Design and characterization of a compact dual channel virus counter.
AuthorsStoffel CL,Kathy RF,Rowlen KL
JournalCytometry. Part A : the journal of the International Society for Analytical Cytology
PubMed ID15830378
Cell-to-cell movement of potato spindle tuber viroid.
AuthorsDing B, Kwon MO, Hammond R, Owens R
JournalPlant J
PubMed ID9375403
Viroids are non-translatable, autonomously replicating circular RNAs that infect only plants. An important component of the viroid infection process is cell-to-cell movement; however, there is virtually no information available about the pathways and mechanisms of this process. In this study, potato spindle tuber viroid (PSTVd) has been used as a ... More
Quantitation of polymerase chain reaction products by capillary electrophoresis using laser fluorescence.
AuthorsButler JM, McCord BR, Jung JM, Wilson MR, Budowle B, Allen RO
JournalJ Chromatogr B Biomed Appl
PubMed ID7820255
In samples where the amount of DNA is limited, the polymerase chain reaction (PCR) can amplify specific regions of the DNA. A quantitative analysis of the PCR product would be desirable to ensure sufficient DNA is available for analysis. In this study, we examine the use of capillary electrophoresis (CE) ... More
Development and evaluation of an automated workstation for single nucleotide polymorphism discrimination using bacterial magnetic particles.
AuthorsTanaka T, Maruyama K, Yoda K, Nemoto E, Udagawa Y, Nakayama H, Takeyama H, Matsunaga T
JournalBiosens Bioelectron
PubMed ID14615090
We designed an automated workstation for magnetic particle-based single nucleotide polymorphism (SNP) discrimination of ALDH genotypes. Bacterial magnetic particles (BMPs) extracted from Magnetospirillum magneticum AMB-1 were used as DNA carriers. The principle for SNP discrimination in this study was based on fluorescence resonance energy transfer (FRET) between FITC (donor) and ... More
Cyclin G2 associates with protein phosphatase 2A catalytic and regulatory B' subunits in active complexes and induces nuclear aberrations and a G1/S phase cell cycle arrest.
AuthorsBennin David A; Don Aruni S Arachchige; Brake Tiffany; McKenzie Jennifer L; Rosenbaum Heidi; Ortiz Linette; DePaoli-Roach Anna A; Horne Mary C;
JournalJ Biol Chem
PubMed ID11956189
Cyclin G2, together with cyclin G1 and cyclin I, defines a novel cyclin family expressed in terminally differentiated tissues including brain and muscle. Cyclin G2 expression is up-regulated as cells undergo cell cycle arrest or apoptosis in response to inhibitory stimuli independent of p53 (Horne, M., Donaldson, K., Goolsby, G., ... More
Development of a real-time PCR assay for detection of Plasmodium falciparum, Plasmodium vivax, and Plasmodium ovale for routine clinical diagnosis.
AuthorsPerandin F, Manca N, Calderaro A, Piccolo G, Galati L, Ricci L, Medici MC, Arcangeletti MC, Snounou G, Dettori G, Chezzi C
JournalJ Clin Microbiol
PubMed ID15004078
A TaqMan-based real-time PCR qualitative assay for the detection of three species of malaria parasites-Plasmodium falciparum, P. ovale, and P. vivax-was devised and evaluated using 122 whole-blood samples from patients who had traveled to areas where malaria is endemic and who presented with malaria-like symptoms and fever. The assay was ... More
Functional overexpression of gamma-secretase reveals protease-independent trafficking functions and a critical role of lipids for protease activity.
AuthorsWrigley JD, Schurov I, Nunn EJ, Martin AC, Clarke EE, Ellis S, Bonnert TP, Shearman MS, Beher D
JournalJ Biol Chem
PubMed ID15613471
'Presenilins appear to form the active center of gamma-secretase but require the presence of the integral membrane proteins nicastrin, anterior pharynx defective 1, and presenilin enhancer 2 for catalytic function. We have simultaneously overexpressed all of these polypeptides, and we demonstrate functional assembly of the enzyme complex, a substantial increase ... More
Drosophila atypical protein kinase C associates with Bazooka and controls polarity of epithelia and neuroblasts.
AuthorsWodarz A, Ramrath A, Grimm A, Knust E
JournalJ Cell Biol
PubMed ID10995441
'The establishment and maintenance of polarity is of fundamental importance for the function of epithelial and neuronal cells. In Drosophila, the multi-PDZ domain protein Bazooka (Baz) is required for establishment of apico-basal polarity in epithelia and in neuroblasts, the stem cells of the central nervous system. In the latter, Baz ... More
Asbestos increases mammalian AP-endonuclease gene expression, protein levels, and enzyme activity in mesothelial cells.
'Only two DNA repair enzymes, DNA polymerase beta and O6-methylguanine-DNA methyltransferase, have been shown to be inducible in mammalian cells by genotoxic agents. We show here that crocidolite asbestos induces the DNA repair enzyme, apurinic/apyrimidinic (AP)-endonuclease, in isolated mesothelial cells, the progenitor cells of malignant mesothelioma. Asbestos at nontoxic concentrations ... More
Active caspase-8 translocates into the nucleus of apoptotic cells to inactivate poly(ADP-ribose) polymerase-2.
AuthorsBenchoua A, Couriaud C, Guégan C, Tartier L, Couvert P, Friocourt G, Chelly J, Ménissier-de Murcia J, Onténiente B
JournalJ Biol Chem
PubMed ID12065591
'Caspase-8 is the prototypic initiator of the death domain receptor pathway of apoptosis. Here, we report that caspase-8 not only triggers and amplifies the apoptotic process at cytoplasmic sites but can also act as an executioner at nuclear levels. In a murine model of acute ischemia, caspase-8 is relocated into ... 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
Sensitive multicolor fluorescence in situ hybridization using catalyzed reporter deposition (CARD) amplification.
AuthorsSpeel EJ, Ramaekers FC, Hopman AH
JournalJ Histochem Cytochem
PubMed ID9313806
'We describe the simultaneous localization of DNA sequences in cell and chromosome preparations by means of differently fluorochrome-labeled (AMCA, FITC, TRITC) tyramides using the catalyzed reporter deposition (CARD) procedure. For this purpose, repeated as well as single-copy DNA probes were labeled with biotin, digoxigenin, and FITC, hybridized, and visualized with ... More
MBD3 and HDAC1, two components of the NuRD complex, are localized at Aurora-A-positive centrosomes in M phase.
AuthorsSakai H, Urano T, Ookata K, Kim MH, Hirai Y, Saito M, Nojima Y, Ishikawa F
JournalJ Biol Chem
PubMed ID12354758
'MBD3, a component of the histone deacetylase NuRD complex, contains the methyl-CpG-binding domain (MBD), yet does not possess appreciable mCpG-specific binding activity. The functional significance of MBD3 in the NuRD complex remains enigmatic, partly because of the limited availability of biochemical approaches, such as immunoprecipitation, to analyze MBD3. In this ... More
Nuclear localization of a non-caspase truncation product of atrophin-1, with an expanded polyglutamine repeat, increases cellular toxicity.
