Molecular analysis of the Drosophila miniature-dusky ( m-dy) gene complex: m-dy mRNAs encode transmembrane proteins with similarity to C. elegans cuticulin

Mutations in the Drosophila miniature-dusky ( m-dy) gene complex were first reported by Morgan and Bridges about 90 years ago. m-dy mutants have abnormally small wings, a phenotype attributed to a cell-autonomous reduction in the size of the epidermal cells comprising the differentiated wing. Using a molecular genetic approach, we have characterized the m-dy chromosomal interval and identified a pair of adjacent transcription units corresponding to m and dy. A dy mutant known as dy (And) has a single base substitution within the protein-coding region that is predicted to result in an amber stop codon and premature translational termination. We show that dy mRNA is expressed at two discrete periods during the life cycle--one during embryonic development and early larval instars, the second during adult development, coincident with wing differentiation. In agreement with the phenotypic similarity of m and dy mutants, sequence comparisons reveal a similarity between the predicted MINIATURE and DUSKY proteins, and indicate that the m and dy genes are members of a larger Drosophila gene family. Both m and dy, as well as other members of this superfamily, are predicted to encode transmembrane proteins with similarity to C. elegans cuticle proteins known as cuticulins. We postulate that m, dy and other members of this protein superfamily function as structural components of the Drosophila cuticulin layer. Such a role for m and dy products in wing differentiation is sufficient to explain the morphological phenotypes associated with m-dy mutants.

Microarray data analysis: a practical approach for selecting differentially expressed genes

BACKGROUND

The biomedical community is rapidly developing new methods of data analysis for microarray experiments, with the goal of establishing new standards to objectively process the massive datasets produced from functional genomic experiments. Each microarray experiment measures thousands of genes simultaneously producing an unprecedented amount of biological information across increasingly numerous experiments; however, in general, only a very small percentage of the genes present on any given array are identified as differentially regulated. The challenge then is to process this information objectively and efficiently in order to obtain knowledge of the biological system under study and by which to compare information gained across multiple experiments. In this context, systematic and objective mathematical approaches, which are simple to apply across a large number of experimental designs, become fundamental to correctly handle the mass of data and to understand the true complexity of the biological systems under study.

RESULTS

The present report develops a method of extracting differentially expressed genes across any number of experimental samples by first evaluating the maximum fold change (FC) across all experimental parameters and across the entire range of absolute expression levels. The model developed works by first evaluating the FC across the entire range of absolute expression levels in any number of experimental conditions. The selection of those genes within the top X% of highest FCs observed within absolute expression bins was evaluated both with and without the use of replicates. Lastly, the FC model was validated by both real time polymerase chain reaction (RT-PCR) and variance data. Semi-quantitative RT-PCR analysis demonstrated 73% concordance with the microarray data from Mu11K Affymetrix GeneChips. Furthermore, 94.1% of those genes selected by the 5% FC model were found to lie above measurement variability using a SDwithin confidence level of 99.9%.

CONCLUSION

As evidenced by the high rate of validation, the FC model has the potential to minimize the number of required replicates in expensive microarray experiments by extracting information on gene expression patterns (e.g. characterizing biological and/or measurement variance) within an experiment. The simplicity of the overall process allows the analyst to easily select model limits which best describe the data. The genes selected by this process can be compared between experiments and are shown to objectively extract information which is biologically & statistically significant.

Semantic processing in visual word recognition: activation blocking and domain specificity

Lexical decision to a target is typically facilitated when a related prime is simply read, but is typically eliminated if subjects carry out a letter search on the prime when probe and prime appear simultaneously. Three experiments involving the addition of a task-irrelevant word to this prime search paradigm address (1) Stolz and Besner's (1996, 1998) account in which semantic priming is eliminated because letter search on the prime instantiates an activation block between lexical and semantic levels of representation, (2) Chiappe, Smith, and Besner's (1996) account that activation blocking is domain specific, and (3) Neely and Kahan's (2001) claim that semantic activation is context independent and capacity free. The results are (1) consistent with the account that activation blocking is general to a level, rather than item specific, (2) consistent with the account that activation blocking is domain specific, and (3) inconsistent with the claim that semantic activation is context independent and capacity free.

