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At least 1,441 records · Page 80Linked to original sources
PubMed2005

Natural antisense transcripts associated with genes involved in eye development.

Natural antisense transcripts (NATs) are a class of genes whose role in controlling gene expression is becoming more and more relevant. We describe the identification of eight novel mouse NATs associated with transcription factors (Pax6, Pax2, Six3, Six6, Otx2, Crx, Rax and Vax2) that play an important role in eye development and function. These newly identified NATs overlap with the mature processed mRNAs or with the primary unprocessed transcript of their corresponding sense genes, are predicted to represent either protein coding or non-coding RNAs and undergo extensive alternative splicing. Expression studies, by both RT-PCR and RNA in situ hybridization, demonstrate that most of these NATs, similarly to their sense counterparts, display a specific or predominant expression in the retina, particularly at postnatal stages. We found a significant reduction of the expression levels of one of these NATs, Vax2OS (Vax2 opposite strand) in a mouse mutant carrying the inactivation of Vax2, the corresponding sense gene. In addition, we overexpressed another NAT, CrxOS, in mouse adult retina using adeno-associated viral vectors and we observed a significant decrease in the expression levels of the corresponding sense gene, Crx. These results suggest that these transcripts are functionally related to their sense counterparts and may play an important role in regulating the molecular mechanisms that underlie eye development and function in both physiological and pathological conditions.

Alternative Splicing↗
PubMed1982

Molecular cloning of human immune interferon cDNA and its expression in eukaryotic cells.

Starting with mRNA derived from Staphylococcal enterotoxin A induced human splenocytes, dsDNA was synthesized and inserted into unique BamHI site of the eukaryotic expression vector pSV529 (1). A recombinant plasmid containing human immune interferon (IFN-gamma) cDNA was identified by hybridization of plasmid inserted DNA bound onto nitrocellulose filters with mRNA derived from SEA-induced splenocytes, translation of the eluted RNA in Xenopus laevis oocytes and assaying for IFN activity. Plasmids containing the entire human IFN-gamma cDNA sequence were identified by colony hybridization and were sequenced. A unique coding region was identified which predicted a protein of 166 amino acids, the 20 N-terminal amino acids of which presumably represent a signal peptide. After transfection of monkey cells with plasmid DNA isolated from one of the recombinant clones (pHIIF-SV-gamma 1), IFN was excreted into the culture medium. This IFN was not distinguishable from human IFN-gamma by serological criteria or by cell target species specificity.

Amino Acid Sequence↗
PubMed1987

Escherichia coli rep gene: sequence of the gene, the encoded helicase, and its homology with uvrD.

The sequence of a 2.67-kilobase section of the Escherichia coli chromosome that contains the rep gene has been determined. This gene codes for a protein of predicted Mr 72,800, a DNA helicase, which is also a single-stranded DNA-dependent ATPase. The sequenced region contains an open reading frame of the correct length and orientation to encode the Rep protein. A secondary structure for the protein can be formulated from the amino acid sequence. We have compared both the primary and the secondary structures of Rep with other proteins and find the greatest homology between Rep and E. coli helicase II, the product of the uvrD gene.

Adenosine Triphosphatases↗
PubMed1987

Characterisation of cDNA clones for hypoxanthine-guanine phosphoribosyltransferase from the human malarial parasite, Plasmodium falciparum: comparisons to the mammalian gene and protein.

The isolation of cDNA clones for hypoxanthine-guanine phosphoribosyltransferase (HPRT) from the human malarial parasite, Plasmodium falciparum, is described. Northern analysis indicates that P. falciparum HPRT mRNA is the same size as that coding for mammalian HPRT. The predicted amino acid sequence of the P. falciparum HPRT protein shows extensive homology to the mammalian enzyme. Homology between the two proteins occurs in distinct blocks and a putative catalytic binding domain in the centre of the protein is also conserved. Five out of the seven characterised mammalian HPRT missense mutations map to regions which are conserved in the P. falciparum protein.

Amino Acid Sequence↗
PubMed1991

A differentially expressed murine RNA encoding a protein with similarities to two types of nucleic acid binding motifs.

Using differential screening, a murine cDNA, termed X16, was isolated corresponding to an mRNA which is more strongly expressed in pre-B cell lines relative to mature B-cell lines. The complete coding sequence of the mRNA predicts a 19kD protein with two domains connected by a proline-rich spacer. The N-terminal domain of about 90 amino acids encodes an RNA binding motif including the ribonucleoprotein consensus octapeptide found in one class of RNA-binding proteins and highly conserved from yeast to man. Within the very basic C-terminal domain of about 60 amino acids, several copies of two different peptides are found which are also present in several proteins which bind DNA or RNA. The expression of X16 is not limited to the lymphoid lineage. In adult mice, although the strongest expression was seen in thymus, mRNA was also found in testis, brain, spleen, and very low in heart. X16 mRNA was not detected in liver and kidney. In tissue culture, the expression of X16 mRNA can be induced by serum. The conserved protein motifs and expression pattern suggest that X16 could be involved in RNA processing correlating with cellular proliferation.

