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J D Watson

Publications and source records attributed to J D Watson.

At least 19 recordsLinked to original sources
PubMed2006

SPINE bioinformatics and data-management aspects of high-throughput structural biology.

SPINE (Structural Proteomics In Europe) was established in 2002 as an integrated research project to develop new methods and technologies for high-throughput structural biology. Development areas were broken down into workpackages and this article gives an overview of ongoing activity in the bioinformatics workpackage. Developments cover target selection, target registration, wet and dry laboratory data management and structure annotation as they pertain to high-throughput studies. Some individual projects and developments are discussed in detail, while those that are covered elsewhere in this issue are treated more briefly. In particular, this overview focuses on the infrastructure of the software that allows the experimentalist to move projects through different areas that are crucial to high-throughput studies, leading to the collation of large data sets which are managed and eventually archived and/or deposited.

Computational Biology↗
PubMed2006

Merkel cell carcinoma in South East Scotland, 1993-2003.

BACKGROUND AND AIMS: Merkel cell carcinoma (MCC) is a rare cutaneous malignancy. The aims of this study were to look at the incidence and distribution of MCC in a predominantly skin type I Caucasian population, review overall management of the disease and assess patient outcomes. METHODS: Cases were identified through the regional pathology database. Twenty patients were diagnosed with MCC over a 10-year period (1993-2003) and managed at the Regional Plastic Surgery Unit at St John's Hospital, Livingston. RESULTS: The disease incidence was found to be 0.133 per 100,000 per annum. All patients were Caucasian, seven males and 13 females (1:1.9 ratio). The mean age at presentation was 77 years (range 58-93 years). The majority of lesions were found to be stage IA (80%), located in the head and neck region. There were two cases (10%) with stage II disease and two (10%) with stage III disease (both with liver metastases) at the time of diagnosis. All patients were managed operatively. Seventeen of the 20 had wide local excisions; of the remaining three, two were only suitable for debulking procedures and one patient (stage II) had only a diagnostic biopsy, refusing intervention thereafter. One patient received adjuvant chemoradiotherapy. CONCLUSION: Surgery remains the mainstay of treatment but adjuvant therapy, in particular chemotherapy, is problematic in a frail, elderly population.

Aged↗
PubMed2004

Crystal structure of Bacillus subtilis YckF: structural and functional evolution.

The crystal structure of the YckF protein from Bacillus subtilis was determined with MAD phasing and refined at 1.95A resolution. YckF forms a tight tetramer both in crystals and in solution. Conservation of such oligomerization in other phosphate sugar isomerases indicates that the crystallographically observed tetramer is physiologically relevant. The structure of YckF was compared to with its ortholog from Methanococcus jannaschii, MJ1247. Both of these proteins have phosphate hexulose isomerase activity, although neither of the organisms can utilize methane or methanol as source of energy and/or carbon. Extensive sequence and structural similarities with MJ1247 and with the isomerase domain of glucosamine-6-phosphate synthase from Escherichia coli allowed us to group residues contributing to substrate binding or catalysis. Few notable differences among these structures suggest possible cooperativity of the four active sites of the tetramer. Phylogenetic relationships between obligatory and facultative methylotrophs along with B. subtilis and E. coli provide clues about the possible evolution of genes as they loose their physiological importance.

Amino Acid Sequence↗
PubMed2001

11: disorders of memory and intellect.

The clinical approach to the patient with a suspected disorder of memory and intellect is to establish whether it is dementia, which parts of the brain are affected, what is the cause, what is the prognosis, and what can be done about it. The diagnosis of dementia usually requires the involvement of memory and at least one other cognitive system. Delirium and depression are important differential diagnoses. Patients with dementia should usually have some simple investigations after a careful history-taking and examination to identify "reversible" causes. The commonest cause of dementia is Alzheimer's disease, in which short-term memory disturbance is usually prominent. Other causes of dementia include cerebrovascular disease, Lewy-body disease and Pick's disease. There is now hope for patients with Alzheimer's disease (which can be treated with some success with cholinesterase inhibitors) and patients with vascular dementia, in whom aggressive control of causal risk factors may retard progression.

Aged↗
PubMed2001

Identification of a new fibroblast growth factor receptor, FGFR5.

A novel fibroblast growth factor receptor (FGFR), designated FGFR5, was identified from an EST database of a murine lymph node stromal cell cDNA library. The EST has approximately 32% identity to the extracellular domain of FGFR1-4. Library screening with this EST identified two full-length alternative transcripts which we designated as FGFR5 beta and FGFR5 gamma. The main difference between these transcripts is that FGFR5 beta contains three extracellular Ig domains whereas FGFR5 gamma contains only two. A unique feature of FGFR5 is that it does not contain an intracellular tyrosine kinase domain. Predictive structural modelling of the extracellular domain of FGFR5 gamma suggested that it was a member of the I-set subgroup of the Ig-superfamily, consistent with the known FGFRs. Northern analysis of mouse and human FGFR5 showed detectable mRNA in a broad range of tissues, including kidney, brain and lung. Genomic sequencing identified four introns but identified no alternative transcripts containing a tyrosine kinase domain. Extracellular regions of FGFR5 beta and 5 gamma were cloned in-frame with the Fc fragment of human IgG(1) to generate recombinant non-membrane bound protein. Recombinant FGFR5 beta Fc and R5 gamma Fc demonstrated specific binding to the ligand FGF-2, but not FGF-7 or EGF. However, biological data suggest that FGF-2 binding to these proteins is with lower affinity than its cognate receptor FGFR2C. The above data indicate that this receptor should be considered as the fifth member of the FGFR family.

