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Biomedical subjects

R J Roberts

Publications and source records attributed to R J Roberts.

At least 19 recordsLinked to original sources
PubMed2006

Analysis of the incidence of infectious pancreatic necrosis mortality in pedigreed Atlantic salmon, Salmo salar L., populations.

A total of 77,124 Atlantic salmon post-smolts, representing 197 full-sib families produced by 149 males and 197 females, experienced a field challenge from infectious pancreatic necrosis virus (IPNV), following transfer to three separate seawater sites. The first IPN mortality was observed 45 days after transfer, and the duration of the epidemic varied between 37 and 92 days among sites. Mortalities were traced to their parental families by PIT (Passive Integrated Transpondes) tag records and DNA genotyping. Full-sib family mean incidence of mortality was calculated for each family on each site. Heritabilities were estimated based on the heterogeneity of chi-square using incidence within half-sib families and the variance in incidence among full-sib families, both on the observed and underlying liability scale. The observed correlation among families across sites was used to estimate genetic correlations. The overall mortality rate was 10.8%, with only small differences between sites, ranging from 10.3% to 11.9%. Heritabilities on the liability scale were found to be moderate to strong, and ranged between 0.24 and 0.81, with a pooled estimate of 0.43, greater than is typically associated with disease traits. Genetic correlations among sites were all substantial, between 0.71 and 0.78, and indicated that a substantial component of the genetic variation displayed within sites was common to all. The results show that field challenges can yield very good genetic information on family differences in resistance, especially when replicated over sites, which may then be developed for use in selection for breeding strains of Atlantic salmon with greater resistance to IPN.

Animals↗
PubMed2005

Exposure to school children as a risk factor in a community outbreak of hepatitis A in young adults: a case control study.

To investigate risk factors during a community outbreak of hepatitis A we carried out a case- control study of 35 cases and 49 matched controls using an interviewer-administered questionnaire on clinical history, travel, household details including domestic toilet facilities, infectious contacts, and food history. Of 99 cases notified in the city during the outbreak year, 50 (51%) were young adults age 15-34 years. Hepatitis A infection was independently associated with household contact with a case (P=0.0005), and sharing a household with children in primary school (OR 3.4, 95% CI 1.2-9.5, P=0.008) with risk increasing with number of primary-school pupils in the household (chi(2) for linear trend 6.47, P=0.01). We concluded that in a population with a low prevalence of hepatitis A, adults who live in the same household as primary-school-age children are at increased risk of acquiring the infection during community outbreaks.

Adolescent↗
PubMed2005

Maternal age in pregnancy and offspring blood pressure in childhood in the Avon Longitudinal Study of Parents and Children (ALSPAC).

Associations between maternal age in pregnancy and offspring blood pressure (BP) at age 7(1/2) were investigated in 7623 singletons from the Avon Longitudinal Study of Parents and Children (ALSPAC). In models adjusted for age and sex there was an inverse relationship between maternal age and BP in children: beta = -0.06 mmHg per year of maternal age (95% CI -0.10 to -0.01, P = 0.02) for systolic BP and beta = -0.04 (95% CI -0.07 to -0.01, P = 0.02) for diastolic BP. However, this association disappeared after adjustment for confounding factors: beta = -0.02 mmHg per year of maternal age (95% CI -0.07 to 0.04, P = 0.5) for systolic BP and beta = -0.03 (95% CI -0.07 to 0.01, P = 0.2) for diastolic BP. We conclude that there is no evidence of a relationship between maternal age in pregnancy and childhood BP in this contemporary birth cohort.

Adult↗
PubMed2005

Infectious pancreatic necrosis in Atlantic salmon, Salmo salar L.

A clinical and histopathological review was carried out of 21 outbreaks of acute infectious pancreatic necrosis (IPN) in Scottish Atlantic salmon, Salmo salar L., farms (13 marine and eight fresh water) during 1991-2004. A distinctive syndrome was evident in both post-smolts in sea water and fry in fresh water, where liver lesions, which had not previously been associated with IPN, became a consistent finding in addition to the more typical pancreatic and intestinal changes. Initial cases were described in post-smolts in Shetland, but by the end of the period of investigation this type of pathology had extended down the West coast of Scotland and into Ireland. Limited viral strain analysis suggested that similar strains were involved in both fresh water and sea water and that these differed from earlier isolates from rainbow trout, Oncorhynchus mykiss (Walbaum). In fresh water, recovered fish frequently developed a greatly distended intestine associated with accumulation of undigested food. In sea water, after the initial, often significant (50% or more), losses, there were many fish which failed to grow and became chronically emaciated and prone to sea louse infection. Although use of transfer diets containing immune enhancers and the selection of IPN resistant broodstock has reduced losses the disease remains a serious cause of economic loss.