Amino Acid Sequence↗
PubMed1992

Chimeric and truncated RNAs in Trypanosoma brucei suggest transesterifications at non-consecutive sites during RNA editing.

RNA editing adds and removes uridines at specific sites in several mitochondrial transcripts in kinetoplastid parasites probably as specified by guide RNAs (gRNAs) that are complementary to the final edited sequence. Editing has been postulated to involve transesterification which predicts (1) chimeric molecules with a gRNA covalently attached by its non-encoded oligo U tail to an internal editing site in the mRNA and (2) the corresponding truncated 5' portions of the mRNAs. We have characterized cDNAs representing a large number of both types of intermediates from Trypanosoma brucei. The lengths of both U tails and encoded gRNA sequences vary greatly in length. The majority of encoded gRNA sequences are shorter than predicted based on their minicircle coding sequences. Analysis of the predominant sites of gRNA attachment in chimeras suggests that the transesterifications that religate the truncated 5' mRNAs may proceed more rapidly at editing sites at the 5' end of an editing domain and at sites of U deletion. Partially edited sequences in the mRNA portion of chimeras and at the 3' ends of truncated 5' mRNAs also indicate a non-consecutive order of site selection during RNA editing.

Animals↗
PubMed1993

Molecular characterisation and stage-specific expression of proliferating cell nuclear antigen (PCNA) from the malarial parasite, Plasmodium falciparum.

The gene encoding the malarial homologue of proliferating cell nuclear antigen, PCNA, has been identified and characterised. It is located on chromosome 13. The coding sequence of 825 nucleotides predicts a protein of 30,586 Da. There are no introns and northern analysis reveals a transcript of approximately 1.6kb. The conserved residues which characterise the PCNAs of human, Drosophila, Saccharomyces and Xenopus are present in PfPCNA but the overall identity of PfPCNA with human and yeast PCNAs is low; 34% and 31% respectively. PfPCNA is longer than the PCNAs of these other species by about 16 amino acids, most of which are present in a block near the carboxy terminus. Antibodies against a purified PfPCNA-glutathione-S-transferase fusion protein recognise a single band in western blots of parasite extracts at 32kDa. The same antiserum has been used to demonstrate that the expression of PfPCNA is regulated during the intraerythrocytic development of the parasite. Expression increases dramatically in late trophozoites and is maintained during the subsequent nuclear divisions which produce schizonts.

Amino Acid Sequence↗
PubMed2001

Aircrew exposure from cosmic radiation on commercial airline routes.

As a result of the recent recommendations of the ICRP 60, and in anticipation of possible regulation on occupational exposure of Canadian-based aircrew, an extensive study was carried out by the Royal Military College of Canada over a one-year period to measure the cosmic radiation at commercial jet altitudes. A tissue-equivalent proportional counter was used to measure the ambient total dose equivalent rate on 62 flight routes, resulting in over 20,000 data points at one-minute intervals at various altitudes and geomagnetic latitudes (i.e. which span the full cut-off rigidity of the Earth's magnetic field). These data were then compared to similar experimental work at the Physikalisch Technische Bundesanstalt, using a different suite of equipment, to measure separately the low and high linear energy transfer components of the mixed radiation field, and to predictions with the LUIN transport code. All experimental and theoretical results were in excellent agreement. From these data, a semiempirical model was developed to allow for the interpolation of the dose rate for any global position, altitude and date (i.e. heliocentric potential). Through integration of the dose rate function over a great circle flight path, a computer code was developed to provide an estimate of the total dose equivalent on any route worldwide at any period in the solar cycle.

Aircraft↗
PubMed1993

Expression and cellular localization of retinol-binding protein messenger ribonucleic acid in bovine blastocysts and extraembryonic membranes.

A cDNA clone encoding retinol-binding protein (RBP) was isolated from a bovine conceptus cDNA library by use of an antiserum specific for bovine conceptus RBP (bcRBP). The RBP cDNA clone, designated bcRBP-700, is 732 bp in length and codes for a protein whose predicted amino acid sequence is identical to that of bovine plasma RBP. The size of the RBP mRNA transcript in bovine chorioallantois was approximately 1.4 kb as determined by Northern blot analysis. Expression of the protein and its mRNA in expanding bovine conceptuses (Day 13) and extraembryonic membranes (Day 45) was determined by immunocytochemistry with anti-bcRBP serum and in situ hybridization with 35S-labeled bcRBP-700 cDNA. Strong immunostaining for RBP and hybridization signals for RBP mRNA were observed in trophectoderm of tubular but not spherical Day 13 blastocysts. RBP mRNA was localized in epithelial cells lining the chorion, allantois, and amnion at Day 45 of pregnancy. In addition, RBP mRNA was detected in cotyledons, the sites of chorionic attachment to the uterine endometrium and physiological exchange between the embryo and its mother. Expression of RBP in expanding conceptuses, developing extraembryonic membranes, and sites of fetal-maternal attachment suggests that the extraembryonic membranes regulate retinol transport and availability within the conceptus.

