Electron microscopy of glutamine synthetase from pea leaf chloroplasts

Using electron microscopy, the spatial structure of glutamine synthetase from pea leaf chloroplasts was studied. The enzyme was shown to consist of eight elongated subunits, which are arranged with a point of 42 symmetry at the vertices of two squares. These squares are twisted about a 4-fold axis at 40 degrees relative to each other.     

Robust analysis of covariance

The simple analysis of covariance situation with two groups and one concomitant variable is considered. The parameters of this model with outliers present are estimated by the methods of at least squares and M-estimation. By use of simulation, several forms of M-estimators are compared with the least squares method. In terms of their efficiencies the tests on the equality of slopes and of adjusted means in the presence of outliers are examined under the null hypothesis by studying the behavior of t-like statistics based on the least squares and M-estimates. An example illustrates the techniques discussed.     

An alternating least squares approach to inferring phylogenies from pairwise distances

A computational method is presented for minimizing the weighted sum of squares of the differences between observed and expected pairwise distances between species, where the expectations are generated by an additive tree model. The criteria of Fitch and Margoliash (1967, Science 155:279-284) and Cavalli-Sforza and Edwards (1967, Evolution 21:550-570) are both weighted least squares, with different weights. The method presented iterates lengths of adjacent branches in the tree three at a time. The weighted sum of squares never increases during the process of iteration, and the iterates approach a stationary point on the surface of the sum of squares. This iterative approach makes it particularly easy to maintain the constraint that branch lengths never become negative, although negative branch lengths can also be allowed. The method is implemented in a computer program, FITCH, which has been distributed since 1982 as part of the PHYLIP package of programs for inferring phylogenies, and is also implemented in PAUP*. The present method is compared, using some simulated data sets, with an implementation of the method of De Soete (1983, Psychometrika 48:621-626); it is slower than De Soete's method but more effective at finding the least squares tree. The relationship of this method to the neighbor-joining method is also discussed.     

Nature reserve selection in the Transvaal, South Africa: what data should we be using?

Iterative reserve selection algorithms were applied to two mammal databases, generalized to sixteenth degree grid squares, for the Transvaal region of South Africa. Based on primary point data, 24 grid squares are required to represent all species at least once, while only 13 grid squares are required when based on distribution map data; only two of these grid squares are common to both analyses. As the number of representations per species is increased from one to five, the number of selected grid squares increased to 86 and 71 or 72 respectively, with only 17 of these common to both analyses. These differences in the selection of sites are further reflected in the degree of congruence between selected grid squares and existing conservation areas which is on average 63.3% for grid squares selected from the primary database and only 42.5% for those selected from the distribution map database. These results emphasize the importance of quality data input when evaluating regional reserve networks. Highly generalized distribution map data sets, on the one hand, are extrapolations of limited data sets and contain non-quantifiable levels of false-positives which could have significant implications if used for establishing regional reserve networks. On the other hand, although there are problems associated with the establishment of primary diversity databases, namely data currency and uneven and non-random sampling (leading to false negatives), they remain our most reliable option for assigning conservation value.     

A robust comparison of biological shapes

Localized differences in the form of two related animal skeletons are more effectively determined when resistant fitting techniques are used rather than at least squares. The repeated median resistant fitting algorithm is introduced. The methods are tested by comparing hominid skulls with those of the least squares fit, in that the differences are more readily identified and agree more closely with the structural differences perceived on biological grounds.     

Procedures for comparing samples with multiple endpoints

Five procedures are considered for the comparison of two or more multivariate samples. These procedures include a newly proposed nonparametric rank-sum test and a generalized least squares test. Also considered are the following tests: ordinary least squares, Hotelling's T2, and a Bonferroni per-experiment error-rate approach. Applications are envisaged in which each variable represents a qualitatively different measure of response to treatment. The null hypothesis of no treatment difference is tested with power directed towards alternatives in which at least one treatment is uniformly better than the others. In all simulations the nonparametric procedure provided relatively good power and accurate control over the size of the test, and is recommended for general use. Alternatively, the generalized least squares procedure may also be useful with normally distributed data in moderate or large samples. A convenient expression for this procedure is obtained and its asymptotic relative efficiency with respect to the ordinary least squares test is evaluated.     