AuthorsNucifora FC, Ellerby LM, Wellington CL, Wood JD, Herring WJ, Sawa A, Hayden MR, Dawson VL, Dawson TM, Ross CA
JournalJ Biol Chem
PubMed ID12464607
'Dentatorubral and pallidoluysian atrophy (DRPLA) is an autosomal dominant neurodegenerative disorder similar to Huntington's disease, with clinical manifestations including chorea, incoordination, ataxia, and dementia. It is caused by an expansion of a CAG trinucleotide repeat encoding polyglutamine in the atrophin-1 gene. Both patients and DRPLA transgenic mice have nuclear accumulation ... More
Visualization of replication initiation and elongation in Drosophila.
AuthorsClaycomb JM, MacAlpine DM, Evans JG, Bell SP, Orr-Weaver TL
JournalJ Cell Biol
PubMed ID12403810
'Chorion gene amplification in the ovaries of Drosophila melanogaster is a powerful system for the study of metazoan DNA replication in vivo. Using a combination of high-resolution confocal and deconvolution microscopy and quantitative realtime PCR, we found that initiation and elongation occur during separate developmental stages, thus permitting analysis of ... More
Murine cytomegalovirus M78 protein, a G protein-coupled receptor homologue, is a constituent of the virion and facilitates accumulation of immediate-early viral mRNA.
AuthorsOliveira SA, Shenk TE
JournalProc Natl Acad Sci U S A
PubMed ID11248062
'The M78 protein of murine cytomegalovirus exhibits sequence features of a G protein-coupled receptor. It is synthesized with early kinetics, it becomes partially colocalized with Golgi markers, and it is incorporated into viral particles. We have constructed a viral substitution mutant, SMsubM78, which lacks most of the M78 ORF. The ... More
Evidence that Sry is expressed in pre-Sertoli cells and Sertoli and granulosa cells have a common precursor.
AuthorsAlbrecht KH, Eicher EM
JournalDev Biol
PubMed ID11784049
'The expression of Sry in the undifferentiated, bipotential genital ridges of mammalian XY fetuses initiates testis development and is hypothesized to do so by directing supporting cell precursors to develop as Sertoli cells and not as granulosa cells. To directly test this hypothesis, transgenic mice expressing EGFP under the control ... More
Quantifying single gene copy number by measuring fluorescent probe lengths on combed genomic DNA.
AuthorsHerrick J, Michalet X, Conti C, Schurra C, Bensimon A
JournalProc Natl Acad Sci U S A
PubMed ID10618399
'An approach was developed for the quantification of subtle gains and losses of genomic DNA. The approach relies on a process called molecular combing. Molecular combing consists of the extension and alignment of purified molecules of genomic DNA on a glass coverslip. It has the advantage that a large number ... More
Disruption of nuclear lamin organization blocks the elongation phase of DNA replication.
AuthorsMoir RD, Spann TP, Herrmann H, Goldman RD
JournalJ Cell Biol
PubMed ID10851016
'The role of nuclear lamins in DNA replication is unclear. To address this, nuclei were assembled in Xenopus extracts containing AraC, a reversible inhibitor that blocks near the onset of the elongation phase of replication. Dominant-negative lamin mutants lacking their NH(2)-terminal domains were added to assembled nuclei to disrupt lamin ... More
A new method for imaging and 3D reconstruction of mammalian cochlea by fluorescent confocal microscopy.
AuthorsHardie NA, MacDonald G, Rubel EW
JournalBrain Res
PubMed ID15053969
'Traditional methods for anatomical and morphometric studies of cochlear tissues have relied upon either microdissection of the organ of Corti or the generation of serial sections of the cochlea. Such methods are time-consuming, disruptive to three-dimensional relationships and often restrict sampling to very limited numbers of cells. We have found ... More
Solution structure and energy calculation of bis-intercalation of homodimeric thiazole orange dye derivatives in DNA: effects of modifying the linker.
AuthorsBondensgaard K, Jacobsen JP
JournalBioconjug Chem
PubMed ID10502338
'We have used two-dimensional (1)H NMR spectroscopy obtained at 750 MHz to determine a high-resolution solution structure of the double-stranded DNA oligonucleotide d(5''-CGCTAGCG-3'')(2) complexed with the bis-intercalating dye 1,1''-(5,5,9,9-tetramethyl-5, 9-diazatridecamethylene)-bis-4-[3-ethyl-2,3-dihydro(benzo-1, 3-thiazolyl)-2-methylidene]quino-linium tetraiodide (TOTO11Et). The determination of the structure was based on a complete relaxation matrix analysis of the NOESY cross-peaks ... More
Cohesin defects lead to premature sister chromatid separation, kinetochore dysfunction, and spindle-assembly checkpoint activation.
AuthorsHoque MT, Ishikawa F
JournalJ Biol Chem
PubMed ID12200439
'Scc1/Mcd1 is a component of the cohesin complex that plays an essential role in sister chromatid cohesion in eukaryote cells. Knockout experiments of this gene have been described in budding yeast, fission yeast, and chicken cells, but no study has been reported on human Scc1 thus far. In this study, ... More
Ribosomes in the squid giant axon.
AuthorsBleher R, Martin R
JournalNeuroscience
PubMed ID11719007
'Ribosome clusters, referred to as endoaxoplasmic plaques, were documented and quantitatively analyzed in the squid giant axon at the light and electron microscopic levels. The methods included nonspecific high affinity fluorescence staining of RNA by YOYO-1, specific immunofluorescence labeling of ribosomal RNA, electron energy loss spectroscopic mapping of ribosomal phosphorus, ... More
Methylated DNA-binding proteins from Arabidopsis.
AuthorsIto M, Koike A, Koizumi N, Sano H
JournalPlant Physiol
PubMed ID14605234
'The 5-methylcytosines (m5C) play a critical role in epigenetic control, often being recognized by proteins containing a methyl-CpG-binding domain (MBD). Database screening has identified at least 12 putative methyl-CpG-binding proteins from Arabidopsis; we have isolated corresponding cDNAs for seven of them. Despite variation in size and amino acid sequence, all ... More
Keratin binding to 14-3-3 proteins modulates keratin filaments and hepatocyte mitotic progression.
AuthorsKu NO, Michie S, Resurreccion EZ, Broome RL, Omary MB
JournalProc Natl Acad Sci U S A
PubMed ID11917136
'Keratin polypeptides 8 and 18 (K8/18) are the major intermediate filament proteins of simple-type epithelia. K18 Ser-33 phosphorylation regulates its binding to 14-3-3 proteins during mitosis. We studied the significance of keratin binding to 14-3-3 in transgenic mice that overexpress wild-type or Ser-33-->Ala (S33A) K18. In S33A but not wild-type ... More
Anomalous radial migration of single DNA molecules in capillary electrophoresis.