Allantois↗
PubMed1987

An evaluation of the U.S. Army fallout prediction model.

The U.S. Army fallout prediction method was evaluated against an advanced fallout prediction model--SIMFIC (Simplified Fallout Interpretive Code). The danger zone areas of the U.S. Army method were found to be significantly greater (up to a factor of 8) than the areas of corresponding radiation hazard as predicted by SIMFIC. Nonetheless, because the U.S. Army's method predicts danger zone lengths that are commonly shorter than the corresponding "hot line distances" of SIMFIC, the U.S. Army's method is not reliably conservative.

Military Medicine↗
PubMed1997

Techniques for determining electron losses at a 1.5 GeV synchrotron light source.

A computer code was developed to simulate the bremsstrahlung dose rate distribution patterns produced by the CAMD electron storage ring. These bremsstralung dose rate distributions were measured along the interior surface of the shield walls (short walls perpendicular to the bending magnets) with TLD chips. Electron losses for each specific magnet was determined by running the computer code and varying the electron loss parameters to fit the measured dose rate distributions. It was determined that (1) bending magnet No. 1 (closest to the injection septum) loses 2.7 x 1010 electrons per minute during electron injection. The loss rate for each of the subsequent seven bending magnets during injection varies from about 25% to 33% of this number; (2) the magnet immediately subsequent to the bending magnet loses more electrons than the magnet immediately prior to the bending magnet does; and (3) the computer code may be used to predict potential problems such as misalignment.

Computer Simulation↗
PubMed1997

Leaching of accelerator-produced radionuclides.

Leaching of radionuclides produced in soil and rock by high energy proton-induced radiation was studied for the SSC site. Comparison was made with predictions of a Monte Carlo code CASIM and previous results for the Fermilab site. The principal long-lived radionuclides were 3H and 22Na in agreement with Fermilab results. A few other radionuclides were present at lower concentrations in a subset of the samples. For example, 134Cs was detected in a few SSC water samples. Leaching from SSC chalk was dependent on previous weathering and on leaching time. The more soil-like marl and shale were leached more rapidly. Results of this study, in conjunction with the SSC groundwater model, show that adequate groundwater protection would have been maintained for an accidental loss of the entire proton beam at a point in the SSC Collider tunnel. Early warning techniques developed are directly applicable to soil activation monitoring at other facilities.

Cesium Radioisotopes↗
PubMed2003

Genetic findings and functional studies of human CYP3A5 single nucleotide polymorphisms in different ethnic groups.

OBJECTIVES: Genetic polymorphisms of cytochromes P450 (CYPs) are a principal reason for inter-individual variations in the metabolism of therapeutic drugs and environmental chemicals in humans. The present study identifies 34 single nucleotide polymorphisms (SNPs) of CYP3A5 including 27 previously unidentified SNPs by direct sequencing of the exons, intron-exon junctions and 5'-upstream region of CYP3A5 from 92 racially diverse individuals (24 Caucasians, 24 Africans, 24 Asians, and 20 individuals of unknown racial origin). RESULTS: Four new CYP3A5 SNPs produced coding changes: R28C, L82R, A337T, and F446S. CYP3A5 R28C occurred in African populations (allelic frequency of 4%). CYP3A5 A337T occurred in Asians (2% allelic frequency), CYP3A5 L82R (occurred in the racially unidentified group) and CYP3A5 F446S (identified in Caucasians with a 2% allelic frequency) were on an allele containing the splice change g.6986A>G known as CYP3A5*3. The newly identified allelic proteins were constructed by site-directed mutagenesis, expressed in Escherichia coli and purified. CYP3A5 L82R was expressed only as denatured CYP420, suggesting it may be unstable. CYP3A5*1 exhibited the highest maximal clearance for testosterone followed by CYP3A5 A337T > CYP3A5 R28C >> CYP3A5 F446S. CYP3A5*1 exhibited a higher V(max) for nifedipine oxidation than CYP3A5 A337T > CYP3A5 R28C >> CYP3A5 F446S. CYP3A5 A337T and CYP3A5 R28C exhibited a 42-64% lower V(max) for nifedipine oxidation than CYP3A5*1. CYP3A5 F446S exhibited a > 95% decrease in the intrinsic clearance for both 6beta-hydroxytestosterone and nifedipine oxidation. CONCLUSION: This study identifies four new potentially defective coding alleles. CYP3A5 F446S is predicted to be more catalytically defective than the splice change alone.

