugates.
AuthorsBerlier JE, Rothe A, Buller G, Bradford J, Gray DR, Filanoski BJ, Telford WG, Yue S, Liu J, Cheung CY, Chang W, Hirsch JD, Beechem JM, Haugland RP, Haugland RP
JournalJ Histochem Cytochem
PubMed ID14623938
'Amine-reactive N-hydroxysuccinimidyl esters of Alexa Fluor fluorescent dyes with principal absorption maxima at about 555 nm, 633 nm, 647 nm, 660 nm, 680 nm, 700 nm, and 750 nm were conjugated to antibodies and other selected proteins. These conjugates were compared with spectrally similar protein conjugates of the Cy3, Cy5, ... More
A fluorescence resonance energy transfer-based approach for investigating late endosome-lysosome retrograde fusion events.
AuthorsKaufmann AM, Goldman SD, Krise JP,
JournalAnal Biochem
PubMed ID19109922
'Traditionally, lysosomes have been considered to be a terminal endocytic compartment. Recent studies suggest that lysosomes are quite dynamic, being able to fuse with other late endocytic compartments as well as with the plasma membrane. Here we describe a quantitative fluorescence energy transfer (FRET)-based method for assessing rates of retrograde ... More
A streptavidin variant with slower biotin dissociation and increased mechanostability.
AuthorsChivers CE, Crozat E, Chu C, Moy VT, Sherratt DJ, Howarth M,
JournalNat Methods
PubMed ID20383133
'Streptavidin binds biotin conjugates with exceptional stability but dissociation does occur, limiting its use in imaging, DNA amplification and nanotechnology. We identified a mutant streptavidin, traptavidin, with more than tenfold slower biotin dissociation, increased mechanical strength and improved thermostability; this resilience should enable diverse applications. FtsK, a motor protein important ... More
Visualization of galectin-3 oligomerization on the surface of neutrophils and endothelial cells using fluorescence resonance energy transfer.
AuthorsNieminen J, Kuno A, Hirabayashi J, Sato S
JournalJ Biol Chem
PubMed ID17082191
'Galectin-3, a member of the galectin family of carbohydrate binding proteins, is widely expressed, particularly in cells involved in the immune response. Galectin-3 has also been indicated to play a role in various biological activities ranging from cell repression to cell activation and adhesion and has, thus, been recognized as ... More
Unified superresolution experiments and stochastic theory provide mechanistic insight into protein ion-exchange adsorptive separations.
'Chromatographic protein separations, immunoassays, and biosensing all typically involve the adsorption of proteins to surfaces decorated with charged, hydrophobic, or affinity ligands. Despite increasingly widespread use throughout the pharmaceutical industry, mechanistic detail about the interactions of proteins with individual chromatographic adsorbent sites is available only via inference from ensemble measurements ... More
The relationship between force and focal complex development.
AuthorsGalbraith CG, Yamada KM, Sheetz MP
JournalJ Cell Biol
PubMed ID12446745
'To adhere and migrate, cells must be capable of applying cytoskeletal force to the extracellular matrix (ECM) through integrin receptors. However, it is unclear if connections between integrins and the ECM are immediately capable of transducing cytoskeletal contraction into migration force, or whether engagement of force transmission requires maturation of ... More
Possible sources of dye-related signal correlation bias in two-color DNA microarray assays.
AuthorsCox WG, Beaudet MP, Agnew JY, Ruth JL
JournalAnal Biochem
PubMed ID15265729
'DNA microarray analyses commonly use two spectrally distinct fluorescent labels to simultaneously compare different mRNA pools. Signal correlation bias currently limits accepted resolution to twofold changes in gene expression. This bias was investigated by (i) examining fluorescence and absorption spectra and changes in relative fluorescence of DNAs labeled with the ... More
Receptor-dependent and -independent axonal retrograde transport of poliovirus in motor neurons.
AuthorsOhka S, Sakai M, Bohnert S, Igarashi H, Deinhardt K, Schiavo G, Nomoto A,
JournalJ Virol
PubMed ID19244317
'Poliovirus (PV), when injected intramuscularly into the calf, is incorporated into the sciatic nerve and causes an initial paralysis of the inoculated limb in transgenic (Tg) mice carrying the human PV receptor (hPVR/CD155) gene. We have previously demonstrated that a fast retrograde axonal transport process is required for PV dissemination ... More
Multiplexed DNA detection using spectrally encoded porous SiO2 photonic crystal particles.
