SPACRCAN, a novel human interphotoreceptor matrix hyaluronan-binding proteoglycan synthesized by photoreceptors and pinealocytes.
AuthorsAcharya S, Foletta VC, Lee JW, Rayborn ME, Rodriguez IR, Young WS, Hollyfield JG
JournalJ Biol Chem
PubMed ID10702256
The interphotoreceptor matrix is a unique extracellular complex occupying the interface between photoreceptors and the retinal pigment epithelium in the fundus of the eye. Because of the putative supportive role in photoreceptor maintenance, it is likely that constituent molecules play key roles in photoreceptor function and may be targets for ... More
Lateral-flow and up-converting phosphor reporters to detect single-stranded nucleic acids in a sandwich-hybridization assay.
AuthorsCorstjens PL, Zuiderwijk M, Nilsson M, Feindt H, Sam Niedbala R, Tanke HJ
JournalAnal Biochem
PubMed ID12531205
'Up-converting Phosphor Technology (UPT) particles were used as reporters in lateral-flow (LF) assays to detect single-stranded nucleic acids. The 400-nm phosphor particles exhibit strong visible luminescence upon excitation with infrared (IR) light resulting in the total absence of background autofluorescence from other biological compounds. A sandwich-type hybridization assay was applied ... More
Naturally occurring mutations in human mitochondrial pre-tRNASer(UCN) can affect the transfer ribonuclease Z cleavage site, processing kinetics, and substrate secondary structure.
AuthorsYan H, Zareen N, Levinger L
JournalJ Biol Chem
PubMed ID16361254
'tRNAs are transcribed as precursors with a 5'' end leader and a 3'' end trailer. The 5'' end leader is processed by RNase P, and in most organisms in all three kingdoms, transfer ribonuclease (tRNase) Z can endonucleolytically remove the 3'' end trailer. Long ((L)) and short ((S)) forms of ... More
Protein-free parallel triple-stranded DNA complex formation.
'A 14 nt DNA sequence 5''-AGAATGTGGCAAAG-3'' from the zinc finger repeat of the human KRAB zinc finger protein gene ZNF91 bearing the intercalator 2-methoxy,6-chloro,9-amino acridine (Acr) attached to the sugar-phosphate backbone in various positions has been shown to form a specific triple helix (triplex) with a 16 bp hairpin (intramolecular) ... More
Phylogenetic assessment of length variation at a microsatellite locus.
AuthorsOrtí G, Pearse DE, Avise JC
JournalProc Natl Acad Sci U S A
PubMed ID9380705
'Sixty-six haplotypes at a locus containing a simple dinucleotide (CA)n microsatellite repeat were isolated by PCR-single-strand conformational polymorphism from populations of the horseshoe crab Limulus polyphemus. These haplotypes were sequenced to assess nucleotide variation directly. Thirty-four distinct sequences (alleles) were identified in a region 570 bp long that included the ... More
An automated microplate-based method for monitoring DNA strand breaks in plasmids and bacterial artificial chromosomes.
AuthorsRock C, Shamlou PA, Levy MS
JournalNucleic Acids Res
PubMed ID12771229
'A method is described for high-throughput monitoring of DNA backbone integrity in plasmids and artificial chromosomes in solution. The method is based on the denaturation properties of double-stranded DNA in alkaline conditions and uses PicoGreen fluorochrome to monitor denaturation. In the present method, fluorescence enhancement of PicoGreen at pH 12.4 ... More
Flow cytometric analysis of bacteria- and virus-like particles in lake sediments.
AuthorsDuhamel S, Jacquet S
JournalJ Microbiol Methods
PubMed ID16081175
'Flow cytometry (FCM) was successfully used to analyze freshwater bacteria and viruses in lake sediments after relatively simple sample treatment and optimization of dilution/fixation/staining procedures. Biological particles from Lakes Geneva and Bourget were first separated from the sediments by using both Sodium Pyrophosphate (0.01 M final concentration) and Polyoxyethylene-Sorbitan Monooleate ... More
Separation of miRNA and its methylation products by capillary electrophoresis.
