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J P Cox

Publications and source records attributed to J P Cox.

At least 19 recordsLinked to original sources
PubMed2001

Long-term data storage in DNA.

This article discusses how DNA might be used to store data. It is argued that, at present, DNA would be best employed as a long-term repository (thousands or millions of years). How data-containing DNA might be packaged and how the data might be encrypted, with particular attention to the encryption of written information, is also discussed. Various encryption issues are touched on, such as how data-containing DNA might be differentiated from genetic material, error detection, data compression and reading frame location. Finally, this article broaches the difficulty of constructing very large pieces of DNA in the laboratory and highlights some complications that might arise when attempting to transmit DNA-encrypted data to recipients who are a long period of time in the future.

Base Sequence↗
PubMed2001

Bar coding objects with DNA.

A bioanalytical scheme is described for bar coding objects with DNA. Several DNA templates of different lengths are mixed together and the mixture used to label the object of interest. To disclose the bar code, the DNA mixture is eluted from the object, amplified by the polymerase chain reaction with a universal pair of primers, and then the amplified templates resolved by agarose gel electrophoresis. In its present state, the bar coding scheme allows for over a million different labels. The reliability of the scheme has been demonstrated in a typical situation by labelling a letter with a template mixture (approximately 1.5 fmol of DNA), sending the letter through the post and successfully reading the bar code on receipt of the letter.

DNA↗
PubMed2000

Isolated hypercalciuria with mutation in CLCN5: relevance to idiopathic hypercalciuria.

UNLABELLED: Isolated hypercalciuria with mutation in CLCN5: Relevance to idiopathic hypercalciuria. BACKGROUND: Idiopathic hypercalciuria (IH) is the most common risk factor for kidney stones and often has a genetic component. Dent's disease (X-linked nephrolithiasis) is associated with mutations in the CLCN5 chloride channel gene, and low molecular weight (LMW) proteinuria was universally observed in affected males. We sought to identify mutations in CLCN5 or abnormalities in LMW protein excretion in a large group of patients with IH and in a rat model of genetic hypercalciuria. METHODS: One hundred and seven patients with IH (82 adults and 25 children) and one asymptomatic hypercalciuric man with a known inactivating mutation in CLCN5 were studied. Secondary causes of hypercalciuria were excluded in all. The excretion of retinol-binding protein and beta2-microglobulin was measured by immunoassay in 101 patients with IH. Mutation analysis of the CLCN5 gene was performed in 32 patients with IH and in the genetic hypercalciuric stone-forming (GHS) rat strain. RESULTS: LMW protein excretion was normal in 92 patients with IH, and only slight abnormalities were found in the other nine, none of whom had a mutation in CLCN5. One 27-year-old man who had a CLCN5 mutation was found to have isolated hypercalciuria without LMW proteinuria, renal failure, or other evidence of renal disease. Mutation analysis was normal in 32 patients with IH. The CLCN5 sequence was normal in the GHS rat. CONCLUSIONS: Inactivation of CLCN5 can be found in the setting of hypercalciuria without other features of X-linked nephrolithiasis. However, mutations in CLCN5 do not represent a common cause of IH.

Adolescent↗
PubMed1999

Renal chloride channel, CLCN5, mutations in Dent's disease.

Dent's disease is an X-linked renal tubular disorder characterized by low-molecular-weight proteinuria, hypercalciuria, nephrocalcinosis, nephrolithiasis, and renal failure. Patients with Dent's disease may also suffer from rickets and other features of the renal Fanconi Syndrome. Patients may have mutations in the X-linked renal chloride channel gene, CLCN5, which encodes a 746-amino-acid protein with 12-13 transmembrane domains. We have investigated the 11 coding exons of CLCN5 for mutations in eight unrelated patients with Dent's disease. Leukocyte DNA was used for the polymerase chain reaction amplification of CLCN5 and the products analyzed for single-stranded conformational polymorphisms (SSCPs). Abnormal SSCPs were sequenced and revealed eight mutations. These consisted of three nonsense mutations (Arg34Stop, Arg648Stop, Arg704Stop), four deletions involving codons 40, 86, 157, and 241, and one acceptor splice consensus sequence mutation tgcag --> tgaag. The mutations were confirmed either by restriction endonuclease or sequence-specific oligonucleotide hybridization analysis. In addition, an analysis of 110 alleles from 74 unrelated normal individuals demonstrated that the DNA sequence changes were not common polymorphisms. All of the mutations predict truncated chloride channels that are likely to result in a functional loss. Thus, our findings expand the spectrum of CLCN5 mutations associated with Dent's disease and the results will help to elucidate further the functional domains of this novel chloride channel.