Cotton harvest at 40% versus 75% boll-splitting on yield and economic return under standard and proactive boll weevil (Coleoptera: Curculionidae) spray regimes

The standard practice of two or three preemptive insecticide applications at the start of pinhead (1-2-mm-diameter) squaring followed by threshold-triggered (when 10% of randomly selected squares have oviposition punctures) insecticide applications for boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), control does not provide reliable protection of cotton, Gossypium hirsutum L., lint production. This study, conducted during 2004 and 2005, showed that three to six fewer spray applications in a "proactive" approach, in which spraying began at the start of large (5.5-8-mm-diameter) square formation and continued at approximately 7-d intervals while large squares were abundant, resulted in fewer infested squares and 1.4- to 1.7-fold more lint than the standard treatment. Fewer sprays and increased yield made proactive spraying significantly more profitable than the standard approach, which resulted in relatively low or negative economic returns. Harvest at 75% boll-split in the proactive spray regime of 2005 resulted in four-fold greater economic return than cotton harvested at 40% boll-split because of improved protection of large squares and the elimination of late-season sprays inherent to standard spray regime despite the cost of an extra irrigation in the 75% boll-split treatments. The earlier, 40% harvest trigger does not avoid high late-season boll weevil pressure, which exerts less impact on bolls, the predominant form of fruiting body at that time, than on squares. Proactive spraying and harvest timing are based on an important relationship between nutrition, boll weevil reproduction, and economic inputs; therefore, the tactic of combining proaction with harvest at 75% boll-split is applicable where boll weevils are problematic regardless of climate or region, or whether an eradication program is ongoing.     

The visual system of the honeybee (Apis mellifera): the maximum length of the orientation detector

Bees were trained to discriminate between two or more black bars and similar bars at right angles, presented on a vertical surface. The positions of the bars were shifted every 5 min to prevent their locations being used as cues. The experiments exploit the fact that bees do not discriminate the global orientation of a straight line of small black squares that are individually resolved, because the local responses to equal lengths of edges at right angles cancel out, and each square has no residual orientation cue. The experiments measure the resolution of this effect by control of the width of the gaps between the squares. At the limit the unit orientation detectors cannot span the gaps. Training with vertical or with horizontal bars in separate experiments, and testing with vertical or horizontal lines of squares, shows that the vertical gaps in horizontal rows are detected with better resolution than horizontal gaps in vertical rows. The results show that unit orientation detectors span not more than 3 ommatidia.     

Relationships of abscised cotton fruit to boll weevil (Coleoptera: Curculionidae) feeding, oviposition, and development

Abscised cotton, Gossypium hirsutum L., fruit in field plots planted at different times were examined to assess adult boll weevil, Anthonomus grandis grandis Boheman (Coleoptera: Curculionidae), use of squares and bolls during 2002 and 2003 in the Lower Rio Grande Valley of Texas. Although boll abscission is not necessarily related to infestation, generally more bolls abscised than squares and abundances of fallen bolls were not related to the planting date treatments. During 2003, fallen squares were most abundant in the late-planted treatment. Although large squares (5.5-8-mm-diameter) on the plant are preferred for boll weevil oviposition, diameter of abscised squares is not a reliable measurement because of shrinkage resulting from desiccation and larval feeding. Fallen feeding-punctured squares and bolls were most abundant in late plantings but differences between fallen feeding-punctured squares versus fallen feeding-punctured bolls were found in only one treatment in 2003. During the same year, fallen oviposition-punctured squares were more numerous in the late-planted treatment than in the earlier treatments. Treatment effects were not found on numbers of oviposition-punctured bolls, but fallen oviposition-punctured squares were more common than bolls in the late-planted treatment compared with earlier treatments each year. Dead weevil eggs, larvae, and pupae inside fallen fruit were few and planting date treatment effects were not detected. Living third instars and pupae were more abundant in fallen squares of the late-planted treatment than in the earlier treatments and bolls of all three treatments. This study shows that fallen squares in late-planted cotton contribute more to adult boll weevil populations than bolls, or squares of earlier plantings.     

