31 results on '"R J Watson"'
Search Results
2. The GPlates Geological Information Model and Markup Language
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X. Qin, R. D. Müller, J. Cannon, T. C. W. Landgrebe, C. Heine, R. J. Watson, and M. Turner
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Geophysics. Cosmic physics ,QC801-809 - Abstract
Understanding tectonic and geodynamic processes leading to the present-day configuration of the Earth involves studying data and models across a variety of disciplines, from geochemistry, geochronology and geophysics, to plate kinematics and mantle dynamics. All these data represent a 3-D spatial and 1-D temporal framework, a formalism which is not exploited by traditional spatial analysis tools. This is arguably a fundamental limit in both the rigour and sophistication in which datasets can be combined for geological deep time analysis, and often confines the extent of data analyses to the present-day configurations of geological objects. The GPlates Geological Information Model (GPGIM) represents a formal specification of geological and geophysical data in a time-varying plate tectonics context, used by the GPlates virtual-globe software. It provides a framework in which relevant types of geological data are attached to a common plate tectonic reference frame, allowing the data to be reconstructed in a time-dependent spatio-temporal plate reference frame. The GPlates Markup Language (GPML), being an extension of the open standard Geography Markup Language (GML), is both the modelling language for the GPGIM and an XML-based data format for the interoperable storage and exchange of data modelled by it. The GPlates software implements the GPGIM allowing researchers to query, visualise, reconstruct and analyse a rich set of geological data including numerical raster data. The GPGIM has recently been extended to support time-dependent geo-referenced numerical raster data by wrapping GML primitives into the time-dependent framework of the GPGIM. Coupled with GPlates' ability to reconstruct numerical raster data and import/export from/to a variety of raster file formats, as well as its handling of time-dependent plate boundary topologies, interoperability with geodynamic softwares is established, leading to a new generation of deep-time spatio-temporal data analysis and modelling, including a variety of new functionalities, such as 4-D data-mining.
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- 2012
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3. Spoofing and Jamming of GNSS Signals: Are They Real and What Can We Do About Them
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R. W. Meggs and R. J. Watson
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safety ,Spoofing attack ,Satellite navigation ,Computer science ,ship systems ,ComputerSystemsOrganization_COMPUTER-COMMUNICATIONNETWORKS ,Real-time computing ,Denial-of-service attack ,Jamming ,radio frequency ,GNSS applications ,denial of service ,Radio frequency ,jamming - Abstract
Put simply, ‘spoofing’ is a means of controlling the reported position and time of a GNSS receiver. Spoofing has now been well demonstrated in the experimental context, but until a few years ago it was regarded as “…a bit like UFOs: much speculation, occasional alarms at suspected instances, but little real-world evidence of its existence” (Ref. 1). In the intervening years spoofing has transformed from a research laboratory into an emerging threat. In this paper we focus on radio-frequency attack as the primary method of spoofing. However there is also the possibility of cyber-attack on GNSS systems, in which there is interception and modification of computed position between the receiver and application. It had perhaps previously been considered that the technology and know-how “barrier to entry” to produce an effective spoofer was itself a significant deterrent. However, the commercial availability of inexpensive (sub £250) software defined radio systems, low-cost computing and open-source GNSS signal generator software has all but eliminated this barrier. This paper will consider various methods of spoofing, means of detecting spoofing through analysis of signal anomalies and also mitigation of spoofing at the physical layer via the antenna and signal processing and at the software application layer through the detection of anomalies.
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- 2020
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4. Scan-directed mini-incision focused parathyroidectomy: how accurate is accurate enough?
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S Jabbar, Iestyn M. Shapey, Z Khan, R J Watson, and J E Nicholson
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Parathyroidectomy ,Male ,medicine.medical_specialty ,medicine.medical_treatment ,Concordance ,Parathyroid Diseases ,Parathyroid Glands/surgery ,030230 surgery ,Focused parathyroidectomy ,Parathyroid Glands ,03 medical and health sciences ,0302 clinical medicine ,Postoperative Complications ,Minimally Invasive Surgical Procedures/adverse effects ,medicine ,Humans ,Minimally Invasive Surgical Procedures ,Parathyroid Diseases/surgery ,Retrospective Studies ,business.industry ,Parathyroidectomy/adverse effects ,Ultrasound ,Retrospective cohort study ,General Medicine ,medicine.disease ,Mini incision ,Treatment Outcome ,030220 oncology & carcinogenesis ,General Surgery ,Surgery ,Female ,Radiology ,business ,Primary hyperparathyroidism ,Preoperative imaging - Abstract
INTRODUCTION Mini-incision focused parathyroidectomy (MI-FP) is advocated as an alternative to bilateral neck exploration (BNE), owing to its reduced morbidity. The site and side of the affected gland is identified preoperatively using a combination of ultrasound and sestamibi scans. However, the acceptable degree of inter-scan concordance required to prompt MI-FP without compromising accuracy is undetermined. METHODS Accuracy of preoperative imaging was determined both individually and in combination for all parathyroidectomies (2007–2014). A grading system (excellent, good, poor) was devised to describe the interscan concordance, which was validated by the operative and histological findings. RESULTS Eighty-nine patients (17 male, 68 female) underwent parathyroidectomy (MI-FP 44, BNE 45). The accuracy of scans interpreted individually was 53% for ultrasound and 60% for sestamibi, with no difference according to surgical technique (P = 0.43, P = 1, respectively). The proportion of interscan concordance was: excellent – 35%, good – 40%, poor 25%. Combined accuracy was 100% for both excellent and good grades but only 13% for those graded poor. Similar rates of normocalcaemia were observed for MI-FP and BNE, while postoperative hypocalcaemia was five times higher in those undergoing BNE. CONCLUSIONS Reduction in the inter-scan concordance from excellent to good does not compromise accuracy. MI-FP could be successfully performed in up to 75% of patients – 25% higher than recommended in national guidelines. Focused parathyroidectomy does not compromise surgical and endocrinological outcomes but boasts a far superior complication rate.