AuthorsZheng J, Yeung ES
JournalAnal Chem
PubMed ID12236367
'We report the unexpected radial migration of DNA molecules in capillary electrophoresis (CE) with applied Poiseuille flow. Such movement can contribute to anomalous migration times, peak dispersion, and size and shape selectivity in CE. When Poiseuille flow is applied from the cathode to the anode, DNA molecules move toward the ... More
Ultrasensitive detection of genetically modified maize DNA by capillary gel electrophoresis with laser-induced fluorescence using different fluorescent intercalating dyes.
AuthorsGarcía-Cañas V, González R, Cifuentes A
JournalJ Agric Food Chem
PubMed ID12137467
'In this work, four different fluorescent intercalating dyes are compared for the ultrasensitive CGE-LIF detection of DNA from transgenic maize in flours. The fluorescent intercalating dyes compared are YOPRO-1, SYBR-Green-I, Ethidium bromide (EthBr), and EnhanCE. For all the four dyes optimum concentrations are established, and efficient separations of DNA fragments ... More
Protein synthesizing units in presynaptic and postsynaptic domains of squid neurons.
AuthorsMartin R, Vaida B, Bleher R, Crispino M, Giuditta A
JournalJ Cell Sci
PubMed ID9763510
'Putative protein synthesizing domains, called plaques, are characterized in the squid giant synapse and axon and in terminals of squid photoreceptor neurons. Plaques are oval-shaped formations of about 1 microm in size, which (1) generate signals that have spectroscopic electron energy loss characteristics of ribosomes, (2) exhibit ribonuclease-sensitive binding of ... More
A functional angiotensin II receptor-GFP fusion protein: evidence for agonist-dependent nuclear translocation.
AuthorsChen R, Mukhin YV, Garnovskaya MN, Thielen TE, Iijima Y, Huang C, Raymond JR, Ullian ME, Paul RV
JournalAm J Physiol Renal Physiol
PubMed ID10966923
'We constructed an expression vector for a fusion protein [ANG II type 1a receptor-green fluorescent protein (AT(1a)R-GFP)] consisting of enhanced GFP attached to the COOH terminus of the rat AT(1a)R. Chinese hamster ovary (CHO) cells transfected with AT(1a)R-GFP demonstrated specific, high-affinity (125)I-labeled ANG II binding (IC(50) 21 nM). ANG II ... More
Protective effect of vitamin C against double-strand breaks in reconstituted chromatin visualized by single-molecule observation.
AuthorsYoshikawa Y, Hizume K, Oda Y, Takeyasu K, Araki S, Yoshikawa K
JournalBiophys J
PubMed ID16284271
'Direct attack to genomic DNA by reactive oxygen species causes various types of lesions, including base modifications and strand breaks. The most significant lesion is considered to be an unrepaired double-strand break that can lead to fatal cell damage. We directly observed double-strand breaks of DNA in reconstituted chromatin stained ... More
Isolation and characterization of a human STAT1 gene regulatory element. Inducibility by interferon (IFN) types I and II and role of IFN regulatory factor-1.
AuthorsWong LH, Sim H, Chatterjee-Kishore M, Hatzinisiriou I, Devenish RJ, Stark G, Ralph SJ
JournalJ Biol Chem
PubMed ID11909852
'The transcription factor STAT1 plays a pivotal role in signal transduction of type I and II interferons (IFNs). STAT1 activation leads to changes in expression of key regulatory genes encoding caspases and cell cycle inhibitors. Deficient STAT1 expression in human cancer cells and virally mediated inhibition of STAT1 function have ... More
Heterodimeric DNA-binding dyes designed for energy transfer: stability and applications of the DNA complexes.
AuthorsBenson SC, Mathies RA, Glazer AN
JournalNucleic Acids Res
PubMed ID8284220
'Spectroscopic studies of the complexes of double-stranded (ds) DNA with the polymethylene-amine linked heterodimers thiazole orange-thiazole blue, thiazole orange-ethidium, and fluorescein-ethidium, in each case show efficient energy transfer from donor to acceptor chromophores (Benson, S.C., Singh, P. and Glazer, A.N. (1993) accompanying manuscript). A quantitative assay of the stability of ... More
Differential effects of deuterium oxide on the fluorescence lifetimes and intensities of dyes with different modes of binding to DNA.
AuthorsSailer BL, Nastasi AJ, Valdez JG, Steinkamp JA, Crissman HA
JournalJ Histochem Cytochem
PubMed ID9016307
'Deuterium oxide (D2O) increases both the fluorescence lifetime and the fluorescence intensity of the intercalating dyes propidium iodide (PI) and ethidium bromide (EB) when bound to nucleic acid structures. We have used spectroscopic analysis coupled with conventional and phase-sensitive flow cytometry to compare the alterations in intensity and lifetime of ... More
Environment-sensitive labels in multiplex fluorescence analyses of protein-DNA complexes.
AuthorsDrees BL, Rye HS, Glazer AN, Nelson HC
JournalJ Biol Chem
PubMed ID8943271
'Fluorescein is widely used for protein labeling because of its high extinction coefficient and fluorescence emission quantum yield. However, its emission is readily quenched by various pathways. We exploit these properties of fluorescein to examine the self-association of a DNA binding protein and determine the amount of the protein in ... More
1H NMR studies of the bis-intercalation of a homodimeric oxazole yellow dye in DNA oligonucleotides.
AuthorsJohansen F, Jacobsen JP
JournalJ Biomol Struct Dyn
PubMed ID9833661
'We have used one and two dimensional 1H NMR spectroscopy to characterize the binding of a homodimeric oxazole yellow dye, 1,1'-(4,4,8,8-tetramethyl-4,8-diaza-undecamethylene)-bis-4-( 3-methyl-2,3-dihydro-(benzo-1,3-oxazole)-2-methylidene)-quinoliniu m tetraiodide (YOYO), to oligonucleotides containing the (5'-CTAG-3')2 and the (5'-CCGG-3')2 binding sites in either different oligonucleotides or in the same oligonucleotide. YOYO bis-intercalates strongly in all the ... More
Transcriptional control of monolignol biosynthesis in Pinus taeda: factors affecting monolignol ratios and carbon allocation in phenylpropanoid metabolism.
AuthorsAnterola AM, Jeon JH, Davin LB, Lewis NG
JournalJ Biol Chem
PubMed ID11891223
'Transcriptional profiling of the phenylpropanoid pathway in Pinus taeda cell suspension cultures was carried out using quantitative real time PCR analyses of all known genes involved in the biosynthesis of the two monolignols, p-coumaryl and coniferyl alcohols (lignin/lignan precursors). When the cells were transferred to a medium containing 8% sucrose ... More
Flow cytometric assessment of viability of lactic acid bacteria.
AuthorsBunthof CJ, Bloemen K, Breeuwer P, Rombouts FM, Abee T
JournalAppl Environ Microbiol
PubMed ID11319119
'The viability of lactic acid bacteria is crucial for their applications as dairy starters and as probiotics. We investigated the usefulness of flow cytometry (FCM) for viability assessment of lactic acid bacteria. The esterase substrate carboxyfluorescein diacetate (cFDA) and the dye exclusion DNA binding probes propidium iodide (PI) and TOTO-1 ... More
Monitoring phytoplankton, bacterioplankton, and virioplankton in a coastal inlet (Bedford Basin) by flow cytometry.