Animals↗
PubMed2004

Control of Salmincola californiensis (Copepoda: Lernaeapodidae) in rainbow trout, Oncorhynchus mykiss (Walbaum): a clinical and histopathological study.

A stock of rainbow trout, Oncorhynchus mykiss, held at an experimental facility, was found to be heavily infested with the lernmaeapodid copepod Salmincola californiensis. The efficacy and effects of treatment were compared with ivermectin or manual removal of parasites as a means of control of S. californiensis. One group of fish was orally intubated with 0.2 mg ivermectin active ingredient kg-1 fish. A second treatment was administered after a further 14 days. In a second group of fish, parasites were manually removed from the gills using forceps. These fish were sampled for up to 21 days post-first removal of parasites. In the ivermectin-treated fish adult parasites became inactive and changed colour within 18 h of the initial treatment. Copepods began to disappear by day 3 post-treatment and by day 31 almost all embedded female parasites had disappeared. Gills were clinically normal apart from cavitation deformity resulting from parasite attachment. Post-ivermectin treatment, there was an increase in the number of eosinophilic granular cells surrounding the bulla of attached S. californiensis, but from day 31 post-treatment these were replaced by macrophages and epithelioid cells to form a necrotic focus. In manually picked fish there was extensive haemorrhage in the interlamellar spaces as a result of parasite removal. At sites of parasite removal tissue necrosis was minimal and healing was rapid. At the end of the sampling period the structure of the gill was improved. The use of oral dosage with ivermectin is an effective treatment for S. californiensis and could be particularly beneficial for use with endangered salmon broodstocks infested with the parasite.

Animals↗
PubMed2004

The pathology of phosphorus deficiency in fish--a review.

Phosphorus (P) is an essential component of fish diets. Its deficiency affects not only hard tissues, where it is responsible for rickets, leading to skeletal malformation, but also influences various aspects of intermediary metabolism, and thus growth and feed conversion. Therefore, optimizing the dietary inclusion level is critical at all times. As the aquaculture industry has expanded, so the effects of P in farm effluents, derived from metabolic and uneaten food sources, have also become recognized. Diets are increasingly formulated on a basis that will not only provide adequate P for fish needs, but also endeavour to ensure minimal acceptable P levels in effluents at the same time. Many variables influence P requirements and P availability in fish diets, so it is inadvisable to feed diets formulated to an assumed minimum dietary requirement level, irrespective of the advantages that such a formulation may provide to environmental impact.

Animal Nutritional Physiological Phenomena↗
PubMed2003

Melano-macrophage centres and their role in fish pathology.

Melano-macrophage centres, also known as macrophage aggregates, are distinctive groupings of pigment-containing cells within the tissues of heterothermic vertebrates. In fish they are normally located in the stroma of the haemopoietic tissue of the spleen and the kidney, although in amphibians and reptiles, and some fish, they are also found in the liver. They may also develop in association with chronic inflammatory lesions elsewhere in the body and during ovarian atresia. In higher teleosts, they often exist as complex discrete centres, containing lymphocytes and macrophages, and may be primitive analogues of the germinal centres of lymph nodes. Melano-macrophage centres usually contain a variety of pigments, including melanins, and these increase in range and volume in older fish or in the presence of cachectic disease. Melano-macrophage centres act as focal depositories for resistant intracellular bacteria, from which chronic infections may develop. Iron capture and storage in haemolytic diseases appears to be a primary function, but antigen trapping and presentation to lymphocytes, sequestration of products of cellular degradation and potentially toxic tissue materials, such as melanins, free radicals and catabolic breakdown products are among other functions that have been ascribed. Recent work suggests that they are a site of primary melanogenesis rather than mere storage. Melano-macrophage centres increase in size or frequency in conditions of environmental stress and have been suggested as reliable biomarkers for water quality in terms of both deoxygenation and iatragenic chemical pollution.

Animals↗
PubMed2003

Parents' attitude towards the second dose of measles, mumps and rubella vaccine: a case-control study.

In response to media scares and subsequent falls in measles, mumps and rubella (MMR) vaccine uptake, a case-control study was conducted to identify factors associated with non-uptake of the second dose of the vaccine in children resident in North Wales. Subjects were selected from parents of children scheduled for the second dose between October and December 1997. Postal questionnaires were used to compare knowledge, attitudes and practice of non-acceptors (cases) and acceptors (controls). Of non-acceptors, 92.1% (95% CI 82.2-97.5%) stated that they would allow another child to have at least one dose of MMR, and 39.2% (95% CI 25.8-53.9%) both doses of MMR vaccine. Non-acceptors were more likely to report having obtained information from newspapers/television (OR 2.04, 95% CI 1.03-4.02) or from the general practitioner (OR 2.02, 95% CI 1.07-3.86) and to report having 'a lot' or 'some' influence from newspapers/television (OR 3.52, 95% CI 1.57-7.86). The 'combination of three vaccines in one jab' was identified as a worry by 55.1% (95% CI 40.2-69.3%) of non-acceptors and 38.5% (95% CI 30.6-46.9%) of acceptors. On this evidence, catch-up campaigns would be an effective way of increasing coverage; also health professionals need tools to enable them to communicate effectively in the face of ongoing scares.

