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Biomedical subjects

S J Clark

Publications and source records attributed to S J Clark.

At least 19 recordsLinked to original sources
PubMed2006

Denaturing gradient gel electrophoresis can rapidly display the bacterial diversity contained in 16S rDNA clone libraries.

Two different strategies for molecular analysis of bacterial diversity, 16S rDNA cloning and denaturing gradient gel electrophoresis (DGGE), were combined into a single protocol that took advantage of the best attributes of each: the ability of cloning to package DNA sequence information and the ability of DGGE to display a community profile. In this combined protocol, polymerase chain reaction products from environmental DNA were cloned, and then DGGE was used to screen the clone libraries. Both individual clones and pools of randomly selected clones were analyzed by DGGE, and these migration patterns were compared to the conventional DGGE profile produced directly from environmental DNA. For two simple bacterial communities (biofilm from a humics-fed laboratory reactor and planktonic bacteria filtered from an urban freshwater pond), pools of 35-50 clones produced DGGE profiles that contained most of the bands visible in the conventional DGGE profiles, indicating that the clone pools were adequate for identifying the dominant genotypes. However, DGGE profiles of two different pools of 50 clones from a lawn soil clone library were distinctly different from each other and from the conventional DGGE profile, indicating that this small number of clones poorly represented the bacterial diversity in soil. Individual clones with the same apparent DGGE mobility as prominent bands in the humics reactor community profiles were sequenced from the clone plasmid DNA rather than from bands excised from the gel. Because a longer fragment was cloned (approximately 1500 bp) than was actually analyzed in DGGE (approximately 350 bp), far more sequence information was available using this approach that could have been recovered from an excised gel band. This clone/DGGE protocol permitted rapid analysis of the microbial diversity in the two moderately complex systems, but was limited in its ability to represent the diversity in the soil microbial community. Nonetheless, clone/DGGE is a promising strategy for fractionating diverse microbial communities into manageable subsets consisting of small pools of clones.

Bacteria↗
PubMed2006

Effects of genetically modified herbicide-tolerant cropping systems on weed seedbanks in two years of following crops.

The Farm Scale Evaluations (FSEs) showed that genetically modified herbicide-tolerant (GMHT) cropping systems could influence farmland biodiversity because of their effects on weed biomass and seed production. Recently published results for winter oilseed rape showed that a switch to GMHT crops significantly affected weed seedbanks for at least 2 years after the crops were sown, potentially causing longer-term effects on other taxa. Here, we seek evidence for similar medium-term effects on weed seedbanks following spring-sown GMHT crops, using newly available data from the FSEs. Weed seedbanks following GMHT maize were significantly higher than following conventional varieties for both the first and second years, while by contrast, seedbanks following GMHT spring oilseed rape were significantly lower over this period. Seedbanks following GMHT beet were smaller than following conventional crops in the first year after the crops had been sown, but this difference was much reduced by the second year for reasons that are not clear. These new data provide important empirical evidence for longer-term effects of GMHT cropping on farmland biodiversity.

Agriculture↗
PubMed2006

Effect of fungal infection on the reproductive potential of aphids and their progeny.

The effect of infection by Pandora neoaphidis and Beauveria bassiana on the reproductive potential of the pea aphid, Acyrthosiphon pisum, and their progeny was assessed. Infection by either P. neoaphidis or B. bassiana reduced the number of nymphs produced within 24 h of inoculation and over the entire infection period compared to uninfected aphids. However, infection by either P. neoaphidis or B. bassiana for 24 or 72 h did not alter the intrinsic rate of increase of the host aphid's progeny. Therefore, fungal infection appears to have no indirect effects on the fitness of the host's progeny.

Animals↗
PubMed2006

Reactivation of latent hepatitis B virus infection with HIV-related immunosuppression.