AuthorsLi WK, Dickie PM
JournalCytometry
PubMed ID11429774
'BACKGROUND: To establish the prevailing state of the ecosystem for the assessment of long-term change, the abundance of microbial plankton in Bedford Basin (Nova Scotia, Canada) is monitored weekly by flow cytometry. METHODS: Phytoplankton are detected by their chlorophyll autofluorescence. Those that contain phycoerythrin are designated as Synechococcus cyanobacteria or ... More
Diverse microglial motility behaviors during clearance of dead cells in hippocampal slices.
AuthorsPetersen MA, Dailey ME
JournalGlia
PubMed ID15042586
'We used two-channel three-dimensional time-lapse fluorescence confocal imaging in live rat hippocampal slice cultures (1-7 days in vitro) to determine the motility behaviors of activated microglia as they engage dead and dying cells following traumatic brain tissue injury. Live microglia were labeled with a fluorescently conjugated lectin (IB(4)), and dead ... More
Photoreversible DNA condensation using light-responsive surfactants.
AuthorsLe Ny AL, Lee CT
JournalJ Am Chem Soc
PubMed ID16683804
'A means to control DNA compaction with light illumination has been developed using the interaction of DNA with a photoresponsive cationic surfactant. The surfactant undergoes a reversible photoisomerization upon exposure to visible (trans isomer, more hydrophobic) or UV (cis isomer, more hydrophilic) light. As a result, surfactant binding to DNA ... More
Dynamic bis-intercalation of a homodimeric thiazole orange dye in DNA: evidence of intercalator creeping.
'We have used one and two dimensional exchange 1H NMR spectroscopy to characterize the dynamics of the binding of a homodimeric thiazole orange dye, 1,1''-(4,4,8,8-tetramethyl-4,8-diaza-undecamethylene)-bis- 4-(3-methyl-2,3-dihydro-(benzo-1,3-thiazole)-2-methylidene)-quinol inium tetraiodide (TOTO), to double stranded DNA (dsDNA). The double stranded oligonucleotides used were d-(CGCTAGCG)2 (1) and d(CGCTAGCTAGCG)2 (2). TOTO binds preferentially to the ... More
Stable fluorescent complexes of double-stranded DNA with bis-intercalating asymmetric cyanine dyes: properties and applications.
AuthorsRye HS, Yue S, Wemmer DE, Quesada MA, Haugland RP, Mathies RA, Glazer AN
JournalNucleic Acids Res
PubMed ID1614866
'The synthesis, proof of structure, and the absorption and fluorescence properties of two new unsymmetrical cyanine dyes, thiazole orange dimer (TOTO; 1,1''-(4,4,7,7-tetramethyl-4,7- diazaundecamethylene)-bis-4-[3-methyl-2,3-dihydro-(benzo-1,3-thiaz ole)-2- methylidene]-quinolinium tetraiodide) and oxazole yellow dimer (YOYO; an analogue of TOTO with a benzo-1,3-oxazole in place of the benzo-1,3-thiazole) are reported. TOTO and YOYO are virtually ... More
Spectroscopic studies of single-stranded DNA ligands and oxazole yellow dyes.
AuthorsAbramo KH, Pitner JB, McGown LB
JournalBiospectroscopy
PubMed ID9547012
'Interactions between short single-stranded DNA ligands and fluorescent DNA indicator dyes were used to investigate binding selectivity of the ligands. Conformational differences among four DNA ligands of different sequence and structure, including two that form a G-quartet and two that do not, were confirmed by circular dichroism spectroscopy. Their interactions ... More
Snapshot blotting: transfer of nucleic acids and nucleoprotein complexes from electrophoresis gels to grids for electron microscopy.
AuthorsJett SD, Bear DG
JournalProc Natl Acad Sci U S A
PubMed ID8041711
'We present a technique, "snapshot blotting," for the electrophoretic transfer of nucleic acids and nucleoprotein complexes in gel electrophoresis bands onto highly stable carbon film-coated grids for imaging by electron microscopy. The method permits structural analysis of macromolecular species that have been resolved by a gel mobility-shift assay. To demonstrate ... More
Kinesin Superfamily Motor Protein KIF17 and mLin-10 in NMDA Receptor-Containing Vesicle Transport
'Experiments with vesicles containing N-methyl-D-aspartate (NMDA)receptor 2B (NR2B subunit) show that they are transported alongmicrotubules by KIF17, a neuron-specific molecular motor in neuronaldendrites. Selective transport is accomplished by direct interaction of theKIF17 tail with a PDZ domain of mLin-10 (Mint1/X11), which is aconstituent of a large protein complex including mLin-2 ... More
Selective detection of individual DNA molecules by capillary polymerase chain reaction.
AuthorsLi H, Xue G, Yeung ES
JournalAnal Chem
PubMed ID11321306
'On-line capillary polymerase chain reaction (PCR) coupled with laser-induced fluorescence detection was successfully demonstrated for individual DNA molecules. A single 30-microm-i.d. fused-silica capillary was used both as the reaction vessel and for isolating single molecules. SYBR green I dye was added into the reaction mixture for dynamic fluorescent labeling. Because ... More
X-ray induced DNA double-strand breaks in human sperm.
AuthorsSingh NP, Stephens RE
JournalMutagenesis
PubMed ID9491398
'A methodology for quantifying DNA double-strand breaks in human sperm is described. Sperm from three healthy human donors on three separate days each were irradiated with 12.5, 25, 50 and 100 cGy X-rays. Linear dose-response effects were observed in migrated DNA from sperm nuclei when electrophoresed under neutral conditions. RNase ... More
High-throughput flow cytometric DNA fragment sizing.
AuthorsVan Orden A, Keller RA, Ambrose WP
JournalAnal Chem
PubMed ID10655632
'The rate of detection and sizing of individual fluorescently labeled DNA fragments in conventional single-molecule flow cytometry (SMFC) is limited by optical saturation, photon-counting statistics, and fragment overlap to approximately 100 fragments/s. We have increased the detection rate for DNA fragment sizing in SMFC to approximately 2000 fragments/s by parallel ... More
Structure-function analysis of the protein-binding domains of Mac1p, a copper-dependent transcriptional activator of copper uptake in Saccharomyces cerevisiae.
AuthorsSerpe M, Joshi A, Kosman DJ
JournalJ Biol Chem
PubMed ID10506178
'The Mac1 protein in Saccharomyces cerevisiae is essential for the expression of yeast high affinity copper uptake. A positive transcription factor, Mac1p binds via its N-terminal domain to GCTC elements in the promoters of CTR1 and FRE1, encoding a copper permease and metal reductase, respectively. Mac1p-dependent transcriptional activation is negatively ... More
High-sensitivity capillary electrophoresis of double-stranded DNA fragments using monomeric and dimeric fluorescent intercalating dyes.
