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Biomedical subjects

R J Roberts

Publications and source records attributed to R J Roberts.

At least 55 records · Page 3Linked to original sources
PubMed1999

REBASE-restriction enzymes and methylases.

REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Also included is a listing of homing endonucleases. Information from REBASE is distributed via monthly electronic mailings as well as through anonymous ftp and the World Wide Web. The REBASE web site (http://www.neb.com/rebase) contains a web page for every enzyme, reference and supplier. Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages.

Base Sequence↗
PubMed1999

A community outbreak of food-borne small round-structured virus gastroenteritis caused by a contaminated water supply.

In August 1994, 30 of 135 (23%) bakery plant employees and over 100 people from South Wales and Bristol in the United Kingdom, were affected by an outbreak of gastroenteritis. Epidemiological studies of employees and three community clusters found illness in employees to be associated with drinking cold water at the bakery (relative risk 3.3, 95%, CI 1.6-7.0), and in community cases with eating custard slices (relative risk 19.8, 95%, CI 2.9-135.1) from a variety of stores supplied by one particular bakery. Small round-structured viruses (SRSV) were identified in stool specimens from 4 employees and 7 community cases. Analysis of the polymerase and capsid regions of the SRSV genome by reverse transcription-polymerase chain reaction (RT-PCR) demonstrated viruses of both genogroups (1 and 2) each with several different nucleotide sequences. The heterogeneity of the viruses identified in the outbreak suggests that dried custard mix may have been inadvertently reconstituted with contaminated water. The incident shows how secondary food contamination can cause wide-scale community gastroenteritis outbreaks, and demonstrates the ability of molecular techniques to support classical epidemiological methods in outbreak investigations.

Adolescent↗
PubMed1999

Relationships between the modulus of elasticity and tensile strength for pharmaceutical drugs and excipients.

The relationship between the modulus of elasticity and tensile strength for a variety of pharmaceutical drugs and excipients has been explored as a means of generating algorithms for use in computer simulations and expert systems. From literature data two equations have been developed to enable the formulator, from knowledge of one property, to predict the other with a reasonable degree of accuracy. Such relationships are invaluable for use in computer simulation programs or formulation expert systems, enabling formulators to screen potential formulations quickly without the need for extensive experimental work.

Algorithms↗
PubMed1998

Post-synaptic inhibitory mechanisms of anaesthesia; glycine receptors.

(1) The effects on human homomeric alpha1 glycine receptors of 11 general anaesthetics; four barbiturates, two other intravenous anaesthetics, three volatile anaesthetics and two simple gaseous anaesthetics are described. (2) Pentobarbital and thiopental potentiate the current response to bath applied glycine (50 microM) by 200 and 300%, respectively, at clinically relevant concentrations. (3) Neither methohexital nor phenobarbital had any effect on the current response to bath applied glycine (50 microM). (4) Using maximal doses of applied glycine (1 mM) all the barbiturates acted as non-competitive antagonists. (5) Propofol and etomidate potentiate the current response to bath applied glycine (50 microM) by 200 and 10%, respectively, at clinically relevant concentrations. (6) Etomidate acts as a non-competitive antagonist for doses of glycine above the EC50 (197 microM). Propofol was without effect using maximal doses of applied glycine (1 mM). (7) Halothane, chloroform and ether potentiated the response to bath applied glycine (50 microM) by 200, 100 and 200%, respectively, at clinically relevant doses. (8) None of the volatile anaesthetics had any effect using maximal doses of applied glycine (1 mM). (9) Nitrous oxide and xenon potentiated the response to bath applied glycine (50 microM) by 75 and 50%, respectively, at clinically relevant doses. Nitrous oxide also potentiated the response using maximal doses of applied glycine (1 mM). (10) These results suggest a role for glycinergic neurotransmission in the production of anaesthesia.

Anesthesia↗
PubMed1998

Chemical display of thymine residues flipped out by DNA methyltransferases.

The DNA cytosine-C5 methyltransferase M. Hha I flips its target base out of the DNA helix during interaction with the substrate sequence GCGC. Binary and ternary complexes between M. Hha I and hemimethylated DNA duplexes were used to examine the suitability of four chemical methods to detect flipped-out bases in protein-DNA complexes. These methods probe the structural peculiarities of pyrimidine bases in DNA. We find that in cases when the target cytosine is replaced with thymine (GTGC), KMnO4proved an efficient probe for positive display of flipped-out thymines. The generality of this procedure was further verified by examining a DNA adenine-N6 methyltransferase, M. Taq I, in which case an enhanced reactivity of thymine replacing the target adenine (TCGT) in the recognition sequence TCGA was also observed. Our results support the proposed base-flipping mechanism for adenine methyltransferases, and offer a convenient laboratory tool for detection of flipped-out thymines in protein-DNA complexes.