3T3 Cells↗
PubMed2001

Cloning and biological activity of epigen, a novel member of the epidermal growth factor superfamily.

High throughput sequencing of a mouse keratinocyte library was used to identify an expressed sequence tag with homology to the epidermal growth factor (EGF) family of growth factors. We have named the protein encoded by this expressed sequence tag Epigen, for epithelial mitogen. Epigen encodes a protein of 152 amino acids that contains features characteristic of the EGF superfamily. Two hydrophobic regions, corresponding to a putative signal sequence and transmembrane domain, flank a core of amino acids encompassing six cysteine residues and two putative N-linked glycosylation sites. Epigen shows 24-37% identity to members of the EGF superfamily including EGF, transforming growth factor alpha, and Epiregulin. Northern blotting of several adult mouse tissues indicated that Epigen was present in testis, heart, and liver. Recombinant Epigen was synthesized in Escherichia coli and refolded, and its biological activity was compared with that of EGF and transforming growth factor alpha in several assays. In epithelial cells, Epigen stimulated the phosphorylation of c-erbB-1 and mitogen-activated protein kinases and also activated a reporter gene containing enhancer sequences present in the c-fos promoter. Epigen also stimulated the proliferation of HaCaT cells, and this proliferation was blocked by an antibody to the extracellular domain of the receptor tyrosine kinase c-erbB-1. Thus, Epigen is the newest member of the EGF superfamily and, with its ability to promote the growth of epithelial cells, may constitute a novel molecular target for wound-healing therapy.

Amino Acid Sequence↗
PubMed2001

Right medial thalamic lesion causes isolated retrograde amnesia.

Pervasive retrograde amnesia without anterograde memory impairment has rarely been described as a consequence of circumscribed brain damage. We report this phenomenon in a 33 yr-old, right-handed man (JG) in association with the extension in the right thalamus of a previously small, bilateral thalamic lesion. JG presented with a dense amnesia for autobiographical material more than a few years old, with some sparing of recent memories. Furthermore, he was completely unable to recognise famous people or world events. Many other aspects of semantic knowledge were intact and there was no evidence of general intellectual impairment, executive dysfunction or loss of visual imagery. Magnetic resonance imaging revealed an acute lesion in the right thalamus and two small, symmetrical, bilateral non-acute thalamic lesions. Follow-up neuropsychological assessment indicated a stable pattern of impaired retrograde and spared anterograde memory over 18 months and psychiatric assessments yielded no evidence of confabulation, malingering or other symptoms to suggest psychogenic amnesia. JG's profile indicates that the division of declarative memory into just two categories - episodic and semantic - is inadequate. Rather, his case adds to the growing body evidence to suggest that world knowledge pertaining to people and events is stored or accessed similarly to autobiographical information and differently from other types of more general factual knowledge. We hypothesize that the right mediodorsal thalamic nucleus and immediately surrounding regions comprise the central processing mechanism referred to by McClelland (Revue Neurologique, 150 (1994) 570) and Markowitsch (Brain Research Review, 21 (1995) 117) as responsible for inducing and co-ordinating the recall of these sorts of cortically stored memory engrams.

Adult↗
PubMed2001

Expression of B-type natriuretic peptide in atrial natriuretic peptide gene disrupted mice.

Atrial natriuretic peptide (ANP) and B-type natriuretic peptide (BNP) are two hormones produced and secreted by the heart to control blood pressure, body fluid homeostasis and electrolyte balance. Each peptide binds to a common family of 3 receptors (GC-A, GC-B and C-receptor) with varying degrees of affinity. The proANP gene disrupted mouse model provides an excellent opportunity to examine the regulation and expression of BNP in the absence ofANP. A new radioimmunoassay (RIA) was developed in order to measure mouse BNP peptide levels in the plasma, atrium and ventricle of the mouse. A detection limit of 3-6 pg/tube was achieved by this assay. Results show that plasma and ventricular level of BNP were unchanged among the three genotypes of mice. However, a significant decrease in the BNP level was noted in the atrium. The homozygous mutant (ANP-/-) had undetectable levels of BNP in the atrium, while the heterozygous (ANP+/-) and wild-type (ANP+/+) mice had 430 and 910 pg/mg in the atrium, respectively. Northern Blot analysis shows the ANP-/- mice has a 40% reduction of BNP mRNA level in the atrium and a 5-fold increase in the ventricle as compared with that of the ANP+/+ mouse. Our data suggest that there is a compensatory response of BNP expression to proANP gene disruption. Despite the changes in the atrial and ventricular tissue mRNA and peptide levels, the plasma BNP level remains unaltered in the ANP-/- mice. We conclude that the inability of BNP to completely compensate for the lack of ANP eventually leads to chronic hypertension in the proANP gene disrupted mice.

