A new approach to graphical analysis of feeding strategy from stomach contents data—modification of the Costello (1990) method

A modification of the graphical Costello method is proposed for the analysis of stomach contents data. The new method allows prey importance, feeding strategy and the interand intra-individual components of niche width to be explored using graphical presentation. The analysis is based on a two-dimensional representation of prey-specific abundance and frequency of occurrence of the different prey types in the diet. The paper describes the new method and the parameters therein, and also present some examples of the utilization of the method. The method may be particularly well-suited for the examination of predictions made from optimal foraging, competition and niche theories.     

Statistical uncertainty and its propagation in the analysis of quantitative polymerase chain reaction data: Comparison of methods

Most methods for analyzing real-time quantitative polymerase chain reaction (qPCR) data for single experiments estimate the hypothetical cycle 0 signal y₀ by first estimating the quantification cycle (C_q) and amplification efficiency (E) from least-squares fits of fluorescence intensity data for cycles near the onset of the growth phase. The resulting y₀ values are statistically equivalent to the corresponding C_q if and only if E is taken to be error free. But uncertainty in E usually dominates the total uncertainty in y₀, making the latter much degraded in precision compared with C_q. Bias in E can be an even greater source of error in y₀. So-called mechanistic models achieve higher precision in estimating y₀ by tacitly assuming E = 2 in the baseline region and so are subject to this bias error. When used in calibration, the mechanistic y₀ is statistically comparable to C_q from the other methods. When a signal threshold y_q is used to define C_q, best estimation precision is obtained by setting y_q near the maximum signal in the range of fitted cycles, in conflict with common practice in the y₀ estimation algorithms.     

Size and shape analysis of mineral resources in arroyo willow and their relation to sawfly densities

The association between host-plant mineral nutrients and insect herbivory is complex, idiosyncratic, and dynamic. Because of this we employed an unusual statistical method to evaluate the relationship between tenthredinid sawfly herbivory and concentrations of foliar nutrients in arroyo willow,Salix lasiolepis. We discovered that among 20 willow clones and between two years arroyo willow varied in the size (absolute concentrations) and shape (relative concentrations) of five mineral nutrients (Ca, Mg, N, P, and K). Similarly, the densities of five sawfly species varied in size and shape among clones and between years. In 1984, relative densities, or shape, of the sawfly community was associated with relative concentrations, or shape, of foliar nutrients in 20 willow clones. In contrast, in 1985 absolute densities, or size, was associated with absolute concentrations, or size, of foliar nutrients. This shift from a shape to a size association between herbivory and foliar mineral nutrients may reflect the large difference in winter precipitation and sawfly densities between years: precipitation and sawfly densities were much greater in 1985 than in 1984.     

Blood fatty acids indicate inter- and intra-annual variation in the diet of Adélie penguins: Comparison with stomach content and stable isotope analysis

Adélie penguin (Pygoscelis adeliae) diet is an important indicator of prevailing environmental conditions and resource availability. In this study, dietary variation within and between years was studied with fatty acid signature analysis (FASA), stomach content analysis (SCA) and stable isotope analysis (SIA). We profiled the fatty acid (FA) composition of whole blood collected from adult penguins throughout the breeding season, and from chicks during the crèche period, in 2001 and 2002. Differences were detected in FA profiles between years, breeding stage and age (adults vs. chicks). These patterns broadly corresponded to those observed from SCA and SIA, with a mix of krill and fish consumed in the early part of the breeding season in both years, krill dominating the diet during the chick-rearing periods in 2001, and fish in 2002. Different metabolic and physiological demands between stages, and ages, may also influence FA profiles but warrants further investigation. In-situ calibrations of adult FA blood profiles were made using corresponding stomach samples to quantify diet composition. Using linear discriminate function analysis, we classified adult FA profiles into 3 meal-types: krill, fish or mixed. A higher proportion of adults had fish-like profiles during the arrival and guard periods. Krill-like profiles dominated during the incubation and crèche periods, although there were a relatively high proportion of fish-like and mixed profiles as well. These patterns corresponded to results from SCA and SIA. This study demonstrates that FASA has the potential to be integrated with other dietary tools to enhance diet monitoring studies, which are currently integral to ecosystem management and conservation measures. The in-situ calibration method used offers a simple and effective alternative to more rigorous calibration techniques developed elsewhere.     

