JournalDrug metabolism and disposition: the biological fate of chemicals
PubMed ID15523049
Rapid quantification of DNA samples extracted from buccal scrapes prior to DNA profiling.
AuthorsHopwood A, Oldroyd N, Fellows S, Ward R, Owen SA, Sullivan K
JournalBiotechniques
PubMed ID9232218
Simultaneous extraction from bacterioplankton of total RNA and DNA suitable for quantitative structure and function analyses.
AuthorsWeinbauer MG, Fritz I, Wenderoth DF, Höfle MG
JournalAppl Environ Microbiol
PubMed ID11872453
The aim of this study was to develop a protocol for the simultaneous extraction from bacterioplankton of RNA and DNA suitable for quantitative molecular analysis. By using a combined mechanical and chemical extraction method, the highest RNA and DNA yield was obtained with sodium lauryl sarcosinate-phenol or DivoLab-phenol as the ... More
Conventional methods versus 16S ribosomal DNA sequencing for identification of nontuberculous mycobacteria: cost analysis.
AuthorsCook VJ, Turenne CY, Wolfe J, Pauls R, Kabani A
JournalJ Clin Microbiol
PubMed ID12624023
The clinical profile of nontuberculous mycobacteria (NTM) has been raised by the human immunodeficiency virus and AIDS pandemic. Different laboratory techniques, often molecular based, are available to facilitate the rapid and accurate identification of NTM. The expense of these advanced techniques has been questioned. At the National Reference Center for ... More
Exo-proofreading, a versatile SNP scoring technology.
AuthorsCahill P, Bakis M, Hurley J, Kamath V, Nielsen W, Weymouth D, Dupuis J, Doucette-Stamm L, Smith DR
JournalGenome Res
PubMed ID12695330
We report the validation of a new assay for typing single nucleotide polymorphisms (SNPs) that takes advantage of the 3'-to-5' exonuclease proofreading activity of many DNA polymerases. The assay uses one or more primers labeled on the 3' nucleotide base, and can be implemented in a variety of formats including ... More
Antibodies highly effective in SCID mice during infection by the intracellular bacterium Ehrlichia chaffeensis are of picomolar affinity and exhibit preferential epitope and isotype utilization.
AuthorsLi JS, Chu F, Reilly A, Winslow GM
JournalJ Immunol
PubMed ID12133967
Although often considered to be ineffective against intracellular bacteria, Abs, in the absence of lymphocytes, have been shown previously to protect SCID mice from lethal infection by the obligate intracellular bacterium Ehrlichia chaffeensis, even when administered well after infection has been established. To identify characteristics of Abs that are critical ... More
Genome-wide loss of heterozygosity analysis from laser capture microdissected prostate cancer using single nucleotide polymorphic allele (SNP) arrays and a novel bioinformatics platform dChipSNP.
AuthorsLieberfarb ME, Lin M, Lechpammer M, Li C, Tanenbaum DM, Febbo PG, Wright RL, Shim J, Kantoff PW, Loda M, Meyerson M, Sellers WR
JournalCancer Res
PubMed ID12941794
Oligonucleotide arrays that detect single nucleotide polymorphisms were used to generate genome-wide loss of heterozygosity (LOH) maps from laser capture microdissected paraffin-embedded samples using as little as 5 ng of DNA. The allele detection rate from such samples was comparable with that obtained with standard amounts of DNA prepared from ... More
Molecular genetic evidence for monoclonal origin of bilateral ovarian serous borderline tumors.
Patients with serous borderline tumors of the ovary often present with multiple tumors at different sites in the abdominal cavity. Whether different foci of ovarian serous borderline tumors are monoclonal in origin, arising as a consequence of spread from a single ovarian site, or whether such deposits are polyclonal and ... More
Growth and methane oxidation rates of anaerobic methanotrophic archaea in a continuous-flow bioreactor.
AuthorsGirguis PR, Orphan VJ, Hallam SJ, DeLong EF
JournalAppl Environ Microbiol
PubMed ID12957936
Anaerobic methanotrophic archaea have recently been identified in anoxic marine sediments, but have not yet been recovered in pure culture. Physiological studies on freshly collected samples containing archaea and their sulfate-reducing syntrophic partners have been conducted, but sample availability and viability can limit the scope of these experiments. To better ... More
Novel ATP6V1B1 and ATP6V0A4 mutations in autosomal recessive distal renal tubular acidosis with new evidence for hearing loss.
AuthorsStover EH, Borthwick KJ, Bavalia C, Eady N, Fritz DM, Rungroj N, Giersch AB, Morton CC, Axon PR, Akil I, Al-Sabban EA, Baguley DM, Bianca S, Bakkaloglu A, Bircan Z, Chauveau D, Clermont MJ, Guala A, Hulton SA, Kroes H, Li Volti G, Mir S, Mocan H, Nayir A, Ozen S, Rodriguez Soriano J, Sanjad SA, Tasic V, Taylor CM, Topaloglu R, Smith AN, Karet FE
JournalJ Med Genet
PubMed ID12414817
Autosomal recessive distal renal tubular acidosis (rdRTA) is characterised by severe hyperchloraemic metabolic acidosis in childhood, hypokalaemia, decreased urinary calcium solubility, and impaired bone physiology and growth. Two types of rdRTA have been differentiated by the presence or absence of sensorineural hearing loss, but appear otherwise clinically similar. Recently, we ... More
Spatial distribution and stability of the eight microbial species of the altered schaedler flora in the mouse gastrointestinal tract.
AuthorsSarma-Rupavtarm RB, Ge Z, Schauer DB, Fox JG, Polz MF
JournalAppl Environ Microbiol
PubMed ID15128534
The overall complexity of the microbial communities in the gastrointestinal (GI) tracts of mammals has hindered observations of dynamics and interactions of individual bacterial populations. However, such information is crucial for understanding the diverse disease-causing and protective roles that gut microbiota play in their hosts. Here, we determine the spatial ... More
Quantitative detection of Listeria monocytogenes and Listeria innocua by real-time PCR: assessment of hly, iap, and lin02483 targets and AmpliFluor technology.
AuthorsRodrÃguez-Lázaro D, Hernández M, Scortti M, Esteve T, Vázquez-Boland JA, Pla M
JournalAppl Environ Microbiol
PubMed ID15006755
We developed and assessed real-time PCR (RTi-PCR) assays for the detection and quantification of the food-borne pathogen Listeria monocytogenes and the closely related nonpathogenic species L. innocua. The target genes were hly and iap for L. monocytogenes and lin02483 for L. innocua. The assays were 100% specific, as determined with ... More
The impact of CYP2C9 genetics and oral contraceptives on cytochrome P450 2C9 phenotype.
