SEARCH · PubMed Health

Results for “Library preparation”

Explore indexed PubMed citations for clinical trials, systematic reviews and public health research. Read source abstracts and follow each citation to its original PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 235 records · Page 13Linked to original sources

PubMed2001

The B cell superantigen-like interaction of intravenous immunoglobin (IVIG) with Fab fragments of V(H) 3-23 and 3-30/3-30.5 germline gene origin cloned from a patient with Kawasaki disease is enhanced after IVIG therapy.

The etiology of Kawasaki disease (KD) is still unknown. Therefore, the diagnosis relies on clinical criteria only. Although a specific therapy for KD is not available, coronary complications can be significantly reduced with the help of intravenous immunoglobulin (IVIG) therapy. It is not clear how IVIG interacts with the immune system. Previously, we selected a large number of IgG and IgM Fab fragments specifically reacting with IVIG molecules by phage display and antiidiotypic panning from three patients with autoimmune thrombocytopenia, a patient with lupus, and a healthy individual. Sequencing revealed that the favored V(H) germline gene segments of these IVIG-bound Fabs were 3-23 or 3-30/3-30.5, the most frequently rearranged V(H) genes among human B cells. The binding pattern suggested a B cell superantigen-like, specific interaction of an IVIG subset with B cells that present B cell receptors derived from these two germline genes. The aim of the current study was to investigate whether treatment with IVIG influences this restricted interaction. Therefore we cloned and selected Fab fragments from a patient with KD before and after IVIG therapy. A favored selection of antibodies derived from both the 3-23 and the 3-30/3-30.5 germline gene segments as before was observed. Importantly, the reactivity with IVIG was significantly higher for clones from the library prepared after the IVIG treatment, providing the first in vivo functional evidence that a subset of IVIG may selectively activate B cells of this germline origin. This mechanism may add to the therapeutic effect of IVIG in the treatment of KD.

B-Lymphocytes↗

PubMed1986

Characterization of cDNA coding for human factor XIIIa.

A cDNA library prepared from human placenta has been screened for sequences coding for factor XIIIa, the enzymatically active subunit of the factor XIII complex that stabilizes blood clots through crosslinking of fibrin molecules. Two oligonucleotides, based on the amino acid sequences of tryptic peptides of factor XIIIa, were used as hybridization probes. Of 0.36 X 10(6) independent recombinants, 1 clone was identified that hybridized to both probes. The insert of 1704 base pairs coded for the amino-terminal 541 amino acid residues of the mature factor XIIIa molecule. Blot-hybridization analysis using this cDNA as a probe showed that the factor XIIIa mRNA from placenta has a size of approximately 4000 bases. The insert was used to rescreen cDNA libraries and to identify further factor XIIIa-specific sequences. The total length of the isolated factor XIIIa cDNA is 3905 bases, and it codes for a protein of 732 amino acids. In spite of the presence of factor XIII in blood plasma, we could not identify a leader sequence typical for secreted proteins.

Amino Acid Sequence↗

PubMed1994

Characterization of multiple unique cDNAs encoding the major surface glycoprotein of rat-derived Pneumocystis carinii.

The major surface glycoprotein (MSG) of rat-derived Pneumocystis carinii represents a group of related molecules that are encoded by multiple genes. We isolated seven unique MSG cDNAs from a library prepared from a single infected rat lung. The cDNAs displayed both conserved and variant regions to previously described cDNAs. These clones contained inserts that ranged in size from 0.4 to 1.8 kb and all contained a poly(A) tail. The largest clone, Pc1410, hybridized to all 15 chromosomes resolved by pulsed-field gel electrophoresis (PFGE). Protein produced by in vitro translation from Pc1410 was immunoprecipitated with affinity-purified MSG antibodies. The clones were characterized by DNA sequencing of their 3' and 5' ends. Analysis of the untranslated and coding regions demonstrated that the clones contained unique and conserved regions of sequence, but none of the clones were identical. Isolation of seven additional unique clones picked from a single screening of a cDNA library suggests that numerous MSG transcripts exist within a population of P. carinii.

Amino Acid Sequence↗

PubMed2005

Pscroph, a parasitic plant EST database enriched for parasite associated transcripts.