Protein energy supplements in unwell elderly patients--a randomized controlled trial

BACKGROUND

To determine whether oral protein energy supplements, prescribed during hospitalization to elderly medical admissions, affect nutritional status and if baseline nutritional state influences this status. We also considered the effects on mortality, length of hospital stay, functional recovery, and institutionalization.

METHODS

A prospective randomized controlled trial with no placebo. Consenting patients were stratified in 3 nutritional categories, and patients from each stratum were randomized into treatment or control. Observers were blinded to randomization. The participants were emergency admissions from home to a Medicine for the Elderly Unit in a Scottish hospital. The inclusion criteria were as follows: no known malignancy, the ability to swallow, and nonobesity (BMI < 75th percentile). The intervention was a prescription of 120 mL sip feed, 3 times daily (540 kcal, 22.5 g protein per day) throughout hospitalization, using the medicine prescription chart. The trial was powered to detect change in mean percentage weight. The following outcomes were also considered: anthropometry; mortality, length of hospital stay, functional recovery, and rates of institutionalization.

RESULTS

Included in the trial were 381 patients. Nutritional supplementation was associated with significantly better energy intake (p = .001) and weight gain (p = .003) pooled across all nutritional categories. In the most poorly nourished patients, the intervention was associated with reduced mortality (5/34 versus 14/40, p < .05) and more patients improved functionally (17/25 versus 11/28, p < .04). Overall mortality results were 21/186 versus 33/195, odds ratio (OR) 0.62, 95% confidence interval (CI) 0.35, 1.13.

CONCLUSIONS

Prescribing sip feed supplements in the medicine prescription chart during hospital stay reduces weight loss. Our data also support other evidence for a reduction in mortality noted in elderly patients on nutritional supplementation. There were suggestions of other clinical benefits.

Genomics: food and nutrition

Nutrition is traditionally a multidisciplinary field applying principles of molecular biochemistry and statistical epidemiology to integrative metabolism and population health. Genomics, with its global perspective, is now reinventing the future of human metabolic health. Creative experimental designs are addressing metabolic questions in nutrition ranging from energy regulation to aging, and from mechanisms of absorption to the interspecies molecular crosstalk of bacteria and human cells within the intestine.

Genetic analysis of functional domains within the Drosophila LARK RNA-binding protein

LARK is an essential Drosophila RNA-binding protein of the RNA recognition motif (RRM) class that functions during embryonic development and for the circadian regulation of adult eclosion. LARK protein contains three consensus RNA-binding domains: two RRM domains and a retroviral-type zinc finger (RTZF). To show that these three structural domains are required for function, we performed a site-directed mutagenesis of the protein. The analysis of various mutations, in vivo, indicates that the RRM domains and the RTZF are required for wild-type LARK functions. RRM1 and RRM2 are essential for viability, although interestingly either domain can suffice for this function. Remarkably, mutation of either RRM2 or the RTZF results in the same spectrum of phenotypes: mutants exhibit reduced viability, abnormal wing and mechanosensory bristle morphology, female sterility, and flightlessness. The severity of these phenotypes is similar in single mutants and double RRM2; RTZF mutants, indicating a lack of additivity for the mutations and suggesting that RRM2 and the RTZF act together, in vivo, to determine LARK function. Finally, we show that mutations in RRM1, RRM2, or the RTZF do not affect the circadian regulation of eclosion, and we discuss possible interpretations of these results. This genetic analysis demonstrates that each of the LARK structural domains functions in vivo and indicates a pleiotropic requirement for both the LARK RRM2 and RTZF domains.

Separation of iota-, kappa and lambda-carrageenans by capillary electrophoresis

The present study reports a novel method for the separation of the high-molecular-weight anionic polysaccharides, iota, kappa, and lambda carrageenans, in capillary electrophoresis (CE). Carrageenan samples are first derivatised with 9-aminopyrene-1,4,6-trisulfonic acid (APTS), separated in an ammonium acetate background electrolyte (BGE) and detected with laser-induced fluorescence (LIF). The effects of changes of instrumental parameters (temperature, injection mode, field strength) and the composition of the BGE (concentration and pH) are reported, and are explained in terms of the physical chemistry of the BGE and the biopolymers. Optimal separation conditions for kappa, iota, and lambda carrageenans, including an APTS internal standard, were found in a polyvinyl alcohol coated capillary with an ammonium acetate BGE of low concentration (25 mM) and moderate pH (8.0). This BGE gave the best reproducibility in tests on iota/kappa mixtures, with relative standard deviations (RSDs) in migration times and normalised peak areas (relative to the APTS internal standard) of less than 0.1% and 1%, respectively. Using this BGE at 50 degrees C and a voltage of 30 kV, all three carrageenan subtypes were separated in a run time of 3 min.