AuthorsZhu H, Clark SM, Benson SC, Rye HS, Glazer AN, Mathies RA
JournalAnal Chem
PubMed ID8067520
'Fluorescence-detected capillary electrophoresis separations of phi X174/HaeIII DNA restriction fragments have been performed using monomeric and dimeric intercalating dyes. Replaceable hydroxyethyl cellulose solutions were used as the separation medium. Confocal fluorescence detection was performed following 488-nm laser excitation. The limits of DNA detection for on-column staining with monomeric dyes (ethidium ... More
Maitotoxin-induced membrane blebbing and cell death in bovine aortic endothelial cells.
AuthorsEstacion M, Schilling WP
JournalBMC Physiol
PubMed ID11231888
'BACKGROUND: Maitotoxin, a potent cytolytic agent, causes an increase in cytosolic free Ca2+ concentration ([Ca2+]i) via activation of Ca2+-permeable, non-selective cation channels (CaNSC). Channel activation is followed by formation of large endogenous pores that allow ethidium and propidium-based vital dyes to enter the cell. Although activation of these cytolytic/oncotic pores, ... More
Stable fluorescent dye-DNA complexes in high sensitivity detection of protein-DNA interactions. Application to heat shock transcription factor.
AuthorsRye HS, Drees BL, Nelson HC, Glazer AN
JournalJ Biol Chem
PubMed ID8227088
'The gel mobility-shift assay is an important tool for the study of protein-nucleic acid interactions. High detection sensitivity is typically attained by radioisotopic labeling of the target nucleic acid fragments. A novel fluorescence methodology offers significant advantages over this conventional approach. Ethidium, thiazole orange, and oxazole yellow homodimers form stable, ... More
Factors governing the assembly of cationic phospholipid-DNA complexes.
AuthorsKennedy MT, Pozharski EV, Rakhmanova VA, MacDonald RC
JournalBiophys J
PubMed ID10692346
'The interaction of DNA with a novel cationic phospholipid transfection reagent, 1,2-dioleoyl-sn-glycero-3-ethylphosphocholine (EDOPC), was investigated by monitoring thermal effects, particle size, vesicle rupture, and lipid mixing. By isothermal titration calorimetry, the heat of interaction between large unilamellar EDOPC vesicles and plasmid DNA was endothermic at both physiological and low ionic ... More
Bis-intercalation of homodimeric thiazole orange dye derivatives in DNA.
AuthorsPetersen M, Hamed AA, Pedersen EB, Jacobsen JP
JournalBioconjug Chem
PubMed ID9893966
'The thiazole orange dye 1,1''-(4,4,8,8-tetramethyl-4, 8-diazaundecamethylene)-bis-4-[(3-methyl-2,3-dihydro-2(3H)-benzo-1 ,3-thiazolylidene)methyl]quinolinium tetraiodide (TOTO) binds to double-stranded DNA (dsDNA) in a sequence selective bis-intercalation. We have examined the binding of derivatives of TOTO with different substituents on the benzothiazole ring. The analogues are the following: 1,1''-(4,4,8,8-tetramethyl-4, 8-diazaundecamethylene)-[4-[3-(benzyl-2, 3-dihydro-2-(3H)-benzothiazolylidene)methyl]quinolinium]-[4-[3-(++ +methy l-2, 3-dihydro-2-(3H)-benzothiazolylidene)methyl]quinolinium]tetraio dide (TOTOBzl) and 1,1''-(4,4,8,8-tetramethyl-4, ... More
Green-light transilluminator for the detection without photodamage of proteins and DNA labeled with different fluorescent dyes.
AuthorsAlba FJ, Bermúdez A, Daban JR
JournalElectrophoresis
PubMed ID11258745
'The excitation spectra of Nile red and SYPRO red, two currently used dyes for the fluorescent staining of protein bands in sodium dodecyl sulfate (SDS)-polyacrylamide gels, show an excitation peak in the UV region and another in the visible region (maximum at about 550 nm). Ethidium bromide and other intercalating ... More
Concerted intercalation and minor groove recognition of DNA by a homodimeric thiazole orange dye.
'The thiazole orange dye TOTO binds to double-stranded DNA (dsDNA) by a sequence selective bis-intercalation. Each chromophore is sandwiched between two base pairs in a (5''-CpT-3''):(5''-ApG-3'') site, and the linker spans two base pairs in the minor groove. We have used one- and two-dimensional NMR spectroscopy to examine the dsDNA ... More
Correlating cell cycle with metabolism in single cells: combination of image and metabolic cytometry.
AuthorsKrylov SN, Zhang Z, Chan NW, Arriaga E, Palcic MM, Dovichi NJ
JournalCytometry
PubMed ID10451502
'BACKGROUND: We coin two terms: First, chemical cytometry describes the use of high-sensitivity chemical analysis techniques to study single cells. Second, metabolic cytometry is a form of chemical cytometry that monitors a cascade of biosynthetic and biodegradation products generated in a single cell. In this paper, we describe the combination ... More
Sharp DNA bends as landmarks of protein-binding sites on straightened DNA.
AuthorsYokota H, Fung K, Trask BJ, van den Engh G, Sarikaya M, Aebersold R
JournalAnal Chem
PubMed ID10330902
'We have developed a fluorescence-based method for mapping single or multiple protein-binding sites on straightened, large-size DNA molecules (> 5 kbp). In the described method, protein-DNA complexes were straightened and immobilized on a flat surface using surface tension. A fraction of the immobilized complexes displayed a sharp DNA bend with ... More
Polarization of scatter and fluorescence signals in flow cytometry.
AuthorsAsbury CL, Uy JL, van den Engh G
JournalCytometry
PubMed ID10805928
'BACKGROUND: The pulses of light scatter and fluorescence measured in flow cytometers exhibit varying degrees of polarization. Flow cytometers are heterogeneously sensitive to this polarization, depending on the light source(s), the optical layout, and the types of mirrors and filters used. Therefore, fluorescence polarization can affect apparent intensity ratios between ... More
Spectral measurements of intercalated PCR-amplified short tandem repeat alleles.
AuthorsMarino MA, Devaney JM, Davis PA, Smith JK, Girard JE
JournalAnal Chem
PubMed ID9823710
'Short tandem repeat (STR) alleles are popular for use as forensic markers due to their highly polymorphic nature. Commonly they are separated by gel electrophoresis and visualized using intercalation dyes. The purpose of this study was to determine the changes in absorbance and fluorescence of DNA-intercalation dye complexes as a ... More
Bisintercalation of homodimeric thiazole orange dyes in DNA: effect of modifying the linker.
'The thiazole orange dye 1,1'-(4,4,8,8-tetramethyl-4,8-diazaundecamethylene)-bis[4-[3-methy l-2, 3-dihydro(benzo-1,3-thiazole)-2-methylidene]]quinolinium tetraiodide (TOTO) binds to double-stranded DNA (dsDNA) in a sequence selective bisintercalation. Each chromophore is sandwiched between two base pairs in a (5'-CpT-3'):(5'-ApG-3') site, and the linker spans over two base pairs in the minor groove. The binding of analogs of TOTO in ... More
Nano-scale imaging of chromosomes and DNA by scanning near-field optical/atomic force microscopy.