Amino Acid Sequence↗
PubMed1998

Sticky egyptians: a technique for assembling genes encoding constrained peptides of variable length.

Naturally occurring peptides, such as those produced by the poisonous marine snails of the genus Conus , have the ability to form tight, highly specific molecular interactions. The rigidity of the peptide framework which promotes these interactions is usually maintained by disulphide bonds, and it seems that the overall main chain conformation (or fold) of the peptide is determined by its length and the sequence distribution of the pairs of cysteine residues participating in these bonds. The fold of the peptide in turn is largely responsible for its shape. Since highly effective molecular interactions occur between species complementary in shape, we reasoned that peptides with the greatest potential in therapy or diagnosis would be found in a library of shapes, those peptides with a shape complementary to a given target being identified, for example, by selection. As a first step towards constructing such a peptide shape library, we have developed a method for assembling DNA fragments which encode an even number of cysteine residues and which are of variable length. We describe this method here.

Cysteine↗
PubMed1998

Clinical features of X-linked nephrolithiasis in childhood.

X-linked recessive nephrolithiasis (XRN) is a rare hereditary form of progressive renal failure characterized by (1) proximal tubular dysfunction and low molecular weight proteinuria; (2) hypercalciuria with nephrocalcinosis and nephrolithiasis. Because the clinical features are non-specific and variable, affected families in different parts of the world were initially thought to have several distinct syndromes. However, positional cloning of the relevant gene (CLCN5) demonstrated that these families have, in common, mutations affecting a chloride channel expressed throughout the renal tubule. To expand the description of early clinical and pathological manifestations of XRN, we describe three patients diagnosed in the 1st decade of life. Renal tubular dysfunction may be evident even in the neonatal period, hypophosphatemic rickets may develop in the first years of life, and nephrocalcinosis (but not nephrolithiasis) with glomerulosclerosis are consistent features in childhood. One of our patients is indistinguishable from the others on clinical grounds, yet no mutations of the coding regions of the CLCN5 gene were found, raising the possibility of genetic heterogeneity in the XRN syndrome.

Adolescent↗
PubMed1997

Mutations of CLCN5 in Japanese children with idiopathic low molecular weight proteinuria, hypercalciuria and nephrocalcinosis.

The annual urinary screening of Japanese children above three years of age has identified a progressive renal tubular disorder characterized by low molecular weight proteinuria, hypercalciuria and nephrocalcinosis. The disorder has been observed in over 60 patients and has a familial predisposition. Mutations of a renal chloride channel gene, CLCN5, have been reported in four such families, and we have undertaken studies in additional patients from 10 unrelated, non-consanguineous Japanese families to further characterize such CLCN5 mutations and to ascertain their prevalence. CLCN5 abnormalities we identified in 7 of the 10 unrelated patients and consisted of 5 mutations (2 nonsense, 1 frameshift and 2 missense), 1 deletion and 1 silent polymorphism. A clustering of these mutations in CLCN5 exons 8 and 10 was observed. Over 80% of the CLCN5 mutations could be readily detected by single stranded conformational polymorphism (SSCP) analysis, thereby providing a useful mutation screening method. Our results, which indicate that over 70% of Japanese patients with this renal tubulopathy have CLCN5 mutations, will help in the genetic and clinical evaluation of children at risk from this disorder.

Adolescent↗
PubMed1997

Skeletal muscle resting metabolism in cold-acclimated rats: effect of age, noradrenaline and hyperosmolarity.

1. A myothermic technique has been used to measure the resting metabolism of small bundles of a fast twitch muscle, extensor digitorum longus (EDL), and a slow twitch muscle, soleus (SOL), in 7-week-old rats. At 27 degrees C, mean (+/-SEM) resting heat rates were 2.33 +/- 0.41 and 2.09 +/- 0.37 mW/g in EDL and SOL, respectively (n = 16). 2. Seven-week-old rats were cold acclimatized at 4 degrees C for 1-4 weeks and the metabolic rates of the fast and slow twitch muscles were monitored and compared with 7- and 11-week-old controls. There was a 160% increase in metabolic rate from week 7 to week 11, but the increase also occurred in the control group. 3. In accordance with several literature reports, noradrenaline at concentrations of 10(-7) and 10(-6) mol/L had no effect on either the control or cold-acclimatized resting heat rate. 4. The osmolarity of the physiological solution bathing the muscle bundles was increased by 100 mosmol using sodium sulphate. Basal metabolism increased by similar amounts (approximately 250%) in both the fast and slow muscle bundles. Periods of cold exposure had no significant effect on the magnitude of the increment. 5. Bumetanide, a potent inhibitor of Na(+)-Cl- co-transport, produced only a slight reduction in the heat increments caused by hyperosmolar challenge.