Attitude to Health↗
PubMed2002

Functional analysis of iceA1, a CATG-recognizing restriction endonuclease gene in Helicobacter pylori.

iceA1 in Helicobacter pylori is a homolog of nlaIIIR, which encodes the CATG-specific restriction endonuclease NlaIII in Neisseria lactamica. Analysis of iceA1 sequences from 49 H.pylori strains shows that a full-length NlaIII-like ORF is present in 10 strains, including CH4, but in other strains, including strain 60190, the ORFs are truncated due to a variety of mutations. Our goal was to determine whether iceA1 can encode a NlaIII-like endonuclease. Overexpression in Escherichia coli of iceA1 from CH4, but not from 60190, yielded NlaIII-like activity, indicating that the full-length iceA1 is a functional endonuclease gene. Repair of the iceA1 frameshift mutation in strain 60190 and its expression in E.coli yielded functional NlaIII-like activity. We conclude that iceA1 in CH4 is a functional restriction endonuclease gene, while iceA1 in 60190 is not, due to a frameshift mutation, but that its repair restores its restriction endonuclease activity.

Amino Acid Sequence↗
PubMed2002

An outbreak of Salmonella enteritidis phage type 34a infection in primary school children: the use of visual aids and food preferences to overcome recall bias in a case control study.

Outbreaks of infectious intestinal disease are common in schools. Case control studies are useful in the investigation of infectious disease outbreaks but the time interval between illness and investigation can lead to recall bias, particularly in young children. We describe an outbreak of Salmonella enteritidis phage type 34a infection involving 54 clinical cases in two adjacent schools, and a novel approach to overcome recall bias. The likely dates of infection were identified from the epidemic curve. We created a visual display of the menu from those days and asked 9 cases and 18 matched controls to identify their food preferences from this display. Preference for chocolate mouse was significantly associated with illness (P = 0.006). The results of the case control study agreed with the findings of the environmental investigation. We believe our approach could be used in other circumstances, where subjects are young children or recall bias is a concern.

Adolescent↗
PubMed2001

AdoMet-dependent methylation, DNA methyltransferases and base flipping.

Twenty AdoMet-dependent methyltransferases (MTases) have been characterized structurally by X-ray crystallography and NMR. These include seven DNA MTases, five RNA MTases, four protein MTases and four small molecule MTases acting on the carbon, oxygen or nitrogen atoms of their substrates. The MTases share a common core structure of a mixed seven-stranded beta-sheet (6 downward arrow 7 upward arrow 5 downward arrow 4 downward arrow 1 downward arrow 2 downward arrow 3 downward arrow) referred to as an 'AdoMet-dependent MTase fold', with the exception of a protein arginine MTase which contains a compact consensus fold lacking the antiparallel hairpin strands (6 downward arrow 7 upward arrow). The consensus fold is useful to identify hypothetical MTases during structural proteomics efforts on unannotated proteins. The same core structure works for very different classes of MTase including those that act on substrates differing in size from small molecules (catechol or glycine) to macromolecules (DNA, RNA and protein). DNA MTases use a 'base flipping' mechanism to deliver a specific base within a DNA molecule into a typically concave catalytic pocket. Base flipping involves rotation of backbone bonds in double-stranded DNA to expose an out-of-stack nucleotide, which can then be a substrate for an enzyme-catalyzed chemical reaction. The phenomenon is fully established for DNA MTases and for DNA base excision repair enzymes, and is likely to prove general for enzymes that require access to unpaired, mismatched or damaged nucleotides within base-paired regions in DNA and RNA. Several newly discovered MTase families in eukaryotes (DNA 5mC MTases and protein arginine and lysine MTases) offer new challenges in the MTase field.

Binding Sites↗
PubMed2001

Recombinant human DNA (cytosine-5) methyltransferase. III. Allosteric control, reaction order, and influence of plasmid topology and triplet repeat length on methylation of the fragile X CGG.CCG sequence.

