Genotyping single nucleotide polymorphisms in barley by tetra-primer ARMS-PCR

Single nucleotide polymorphisms (SNPs) are the most abundant form of DNA polymorphism. These polymorphisms can be used in plants as simple genetic markers for many breeding applications, for population studies, and for germplasm fingerprinting. The great increase in the available DNA sequences in the databases has made it possible to identify SNPs by "database mining", and the single most important factor preventing their widespread use appears to be the genotyping cost. Many genotyping platforms rely on the use of sophisticated, automated equipment coupled to costly chemistry and detection systems. A simple and economical method involving a single PCR is reported here for barley SNP genotyping. Using the tetra-primer ARMS-PCR procedure, we have been able to assay unambiguously five SNPs in a set of 132 varieties of cultivated barley. The results show the reliability of this technique and its potential for use in low- to moderate-throughput situations; the association of agronomically important traits is discussed.

Safety, tolerability and pharmacokinetics of subcutaneous Å6, an 8-amino acid peptide with anti-angiogenic properties, in healthy men

AIMS

To assess the safety, tolerability and pharmacokinetics of subcutaneous A6, an 8-amino acid peptide with anti-angiogenic properties, in healthy men.

METHODS

Double-blind, placebo-controlled, parallel-group, dose-rising, phase I study of single and repeated doses. In the single dose phase, successive groups of 5 subjects received A6 15, 35, 75, 150, 300 mg, or placebo, as subcutaneous injections in the upper thigh. In the repeat dose phase, 2 groups of 6 subjects received repeat doses of A6 35 mg and 75 mg, or placebo, and 1 group of 5 subjects received 150 mg, or placebo, 12-hourly for 6 days (11 doses in total). In each group, 4 subjects received active treatment, the remainder placebo. Pharmacokinetics of A6 were assessed up to 24 h after single doses, for 12 h after the first of the repeated doses, and up to 24 h after the last of the repeated doses.

MATERIALS

A6 for subcutaneous injection in phosphate buffer, pH 5.6-6.0. Phosphate-buffered saline was used as placebo.

RESULTS

All dose regimens of A6 were safe and well-tolerated, both systemically and locally. Time to peak plasma concentration was similar (0.5-2.1 h) in all dosage groups. Cmax and AUC(0-inf) were linearly proportional to dose. Mean Cmax ranged from 454-10,333 ng/ml and mean AUC(0-inf) from 1,690-43,371 ng x h/ml after the 15 and 300 mg single doses, respectively. Terminal t(1/2) was 1.4-1.8 h, and there was no evidence of unexpected drug accumulation. Urinary excretion of unchanged A6 was 94.6% (SD 20.7) after the 300 mg single dose (0-24 h collection), and 78.4% (SD 13.0) after the 150 mg repeated dose (0-12 h collection). A6 did not trigger production of anti-A6 IgG antibodies within 14 days of the first dose.

CONCLUSION

Single doses of A6 up to 300 mg, and repeated doses up to 150 mg, were well-tolerated and safe in healthy young men. A6 was rapidly absorbed; it was eliminated, mainly unchanged, in urine. Plasma concentrations were dose-proportional. A6 did not trigger an early immunogenic response.

Rethinking sedation and agitation management in critical illness

OBJECTIVE

To examine difficulties in sedation management in the critically ill patient and explore how a semi automated sedation controller can improve agitation control. To present recent work on measurements of agitation, dynamic systems modelling and control of patient agitation response.

DATA SOURCES

Articles and peer-reviewed studies identified through a PUBMED search and selected original works from the biomedical engineering literature of relevance to agitation control and management.

SUMMARY OF REVIEW

Over-sedation has an adverse impact on intensive care resources. Interventions to constrain sedation delivery through development of protocols or regular cessation of infusions result in reduction in resource utilisation, but have not significantly addressed existing difficulties in agitation control. We develop a paradigm in which control of agitation in critically ill patients becomes the primary objective of sedation management. This principle is central to the function of a nurse-managed semi-automated sedation delivery device. The clinical application of this device using subjective assessments of agitation is presented. A framework for the development of improved automated sedation delivery systems using objective measurements of agitation and control, based on agitation feedback, is described. Using dynamic systems modelling and a simulated nurse, a bolus-driven approach significantly reduced agitation and minimised drug utilisation. This result challenges the current practice of sedating patients using continuous infusions.

