Enlarged Similarity of Nucleic Acid Sequences

The concept of nucleic acid sequence base alternations is presented.The number of base alterations for the sequences of differentlength is established. The definition of "enlarged similarity"of nucleic acids sequences on the basis of sequence base alterationsis introduced. Mutual information between sequences is usedas a quantitative measure of enlarged similarity for two comparedsequences. The method of mutual information calculation is developedconsidering the correlation of bases in compared sequences.The definitions of correlated similarity and evolution similaritybetween compared sequences are given. Results of the use ofenlarged similarity approach for DNA sequences analysis arediscussed.     

The distribution of Gossypium hirsutum chromatin in G. barbadense germ plasm: molecular analysis of introgressive plant breeding

Cotton is unusual among major crop plants in that two cross-fertile species are widely cultivated for a common economic product, fiber. Both historical evidence and classical genetic studies suggest that many improved forms of Gossypium barbadense (Sea Island, Egyptian, and Pima cottons) may include chromatin derived from G. hirsutum. Using 106 restriction fragment length polymorphism (RFLP) loci well distributed across the cotton genome, we revealed the amount and genomic distribution of G. hirsutum chromatin in 54 G. barbadense collections from around the world. The average G. barbadense collection was comprised of 8.9% alleles apparently derived from G. hirsutum. Pima cultivars (7.3 %) had fewer G. hirsutum alleles than Sea Island (9.0%) or Egyptian (9.6%) cultivars. G. hirsutum alleles were not randomly distributed, as 57.5% of the total introgression observed was accounted for by five specific chromosomal regions that span less than 10% of the genome. The average length of an introgressed chromosome segment was 12.9 cM. Overlap of introgressed chromatin in different breeding programs hints that retention of these G. hirsutum chromosomal segments may impart a selective advantage to G. barbadense genotypes. Although cluster analysis generally grouped germ plasm from common classes and/or breeding programs together, no 2 genotypes were identical — thus differences in the length and repertoire of introgressed chromosome segments also permit DNA fingerprinting of G. barbadense cultivars.     

Male larval nutrition in Choristoneura rosaceana (Lepidoptera: Tortricidae): an important factor in reproductive success

This study examines how Choristoneura rosaceana male quality, as determined by larval diet, age and mating history, affects the reproductive success of both sexes. While the size of the spermatophore produced at first mating increased linearly with male age, the frequency of mating was significantly higher for middle-aged males (2–4 days old) than younger (0–2 days old) or older (6–8 days old) individuals, when both sexes were fed on artificial diet. However, the duration of copulation was longer in couples with older than younger males. The observed age-related changes in spermatophore size had no significant effect on female longevity, fecundity or fertility, suggesting no direct relationship between male investment and spermatophore size under these experimental conditions. Different larval food sources (artificial diet, maple and hazelnut) did not affect the proportion of 2-day-old virgin males that mated; however, the proportion that remated was significantly higher for males reared on high-quality food (maple and artificial diet) than those on hazelnut, a poorer food source. There was a 5-fold decline in spermatophore size between the first and second matings on all diets, but female reproductive output was reduced by only 25%. In contrast, while the first spermatophore produced by males on hazelnut was 1.5 times smaller than those produced on maple and artificial diet, the fecundity of their mates was 40% less than those mated with high-quality virgin males. These results provide additional support to the idea that spermatophore size is not a valuable indicator of male quality. Most tethered females placed in the field during the first flight period mated with virgin males (based on the size of the spermatophore), suggesting that female choice exists in this species. These results are discussed in relation to the incidence of polyandry in naturally occurring populations of Choristoneura and the potential use of size and/or chemical cues by females to assess male quality.     