Discriminant alleles and discriminant analysis: efficient characters to separate closely related species: the example of Lathyrus latifolius L. and Lathyrus sylvestris L. (Leguminosae)

VALERO, M. & HOSSAERT-MCKEY, M., 1991. Discriminant alleles and discriminant analysis: efficient characters to separate closely related species: the example of Lathyrus latifolius L. and Lathyrus sylvestris L. (Leguminosae). Two species of Lathyrus (L. latifolius and L. sylvestris) were compared using allozymes and quantitative vegetative and reproductive traits. The variation in these characters was analysed in several populations of the two species located in south-western, central and northern France. In a site where the two species are syrapatric, intermediate plants are described. The two species can be identified by discriminant alleles. The genetic structure observed for intermediate plants in the zone of sympatry indicates, paradoxically, the occurrence of a strong reproductive barrier between the two species. The discriminant analysis performed on the quantitative traits readily distinguishes the two species and confirms the reproductive isolation between them. The quantitative character that best discriminates between the species is the number of ovules per ovary, a variable which has non-overlapping distributions in the two species. We discuss how this character, usually ignored, may be better for distinguishing species than some traditionally used reproductive traits such as the number of seeds per fruit. The vegetative traits studied (e.g. degree and intensity of branching) also differ significantly between the two species. Divergent evolution of these traits in the two species is discussed in relation to differences in the original habitats of the two species.     

A simple and accurate method for generating co-dominant markers: an application of conformation-sensitive gel electrophoresis to linkage analysis in the silkworm

A simple and sensitive method for linkage analysis is described, which is based on conformation-sensitive gel electrophoresis (CSGE). Using urea-containing agarose gels or a commercially available polyacrylamide-derived matrix, 13 polymorphic markers were newly identified for known genes of the silkworm, Bombyx mori, which had been scored as monomorphic by PCR-RFLP analysis. This method for detecting polymorphisms is quite sensitive, and can be performed with inexpensive reagents and apparatus that is available in most molecular biology laboratories. Received: 19 November 1998 / Accepted: 2 March 1999     

氮、磷、钾肥配施对'红叶'南天竹叶片色素和 可溶性糖含量的影响及相关性分析

以2年生'红叶'南天竹(Nandina domestica'Hongye')盆栽苗为实验材料,根据L16(45)正交实验设计进行3因素(包括氮、磷和钾肥)4水平(N单株施用量分别为0.0、18.4、36.8和55.2 mg,P2O5单株施用量分别为0.0、14.4、28.8和43.2 mg,K2 O单株施用量分别为0.0、0.8、1.6和2.4 mg)施肥实验,对2015年11月5日至2016年1月20日期间各组叶片的光合色素(包括叶绿素a、叶绿素b、总叶绿素和类胡萝卜素)、花色素苷和可溶性糖含量进行了比较;在此基础上,对叶片色素和可溶性糖含量及各肥料单株施用量进行了Pearson相关性分析.结果表明:总体来看,各组的光合色素和可溶性糖含量显著高于对照(N、P2O5和K2O单株施用量均为0.0 mg)组,而花色素苷含量则显著低于对照组.其中,T14(N、P2O5和K2O单株施用量分别为55.2、14.4和1.6 mg)、T15(N、P2O5和K2O单株施用量分别为55.2、28.8和0.8 mg)和T16(N、P2O5和K2O单株施用量分别为55.2、43.2和0.0 mg)组的光合色素含量均较高,T2(N、P2O5和K2O单株施用量分别为0.0、14.4和0.8 mg)、T3(N、P2O5和K2O单株施用量分别为0.0、28.8和1.6 mg)和T4(N、P2O5和K2O单株施用量分别为0.0、43.2和2.4 mg)组的花色素苷含量均较高,T3和T4组的可溶性糖含量均较低.极差分析结果表明:N单株施用量对光合色素含量的影响最大,K2 O单株施用量的影响最小;N单株施用量对花色素苷和可溶性糖含量的影响最大,P2 O5单株施用量的影响最小.相关性分析结果表明:N单株施用量与各光合色素含量呈极显著正相关,与可溶性糖含量呈显著正相关,与花色素苷含量呈极显著负相关;而P2O5和K2O单株施用量与上述指标的相关性均不显著.各光合色素含量间存在极显著正相关,并与可溶性糖含量呈显著正相关,与花色素苷含量呈极显著负相关.此外,花色素苷含量与可溶性糖含量呈显著负相关.研究结果显示:高氮能够延长'红叶'南天竹的绿叶期,低氮能够促进其叶片呈现红色,因此,在园林栽培过程中应根据实际需要施肥.     