Acclimatization↗
PubMed1995

The structural repertoire of the human V kappa domain.

In humans, the gene for the V kappa domain is produced by the recombination of one of 40 functional V kappa segments and one of five functional J kappa segments. We have analysed the sequences of these germline segments and of 736 rearranged V kappa genes to determine the repertoire of main chain conformations, or canonical structures, they encode. Over 96% of the sequences correspond to one of four canonical structures for the first antigen binding loop (L1) and one canonical structure for the second antigen binding loop (L2). Junctional diversity produces some variation in the length of the third antigen binding loop (L3) and in the identity of residues at the V kappa-J kappa join. However, this is limited and 70% of the rearranged sequences correspond to one of three known canonical structures for the L3 region. Furthermore, we show that the canonical structures selected during the primary response are conserved during affinity maturation: the key residues that determine the conformations of the antigen binding loops are unmutated or undergo conservative mutation. The implications of these results for immune recognition are discussed.

Amino Acid Sequence↗
PubMed1994

A directory of human germ-line V kappa segments reveals a strong bias in their usage.

From the genomic DNA of a single individual, we have amplified, cloned and sequenced 37 human germ-line V kappa segments. Four of these segments were new. We then compiled a comprehensive directory of all germ-line V kappa segments and identified 50 different sequences with open reading frames. Comparison with 236 rearranged sequences revealed that no more than 24 of these germ-line sequences could be assigned rearranged counterparts, that some of these were rarely used, and that only about 11 sequences are used frequently. This suggests that the expressed V kappa repertoire is mainly derived from a limited number of segments. Most surprisingly, the J kappa-distal region of the locus appears to be rarely used: we could unambiguously assign 162 rearranged sequences to V kappa segments of the J kappa-proximal region, but only 5 to segments of the J kappa-distal region.

Amino Acid Sequence↗
PubMed1993

Dissecting the structure of a partially folded protein. Circular dichroism and nuclear magnetic resonance studies of peptides from ubiquitin.

The nature and interaction of structural elements in a partially ordered form of ubiquitin, the A-state, which is populated at low pH in 40 to 60% aqueous methanol, have been investigated. Two synthetic peptides have been studied under the same conditions: U(1-21), corresponding to the N-terminal beta-hairpin in the native (N) and A-states of ubiquitin and U(1-35), which includes this hairpin plus an alpha-helix. Circular dichroism studies indicate that, although these peptides are largely unfolded in water, their structural content in 30 and 60% methanol is comparable with the corresponding native secondary structure. Sequence-specific assignments of the 1H n.m.r. spectra of U(1-35) in aqueous methanol and subsequent secondary structure determination confirm the conservation in detail of native-like secondary structure. Corresponding resonances in spectra of U(1-35), U(1-21) and the A-state itself were found to have closely similar chemical shifts, suggesting that the beta-hairpin exists independently in the partially folded protein, with little or no influence from the rest of the molecule. This is confirmed by the virtual absence in nuclear Overhauser enhancement spectroscopy and rotating frame nuclear Overhauser enhancement spectroscopy spectra of nuclear Overhauser enhancement effects between structural elements. c.d. and n.m.r. evidence suggests that structure in the C-terminal half of the molecule in the A-state is largely non-native. Thus, although methanol is necessary to assure its stability in the absence of wider native interactions, the structure of the beta-hairpin, including the register of its hydrogen bonding, appears to be determined entirely by its own sequence. This intrinsic structural preference in the first part of the ubiquitin sequence is much stronger than in the C-terminal half, a conclusion reflected in the results from a variety of secondary structure prediction algorithms.

Amino Acid Sequence↗
PubMed1993

Retention of native-like structure in an acyclic counterpart of a beta-sheet antibiotic.

An acyclic derivative of the cyclic peptide antibiotic, ramoplanin, has been prepared. In aqueous solution, two-dimensional NMR spectroscopy indicates that the acyclic form adopts a threshold population of conformers in which at least part of the beta-sheet characteristic of the intact ramoplanin persists. Thus, despite losing the entropic benefit which the macrocycle must lend to beta-sheet formation, the polypeptide chain of the acyclic ramoplanin appears to display an innate tendency to adopt a native-like conformation.