The effect of HIV-related immunosuppression and antiretroviral therapy on the reactivation of latent hepatitis B virus (HBV) infection is unclear. We report four patients with advanced HIV-related immunosuppression and abnormal liver function tests who had evidence of HBV reactivation. Reclearance of hepatitis B occurred in two cases with HIV treatment regimens not containing lamivudine, suggesting that improved immune function may be responsible. In three cases, HBV reactivation was recognized during investigation for abnormal liver function initially attributed to drug toxicity. The possibility of HBV reactivation must be considered in the differential diagnosis of abnormal liver function in cases with advanced HIV.

Antiretroviral Therapy, Highly Active↗
PubMed2005

Ab initio dynamics study of poly-para-phenylene vinylene.

We present an ab initio dynamics investigation within a density-functional perturbation theory framework of the properties of the conjugated polymer poly-para-phenylene vinylene (PPV) in both the isolated chain and crystalline states. The calculated results show that for an isolated chain, most of the vibrational modes correspond to experimentally observed modes in crystalline PPV. However, additional hitherto unidentified modes have been observed in experiment and our calculations on crystalline material have allowed us to assign these. We also present the results of calculations of the polarizability and permittivity tensors of the material, which are in reasonable agreement with the typical values for conjugated polymers. Dynamical Born effective charges [S. Baroni, S. de Gironcoli, A. Dal Corso, and P. Giannozzi, Rev. Mod. Phys. 73, 515 (2001)] are calculated and compared with atomic charges obtained from Mulliken population analysis [M. D. Segall, C. J. Pickard, R. Shah, and M. C. Payne, Mol. Phys. 89, 571 (1996)] and we conclude that effective charges are more appropriate for use in the study of the dynamics of the system. Notable differences are found in the infrared-absorption spectra obtained for the isolated chain and crystalline states, which can be attributed to the differences in the crystalline packing effects, which clearly play a key role in influencing the lattice dynamics of PPV.

Journal Article↗
PubMed2005

Wheat containing snowdrop lectin (GNA) does not affect infection of the cereal aphid Metopolophium dirhodum by the fungal natural enemy Pandora neoaphidis.

Studies were carried out to determine if susceptibility of the cereal aphid Metopolophium dirhodum to the fungus Pandora neoaphidis was affected by wheat expressing snowdrop lectin (GNA). Aphid infection did not differ significantly between the transgenic GNA and non-transformed lines (91 and 82%, respectively). Fecundity also did not differ between aphids on the two lines, and was ca. 18 nymphs adult(-1). Time to infection was ca. 5 days for M. dirhodum on both lines in two of three assays. Our results indicate that wheat expressing GNA would not compromise the efficacy of P. neoaphidis as a biocontrol agent.

Animals↗
PubMed2005

Mutation and methylation analysis of TP53 in adrenal carcinogenesis.

AIM: To investigate the role of coding region mutation and promoter hypermethylation of TP53 in adrenocortical cancer formation. METHODS: Twenty sporadic adrenocortical cancers (ACCs) and five normal adrenal tissue samples were available for analysis. Coding region mutation of TP53 in 20 ACCs was examined by polymerase chain amplification using intronic primers for exons 2-11 and direct sequencing of the product. In 10 ACCs and five normal adrenal tissue specimens, methylation of the 16 CpG sites within the TP53 promoter was examined using bisulphite methylation sequencing. RESULTS: Coding region mutation in TP53 was demonstrated in 5 of 20 ACCs. There were four mis-sense mutations and one frameshift mutation. Four of 5 patients with a TP53 mutation had metastases at diagnosis or detected soon thereafter and 3 of 4 died of disease within 12 months of surgical resection. No methylation was seen in the TP53 promoter in 10 ACC and the five normal adrenal tissues examined. CONCLUSION: Coding region mutation in TP53 occurs in 25% of ACCs with a trend toward a poorer prognosis. Promoter methylation of TP53 is not present in ACC as a mechanism for tumour suppressor gene (TSG) inactivation and, therefore, other genes in the 17p13 region are implicated in adrenal carcinogenesis.

Adrenal Gland Neoplasms↗
PubMed2005

Laboratory studies of the effects of reduced prey choice caused by Bt plants on a predatory insect.