Stochastically Independent Components in the Analysis of Variance

In this paper an analysis of a sum of squares for linear hypothesis in a fixed linear model is presented. The analysis is based on a partition of sum of squares into independent components. These components are treated as sums of squares for hypotheses implied by an overall one. In the special case components of a sum of squares are distributed with one degree of freedom each and hypotheses concern single parametric functions. In the model not of full rank the form of a sum of squares is transformed before partitioning. The case of the model for cross classification is considered in details. Next the cases of the model of full rank and the one with restrictions on parameters are discussed. The model for balanced design with unweighted restrictions on parameters is considered in details. In this case sume of squares for orthogonal contrasts are obtained from analysis of the sum of squares for hypothesis concerning main or interaction effects.     

Progressive bias in species status is symptomatic of fine-grained mapping units subject to repeated sampling

Atlas maps of butterflies invariably fail to distinguish the status of records, that is, whether they are observations of breeding populations or vagrant individuals. Yet, for conservation purposes, it is clearly important to know whether records relate to breeding populations in suitable habitats or not. The high mobility of butterfly adults carries two expectations. First, vagrants will frequently be recorded within grid squares, particularly when mapping is fine grained. Second, the frequency of vagrants is likely to be higher in mapping units comprising biotopes with few butterfly habitats, than in those rich in butterfly habitats, if only because there is a greater regional pool of potential vagrants for biotopes depleted in butterfly habitats. It follows that with repeated sampling of squares or biotopes differences in species breeding status will be cumulative between those rich and poor in butterfly habitats. In this paper, these predictions have been tested using data from 30, 1 ha grid squares on Alderley Edge Site of Special Scientific Interest (SSSI) (UK), half of which are in woodland (few butterfly habitats) and half with open habitats (non-woodland; rich in butterfly habitats). Butterflies have been recorded during 38 visits over 4 years. Within squares, vagrants have been distinguished from breeding species on the basis of the presence of larval hostplants and other suitable resources for seasonal maintenance. Owing to the occurrence of vagrants, number of breeding species was found to be significantly fewer than total species in mapping units. Vagrants were found to be significantly more abundant in woodland squares, which contain few species larval hostplants, than in squares dominated by open biotopes with many species larval hostplants. Repeated sampling resulted in a cumulative increase in the frequency of vagrant species. Furthermore, the relative frequency of vagrants increased at a greater rate in woodland squares compared to non-woodland squares. Suggestions are made as to how recording for atlases may be improved.     

Proactive spraying against boll weevils (Coleoptera: Curculionidae) reduces insecticide applications and increases cotton yield and economic return

The current standard practice of two to three preemptive insecticide applications at the start of pinhead (1-2-mm-diameter) squaring followed by threshold-triggered (whenever 10% of randomly selected squares have oviposition punctures) insecticide applications for boll weevil, Anthonomus grandis grandis Boheman, control does not provide a reliably positive impact on cotton, Gossypium hirsutum L., yields in subtropical conditions. This study showed that four fewer spray applications in a "proactive" approach, where spraying began at the start of large (5.5- 8-mm-diameter) square formation and continued at 7- to 8-d intervals while large squares were abundant, resulted in fewer infested squares and 46-56% more yield than the standard treatment at two locations during 2004. The combination of fewer sprays and increased yield made the proactive approach 115-130% more profitable than the standard. The proactive approach entails protection only at the crop's most vulnerable stage (large squares) that, as a source of food, accelerates boll weevil reproduction. In contrast, the standard approach protects early season small squares and later season bolls, both of which contribute less to boll weevil reproduction than large squares. Proaction is an in-season crop protection approach that can be used to increase yield in individual fields during the same season and that could be incorporated into boll weevil eradication strategy that involves later diapause sprays. Because proaction is based on an important relationship between the cotton plant and boll weevil reproduction, the tactic will probably be effective regardless of climate or region.     