Estimation of growth and survival in size-structured cohort data: an application to larval striped bass (Morone saxatilis)

We present a method for estimating growth and mortality rates in size-structured population models. The methods are based on least-square fits to data using approximate models (using spline approximations) for the underlying partial differential equation population model. In a series of numerical tests, we compare our approach to an existing method (due to Hackney and Webb). As an example, we apply our techniques to experimental data from larval striped bass field studies.Research supported in part under grants at Brown University from the National Science Foundation: UINT-8521208, NSFDMS-8818530 (H.T.B., F.K. and CW.); from the Air Force Office of Scientific Research: AFOSR F49620-86-C-0111 (H.T.B., C.W.); and at University of California, Davis from the Alford P. Sloan Foundation (L.W.B.)     

An image analysis method for the precise selection and quantitation of fluorescently labeled cellular constituents: application to the measurement of human muscle cells in culture

The accurate measurement of the morphological characteristics of cells with nonuniform conformations presents difficulties. We report here a straightforward method using immunofluorescent staining and the commercially available imaging program Adobe Photoshop, which allows objective and precise information to be gathered on irregularly shaped cells. We have applied this measurement technique to the analysis of human muscle cells and their immunologically marked intracellular constituents, as these cells are prone to adopting a highly branched phenotype in culture. Use of this method can be used to overcome many of the long-standing limitations of conventional approaches for quantifying muscle cell size in vitro. In addition, wider applications of Photoshop as a quantitative and semiquantitative tool in immunocytochemistry are explored.     

Fatty acid signatures of stomach oil and adipose tissue of northern fulmars (<Emphasis Type="Italic">Fulmarus glacialis</Emphasis>) in Alaska: implications for diet analysis of Procellariiform birds

Procellariiforms are unique among seabirds in storing dietary lipids in both adipose tissue and stomach oil. Thus, both lipid sources are potentially useful for trophic studies using fatty acid (FA) signatures. However, little is known about the relationship between FA signatures in stomach oil and adipose tissue of individuals or whether these signatures provide similar information about diet and physiology. We compared the FA composition of stomach oil and adipose tissue biopsies of individual northern fulmars (N = 101) breeding at three major colonies in Alaska. Fatty acid signatures differed significantly between the two lipid sources, reflecting differences in dietary time scales, metabolic processing, or both. However, these signatures exhibited a relatively consistent relationship between individuals, such that the two lipid sources provided a similar ability to distinguish foraging differences among individuals and colonies. Our results, including the exclusive presence of dietary wax esters in stomach oil but not adipose tissue, are consistent with the notion that stomach oil FA signatures represent lipids retained from prey consumed during recent foraging and reflect little metabolic processing, whereas adipose tissue FA signatures represent a longer-term integration of dietary intake. Our study illustrates the potential for elucidating short- versus longer-term diet information in Procellariiform birds using different lipid sources.     

A 3D interactive method for estimating body segmental parameters in animals: application to the turning and running performance of Tyrannosaurus rex

We developed a method based on interactive B-spline solids for estimating and visualizing biomechanically important parameters for animal body segments. Although the method is most useful for assessing the importance of unknowns in extinct animals, such as body contours, muscle bulk, or inertial parameters, it is also useful for non-invasive measurement of segmental dimensions in extant animals. Points measured directly from bodies or skeletons are digitized and visualized on a computer, and then a B-spline solid is fitted to enclose these points, allowing quantification of segment dimensions. The method is computationally fast enough so that software implementations can interactively deform the shape of body segments (by warping the solid) or adjust the shape quantitatively (e.g., expanding the solid boundary by some percentage or a specific distance beyond measured skeletal coordinates). As the shape changes, the resulting changes in segment mass, center of mass (CM), and moments of inertia can be recomputed immediately. Volumes of reduced or increased density can be embedded to represent lungs, bones, or other structures within the body. The method was validated by reconstructing an ostrich body from a fleshed and defleshed carcass and comparing the estimated dimensions to empirically measured values from the original carcass. We then used the method to calculate the segmental masses, centers of mass, and moments of inertia for an adult Tyrannosaurus rex, with measurements taken directly from a complete skeleton. We compare these results to other estimates, using the model to compute the sensitivities of unknown parameter values based upon 30 different combinations of trunk, lung and air sac, and hindlimb dimensions. The conclusion that T. rex was not an exceptionally fast runner remains strongly supported by our models-the main area of ambiguity for estimating running ability seems to be estimating fascicle lengths, not body dimensions. Additionally, the craniad position of the CM in all of our models reinforces the notion that T. rex did not stand or move with extremely columnar, elephantine limbs. It required some flexion in the limbs to stand still, but how much flexion depends directly on where its CM is assumed to lie. Finally we used our model to test an unsolved problem in dinosaur biomechanics: how fast a huge biped like T. rex could turn. Depending on the assumptions, our whole body model integrated with a musculoskeletal model estimates that turning 45 degrees on one leg could be achieved slowly, in about 1-2s.     

