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At least 1,009 records · Page 56Linked to original sources
PubMed1990

DNA alterations in prostatic adenocarcinoma and benign prostatic hyperplasia: detection by DNA fingerprint analyses.

DNA fingerprinting can be utilized to examine a large number of autosomal loci throughout the human genome. Alterations in banding patterns observed on DNA fingerprint analyses reflect DNA alterations ranging from single base changes to complex chromosomal rearrangements. In this report, we describe the application of this technique to prostatic adenocarcinoma (CAP) and benign prostatic hyperplasia (BPH). The majority of CAP cases (12 of 14) displayed alterations in at least 1 of the approximately 30 resolvable bands obtained by fingerprint analyses when compared with DNA obtained from peripheral white blood cells. Unexpectedly, 5 of the 12 cases of BPH examined revealed at least 1 identifiable band alteration in the prostatic tissue. These findings demonstrate the usefulness of fingerprint analyses in the examination of cancer-associated genetic alterations. They also suggest the presence of observable genetic alterations in BPH.

Adenocarcinoma↗
PubMed1989

Acetylaminofluorene-labelled ribosomal RNA for use in molecular epidemiology and taxonomy.

The use of acetylaminofluorene-labelled 16 + 23S rRNA (from Escherichia coli) is described for determining rRNA-gene-restriction patterns. The labelled probe allowed molecular fingerprinting of bacteria belonging to diverse phylogenetic branches (Enterobacteriaceae, Haemophilus, Pseudomonas, Acinetobacter, Brucella, Leptospira, Cytophaga, Campylobacter, Methylophaga). The labelled probe can be stored frozen (-20 degrees C) for at least a year and can endure vacuum dessication, ethanol precipitation or lyophilization.

2-Acetylaminofluorene↗
PubMed1992

Quantitative analysis of DNA-sequencing electrophoresis.

At the heart of the DNA-sequencing process is a remarkably selective electrophoretic separation of up to 1000 oligonucleotide fragments, each differing in size by only a single nucleotide unit. A quantitative analysis of this separation is performed in terms of both selectivity and efficiency. It is shown that both the Ogston sieving and reptation migration mechanisms are operative. It is demonstrated that, under the conditions used in traditional sequencing electrophoresis, Joule heating does not significantly contribute to band broadening, and that diffusion is the primary contributor to plate height. An analytic expression is derived relating the peak width for each fragment to its molecular size. Calculations are presented showing that, when longer sequences are required, the maximum electrical field strength will be limited by the influence of biased reptation on the separation selectivity. Finally, it is shown that, when short sequences are required, the electrical field strength is limited by the ability to dissipate Joule heat, and that in these cases a tube format will be approximately 50% faster than a slab having a thickness equivalent to the tube diameter.

DNA↗
PubMed1995

Group II intron ribozymes that cleave DNA and RNA linkages with similar efficiency, and lack contacts with substrate 2'-hydroxyl groups.

BACKGROUND: Group II introns are self-splicing RNAs that have mechanistic similarity to the spliceosome complex involved in messenger RNA splicing in eukaryotes. These autocatalytic molecules can be reconfigured into highly specific, multiple-turnover ribozymes that cleave oligonucleotides in trans. We set out to use a simplified system of this kind to study the mechanism of cleavage. RESULTS: Unlike other catalytic RNA molecules, the group II ribozymes cleave DNA linkages almost as readily as RNA linkages. One ribozyme variant cleaves DNA linkages with an efficiency comparable to that of restriction endonuclease EcoRI. Single deoxynucleotide substitutions in the substrate showed that the ribozymes bind substrate without engaging 2'-hydroxyl groups. CONCLUSIONS: The ribose 2'-hydroxyl group at the cleavage site has little role in transition-state stabilization by group II ribozymes. Substrate 2'-hydroxyl groups are not involved in substrate binding, suggesting that only base-pairing is required for substrate recognition.

Animals↗
PubMed2003

Suppression of apolipoprotein AI gene expression in HepG2 cells by TNF alpha and IL-1beta.