BACKGROUND: Parasitic plants in the Orobanchaceae develop invasive root haustoria upon contact with host roots or root factors. The development of haustoria can be visually monitored and is rapid, highly synchronous, and strongly dependent on host factor exposure; therefore it provides a tractable system for studying chemical communications between roots of different plants. DESCRIPTION: Triphysaria is a facultative parasitic plant that initiates haustorium development within minutes after contact with host plant roots, root exudates, or purified haustorium-inducing phenolics. In order to identify genes associated with host root identification and early haustorium development, we sequenced suppression subtractive libraries (SSH) enriched for transcripts regulated in Triphysaria roots within five hours of exposure to Arabidopsis roots or the purified haustorium-inducing factor 2,6 dimethoxybenzoquinone. The sequences of over nine thousand ESTs from three SSH libraries and their subsequent assemblies are available at the Pscroph database http://pscroph.ucdavis.edu. The web site also provides BLAST functions and allows keyword searches of functional annotations. CONCLUSION: Libraries prepared from Triphysaria roots treated with host roots or haustorium inducing factors were enriched for transcripts predicted to function in stress responses, electron transport or protein metabolism. In addition to parasitic plant investigations, the Pscroph database provides a useful resource for investigations in rhizosphere interactions, chemical signaling between organisms, and plant development and evolution.

Arabidopsis↗

PubMed1996

Oncogenic activation of the tyrosine kinase domain of the human trk proto-oncogene by fusion to a cell adhesion molecule.

To investigate the mechanisms of radiation-induced neoplastic conversion, DNA from X-ray transformed human epidermal keratinocytes (RHEK-1) was used in sequential cycles of NIH3T3 transfection followed by nude mice tumorigenicity assays. NIH3T3-derived transformants retained discrete DNA fragments hybridizing to human alu probes. Four clones were isolated from a cosmid library prepared from one of these transformants (49-7G) using human DNA as the probe. Analyses of DNAs from 49-7G cells and the four cosmid clones with probes for a number of human oncogenes demonstrated that the cloned sequences were related to the trk oncogene. Transfection of NIH3T3 cells with the cosmid DNAs did not result in the appearance of transformed foci when the murine fibroblasts were cultured on plastic. However, foci developed when transfected cells were cultured on plates coated with various extracellular matrix (ECM) components. Neomycin-resistant cosmid-transfected NIH3T3 cells did induce tumors in nude mice, and their tumorigenicity correlated with their level of trk expression. Nucleotide sequence analyses of cDNA clones isolated from a 49-7G library with a human trk probe revealed that the cloned sequences resulted from the fusion between 5' sequences from the human beta-1,4-galactosyltransferase gene, which encodes a membrane protein involved in cell-cell and cell-matrix interactions, and 3' sequences from the human trk proto-oncogene. The 76 kDa protein product of the chimeric gene, designated bgt-trk, has been identified in NIH3T3 cells transfected with cosmid 19/2 or with bgt-trk cDNA expression constructs, and its phosphorylation in tyrosine has been found to increase when the transfected cells were seeded on plates coated with ECM components which also elicited foci formation in NIH3T3 transformation assays. The fusion of the trk tyrosine kinase domain to a cell adhesion molecule may explain the ECM dependence for the expression of the full transforming potential of the resulting oncogene product.

3T3 Cells↗

PubMed1995

B-ATF: a novel human bZIP protein that associates with members of the AP-1 transcription factor family.

A new member of the ATF/CREB family of transcription factors, called B-ATF, has been isolated from a cDNA library prepared from Epstein-Barr virus stimulated human B cells. B-ATF is a 125 amino acid nuclear protein possessing a basic leucine zipper domain that is most similar to the basic leucine zipper of ATF-3. Northern blot analysis of polyadenylated mRNA isolated from a variety of human tissues and established cell lines indicates that the 1.0 kilobase B-ATF mRNA is expressed differentially, with the strongest hybridization detected in lung and in Raji Burkitt's lymphoma. Efficient homodimerization of the B-ATF protein cannot be detected using the yeast two hybrid system or using in vitro binding assays with glutathione-s-transferase-B-ATF and maltose binding protein-B-ATF fusion proteins produced in E. coli. However, a yeast two hybrid library screen has identified the human oncoprotein JunB as a specific binding partner for B-ATF. Glutathione-s-transferase-B-ATF heterodimerizes efficiently with in vitro translated JunB, c-Jun, and JunD, but only weakly associates with c-Fos. In addition, electrophoretic mobility shift assays demonstrate that a B-ATF/c-Jun protein complex can interact with DNA containing a consensus binding site for AP-1, suggesting that B-ATF functions as a tissue-specific modulator of the AP-1 transcription complex in human cells.