Animals↗
PubMed2001

Improvement in psoriasis after intradermal administration of delipidated, deglycolipidated Mycobacterium vaccae (PVAC): results of an open-label trial.

The aim of new treatments for psoriasis is to induce extended remissions with fewer side-effects. Previous studies suggest that Mycobacterium vaccae, a harmless organism prepared as a heat-killed suspension, may induce periods of remission in some psoriasis patients after intradermal administration. To assess a more potent derivative of M. vaccae, we conducted an open-label study in which 20 patients with moderate to severe psoriasis (Psoriasis Area and Severity Index of 12-35) received two intradermal inoculations of heat-killed, delipidated, deglycolipidated M. vaccae (DD-MVAC or 'PVAC') in lesion-free deltoid skin, separated by a period of 3 weeks. Twelve weeks after the injections, 13 out of 20 patients (65%) showed marked improvement in the PASI score (> 50% reduction), three were unchanged (< 25% reduction), three had worsened (> 5% increase), and one was withdrawn from the trial because of an exfoliative flare. At 24 weeks, 13 out of 19 patients continued to show > 50% improvement that, in some, lasted for 6 months or longer. Patients classified as good responders at 12 or 24 weeks were then offered additional PVAC injections after 24 weeks if the PASI reached 8 or higher. Intra-dermal administration of PVAC was safe, well tolerated, and induced clinically significant improvement in many psoriasis patients. A randomized, double-blind, controlled study is warranted.

Adolescent↗
PubMed2000

Gene expression in rat dermal papilla cells: analysis of 2529 ESTs.

Dermal papilla (DEPA) cells are resident at the base of hair follicles and are fundamental to hair growth and development. Cultured DEPA cells, in contrast to normal fibroblast cells, are capable of inducing de novo hair follicle growth in vivo. By differential screening of a DEPA cDNA library, we have demonstrated that dermal papilla cells are different from fibroblasts at the molecular level. We further studied these cells by random sequencing of 5130 clones from the DEPA cDNA library. Fifty percent had a BLASTX E value < or =1 x 10(-25). Twenty-one percent had similarity to proteins involved in cell structure/motility with 4 of the top 10 most abundant clones encoding extracellular matrix proteins. Clones encoding growth factor molecules were also abundant. The remaining 50.7% of clones had low similarity scores, demonstrating many novel molecules. For example, we identified a new CTGF family member, the rat homologue of Elm1.

Amino Acid Sequence↗
PubMed2000

Pravastatin therapy and the risk of stroke.

BACKGROUND: Several epidemiologic studies have concluded that there is no relation between total cholesterol levels and the risk of stroke. In some studies that classified strokes according to cause, there was an association between increasing cholesterol levels and the risk of ischemic stroke and a possible association between low cholesterol levels and the risk of hemorrhagic stroke. Recent reviews of trials of 3-hydroxy-3-methylglutaryl-coenzyme A reductase inhibitors have suggested that these agents may reduce the risk of stroke. METHODS: In a double-blind trial (the Long-Term Intervention with Pravastatin in Ischaemic Disease study), we compared the effects of pravastatin on mortality due to coronary heart disease (the primary end point) with the effects of placebo among 9014 patients with a history of myocardial infarction or unstable angina and a total cholesterol level of 155 to 271 mg per deciliter (4.0 to 7.0 mmol per liter). Our goal in the present study was to assess effects on stroke from any cause and nonhemorrhagic stroke, which were secondary end points. RESULTS: There were 419 strokes among 373 patients over a follow-up period of six years. A total of 309 strokes were classified as ischemic, 31 as hemorrhagic, and 79 as of unknown type. Among the patients given placebo, the risk of stroke was 4.5 percent, as compared with 3.7 percent among those given pravastatin (relative reduction in risk, 19 percent; 95 percent confidence interval, 0 to 34 percent; P=0.05). Non-hemorrhagic stroke occurred in 4.4 percent of the patients given placebo, as compared with 3.4 percent of those given pravastatin (reduction in risk, 23 percent; 95 percent confidence interval, 5 to 38 percent; P=0.02). Pravastatin had no effect on hemorrhagic stroke (incidence, 0.2 percent in the placebo group vs. 0.4 percent in the pravastatin group; P=0.28). CONCLUSIONS: Pravastatin has a moderate effect in reducing the risk of stroke from any cause and the risk of nonhemorrhagic stroke in patients with previous myocardial infarction or unstable angina.

Adult↗