Alleles↗
PubMed1987

The complete nucleotide sequence of tobacco rattle virus RNA-1.

The complete nucleotide sequence of tobacco rattle virus (TRV) strain SYM RNA-1 was determined from a series of overlapping cDNA clones. cDNA prepared by primer extension was used to determine the exact 5' terminus. The RNA sequence was 6791 nucleotides in length and contained four open reading frames (ORFs). The ORF nearest the 5' terminus coded for a polypeptide of predicted mol. wt. 134,000 (134K) and terminated at an opal (UGA) stop codon. Readthrough of this stop codon would result in the production of a protein of 194K. The gene for a 29K polypeptide started one base beyond the 194K stop codon and, in turn, was followed by the gene for a 16K protein at the 3' end of RNA-1. Amino acid comparisons of the 194K protein with the putative replicase of tobacco mosaic virus showed three regions of strong homology, suggesting that the 134K and 194K proteins were similarly involved in virus replication. The 5' terminal sequences of both genome RNA species of TRV strains ORY, N5 and PRN together with that of SYM RNA-2 were also determined. Alignments of these sequences showed that there was a 22 base repeated sequence close to the 5' terminus in all these RNA species. It was also shown that the 5' terminus of RNA-1 was homologous with the same region in RNA-2.

Amino Acid Sequence↗
PubMed1994

Characterization of the herpes simplex virus type 1 strain 17+ neurovirulence gene RL1 and its expression in a bacterial system.

The DNA sequence of herpes simplex virus type 1 (HSV-1) strain 17+ in the region coding for the polypeptide ICP34.5 predicts a protein of 248 amino acids with a proposed M(r) of 26,158. The entire RL1 open reading frame was cloned into the expression vector pET8c to enable over-expression of ICP34.5 in Escherichia coli. The expressed protein was partially purified and used as an immunogen to produce a polyclonal antiserum in rabbits. Construction of an ICP34.5 null mutant (1771), demonstrated that the predicted open reading frame for ICP34.5 in strain 17+ is correct and confirmed that HSV-1 strain 17+ ICP34.5 specifically determines neurovirulence. The specificity of the anti-serum directed against the E. coli-expressed ICP34.5 was defined by Western blotting of wild-type and RL1-negative infected cell extracts.

Animals↗
PubMed2003

Suppression of third-order intermodulation in a klystron by third-order injection.

The first observations and measurements are reported on suppression of the third-order intermodulation (IM3) product arising from nonlinear mixing of two drive frequencies in a klystron, by externally injecting a wave at the IM3 product frequency. Optimum amplitude and phase of the injected wave for maximum suppression are examined. Results indicate that suppression of the IM3 product by as much as 30 dB can be achieved. Experimental results compare favorably with predictions of a 1D simulation code that takes into account all kinematical and dynamical effects including charge overtaking and space charge forces.

Journal Article↗
PubMed2004

Particle-transport analysis in reversed field pinch helical states.

This Letter reports the result of a numerical study of particle transport in self-organized single helicity (SH) and quasi-SH reversed field pinch plasmas. Our code, benchmarked against experimental data, predicts a large improvement in particle transport for SH compared to the standard multiple helicity states. The contribution of neoclassical effects is noted. An estimate of the ambipolar electric field in helical states and in fully stochastic magnetic fields is given.

Journal Article↗
PubMed2005

Improving the thermal stability of 1-3 piezoelectric composite transducers.

The effect of temperature on the behavior of 1-3 piezoelectric composites manufactured using various polymeric materials was assessed experimentally through electrical impedance analysis and laser vibrometry. Device behavior varied with temperature irrespective of the polymer filler. Most significant changes in the piezoelectric composites were recorded around the glass transition temperature (Tg) of the polymer; movement to lower fundamental resonant frequencies and higher values of electrical impedance minima were observed at higher temperatures. Decoupling of the pillars from the polymer matrix was observed by laser vibrometry at high temperatures. The use of high Tg polymer extended the operational temperature range of a piezoelectric composite, and a high Tg polymer with improved thermal conductivity also proved beneficial. For all devices, at temperatures very close to room temperature, subtle changes in device performance, linked to polymer softening, were observed. Particulate filled materials have been investigated, and it is recognized that the high viscosities and low mechanical damping of such materials could be problematic for piezoelectric composite manufacture. The thermal solver of the PZFlex finite element code has been used to predict the temporal and spatial temperature response of a selection of the devices presented. The simulated and experimental data compare favorably.

Journal Article↗