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- 2017
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5. Epstein-Barr virus nuclear antigen 3C is a powerful repressor of transcription when tethered to DNA
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Martin J. Allday, M Bain, Paul J. Farrell, and R J Watson
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Gene Expression Regulation, Viral ,Herpesvirus 4, Human ,Saccharomyces cerevisiae Proteins ,Transcription, Genetic ,Recombinant Fusion Proteins ,Immunology ,Repressor ,Biology ,Microbiology ,Fungal Proteins ,Mice ,Transcription (biology) ,Virology ,Tumor Cells, Cultured ,Animals ,Humans ,Binding site ,Promoter Regions, Genetic ,Antigens, Viral ,Transcription factor ,chemistry.chemical_classification ,B-Lymphocytes ,Reporter gene ,Binding Sites ,General transcription factor ,3T3 Cells ,DNA ,Cell Transformation, Viral ,Molecular biology ,Amino acid ,DNA-Binding Proteins ,Repressor Proteins ,Epstein-Barr Virus Nuclear Antigens ,chemistry ,Insect Science ,Transcription factor II D ,Protein Binding ,Transcription Factors ,Research Article - Abstract
The expression of Epstein-Barr virus (EBV) nuclear antigen 3C (EBNA3C) is essential for the activation and immortalization of human B lymphocytes by EBV. EBNA3C consists of 992 amino acids and includes a potential bZIP motif and regions rich in acidic, proline, and glutamine residues. Thus, EBNA3C resembles several trans regulators of gene expression. It has recently been shown that a fragment of EBNA3C can activate reporter gene expression when fused to the DNA-binding domain of GAL4 (D. Marshall and C. Sample, J. Virol. 69:3624-3630,1995). Although EBNA3C binds DNA, a specific site for EBNA3C binding has not been identified; to test the ability of full-length EBNA3C to regulate transcription, EBNA3C (amino acids 11 to 992) was fused to the DNA-binding domain of GAL4. We show that this fusion protein does not transactivate but rather is a potent repressor of reporter gene expression. Repression is dependent on the dose of GAL4-EBNA3C and on the presence of GAL4-binding sites within reporter plasmids. Repression is not restricted to B cells nor is it species or promoter specific. Repression is independent of the location of the GAL4-binding sites relative to the transcription start site. A fragment of EBNA3C (amino acids 280 to 525) which represses expression in a manner which is nearly identical to that of the full-length protein has been identified; this fragment is rich in acidic and proline residues. A second, less potent repressor region located C terminal to amino acids 280 to 525 has also been identified; this domain is rich in proline and glutamine residues. We also show binding of EBNA3C, in vitro, to the TATA-binding protein component of TFIID, and this suggests a mechanism by which EBNA3C may communicate with the basal transcription complex.
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- 1996
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6. Aspartate transport in Rhizobium meliloti
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R. J. Watson, Y.-K. Chan, and V. K. Rastogi
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Sinorhizobium meliloti ,endocrine system diseases ,biology ,nutritional and metabolic diseases ,Metabolism ,Glutamic acid ,Membrane transport ,biology.organism_classification ,Microbiology ,body regions ,Non-competitive inhibition ,Biochemistry ,Aspartic acid ,Rhizobium ,Aspartate transport ,hormones, hormone substitutes, and hormone antagonists - Abstract
Summary: Aspartate transport in Rhizobium meliloti was found to be mediated by at least two transport systems. High rates of aspartate uptake, necessary for growth on aspartate as a carbon source, required the dicarboxylate transport (Dct) system, which also transports succinate, fumarate and malate. The apparent K m for aspartate transport by this system was about 10 mm, compared to 15 μm for succinate. This difference in affinity was also apparent in competitive inhibition studies, which showed that succinate effectively inhibits aspartate transport. Although aspartate was not a preferred substrate, it was a very efficient inducer of the Dct system. Both the Dct system and a second aspartate transport system were capable of supplying aspartate for use as a nitrogen source. The second system had a lower apparent K m for aspartate transport (1.5 mm), and was competitively inhibited by glutamate. This aspartate-glutamate system was regulated independently from the Dct system, since it functioned in mutants lacking the Dct system regulatory genes dctB and dctD, and its induction did not coactivate the Dct system. Uptake kinetics in cultures growing on aspartate as nitrogen source showed rapid substrate exchange between extracellular and internal aspartate. R. meliloti was shown to be able to selectively activate the two uptake systems, and also regulated its metabolism as required to utilize aspartate as either carbon or nitrogen source.
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- 1993
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7. Cloning and nucleotide sequencing of Rhizobium meliloti aminotransferase genes: an aspartate aminotransferase required for symbiotic nitrogen fixation is atypical
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R J Watson and V K Rastogi
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Transcription, Genetic ,Sequence analysis ,Molecular Sequence Data ,Restriction Mapping ,Molecular cloning ,Polymerase Chain Reaction ,Microbiology ,Homology (biology) ,Species Specificity ,Nitrogen Fixation ,Amino Acid Sequence ,Aspartate Aminotransferases ,Cloning, Molecular ,Symbiosis ,Molecular Biology ,Gene ,Tyrosine Transaminase ,Sinorhizobium meliloti ,Base Sequence ,Sequence Homology, Amino Acid ,biology ,Nucleic acid sequence ,Nucleic Acid Hybridization ,Sequence Analysis, DNA ,biology.organism_classification ,Molecular biology ,Recombinant Proteins ,Open reading frame ,Subcloning ,Biochemistry ,Genes, Bacterial ,Research Article - Abstract
In Rhizobium meliloti, an aspartate aminotransferase (AspAT) encoded within a 7.3-kb HindIII fragment was previously shown to be required for symbiotic nitrogen fixation and aspartate catabolism (V. K. Rastogi and R.J. Watson, J. Bacteriol. 173:2879-2887, 1991). A gene coding for an aromatic aminotransferase located within an 11-kb HindIII fragment was found to complement the AspAT deficiency when overexpressed. The genes encoding these two aminotransferases, designated aatA and tatA, respectively, have been localized by subcloning and transposon Tn5 mutagenesis. Sequencing of the tatA gene revealed that it encodes a protein homologous to an Escherichia coli aromatic aminotransferase and most of the known AspAT enzymes. However, sequencing of the aatA gene region revealed two overlapping open reading frames, neither of which encoded an enzyme with homology to the typical AspATs. Polymerase chain reaction was used to selectively generate one of the candidate sequences for subcloning. The cloned fragment complemented the original nitrogen fixation and aspartate catabolism defects and was shown to encode an AspAT with the expected properties. Sequence analysis showed that the aatA protein has homology to AspATs from two thermophilic bacteria and the eukaryotic tyrosine aminotransferases. These aminotransferases form a distinct class in which only 13 amino acids are conserved in comparison with the well-known AspAT family. DNA homologous to the aatA gene was found to be present in Agrobacterium tumefaciens and other rhizobia but not in Klebsiella pneumoniae or E. coli.