DNA (Cytosine-5-)-Methyltransferases↗
PubMed1998

Isolation, characterization and baculovirus-mediated expression of the cDNA encoding cytosine DNA methyltransferase from Pisum sativum.

A series of overlapping clones complementary to the Arabidopsis cytosine-5 DNA methyltransferase (C-5 MTase) has been isolated from pea cDNA libraries. The assembled nucleic acid sequence contains an open reading frame of 4761 bp encoding a protein of 1554 amino acids. Like other eukaryotic C-5 MTases, the inferred protein has a presumed regulatory N-terminal region linked to a catalytic C-terminal domain, which has eight of the ten conserved motifs found in prokaryotic C-5 MTases. The pea C-5 MTase has 65% identity at the nucleotide level and 61% identity at the protein level, with the Arabidopsis C-5 MTase. The catalytic domain of the pea enzyme shares 78% identity with Arabidopsis and approximately 52% identity with murine and human C-5 MTases, including the relative position of the proline-cysteine dipeptides of the catalytic centre. Using the conserved region of the cDNA as a probe, we have identified a transcript of 5 kb. Southern blot analysis of pea genomic DNA with the above probe indicates the presence of a single gene. Using poly(A)+ RNA from different developmental stages and different tissues, we have observed that expression is confined mostly to the rapidly dividing tissues of the plant. Expression of this assembled cDNA in a baculovirus system gives a protein of approximately 174 kDa. The expressed protein can be cross-linked, in an AdoMet-dependent manner, to duplex oligonucleotide substrates containing FdC in place of target cytosines in either CG or CAG/CTG sequences.

Amino Acid Sequence↗
PubMed1998

REBASE - restriction enzymes and methylases.

REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Also included is a listing of homing endonucleases. Information from REBASE is available via monthly electronic mailings as well as via anonymous ftp and through the World Wide Web. The REBASE web site, http://www. neb.com/rebase , is where we maintain a web page for every enzyme, reference and supplier. Additionally, there is a search facility, help and NEWS pages, and a complete description of our various services. Specialized files are available that can be used directly by many software packages.

Computer Communication Networks↗
PubMed1998

Structures of HhaI methyltransferase complexed with substrates containing mismatches at the target base.

Three structures have been determined for complexes between HhaI methyltransferase (M.HhaI) and oligonucleotides containing a G:A, G:U or G:AP (AP = abasic or apurinic/apyrimidinic) mismatch at the target base pair. The mismatched adenine, uracil and abasic site are all flipped out of the DNA helix and located in the enzyme's active-site pocket, adopting the same conformation as in the flipped-out normal substrate. These results, particularly the flipped-out abasic deoxyribose sugar, provide insight into the mechanism of base flipping. If the process involves the protein pushing the base out of the helix, then the push must take place not on the base, but rather on the sugar-phosphate backbone. Thus rotation of the DNA backbone is probably the key to base flipping.

Base Pair Mismatch↗
PubMed1998

Base flipping.

Base flipping is the phenomenon whereby a base in normal B-DNA is swung completely out of the helix into an extrahelical position. It was discovered in 1994 when the first co-crystal structure was reported for a cytosine-5 DNA methyltransferase binding to DNA. Since then it has been shown to occur in many systems where enzymes need access to a DNA base to perform chemistry on it. Many DNA glycosylases that remove abnormal bases from DNA use this mechanism. This review describes systems known to use base flipping as well as many systems where it is likely to occur but has not yet been rigorously demonstrated. The mechanism and evolution of base flipping are also discussed.

Base Pair Mismatch↗
PubMed1997

Baculovirus-mediated expression and characterization of the full-length murine DNA methyltransferase.

The original cDNA sequence reported for the murine DNA methyltransferase (MTase) was not full length. Recently, additional cDNA sequences have been reported that lie upstream of the original and contain an extended open reading frame with three additional ATGs in frame with the coding region [Tucker et al . (1996) Proc. Natl. Acad. Sci. USA , 93, 12920-12925; Yoder et al . (1996) J. Biol. Chem . 271, 31092-31097]. Genomic DNA upstream of this ATG contains two more ATGs in frame and no obvious splice site. We have constructed, and expressed in baculovirus, MTase clones that begin at each of these four ATGs and examined their properties. Constructs beginning with any of the first three ATGs as their initiator methionines give a predominant DNA MTase band of approximately 185 kDa on SDS-PAGE corresponding to translational initiation at the third ATG. The fourth ATG construct gives a much smaller protein band of 173 kDa. The 185 kDa protein was purified by HPLC, characterized by mass spectrometry and has a measured molecular mass of 184 +/- 0.5 kDa. All of these MTases were functional in vitro and steady state kinetic analysis showed that the recombinant proteins exhibit similar kinetic properties irrespective of their length. The homogeneous recombinant enzyme from the fourth ATG construct shows a 2.5-fold preference for a hemi-methylated DNA substrate as compared to an unmethylated substrate, whereas the 185 kDa protein is equally active on both substrates. The kinetic properties of the recombinant enzyme are similar to those reported for the native MTase derived from murine erythroleukemia cells. The new clones are capable of yielding large quantities of intact MTases for further structural and functional studies.