Crops transformed to express Bacillus thuringiensis (Bt) toxins can cause close to 100% mortality of certain target pest species. This study assessed the effect of target pest reduction on the predatory insect Chrysoperla carnea (Stephens) in the presence of alternative prey. Numbers of lacewings recovered from Bt oilseed rape (cultivar Oscar, event O52) did not differ significantly from numbers of lacewings recovered from conventional oilseed rape in cage experiments with the target pest Plutella xylostella (Linnaeus) and the non-target pest Myzus persicae (Sulzer) when aphid densities were high. However, significantly fewer lacewings were recovered from Bt plants as aphid densities were lowered. Lacewing weights were not affected by plant type.

Animals↗
PubMed2004

Dielectric and vibrational properties of amino acids.

We calculate polarizability tensors and normal mode frequencies for the amino acids alanine, leucine, isoleucine, and valine using density functional perturbation theory implemented within the plane wave pseudopotential framework. It is found that the behavior of the electron density under external fields depends to a large extent on the geometrical structure of the molecule in question, rather than simply on the constituent functional groups. The normal modes are able to help distinguish between the different types of intramolecular hydrogen bonding present, and help to explain why leucine is found in the zwitterionic form for the gaseous phase. Calculated IR spectra show a marked difference between those obtained for zwitterionic and nonzwitterionic molecules. These differences can be attributed to the different chemical and hydrogen bonds present. Effective dynamical charges are calculated, and compared to atomic charges obtained from Mulliken population analysis. It is found that disagreement exists, largely due to the differing origins of these quantities.

Amino Acids↗
PubMed2004

Ban on triazine herbicides likely to reduce but not negate relative benefits of GMHT maize cropping.

The UK Farm-Scale Evaluations (FSE) compared the effects on biodiversity of management of genetically modified herbicide-tolerant (GMHT) spring-sown crops with conventional crop management. The FSE reported larger weed abundance under GMHT management for fodder maize, one of three crops studied. Increased seed production may be important for the long-term persistence of these arable weeds and may benefit invertebrates, small mammals and seed-eating birds. In three-quarters of FSE maize fields, growers used atrazine on the conventionally managed half, reflecting contemporary commercial practice. Withdrawal of the triazine herbicides atrazine, simazine and cyanazine from approved lists of EU chemicals could therefore reduce or even reverse the reported benefits of GMHT maize. Here we analyse effects of applications of triazine herbicides in conventional maize regimes on key indicators, using FSE data. Weed abundances were decreased greatly relative to all other regimes whenever atrazine was applied before weeds emerged. Here, we forecast weed abundances in post-triazine herbicide regimes. We predict weed abundances under future conventional herbicide management to be considerably larger than that for atrazine used before weeds emerged, but still smaller than for the four FSE sites analysed that used only non-triazine herbicides. Our overall conclusion is that the comparative benefits for arable biodiversity of GMHT maize cropping would be reduced, but not eliminated, by the withdrawal of triazines from conventional maize cropping.

Atrazine↗
PubMed2004

Right ventricular volume measurements in ventilated preterm neonates.

Pulmonary hypertension is associated with worse perinatal outcomes in infants with respiratory disorders. In these infants, right ventricular dysfunction may result in poor pulmonary blood flow. The objective of this study was to follow changes in right ventricular volumes during the first 2 days of life in infants with respiratory distress syndrome. Serial echocardiographic examinations were performed on days 0-2 on infants ventilated for respiratory distress syndrome. Two-dimensional echocardiography with the ellipsoid approximation was used to calculate systolic and diastolic volumes. In 17 ventilated preterm infants, right ventricular volumes were significantly lower on day 2 compared with day 0 and decreased from a median (interquartile range) end systolic volume of 0.80 ml/kg (0.66-0.91 ml/kg) to 0.45 ml/kg (0.39-0.54 ml/kg) ( p < 0.001). End diastolic volume decreased from a median (interquartile range) of 1.54 ml/kg (1.44-1.65 ml/kg) to 1.30 ml/kg (1.22-1.60 ml/kg) ( p = 0.039). Right ventricular ejection fraction increased from a median (interquartile range) of 0.48 ml/kg (0.44-0.56 ml/kg) to 0.62 ml/kg (0.58-0.71 ml/kg) during the same period ( p < 0.001), as did right ventricular output from a median (interquartile range) 120 ml/kg/min (96-125 ml/kg/min) to 140 ml/kg/min (113-168 ml/kg/min) ( p = 0.044). Right ventricular volume decreases during the first 2 days of life in ventilated preterm infants. However, right ventricular performance is maintained.