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- 1993
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8. Characterization of the sequence-specific interaction of mouse c-myb protein with DNA
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K. M. Howe, R. J. Watson, and C. F. L. Reakes
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Transcription, Genetic ,Protein subunit ,Molecular Sequence Data ,Biology ,Polymerase Chain Reaction ,General Biochemistry, Genetics and Molecular Biology ,Mice ,Proto-Oncogene Proteins c-myb ,chemistry.chemical_compound ,Proto-Oncogene Proteins ,Protein biosynthesis ,Animals ,Amino Acid Sequence ,Binding site ,Molecular Biology ,Peptide sequence ,Repetitive Sequences, Nucleic Acid ,chemistry.chemical_classification ,Gel electrophoresis ,Binding Sites ,Base Sequence ,General Immunology and Microbiology ,General Neuroscience ,DNA ,Molecular biology ,Amino acid ,chemistry ,Biochemistry ,Protein Biosynthesis ,Mutation ,Electrophoresis, Polyacrylamide Gel ,Sequence motif ,Plasmids ,Research Article - Abstract
We have examined parameters that affect sequence-specific interactions of the mouse c-myb protein with DNA oligomers containing the Myb-binding motif (CA/CGTTPu). Complexes formed between these oligomers and in vitro translated c-myb proteins were analysed by electrophoresis on non-denaturing polyacrylamide gels using the mobility-shift assay. By progressive truncation of c-myb coding sequences it was demonstrated that amino acids downstream of a region of three imperfect 51-52 residue repeats (designated R1, R2 and R3), which are located close to the amino terminus of the protein, had no qualitative or quantitative effect on the ability to interact specifically with this DNA motif. However, removal of only five amino acids of the R3 repeat completely abolished this activity. The contribution of individual DNA-binding domain repeats to this interaction was investigated by precisely deleting each individually: it was demonstrated that a combination of R2 and R3 was absolutely required for complex formation while the R1 repeat was completely dispensible. c-myb proteins showed quantitatively greater interaction with oligomers containing duplicated rather than single Myb-binding motif, in particular where these were arranged in tandem. Moreover, it was observed that c-myb protein interacted with these tandem motifs as a monomer. These findings imply that a single protein subunit straddles adjacent binding sites and the implications for c-myb activity are discussed.
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- 1990
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9. Cell cycle regulation by the B-Myb transcription factor
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R. J. Watson and Manel Joaquin
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Transcription, Genetic ,Cyclin A ,Cell Cycle Proteins ,Cellular and Molecular Neuroscience ,Serum response factor ,E2F1 ,Animals ,Humans ,Cyclin D1 ,Phosphorylation ,E2F ,Cell Cycle Protein ,Promoter Regions, Genetic ,Molecular Biology ,Pharmacology ,Cyclin-dependent kinase 1 ,biology ,Ubiquitin ,Cell Cycle ,Nuclear Proteins ,Cell Biology ,E2F Transcription Factors ,DNA-Binding Proteins ,biology.protein ,Cancer research ,Trans-Activators ,Molecular Medicine ,Restriction point ,Transcription Factors - Abstract
The expression of genes required for progression through the cell cycle is highly modulated through a regulatory axis containing the E2F transcription factor and retinoblastoma tumour suppressor protein families. One of the genes regulated through this mechanism encodes the B-Myb transcription factor, which has been shown to be critically required for early embryonal development in the mouse. Transcriptional activity of B-Myb is substantially enhanced in S phase through modification by cyclin A/cdk2, and the evidence points squarely to the major role being played by B-Myb during this phase of the cell cycle. We discuss in this review recent findings suggesting that B-Myb is a multifunctional protein that has, in addition to its transcriptional properties, the ability to interact directly with other regulators of the cell cycle.
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- 2003
10. Fine-wire localization and biopsy of non-palpable breast lesions
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Hartley G, R. J. Watson, Asbury Dl, J. C. Tresadern, A. Borg‐Grech, and Sellwood Ra
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Pathology ,medicine.medical_specialty ,Wire localization ,Breast Neoplasms ,Malignancy ,Asymptomatic ,Breast Diseases ,Biopsy ,medicine ,Humans ,Mammography ,Breast ,Mastectomy ,medicine.diagnostic_test ,business.industry ,Biopsy, Needle ,medicine.disease ,Female ,Surgery ,Radiology ,Microcalcification ,Non palpable ,medicine.symptom ,business ,Breast carcinoma - Abstract
We have undertaken fine-wire localization and biopsy of 130 impalpable breast lesions identified by mammography and considered suspicious of malignancy. Histologically 22 of these lesions were invasive carcinomas and 24 were in situ carcinomas (35 per cent malignant). Twenty-nine per cent of the lesions were identified during the screening of asymptomatic women. In the remainder, the presenting symptoms bore no relation to the eventual histological diagnosis. Clusters of micro-calcification were more often malignant than were abnormal soft-tissue masses. Malignancy in the absence of microcalcification was almost always invasive.
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- 1990
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11. PMO-016 Big brother is watching you! Is data from the BSG colonoscopy audit period a true reflection of normal practice?