AuthorsSandberg M, Johansson I, Christensen M, Rane A, Eliasson E
JournalDrug Metab Dispos
PubMed ID15100169
CYP2C9-dependent drug metabolism is subject to large interindividual variation. To some extent, this is explained by genetic polymorphism with expression of enzyme variants that differ in catalytic activity. The aim of this study was to characterize the variation in CYP2C9 phenotype in relation to genotype, with further analysis of the ... More
Spatial and temporal distribution of two diazotrophic bacteria in the Chesapeake Bay.
AuthorsShort SM, Jenkins BD, Zehr JP
JournalAppl Environ Microbiol
PubMed ID15066812
The aim of this study was to initiate autecological studies on uncultivated natural populations of diazotrophic bacteria by examining the distribution of specific diazotrophs in the Chesapeake Bay. By use of quantitative PCR, the abundance of two nifH sequences (907h22 and 912h4) was quantified in water samples collected along a ... More
A novel strategy to engineer DNA polymerases for enhanced processivity and improved performance in vitro.
AuthorsWang Y, Prosen DE, Mei L, Sullivan JC, Finney M, Vander Horn PB
JournalNucleic Acids Res
PubMed ID14973201
Mechanisms that allow replicative DNA polymerases to attain high processivity are often specific to a given polymerase and cannot be generalized to others. Here we report a protein engineering-based approach to significantly improve the processivity of DNA polymerases by covalently linking the polymerase domain to a sequence non-specific dsDNA binding ... More
Whole genome amplification of DNA from laser capture-microdissected tissue for high-throughput single nucleotide polymorphism and short tandem repeat genotyping.
AuthorsRook MS, Delach SM, Deyneko G, Worlock A, Wolfe JL
JournalAm J Pathol
PubMed ID14695315
Genome-wide screening of genetic alterations between normal and cancer cells, as well as among subgroups of tumors, is important for establishing molecular mechanism and classification of cancer. Gene silencing through loss of heterozygosity is widely observed in cancer cells and detectable by analyzing allelic loss of single nucleotide polymorphism and/or ... More
Balanced-PCR amplification allows unbiased identification of genomic copy changes in minute cell and tissue samples.
AuthorsWang G, Brennan C, Rook M, Wolfe JL, Leo C, Chin L, Pan H, Liu WH, Price B, Makrigiorgos GM
JournalNucleic Acids Res
PubMed ID15155823
Analysis of genomic DNA derived from cells and fresh or fixed tissues often requires whole genome amplification prior to microarray screening. Technical hurdles to this process are the introduction of amplification bias and/or the inhibitory effects of formalin fixation on DNA amplification. Here we demonstrate a balanced-PCR procedure that allows ... More
Reduction in diversity of the colonic mucosa associated bacterial microflora in patients with active inflammatory bowel disease.
AuthorsOtt SJ, Musfeldt M, Wenderoth DF, Hampe J, Brant O, Fölsch UR, Timmis KN, Schreiber S
JournalGut
PubMed ID15082587
BACKGROUND AND AIMS: The intestinal bacterial microflora plays an important role in the aetiology of inflammatory bowel disease (IBD). As most of the colonic bacteria cannot be identified by culture techniques, genomic technology can be used for analysis of the composition of the microflora. PATIENTS AND METHODS: The mucosa associated ... More
Chromosomal proteins HMGN3a and HMGN3b regulate the expression of glycine transporter 1.
AuthorsWest KL, Castellini MA, Duncan MK, Bustin M
JournalMol Cell Biol
PubMed ID15082770
HMGN proteins promote chromatin unfolding, enhance access to nucleosomes, and modulate transcription from chromatin templates. It is not known whether they act indiscriminately as general modulators of transcription or whether they regulate specific gene expression. Here, we investigated the role of HMGN3, a recently discovered HMGN family member, in transcription ... More
Quantitative analysis of diverse Lactobacillus species present in advanced dental caries.
AuthorsByun R, Nadkarni MA, Chhour KL, Martin FE, Jacques NA, Hunter N
JournalJ Clin Microbiol
PubMed ID15243071
Our previous analysis of 65 advanced dental caries lesions by traditional culture techniques indicated that lactobacilli were numerous in the advancing front of the progressive lesion. Production of organic acids by lactobacilli is considered to be important in causing decalcification of the dentinal matrix. The present study was undertaken to ... More
Human stem cell delivery for treatment of large segmental bone defects.
AuthorsDupont KM, Sharma K, Stevens HY, Boerckel JD, García AJ, Guldberg RE,
JournalProc Natl Acad Sci U S A
PubMed ID20133731
'Local or systemic stem cell delivery has the potential to promote repair of a variety of damaged or degenerated tissues. Although various stem cell sources have been investigated for bone repair, few comparative reports exist, and cellular distribution and viability postimplantation remain key issues. In this study, we quantified the ... More
Apical, lateral, and basal polarization cues contribute to the development of the follicular epithelium during Drosophila oogenesis.
AuthorsTanentzapf G, Smith C, McGlade J, Tepass U
JournalJ Cell Biol
PubMed ID11076972
'Analysis of the mechanisms that control epithelial polarization has revealed that cues for polarization are mediated by transmembrane proteins that operate at the apical, lateral, or basal surface of epithelial cells. Whereas for any given epithelial cell type only one or two polarization systems have been identified to date, we ... More
A Novel Pathway for Nickel-induced Interleukin-8 Expression.
'Inhalation of particulate nickel subsulfide (Ni(3)S(2)) causes chronic active inflammation and fibrosis of the lungs. However, the mechanisms for these effects are not well understood. Therefore, cell culture experiments with BEAS-2B human airway epithelial cells were conducted to test the hypothesis that exposure to non-cytotoxic levels of Ni(3)S(2) induces expression ... More
Modulation of gene expression in Leishmania drug resistant mutants as determined by targeted DNA microarrays.
AuthorsGuimond C, Trudel N, Brochu C, Marquis N, El Fadili A, Peytavi R, Briand G, Richard D, Messier N, Papadopoulou B, Corbeil J, Bergeron MG, Légaré D, Ouellette M
JournalNucleic Acids Res
PubMed ID14530437
'In the protozoan parasite Leishmania, drug resistance can be a complex phenomenon. Several metabolic pathways and membrane transporters are implicated in the resistance phenotype. To monitor the expression of these genes, we generated custom DNA microarrays with PCR fragments corresponding to 44 genes involved with drug resistance. Transcript profiling of ... More
High-throughput measurement of the Tp53 response to anticancer drugs and random compounds using a stably integrated Tp53-responsive luciferase reporter.