AuthorsYoshino T, Sugiyama S, Hagiwara S, Fukushi D, Shichiri M, Nakao H, Kim JM, Hirose T, Muramatsu H, Ohtani T
JournalUltramicroscopy
PubMed ID12801660
'Nano-scale structures of the YOYO-1-stained barley chromosomes and lambda-phage DNA were investigated by scanning near-field optical/atomic force microscopy (SNOM/AFM). This technique enabled precise analysis of fluorescence structural images in relation to the morphology of the biomaterials. The results suggested that the fluorescence intensity does not always correspond to topographic height ... More
Visible diode lasers can be used for flow cytometric immunofluorescence and DNA analysis.
AuthorsDoornbos RM, De Grooth BG, Kraan YM, Van Der Poel CJ, Greve J
JournalCytometry
PubMed ID8187585
'This report describes a feasibility study concerning the use of a visible diode laser for two important fluorescence applications in a flow cytometer. With a 3 mW 635 nm diode laser, we performed immunofluorescence measurements using the fluorophore allophycocyanin (APC). We have measured CD8 positive lymphocytes with a two-step labeling ... More
Role of endocytosis in the transfection of L929 fibroblasts by polyethylenimine/DNA complexes.
AuthorsRémy-Kristensen A, Clamme JP, Vuilleumier C, Kuhry JG, Mély Y
JournalBiochim Biophys Acta
PubMed ID11513802
'Polyethylenimine (PEI) is one of the most efficient nonviral vectors for gene therapy. The aim of this study was to investigate the role of endocytosis in the transfection of synchronized L929 fibroblasts by PEI/DNA complexes. This was performed by confocal microscopy and flow cytometry, using the endocytosis marker FM4-64 and ... More
Dynamics of individual flexible polymers in a shear flow.
AuthorsLeDuc P, Haber C, Bao G, Wirtz D
JournalNature
PubMed ID10376595
'Polymer dynamics are of central importance in materials science, mechanical engineering, biology and medicine. The dynamics of macromolecular solutions and melts in shear flow are typically studied using bulk experimental methods such as light and neutron scattering and birefringence. But the effect of shear on the conformation and dynamics of ... More
Maitotoxin activates a nonselective cation channel and a P2Z/P2X(7)-like cytolytic pore in human skin fibroblasts.
AuthorsSchilling WP, Sinkins WG, Estacion M
JournalAm J Physiol
PubMed ID10516106
'Maitotoxin (MTX), a potent cytolytic agent, activates Ca(2+) entry via nonselective cation channels in virtually all types of cells. The identity of the channels involved and the biochemical events leading to cell lysis remain unknown. In the present study, the effect of MTX on plasmalemmal permeability of human skin fibroblasts ... More
Reduced survival of lens epithelial cells in the alphaA-crystallin-knockout mouse.
AuthorsXi JH, Bai F, Andley UP
JournalJ Cell Sci
PubMed ID12584250
'alphaA-Crystallin (alphaA) is a molecular chaperone expressed preferentially in the lens. alphaA transcripts are first detected during the early stages of lens development and its synthesis continues as the lens grows throughout life. alphaA(-/-) mouse lenses are smaller than controls, and lens epithelial cells derived from these mice have diminished ... More
Dynamics of transitional endoplasmic reticulum sites in vertebrate cells.
AuthorsHammond AT, Glick BS
JournalMol Biol Cell
PubMed ID10982397
'A typical vertebrate cell contains several hundred sites of transitional ER (tER). Presumably, tER sites generate elements of the ER-Golgi intermediate compartment (ERGIC), and ERGIC elements then generate Golgi cisternae. Therefore, characterizing the mechanisms that influence tER distribution may shed light on the dynamic behavior of the Golgi. We explored ... More
Interaction of dimeric intercalating dyes with single-stranded DNA.
AuthorsRye HS, Glazer AN
JournalNucleic Acids Res
PubMed ID7739900
'The unsymmetrical cyanine dye thiazole orange homodimer (TOTO) binds to single-stranded DNA (ssDNA, M13mp18 ssDNA) to form a fluorescent complex that is stable under the standard conditions of electrophoresis. The stability of this complex is indistinguishable from that of the corresponding complex of TOTO with double-stranded DNA (dsDNA). To examine ... More
Internal structure and dynamics of isolated Escherichia coli nucleoids assessed by fluorescence correlation spectroscopy.
AuthorsRomantsov T, Fishov I, Krichevsky O
JournalBiophys J
PubMed ID17259281
'The morphology and dynamics of DNA in a bacterial nucleoid affects the kinetics of such major processes as DNA replication, gene expression. and chromosome segregation. In this work, we have applied fluorescence correlation spectroscopy to assess the structure and internal dynamics of isolated Escherichia coli nucleoids. We show that structural ... More
Comet assay with nuclear extract incubation.
AuthorsWang AS, Ramanathan B, Chien YH, Goparaju CM, Jan KY
JournalAnal Biochem
PubMed ID15649377
'Alkaline comet assay is a simple sensitive method for detecting DNA strand breaks. However, at the time of cell lysis, only a fraction of the entire DNA damage appears as DNA strand breaks, while some DNA strand breaks may have been rejoined and some DNA lesions may still remain unexcised. ... More
Quantitative RNA-polymerase chain reaction-DNA analysis by capillary electrophoresis and laser-induced fluorescence.
AuthorsFasco MJ, Treanor CP, Spivack S, Figge HL, Kaminsky LS
JournalAnal Biochem
PubMed ID7710061
'Quantitative RNA-polymerase chain reaction (RNA-PCR) is an extremely powerful analytical tool owing to its specificity and high level of sensitivity. Quantitative RNA-PCR is, however, highly labor intensive. No analytical method currently exists that can accurately and rapidly quantitate the small quantities of DNA in RNA-PCR reaction mixtures. We have developed ... More
Single molecule analysis of DNA replication.
AuthorsHerrick J, Bensimon A
JournalBiochimie
PubMed ID10572299
'We describe here a novel approach for the study of DNA replication. The approach is based on a process called molecular combing and allows for the genome wide analysis of the spatial and temporal organization of replication units and replication origins in a sample of genomic DNA. Molecular combing is ... More
TOTO and YOYO: new very bright fluorochromes for DNA content analyses by flow cytometry.
AuthorsHirons GT, Fawcett JJ, Crissman HA
JournalCytometry
PubMed ID7513274
'Flow cytometric (FCM) studies were performed on nuclei, ethanol-fixed CHO cells, and isolated human GM130 chromosomes stained with two new cyanine dyes, TOTO and YOYO. These fluorochromes, which are dimers of thiazole orange and oxazole yellow, respectively, have high quantum efficiencies and exhibit specificities for both DNA and RNA. Bound ... More
Design and formulation of polyplexes based on pluronic-polyethyleneimine conjugates for gene transfer.