Soil microbial diversity and the sustainability of agricultural soils

Many world ecosystems are in various states of decline evidenced by erosion, low productivity, and poor water quality caused by forest clearing, intensive agricultural production, and continued use of land resources for purposes that are not sustainable. The biological diversity of these systems is being altered. Little research has been conducted to quantify the beneficial relationships between microbial diversity, soil and plant quality, and ecosystem sustainability. Ecosystem functioning is governed largely by soil microbial dynamics. Differences in microbial properties and activities of soils have been reported but are restricted to general ecological enumeration methods or activity levels, which are limited in their ability to describe a particular ecosystem. Microbial populations and their responses to stresses have been traditionally studied at the process level, in terms of total numbers of microorganisms, biomass, respiration rates, and enzyme activities, with little attention being paid to responses at the community or the organismal levels. These process level measurements, although critical to understanding the ecosystem, may be insensitive to community level changes due to the redundancy of these functions. As microbial communities comprise complex interactions between diverse organisms, they should be studied as such, and not as a black box into which inputs are entered and outputs are received at measured rates. Microbial communities and their processes need to be examined in relation to not only the individuals that comprise the community, but the effect of perturbations or environmental stresses on those communities.     

An evaluation of ‘rapid review’ as a method of quality control of cervical smears using the AxioHOME microscope

An evaluation of ‘rapid review’ as a method of quality control of cervical smears using the AxioHOME miscroscope One method of quality control which has recently been recommended by professional bodies in the UK is the ‘rapid review’ method. This involves the microscopic 30 s review of all negative cervical smears with the intention of flagging potential missed abnormalities. Although it has been suggested that rapid review is better than 10% random rescreening of negative smears, the efficiency and efficacy of this method of quality control have not been thoroughly evaluated. We have used the AxioHOME system, which can record the area of a slide covered and the screening time, to investigate slide coverage during rapid review quality control, as performed by 15 cytoscreeners and MLSOs reviewing a test set of 22 slides each. The test set comprised 18 negative slides, three positive slides, and one unsatisfactory slide. We have recorded two distinct methods of rapid review in use amongst cytotechnologists, the step method and the whole slide method. The data show that rapid review takes longer on average than the recommended 30 s, the mean screening times being 76 s and 82 s for the step and whole slide methods, respectively. Abnormal smears were missed on three of 15 occasions by the step method (sensitivity 80%, positive predictive value 85%), and on seven of 30 occasions by the whole slide method (sensitivity 76.6%, positive predictive value 45%). However, the 95% confidence intervals were wide (57.7–90.7% for the step method, and 51.9–95.7% for the whole slide method). Analysis of scanning tracks and screening rates shows significant flaws in the methodology of rapid review. Abnormal cells were not identified, although dyskaryotic cells were included in the scanning track on nine occasions, seven using the whole slide method and two using the step method. On one occasion (using the step method) abnormal cells were not identified because they were not included in the scanning track. Further research is in progress to determine optimal methods of rapid review, and whether the rapid review technique is as effective as automated screening systems for quality assurance in cytology. Evaluation de la technique de ‘Relecture Rapide’ comme méthode de contrôle de qualité des frottis