AuthorsSohn TA, Bansal R, Su GH, Murphy KM, Kern SE
JournalCarcinogenesis
PubMed ID12082016
'Human Tp53 is normally a short-lived protein. Tp53 protein is stabilized and levels are increased in response to a variety of cellular stresses, including those induced by genotoxic anticancer drugs and environmental exposures. To engineer an efficient assay based on this property, we constructed and integrated a Tp53-specific reporter system ... More
Selection of cysteine protease inhibitor-resistant malaria parasites is accompanied by amplification of falcipain genes and alteration in inhibitor transport.
AuthorsSingh A, Rosenthal PJ
JournalJ Biol Chem
PubMed ID15192087
'Cysteine protease inhibitors are being studied as possible new antimalarial agents. To evaluate the potential for resistance to these compounds, we subjected chloroquine-resistant (W2 strain) Plasmodium falciparum to increasing concentrations of a vinyl sulfone cysteine protease inhibitor. After incubation with 1-200 nm morpholine urea-leucine-homophenylalanine-phenyl vinyl sulfone over approximately 8 months, ... More
Quantitation of DNA extracted after micropreparation of cells from frozen and formalin-fixed tissue sections.
AuthorsSerth J, Kuczyk MA, Paeslack U, Lichtinghagen R, Jonas U
JournalAm J Pathol
PubMed ID10751344
'Quantitation of DNA from microdissected fresh-frozen or paraffin-embedded tissue sections would be not only a valuable tool for ensuring optimum reaction conditions for many types of qualitative polymerase chain reaction (PCR) analyses, but also a prerequisite for any kind of subsequently performed genetic analyses aimed at the absolute quantitation of ... More
Factors affecting quantification of total DNA by UV spectroscopy and PicoGreen fluorescence.
AuthorsHolden MJ, Haynes RJ, Rabb SA, Satija N, Yang K, Blasic JR,
JournalJ Agric Food Chem
PubMed ID19627145
'The total amount of DNA in a preparation extracted from tissues can be measured in several ways, each method offering advantages and disadvantages. For the sake of accuracy in quantitation, it is of interest to compare these methodologies and determine if good correlation can be achieved between them. Different answers ... More
Identification and purification of functional human beta-cells by a new specific zinc-fluorescent probe.
'Pancreatic beta-cells contain large amounts of zinc. We took advantage of this to try to localize, quantify, and isolate insulin-producing cells from islet preparations. Our study was designed to identify a non-toxic zinc-sensitive fluorescent probe able to selectively label labile zinc in viable beta-cells and to exhibit excitation and emission ... More
Performance of high-throughput DNA quantification methods.
AuthorsHaque KA, Pfeiffer RM, Beerman MB, Struewing JP, Chanock SJ, Bergen AW
JournalBMC Biotechnol
PubMed ID14583097
'BACKGROUND: The accuracy and precision of estimates of DNA concentration are critical factors for efficient use of DNA samples in high-throughput genotype and sequence analyses. We evaluated the performance of spectrophotometric (OD) DNA quantification, and compared it to two fluorometric quantification methods, the PicoGreen assay (PG), and a novel real-time ... More
Seasonal changes in an alpine soil bacterial community in the colorado rocky mountains.
AuthorsLipson DA, Schmidt SK
JournalAppl Environ Microbiol
PubMed ID15128545
'The period when the snowpack melts in late spring is a dynamic time for alpine ecosystems. The large winter microbial community begins to turn over rapidly, releasing nutrients to plants. Past studies have shown that the soil microbial community in alpine dry meadows of the Colorado Rocky Mountains changes in ... More
Selective induction of Th2-attracting chemokines CCL17 and CCL22 in human B cells by latent membrane protein 1 of Epstein-Barr virus.
AuthorsNakayama T, Hieshima K, Nagakubo D, Sato E, Nakayama M, Kawa K, Yoshie O
JournalJ Virol
PubMed ID14747532
'Chemokines are likely to play important roles in the pathophysiology of diseases associated with Epstein-Barr virus (EBV). Here, we have analyzed the repertoire of chemokines expressed by EBV-infected B cells. EBV infection of B cells induced expression of TARC/CCL17 and MDC/CCL22, which are known to attract Th2 cells and regulatory ... More
5-Chlorouracil, a marker of DNA damage from hypochlorous acid during inflammation. A gas chromatography-mass spectrometry assay.
AuthorsJiang Q, Blount BC, Ames BN
JournalJ Biol Chem
PubMed ID12810714
'Hypochlorous acid (HOCl), generated from H2O2 and Cl- by myeloperoxidase in activated neutrophils, causes tissue damage during inflammation. We have developed a simple, sensitive (approximately 0.2 fmol on column) and specific GC-MS assay for the detection of 5-chlorouracil (5-ClUra), a signature product of HOCl-mediated damage to nucleobases. In this assay, ... More
Performance assessment of eight high-throughput PCR assays for viral load quantitation of oncogenic HPV types.
AuthorsFlores-Munguia R, Siegel E, Klimecki WT, Giuliano AR
JournalJ Mol Diagn
PubMed ID15096567
'Infection with mucosotropic human papillomavirus (HPV) is the necessary cause of cervical intraepithelial neoplasia. Several epidemiological studies suggest that HPV viral load can be a risk factor of cervical dysplasia. The purpose of the present study was to evaluate a methodology to determine HPV viral load of eight oncogenic HPV ... More
mRNA extraction and reverse transcription-PCR protocol for detection of nifH gene expression by Azotobacter vinelandii in soil.
AuthorsBürgmann H, Widmer F, Sigler WV, Zeyer J
JournalAppl Environ Microbiol
PubMed ID12676666
'The study of free-living nitrogen-fixing organisms in bulk soil is hampered by the great diversity of soil microbial communities and the difficulty of relating nitrogen fixation activities to individual members of the diazotroph populations. We developed a molecular method that allows analysis of nifH mRNA expression in soil in parallel ... More
Ku entry into DNA inhibits inward DNA transactions in vitro.
AuthorsFrit P, Li RY, Arzel D, Salles B, Calsou P
JournalJ Biol Chem
PubMed ID10945984
'Association of the DNA end-binding Ku70/Ku80 heterodimer with the 460-kDa serine/threonine kinase catalytic subunit forms the DNA-dependent protein kinase (DNA-PK) that is required for double-strand break repair by non-homologous recombination in mammalian cells. Recently, we have proposed a model in which the kinase activity is required for translocation of the ... More
Use of isogenic human cancer cells for high-throughput screening and drug discovery.