Plasma inflammatory cytokines are elevated in obese subjects as well as in those with type 2 diabetes. This presumably results in systemic insulin resistance, characterized by a pro-atherogenic plasma lipid profile and reduced apolipoprotein AI (apoAI) protein levels. To determine how cytokine-mediated insulin resistance suppresses apoAI gene expression, we investigated the effect of tumor necrosis factor alpha (TNF alpha) and interleukin-1beta (IL-1beta) on apoAI protein, mRNA, and transcriptional activity in the human hepatoma cell line HepG2. ApoAI secretion was suppressed in a dose-dependent manner in HepG2 cells treated with both cytokines. ApoAI protein levels were 2892+/-22.0, 2263+/-117, 2458+/-25.0, 3401+/-152, 2333+/-248, 1520+/-41.5 and 956.0+/-11.0 arbitrary units (AU) in cells treated with 0, 0.3, 1.0, 3.0, 10, 30, and 100 ng/ml TNF alpha, achieving statistical significance in the 30 and 100 ng/ml range (P<0.0009). ApoAI protein levels were 4055+/-360, 3697+/-101, 3347+/-327, 1561+/-33.0, 1581+/-182, 810.0+/-59.5, and 1766+/-717 AU in cells treated with similar doses of IL-1beta, achieving statistical significance within the range of 3-100 ng/ml (P<0.02). ApoAI mRNA levels were suppressed 50.8% in HepG2 cells treated with 30 ng/ml TNF alpha for 24 h (P<0.05), and remained suppressed for up to 96 h. Similarly, treatment of cells with 30 ng/ml IL-1beta for 24 h, resulted in 42.9% reduction in apoAI mRNA levels (P<0.05) and remained suppressed for up to 96 h. In order to determine if the effect of TNF alpha and IL-1beta occurs at the transcriptional level, HepG2 cells were transfected with a chloramphenicol acetyltransferase (CAT) reporter gene plasmid containing the full-length apoAI promoter, and after 24 h, treated with TNF alpha (30 ng/ml), IL-1beta (30 ng/ml), or both cytokines. CAT activity was suppressed by both cytokines (24.0+/-1.9% acetylation in control cells vs. 5.6+/-1.2% (P<0.0004), 10.2+/-1.5% (P<0.0006), and 3.9+/-0.9% acetylation (P<0.0002) in cells treated with TNF alpha, IL-1beta, and the combination of both cytokines, respectively) suggesting that cytokine-mediated suppression occurs at the transcriptional level. Using a series of apoAI deletion constructs, the cytokine response element was mapped between nucleotides -325 and -186 (relative to the transcriptional start site). This region contains a previously identified and characterized cis-element, site A, which binds several different transcription factors. Finally, electrophoretic mobility shift assays (EMSA) showed that TNF alpha treatment of HepG2 cells is associated with reduced nuclear factor binding to site A. These studies suggest that inflammatory cytokines down-regulate apoAI expression at least partly through inhibition of binding of the nuclear factors to site A of the apoAI promoter.

Apolipoprotein A-I↗
PubMed2005

No evidence for association of the TATA-box binding protein glutamine repeat sequence or the flanking chromosome 6q27 region with type 1 diabetes.

Susceptibility to the autoimmune disease type 1 diabetes has been linked to human chromosome 6q27 and, moreover, recently associated with one of the genes in the region, TATA box-binding protein (TBP). Using a much larger sample of T1D families than those studied by others, and by extensive re-sequencing of nine other genes in the proximity, in which we identified 279 polymorphisms, 83 of which were genotyped in up to 725 T1D multiplex and simplex families, we obtained no evidence for association of the TBP CAG/CAA (glutamine) microsatellite repeat sequence with disease, or for nine other genes, PDCD2, PSMB1, KIAA1838, DLL1, dJ894D12.4, FLJ25454, FLJ13162, FLJ11152, PHF10 and CCR6. This study also provides an exon-based tag single nucleotide polymorphism map for these 10 genes that can be used for analysis of other diseases.

Chromosomes, Human, Pair 6↗
PubMedDate not supplied

Identification of a rare point mutation at C-terminus of merozoite surface antigen-1 gene of Plasmodium falciparum in eastern Indian isolates.