AuthorsMeade SO, Chen MY, Sailor MJ, Miskelly GM,
JournalAnal Chem
PubMed ID19271746
A particle-based multiplexed DNA assay based on encoded porous SiO(2) photonic crystal disks is demonstrated. A
Organization of the archaeal MCM complex on DNA and implications for the helicase mechanism.
AuthorsMcGeoch AT, Trakselis MA, Laskey RA, Bell SD
JournalNat Struct Mol Biol
PubMed ID16116441
The homomultimeric archaeal mini-chromosome maintenance (MCM) complex serves as a simple model for the analogous heterohexameric eukaryotic complex. Here we investigate the organization and orientation of the MCM complex of the hyperthermophilic archaeon Sulfolobus solfataricus (Sso) on model DNA substrates. Sso MCM binds as a hexamer and slides on the ... More
Retention of mutant low density lipoprotein receptor in ER leads to ER stress.
Familial hypercholesterolemia (FH) is an autosomal dominant disease caused by mutations in the gene encoding the low density lipoprotein receptor (LDLR). More than 50% of these mutations lead to receptor proteins that are completely or partly retained in the endoplasmic reticulum (ER). The mechanisms involved in the intracellular processing and ... More
Measurement of replication structures at the nanometer scale using super-resolution light microscopy.
AuthorsBaddeley D, Chagin VO, Schermelleh L, Martin S, Pombo A, Carlton PM, Gahl A, Domaing P, Birk U, Leonhardt H, Cremer C, Cardoso MC,
JournalNucleic Acids Res
PubMed ID19864256
DNA replication, similar to other cellular processes, occurs within dynamic macromolecular structures. Any comprehensive understanding ultimately requires quantitative data to establish and test models of genome duplication. We used two different super-resolution light microscopy techniques to directly measure and compare the size and numbers of replication foci in mammalian cells. ... More
Design of recombinant antibody microarrays for complex proteome analysis: choice of sample labeling-tag and solid support.
AuthorsWingren C, Ingvarsson J, Dexlin L, Szul D, Borrebaeck CA,
JournalProteomics
PubMed ID17787036
Antibody-based microarray is a novel technology with great potential within high-throughput proteomics. The process of designing high-performing antibody (protein) microarrays has, however, turned out to be a challenging process. In this study, we have developed further our human recombinant single-chain variable-fragment (scFv) antibody microarray methodology by addressing two crucial technological ... More
Low-density Lipoprotein Receptor-related Protein-1 (LRP1) Mediates Autophagy and Apoptosis Caused by Helicobacter pylori VacA.
AuthorsYahiro K, Satoh M, Nakano M, Hisatsune J, Isomoto H, Sap J, Suzuki H, Nomura F, Noda M, Moss J, Hirayama T,
JournalJ Biol Chem
PubMed ID22822085
In Helicobacter pylori infection, vacuolating cytotoxin (VacA)-induced mitochondrial damage leading to apoptosis is believed to be a major cause of cell death. It has also been proposed that VacA-induced autophagy serves as a host mechanism to limit toxin-induced cellular damage. Apoptosis and autophagy are two dynamic and opposing processes that ... More
Novel anti-cholesterol monoclonal immunoglobulin G antibodies as probes and potential modulators of membrane raft-dependent immune functions.
AuthorsBíró A, Cervenak L, Balogh A, Lorincz A, Uray K, Horváth A, Romics L, Matkó J, Füst G, László G,
JournalJ Lipid Res
PubMed ID17023738
Natural autoantibodies against cholesterol are present in the sera of all healthy individuals; their function, production, and regulation, however, are still unclear. Here, we managed to produce two monoclonal anti-cholesterol antibodies (ACHAs) by immunizing mice with cholesterol-rich liposomes. The new ACHAs were specific to cholesterol and to some structurally closely ... More
Effects of atmospheric ozone on microarray data quality.
AuthorsFare TL, Coffey EM, Dai H, He YD, Kessler DA, Kilian KA, Koch JE, LeProust E, Marton MJ, Meyer MR, Stoughton RB, Tokiwa GY, Wang Y
JournalAnal Chem
PubMed ID14632079
A data anomaly was observed that affected the uniformity and reproducibility of fluorescent signal across DNA microarrays. Results from experimental sets designed to identify potential causes (from microarray production to array scanning) indicated that the anomaly was linked to a batch process; further work allowed us to localize the effect ... More
Quantum dot/peptide-MHC biosensors reveal strong CD8-dependent cooperation between self and viral antigens that augment the T cell response.