Amino Acid Sequence↗

PubMed1994

Evolutionary conservation of the AU-rich 3' untranslated region of messenger RNA.

AU-rich sequence motifs (specifically sequences containing reiterations of AUUUA) are found in the 3' untranslated region of mammalian mRNAs encoding cytokines, adhesion molecules, and protooncogenes. Because these AU-rich elements (3'AURE) have been observed to reduce the stability and translational efficiency of transcripts that contain them, and because many of these transcripts accumulate in cells exposed to inflammatory stimuli, we reasoned that mRNAs with 3'AURE may be highly conserved and that the AURE is a marker of mRNAs that are inducible by environmental stressors. To test this hypothesis, we developed a polymerase chain reaction (PCR) strategy to isolate specifically mRNAs with 3'AURE. We first validated the effectiveness of this approach by selectively amplifying two mRNAs containing 3'AURE from interleukin 1 (IL-1)-induced human endothelial cells, then used the same primers in reverse transcriptase-PCR of sea urchin RNA, and used the radiolabeled reaction products to screen a cDNA library prepared from endotoxin-exposed sea urchin coelomocytes. We identified 124 positive clones and isolated a 1608-base-pair fragment that contains an AU-rich consensus sequence upstream from a poly(A) tail. This sea urchin transcript hybridizes with immobilized poly(A)(+)-selected RNA prepared from living coelomocytes maintained in vitro for 8.5-13 h but not with RNA prepared from freshly harvested coelomocytes. Our results provide support for the growing body of evidence that 3' AURE are both conserved and functional and indicate further that isolation and short-term in vitro culture of sea urchin coelomocytes is sufficient to induce the expression of transcripts containing 3'AURE.

Animals↗

PubMed1997

Synthesis of oligopeptide and peptidomimetic libraries.

The elaboration of peptide libraries prepared by either chemical or biological methods in a format useful for discovery of peptides with specific biological activities was first introduced in the 1980s. A virtual explosion of activity in this area has occurred recently, and the basic approaches have been applied to a wide variety of chemistries and for all manner of biological, chemical and physical targets. Recent advances include new synthetic methodologies, new analytical methods, new design methods and new assay procedures.

Bacteriophages↗

PubMed1996

Molecular diversity of soil and marine 16S rRNA gene sequences related to beta-subgroup ammonia-oxidizing bacteria.

We have conducted a preliminary phylogenetic survey of ammonia-oxidizing beta-proteobacteria, using 16S rRNA gene libraries prepared by selective PCR and DNA from acid and neutral soils and polluted and nonpolluted marine sediments. Enrichment cultures were established from samples and analyzed by PCR. Analysis of 111 partial sequences of c. 300 bases revealed that the environmental sequences formed seven clusters, four of which are novel, within the phylogenetic radiation defined by cultured autotrophic ammonia oxidizers. Longer sequences from 13 cluster representatives support their phylogenetic positions relative to cultured taxa. These data suggest that known taxa may not be representative of the ammonia-oxidizing beta-proteobacteria in our samples. Our data provide further evidence that molecular and culture-based enrichment methods can select for different community members. Most enrichments contained novel Nitrosomonas-like sequences whereas novel Nitrosospira-like sequences were more common from gene libraries of soils and marine sediments. This is the first evidence for the occurrence of Nitrosospira-like strains in marine samples. Clear differences between the sequences of soil and marine sediment libraries were detected. Comparison of 16S rRNA sequences from polluted and nonpolluted sediments provided no strong evidence that the community composition was determined by the degree of pollution. Soil clone sequences fell into four clusters, each containing sequences from acid and neutral soils in varying proportions. Our data suggest that some related strains may be present in both samples, but further work is needed to resolve whether there is selection due to pH for particular sequence types.