AuthorsLi N, Nguyen A, Diedrich J, Zhong W,
JournalJ Chromatogr A
PubMed ID18649888
'Methylation is a crucial step in plant microRNA biogenesis. To improve our understanding of the methylation process and its regulation, a rapid and convenient high-throughput method should be sought to help with the study of reaction kinetics and assist the search for chemical inhibitors of the methyltransferase, HEN1. In this ... More
Normalization of RNA hybridization signals by means of SYBR green II-stained 28S or 18S ribosomal RNA and a phosphor imager.
AuthorsSpiess AN, Ivell R
JournalBiotechniques
PubMed ID9894590
A rapid, sensitive, and nonradioactive method for assay of FHIT Ap3A hydrolase activity by fluorescence thin-layer chromatographic image analysis.
AuthorsJi L, Fang B, Roth JA
JournalAnal Biochem
PubMed ID10361018
A fluorometric assay for the quantification of RNA in solution with nanogram sensitivity.
AuthorsSchmidt DM, Ernst JD
JournalAnal Biochem
PubMed ID8600826
An evaluation of four staining methods for the detection of DNA in nondenaturing polyacrylamide gels.
AuthorsStothard JR, Frame IA, Miles MA
JournalAnal Biochem
PubMed ID9367513
Rapid and simple quantification of bacterial cells by using a microfluidic device.
AuthorsSakamoto C, Yamaguchi N, Nasu M,
JournalAppl Environ Microbiol
PubMed ID15691978
This study investigated a microfluidic chip-based system (on-chip flow cytometry) for quantification of bacteria both in culture and in environmental samples. Bacterial numbers determined by this technique were similar to those obtained by direct microscopic count. The time required for this on-chip flow cytometry was only 30 min per 6 ... More
Utility of green fluorescent nucleic acid dyes and aluminum oxide membrane filters for rapid epifluorescence enumeration of soil and sediment bacteria.
AuthorsWeinbauer MG, Beckmann C, Höfle MG
JournalAppl Environ Microbiol
PubMed ID9835595
High background fluorescence and unspecific staining hampered the epifluorescence enumeration of bacteria in 45% of the tested soil and sediment samples with 4',6-diamidino-2-phenylindole (DAPI) and polycarbonate membrane filters. These problems of the determination of total cell counts can be circumvented by using green fluorescent high-affinity nucleic acid dyes and aluminum ... More
Analysis of DNA microarrays by non-destructive fluorescent staining using SYBR green II.
AuthorsBattaglia C, Salani G, Consolandi C, Bernardi LR, De Bellis G
JournalBiotechniques
PubMed ID10907080
A simple, non-destructive procedure is described to determine the quality of DNA arrays before they are used. It consists of a preliminary staining step of the DNA microarray by using SYBR green II, a fluorophore with specific affinity for ssDNA, followed by a laser scan analysis. The surface quality, integrity ... More
Flow cytometric detection of viruses.
AuthorsBrussaard CP, Marie D, Bratbak G
JournalJ Virol Methods
PubMed ID10716350
Representatives from several different virus families (Baculoviridae, Herpesviridae, Myoviridae, Phycodnaviridae, Picornaviridae, Podoviridae, Retroviridae, and Siphoviridae) were stained using a variety of highly fluorescent nucleic acid specific dyes (SYBR Green I, SYBR Green II, OliGreen, PicoGreen) and examined using a standard flow cytometer equipped with a standard 15 mW argon-ion laser. ... More
Nucleic acid detection using non-radioactive labelling methods.
AuthorsMansfield ES, Worley JM, McKenzie SE, Surrey S, Rappaport E, Fortina P
JournalMol Cell Probes
PubMed ID7477006
Nucleic acid probe-based assays are now widely used in genetic research, human identification, forensics and in a broad spectrum of clinical assays in the fields of microbiology, haematology/oncology and virology. Labelled probes are used in a variety of assay formats including dot-blots, Southern blots (DNA target), Northern blots (RNA target), ... More
Herp, a new ubiquitin-like membrane protein induced by endoplasmic reticulum stress.