Use of randomly amplified polymorphic DNA as a means of developing genus- and strain-specific Streptomyces DNA probes

We have analyzed 20 randomly amplified polymorphic DNA (RAPD) primers against 36 Streptomyces strains, including 17 taxonomically undefined strains, 25 nonstreptomycete actinomycetes, and 12 outgroups consisting of gram-positive and -negative species. Most of the primers were useful in identifying unique DNA polymorphisms of all strains tested. We have used RAPD techniques to develop a genus-specific probe, one not necessarily targeting the ribosomal gene, for Streptomyces, and a strain-specific probe for the biological control agent Streptomyces lydicus WYEC108. In the course of these investigations, small-scale DNA isolations were also developed for efficiently isolating actinomycete DNA. Various modifications of isolation procedures for soil DNA were compared, and the reliability and specificity of the RAPD methodology were tested by specifically detecting the S. lydicus WYEC108 in DNA isolated from soil.

Predictors of adult height and weight in boys treated with methylphenidate for childhood behavior problems

OBJECTIVE

To examine associations between childhood treatment with methylphenidate (MPH) and adult height and weight.

METHOD

Subjects were 97 boys, aged 4 to 12 years, with behavior problems who were (1) referred to a child psychiatry outpatient clinic, (2) treated clinically with MPH for an average of 36 months, and (3) reevaluated between ages 21 and 23 years. Hierarchical analyses predicted adult height and weight from sets of non-medication and medication-related variables.

RESULTS

Medicated subjects' age, height, and parental socioeconomic status (SES) at referral predicted 44.8% of variation in adult height. Medicated subjects' birth weight, age, height and weight at referral, and parental SES predicted 61.8% of variation in adult weight. With these non-medication variables held constant, initial nausea and vomiting side effects predicted 4.4% incremental variation in adult height, and MPH maintenance dose predicted 3.2% incremental variation in adult weight.

CONCLUSIONS

Medicated individuals who had attained their final stature did not differ in average height or weight from family, community, or unmedicated controls. Most aspects of medication were not associated with adult height or weight. In some individuals, nausea and vomiting side effects and treatment with higher doses of MPH were associated with adult growth decrements.

Cryosolvents useful for protein and enzyme studies below -100 degrees C

For the study of protein structure, dynamics, and function, at very low temperatures it is desirable to use cryosolvents that resist phase separation and crystallisation. We have examined these properties in a variety of cryosolvents. Using visual and X-ray diffraction criteria, methanol:ethanediol (70%:10%), methanol:glycerol (70%:10%), acetone:methoxy-ethanol:ethanediol (35%:35%:10%), dimethylformamide:ethanediol (70%:10%), dimethylformamide (80%), methoxyethanol (80%), and methoxyethanol:ethanediol (70%:10%) were all found to be free of phase-changes down to at least -160 degrees C. The least viscous of these, methanol:ethanediol (70%:10%), was miscible down to -125 degrees C and showed no exo or endothermic transitions when examined using DSC. It is therefore potentially particularly suitable for very low temperature cryoenzymology.

The use of cyclic voltammetry for the evaluation of antioxidant capacity

Low-molecular weight antioxidants (LMWAs) play a major role in protecting biological systems against reactive oxygen-derived species and reflect the antioxidant capacity of the system. Cyclic voltammetry (CV), shown to be convenient methodology, has been validated for quantitation of the LMWA capacity of blood plasma, tissue homogenates, and plant extracts. Analysis of the CV tracing yields the values of (i) the biological oxidation potential, E and E(1/2), which relate to the nature of the specific molecule(s); (ii) the intensity (Ia) of the anodic current; and (iii) the area of the anodic wave (S). Both Ia and S relate to the concentration of the molecule(s). LMWA components of human plasma and animal tissues were identified and further validated by reconstruction of the CV tracing and by high-performance liquid chromatography-electrochemical detection. To reflect the oxidative stress status, the use of an additional parameter, R, has been proposed. R represents the level (%) of oxidized ascorbate (compared with total ascorbate) and is measured by high-performance liquid chromatography-electrochemical detection. All these parameters were monitored in healthy human subjects as well as in chronic (diabetes mellitus) and acute care patients (subjected to total body irradiation before bone marrow transplantation). The electroanalytical methodologies presented here could be widely employed for rapid evaluation of the status of subjects (in health and disease) for monitoring of their response to treatment and/or nutritional supplementation as well as for screening of specific populations.