'Cell-based screening for novel tumor-specific drugs has been compromised by the lack of appropriate control cells. We describe a strategy for drug screening based on isogenic human cancer cell lines in which key tumorigenic genes have been deleted by targeted homologous recombination. As a test case, a yellow fluorescent protein ... More
Isothermal reactions for the amplification of oligonucleotides.
AuthorsVan Ness J, Van Ness LK, Galas DJ
JournalProc Natl Acad Sci U S A
PubMed ID12679520
'We have devised a class of isothermal reactions for amplifying DNA. These homogeneous reactions rapidly synthesize short oligonucleotides (8-16 bases) specified by the sequence of an amplification template. Versions of the reactions can proceed in either a linear or an exponential amplification mode. Both of these reactions require simple, constant ... More
Characterization of recombinant HPV6 and 11 E1 helicases: effect of ATP on the interaction of E1 with E2 and mapping of a minimal helicase domain.
AuthorsWhite PW, Pelletier A, Brault K, Titolo S, Welchner E, Thauvette L, Fazekas M, Cordingley MG, Archambault J
JournalJ Biol Chem
PubMed ID11304544
'To better characterize the enzymatic activities required for human papillomavirus (HPV) DNA replication, the E1 helicases of HPV types 6 and 11 were produced using a baculovirus expression system. The purified wild type proteins and a version of HPV11 E1 lacking the N-terminal 71 amino acids, which was better expressed, ... More
Extraction of plasmid DNA from Escherichia coli cell lysate in a thermoseparating aqueous two-phase system.
AuthorsKepka C, Rhodin J, Lemmens R, Tjerneld F, Gustavsson PE
JournalJ Chromatogr A
PubMed ID14753711
'The primary purification of a 6.1 kilo base pair (kbp) plasmid from a desalted alkaline lysate has been accomplished by a thermoseparating aqueous two-phase system [(50% ethylene oxide-50% propylene oxide)-Dextran T 500]. The partitioning of the different nucleic acids (plasmid DNA, RNA, genomic DNA) in the thermoseparating aqueous two-phase system ... More
Autoinhibition of TFIIIB70 binding by the tetratricopeptide repeat-containing subunit of TFIIIC.
AuthorsMoir RD, Puglia KV, Willis IM
JournalJ Biol Chem
PubMed ID11684692
'An important step in the assembly of RNA polymerase (pol) III transcription complexes on tRNA and 5 S genes is the interaction between the tetratricopeptide repeat (TPR)-containing subunit of TFIIIC (TFIIIC131) and the TFIIB-related subunit of TFIIIB (TFIIIB70/Brf1). A fragment of TFIIIC131 that contains the hydrophilic amino terminus and two ... More
Microchip-based purification of DNA from biological samples.
'A microchip solid-phase extraction method for purification of DNA from biological samples, such as blood, is demonstrated. Silica beads were packed into glass microchips and the beads immobilized with sol-gel to provide a stable and reproducible solid phase onto which DNA could be adsorbed. Optimization of the DNA loading conditions ... 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
Carbon nanotubes as electrodes for dielectrophoresis of DNA.
AuthorsTuukkanen S, Toppari JJ, Kuzyk A, Hirviniemi L, Hytönen VP, Ihalainen T, Törmä P
JournalNano Lett
PubMed ID16834407
'Dielectrophoresis can potentially be used as an efficient trapping tool in the fabrication of molecular devices. For nanoscale objects, however, the Brownian motion poses a challenge. We show that the use of carbon nanotube electrodes makes it possible to apply relatively low trapping voltages and still achieve high enough field ... More
Biochemical quantification of DNA in human articular and septal cartilage using PicoGreen and Hoechst 33258.
AuthorsMcGowan KB, Kurtis MS, Lottman LM, Watson D, Sah RL
JournalOsteoarthritis Cartilage
PubMed ID12127839
'OBJECTIVE: To compare two fluorometric assays, utilizing (1) the bisbenzimidazole Hoechst 33258 and (2) PicoGreen, for determining DNA content in human cartilage. METHODS: Human articular and nasal septal cartilage explants were digested using proteinase K. Portions of sample digest were analysed for intrinsic and dye-enhanced fluorescence with either Hoechst 33258 ... More
Rapid-cycle PCR and fluorimetry for detection of mycobacteria.
AuthorsLachnik J, Ackermann B, Bohrssen A, Maass S, Diephaus C, Puncken A, Stermann M, Bange FC
JournalJ Clin Microbiol
PubMed ID12202580
'In this study we used LightCycler PCR amplification and product detection by fluorescence resonance energy transfer probes to identify mycobacteria and differentiate between Mycobacterium tuberculosis complex, Mycobacterium avium, and other nontuberculous mycobacteria. Targeting the 16S rRNA gene, three different probes specific for mycobacteria, M. tuberculosis complex, and M. avium were ... More
Flow cytometric analysis of 5-cyano-2,3-ditolyl tetrazolium chloride activity of marine bacterioplankton in dilution cultures.
AuthorsSieracki ME, Cucci TL, Nicinski J,
JournalAppl Environ Microbiol
PubMed ID10347021
'The respiratory activity of marine bacteria is an important indication of the ecological functioning of these organisms in marine ecosystems. The redox dye 5-cyano-2,3-ditolyl tetrazolium chloride (CTC) is reduced intracellularly in respiring cells to an insoluble, fluorescent precipitate. This product is detectable and quantifiable by flow cytometry in individual cells. ... More
Analysis and accurate quantification of CpG methylation by MALDI mass spectrometry.
AuthorsTost J, Schatz P, Schuster M, Berlin K, Gut IG
JournalNucleic Acids Res
PubMed ID12711695
'As the DNA sequence of the human genome is now nearly finished, the main task of genome research is to elucidate gene function and regulation. DNA methylation is of particular importance for gene regulation and is strongly implicated in the development of cancer. Even minor changes in the degree of ... More
Heterozygote and mutation detection by direct automated fluorescent DNA sequencing using a mutant Taq DNA polymerase.
'We describe a method for direct cycle sequencing of PCR fragments amplified from genomic DNA or cDNA. DNA sequencing template is amplified using PCR and oligonucleotide primers flanking the region of interest. The amplified fragment is directly cycle sequenced using fluorescent sequencing primers, Sanger dideoxy sequencing chemistry and an enzyme ... More
Analytical methods for the characterization of cationic lipid-nucleic acid complexes.
AuthorsFerrari ME, Nguyen CM, Zelphati O, Tsai Y, Felgner PL
JournalHum Gene Ther
PubMed ID9508052
'Five analytical assays are described that provide a platform for systematically evaluating the effect of formulation variables on the physical properties of cationic lipid-DNA complexes (lipoplexes). The assays are for (i) lipid recovery, (ii) total DNA, (iii) free DNA, (iv) nuclease sensitivity, and (v) physical stability by filtration. Lipid recovery ... More
The connection between chromatin motion on the 100 nm length scale and core histone dynamics in live XTC-2 cells and isolated nuclei.