CONCLUSIONS

A simple computerised interface with an algorithm that continually reduces the infusion rate in the absence of agitation has successfully been introduced into clinical practice. Nursing staff reported high levels of satisfaction with this device and it has enabled detailed data on patterns of sedation administration to be extracted for analysis. This data has been used to validate a model of the fundamental agitation-sedation dynamics.

Molecular genetic variation in the East Midlands, England: analysis of VNTR, STR and Alu insertion/deletion polymorphisms

BACKGROUND

Short tandem repeats (STRs) and variable number of tandem repeats (VNTRs) have been used successfully in disease analysis and studies of human evolution and population genetic diversity. However DNA-based comprehensive population genetic studies of the East Midlands, England are limited.

SUBJECTS AND METHODS

To enlarge our understanding of genetic variation in the East Midlands, a study was conducted on five regional populations: north-west Derbyshire,north-east Derbyshire, south Derbyshire, Nottinghamshire and Leicestershire. Blood samples were collected from donors whose ancestors had lived in the region for at least three generations. Seven VNTRs (MSI (DIS7), MS31 (D7S21), MS43A (D12SII) and YNH24 (D2S44), DIS0, APOB, YNZ22 (D17S5)), six STRs (HumTHOI, HumVWA31A, HumF13AOl1, HumFESFPS, HumCSFIPO, HumTPOX) and six Alu insertion/deletion polymorphisms (TPA25, ACE, PV92, F13B, APO, DI) were analysed in approximately 500 individuals. Allele or bin frequencies were calculated using gene counting and fixed bin methods. The chi-square method and exact tests were used to assess Hardy-Weinberg equilibrium. Genetic distances were calculated using Nei's DA method and correspondence analysis was used to assess population affinities.

RESULTS

The overall pattern of allele frequencies was similar to many European and UK populations for a number of genetic systems. Overall heterogeneity was observed for five loci: MS43A, MS31, HumF13A0l, HumFESFPS and HumTHOI. Twenty-three of 190 pairwise population comparisons were also statistically significant at the 5% level. Average molecular genetic system heterozygosity was 1.5 times higher than observed with conventional blood group systems. GsT values for molecular systems were also higher than conventional systems (0.012 vs 0.005) and suggest a low to moderate level of differentiation.

CONCLUSION

The allele frequency spectrum and inter-population comparisons show that there is significant genetic variation in the five contiguous regional populations of the East Midlands. Some of this variation may be due to local geographical barriers, genetic drift and possibly the settlement patterns of Continental European invaders.

Transanal endoscopic microsurgery and radical surgery for T1 and T2 rectal cancer

BACKGROUND

Transanal endoscopic microsurgery (TEM) has gained increasing acceptance as a local treatment of early rectal cancer. The purpose of this study was to compare the results of TEM and radical surgery in patients with T1 and T2 rectal cancer.

METHODS

From October 1994 to December 2000, 74 patients with T1 and T2 rectal adenocarcinoma treated with TEM were compared with 100 patients with T1N0M0 and T2N0M0 rectal adenocarcinoma treated with radical surgery. Retrospective analysis was performed regarding to recurrence and survival rate. Neither group received adjuvant chemoradiation. There was no significant difference in age, gender, tumor location, or follow-up period between the two groups. The only difference was in tumor size.

RESULTS

Of the 74 patients in TEM group, 52 were T1 (70.3%) and 22 were T2 (29.7%). Of the 100 patients in radical surgery group, 17 were T1 (17%) and 83 patients were T2 (83%). The 5-year local recurrence rates were 4.1% for T1, 19.5% for T2 after TEM, 0% for T1, and 9.4% for T2 after radical surgery. There was no statistical difference between the TEM and radical surgery groups for T1 rectal cancer ( p = 0.95), but for T2 rectal cancer, the 5-year local recurrence rate was higher after TEM than after radical surgery ( p = 0.04). There were no significant statistical difference between the two groups in terms of the 5-year disease-free survival rate and the survival rate.

CONCLUSIONS

For T1 rectal cancer, there was no difference in recurrence or 5-year survival rate between the TEM and the radical surgery groups. For T2 rectal cancer, there was no statistical difference in the 5-year survival rate between the two groups, but TEM carried higher risk of local recurrence. Therefore, careful selection of the patients is required for TEM, and when proper muscle invasion is proven, the TEM procedure should be supplemented by further treatment, or radical surgery should be performed.