Organisation of services for acute stroke in Scotland--report of the Scottish stroke services audit

An audit was undertaken of hospital service provision for acute strokes in Scotland, using as a template key recommendations in the four SIGN guidelines on management of stroke. A questionnaire and structured interview was undertaken of key personnel in the 43 Trusts and three directly managed units providing in-patient stroke care in Scotland, and the 15 Health Boards commissioning stroke care. All Trusts and Health Boards participated and a complete set of information for each was recorded on a data-base and analysed. This report gives an overview for 14 key components of an integrated stroke service with results presented in four bands according to Trust type determined by the number of strokes admitted. No Trust provided all key components and for a few components a lack of provision was widespread, e.g. fast-track assessment clinics for TIA and minor stroke, access to CT scanning within 48 hours. Variation occurred between Trusts of similar size, between Trusts of different sizes. Overall the Health Boards were at a preliminary stage in the development of stroke specific service specifications. The results of the audit are a view of stroke services around April 1998, and should enable commissioners and providers to consider how to progress implementation of the clinical guidelines on stroke care.

Induction and characterization of Ph1 wheat mutants

The cloning of genes for complex traits in polyploid plants that possess large genomes, such as hexaploid wheat, requires an efficient strategy. We present here one such strategy focusing on the homologous pairing suppressor (Ph1) locus of wheat. This locus has been shown to affect both premeiotic and meiotic processes, possibly suggesting a complex control. The strategy combined the identification of lines carrying specific deletions using multiplex PCR screening of fast-neutron irradiated wheat populations with the approach of physically mapping the region in the rice genome equivalent to the deletion to reveal its gene content. As a result, we have located the Ph1 factor controlling the euploid-like level of homologous chromosome pairing to the region between two loci (Xrgc846 and Xpsr150A). These loci are located within 400 kb of each other in the rice genome. By sequencing this region of the rice genome, it should now be possible to define the nature of this factor.

An extraretinally expressed insect cryptochrome with similarity to the blue light photoreceptors of mammals and plants

Photic entrainment of insect circadian rhythms can occur through either extraretinal (brain) or retinal photoreceptors, which mediate sensitivity to blue light or longer wavelengths, respectively. Although visual transduction processes are well understood in the insect retina, almost nothing is known about the extraretinal blue light photoreceptor of insects. We now have identified and characterized a candidate blue light photoreceptor gene in Drosophila (DCry) that is homologous to the cryptochrome (Cry) genes of mammals and plants. The DCry gene is located in region 91F of the third chromosome, an interval that does not contain other genes required for circadian rhythmicity. The protein encoded by DCry is approximately 50% identical to the CRY1 and CRY2 proteins recently discovered in mammalian species. As expected for an extraretinal photoreceptor mediating circadian entrainment, DCry mRNA is expressed within the adult brain and can be detected within body tissues. Indeed, tissue in situ hybridization demonstrates prominent expression in cells of the lateral brain, which are close to or coincident with the Drosophila clock neurons. Interestingly, DCry mRNA abundance oscillates in a circadian manner in Drosophila head RNA extracts, and the temporal phasing of the rhythm is similar to that documented for the mouse Cry1 mRNA, which is expressed in clock tissues. Finally, we show that changes in DCry gene dosage are associated predictably with alterations of the blue light resetting response for the circadian rhythm of adult locomotor activity.

The epidemiology of women's rugby injuries

OBJECTIVE

The purpose of this study was to identify all injuries to members of an elite women's rugby team and to compare these injuries with published data on injuries in other women's contact and collision sports.

DESIGN

This was a prospective cohort observational study conducted using a monthly log completed by the team's certified athletic therapist to closely monitor attendance at practices and games along with the type and severity of injuries.