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G Lipman, R J Watson, and A R Watson
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medicine.medical_specialty ,Pediatrics ,medicine.diagnostic_test ,medicine.drug_class ,business.industry ,Hawthorne effect ,Sedation ,Gastroenterology ,Psychological intervention ,Colonoscopy ,Audit ,Confidence interval ,Sedative ,Emergency medicine ,medicine ,medicine.symptom ,business ,Null hypothesis - Abstract
Introduction The “Hawthorne Effect” is the phenomenon in which subjects modify practice as a consequence of the knowledge that they are being observed. This is a potential confounder during periods of national endosocopy audit and may result in spuriously improved outcome reporting during audit periods. We aimed to investigate whether the Hawthorne Effect influences colonoscopy practice. We also aimed to ascertain if the national colonscopy audit could result in a change in practice, and whether any such change was maintained. Methods The Unisoft endoscopy database at Whipps Cross University Hospital was interrogated to determine patient demographics, sedation rates, quality of bowel preparation, diagnoses and therapeutic interventions during 5 2-week time periods; The national colonoscopy audit period (t), t−1 year, t−2 weeks, t+2 weeks and t+3 months. Results were compared to determine whether there was a statistically significant difference in measurable indices of clinical practice that may be due to the Hawthorne Effect. Time periods following the audit period were included to establish whether there was any evidence of a “washout period” of improved outcomes following the national audit—that is, if the process of observed audit results in a lasting improvement in clinical practice. The null hypothesis was suggested that all periods would be similar, and tested to a 95% confidence level. Results Colonoscopies performed during the national colonoscopy audit period (t) were compared with 2-week periods t−1 year, t−2 weeks, t+2 weeks and t+3 months. Similar numbers of procedures were carried out during the five time periods. Basic patient demographics were similar, as were the numbers of male and female patients. No statistically significant differences were found in the sedative dose, ceacal or TI intubation rates between the audit period and any other time period. Moreover, polyp detection and retrieval was likewise also not statistically significantly different when the four time periods were compared with the fortnight of the national colonscopy audit. Small differences were noted in the colonscopists assessment of bowel preparation—there was more likely be a comment on poor bowel preparation during the audit period than any of the other time periods. Conclusion Data from Whipps Cross University Hospital demonstrate that observation of colonoscopists during the recent BSG national colonoscopy audit does not alter significantly the clinical practice or interpretation of findings when compared to time periods before or after the audit period. This validates the national colonoscopy audt findings; the data are indeed a true reflection of “normal” colonsocopy practice—colonoscopists are apparently not affected by the “Hawthorne Effect”. Competing interests None declared.
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- 2012
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12. Complex Symbiotic Phenotypes Result from Gluconeogenic Mutations inRhizobium meliloti
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E. Mcwhinnie, R. J. Watson, B. Driscoll, and Turlough M. Finan
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Mutation ,Rhizobiaceae ,biology ,Plant nodule ,Physiology ,General Medicine ,biology.organism_classification ,medicine.disease_cause ,Phenotype ,Biochemistry ,Symbiosis ,Nitrogen fixation ,medicine ,Rhizobium ,Agronomy and Crop Science ,Bacteria - Published
- 1991
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13. Cloning the spoT gene of Escherichia coli: identification of the spoT gene product
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J Justesen, J D Friesen, G An, and R J Watson
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DNA, Bacterial ,DNA, Recombinant ,Guanosine ,Guanosine Tetraphosphate ,Biology ,medicine.disease_cause ,Coliphages ,Microbiology ,Pyrophosphate ,Gene product ,chemistry.chemical_compound ,Plasmid ,Transduction, Genetic ,Escherichia coli ,medicine ,Pyrophosphatases ,Molecular Biology ,Alleles ,Pyrophosphatase ,Molecular biology ,PBR322 ,Biochemistry ,chemistry ,Plasmids ,Research Article - Abstract
We have isolated five specialized transducing lambda bacteriophages (lambda dpyrE spoT) carrying the pyrE and spoT genes of Escherichia coli. A fragment from one of these phages was used as the source of DNA to clone the spoT and pyrE genes on a multicopy plasmid, pBR322. Insertions and deletions in this plasmid were obtained. These plasmids were used to transform a minicell-producing strain, and the gene products synthesized were determined. Our experiments demonstrate that the spoT and pyrE genes are separated by about 4 magadaltons and suggest that the spoT gene product is a protein whose molecular weight is 80,000. The strain in which the spoT+ allele is carried on a plasmid produced nine times more spoT gene activity than a normal spoT+ strain when assayed in crude extracts. This strain was used to prepare partially purified gene product, guanosine 5'-diphosphate, 3'-diphosphate pyrophosphatase. The enzyme has the following characteristics. (i) It hydrolyzes pyrophosphate from the 5'-pyrophosphate of guanosine 5'-diphosphate, 3'-diphosphate, yielding GDP and pyrophosphate. (ii) Its activity is strongly stimulated by Mn2+ and slightly stimulated by salt. (iii) Its activity is inhibited by uncharged tRNA. There are also two additional activities in the cell extract which degrade guanosine in 5'-diphosphate, 3'-diphosphate in vitro but which are not specified by the spoT gene.
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- 1979
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14. Human DNA sequence homologous to the transforming gene (mos) of Moloney murine sarcoma virus
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M Oskarsson, G F Vande Woude, and R J Watson
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Placenta ,Molecular cloning ,Biology ,DNA sequencing ,Mice ,chemistry.chemical_compound ,Pregnancy ,Animals ,Humans ,Coding region ,Cloning, Molecular ,Gene ,Genetics ,Multidisciplinary ,Base Sequence ,DNA ,DNA Restriction Enzymes ,Molecular biology ,Long terminal repeat ,Open reading frame ,Cell Transformation, Neoplastic ,chemistry ,DNA, Viral ,Female ,Moloney murine leukemia virus ,BamHI ,Research Article - Abstract
We describe the molecular cloning of a 9-kilo-base-pair BamHI fragment from human placental DNA containing a sequence homologous to the transforming gene (v-mos) of Moloney murine sarcoma virus. The DNA sequence of the homologous region of human DNA (termed humos) was resolved and compared to that of the mouse cellular homolog of v-mos (termed mumos) [Van Beveren, C., van Straaten, F., Galleshaw, J.A. & Verma, I.M. (1981) Cell 27, 97-108]. The humos gene contained an open reading frame of 346 codons that was aligned with the equivalent mumos DNA sequence by the introduction of two gaps of 15 and 3 bases into the mumos DNA and a single gap of 9 bases into the humos DNA. The aligned coding sequences were 77% homologous and terminated at equivalent opal codons. The humos open reading frame initiated at an ATG found internally in the mumos coding sequence. The polypeptides predicted from the DNA sequence to be encoded by humos and mumos also were found to be extensively homologous, and 253 of 337 amino acids were shared between the two polypeptides. The first five NH2-terminal and last two COOH-terminal amino acids of the humos gene product were in common with those of mumos. In addition, near the middle of the polypeptide chains, four regions ranging from 19 to 26 consecutive amino acids were conserved. However, we have not been able to transform mouse cells with transfected humos DNA fragments or with hybrid DNA recombinants containing humos and retroviral long terminal repeat (LTR) sequences.