Ammonia↗

PubMed1995

Identification of novel differentially expressed hepatic genes in cholesterol-fed rabbits by a non-targeted gene approach.

Several key genes involved in cholesterol metabolism are known to be directly regulated by cholesterol. The possible indirect effect, however, of increased levels of cellular cholesterol on gene expression and its possible role in cholesterol metabolism and atherosclerosis has not been thoroughly explored. In order to determine the overall effect of cholesterol on gene expression, we isolated differentially expressed genes from a PCR-based subtraction library prepared from the liver of chow-fed and cholesterol-fed rabbits. A total of nine upregulated and four down-regulated cDNA fragments were isolated. As determined by Northern blot analysis, the expression of the isolated cDNAs began to change as early as the first week on the cholesterol-rich diet or as late as 4 weeks, which corresponded with hepatic cholesterol accumulation. Three of the cDNAs were identified by DNA sequence homology, whereas the remaining cDNAs had no significant homology match. CYP1A1, a cytochrome P450 isoenzyme, was found to be down-regulated in hepatocytes by cholesterol feeding. Osteopontin and Mac-2, which are produced by macrophages, were found to be up-regulated in Kupffer cells by cholesterol feeding. Overall these results demonstrate the usefulness of the subtraction library approach for identifying new candidate genes for exploring the pathogenesis of atherosclerosis.

Animals↗

PubMed2005

Variations in the abundance and identity of class II aromatic ring-hydroxylating dioxygenase genes in groundwater at an aromatic hydrocarbon-contaminated site.

The abundance of genes encoding aromatic ring-hydroxylating dioxygenases (RHDs) in the groundwater at an aromatic hydrocarbon-contaminated landfill near Sydney, Australia, was determined by quantitative DNA-DNA hybridization using class II RHD genes as probes. There were marked differences in hybridization signal intensity against DNA extracted from the groundwater at seven different locations across this heterogeneous site. This was interpreted as indicating variation in RHD gene abundance. Clone libraries of polymerase chain reaction (PCR)-amplified RHD gene fragments were constructed from DNA from each of the groundwater samples. The libraries from the samples with greater RHD gene abundance were dominated by a group of bacterial class II RHD genes, designated the S-cluster, that has yet to be found in cultured isolates. These groundwater samples contained no detectable petroleum hydrocarbons. A second group of class II RHD gene sequences, designated the T-cluster, dominated RHD gene clone libraries prepared from groundwater samples that contained detectable levels of total petroleum and aromatic hydrocarbons but lower RHD gene abundance. The hosts and in situ expression of these novel genes, and the substrates of the enzymes they encode, remain unknown. The scarcity of genes from known aromatic hydrocarbon-degrading bacteria and the numerical dominance of the novel genes suggest that the hosts of these novel genes may play an important role in aromatic hydrocarbon degradation at this site.

Australia↗

PubMed1994

Expression and localization of amiloride-sensitive sodium channel indicate a role for non-taste cells in taste perception.

Salty taste is blocked by the diuretic amiloride, which inhibits specific sodium channels. We have isolated an amiloride-sensitive sodium channel (ASSC) from taste tissues by polymerase chain reaction and screening of a cDNA library prepared from rat circumvallate papillae. Northern analysis reveals ASSC in taste and non-taste tissues with the highest level of expression of ASSC in the lung. In situ hybridization establishes ASSC localizations in the epithelia of lung and colon as well as tongue epithelial layers containing and lacking taste buds. These results support a model in which ASSC in non-taste cells regulates responses of taste cells to salt as well as other tastants.

Amiloride↗

PubMed2000

Screening of environmental DNA libraries for the presence of genes conferring lipolytic activity on Escherichia coli.

Environmental DNA libraries prepared from three different soil samples were screened for genes conferring lipolytic activity on Escherichia coli clones. Screening on triolein agar revealed 1 positive clone out of 730,000 clones, and screening on tributyrin agar revealed 3 positive clones out of 286,000 E. coli clones. Substrate specificity analysis revealed that one recombinant strain harbored a lipase and the other three contained esterases. The genes responsible for the lipolytic activity were identified and characterized.

Amino Acid Sequence↗

PubMed1988

Primary structure of prostaglandin G/H synthase from sheep vesicular gland determined from the complementary DNA sequence.