Correlation of age, acromial morphology, and rotator cuff tear pathology diagnosed by ultrasound in asymptomatic patients

The importance of acromial morphology in the pathogenesis of rotator cuff tears remains controversial. Some surgeons place great emphasis on acromial morphology and others feel that acromial shape is a result of cuff tear pathology rather than the cause. The purpose of this study was to determine if there was an association between acromial morphology, age, and rotator cuff tears found by ultrasound in asymptomatic volunteer subjects with no past history of shoulder symptoms. One hundred eighteen outlet x-rays and ultrasound scans were performed in 59 asymptomatic patients in various age groups. Acromial morphology and the age of the patients were then correlated with the ultrasound findings. Older patients were noted to have a high incidence of type II and type III acromions (93% of those over 70). Full- and partial-thickness tears were more commonly seen in patients with type II or type III acromions compared with type I. Patients over 50 years had a high incidence of full-thickness tears (40%), but the incidence did not increase with increasing age past 50. These findings lend credence to the multifactorial etiology of rotator cuff tears. The patient's age (degeneration) and acromial morphology (impingement) are two of the factors involved in causing rotator cuff tears. The incidence of cuff tears and type III acromions was high in this group of entirely asymptomatic volunteer subjects. Surgeons should interpret radiologically hooked or curved acromions as well as rotator cuff tears diagnosed with ultrasound or other modalities with caution. It may well be that both of these findings should be regarded as part of the natural ageing process.

Comparison of the utility of barley retrotransposon families for genetic analysis by molecular marker techniques

The Sequence-Specific Amplification Polymorphism (S-SAP) method, and the related molecular marker techniques IRAP (inter-retrotransposon amplified polymorphism) and REMAP (retrotransposon-microsatellite amplified polymorphism), are based on retrotransposon activity, and are increasingly widely used. However, there have been no systematic analyses of the parameters of these methods or of the utility of different retrotransposon families in producing polymorphic, scorable fingerprints. We have generated S-SAP, IRAP, and REMAP data for three barley (Hordeum vulgare L.) varieties using primers based on sequences from six retrotransposon families (BARE-1, BAGY-1, BAGY-2, Sabrina, Nikita and Sukkula). The effect of the number of selective bases on the S-SAP profiles has been examined and the profiles obtained with eight MseI+3 selective primers compared for all the elements. Polymorphisms detected in the insertion pattern of all the families show that each can be used for S-SAP. The uniqueness of each transposition event and differences in the historic activity of each family suggest that the use of multiple retrotransposon families for genetic analysis will find applications in mapping, fingerprinting, and marker-assisted selection and evolutionary studies, not only in barley and other Hordeum species and related taxa, but also more generally.

[HUMANS: a neuropsychological battery for evaluating HIV 1 infected patients]

OBJECTIVE

To develop a neuropsychological test battery in Spanish for the cognitive evaluation of HIV 1 infected patients.

DEVELOPMENT

Departing from the suggestions presented by the work group of the National Institute of Mental Health (USA), a neuropsychological assessment battery was developed. It was named HUMANS (HIV/University of Miami Annotated Neuropsychological test battery in Spanish). This battery includes the following domains: 1) attention and speed of processing information, 2) memory, 3) executive function, 4) language, 5) visuospacial/visuoconstructive abilities, and 6) motor abilities. Administration takes about 3 4 hours. The English parallel version of this battery has been successfully used in English for over a decade with HIV 1 infected patients. In the paper the development and adaptation to Spanish language of the HUMANS neuropsychology section is presented.

CONCLUSIONS

HUMANS neuropsychological test battery fulfill the recommendations presented by the work group of the National Institute of Mental Health for evaluating HIV 1 infected patients. Studies regarding validity and reliability are still required.