Quantitative description of cell cycle kinetics under chemotherapy utilizing flow cytometry.

A discrete time cell cycle kinetics model is developed to account for the effects of cytotoxic chemotherapy, particularly including the existence of cells destined to die. A model structure is determined from related experiments, leaving key parameter values undetermined. These values are found by determining the best least squares fit of the predicted to the observed DNA distribution data at a series of time intervals. The numerical methods include separable least squares, linear inequality constrained least squares and the Gauss--Newton method. This approach is applied to an experiment in which the Ehrlich ascites tumour was given a single dose of bleomycin. The results include several different parameters, including the age response function and a time series of cell age and DNA distributions, which can be used as a basis for further treatment.     

Bias in Butterfly Distribution Maps: The Influence of Hot Spots and Recorder's Home Range

We use data from the Mersey Valley zone (3×2km area; N = 600Iha squares) of the Greater Manchester butterfly atlas to investigate whether recorder visits are biased by access (viz. distance from recorder's home base) and by the locations of potential hot spots. In a multiple regression analysis, visits were found to correlate significantly both with distance from home base of the recorder and with the mean and maximum number of species found in squares. Sites close to the home base of the recorder were visited more frequently than those further afield and squares with more species were visited more frequently than those squares with fewer species. Visits were also made significantly more frequently to squares with greater numbers of butterfly resources (e.g. hostplants, nectar). Furthermore, recording is biased to and away from distinct land uses, which vary significantly in species richness. Reasons are given why these biases are to be expected at all scales. The message is that future distribution mapping should be based on rigorous sampling approaches.     

Least squares regression methods for clustered ROC data with discrete covariates

The receiver operating characteristic (ROC) curve is a popular tool to evaluate and compare the accuracy of diagnostic tests to distinguish the diseased group from the nondiseased group when test results from tests are continuous or ordinal. A complicated data setting occurs when multiple tests are measured on abnormal and normal locations from the same subject and the measurements are clustered within the subject. Although least squares regression methods can be used for the estimation of ROC curve from correlated data, how to develop the least squares methods to estimate the ROC curve from the clustered data has not been studied. Also, the statistical properties of the least squares methods under the clustering setting are unknown. In this article, we develop the least squares ROC methods to allow the baseline and link functions to differ, and more importantly, to accommodate clustered data with discrete covariates. The methods can generate smooth ROC curves that satisfy the inherent continuous property of the true underlying curve. The least squares methods are shown to be more efficient than the existing nonparametric ROC methods under appropriate model assumptions in simulation studies. We apply the methods to a real example in the detection of glaucomatous deterioration. We also derive the asymptotic properties of the proposed methods.     

Influence of cotton fruit stages as food sources on boll weevil (Coleoptera: Curculionidae) fecundity and oviposition

Boll weevil, Anthonomus grandis grandis Boheman (Coloeoptera: Curculionidae), populations in the Lower Rio Grande Valley of Texas increase strongly during the squaring stage, and preemptive insecticide sprays at the pinhead square stage were designed to capitalize on that association. Laboratory assays showed that cotton plant volatiles, or leaves as a food source, do not elicit egg production in wild weevils. Boll weevils fed on large (5.5-8-mm diameter) squares for 7 d resulted in > or = 3.8-fold more gravid females that developed 4.8-fold more chorionated eggs per female than weevils fed on match-head-sized squares, or postbloom, young (5-10-d-old), or old (3-5-wk-old) bolls. When presented with a choice, nongravid females preferred to feed on young and old bolls 4.7- and 8.4-fold more, respectively, than on large squares. In the field, large squares had 7.8- and 25-fold more feeding punctures than match-head-sized squares and bolls, respectively. Oviposition increased > or = 2.7-fold when females fed on large squares compared with match-head-sized squares and bolls. Greater feeding on large squares during squaring and the associated greater fecundity explain rapid weevil population buildups shortly after large squares become well established.     