Prostaglandin G/H synthase (8,11,14-icosatrienoate, hydrogen-donor:oxygen oxidoreductase, EC 1.14.99.1) catalyzes the first step in the formation of prostaglandins and thromboxanes, the conversion of arachidonic acid to prostaglandin endoperoxides G and H. This enzyme is the site of action of nonsteroidal anti-inflammatory drugs. We have isolated a 2.7-kilobase complementary DNA (cDNA) encompassing the entire coding region of prostaglandin G/H synthase from sheep vesicular glands. This cDNA, cloned from a lambda gt 10 library prepared from poly(A)+ RNA of vesicular glands, hybridizes with a single 2.75-kilobase mRNA species. The cDNA clone was selected using oligonucleotide probes modeled from amino acid sequences of tryptic peptides prepared from the purified enzyme. The full-length cDNA encodes a protein of 600 amino acids, including a signal sequence of 24 amino acids. Identification of the cDNA as coding for prostaglandin G/H synthase is based on comparison of amino acid sequences of seven peptides comprising 103 amino acids with the amino acid sequence deduced from the nucleotide sequence of the cDNA. The molecular weight of the unglycosylated enzyme lacking the signal peptide is 65,621. The synthase is a glycoprotein, and there are three potential sites for N-glycosylation, two of them in the amino-terminal half of the molecule. The serine reported to be acetylated by aspirin is at position 530, near the carboxyl terminus. There is no significant similarity between the sequence of the synthase and that of any other protein in amino acid or nucleotide sequence libraries, and a heme binding site(s) is not apparent from the amino acid sequence. The availability of a full-length cDNA clone coding for prostaglandin G/H synthase should facilitate studies of the regulation of expression of this enzyme and the structural features important for catalysis and for interaction with anti-inflammatory drugs.

Amino Acid Sequence↗

PubMed1998

Cloning and expression of a cDNA encoding the large subunit of duck replication factor C.

A cDNA encoding an avian homologue of the large subunit of replication factor C (RFC-L) has been cloned from a duck liver cDNA expression library prepared in bacteriophage lambda. The full length cDNA encodes a protein with a predicted size of approximately 130 kDa, consistent with the size of the polypeptide detected in duck liver. The duck RFC-L amino acid sequence shares 66.4% and 68.4% identity with mouse and human RFC-L proteins, respectively. We identified a 4kb RFC-L mRNA expressed in most duck tissues.

Amino Acid Sequence↗

PubMed2003

The granulin-epithelin precursor/PC-cell-derived growth factor is a growth factor for epithelial ovarian cancer.

PURPOSE: The role of growth factors in ovarian cancer development and progression is complex and multifactorial. We hypothesized that new growth factors may be identified through the molecular analysis of ovarian tumors as they exist in their native environment. EXPERIMENTAL DESIGN: RNA extracted from microdissected serous low malignant potential (LMP) and invasive ovarian tumors was used to construct cDNA libraries. A total of 7300 transcripts were randomly chosen for sequencing, and those transcripts were statistically evaluated. Reverse transcription-PCR and immunohistochemistry were used to validate the findings in tumor tissue samples. Ovarian cancer cell lines were used to test gene effects on monolayer growth, proliferative capacity, and density-independent growth. RESULTS: Analysis of the pooled library transcripts revealed 26 genes differentially expressed between LMP and invasive ovarian cancers. The granulin-epithelin precursor [GEP/PC-cell derived growth factor (PCDGF)] was expressed only in the invasive ovarian cancer libraries (P < 0.028) and was absent in the LMP libraries (0 of 2872 clones). All of the invasive tumor epithelia, 20% of the LMP tumor epithelia, and all of the stroma from both subsets expressed GEP by reverse transcription-PCR. Immunohistochemical staining for GEP was diffuse and cytosolic in invasive ovarian cancer tumor cells compared with occasional, punctate, and apical staining in LMP tumor epithelia. Antisense transfection of GEP into ovarian cancer cell lines resulted in down-regulation of GEP production, reduction in cell growth (P < 0.002), decrease in the S-phase fraction (P < 0.04), and loss of density-independent growth potential (P < 0.01). CONCLUSION: cDNA library preparation from microdissected tumor epithelium provided a selective advantage for the identification of growth factors for epithelial ovarian cancer. Differential granulin expression in tumor samples and the antiproliferative effects of its antisense down-regulation suggest that GEP may be a new autocrine growth factor and molecular target for epithelial ovarian cancer.