'Previously, we reported the evaluation of several polyplex-based gene delivery systems with respect to their effectiveness, toxicity, and cell type dependence in vitro. One system, P123-g-PEI(2K), a cationic graft block copolymer, is of particular interest as it has been demonstrated to successfully deliver genetic material to murine liver following systemic ... More
Whole-genome shotgun optical mapping of Rhodobacter sphaeroides strain 2.4.1 and its use for whole-genome shotgun sequence assembly.
AuthorsZhou S, Kvikstad E, Kile A, Severin J, Forrest D, Runnheim R, Churas C, Hickman JW, Mackenzie C, Choudhary M, Donohue T, Kaplan S, Schwartz DC
JournalGenome Res
PubMed ID12952882
'Rhodobacter sphaeroides 2.4.1 is a facultative photoheterotrophic bacterium with tremendous metabolic diversity, which has significantly contributed to our understanding of the molecular genetics of photosynthesis, photoheterotrophy, nitrogen fixation, hydrogen metabolism, carbon dioxide fixation, taxis, and tetrapyrrole biosynthesis. To further understand this remarkable bacterium, and to accelerate an ongoing sequencing project, ... More
Gene transfer by cationic surfactants is essentially limited by the trapping of the surfactant/DNA complexes onto the cell membrane: a fluorescence investigation.
AuthorsClamme JP, Bernacchi S, Vuilleumier C, Duportail G, Mély Y
JournalBiochim Biophys Acta
PubMed ID11030593
'The interaction between complexes of plasmid DNA with cetyltrimethylammonium bromide (CTAB) and L929 fibroblasts was first examined using confocal microscopy. The complexes labeled with the DNA intercalator, YOYO-1, were found to be trapped onto the external face of the plasma membrane; a feature that may constitute a major limiting step ... More
Bacterial fingerprinting by flow cytometry: bacterial species discrimination.
AuthorsKim Y, Jett JH, Larson EJ, Penttila JR, Marrone BL, Keller RA
JournalCytometry
PubMed ID10404148
'BACKGROUND: A flow cytometric measurement (FCM) technique has been developed to size DNA fragments. Individual fragments of a restriction digest of genomic DNA, stained with an intercalating dye, are passed through an ultrasensitive cytometer. The measured fluorescence intensity from each fragment is proportional to the fragment length. METHODS: The isolation ... More
The two nuclei of Giardia each have complete copies of the genome and are partitioned equationally at cytokinesis.
AuthorsYu LZ, Birky CW, Adam RD
JournalEukaryot Cell
PubMed ID12455954
'Giardia lamblia is medically important as a cause of diarrhea and malabsorption throughout the world and is thought to be one of the earliest-branching eukaryotes on a phylogenetic tree. Nevertheless, the mechanisms of inheritance are largely unknown. The trophozoites of Giardia and other diplomonads are interesting in their possession of ... More
Zebrafish vasa RNA but not its protein is a component of the germ plasm and segregates asymmetrically before germline specification.
AuthorsKnaut H, Pelegri F, Bohmann K, Schwarz H, Nüsslein-Volhard C
JournalJ Cell Biol
PubMed ID10811828
'Work in different organisms revealed that the vasa gene product is essential for germline specification. Here, we describe the asymmetric segregation of zebrafish vasa RNA, which distinguishes germ cell precursors from somatic cells in cleavage stage embryos. At the late blastula (sphere) stage, vasa mRNA segregation changes from asymmetric to ... More
Hyperproliferation and p53 status of lens epithelial cells derived from alphaB-crystallin knockout mice.
AuthorsBai F, Xi JH, Wawrousek EF, Fleming TP, Andley UP
JournalJ Biol Chem
PubMed ID12826669
'alphaB-Crystallin, a major protein of lens fiber cells, is a stress-induced chaperone expressed at low levels in the lens epithelium and numerous other tissues, and its expression is enhanced in certain pathological conditions. However, the function of alphaB in these tissues is not known. Lenses of alphaB-/- mice develop degeneration ... More
Groove-binding unsymmetrical cyanine dyes for staining of DNA: syntheses and characterization of the DNA-binding.
AuthorsKarlsson HJ, Eriksson M, Perzon E, Akerman B, Lincoln P, Westman G
JournalNucleic Acids Res
PubMed ID14576310
'Two new crescent-shaped unsymmetrical cyanine dyes have been synthesised and their interactions with DNA have been investigated by different spectroscopic methods. These dyes are analogues to a minor groove binding unsymmetrical cyanine dye, BEBO, recently reported by us. In this dye, the structure of the known intercalating cyanine dye BO ... More
Modifications of alkaline microgel electrophoresis for sensitive detection of DNA damage.
AuthorsSingh NP, Stephens RE, Schneider EL
JournalInt J Radiat Biol
PubMed ID8027608
'The alkaline microgel electrophoresis technique was modified to achieve a substantial increase in sensitivity for the detection of radiation-induced DNA damage in human lymphocytes. This increased sensitivity was achieved through: (1) the addition of free radical scavengers to the electrophoresis solution to reduce DNA damage generated during alkaline unwinding and ... More
Organized arrays of individual DNA molecules tethered to supported lipid bilayers.
AuthorsGranéli A, Yeykal CC, Prasad TK, Greene EC
JournalLangmuir
PubMed ID16378434
'An unappreciated aspect of many single-molecule techniques is the need for an inert surface to which individual molecules can be anchored without compromising their biological integrity. Here, we present new methods for tethering large DNA molecules to the surface of a microfluidic sample chamber that has been rendered inert by ... More
Observation by fluorescence microscopy of transcription on single combed DNA.
AuthorsGueroui Z, Place C, Freyssingeas E, Berge B
JournalProc Natl Acad Sci U S A
PubMed ID11983896
'Molecular combing is a powerful procedure for aligning a large array of DNA molecules onto a surface. This technique usually leads to an overstretching of about 150% of the molecules'' contour length. By changing the magnitude of capillary forces during the combing process, we were able to reduce the relative ... More
Fluorescent DNA nanotags: supramolecular fluorescent labels based on intercalating dye arrays assembled on nanostructured DNA templates.
AuthorsBenvin AL, Creeger Y, Fisher GW, Ballou B, Waggoner AS, Armitage BA
JournalJ Am Chem Soc
PubMed ID17256855
'Fluorescence detection and imaging are vital technologies in the life sciences and clinical diagnostics. The key to obtaining high-resolution images and sensitive detection is to use fluorescent molecules or particles that absorb and emit visible light with high efficiency. We have synthesized supramolecular complexes consisting of a branched DNA template ... More
Spatial organization of large-scale chromatin domains in the nucleus: a magnified view of single chromosome territories.
AuthorsFerreira J, Paolella G, Ramos C, Lamond AI
JournalJ Cell Biol
PubMed ID9412456
'We have analyzed the spatial organization of large scale chromatin domains in chinese hamster fibroblast, human lymphoid (IM-9), and marsupial kidney epithelial (PtK) cells by labeling DNA at defined stages of S phase via pulsed incorporation of halogenated deoxynucleosides. Most, if not all, chromosomes contribute multiple chromatin domains to both ... More
High-speed screening of polymerase chain reaction products by capillary electrophoresis.