Anti-Bacterial Agents↗
PubMed1992

The J-shaped curve in elderly hypertensives.

PURPOSE: To review the relationship between mortality and morbidity and achieved blood pressure, after drug treatment in elderly hypertensive patients. CONTENTS: Recent studies have suggested that a reduction in systolic blood pressure, with drug treatment, to levels below about 140 mmHg in elderly patients (greater than 60 years) may increase the risk of stroke. However, a J-shaped relationship between both mortality and morbidity and blood pressure has been reported in the untreated controls of the Hypertension in Elderly Patients in primary care (HEP) study. In the European Working Party on High Blood Pressure in the Elderly trial (EWPHE) there was a U-shaped relationship between total mortality and treated systolic pressure, but a similar U-shaped relationship was observed with diastolic pressure in patients on placebo. In addition, patients with the lowest pressure during treatment showed the greatest falls in body weight and haemoglobin concentrations, suggesting that the increased mortality seen with lower blood pressure levels may have been an expression of a deterioration in general health. Moreover, a U-shaped relationship between blood pressure and mortality has been observed in the very old (aged 80 + years). CONCLUSIONS: While it is premature to conclude, on the basis of present evidence, that reducing blood pressure to the lower part of the normal range is harmful in older patients, it appears prudent, nonetheless, not to lower blood pressure excessively with treatment in this age group.

Aged↗
PubMed1991

Further learnings from the European Working Party on High Blood Pressure in the Elderly (EWPHE) study: focus on systolic hypertension.

Event rates in relation to the number of elderly hypertensives treated were calculated from randomized analysis data from the 840 patients who completed the European Working Party on High Blood Pressure in the Elderly (EWPHE) trial. In all, the actively treated group had 29 fewer cardiovascular events per 1000 patient years. Putting this another way, treating 34 patients for 1 year would prevent one cardiovascular event. Moreover, as there were 14 fewer cardiovascular deaths and 11 fewer nonfatal strokes per 1000 patient years in the actively treated groups, we calculated that treating 71 or 91 elderly patients for 1 year would prevent one cardiovascular death or nonfatal stroke, respectively. Because of the higher baseline incidence of cardiovascular events in this study, there were greater gains in terms of absolute reductions in mortality and morbidity in treated elderly hypertensive patients than in younger patients in similar studies. Of the 840 patients who participated in the trial, 247 had systolic blood pressure greater than or equal to 160 mmHg and diastolic blood pressure less than or equal to 95 mmHg. In this group, blood pressure was reduced by 13/8 mmHg after 3 years in those randomized to active treatment compared to placebo. While patient numbers were insufficient to draw firm conclusions, their outcome on treatment was similar to that for patients on active treatment in the overall study. These results high-light the need for a rigorous assessment of the value of treating isolated systolic hypertension in the elderly.

Aged↗
PubMed1991

Choice of drug treatment for elderly hypertensive patients.

It is generally agreed that moderate and severe hypertension in the elderly should be treated, but it is not clear which drug or drugs are most appropriate. Thiazide diuretics are inexpensive and effective, but they are associated with metabolic side effects that are becoming less acceptable as newer agents become available. Beta blockers are effective, but can be associated with central nervous system side effects and are often contraindicated by coexisting disease. Recently, attention has been focused on the newer agents, including calcium antagonists and angiotensin-converting enzyme inhibitors. The advantage of calcium antagonists is that they do not produce metabolic side effects. However, they are expensive and may cause vasodilatory side effects. The angiotensin-converting enzyme inhibitors are effective and relatively free of side effects and may be particularly useful for elderly hypertensive patients with congestive heart failure.

Aged↗
PubMed1991

The in vivo release of 90Y from cyclic and acyclic ligand-antibody conjugates.

Yttrium binding ligands DOTA, caDTPA and CT-DTPA were each conjugated to monoclonal antibody B72.3, labelled with 90Y and injected into mice in order to assess the in vivo inertness of the antibody-linked 90Y-ligand complexes. Levels of 90Y in femur shafts of the DOTA-B72.3 mice were low, being approximately 7 and 44%, respectively, of levels in the femur shafts of the caDTPA-B72.3 and CT-DTPA-B72.3 treated mice. This finding demonstrates the greater inertness and by implication the greater suitability for immunotherapy of the DOTA-90Y complex.

Animals↗