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- 1982
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15. Pseudorabies virus gene encoding glycoprotein gIII is not essential for growth in tissue culture
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A. K. Robbins, Lynn W. Enquist, M. E. Whealy, and R. J. Watson
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XhoI ,Genes, Viral ,Swine ,viruses ,Immunology ,Transfection ,medicine.disease_cause ,Microbiology ,Virus ,Cell Line ,Viral Proteins ,Plasmid ,Viral Envelope Proteins ,Virology ,medicine ,Animals ,Gene ,chemistry.chemical_classification ,Mutation ,biology ,RNA ,Herpesvirus 1, Suid ,Molecular biology ,chemistry ,Cell culture ,Protein Biosynthesis ,Insect Science ,biology.protein ,Glycoprotein ,Research Article - Abstract
We have established that in the Becker strain of pseudorabies virus (PRV), the glycoprotein gIII gene is not essential for growth in cell culture. This was accomplished by construction and analysis of viral mutants containing two defined deletion mutations affecting the gIII gene. These mutations were first constructed in vitro and introduced into Escherichia coli expression plasmids to verify structure and protein production. Each mutation was then crossed onto PRV by cotransfection of plasmid DNA and parental viral DNA by using gIII-specific monoclonal antibodies as selective and screening reagents. One resultant virus strain, PRV-2, contained an in-frame deletion of a 402-base-pair (bp) SacI fragment contained within the gIII gene. Another virus strain, PRV-10, contained a deletion of a 1,480-bp XhoI fragment removing 230 bp of the upstream, putative transcriptional control sequences and 87% of the gIII coding sequence. The deletion mutants were compared with parental virus by analysis of virion DNA, gIII specific RNA, and proteins reacting with gIII specific antibodies. Upon infection of PK15 cells, the deletion mutants did not produce any proteins that reacted with two gIII specific monoclonal antibodies. However, two species of truncated glycosylated proteins were observed in PRV-2 infected cells that reacted with antiserum raised against bacterially produced gIII protein. PRV-10 produced no detectable gIII-specific RNA or protein. PRV-10 could be propagated without difficulty in tissue culture. Virus particles lacking gIII were indistinguishable from parental PRV virus particles by analysis of infected-cell thin sections in the electron microscope. We therefore conclude that expression of the gIII gene was not absolutely essential for PRV growth in tissue culture.
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- 1986
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16. Multiple c-myb transcript cap sites are variously utilized in cells of mouse haemopoietic origin
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P. J. Dyson, J. McMahon, and R. J. Watson
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Transcription, Genetic ,RNase P ,T cell ,Biology ,General Biochemistry, Genetics and Molecular Biology ,Cell Line ,Mice ,Myeloid stem cell ,Proto-Oncogenes ,Gene expression ,medicine ,Animals ,Coding region ,RNA, Messenger ,Molecular Biology ,Gene ,Mice, Inbred BALB C ,Messenger RNA ,Leukemia, Experimental ,General Immunology and Microbiology ,General Neuroscience ,Nucleotide Mapping ,RNA ,Neoplasms, Experimental ,Hematopoietic Stem Cells ,Molecular biology ,Mice, Inbred C57BL ,medicine.anatomical_structure ,Research Article - Abstract
Mouse c-myb gene transcripts in various cells of haemopoietic origin were analysed using S1 nuclease and RNase mapping techniques and by Northern blotting. It was found that the prevalent 3.8-kb c-myb mRNA present in thymocytes, T cell leukaemias, myelomonocytic leukaemias, erythroleukaemias and myeloid stem cells was initiated at several cap sites mapping within a region 97-244 bp upstream from the protein coding sequence. Utilization of additional cap sites mapping further upstream was also observed in certain cells, most notably thymocytes, and this gave rise to RNA species (4.3-5.6 kb) larger than the presumptive mRNA. In contrast, myeloma cell c-myb transcripts, which are much less abundant than those in more immature haemopoietic cells, were found to be initiated at a restricted set of cap sites mapping 244-277 bp upstream of the coding sequence. Hence, these data suggest that the abundance of the c-myb mRNA may be regulated by a process involving selective utilization of mRNA cap sites. Sites hypersensitive to DNase I were associated with mRNA cap sites in cells that expressed c-myb.
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- 1987
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17. Localization of a type-specific antigenic site on herpes simplex virus type 2 glycoprotein D
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R J Watson, G Sisson, N Balachandran, and William E. Rawls
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Adult ,Sequence analysis ,medicine.drug_class ,Immunology ,Fluorescent Antibody Technique ,Biology ,medicine.disease_cause ,Monoclonal antibody ,Microbiology ,Herpesviridae ,Virus ,Epitope ,Epitopes ,Viral Proteins ,Viral Envelope Proteins ,Virology ,medicine ,Humans ,Simplexvirus ,Amino Acid Sequence ,Peptide sequence ,chemistry.chemical_classification ,Base Sequence ,Antibodies, Monoclonal ,Molecular biology ,Herpes simplex virus ,chemistry ,Insect Science ,DNA, Viral ,Female ,Glycoprotein ,Research Article - Abstract
A herpes simplex virus type 1 strain isolated from a recurrent lesion of the nose reacted with monoclonal antibodies recognizing a type 2-specific site on glycoprotein D but not with monoclonal antibodies recognizing other type 2-specific sites. DNA sequence analysis of the glycoprotein D gene of the isolate revealed a single nucleotide alteration which changed the codon for asparagine to one encoding histidine at amino acid 97 in the protein. Histidine is located at this position in glycoprotein of herpes simplex virus type 2; thus, the monoclonal antibody 17 beta A3 recognizes an epitope located at this region of the protein.