Cardiotonic Agents↗
PubMed2004

Evidence for gene flow and local clonal selection in field populations of the grain aphid (Sitobion avenae) in Britain revealed using microsatellites.

Samples of the grain aphid, Sitobion avenae (F.), a major European pest of cereals, were collected in June and July 1997 from fields sown with winter wheat in a rough transect south-west of Rothamsted, UK. These aphids were genotyped at four microsatellite loci known from previous studies to be highly polymorphic. Allelic frequencies were similar between samples collected in the fields and in the 12.2 m high suction trap at Rothamsted, and there were many widespread genotypes (clones), providing evidence that the species is highly migratory. However, field samples were found to display a high level of genotypic heterogeneity (= variable clonal composition), most probably the result of clonal selection. The suction trap genotypes sample were slightly different from the field samples, indicative of the inclusion of genotypes from plant hosts (cereals and grasses, Poaceae) other than winter wheat and/or genotype-biased emigration from the field. The relevance of these data to modelling of aphid outbreaks is briefly discussed.

Animals↗
PubMed2004

Concentrations of cardiac troponin T in neonates with and without respiratory distress.

AIMS: To establish a practical postnatal reference range for cardiac troponin T in neonates and to investigate concentrations in neonates with respiratory distress. METHODS: Prospective investigation in a tertiary neonatal unit, recruiting infants with and without respiratory distress (sick and healthy infants respectively). Concentrations of cardiac troponin T were compared between sick and healthy infants, accounting for confounding variables. RESULTS: A total of 162 neonates (113 healthy and 49 sick infants) had samples taken. The median (interquartile range) cardiac troponin T concentration in the healthy infants was 0.025 (0.01-0.062) ng/ml, and the 95th centile was 0.153 ng/ml. There were no significant relations between cardiac troponin T and various variables. The median (interquartile range) cardiac troponin T concentration in the sick infants was 0.159 (0.075-0.308) ng/ml. This was significantly higher (p < 0.0001) than in the healthy infants. In a linear regression model, the use of inotropes and oxygen requirement were significant associations independent of other basic and clinical variables in explaining the variation in cardiac troponin T concentrations. CONCLUSIONS: Cardiac troponin T is detectable in the blood of many healthy neonates, but no relation with important basic and clinical variables was found. Sick infants have significantly higher concentrations than healthy infants. The variations in cardiac troponin T concentration were significantly associated with oxygen requirement or the use of inotropic support in a regression model. Cardiac troponin T may be a useful marker of neonatal and cardiorespiratory morbidity.

Female↗
PubMed2003

Weeds in fields with contrasting conventional and genetically modified herbicide-tolerant crops. II. Effects on individual species.

We compared the effects of the management of genetically modified herbicide-tolerant (GMHT) and conventional beet, maize and spring oilseed rape on 12 weed species. We sampled the seedbank before and after cropping. During the season we counted plants and measured seed rain and biomass. Ratios of densities were used to calculate emergence, survival, reproduction and seedbank change. Treatments significantly affected the biomass of six species in beet, eight in maize and five in spring oilseed rape. The effects were generally consistent, with biomass lower in GMHT beet and spring oilseed rape and higher in GMHT maize. With few exceptions, emergence was higher in GMHT crops. Subsequent survival was significantly lowered for eight species in beet and six in spring oilseed rape in the GMHT treatments. It was increased for five species in maize and one in spring oilseed rape. Significant effects on seedbank change were found for four species. However, for many species in beet and spring oilseed rape (19 out of 24 cases), seed densities were lower in the seedbank after GMHT cropping. These differences compounded over time would result in large decreases in population densities of arable weeds. In maize, populations may increase.