Cell Division↗

PubMed1999

Nuclear localisation of NOVH protein: a potential role for NOV in the regulation of gene expression.

AIMS: To identify the NOV protein detected by immunofluorescence in the nucleus of human cancer cell lines to establish whether targeting to the nucleus reflects dual paracrine and intracrine biological functions of NOV, as has been reported previously for several signalling peptides and proteins. METHODS: Nuclear and cytoplasmic fractions were prepared from 143 and HeLa cells in which nuclear NOV protein was detected. Western blotting analysis of NOV proteins in both types of fractions was performed using two NOV specific antibodies. Confocal microscopy was used to visualise the nuclear NOV protein in HeLa and 143 cells. A yeast two hybrid screening system was used to isolate cDNAs encoding proteins able to interact with the human NOV protein. RESULTS: A 31/32 kDa doublet of NOV protein was identified in the nuclear fraction of 143 and HeLa cells. Because the antibodies were directed against the C-terminus of NOV, the 31/32 kDa NOV isoform is probably truncated at the N-terminus and might correspond to the secreted 32 kDa NOV isoform detected in cell culture medium. Confocal microscopy indicated that in addition to the cytoplasmic NOV protein already identified, a nuclear NOV protein was present in both the nucleoplasm and nucleoli of Hela and 143 cells. Screening of cDNA libraries prepared from HeLa cells, Epstein-Barr virus transformed lymphocytes, and normal human brain showed that the NOV protein interacts with the rpb7 subunit of RNA polymerase in a yeast two hybrid system. CONCLUSIONS: The NOV protein detected in the nucleus of 143 and HeLa cells is probably an N-terminus truncated isoform of the secreted 48 kDa NOV protein. A growing body of evidence suggests that novH expression is closely associated with differentiation in normal human tissues and that the nov gene encodes a signalling protein that belongs to an emerging family of cell growth regulators. The nuclear localisation of a NOV isoform potentially provides an additional degree of signalling specificity. The interaction of the NOV protein and the rpb7 subunit of RNA polymerase II in the two hybrid system suggests that NOV might be involved in regulating gene expression at the transcriptional level. As has already been suggested for several other nuclearly located cytokines, the NOV protein does not contain a typical nuclear localisation signal. Therefore, it is possible that it combines with either a receptor or a chaperone during its translocation. Disruption of the balance between the secreted and nuclear NOV isoforms might affect the putative autocrine and paracrine functions of NOV and might be of considerable importance in the development of cancers in which the expression of novH has been shown to be impaired.

Base Sequence↗

PubMed2002

Functional and comparative bioinformatic analysis of expressed genes from wheat spikes infected with Fusarium graminearum.

Fusarium head blight, caused by the fungus Fusarium graminearum, is a major disease on wheat (Triticum aestivum L.). Expressed sequence tags (ESTs) were used to identify genes expressed during the wheat-F. graminearum interaction. We generated 4,838 ESTs from a cDNA library prepared from spikes of the partially resistant cultivar Sumai 3 infected with F. graminearum. These ESTs were composed of 2,831 singlet (single-copy transcripts) and 715 contigs (multiple-copy transcripts) for a total of 3,546 non-redundant sequences. Four sets of nonredundant sequences were identified. One set contains numerous, common biotic and abiotic stress-related genes. Many of these stress-related genes were represented by multiple ESTs, indicating that they are abundantly expressed. A second set comprised 16 nonredundant sequences from F. graminearum that may be required for pathogenicity. A subset of these fungal genes encodes proteins associated with plant cell wall degradation. A third set of 326 nonredundant sequences had no DNA or amino acid sequence similarity to almost 1 million plant and over 7 million animal sequences in dbEST (as of 22 June 2001). Thus, these 326 nonredundant sequences have only been found in our F. graminearum-infected 'Sumai 3' cDNA library. A fourth set of 29 nonredundant sequences was found in our F. graminearum-infected wheat and another plant-pathogen interaction cDNA library. Some of these sequences encode proteins that may act in establishing various plant-fungal interactions.

Cell Wall↗