An in vitro method generating base substitutions in preselected regions of plasmid DNA: application to structural analysis of the replication origin of the Escherichia coli K-12 chromosome

A method for introducing base substitutions in defined regions of plasmid DNA has been developed. In principle, a circular heteroduplex DNA containing a gap is constructed by annealing of two kinds of linear molecules derived from the same plasmid: One is the molecule shortened either by exonucleolytic digestion from the termini generated at a restriction site or by removal of a region flanked by two restriction sites, and the other the full-length molecule linearized at a different site. The deleted region in the shorter linear molecule becomes a single-stranded gap in the circular heteroduplex DNA. The heteroduplex is then treated with sodium bisulfite that converts specifically cytosine residues to uracil residues in single-stranded regions. After filling in the gap by repair synthesis, transformation is carried out to isolate mutant plasmids. Since two kinds of circular heteroduplexes are formed by annealing in which the sequences in the gaps are complementary to each other, mutagenesis of both strands can be accomplished in one experiment. This method was applied to construction of mutants with base substitutions in the replication origin region (oriC) of the Escherichia coli K-12 chromosome which had previously been cloned in colicin E1 plasmid vectors, and various mutants in defined regions of oriC were successfully isolated at high efficiencies. Analysis of these mutants provided evidence that oriC contains special regions, designated spacers, which separate neighboring important sequences specifying interactions with initiation factors for DNA replication at precise distances.     

Development of an LC‐MS method for simultaneous quantitation of amentoflavone and biapigenin,the minor and major biflavones from Hypericum perforatum L., in human plasma and its application to real blood

Introduction – Biflavones of Hypericum perforatum L. are bioactive compounds used in the treatment of inflammation and depression. Determination of amentoflavone and biapigenin from blood is challenging owing to their similar structures and low concentrations. Objective – To develop a rapid, sensitive and accurate method based on liquid‐phase extraction followed by high‐performance liquid chromatography and electrospray ionisation mass spectrometry (HPLC‐ESI‐MS) for quantification of biflavones in human plasma. Methodology – After extraction from blood, the analytes were subjected to HPLC with an XTerra® MS C₁₈ column and a binary mobile phase consisting of 2% formic acid in water and acetonitrile under isocratic elution conditions, with ESI‐MS detection in the negative ion mode and multiple reaction monitoring (MRM). Results – Both calibration curves showed good linearity within the concentration range 1–500 ng/mL. Limits of detection (S/N = 3) were 0.1 ng for pure substances and the limits of quantitation (S/N = 5) were 1.0 ng/mL from analyte‐spiked serum. The grand mean recovery was 90% from several subsamples of each biflavone. The imprecision (RSD) of peak areas was between 5% (intraday) and 10% (interday) for high concentrations (250 ng/mL) and between 10% (intraday) and 15% (interday) for low concentrations (1 ng/mL). Inaccuracy of the mean was less than 20% at the lower limit of quantitation. Conclusion – The developed and validated method for determination of biflavones from human plasma was effectively applied to pharmacokinetic studies of 13 probands and preliminary results indicate biphasic concentration–time curves. Copyright © 2010 John Wiley & Sons, Ltd.     

Unidirectional sodium fluxes in red beet storage tissue (Beta vulgaris L. cv. Platronde Egyptische): effects of the phytohormones indol-3yl-acetic acid and abscisic acid

Abstract. The influence of indol-3yl-acetic acid (IAA) and abscisic acid (ABA) on the capacities of the cytoplasm and vacuole and their effects on unidirectional sodium fluxes across the plasmalemma and the tonoplast of aged red beet storage tissue was investigated. After loading the tissue in a labelled NaCl solution the efflux of radio-activity was measured in unlabelled NaCl. By means of compartmental analysis the capacities and fluxes were determined and compared with those obtained after loading and elution in the presence of IAA or ABA.
It was established that both IAA and ABA affect sodium transport across the principal cell membranes. Both hormones inhibited the efflux across the plasma-lemma, possibly by affecting a Na⁺ for H⁺ exchanging system. Efflux across the tonoplast was stimulated by IAA and influx across the same membrane was enhanced by ABA. It was suggested that IAA stimulated a proton pump at this level while the influence of ABA remained difficult to explain.     