cervico-utérins, à l'aide du microscope AxioHOME Une des méthodes de contrôle de qualité récemment recommandée par le corps professionnel du Royaume Uni est la méthode dite de ‘relecture rapide’. Cette méthode consiste en une deuxième lecture d'une durée de trente secondes de tous les frottis cervicaux négatifs et dont l'objectif est de détecter les anomalies ayant pu échapper au premier examen. Bien qu'il ait été suggéré que cette méthode de relecture rapide soit meilleure que la relecture de 10% des frottis négatifs tirés au sort, le rendement et l'efficacité de cette méthode de contrôle de qualité n'ont pas été évalués complètement. Nous avons utilisé le système AxioHOME capable d'enregistrer la plage de la lame qui a été explorée ainsi que le temps de lecture afin d'étudier la surface explorée au cours de cette relecture rapide telle qu'elle a pu être pratiquée par quinze cytotechniciens et MLSOs, chacun ayant relu une série test de vingt deux lames. Cette série test comprenait dix huit lames négatives, trois lames positives et un frottis non satisfaisant. Nous avons noté que les cytotechniciens utilisaient deux méthodes de relecture rapide différentes, la méthode ‘pas à pas’ et la méthode ‘globale’. Les données montrent que la relecture rapide prend, en moyenne, un temps supérieur aux trente secondes recommandées, la moyenne des temps de lecture étant de 76 secondes et de 82 secondes respectivement pour la méthode ‘pas à pas’ et la méthode ‘globale’. Les anomalies n'ont pas été détectées dans trois cas sur quinze par la méthode ‘pas à pas’ (sensibilité 80%, valeur prédictive positive 85%), et dans 7 cas sur 30 par la méthode globale (sensibilité 76,6%, valeur prédictive positive 45%). Toutefois, l'intervalle de confiance à 95% est important (57,7%-90,7% pour la méthode ‘pas à pas’ et 51,9%-95,7% pour la méthode globale). L'analyse des surfaces balayées et des taux de détection montre des points faibles significatifs de cette méthodologie de relecture rapide. Dans 9 cas, les anomalies n'ont pas été identifiées alors que des cellules dyskaryotiques étaient présentes dans les plages balayées au cours de la relecture (sept utilisant la méthode globale et deux utilisant la méthode ‘pas à pas’). Dans un cas (avec la méthode ‘pas à pas’) les cellules anormales n'ont pas été identifiées parce qu'elles étaient absentes des plages de relecture. Des études sont en cours afin de déterminer quelles sont les méthodes optimales de relecture rapide et si ces techniques de relecture rapide sont aussi efficaces que les systèmes de lecture automatisée pour l'assurance de qualité en cytologie cervico-utérine. ‘Rapid Review’ als Methode der Qualitätskontrolle gynäkologischer Abstriche, Überprüfung mit dem AxioHOME-Mikroskop Die empfohlene ‘Rapid Review’ Kontrolle aller negativen Abstriche in nur 30 Sekunden anstelle des Nachscreenens von 10% der Präparate ist in ihrer Zuverlässigkeit bislang nicht überprüft worden. Mit Hilfe des AxioHOME-Mikroskops ist es möglich sowohl die ausgewertete Fläche, als auch die erforderliche Zeit zu erfassen. 15 Auswerter prüften mit der Methode jeweils einen Testsatz von 22 Präparaten. Er enhielt 18 negative, 3 positive und 1 nichtauswertbaren Abstrich. Getestet wurden zwei verschiedene Vorgehensweisen: die schrittweise und die das ganze Präparat erfassende. Beide erfordern mehr Zeit als 30 Sekunden; der mittlere Zeitaufwand betrug für die Schrittmethode 76 und für die Ganzheitsmethode 82 Sekunden. Die Schrittmethode verfehlte 3/15 Anomalien (Sensitivität 80%, positiver prädiktiver Wert 85%), die Ganzheitsmethode 7/30 (Sensitivität 76,6%, positiver prädiktiver Wert 45%). Der 95% Konfi denzbereich reichte für die Schrittmethode von 57,5–90,7% und für die Ganzheitsmethode von 51,9–95,7%). Die Analyse deckt wesentliche Schwachstellen des Rapid Review-Verfahrens auf. In 9 Fällen lagen nicht erkannte Zellatypien in den kontroll ierten Bahnen (7 bei des Schrittmethode, 2 bei der Ganzheitsmethode). Einmal lagen sie bei der Schrittmethode ausserhalb der geprüften Bahnen. Weitere Studien werden prüfen ab das Rapid Review-Verfahren automatisierten Systemen vergleichbar ist.     