'In an effort to develop capillary electrophoresis (CE) for high-throughput polymerase chain reaction (PCR) molecular diagnostics, a method was developed to rapidly screen small PCR products of similar molecular weights. The assay of interest required the separation of two PCR products (375 and 400 bp) in an assay of TGF-beta ... More
Connexin 47 (Cx47)-deficient mice with enhanced green fluorescent protein reporter gene reveal predominant oligodendrocytic expression of Cx47 and display vacuolized myelin in the CNS.
'To further characterize the recently described gap junction gene connexin 47 (Cx47), we generated Cx47-null mice by replacing the Cx47 coding DNA with an enhanced green fluorescent protein (EGFP) reporter gene, which was thus placed under control of the endogenous Cx47 promoter. Homozygous mutant mice were fertile and showed no ... More
Targeting Janus kinase 3 in mast cells prevents immediate hypersensitivity reactions and anaphylaxis.
AuthorsMalaviya R, Zhu D, Dibirdik I, Uckun FM
JournalJ Biol Chem
PubMed ID10480916
'Janus kinase 3 (JAK3), a member of the Janus family protein-tyrosine kinases, is expressed in mast cells, and its enzymatic activity is enhanced by IgE receptor/FcepsilonRI cross-linking. Selective inhibition of JAK3 in mast cells with 4-(4''-hydroxylphenyl)-amino-6, 7-dimethoxyquinazoline) (WHI-P131) blocked the phospholipase C activation, calcium mobilization, and activation of microtubule-associated protein ... More
Opposing actions of inositol 1,4,5-trisphosphate and ryanodine receptors on nuclear factor of activated T-cells regulation in smooth muscle.
AuthorsGomez MF, Stevenson AS, Bonev AD, Hill-Eubanks DC, Nelson MT,
JournalJ Biol Chem
PubMed ID12145283
'The nuclear factor of activated T-cells (NFAT), originally identified in T-cells, has since been shown to play a role in mediating Ca(2+)-dependent gene transcription in diverse cell types outside of the immune system. We have previously shown that nuclear accumulation of NFATc3 is induced in ileal smooth muscle by platelet-derived ... More
Selection of fluorescent probes for flow cytometric viability assessment of Listeria monocytogenes exposed to membrane-active and oxidizing disinfectants.
AuthorsLuppens SB, Barbaras B, Breeuwer P, Rombouts FM, Abee T
JournalJ Food Prot
PubMed ID12929825
'The aim of this study was to select fluorescence methods for use as alternatives to plate counting to assess the viability of Listeria monocytogenes cells exposed to benzalkonium chloride (BAC) and hydrogen peroxide, two disinfectants with different mechanisms of action. A further aim of this study was to determine whether ... More
Orientation of the chromophore dipoles in the TOTO-DNA system.
AuthorsSchins JM, Agronskaia A, de Grooth BG, Greve J
JournalCytometry
PubMed ID10520204
'BACKGROUND:Flow cytometry has been applied successfully to the sizing of medium to large-sized DNA molecules, thanks to the excellent staining properties of cyanine chromophores such as TOTO (homodimer of thiazole orange) (Petty et al.: Anal Chem 67:1755-1761, 1995). The hydrodynamic flow, used to focus the sample molecules in a small ... More
Entropic recoil separation of long DNA molecules.
AuthorsCabodi M, Turner SW, Craighead HG
JournalAnal Chem
PubMed ID12403567
'A novel technique that can rapidly separate long-strand polymers according to length is presented. The separation mechanism is mediated by a confinement-induced entropic force at the abrupt interface between regions of vastly different configuration entropy. To demonstrate this technique, DNA molecules were partially inserted into a dense array of nanopillars ... More
Intercalating fluorescence dye YOYO-1 prevents the folding transition in giant duplex DNA.
AuthorsYoshinaga N, Akitaya T, Yoshikawa K
JournalBiochem Biophys Res Commun
PubMed ID11500031
'Recently, it has become clear that with the addition of polyamines, giant DNA molecules of size greater than 10 kbp exhibit all-or-none switching between elongated coil and folded compact states. Here the effects of the intercalating fluorescent labeling dye, YOYO-1, and the minor-groove binding fluorescent labeling dye, DAPI, on the ... More
Use of locked nucleic acid oligonucleotides to add functionality to plasmid DNA.
AuthorsHertoghs KM, Ellis JH, Catchpole IR
JournalNucleic Acids Res
PubMed ID14530430
'The available reagents for the attachment of functional moieties to plasmid DNA are limiting. Most reagents bind plasmid DNA in a non-sequence- specific manner, with undefined stoichiometry, and affect DNA charge and delivery properties or involve chemical modifications that abolish gene expression. The design and ability of oligonucleotides (ODNs) containing ... More
The yeast Sgs1 helicase is differentially required for genomic and ribosomal DNA replication.
AuthorsVersini G, Comet I, Wu M, Hoopes L, Schwob E, Pasero P
JournalEMBO J
PubMed ID12682026
'The members of the RecQ family of DNA helicases play conserved roles in the preservation of genome integrity. RecQ helicases are implicated in Bloom and Werner syndromes, which are associated with genomic instability and predisposition to cancers. The human BLM and WRN helicases are required for normal S phase progression. ... More
Applications of cytotoxicity assays and pre-lethal mechanistic assays for assessment of human hepatotoxicity potential.
AuthorsXu JJ, Diaz D, O'Brien PJ
JournalChem Biol Interact
PubMed ID15522265
'While drug toxicity (especially hepatotoxicity) is the most frequent reason cited for withdrawal of an approved drug, no simple solution exists to adequately predict such adverse events. Simple cytotoxicity assays in HepG2 cells are relatively insensitive to human hepatotoxic drugs in a retrospective analysis of marketed pharmaceuticals. In comparison, a ... More
Optimisation of flow cytometric measurement of parasitaemia in plasmodium-infected mice.
AuthorsBarkan D, Ginsburg H, Golenser J
JournalInt J Parasitol
PubMed ID10779580
'Mouse malaria is often used as a model for drug testing. The results of drug trials are monitored by tedious (and consequently, sometimes inaccurate) microscopic counting of blood smears, or by flow cytometry. We suggest an improved, accurate and time-saving flow cytometric method for determination of parasitaemias in mice infected ... More
Two proteins of a plant DNA virus coordinate nuclear and plasmodesmal transport.
AuthorsNoueiry AO, Lucas WJ, Gilbertson RL
JournalCell
PubMed ID8124726
'Plant viruses establish a systemic infection by moving through plasmodesmata, but little is known of the mechanism(s) involved. The roles of two movement-associated proteins of a single-stranded DNA virus were investigated in vivo, using functional proteins expressed in E. coli and microinjection into plant cells. We report here that the ... More