SETTING

Rugby games and practices held in Ontario, Quebec, and the Netherlands.

PARTICIPANTS

Forty members of the Ontario Women's Senior Provincial Rugby Team over the 1997 season and the 1998 World Championships.

MAIN OUTCOME MEASURES

An injury was defined as a rugby-related event that kept a player out of practice or competition for >24 hours or required the attention of a physician (e.g., suturing lacerations) and in addition included all dental, eye, and nerve injuries and concussions.

RESULTS

There were a total of 35 injuries in 4,958 player-hours and 2,926 athletic exposures. This resulted in a rugby injury rate of 7.1+/-0.4 per 1,000 player-hours and 12.0+/-2 per 1,000 athletic exposures.

CONCLUSION

The incidence of injuries in women's rugby is comparable with that in other women's contact and collision sports, indicating that the sport may be safer than stated in the literature and media.

Biogenesis and biological function of marine algal oxylipins

The biogenetic source of most marine algal oxylipins, which are many and of diverse structure, can logically be unified through a common lipoxygenase-derived hydroperoxide to epoxy allylic carbocation transformation. The biological role of oxylipins in algae remains an enigma, although numerous ideas have been put forth. Herein, we hypothesize and provide some evidence for an osmoregulatory role for these metabolites.

Serological response to influenza vaccination and nutritional and functional status of patients in geriatric medical long-term care

INTRODUCTION

in the UK the Department of Health recommends influenza vaccination for elderly people resident in institutional care. However, the efficacy of vaccination may be reduced in very frail elderly people with functional impairment, undernutrition and multiple pathologies. Nutritional and functional status is claimed to affect vaccine responses in healthy elderly subjects. We wished to determine if a relationship could be seen between nutritional and functional status and seroconversion in patients receiving long- term care.

METHODS

all patients in geriatric medical long-term care were offered vaccine. Consenting patients had pre- and post-vaccine serology measured using single radial haemolysis. Anthropometry was measured to enable body mass index (BMI) to be calculated. Functional independence was assessed using the 20-point Barthel index.

RESULTS

of 260 patients who received influenza vaccine, 137 (36 male, 101 female) consented to venesection for serology and thus form the study population. Mean age was 82 years (SD 7.9). The median Barthel score was 3/20 and the mean BMI was 21.6 (SD 4.6, range 13-36.2). Antibodies to influenza A were undetectable both pre- and post-vaccination in 63/137 patients. In 49 patients the antibody titre rose after vaccination and 25 had detectable antibody titres pre-vaccination which failed to rise post-vaccine. There were no significant associations between post-vaccination influenza antibody responses and BMI, Barthel score or age.

CONCLUSION

frail elderly patients in geriatric medical long-term care had a poor antibody response to influenza vaccination. Within this group, serological responses could not be predicted by nutritional or functional status.

Cognitive outcome in children and adolescents following severe traumatic brain injury: influence of psychosocial, psychiatric, and injury-related variables

Previous studies of childhood traumatic brain injury (TBI) have emphasized injury-related variables rather than psychiatric or psychosocial factors as correlates of cognitive outcomes. We addressed this concern by recruiting a consecutive series (N = 24) of children age 5 through 14 years who suffered a severe TBI, a matched group who sustained a mild TBI, and a second matched group who sustained an orthopedic injury. Standardized intellectual, memory, psychiatric, family functioning, family psychiatric history, neurological, and neuroimaging assessments were conducted at an average of 2 years following injury. Severe TBI, when compared to mild TBI and orthopedic injury, was associated with significant decrements in intellectual and memory function. A principal components analysis of independent variables that showed significant (p < .05) bivariate correlations with the outcome measures yielded a neuropsychiatric factor encompassing severity of TBI indices and postinjury psychiatric disorders and a psychosocial disadvantage factor. Both factors were independently and significantly related to intellectual and memory function outcome. Postinjury psychiatric disorders added significantly to severity indices and family functioning and family psychiatric history added significantly to socioeconomic status in explaining several specific cognitive outcomes. These results may help to define subgroups of children who will require more intensive services following their injuries.