AuthorsDavis SK, Bardeen CJ
JournalBiophys J
PubMed ID14695300
'The diffusive motion of DNA-containing chromatin in live cells and isolated nuclei is investigated using a two-photon standing wave fluorescence photobleaching experiment with 100 nm spatial resolution. The chromatin is labeled using the minor groove binding dye Hoechst 33342. In live cells, the mean diffusion rate is 5 x 10(-4) ... More
Improving DNA array data quality by minimising 'neighbourhood' effects.
AuthorsMachl AW, Schaab C, Ivanov I
JournalNucleic Acids Res
PubMed ID12434009
'Gene expression studies using cDNA arrays require robust and sensitive detection methods. Being extremely sensitive, radioactive detection suffers from the influence of signals positioned in each other''s vicinity, the ''neighbourhood'' effect. This limits the gene density of arrays and the quality of the results obtained. We have investigated the quantitative ... More
Overexpression of Phex in osteoblasts fails to rescue the Hyp mouse phenotype.
Authors Liu Shiguang; Guo Rong; Tu Qisheng; Quarles L Darryl;
JournalJ Biol Chem
PubMed ID11713245
'Inactivating mutations of Phex, a phosphate-regulating endopeptidase, cause hypophosphatemia and impaired mineralization in X-linked hypophosphatemia (XLH) and its mouse homologue, Hyp. Because Phex is predominantly expressed in bone and cultured osteoblasts from Hyp mice display an apparent intrinsic mineralization defect, it is thought that reduced expression of Phex in mature ... More
Impact of the physical and topographical characteristics of adsorbent solid-phases upon the fluidised bed recovery of plasmid DNA from Escherichia coli lysates.
AuthorsThwaites E, Burton SC, Lyddiatt A
JournalJ Chromatogr A
PubMed ID11820283
'A comparison is made of the performance of two types of adsorbent solid phases (commercially sourced Streamline composites and custom-assembled Zirblast pelliculates), derivatised with similar anion exchange chemistries and applied to the recovery of plasmid DNA from Escherichia coli extracts prepared by chemical lysis and coarse filtration. Streamline and Zirblast ... More
Enrichment followed by quantitative PCR both for rapid detection and as a tool for quantitative risk assessment of food-borne thermotolerant campylobacters.
AuthorsJosefsen MH, Jacobsen NR, Hoorfar J
JournalAppl Environ Microbiol
PubMed ID15184161
'As part of a large international project for standardization of PCR (Food-PCR; www.pcr.dk), a multiplex, multiplatform, ready-to-go enrichment followed by a real-time PCR method, including an internal amplification control, was developed for detection of food-borne thermotolerant campylobacters in chickens. Chicken rinse samples were enriched in Bolton broth for 20 h, ... More
Heat stress- and heat shock transcription factor-dependent expression and activity of ascorbate peroxidase in Arabidopsis.
AuthorsPanchuk II, Volkov RA, Schöffl F
JournalPlant Physiol
PubMed ID12068123
'To find evidence for a connection between heat stress response, oxidative stress, and common stress tolerance, we studied the effects of elevated growth temperatures and heat stress on the activity and expression of ascorbate peroxidase (APX). We compared wild-type Arabidopsis with transgenic plants overexpressing heat shock transcription factor 3 (HSF3), ... More
Effects of Resources and Trophic Interactions on Freshwater Bacterioplankton Diversity.
AuthorsFisher MM, Klug JL, Lauster G, Newton M, Triplett EW
JournalMicrob Ecol
PubMed ID11029081
'In a study of bacterioplankton in an oligotrophic lake in northern Wisconsin, a community fingerprinting technique, automated ribosomal intergenic spacer analysis (ARISA), was used to determine the effect of resources and trophic interactions on bacterioplankton diversity. Inorganic nitrogen and phosphorus (NP), carbon in the form of glucose (G) or dissolved ... More
Increased integrity of free circulating DNA in sera of patients with colorectal or periampullary cancer: direct quantitative PCR for ALU repeats.
AuthorsUmetani N, Kim J, Hiramatsu S, Reber HA, Hines OJ, Bilchik AJ, Hoon DS
JournalClin Chem
PubMed ID16723681
'BACKGROUND: Cell-free DNA circulating in blood is a candidate biomarker for malignant tumors. Unlike uniformly truncated DNA released from apoptotic nondiseased cells, DNA released from dead cancer cells varies in size. We developed a novel method to measure the ratio of longer to shorter DNA fragments (DNA integrity) in serum ... More
A genomic rearrangement resulting in a tandem duplication is associated with split hand-split foot malformation 3 (SHFM3) at 10q24.
Authorsde Mollerat XJ, Gurrieri F, Morgan CT, Sangiorgi E, Everman DB, Gaspari P, Amiel J, Bamshad MJ, Lyle R, Blouin JL, Allanson JE, Le Marec B, Wilson M, Braverman NE, Radhakrishna U, Delozier-Blanchet C, Abbott A, Elghouzzi V, Antonarakis S, Stevenson RE, Munnich A, Neri G, Schwartz CE
JournalHum Mol Genet
PubMed ID12913067
'Split hand-split foot malformation (SHFM) is characterized by hypoplasia/aplasia of the central digits with fusion of the remaining digits. SHFM is usually an autosomal dominant condition and at least five loci have been identified in humans. Mutation analysis of the DACTYLIN gene, suspected to be responsible for SHFM3 in chromosome ... More
Detection of residual donor leucocytes in leucoreduced red blood cell components using a fluorescence microplate assay.
'In November 1999, universal leucoreduction of blood components was introduced in the UK to minimise the risk of variant Creutzfeldt-Jakob Disease (vCJD) transmission by blood transfusion. The UK specifications for leucodepletion processes state that 99% of leucodepleted components should contain < 5 x 10(6) leucocytes/unit, within 95% confidence limits. However, ... More
A full-coverage, high-resolution human chromosome 22 genomic microarray for clinical and research applications.