Merozoite surface antigen-1 (MSA-1) of Plasmodium falciparum is highly immunogenic in human. Several studies suggest that MSA-1 protein is an effective target for a protective immune response. Attempt has been made to find new point mutations by analyzing 244 bp [codon 1655(R) to 1735 (I)] relatively conserved C-terminus region of MSA-1 gene in 125 isolates. This region contains two EGF like domains, which are involved in generating protective immune response in human. Point mutations in this region are very much important in view of vaccine development. Searching of mutational hot spots in MSA-1 protein by sequencing method in a representative number of isolates is quite critical and expensive. Therefore, in this study slot blot and PCR-SSCP method have been used to find out new mutations in the individual isolates showing alterations in the mobility of DNA fragment. Sequencing of the altered bands from the SSCP gel shows a rare non-synonymous point mutation in 7 (5.6%) of the 125 isolates at amino acid position 1704 of MSA-1 gene where isoleucine is replaced by valine.

Animals↗
PubMed2005

Untying the FIV frameshifting pseudoknot structure by MS3D.

The structure of the putative feline immunodeficiency virus (FIV) ribosomal frameshifting pseudoknot (PK) has been investigated by a mass spectrometric three-dimensional (MS3D) approach, which involves the application of established solvent-accessibility probes and chemical crosslinkers with detection by electrospray ionization (ESI) Fourier transform mass spectrometry (FTMS). Regardless of their size, probed substrates can be treated with ribonucleases and analyzed by ESI-FTMS to obtain the correct position of chemically modified nucleotides. Protection maps and distance information can be utilized to generate 3D models using the constraint satisfaction algorithm provided by MC-SYM and the energy minimization modules included in CNS. Control experiments were performed on a mutant of mouse mammary tumor virus pseudoknot (VPK), for which an NMR structure is available. Comparison between the MS3D model and the high-resolution structure provided a approximately 3A root-mean-square deviation calculated from all the atoms present in double-stranded regions. Applied to FIV-PK, the MS3D approach confirmed that the selected sequence could fold into an actual pseudoknot, supporting the sequence alignment predictions. Characteristic features of H-type pseudoknots were recognized immediately, but a putative A13-U30 pair was not observed at the stem junction, making FIV-PK resemble VPK more closely than the initially suggested simian retrovirus type-1 pseudoknot. In our model, the unpaired U30 protrudes into the medium, while the hinging A13 assumes a stacked conformation that enables the stems to form a approximately 60 degrees bend and relieve the strain caused by a short loop 1. The model provided the basis to explain the different alkylation patterns observed in the absence and presence of Mg(2+), suggesting the possible formation of a specific metal-binding site between loop 1 and stem 2. This instance illustrates how the MS3D model of FIV-PK can be utilized effectively to generate hypotheses and support functional observations in the absence of a high-resolution structure.

Algorithms↗
PubMed2006

Drug interactions and pharmacogenetic reactions are the basis for chloroquine and mefloquine-induced psychosis.

BACKGROUND: Chloroquine and mefloquine used for prophylaxis and treatment of malaria sometimes causes severe mental status changes, through mechanisms that are poorly understood. PRESENTATION OF THE HYPOTHESIS: Psychosis is caused by interactions with other drugs or by pharmacogenetic vulnerabilities that cause heightened responses to chloroquine or mefloquine alone, mediated through dopamine, acetylcholine, serotonin, P-glycoprotein, inhibited cortical activity, deranged calcium homeostasis, and impaired synaptogenesis. TESTING THE HYPOTHESIS: Retrospective studies can identify all other drugs taken coincident with chloroquine or mefloquine psychosis. Various genes from patients could be cloned and compared to those from individuals who tolerated chloroquine and mefloquine, culminating with transgenic animal studies. Identification of candidate genes may be aided by pharmacogenomic analysis of single nucleotide polymorphism maps. Finally, prospective studies with cerebrospinal fluid analysis and PET scanning could help verify the hypothesis. IMPLICATIONS OF THE HYPOTHESIS: If this hypothesis is correct, the incidence of chloroquine and mefloquine psychosis can be greatly reduced by avoiding interacting medications and by conducting genetic screening prior to initiating chloroquine and mefloquine. Validation of the hypothesis would also provide a paradigm to follow for avoiding neuropsychiatric side effects if antidepressants and neuroleptics are used to overcome chloroquine resistance, if new antimalarial drugs chemically related to chloroquine and mefloquine are developed and if chloroquine and mefloquine are used for non-malarial applications such as HIV and cancer.