Statistical analysis of algal and water quality data

Data on cyanobacteria (blue-green algae) are generallycollected on a reactive basis, frequently in responseto bloom events. Such data presents a biased andincomplete snapshot of water quality. This paper looksat two typical data sets for UK waters showing thatwhile statistics may be used to describe the data theyare of limited use in forecasting. Suggestions ofappropriate tests for small and sparse data sets aremade.     

Construct Validity of the Impact of Weight on Quality of Life Questionnaire

KOLOTKIN, RONETTE L, SUSAN HEAD, ALAN BROOKHART. Construct validity of the Impact of Weight on Quality of Life questionnaire. The Impact of Weight on Quality of Life questionnaire (IWQOL) is a 74-item self-report, condition-specific instrument that (1) assesses the effect of weight on quality of life in eight key areas, and (2) may be used as a treatment outcome measure and/or an evaluation tool for healthcare policy makers and third-party payers. This study explores IWQOL construct validity and provides new information on internal consistency, treatment effects, and differences between men and women. IWQOL total scores correlated highly with other measures of overall quality of life, and subscale scores correlated well with counterparts in the assessment battery. Internal consistency estimates for the IWQOL scales generally were high. For the women, 4-week participants, and the total sample, pretreatment-posttreatment differences were significant for all IWQOL scales and total score. For men, treatment differences were significant for the total score and all subscales except for Work and Mobility. Treatment differences for 2-week participants were significant for all scales except for Work. Consistent with previous IWQOL study results, the Comfort With Food scale scores reflected more discomfort at posttreatment as compared with pretreatment. The IWQOL, already translated into French and Italian, currently is demonstrating clinical and research utility as a quality-of-life outcome measure for clinical trials of antiobesity drugs and surgical treatments for patients with obesity.     

Factors determining the pest status of the rose-grain aphid, Metopolophium dirhodum (Walker), on winter barley in the United Kingdom

To test the hypothesis that early maturation of barley affords it some resistance to cereal aphids, the colonisation, survival, growth, reproduction and emigration of M. dirhodum on barley was measured and compared with previously published results for this aphid on wheat.
Barley plants were colonised as readily as wheat plants. Survival to maturity was similar on both hosts. Relative growth rate was higher on wheat than on barley for most of the season while reproduction was similar on both. Emigration, measured alate production, was significantly higher on mature wheat than on mature barley.
It is proposed that the increase of M. dirhodum populations on barley is normally terminated early in the year directly plant maturation and consequent drying out of the leaves, resulting in the death of aphids. This is different to the situation on wheat, which matures later, and where emigration following plant induced alate induction has been shown to be the major factor affecting the decline in population growth.
These results support the hypothesis that early maturation of barley provides some resistance to M. dirhodum.     

Prolonged aerated hydration for improvement of seed quality in Brassica oleracea L.

Seeds of cauliflower cv. Hipop and Brussels sprouts cv. Asmer Aries were aged at 20% moisture content for 24 h; all seeds retained a germination of over 70% after ageing although the mean germination time increased. Prolonged aerated hydration for up to 32 h at 20°C followed drying resulted in improved performance of both unaged and aged cauliflower seeds and aged Brussels sprouts. Thus, all seed showed reductions in the mean germination time to the extent that after 32 h hydration the aged cauliflower seeds performed as well as high quality unaged seed. The improvement of aged seeds was also revealed an increase in germination after the controlled deterioration test following up to 24 h (cauliflower) or 32 h (Brussels sprouts) aerated hydration. This increase was indicative of a decrease in the extent of deterioration present after aerated hydration. Deleterious effects of prolonged hydration were observed in Brussels sprouts after 32 h although these may be explained desiccation injury after treatment since radicle emergence had occurred during hydration. The improvements in seed performance may be explained the activation of metabolic repair occurring during the early part of the hydration period therereducing the extent of deterioration that has been sustained during ageing, with further improvements due to the advancement of the germination process.     

Frequency modulated sound pattern analysis in the lesser bulldog bat: the role of interactions between adjacent frequency elements of complex sounds

A stereotyped approach phase vocalization response of Noctilio albiventris to artificial echoes simulating a virtual approaching object was used to assess the ability of the bat to analyze and extract distance information from the artificial echoes. The performance of the bats depended on the temporal pattern of frequency change of the continuously sweeping frequency modulated (FM) component of the signals. When the bats were presented with a CF/FM signal containing a time-reversed upward FM sweep, they responded with approach phase behavior at a performance level that was significantly below that seen with a CF/FM signal containing a naturally structured downward FM sweep. When the FM sweep was divided into a series of brief pure tone steps, the extent to which the bats showed a difference in their capability to process upward versus downward FM sweeps depended on the difference in frequency between the pure tone steps. The bats effectively processed downward but not upward FM sweeps when the difference in frequency between pure tone frequency elements of the FM sweeps was from about 100–200 Hz, but they effectually processed both downward and upward FM sweeps when the tonal elements composing the FM sweeps were separated by more than about 200 Hz. This suggests that the ability of the bats to effectively process downward but not upward FM sweeps is based on local interactions between adjacent frequency elements of the complex sounds.Abbreviations CF constant frequency - FM frequency modulated