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- 1984
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18. The pseudorabies virus gII gene is closely related to the gB glycoprotein gene of herpes simplex virus
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M Levine, C Gold, M. E. Whealy, D J Dorney, L E Holland, M W Wathen, R. J. Watson, J C Glorioso, A. K. Robbins, and S D Weed
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Genes, Viral ,Transcription, Genetic ,Sequence analysis ,viruses ,Immunology ,Biology ,Microbiology ,Viral Proteins ,Virology ,Sequence Homology, Nucleic Acid ,Coding region ,Simplexvirus ,Amino Acid Sequence ,Peptide sequence ,Gene ,Southern blot ,Glycoproteins ,Base Sequence ,Antibodies, Monoclonal ,Molecular biology ,Herpesvirus glycoprotein B ,Herpesvirus 1, Suid ,Restriction enzyme ,Open reading frame ,Insect Science ,DNA, Viral ,RNA, Viral ,Research Article - Abstract
We have looked for conserved DNA sequences between four herpes simplex virus type 1 (HSV-1) glycoprotein genes encoding gB, gC, gD, and gE and pseudorabies virus (PRV) DNA, HSV-1 DNA fragments representing these four glycoprotein-coding sequences were hybridized to restriction enzyme fragments of PRV DNA by the Southern blot procedure. Specific hybridization was observed only when HSV-1 gB DNA was used as probe. This region of hybridization was localized to a 5.2-kilobase (kb) region mapping at approximately 0.15 map units on the PRV genome. Northern blot (RNA blot) analysis, with a 1.2-kb probe derived from this segment, revealed a predominant hybridizing RNA species of approximately 3 kb in PRV-infected PK15 cells. DNA sequence analysis of the region corresponding to this RNA revealed a single large open reading frame with significant nucleotide homology with the gB gene of HSV-1 KOS 321. In addition, the beginning of the sequenced PRV region also contained the end of an open reading frame with amino acid homology to HSV-1 ICP 18.5, a protein that may be involved in viral glycoprotein transport. This sequence partially overlaps the PRV gB homolog coding sequence. We have shown that the PRV gene with homology to HSV-1 gB encoded the gII glycoprotein gene by expressing a 765-base-pair segment of the PRV open reading frame in Escherichia coli as a protein fused to beta-galactosidase. Antiserum, raised in rabbits, against this fusion protein immunoprecipitated a specific family of PRV glycoproteins of apparent molecular mass 110, 68, and 55 kilodaltons that have been identified as the gII family of glycoproteins. Analysis of the predicted amino acid sequence indicated that the PRV gII protein shares 50% amino acid homology with the aligned HSV-1 gB protein. All 10 cysteine residues located outside of the signal sequence, as well as 4 of 6 potential N-linked glycosylation sites, were conserved between the two proteins. The primary protein sequence for HSV-1 gB regions known to be involved in the rate of virus entry into the cells and cell-cell fusion, as well as regions known to be associated with monoclonal antibody resistance, were highly homologous with the PRV protein sequence. Furthermore, monospecific antibody made against PRV gII immunoprecipitated HSV-1 gB from infected cells. Taken together, these findings suggest significant conservation of structure and function between the two proteins and may indicate a common evolutionary history.
- Published
- 1987
19. Structures of two spliced herpes simplex virus type 1 immediate-early mRNA's which map at the junctions of the unique and reiterated regions of the virus DNA S component
- Author
-
M Sullivan, R J Watson, and G F Vande Woude
- Subjects
Base pair ,Immunology ,Biology ,medicine.disease_cause ,Microbiology ,Virus ,chemistry.chemical_compound ,Virology ,medicine ,Simplexvirus ,RNA, Messenger ,Gene ,RNA, Double-Stranded ,Repetitive Sequences, Nucleic Acid ,Genetics ,Electrophoresis, Agar Gel ,Base Sequence ,Intron ,RNA ,Nucleic Acid Hybridization ,Exonuclease VII ,Molecular biology ,Microscopy, Electron ,Herpes simplex virus ,chemistry ,Insect Science ,DNA, Viral ,Nucleic Acid Conformation ,RNA, Viral ,Poly A ,DNA ,Research Article - Abstract
We have examined the structures of two herpes simplex virus type 1 immediate-early (IE) RNAs (IE mRNA-4 and IE mRNA-5) which map at the junctions of the unique (Us) and reiterated regions (TRs/IRs) of the virus DNA short component. Hybrids between IE cytoplasmic RNA and herpes simplex virus type 1 DNA restriction fragments were digested with single-strand-specific nucleases S1 and exonuclease VII, and the products were analyzed by agarose gel electrophoresis. Data obtained with the nuclease digestion technique were confirmed by electron microscopy of R-loop structures formed with polyadenylated IE RNA and virus DNA fragments. It was found that both IE mRNA-4 and IE mRNA-5 contained a 260-base 5'-terminal cotranscript which mapped at equivalent loci within TRs/IRs. These 5'-terminal sequences were shown to be spliced to 3'-terminal cotranscripts of 1,450 bases (for IE mRNA-4) and 1,540 bases (for IE mRNA-5). The 3'-terminal cotranscripts contained sequences encoded by both TRs/IRs and opposite ends of Us, indicating that the introns contained by the IE mRNA-4 and IE mRNA-5 genes, found to be approximately 150 base pairs in size, mapped entirely within the reiterated sequences. The data suggest that these genes may contain common and unique components, and the implications of this model are discussed.
- Published
- 1981
20. Separation and characterization of herpes simplex virus type 1 immediate-early mRNA's
- Author
-
R J Watson, C M Preston, and J B Clements
- Subjects
Polyadenylation ,Immunology ,Cycloheximide ,Biology ,medicine.disease_cause ,Kidney ,Microbiology ,Virus ,Cell Line ,chemistry.chemical_compound ,Nucleic acid thermodynamics ,Viral Proteins ,Virology ,Cricetinae ,medicine ,Protein biosynthesis ,Animals ,Simplexvirus ,RNA, Messenger ,Messenger RNA ,Cell-Free System ,Nucleic Acid Hybridization ,Molecular biology ,Herpes simplex virus ,chemistry ,Insect Science ,Protein Biosynthesis ,DNA, Viral ,RNA, Viral ,Poly A ,DNA ,Research Article - Abstract
Polyadenylated immediate-early transcripts of herpes simplex virus type 1, made in BHK cells infected and maintained in the presence of cycloheximide, have been separated on denaturing agarose gels containing methyl mercuric hydroxide. Three virus-specific mRNA bands of estimated sizes 4.7, 3.0, and 2.0 kilobases (kb) were detected, and these mRNA's were mapped on the virus genome and also used to direct protein synthesis in vitro. The 4.7- and 3.0-kb mRNA's hybridized predominantly to certain DNA fragments which are located in the short and long repetitive regions of the genome, respectively, whereas the 2.0-kb mRNA's mapped to three discrete regions of the virus DNA. In vitro translation of these separated mRNA size classes indicated that the 3.0-kb mRNA specified the synthesis of virus polypeptide Vmw 110, whereas the 2.0-kb mRNA's specified Vmw 68, 63, and 12. The synthesis of small amounts of Vmw 175 was specified by the 4.7-kb mRNA. In contrast with the mRNA's which specify these other immediate-early polypeptides, that specifying Vmw 12 is much larger than required for its coding sequences.