AuthorsBuckley PG, Mantripragada KK, Benetkiewicz M, Tapia-Páez I, Diaz De Ståhl T, Rosenquist M, Ali H, Jarbo C, De Bustos C, Hirvelä C, Sinder Wilén B, Fransson I, Thyr C, Johnsson BI, Bruder CE, Menzel U, Hergersberg M, Mandahl N, Blennow E, Wedell A, Beare DM, Collins JE, Dunham I, Albertson D, Pinkel D, Bastian BC, Faruqi AF, Lasken RS, Ichimura K, Collins VP, Dumanski JP
JournalHum Mol Genet
PubMed ID12444106
'We have constructed the first comprehensive microarray representing a human chromosome for analysis of DNA copy number variation. This chromosome 22 array covers 34.7 Mb, representing 1.1% of the genome, with an average resolution of 75 kb. To demonstrate the utility of the array, we have applied it to profile ... More
Manufacturing DNA microarrays from unpurified PCR products.
'For the production of DNA microarrays from PCR products, purification of the the DNA fragments prior to spotting is a major expense in cost and time. Also, a considerable amount of material is lost during this process and contamination might occur. Here, a protocol is presented that permits the manufacture ... More
Specific down-modulation of Notch1 signaling in cervical cancer cells is required for sustained HPV-E6/E7 expression and late steps of malignant transformation.
AuthorsTalora C, Sgroi DC, Crum CP, Dotto GP
JournalGenes Dev
PubMed ID12208848
'The Notch family of cell surface receptors plays a key role in cell-fate determination and differentiation, functioning in a cell- and context-specific manner. In mammalian cells, Notch activation is generally thought to maintain stem cell potential and inhibit differentiation, thereby promoting carcinogenesis. However, in other contexts such as primary epithelial ... More
Constitutive androstane receptor and pregnane X receptor gene expression in human liver: interindividual variability and correlation with CYP2B6 mRNA levels.
AuthorsChang TK, Bandiera SM, Chen J
JournalDrug Metab Dispos
PubMed ID12485946
'The constitutive androstane receptor (CAR) and pregnane X receptor (PXR) mediate the expression of mammalian cytochrome p450 (p450) 2B genes, including CYP2B6 in humans. Large interindividual differences exist in hepatic CYP2B6 expression, but the molecular basis for this variability is not well understood. In the present study, we developed real-time ... More
TempliPhi: A sequencing template preparation procedure that eliminates overnight cultures and DNA purification.
AuthorsReagin MJ, Giesler TL, Merla AL, Resetar-Gerke JM, Kapolka KM, Mamone JA
JournalJ Biomol Tech
PubMed ID14676313
'Preparing plasmid templates for DNA sequencing is the most time-consuming step in the sequencing process. Current template preparation methods rely on a labor-intensive, multistep procedure that takes up to 24 h and produces templates of varying quality and quantity. The TempliPhi DNA Sequencing Template Amplification Kit eliminates the requirement for ... More
Mesenchymal stem cells, MG63 and HEK293 transfection using chitosan-DNA nanoparticles.
AuthorsCorsi K, Chellat F, Yahia L, Fernandes JC
JournalBiomaterials
PubMed ID12527266
'Chitosan-DNA nanoparticles were synthesized from the complexation of the cationic polymer with a ss-gal DNA plasmid, in order to study the efficacy of chitosan to develop a non-viral gene delivery system that can be optimized for efficient gene therapy. The optimal binding conditions were determined with the fluorescamine and PicoGreen ... More
Regulation of maternal transcript destabilization during egg activation in Drosophila.
AuthorsTadros W, Houston SA, Bashirullah A, Cooperstock RL, Semotok JL, Reed BH, Lipshitz HD
JournalGenetics
PubMed ID12871909
'In animals, the transfer of developmental control from maternal RNAs and proteins to zygotically derived products occurs at the midblastula transition. This is accompanied by the destabilization of a subset of maternal transcripts. In Drosophila, maternal transcript destabilization occurs in the absence of fertilization and requires specific cis-acting instability elements. ... More
Quality and quantity of saliva DNA obtained from the self-administrated oragene method--a pilot study on the cohort of Swedish men.
AuthorsRylander-Rudqvist T, Håkansson N, Tybring G, Wolk A
JournalCancer Epidemiol Biomarkers Prev
PubMed ID16985039
'Self-collection of saliva has the potential to provide molecular epidemiologic studies with DNA in a user-friendly way. We evaluated the new Oragene saliva collection method and requested saliva samples by mail from 611 men (ages 53-87 years). We obtained a response rate of, on average, 80% [varying from 89% (ages ... More
Cell cycle-dependent modulation of telomerase activity in tumor cells.
AuthorsZhu X, Kumar R, Mandal M, Sharma N, Sharma HW, Dhingra U, Sokoloski JA, Hsiao R, Narayanan R
JournalProc Natl Acad Sci U S A
PubMed ID8650224
'Telomerase is a ribonucleoprotein complex that is thought to add telomeric repeats onto the ends of chromosomes during the replicative phase of the cell cycle. We tested this hypothesis by arresting human tumor cell lines at different stages of the cell cycle. Induction of quiescence by serum deprivation did not ... More
L-type voltage-gated Ca2+ channels modulate expression of smooth muscle differentiation marker genes via a rho kinase/myocardin/SRF-dependent mechanism.
'Vascular smooth muscle cell (SMC) contraction is mediated in part by calcium influx through L-type voltage-gated Ca2+ channels (VGCC) and activation of the RhoA/Rho kinase (ROK) signaling cascade. We tested the hypothesis that Ca2+ influx through VGCCs regulates SMC differentiation marker expression and that these effects are dependent on RhoA/ROK ... More
Fingerprinting diazotroph communities in the Chesapeake Bay by using a DNA macroarray.
AuthorsJenkins BD, Steward GF, Short SM, Ward BB, Zehr JP
JournalAppl Environ Microbiol
PubMed ID15006803
'Investigations of the distribution and diversity of nitrogen-fixing microorganisms in natural environments have often relied on PCR amplification and sequence analysis of a portion of one of the key enzymes in nitrogen fixation, dinitrogenase reductase, encoded by nifH. Recent work has suggested that DNA macroarrays provide semiquantitative fingerprints of diversity ... More
A plastic microchip for nucleic acid purification.
AuthorsLiu Y, Cady NC, Batt CA
JournalBiomed Microdevices
PubMed ID17530410
'A microchip for purifying nucleic acids from bacterial pathogens was designed and fabricated in plastic. The fabricated plastic microchips were tested for their ability to purify nucleic acids from the bacteria Listeria monocytogenes (L. monocytogenes), Escherichia coli (E. coli), and Salmonella typhimurium (S. typhimurium). These chips were constructed using rapid ... More
Tal1/SCL binding to pericentromeric DNA represses transcription.
'Tal1/SCL is a basic helix-loop-helix transcription factor critical for normal hematopoiesis. To understand the mechanisms underlying transcriptional regulation by Tal1/SCL, we combined an in vitro DNA binding strategy and an in vivo chromatin immunoprecipitation analysis to search for Tal1/SCL target regions in K562 erythroleukemia cells. A 0.4-kb genomic DNA clone ... More
Quantitation of DNA copy number in individual mitochondrial particles by capillary electrophoresis.