The development of multiplex simple sequence repeat (SSR) markers to complement distinctness, uniformity and stability testing of rape (Brassica napus L.) varieties

To assess the potential of multiplex SSR markers for testing distinctness, uniformity and stability of rape (Brassica napus L.) varieties, we developed three multiplex SSR sets composed of five markers each. These were used to measure the extent of diversity within and between a set of ten varieties using a fluorescence-based semi-automated detection technology. Also, we evaluated the significance of any correlation between SSRs, pedigree and five of the morphological characters currently used for statutory distinctness, uniformity and stability testing of rape varieties. An assignment test was allowed to identify 99% of the plants examined, with the correct variety based on the analysis of 48 individual plants for each variety. Principal coordinate analysis confirmed that a high degree of separation between varieties could be achieved. Varieties were separated in three groups corresponding to winter, spring and forage types. These results suggested that it should be possible to select a set of markers for obtaining a suitable separation. Diversity within varieties varied considerably, according to the variety and the locus examined. No significant correlation was found between SSR and morphological data. However, genetic distances measured by SSRs were correlated to pedigree. These results suggested that SSRs could be used for pre-screening or grouping of existing and candidate varieties, allowing the number of varieties that need to be grown for comparison to be reduced. Multiplex SSR sets gave high-throughput reproducible results, thus reducing the costs of SSR assessment. Multiplex SSR sets are a promising way forward for complementing the current variety testing system in B. napus.

Generation of expression constructs that secrete bioactive alphaMSH and their use in the treatment of experimental autoimmune encephalomyelitis

alpha Melanocyte-stimulating hormone (alphaMSH) is a 13 amino acid peptide with potent anti-inflammatory effects. We created two DNA expression constructs (miniPOMC and pACTH1-17) that encode bioactive versions of the alphaMSH peptide, and tested these constructs for therapeutic effects in experimental autoimmune encephalomyelitis (EAE). Each construct contained the sequences for alphaMSH, as well as the sequences that are involved in the secretion and processing of the POMC gene with the assumption that these sequences would promote processing and release of the encoded alphaMSH peptide. The differences between the two constructs lie at the C-terminal end where amino acids necessary for amidation of alphaMSH were included in only the pACTH1-17 construct. These two constructs were tested in vitro in bioassays, and in vivo in a mouse model of EAE. The results show that although bioactive peptides are secreted from cells transfected with either construct, there appears to be a significant therapeutic effect only with the pACTH1-17 construct which contains the extra C-terminal amino acids. The data suggest that it is possible to engineer DNA expression vectors encoding small secreted peptides such as alphaMSH, and that similar type constructs may be useful as therapeutics for the treatment of inflammatory diseases.

Rheumatoid arthritis susceptibility and interleukin 10: a study of two ethnically diverse populations

INTRODUCTION

IL-10 is an immunoregulatory cytokine which may modulate disease expression in rheumatoid arthritis (RA). The IL-10 gene is highly polymorphic with a number of single nucleotide polymorphisms in the promoter region and two microsatellite loci, IL10.R and IL10.G, 4 kb and 1.1 kb 5' of the transcription initiation site. It has been reported that allele 2 of the IL10.R microsatellite (IL10.R2) is associated with increased IL-10 secretion and IL10.R3 with reduced secretion. Subsequently, over-representation of IL10.R2 and under-representation of IL10.R3 in three independent RA groups has been reported. The aim of the current study is to determine whether there is an association between the IL10.R2 allele and RA in two ethnically distinct populations.

METHODS

IL10.R genotypes were determined by semi-automated DNA sequencing technology in 186 UK Caucasians and 138 South Africans of Zulu or Sotho origin, fulfilling the 1987 American College of Rheumatology (ACR) criteria for RA. The Caucasian patients had relatively severe disease and comprised 75 patients with RA vasculitis, 22 with Felty's syndrome and 89 who had undergone a joint replacement (hip or knee) within 15 years of the onset of disease. Allele frequencies were compared with 296 Caucasians and/or 73 South Africans.

RESULTS

The frequency of the IL10.R2 allele was significantly greater in the South Africans (RA and controls) than in the Caucasians (0.78 vs 0.66, P=1 x 10(-6)), while the frequency of IL10.R3 was less common (0.16 vs 0.3, P=1 x 10(-8)). No differences were observed in either IL10.R2 or IL10.R3 frequencies between patients and controls in either population.

CONCLUSIONS

We were unable to confirm any association between IL10.R alleles and RA in this study. However, significant differences were demonstrated in the frequency of IL10.R2 and IL10.R3 between the two ethnic groups. The relatively high frequency of IL10.R2 in the South African population (0.78) would have reduced the power to detect an association with RA.