- Published
- 1979
21. Rhizobium meliloti genes required for C4-dicarboxylate transport and symbiotic nitrogen fixation are located on a megaplasmid
- Author
-
S H Han, R J Watson, Yiu-Kwok Chan, R Wheatcroft, and A F Yang
- Subjects
DNA, Bacterial ,Rhizobiaceae ,Mutant ,EcoRI ,Mutagenesis (molecular biology technique) ,Deoxyribonuclease HindIII ,medicine.disease_cause ,Microbiology ,Deoxyribonuclease EcoRI ,Plasmid ,Nitrogen Fixation ,medicine ,Dicarboxylic Acids ,Symbiosis ,Molecular Biology ,Mutation ,biology ,food and beverages ,Nucleic Acid Hybridization ,DNA Restriction Enzymes ,biology.organism_classification ,Cosmids ,Microscopy, Electron ,Biochemistry ,Genes, Bacterial ,biology.protein ,Cosmid ,Rhizobium ,Research Article ,Medicago sativa ,Plasmids - Abstract
A mutant of Rhizobium meliloti unable to transport C4 dicarboxylates (dct) was isolated after Tn5 mutagenesis. The mutant, 4F6, could not grow on aspartate or the tricarboxylic acid cycle intermediates succinate, fumarate, or malate. It produced symbiotically ineffective nodules on Medicago sativa in which bacteroids appeared normal, but the symbiotic zone was reduced and the plant cells contained numerous starch granules at their peripheries. Cosmids containing the dct region were obtained by selecting those which restored the ability of 4F6 to grow on succinate. The Tn5 insertion in 4F6 was found to be within a 5.9-kilobase (kb) EcoRI fragment common to the complementing cosmids. Site-specific Tn5-mutagenesis revealed dct genes in a segment of DNA about 4 kb in size extending from within the 5.9-kb EcoRI fragment into an adjacent 2.9-kb EcoRI fragment. The 4F6 mutation was found to be in a complementation group in which mutations yielded a Fix- phenotype, whereas other dct mutations in the region resulted in mutants which produced effective nodules in most, although not all, plant tests (partially Fix-). The dct region was found to be located on a megaplasmid known to carry genes required for exopolysaccharide production.
- Published
- 1988
22. Ultrastructural observations on the basal lamina in the normal human breast
- Author
-
R J, Watson, B P, Eyden, A, Howell, and R A, Sellwood
- Subjects
Microscopy, Electron ,Biopsy ,Humans ,Female ,Breast ,Fibrocystic Breast Disease ,Basement Membrane ,Menstrual Cycle ,Research Article - Abstract
The ultrastructure of the basal lamina of histologically normal human breast tissue was determined in 19 women undergoing operations for removal of a fibroadenoma or reduction mammoplasty. The day of the menstrual cycle was determined by hormone assay and direct questioning. Previously documented ultrastructural appearances were confirmed: in addition, three morphological variants were found. In all tissue examined, there was reduplication of basal lamina in some areas, which has been described previously as a pathological feature. Also, there was complex branching of the basal lamina into the periductular connective tissue. Some projections contained cytoplasmic processes and, in almost all, hemidesmosomes were seen. The third variant consisted of loops of basal lamina thrown up in folds into the collagenous stromal cuff. Reduplication of basal lamina was detected in breast tissue removed at all stages of the menstrual cycle, looping was not and could not be related to any particular phase of the menstrual cycle. However, complex branching was seen predominantly in the periovulatory and early luteal phase. We conclude that these appearances are normal variants of basal lamina. The appearance of branching basal lamina in the luteal phase suggests that this may be produced in response to endocrine stimulation.
- Published
- 1988
23. Isolation of a lambda transducing bacteriophage carrying the relA gene of Escherichia coli
- Author
-
N P Fill, J Parker, J D Friesen, F S Pedersen, S Pedersen, and R J Watson
- Subjects
Hot Temperature ,medicine.disease_cause ,Microbiology ,Coliphages ,Bacteriophage ,Gene product ,Plasmid ,Lysogen ,Bacterial Proteins ,Transduction, Genetic ,medicine ,Escherichia coli ,Amino Acids ,Molecular Biology ,Polyacrylamide gel electrophoresis ,Gene ,Lysogeny ,Gel electrophoresis ,biology ,biology.organism_classification ,Molecular biology ,Guanine Nucleotides ,RNA, Bacterial ,Genes ,Research Article - Abstract
In Escherichia coli the relA and pyrG loci are 99% cotransducible. On the basis of this knowledge, we have isolated lambdacI857S7dpyrG transducing bacteriophages carrying both the pyrG and relA genes. Single lysogens of this bacteriophage show basal levels of ppGpp that are 10-fold higher than normal. Stringent factor is present among the gene products synthesized by lambdadpyrG relA after infection of ultraviolet-killed cells, as analyzed by polyacrylamide gel electrophoresis. The intracellular content of stringent factor, as determined by enzymatic activity, rises 20-fold after induction of a single lysogen of lambdadpyrG relA. As measured by two-dimensional gel electrophoresis, the amount of stringent factor in an exponentially growing strain carrying a pyrG relA plasmid is at least 10-fold greater than in a normal strain. These data constitute strong evidence that stringent factor is the relA gene product.
- Published
- 1976
24. DNA sequence of an immediate-early gene (IEmRNA-5) of herpes simplex virus type I
- Author
-
R J Watson and G F Vande Woude
- Subjects
Genetics ,Base Composition ,Base Sequence ,Genes, Viral ,Transcription, Genetic ,Oligonucleotide ,Base pair ,Intron ,DNA Restriction Enzymes ,Biology ,Molecular biology ,DNA sequencing ,Open reading frame ,chemistry.chemical_compound ,chemistry ,Transcription (biology) ,DNA, Viral ,Animals ,Simplexvirus ,RNA, Messenger ,Gene ,DNA ,Plasmids ,Research Article - Abstract
We describe a 2560 base pair herpes simplex virus type 1 (HSV-1) DNA sequence containing the entire immediate-early mRNA-5 (IEmRNA-5) gene. The 3' and 5' termini of IEmRNA-5 were mapped within this DNA sequence by single-strand specific endonuclease protection experiments. The IEmRNA-5 gene contains DNA sequences from both the unique (Us) and reiterated (TRs/IRs) regions of the HSV-1 DNA short component and is interrupted by a single intron mapping in TRs/IRs. A search of the transcribed DNA sequence revealed no initiator codon within TRs/IRs. The first ATG was located 6 bases into Us sequences and this reading frame (316 codons) was also observed in the 3' transcribed region. The oligonucleotide sequences adjacent to the IEmRNA-5 termini are discussed in relation to those of the HSV-1 thymidine kinase gene and other genes transcribed by RNA polymerase II.