Steady-state kinetic analyses revealed that the methylation reaction of the human DNA (cytosine-5) methyltransferase 1 (DNMT1) is repressed by the N-terminal domain comprising the first 501 amino acids, and that repression is relieved when methylated DNA binds to this region. DNMT1 lacking the first 501 amino acids retains its preference for hemimethylated DNA. The methylation reaction proceeds by a sequential mechanism, and either substrate (S-adenosyl-l-methionine and unmethylated DNA) may be the first to bind to the active site. However, initial binding of S-adenosyl-l-methionine is preferred. The binding affinities of DNA for both the regulatory and the catalytic sites increase in the presence of methylated CpG dinucleotides and vary considerably (more than one hundred times) according to DNA sequence. DNA topology strongly influences the reaction rates, which increased with increasing negative superhelical tension. These kinetic data are consistent with the role of DNMT1 in maintaining the methylation patterns throughout development and suggest that the enzyme may be involved in the etiology of fragile X, a syndrome characterized by de novo methylation of a greatly expanded CGG.CCG triplet repeat sequence.

Allosteric Regulation↗
PubMed2001

The sequence of the human genome.

A 2.91-billion base pair (bp) consensus sequence of the euchromatic portion of the human genome was generated by the whole-genome shotgun sequencing method. The 14.8-billion bp DNA sequence was generated over 9 months from 27,271,853 high-quality sequence reads (5.11-fold coverage of the genome) from both ends of plasmid clones made from the DNA of five individuals. Two assembly strategies-a whole-genome assembly and a regional chromosome assembly-were used, each combining sequence data from Celera and the publicly funded genome effort. The public data were shredded into 550-bp segments to create a 2.9-fold coverage of those genome regions that had been sequenced, without including biases inherent in the cloning and assembly procedure used by the publicly funded group. This brought the effective coverage in the assemblies to eightfold, reducing the number and size of gaps in the final assembly over what would be obtained with 5.11-fold coverage. The two assembly strategies yielded very similar results that largely agree with independent mapping data. The assemblies effectively cover the euchromatic regions of the human chromosomes. More than 90% of the genome is in scaffold assemblies of 100,000 bp or more, and 25% of the genome is in scaffolds of 10 million bp or larger. Analysis of the genome sequence revealed 26,588 protein-encoding transcripts for which there was strong corroborating evidence and an additional approximately 12,000 computationally derived genes with mouse matches or other weak supporting evidence. Although gene-dense clusters are obvious, almost half the genes are dispersed in low G+C sequence separated by large tracts of apparently noncoding sequence. Only 1.1% of the genome is spanned by exons, whereas 24% is in introns, with 75% of the genome being intergenic DNA. Duplications of segmental blocks, ranging in size up to chromosomal lengths, are abundant throughout the genome and reveal a complex evolutionary history. Comparative genomic analysis indicates vertebrate expansions of genes associated with neuronal function, with tissue-specific developmental regulation, and with the hemostasis and immune systems. DNA sequence comparisons between the consensus sequence and publicly funded genome data provided locations of 2.1 million single-nucleotide polymorphisms (SNPs). A random pair of human haploid genomes differed at a rate of 1 bp per 1250 on average, but there was marked heterogeneity in the level of polymorphism across the genome. Less than 1% of all SNPs resulted in variation in proteins, but the task of determining which SNPs have functional consequences remains an open challenge.

Algorithms↗
PubMed2001

Comparative genomics of the restriction-modification systems in Helicobacter pylori.

Helicobacter pylori is a Gram-negative bacterial pathogen with a small genome of 1.64-1.67 Mb. More than 20 putative DNA restriction-modification (R-M) systems, comprising more than 4% of the total genome, have been identified in the two completely sequenced H. pylori strains, 26695 and J99, based on sequence similarities. In this study, we have investigated the biochemical activities of 14 Type II R-M systems in H. pylori 26695. Less than 30% of the Type II R-M systems in 26695 are fully functional, similar to the results obtained from strain J99. Although nearly 90% of the R-M genes are shared by the two H. pylori strains, different sets of these R-M genes are functionally active in each strain. Interestingly, all strain-specific R-M genes are active, whereas most shared genes are inactive. This agrees with the notion that strain-specific genes have been acquired more recently through horizontal transfer from other bacteria and selected for function. Thus, they are less likely to be impaired by random mutations. Our results also show that H. pylori has extremely diversified R-M systems in different strains, and that the diversity may be maintained by constantly acquiring new R-M systems and by inactivating and deleting the old ones.

Cloning, Molecular↗
PubMed2001

REBASE--restriction enzymes and methylases.

REBASE contains comprehensive information about restriction enzymes, DNA methylases and related proteins such as nicking enzymes, specificity subunits and control proteins. It contains published and unpublished references, recognition and cleavage sites, isoschizomers, commercial availability, methylation sensitivity, crystal data and sequence data. Homing endonucleases are also included. Most recently, extensive information about the methylation sensitivity of restriction enzymes has been added and a new feature contains complete analyses of the putative restriction systems in the sequenced bacterial and archaeal genomes. The data is distributed via email, ftp (ftp.neb.com) and the Web (http://rebase. neb.com).

Base Sequence↗