Angular resolution of parallel foils on a synchrotron powder diffractometer

In an attempt to improve the resolution in flat-plate diffraction geometry, a new set of parallel foils, 100 microm spacing, 365 mm long with an aperture of 20 x 20 mm(2), has been commissioned. The study was carried out using the two-circle diffractometer of station 2.3 at the SRS. In order to properly quantify the improvements, a detailed and comparative study of the instrumental resolution using the new and existing foils, of 200 micron spacing, is reported. A number of cubic materials, BaF2, Si and CeO2, that are known to show well defined Bragg peaks over the full 2theta angular range available, were investigated.

Small-scale isolation of genomic DNA from Streptomyces mycelia or spores

We have developed a small-scale method for isolating high-quality chromosomal DNA from Streptomyces species. The entire procedure may be carried out in 2-mL microcentrifuge tubes in one day. It has been tested both quantitatively and qualitatively to ensure reliability and reproducibility. DNA yields from a variety of Streptomyces species ranged from 30 micrograms DNA/50 mg cells to over 225 micrograms DNA/50 mg cells. We used the method to isolate DNA from cells grown in liquid culture, on solid media and from spore suspensions. DNA yields and quality were assessed by spectrophotometry, restriction endonuclease digestion and random-amplified polymorphic DNA-PCR (RAPD-PCR) analysis. These confirmed that this procedure is an efficient method for isolating large amounts of high-quality DNA from a wide range of Streptomyces species.

A simple PCR-based method for scoring the ph1b deletion in wheat

The amplified fragment length polymorphism (AFLP) technique was used to isolate DNA sequences present in the euploid wheat Chinese Spring but not in the Chinese Spring ph1b mutant (which has a deletion of the Ph1 gene, a suppressor of homoeologous chromosome pairing). The polymorphic DNA fragments identified by AFLP were then cloned, sequenced, and used to design two primer pairs. These primers were used in a PCR-based assay to specifically amplify products from the Chinese Spring euploid but not from the ph1b mutant. This PCR assay can be carried out from extracted genomic DNA or directly from alkaline-treated wheat leaves, and the reaction products can be scored on a plus-minus basis, making the screening amenable to automation. The reliability of the assay was tested using a F1-derived doubled-haploid population of 55 lines which segregate for the ph1b deletion. This PCR-screening technique is less time and labour consuming, and more accurate and reliable, than cytologically based conventional methods.

Redefining reductive sulfate assimilation in higher plants: a role for APS reductase, a new member of the thioredoxin superfamily?

The reaction steps leading from the intermediate adenosine 5'-phosphosulfate (APS) to sulfide within the higher plant reductive sulfate assimilation pathway are the subject of controversy. Two pathways have been proposed: a 'bound intermediate' pathway in which the sulfo group of APS is first transferred by APS sulfotransferase to a carrier molecule to form a bound sulfite intermediate and is then further reduced by thiosulfonate reductase to bound sulfide; and a 'free intermediate' pathway in which APS is further activated to 3'-phosphoadenosine 5'-phosphosulfate (PAPS) by APS kinase followed by reduction of the sulfo group to free sulfite by PAPS reductase. Sulfite is then reduced to free sulfide by sulfite reductase. Sulfide, either free or bound, is then incorporated into organic form (as cysteine) by the enzyme O-acetylserine (thiol) lyase. In order to better characterize the pathway we attempted to clone PAPS reductase cDNAs by functional complementation of an Escherichia coli cysH mutant to prototrophy. We found no evidence for PAPS reductase cDNAs but did identify cDNAs that encode a small family of novel, chloroplast-localized proteins with APS reductase activity that are new members of the thioredoxin superfamily. We show here that the thioredoxin domain of these proteins is functional. We speculate that rather than proceeding via either of the pathways proposed above, reductive sulfate assimilation proceeds via the reduction of APS to sulfite by APS reductase and the subsequent reduction of sulfite to sulfide by sulfite reductase. In this scheme the product of the APS kinase reaction, PAPS, is not a direct intermediate in the pathway but rather acts as a substrate for sulfotransferase action and perhaps as a store of activated sulfate that can be returned to the pathway as APS via phosphohydrolase action on PAPS. Interactions between enzyme isoforms within the chloroplast stroma may bring about substrate channeling of APS and contribute to the partitioning of APS between sulfotransferase reactions on the one hand and the synthesis of cysteine and related metabolites via the reductive sulfate assimilation pathway on the other.