Agriculture↗
PubMed2003

Weeds in fields with contrasting conventional and genetically modified herbicide-tolerant crops. I. Effects on abundance and diversity.

We compared the seedbanks, seed rains, plant densities and biomasses of weeds under two contrasting systems of management in beet, maize and spring oilseed rape. Weed seedbank and plant density were measured at the same locations in two subsequent seasons. About 60 fields were sown with each crop. Each field was split, one half being sown with a conventional variety managed according to the farmer's normal practice, the other half being sown with a genetically modified herbicide-tolerant (GMHT) variety, with weeds controlled by a broad-spectrum herbicide. In beet and rape, plant densities shortly after sowing were higher in the GMHT treatment. Following weed control in conventional beet, plant densities were approximately one-fifth of those in GMHT beet. In both beet and rape, this effect was reversed after the first application of broad-spectrum herbicide, so that late-season plant densities were lower in the GMHT treatments. Biomass and seed rain in GMHT crops were between one-third and one-sixth of those in conventional treatments. The effects of differing weed-seed returns in these two crops persisted in the seedbank: densities following the GMHT treatment were about 20% lower than those following the conventional treatment. The effect of growing maize was quite different. Weed density was higher throughout the season in the GMHT treatment. Late-season biomass was 82% higher and seed rain was 87% higher than in the conventional treatment. The difference was not subsequently detectable in the seedbank because the total seed return was low after both treatments. In all three crops, weed diversity was little affected by the treatment, except for transient effects immediately following herbicide application.

Agriculture↗
PubMed2003

Invertebrates and vegetation of field margins adjacent to crops subject to contrasting herbicide regimes in the Farm Scale Evaluations of genetically modified herbicide-tolerant crops.

The effects of management of genetically modified herbicide-tolerant (GMHT) crops on adjacent field margins were assessed for 59 maize, 66 beet and 67 spring oilseed rape sites. Fields were split into halves, one being sown with a GMHT crop and the other with the equivalent conventional non-GMHT crop. Margin vegetation was recorded in three components of the field margins. Most differences were in the tilled area, with fewer smaller effects mirroring them in the verge and boundary. In spring oilseed rape fields, the cover, flowering and seeding of plants were 25%, 44% and 39% lower, respectively, in the GMHT uncropped tilled margins. Similarly, for beet, flowering and seeding were 34% and 39% lower, respectively, in the GMHT margins. For maize, the effect was reversed, with plant cover and flowering 28% and 67% greater, respectively, in the GMHT half. Effects on butterflies mirrored these vegetation effects, with 24% fewer butterflies in margins of GMHT spring oilseed rape. The likely cause is the lower nectar supply in GMHT tilled margins and crop edges. Few large treatment differences were found for bees, gastropods or other invertebrates. Scorching of vegetation by herbicide-spray drift was on average 1.6% on verges beside conventional crops and 3.7% beside GMHT crops, the difference being significant for all three crops.

Agriculture↗
PubMed2003

Crop management and agronomic context of the Farm Scale Evaluations of genetically modified herbicide-tolerant crops.

The Farm Scale Evaluations of genetically modified herbicide-tolerant crops (GMHT) were conducted in the UK from 2000 to 2002 on beet (sugar and fodder), spring oilseed rape and forage maize. The management of the crops studied is described and compared with current conventional commercial practice. The distribution of field sites adequately represented the areas currently growing these crops, and the sample contained sites operated at a range of management intensities, including low intensity. Herbicide inputs were audited, and the active ingredients used and the rates and the timings of applications compared well with current practice for both GMHT and conventional crops. Inputs on sugar beet were lower than, and inputs on spring oilseed rape and forage maize were consistent with, national averages. Regression analysis of herbicide-application strategies and weed emergence showed that inputs applied by farmers increased with weed densities in beet and forage maize. GMHT crops generally received only one herbicide active ingredient per crop, later and fewer herbicide sprays and less active ingredient (for beet and maize) than the conventional treatments. The audit of inputs found no evidence of bias.

Agriculture↗