Expression profiling of the 14-3-3 gene family in response to salt stress and potassium and iron deficiencies in young tomato (Solanum lycopersicum) roots: analysis by real-time RT-PCR

BACKGROUND AND AIMS Mineral nutrient deficiencies and salinity constitute major limitations for crop plant growth on agricultural soils. 14-3-3 proteins are phosphoserine-binding proteins that regulate the activities of a wide array of targets via direct protein-protein interactions and may play an important role in responses to mineral nutrients deficiencies and salt stress. In the present study, the expression profiling of the 14-3-3 gene family in response to salt stress and potassium and iron deficiencies in young tomato (Solanum lycopersicum) roots was investigated in order to analyse the 14-3-3 roles of the proteins in these abiotic stresses. METHODS: Sequence identities and phylogenetic tree creation were performed using DNAMAN version 4.0 (Lynnon Biosoft Company). Real-time RT-PCR was used to examine the expression of each 14-3-3 gene in response to salt stress and potassium and iron deficiencies in young tomato roots. KEY RESULTS: The phylogenetic tree shows that the 14-3-3 gene family falls into two major groups in tomato plants. By using real-time RT-PCR, it was found that (a) under normal growth conditions, there were significant differences in the mRNA levels of 14-3-3 gene family members in young tomato roots and (b) 14-3-3 proteins exhibited diverse patterns of gene expression in response to salt stress and potassium and iron deficiencies in tomato roots. CONCLUSIONS: The results suggest that (a) 14-3-3 proteins may be involved in the salt stress and potassium and iron deficiency signalling pathways in young tomato roots, (b) the expression pattern of 14-3-3 gene family members in tomato roots is not strictly related to the position of the corresponding proteins within a phylogenetic tree, (c) gene-specific expression patterns indicate that isoform-specificity may exist in the 14-3-3 gene family of tomato roots, and (d) 14-3-3 proteins (TFT7) might mediate cross-talk between the salt stress and potassium and iron-deficiency signalling pathways in tomato roots.     

A comparative anatomical and biochemical analysis in salsola (Chenopodiaceae) species with and without a Kranz type leaf anatomy: a possible reversion of C4 to C3 photosynthesis

Leaf anatomy was studied by light and electron microscopy and the leaf activities of RUBP carboxylase, PEP carboxylase, and malic enzyme were assayed in: Salsola australis and S. oreophila grown on the West Pamirs at 1800 m altitude; in S. australis grown on the East Pamirs at 3860 m; and in S. arbusculiformis grown in the Kisil-Kum desert in Middle Asia near 500 m. Carbon isotope fractionation ratio values also were measured on whole leaf tissue for 18 Salsola species field collected in these and other regions of the former USSR. S. australis leaves are cylindrical and in cross section exhibit a peripheral ring of mesophyll and then an inner ring of bundle sheath type cells; and its biochemical characteristics and deltaC values are typical of a C4 species of the NADP-malic enzyme malate-forming group. These traits were expressed independent of the plant growth altitude up to 4000 m. C4 type deltaC values were obtained in 14 of the Salsola species. Anatomical, structural, and biochemical features typical of the C4 syndrome were absent in S. oreophila and S. arbusculiformis. Four Salsola species, including these two, had C3-type deltaC values. Their cylindrical leaves in cross section exhibited two to three peripheral rings as layers of palisade parenchyma. Although their vascular bundles were surrounded by green bundle sheath cells, their organelle numbers were comparable to those in mesophyll cells. Neither bundle sheath cell wall thickenings nor dimorphic chloroplasts in two leaf cell types were observed. In S. oreophila, there was a high activity of RuBP carboxylase, but a low activity of C4 cycle enzymes. Interpretation of these data lends evidence to the hypothesis that a small group of C3 Salsola species, including S. oreophila, S. arbusculiformis, S. montana, and S. pachyphylla, arose as the result of a reversion of a C4 to a C3 type of photosynthetic CO2 fixation in the cooler climates of Middle Asia.