- Published
- 1982
25. Expression of the c-myb and c-myc genes is regulated independently in differentiating mouse erythroleukemia cells by common processes of premature transcription arrest and increased mRNA turnover
- Author
-
R J Watson
- Subjects
Transcription, Genetic ,Cellular differentiation ,Biology ,Mice ,Transcription (biology) ,hemic and lymphatic diseases ,Gene expression ,Proto-Oncogenes ,Animals ,MYB ,Dimethyl Sulfoxide ,RNA, Messenger ,Gene ,Molecular Biology ,Regulation of gene expression ,Messenger RNA ,Leukemia, Experimental ,RNA ,Nucleic Acid Hybridization ,Cell Biology ,DNA Restriction Enzymes ,Molecular biology ,Kinetics ,Gene Expression Regulation ,Leukemia, Erythroblastic, Acute ,Research Article - Abstract
The mechanisms that modulate c-myb mRNA levels in mouse erythroleukemia cells induced toward erythroid differentiation were compared with those that act on c-myc. Both genes exhibited regulation at the levels of premature transcription arrest and RNA turnover. However, these common processes allowed temporally distinct control of gene expression.
- Published
- 1988
26. Gastric pseudolymphoma (lymphofollicular gastritis)
- Author
-
R J Watson and M T O'Brien
- Subjects
Adult ,medicine.medical_specialty ,Lymphoma ,business.industry ,Stomach ,Gastric pseudolymphoma ,Gastroenterology ,Diagnosis, Differential ,Radiography ,Stomach Neoplasms ,Internal medicine ,Gastritis ,medicine ,Humans ,Surgery ,Female ,medicine.symptom ,business ,Research Article - Published
- 1970
27. Splenic aspirations in multiple myeloma
- Author
-
H D, SHAPIRO and R J, WATSON
- Subjects
Plasma Cells ,Humans ,Multiple Myeloma ,Spleen - Published
- 1953
28. Studies on thalassemia. I. An extracorpuscular defect in thalassemia major. II. The effects of splenectomy in thalassemia major with an associated acquired hemolytic anemia
- Author
-
H C, LICHTMAN, R J, WATSON, F, FELDMAN, V, GINSBERG, and J, ROBINSON
- Subjects
Anemia, Hemolytic ,Erythrocytes ,Sodium ,beta-Thalassemia ,Splenectomy ,Humans ,Thalassemia ,Anemia ,Blood Transfusion ,Articles ,Spleen - Published
- 1953
29. Splenic aspiration in clinical and experimental hematology
- Author
-
R J, WATSON, H D, SHAPIRO, R R, ELLISON, and H C, LICHTMAN
- Subjects
Humans ,Hematology ,Punctures ,Spleen - Published
- 1955
30. The effect of age and menstrual cycle upon proliferative activity of the normal human breast
- Author
-
Martin Harris, Christopher S Potten, S Tickle, Anthony Howell, R J Watson, Geraint T. Williams, and Stephen A Roberts
- Subjects
Adult ,Cancer Research ,medicine.medical_specialty ,Mitotic index ,Time Factors ,Adolescent ,Cell Survival ,media_common.quotation_subject ,Physiology ,Patient age ,Cytology ,Internal medicine ,medicine ,Mitotic Index ,Humans ,Breast ,Menstrual cycle ,Menstrual Cycle ,media_common ,business.industry ,Age Factors ,Histology ,Epithelial Cells ,Middle Aged ,medicine.disease ,Fibroadenoma ,Middle age ,Parity ,Endocrinology ,Oncology ,Female ,business ,Human breast ,Contraceptives, Oral ,Research Article - Abstract
The aim of this study was to determine the proliferative activity within the epithelial cells of the normal human breast in 122 patients (6 reduction mammoplasties and 116 fibroadenoma excisions) in relation to age and the phase of the menstrual cycle. Thirty three of the patients were on oral contraceptives and 33 were parous. Thin tissue slices were incubated with tritiated thymidine and processed for autoradiography. Other samples were fixed directly and prepared for histology. The labelling, mitotic and apoptotic indices (LI, MI and AI) were determined and all illustrated considerable variability. The labelling indices are significantly (P less than 0.05) influenced by both patient age and stage during the menstrual cycle and ranged from 0-11.5%. Maximum LI values were obtained on the 20.8th day of the cycle. A square root transformation of the data was used to reduce the skewness of the data to a more normal distribution. The square root of the LI declined by 0.22 per decade. The mitotic data showed similar significant (P less than 0.05) correlations against age and day of cycle with a peak on the 21.5th day of the cycle, a decline by 0.072 per decade and a range from 0-0.6%. The data for apoptotic cells were less clearly influenced by the stage of the menstrual cycle but showed a significant (P less than 0.5) decline with age. The AI in parous patients was significantly higher than that in non-parous patients. There was no significant effect of oral contraceptives on any of the parameters measured when age and stage of cycle were taken into account. The considerable variability in the data could not be fully accounted for by either technical factors, the age of the patients, or the day of the cycle. We conclude that proliferation is negatively related to age and is influenced by the menstrual cycle but that additional as yet unknown factors must account for a large part of the variability seen in the data. Images Figure 1
31. Optimal timing of operation for bleeding peptic ulcer
- Author
-
R. J. Watson, T. L Hooper, and G. Ingram
- Subjects
medicine.medical_specialty ,business.industry ,General surgery ,General Engineering ,General Medicine ,medicine.disease ,Data science ,Text mining ,Peptic ulcer ,Correspondence ,General Earth and Planetary Sciences ,Medicine ,business ,General Environmental Science - Published
- 1984
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