AuthorsAnikeeva N, Lebedeva T, Clapp AR, Goldman ER, Dustin ML, Mattoussi H, Sykulev Y
JournalProc Natl Acad Sci U S A
PubMed ID17077145
Cytotoxic T lymphocytes (CTL) can respond to a few viral peptide-MHC-I (pMHC-I) complexes among a myriad of virus-unrelated endogenous self pMHC-I complexes displayed on virus-infected cells. To elucidate the molecular recognition events on live CTL, we have utilized a self-assembled biosensor composed of semiconductor nanocrystals, quantum dots, carrying a controlled ... More
CpG Island microarray probe sequences derived from a physical library are representative of CpG Islands annotated on the human genome.
AuthorsHeisler LE, Torti D, Boutros PC, Watson J, Chan C, Winegarden N, Takahashi M, Yau P, Huang TH, Farnham PJ, Jurisica I, Woodgett JR, Bremner R, Penn LZ, Der SD
JournalNucleic Acids Res
PubMed ID15911630
An effective tool for the global analysis of both DNA methylation status and protein-chromatin interactions is a microarray constructed with sequences containing regulatory elements. One type of array suited for this purpose takes advantage of the strong association between CpG Islands (CGIs) and gene regulatory regions. We have obtained 20,736 ... More
Modulation of antigen presentation by autoreactive B cell clones specific for GAD65 from a type I diabetic patient.
AuthorsBanga JP, Moore JK, Duhindan N, Madec AM, van Endert PM, Orgiazzi J, Endl J
JournalClin Exp Immunol
PubMed ID14678267
We used a GAD65-specific human B-T cell line cognate system in vitro to investigate the modulation of GAD65 presentation by autoantibody, assessed in a proliferation assay. Generally, if the T cell determinant overlaps or resides within the antibody epitope, effects of presentation are blunted while if they are distant can ... More
Ligand-induced dimer-tetramer transition during the activation of the cell surface epidermal growth factor receptor-A multidimensional microscopy analysis.
The epidermal growth factor receptor (EGFR) is a member of the erbB tyrosine kinase family of receptors. For many years it has been believed that receptor activation occurs via a monomer-dimer transition that is associated with a conformational change to activate the kinase. However, little is known about the quaternary ... More
Exploring the regulation of tRNA distribution on the genomic scale.
AuthorsDittmar KA, Mobley EM, Radek AJ, Pan T
JournalJ Mol Biol
PubMed ID15001350
Though up to 20% of the total RNA in bacterial cells is tRNA, the regulation of tRNA distribution on the genomic level remains unclear. tRNA distribution is governed by four processes: transcription, processing of precursor tRNA, degradation of precursor tRNA and degradation of mature tRNA. To elucidate the relationship between ... More
Annexin 2 binding to phosphatidylinositol 4,5-bisphosphate on endocytic vesicles is regulated by the stress response pathway.
AuthorsHayes MJ, Merrifield CJ, Shao D, Ayala-Sanmartin J, Schorey CD, Levine TP, Proust J, Curran J, Bailly M, Moss SE
JournalJ Biol Chem
PubMed ID14734570
Annexin 2 is a Ca(2+)-binding protein that has an essential role in actin-dependent macropinosome motility. We show here that macropinosome rocketing can be induced by hyperosmotic shock, either alone or synergistically when combined with phorbol ester or pervanadate. Rocketing was blocked by inhibitors of phosphatidylinositol-3-kinase(s), p38 mitogen-activated protein (MAP) kinase, ... More
New insights into extracellular matrix assembly and reorganization from dynamic imaging of extracellular matrix proteins in living osteoblasts.
AuthorsSivakumar P, Czirok A, Rongish BJ, Divakara VP, Wang YP, Dallas SL
JournalJ Cell Sci
PubMed ID16537652
The extracellular matrix (ECM) has been traditionally viewed as a static scaffold that supports cells and tissues. However, recent dynamic imaging studies suggest that ECM components are highly elastic and undergo continual movement and deformation. Latent transforming growth factor beta (TGFbeta) binding protein-1 (LTBP1) is an ECM glycoprotein that binds ... More