Loss rates of butterfly species with urban development. A test of atlas data and sampling artefacts at a fine scale

Data for the United Kingdom (UK) Manchester Butterfly Atlas produced conflicting species loss rates for increased urban development. In particular, a very low rate of loss was recorded (0.19 species for every 10% increase in urban cover) for the Mersey Valley mapped at a high resolution of 1 ha units. It was suggested that sampling artefacts (uneven recording) or failure to distinguish vagrant individuals from breeding populations cause this. Herein, results are reported for 30 sample squares, within the Mersey Valley, surveyed uniformly throughout 1999. It is shown that loss rates are as high as areas mapped at lower resolution over wider areas (0.67–0.68 species for every 10% increase in urban cover) and that increasingly stringent definitions of urban cover result in higher loss rates. Comparison with the data from the Atlas, but for the same 30 sample squares, indicate that the low rates at a fine scale for the complete Atlas data are more likely to be caused by uneven recording than from failure to record species status. However, progressive sampling of squares, despite uniform recording, will inevitably cause a reduction in loss rates of total species for increases in urban development.     

Quantitative Description of Cell Cycle Kinetics Under Chemotherapy Utilizing Flow Cytometry

A discrete time cell cycle kinetics model is developed to account for the effects of cytotoxic chemotherapy, particularly including the existence of cells destined to die. A model structure is determined from related experiments, leaving key parameter values undetermined. These values are found by determining the best least squares fit of the predicted to the observed DNA distribution data at a series of time intervals. the numerical methods include separable least squares, linear inequality constrained least squares and the Gauss-Newton method. This approach is applied to an experiment in which the Ehrlich ascites tumour was given a single dose of bleomycin. the results include several different parameters, including the age response function and a time series of cell age and DNA distributions, which can be used as a basis for further treatment.     

Effects of kaolin-based particle film application on boll weevil (Coleoptera: Curculionidae) injury to cotton

This study examined a non-insecticidal tactic for suppressing boll weevil, Anthonomus grandis grandis Boheman, damage to cotton, Gossypium hirsutum L. In cage assays, kaolin, a reflective white mineral, applied to excised cotton squares or to the cotton foliage, initially resulted in lower levels of boll weevil injury to squares than nontreated squares. Boll weevil oviposition and feeding on kaolin-treated squares and squares on kaolin-treated cotton plants increased when nontreated squares and cotton plants were in short supply. A laboratory assay and field trials suggested that boll weevils distinguished between cotton plots based on color differences caused by kaolin and this appeared to influence levels of damage to squares. Random sampling in small plots indicated that oviposition damage to squares in plots treated with kaolin was reduced (P < 0.05) compared with nontreated controls, except when rain washed the kaolin off the foliage. Lint yield differences were not detected between the small plots, but the kaolin-treated small plots yielded as much as 2.36 times more cotton lint than a large but unreplicated adjacent nontreated control plot, and up to 1.39 times more than another large but unreplicated adjacent plot sprayed twice with preemptive applications of azinphosmethyl when cotton squares were first developing (pinhead stage). Potentially important avenues for future research on boll weevil injury suppression using kaolin are discussed.     

Expanding ranges of wild and feral deer in Great Britain

1. It is often stated that wild deer in Great Britain are increasing in range and number. This study presents the first quantified estimate of national range expansion for all six species. From national surveys of deer presence in 10 km squares between 1972 and 2002, the red deer range is estimated to have expanded at a compound rate of 0.3% per year, fallow deer at 1.8%, Chinese water deer at 2.0%, roe deer at 2.3%, Japanese sika at 5.3% and Reeves’ muntjac at 8.2%. 2. Each species is expected to expand its range further for the foreseeable future. The most widespread species, roe deer, is predicted to be present within 79% of all 10 km squares in mainland Britain within 10 years. 3. Deer range expansion brings a combination of benefits and costs, and some degree of management is considered necessary to limit both environmental damage and deer suffering.