Amino Acid Sequence↗
PubMed1997

Homing endonucleases: keeping the house in order.

Homing endonucleases are rare-cutting enzymes encoded by introns and inteins. They have striking structural and functional properties that distinguish them from restriction enzymes. Nomenclature conventions analogous to those for restriction enzymes have been developed for the homing endonucleases. Recent progress in understanding the structure and function of the four families of homing enzymes is reviewed. Of particular interest are the first reported structures of homing endonucleases of the LAGLIDADG family. The exploitation of the homing enzymes in genome analysis and recombination research is also summarized. Finally, the evolution of homing endonucleases is considered, both at the structure-function level and in terms of their persistence in widely divergent biological systems.

Base Sequence↗
PubMed1997

DNA containing 4'-thio-2'-deoxycytidine inhibits methylation by HhaI methyltransferase.

4'-Thio-2'-deoxycytidine was synthesized as a 5'- protected phosphoramidite compatible with solid phase DNA synthesis. When incorporated as the target cytosine (C*) in the GC*GC recognition sequence for the DNA methyltransferase M. HhaI, methyl transfer was strongly inhibited. In contrast, these same oligonucleotides were normal substrates for the cognate restriction endonuclease R. HhaI and its isoschizomer R. Hin P1I. M. HhaI was able to bind both 4'-thio-modified DNA and unmodified DNA to equivalent extents under equilibrium conditions. However, the presence of 4'-thio-2'-deoxycytidine decreased the half-life of the complex by >10-fold. The crystal structure of a ternary complex of M. HhaI, AdoMet and DNA containing 4'-thio-2'-deoxycytidine was solved at 2.05 A resolution with a crystallographic R-factor of 0.186 and R-free of 0.231. The structure is not grossly different from previously solved ternary complexes containing M. HhaI, DNA and AdoHcy. The difference electron density suggests partial methylation at C5 of the flipped target 4'-thio-2'-deoxycytidine. The inhibitory effect of the 4'sulfur atom on enzymatic activity may be traced to perturbation of a step in the methylation reaction after DNA binding but prior to methyl transfer. This inhibitory effect can be partially overcome after a considerably long time in the crystal environment where the packing prevents complex dissociation and the target is accurately positioned within the active site.

DNA↗
PubMed1997

Jak1 kinase is required for cell migrations and anterior specification in zebrafish embryos.

Establishment of the vertebrate body plan requires a variety of signaling molecules. In a search for tyrosine kinases expressed in early zebrafish embryos, a model system for the study of vertebrate development, we discovered Jak1 kinase to be maternally encoded and the mRNA evenly distributed among the cells of blastula-stage embryos. Injection of RNA-encoding dominant-negative Jak1 kinases reduces a specific cell migration, epiboly, and results in the reduction of goosecoid expression and of anterior structures. This work establishes that, in addition to its role in signal transduction of cytokines in adult tissues, Jak1 kinase has a role in early vertebrate development.

Animals↗
PubMed1997

REBASE-restriction enzymes and methylases.

REBASE is a comprehensive database of information about restriction enzymes and their associated methylases, including their recognition and cleavage sites and their commercial availability. Information from REBASE is available via monthly electronic mailings as well as via anonymous ftp, WAIS/gopher and through the World Wide Web (http://www.neb.com/rebase ). Specialized files are available that can be used directly by many software packages.

DNA Modification Methylases↗
PubMed1997

Neuropsychiatric sequelae of cerebral malaria in Vietnam veterans.

Approximately 250,000 Vietnam veterans suffered cerebral malaria, an illness that often results in damage to subcortical white matter and fronto-temporal areas of neocortex. Case reports dating back 2500 years indicate that survivors of cerebral malaria show depression, poor memory, personality change, and irritability/violence. The purpose of the present study was to compare the neuropsychiatric status of Vietnam veterans who had suffered cerebral malaria in the remote past (i.e., 1966 to 1969) with that of Vietnam veterans wounded in combat who had not suffered malaria or other neurological conditions. Findings indicate that cerebral malaria results in multiple, major, substantially underappreciated neuropsychiatric symptoms in Vietnam veterans, including poor dichotic listening, "personality change," depression, and, in some cases, partial seizure-like symptoms. Findings strongly suggest that history of malaria should be considered in any medical, psychological, or psychiatric workup of a Vietnam War veteran because a positive response could result in substantial changes in diagnosis and treatment.

Adult↗