AuthorsNavratil M, Poe BG, Arriaga EA
JournalAnal Chem
PubMed ID17877423
'Here, we present a direct method for determining mitochondrial DNA (mtDNA) copy numbers in individual mitochondrial particles, isolated from cultured cells, by means of capillary electrophoresis with laser-induced fluorescence (CE-LIF) detection. We demonstrate that this method can detect a single molecule of PicoGreen-stained mtDNA in intact DsRed2-labeled mitochondrial particles isolated ... More
Selective deficiency of the "bone-related" Runx2-II unexpectedly preserves osteoblast-mediated skeletogenesis.
AuthorsXiao ZS, Hjelmeland AB, Quarles LD
JournalJ Biol Chem
PubMed ID15007057
'Runx2 (runt-related transcription factor 2) is a master regulator of skeletogenesis. Distinct promoters in the Runx2 gene transcribe the "bone-related" Runx2-II and non-osseous Runx2-I isoforms that differ only in their respective N termini. Existing mutant mouse models with both isoforms deleted exhibit an arrest of osteoblast and chondrocyte maturation and ... More
Microbial diversity in the deep sea and the underexplored "rare biosphere".
'The evolution of marine microbes over billions of years predicts that the composition of microbial communities should be much greater than the published estimates of a few thousand distinct kinds of microbes per liter of seawater. By adopting a massively parallel tag sequencing strategy, we show that bacterial communities of ... More
Mechanisms underlying the impact of humic acids on DNA quantification by SYBR Green I and consequences for the analysis of soils and aquatic sediments.
'DNA quantification of soils and sediments is useful for the investigation of microbial communities and for the acquisition of their genomes that are exploited for the production of natural products. However, in such samples DNA quantification is impaired by humic acids (HA). Due to its lack of specificity and sensitivity, ... More
Inhibition of apoptosis in pulmonary endothelial cells by altered pH, mitochondrial function, and ATP supply.
AuthorsTerminella C, Tollefson K, Kroczynski J, Pelli J, Cutaia M
JournalAm J Physiol Lung Cell Mol Physiol
PubMed ID12424147
'We investigated the effect of altered extracellular pH, mitochondrial function, and ATP content on development of apoptosis in human pulmonary artery endothelial cells after treatment with staurosporine (STS). STS produced a concentration- and time-dependent increase in caspase-3 activity in pH 7.4 medium that reached a peak at 6 h. The ... More
Iron acquisition and regulation in Campylobacter jejuni.
AuthorsPalyada K, Threadgill D, Stintzi A
JournalJ Bacteriol
PubMed ID15231804
'Iron affects the physiology of bacteria in two different ways: as a micronutrient for bacterial growth and as a catalyst for the formation of hydroxyl radicals. In this study, we used DNA microarrays to identify the C. jejuni genes that have their transcript abundance affected by iron availability. The transcript ... More
Cell cycle synchronization of Escherichia coli using the stringent response, with fluorescence labeling assays for DNA content and replication.
AuthorsFerullo DJ, Cooper DL, Moore HR, Lovett ST,
JournalMethods
PubMed ID19245839
'We describe a method for synchronization of the cell cycle in the bacterium Escherichia coli. Treatment of asynchronous cultures with the amino acid analog, dl-serine hydroxamate, induces the stringent response, with concomitant arrest of DNA replication at initiation. Following release of the stringent response, cells initiate DNA replication in synchrony, ... More
Pax5 is required for recombination of transcribed, acetylated, 5' IgH V gene segments.
'Pax5-deficient progenitor B (pro-B) cells are thought to be severely defective for recombination of all immunoglobulin heavy chain (IgH) V gene segments, but the mechanism by which Pax5 regulates this process has not been defined. To address this issue, we have examined the assembly of the IgH locus in Pax5-deficient ... More
Amplicon mapping and transcriptional analysis pinpoint cyclin L as a candidate oncogene in head and neck cancer.
AuthorsRedon R, Hussenet T, Bour G, Caulee K, Jost B, Muller D, Abecassis J, du Manoir S
JournalCancer Res
PubMed ID12414649
'DNA gains targeting the 3q chromosome are common in head and neck squamous cell carcinomas, as well as in lung, ovarian, and cervical cancer. Several candidate oncogenes located on 3q were proposed, i.e., PIK3CA, p63, and eIF-5A2. However, none of these genes was found included in a narrow high-level amplification. ... More
Fluorimetric DNA assay of cell number.
AuthorsOtto WR
JournalMethods Mol Biol
PubMed ID15502190
'This fluorimetric assay has utility for the accurate assessment of cultured epidermal cell numbers by virtue of their deoxyribonucleic acid content, which is the most significant correlate available. The improvement in fluorochromes in the recent past makes PicoGreen the dye of choice for this, with its greatly increased sensitivity (+/- ... More
A novel DNA-based microfluorimetric method to evaluate antimalarial drug activity.
AuthorsCorbett Y, Herrera L, Gonzalez J, Cubilla L, Capson TL, Coley PD, Kursar TA, Romero LI, Ortega-Barria E
JournalAm J Trop Med Hyg
PubMed ID14993620
'This paper describes the development of a novel microfluorimetric assay to measure the inhibition of Plasmodium falciparum based on the detection of parasitic DNA by intercalation with PicoGreen. The method was used to determine parasite inhibition profiles and 50% inhibitory concentration values of known or potential antimalarial drugs. Values for ... More
Mitochondrial DNA is a direct target of anti-cancer anthracycline drugs.
AuthorsAshley N, Poulton J,
JournalBiochem Biophys Res Commun
PubMed ID19032935
'The anthracyclines, such as doxorubicin (DXR), are potent anti-cancer drugs but they are limited by their clinical toxicity. The mechanisms involved remain poorly understood partly because of the difficulty in determining sub-cellular drug localisation. Using a novel method utilising the fluorescent DNA dye PicoGreen, we found that anthracyclines intercalated not ... More
Metal-enhanced PicoGreen fluorescence: application to fast and ultra-sensitive pg/ml DNA quantitation.
'In this paper we provide both a theoretical and experimental analysis of the sensitivity of a DNA quantitation assay using a fluorescent chromophore which non-covalently binds dsDNA. It is well-known that the range of DNA concentrations available for fluorescence quantitation depends on the concentration of the chromophore, its affinity for ... More
Effect of signal compounds and incubation conditions on the culturability of freshwater bacterioplankton.