ATP Binding Cassette Transporter, Subfamily B, Mem↗
PubMed2004

rDNA enhancer affects replication initiation and mitotic recombination: Fob1 mediates nucleolytic processing independently of replication.

To investigate the influence of the ribosomal DNA enhancer on initiation of replication and recombination at the ribosomal array, we used yeast S. cerevisiae strains with adjacent, tagged rRNA genes. We found that the enhancer is an absolute requirement for replication fork barrier function, while it only modulates initiation of replication. Moreover, the formation of monomeric extrachromosomal ribosomal circles depends on this element. Our data indicate that DNA double-strand breaks occur at specific sites in the parental leading arm of replication forks stalled at the replication fork barrier. Additionally, nicks upstream of the replication fork barrier were visualized by nucleotide-resolution mapping. They coincide with essential sequences of the mitotic hyperrecombination site HOT1, which previously has been determined at ectopic sites. Interestingly, these nicks are strictly dependent on the replication fork blocking-protein (Fob1), but are replication independent, suggesting that intrachromosomal ribosomal DNA recombination may occur outside of S phase.

Base Sequence↗
PubMed2004

JAB1 participates in unfolded protein responses by association and dissociation with IRE1.

Recent papers have reported that neuronal death in patients with Alzheimer's disease, Parkinson's disease, and cerebral ischemia has its origin in the endoplasmic reticulum (ER). IRE1alpha is one of the ER stress transducers that detect the accumulation of unfolded proteins in the ER. IRE1alpha mediates two major cellular responses, which are the unfolded protein response (UPR), a defensive response, and apoptosis that leads to cell death. However, little is known about the regulatory mechanisms that select between the UPR and apoptosis. We identified Jun activation domain-binding protein-1 (JAB1) as a molecule that interacts with IRE1alpha using a yeast two-hybrid system. We demonstrated that JAB1 binds to IRE1alpha in the absence of stress, but that binding is decreased by ER stress inducers. Moreover, mutant JAB1 down-regulates the UPR signaling pathway through tight binding with IRE1alpha. These results suggested that JAB1 may act as a key molecule in selecting the UPR or cell death by association and dissociation with IRE1alpha.

Antibodies↗
PubMed2026

Genome-Wide and Rare Variant Association Studies of Amblyopia in Admixed American and African Ancestry Groups.

OBJECTIVE: To identify genetic variants associated with amblyopia in African (AFR) and Admixed American (AMR) ancestry groups, expanding on previous studies conducted in European ancestry. DESIGN: Retrospective ancestry-stratified genome-wide association study (GWAS) and gene-level rare variant association study (RVAS). PARTICIPANTS: Participants in the All of Us Research Program from AFR and AMR ancestry groups who had whole-genome sequencing available. Cases and controls were distinguished based on the presence of International Classification of Diseases 9/10/SNOMED diagnosis codes for amblyopia in electronic health records. This yielded ancestry-stratified subsets of 269 cases and 71 585 controls of AMR ancestry and 366 cases and 79 460 controls of AFR ancestry. METHODS: Stratified logistic regression models were adjusted for age, biological sex, and the top 10 principal components of genomic ancestry. GWAS was limited to common variants (minor allele frequency &#x2265;1%), and RVAS was limited to rare variants with coding sequence-altering effects (minor allele frequency >1%, exonic only, excluding synonymous variants) aggregated at the gene level using the SKAT algorithm. Downstream analyses of the significant variants were performed using KEGG and GO pathway analysis and STRING database queries for protein-protein interactions and gene-gene interactions. MAIN OUTCOME MEASURES: Single-nucleotide polymorphisms were determined to have genome-wide significance if P < 5e-8 in the GWAS, and genes were determined to have significant association with amblyopia in the RVAS if P < 8.0 &#xd7; 10-4. RESULTS: In the AMR GWAS, 245 unique single-nucleotide polymorphisms mapping to 97 distinct loci were identified, notably within neurodevelopmental and axonal guidance genes, including ROBO1, SEMA4B, PTPRD, NRXN1, and CAMK2D. The AFR GWAS identified 11 significant variants corresponding to 6 loci mapping primarily to long noncoding RNAs and pseudogenes. The AMR RVAS identified 15 genes, including axonal transport genes (KIF1B and KIF7) and growth factor signaling genes (EGF, ERBIN, and AKAP17A). The AFR RVAS identified a single gene, DLG2, which encodes the postsynaptic protein PSD-93, which promotes the closure of the sensitive period of neuroplasticity for vision in early childhood. CONCLUSIONS: Genetic risk architectures for amblyopia differ across ancestries but fundamentally converge on neurodevelopmental signaling, cortical synapse assembly, and sensitive period plasticity rather than ocular structural dynamics. FINANCIAL DISCLOSURE(S): The authors have no proprietary or commercial interest in any materials discussed in this article.