AuthorsKokame K, Agarwala KL, Kato H, Miyata T
JournalJ Biol Chem
PubMed ID10922362
Hyperhomocysteinemia, a risk factor for vascular disease, injures endothelial cells through undefined mechanisms. We previously identified several homocysteine-responsive genes in cultured human vascular endothelial cells, including the endoplasmic reticulum (ER)-resident molecular chaperone GRP78/BiP. Here, we demonstrate that homocysteine induces the ER stress response and leads to the expression of a ... More
Microarray optimizations: increasing spot accuracy and automated identification of true microarray signals.
AuthorsTran PH, Peiffer DA, Shin Y, Meek LM, Brody JP, Cho KW
JournalNucleic Acids Res
PubMed ID12060692
In this paper, fluorescent microarray images and various analysis techniques are described to improve the microarray data acquisition processes. Signal intensities produced by rarely expressed genes are initially correctly detected, but they are often lost in corrections for background, log or ratio. Our analyses indicate that a simple correlation between ... More
In situ analysis of single-stranded and duplex siRNA integrity in living cells.
AuthorsRaemdonck K, Remaut K, Lucas B, Sanders NN, Demeester J, De Smedt SC
JournalBiochemistry
PubMed ID16939213
To attain the full therapeutic promise of short interfering RNA (siRNA), it is believed that improvements such as increased biostability are critical. Regrettably, thus far, insufficient in situ data are on hand regarding the intracellular stability of siRNAs. We report on the use of an advanced fluorescence-based method to probe ... More
Mutational analysis of the transforming growth factor beta receptor type II gene in human ovarian carcinoma.
AuthorsLynch MA, Nakashima R, Song H, DeGroff VL, Wang D, Enomoto T, Weghorst CM
JournalCancer Res
PubMed ID9766642
In the present study, we evaluated a series of sporadic ovarian carcinomas for mutations within the entire coding region of TbetaR-II. Using reverse transcription-PCR and "Cold" single-strand conformational polymorphism analysis, 6 of 24 samples (25%) were found to contain code-altering mutations in TbetaR-II: (a) four mutations resulting in amino acid ... More
Enumeration of water-borne bacteria using viability assays and flow cytometry: a comparison to culture-based techniques.
AuthorsHoefel D, Grooby WL, Monis PT, Andrews S, Saint CP
JournalJ Microbiol Methods
PubMed ID14607402
Maintaining optimal conditions in catchments or distribution systems relies heavily on water authorities having access to rapid and accurate water quality data, including an indication of bacteriological quality. In this study, the BacLight bacterial viability kit and carboxyfluorescein diacetate (CFDA) were coupled with flow cytometry (FCM) for rapid detection of ... More
Molecular and biochemical characterization of a novel oxysterol-binding protein (OSBP2) highly expressed in retina.
AuthorsMoreira EF, Jaworski C, Li A, Rodriguez IR
JournalJ Biol Chem
PubMed ID11278871
We are interested in understanding the possible function(s) of the oxysterol-binding proteins in mediating oxysterol cytotoxicity in the retina. In this study we describe the cloning, localization, and biological activity of a novel oxysterol-binding protein (OSBP2), and complete the molecular characterization of the previously known OSBP1. Both OSBP genes contain ... More
Sensitive determination of microbial growth by nucleic acid staining in aqueous suspension.
AuthorsMartens-Habbena W, Sass H
JournalAppl Environ Microbiol
PubMed ID16391029
The determination of cell numbers or biomass in laboratory cultures or environmental samples is usually based on turbidity measurements, viable counts, biochemical determinations (e.g., protein and lipid measurements), microscopic counting, or recently, flow cytometric analysis. In the present study, we developed a novel procedure for the sensitive quantification of microbial ... More
Detailed characterization of the posttranscriptional gene-silencing-related small RNA in a GUS gene-silenced tobacco.
AuthorsHutvágner G, Mlynárová L, Nap JP
JournalRNA
PubMed ID11073220
Posttranscriptional gene-silencing phenomena such as cosuppression and RNA interference are associated with the occurrence of small, about 21-23 nt short RNA species homologous to the silenced gene. We here show that the small RNA present in silenced transgenic plants can easily be detected in total RNA isolated according to standard ... More