AuthorsBruns A, Nübel U, Cypionka H, Overmann J
JournalAppl Environ Microbiol
PubMed ID12676673
'The effect of signal compounds and of different incubation conditions on the culturability (i.e., the fraction of all cells capable of growth) of natural bacterioplankton from the eutrophic lake Zwischenahner Meer was investigated over a period of 20 months. Numbers of growing cells were determined by the most-probable-number technique in ... More
'An analysis of the Pseudomonas aeruginosa genomic sequence revealed three gene clusters, PA1381-1393, PA2231-2240, and PA3552-3558, in addition to the alginate biosynthesis gene cluster, which appeared to encode functions for exopolysaccharide (EPS) biosynthesis. Recent evidence indicates that alginate is not a significant component of the extracellular matrix in biofilms of ... More
SNP genotyping on pooled DNAs: comparison of genotyping technologies and a semi automated method for data storage and analysis.
'We have compared the accuracy, efficiency and robustness of three methods of genotyping single nucleotide polymorphisms on pooled DNAs. We conclude that (i) the frequencies of the two alleles in pools should be corrected with a factor for unequal allelic amplification, which should be estimated from the mean ratio of ... More
Detection and quantification of oral treponemes in subgingival plaque by real-time PCR.
AuthorsAsai Y, Jinno T, Igarashi H, Ohyama Y, Ogawa T
JournalJ Clin Microbiol
PubMed ID12202575
'Oral treponemes have been associated with periodontal diseases. We developed a highly sensitive and specific method to detect and quantify cultivable oral treponemes (Treponema denticola, Treponema vincentii, and Treponema medium) in 50 subgingival plaque samples from 13 healthy subjects as well as 37 patients with periodontal diseases using real-time PCR ... More
The two variants of oxysterol binding protein-related protein-1 display different tissue expression patterns, have different intracellular localization, and are functionally distinct.
AuthorsJohansson M, Bocher V, Lehto M, Chinetti G, Kuismanen E, Ehnholm C, Staels B, Olkkonen VM
JournalMol Biol Cell
PubMed ID12631712
'Oxysterol binding protein (OSBP) homologs comprise a family of 12 proteins in humans (Jaworski et al., 2001; Lehto et al., 2001). Two variants of OSBP-related protein (ORP) 1 have been identified: a short one that consists of the carboxy-terminal ligand binding domain only (ORP1S, 437 aa) and a longer N-terminally ... More
Rapid DNA fingerprinting of pathogens by flow cytometry.
'BACKGROUND: A new method for rapid discrimination among bacterial strains based on DNA fragment sizing by flow cytometry is presented. This revolutionary approach combines the reproducibility and reliability of restriction fragment length polymorphism (RFLP) analysis with the speed and sensitivity of flow cytometry. METHODS: Bacterial genomic DNA was isolated and ... More
Difference between free circulating plasma and serum DNA in patients with colorectal liver metastases.
AuthorsThijssen MA, Swinkels DW, Ruers TJ, de Kok JB
JournalAnticancer Res
PubMed ID12017326
'BACKGROUND: Previous studies suggest that the amount of circulating cell-free DNA in plasma or serum may be a promising marker for diagnosis and prediction of prognosis in patients with tumours. However, it is unclear whether DNA from plasma or from serum better reflects the clinical status. PATIENTS AND METHODS: To ... More
Optimizing primer--probe design for fluorescent PCR.
AuthorsProudnikov D, Yuferov V, Zhou Y, LaForge KS, Ho A, Kreek MJ
JournalJ Neurosci Methods
PubMed ID12581847
'TaqMan, a variation of fluorescent PCR, is a powerful tool for gene expression and polymorphism studies. Here we describe the design and evaluation of 27 new TaqMan primer-probe sets for rat genes that play a key role in neural signaling. These newly designed and synthesized probes were tested and then ... More
Induction of NFATc2 expression by interleukin 6 promotes T helper type 2 differentiation.
AuthorsDiehl S, Chow CW, Weiss L, Palmetshofer A, Twardzik T, Rounds L, Serfling E, Davis RJ, Anguita J, Rincón M
JournalJ Exp Med
PubMed ID12093869
'Interleukin (IL)-6 is produced by professional antigen-presenting cells (APCs) such as B cells, macrophages, and dendritic cells. It has been previously shown that APC-derived IL-6 promotes the differentiation of naive CD4+ T cells into effector T helper type 2 (Th2) cells. Here, we have studied the molecular mechanism for IL-6-mediated ... More
An evaluation of the performance of cDNA microarrays for detecting changes in global mRNA expression.
AuthorsYue H, Eastman PS, Wang BB, Minor J, Doctolero MH, Nuttall RL, Stack R, Becker JW, Montgomery JR, Vainer M, Johnston R
JournalNucleic Acids Res
PubMed ID11292855
'The cDNA microarray is one technological approach that has the potential to accurately measure changes in global mRNA expression levels. We report an assessment of an optimized cDNA microarray platform to generate accurate, precise and reliable data consistent with the objective of using microarrays as an acquisition platform to populate ... More
The expression of plasma nucleosomes in mice undergoing in vivo apoptosis.
AuthorsJiang N, Reich CF, Monestier M, Pisetsky DS
JournalClin Immunol
PubMed ID12672404
'Nucleosomes occur in the blood of patients with systemic lupus erythematosus and are thought to result from in vivo cell death. To determine the conditions for the release of nucleosomes into the blood, normal mice were treated with four agents that have the potential to induce apoptosis or immune cell ... More
Salt dependence of the elasticity and overstretching transition of single DNA molecules.
AuthorsWenner JR, Williams MC, Rouzina I, Bloomfield VA
JournalBiophys J
PubMed ID12023240
'As double-stranded DNA is stretched to its B-form contour length, models of polymer elasticity can describe the dramatic increase in measured force. When the molecule is stretched beyond this contour length, it shows a highly cooperative overstretching transition. We have measured the elasticity and overstretching transition as a function of ... More
Insulin augmentation of 17alpha-hydroxylase activity is mediated by phosphatidyl inositol 3-kinase but not extracellular signal-regulated kinase-1/2 in human ovarian theca cells.
AuthorsMunir I, Yen HW, Geller DH, Torbati D, Bierden RM, Weitsman SR, Agarwal SK, Magoffin DA
JournalEndocrinology
PubMed ID14512432
'Polycystic ovary syndrome, characterized by hyperandrogenism and chronic anovulation, is frequently associated with insulin resistance. Ample evidence implicates a role for insulin in the genesis of ovarian hyperandrogenism. The objective of this study was to begin to define the intracellular signaling pathway(s) that mediates insulin regulation of 17alpha-hydroxylase activity in ... More