Amblyopia↗
PubMed1990

Discrepancy in the diagnoses of hydatidiform mole by macroscopic and microscopic findings and the deoxyribonucleic acid fingerprint method.

Ten cases of hydatidiform mole were analyzed by the deoxyribonucleic acid fingerprint method. Deoxyribonucleic acid samples were prepared from hydatidiform mole tissue of hydatidiform mole and maternal and paternal blood. A case of partial hydatidiform mole diagnosed by histologic findings was revealed to be complete hydatidiform mole by deoxyribonucleic acid fingerprinting.

Chorionic Gonadotropin↗
PubMed1989

Zygosity determination of multiple pregnancy by deoxyribonucleic acid fingerprints.

We used a new method of deoxyribonucleic acid analysis to determine zygosity in multiple pregnancies. This method uses a minisatellite core probe, requires only a small amount of deoxyribonucleic acid, and detects the restriction fragment length polymorphisms that are a result of allelic differences in the number of tandem repeats that contain the core sequence. Southern blot hybridization showed an individual-specific deoxyribonucleic acid fingerprint and each polymorphic band in the sibling could be identified within one (but not both) of the parents. Identical deoxyribonucleic acid fingerprints among the siblings of multiple pregnancy indicate they must be monozygotic. This method is sufficiently reliable and rapid so the determination of zygosity in multiple pregnancy can be made the same day the fetal deoxyribonucleic acid is made available.

DNA↗
PubMed1984

Synthesis of rat apolipoprotein E by Escherichia coli infected with recombinant bacteriophage.

A cDNA library was constructed from rat liver polyadenylated RNA using the expression vector lambda gt11-Amp3. Several clones expressing antigenic determinants for rat apolipoprotein E were identified. The cDNA insert in one clone was further characterized and found to have a sufficient length (1120 base pairs) to code for full length apolipoprotein E. Restriction mapping and nucleotide sequencing showed the clone to contain the coding region for apolipoprotein E flanked by about 120 nucleotides at the 3'-side and by about 64 nucleotides on the 5'-side. One of the proteins produced by the clone was found to be a prokaryotic/eukaryotic hybrid protein reacting with antibodies to both bacterial beta-galactosidase and rat apolipoprotein E.

Animals↗
PubMed1988

Distinct nuclear 7S RNAs hybridize to regulatory regions of two oncogenes.

The role of 7SK nuclear RNA remains obscure despite indications that it might be involved in the control of gene expression and associated with transformation. Here we identify distinct 7S nuclear transcripts by hybridization with DNA and RNA probes derived from regulatory regions of SV40 and c-myc genes. 7SK RNA hybridized to both early and late strands within the 21bp repeat region of SV4C and only to the sense strand within the first c-myc intron. Another nuclear 7S RNA, distinct from cytoplasmic 7SL, hybridized selectively to the SV40 late strand within the 72bp region. This RNA, designated 7SN, also hybridized to the c-myc first intron but with opposite polarity to 7SK. The identification of a novel 7S transcript and the observed selective hybridization of nuclear 7S RNAs with oncogene promoters raises interesting possibilities about their function.

Animals↗