Growth-band counts from elephantfish Callorhinchus milii fin spines do not correspond with independently estimated ages

Fin spines from elephantfish Callorhinchus milii were sectioned and viewed with transmitted white light under a compound microscope. The sections displayed growth bands but their interpretation and significance were unclear. Three different methods were used for counting growth bands. The results were compared with reference growth curves based on length-at-age estimates for six juvenile year classes derived from length-frequency distributions, and tagging data that showed longevity is at least 20 years. None of the three ageing methods showed good correspondence with the reference curves and all methods departed markedly from the reference curves at ages above 2 years old. Therefore, growth bands present in C. milii spines are not useful for ageing, at least with the three methods tested here. Spine bands may not represent age marks, but instead may be layers of material deposited irregularly to strengthen the spine.     

The age distribution of cells in stratified squamous epithelium

In structured tissues such as stratified squamous epithelium the age distribution of cycling cells in a particular part of the tissue is influenced by cell migration. Age distributions are derived for the proliferative cells of stratified squamous epithelium, dependent on the mode of migration; and the effect of using analytical methods which assume exponential or rectangular age distributions is discussed with particular reference to the analysis of stathmokinetic experiments.     

Species diversity and ecological range in relation to ploidy level in the flora of the Pyrenees

Polyploidy is a major process in plant evolution. Surprisingly, no study has examined its role in species diversification and ecological distribution in relation to other life history traits. In this study, we examine to what extent polyploidy and the other traditionally examined biological traits (pollination mode, dispersal mode and growth form) account for ecological and taxonomic diversity in the flora of the Pyrenees. Fifty genera (in 22 angiosperm families) were classified according to ploidy level, growth form, pollination mode and dispersal mode, and 451 species and/or subspecies in these 50 genera were classified according to ploidy level and growth form. We examined the contribution of ploidy level, pollination and dispersal modes and growth form to (i) the ecological range of species and genera, i.e., the number of natural habitats (defined by a combination of ecological characteristics) where they occur, and (ii) the taxonomic diversity of the 50 genera. Ploidy level and dispersal mode had significant effects on the taxonomic diversity of the 50 genera. Taxonomic diversity, but not polyploidy per se, was significantly correlated with ecological range of genera. For individual species, diploids had a larger ecological range than polyploids, and herbaceous growth forms had wider ecological distributions than other growth forms. Our results indicate that polyploidisation may be a source of ecological diversification of genera, not by increasing the ecological range of particular polyploid species compared to diploids, but rather by creating taxonomic diversity that leads in some genera to a diversification of the habitats occupied by different ploidy levels. This observation is consistent with previous observations of ecological divergence of chromosomal races in some species in the Alps and in the Pyrenees. As found in other studies, species diversification in the studied flora appears to be greatly influenced by the occurrence of multiple dispersal modes, while ecological range of species or subspecies is significantly increased by the presence of herbaceous species.     

Population structure, growth and distribution of Lingula anatina (Brachiopoda) in Queensland, Australia

Size-frequency data collected in large samples from five populations of Lingula anatina from North Queensland intertidal sandflats conformed to previously known brachiopod size-frequency distributions. Probability paper analysis of the samples and constituent sub-samples confirmed that all the distributions had a hidden poly-modality resulting from a long but defined breeding season. Two patterns of annual recruitment were revealed; the first is the periodic failure of the populations to gain recruits and the second is one of patchy distribution of settlement cohorts. These patterns introduce sampling bias into the derivation of lingulid size frequency curves unless compensated by more extensive sampling methods than have previously been considered adequate. The interpretation of year classes has enabled a growth curve to be derived. The populations inhabited predominantly sandy sub-strates and displayed aggregated distributions. Littoral distribution of the species is regarded as optimal rather than marginal.     

BREAKING UP AND GETTING TOGETHER: EVOLUTION OF SYMBIOSIS AND CLONING BY FISSION IN SEA ANEMONES (GENUS ANTHOPLEURA)

Abstract Clonal growth and symbiosis with photosynthetic zooxanthellae typify many genera of marine organisms, suggesting that these traits are usually conserved. However, some, such as Anthopleura , a genus of sea anemones, contain members lacking one or both of these traits. The evolutionary origins of these traits in 13 species of Anthopleura were inferred from a molecular phylogeny derived from 395 bp of the mitochondrial 16S rRNA gene and 410 bp of the mitochondrial cytochrome oxidase subunit III gene. Sequences from these genes were combined and analyzed by maximum-parsimony, maximum-likelihood, and neighbor-joining methods. Best trees from each method indicated a minimum of four changes in growth mode and that symbiosis with zooxanthellae has arisen independently in eastern and western Pacific species. Alternative trees in which species sharing growth modes or the symbiotic condition were constrained to be monophyletic were significantly worse than best trees. Although clade composition was mostly consistent with geographic sympatry, A. artemisia from California was included in the western Pacific clade. Likewise, A. midori from Japan was not placed in a clade containing only other Asian congeners. The history of Anthopleura includes repeated shifts between clonality and solitariness, repeated attainment of symbiosis with zooxanthellae, and intercontinental dispersal.     

A Bayesian Latent Variable Mixture Model for Longitudinal Fetal Growth

Summary Fetal growth restriction is a leading cause of perinatal morbidity and mortality that could be reduced if high‐risk infants are identified early in pregnancy. We propose a Bayesian model for aggregating 18 longitudinal ultrasound measurements of fetal size and blood flow into three underlying, continuous latent factors. Our procedure is more flexible than typical latent variable methods in that we relax the normality assumptions by allowing the latent factors to follow finite mixture distributions. Using mixture distributions also permits us to cluster individuals with similar observed characteristics and identify latent classes of subjects who are more likely to be growth or blood flow restricted during pregnancy. We also use our latent variable mixture distribution model to identify a clinically meaningful latent class of subjects with low birth weight and early gestational age. We then examine the association of latent classes of intrauterine growth restriction with latent classes of birth outcomes as well as observed maternal covariates including fetal gender and maternal race, parity, body mass index, and height. Our methods identified a latent class of subjects who have increased blood flow restriction and below average intrauterine size during pregnancy. These subjects were more likely to be growth restricted at birth than a class of individuals with typical size and blood flow.     

A computer-aided measuring system for the characterization of yeast populations combining 2D-image analysis, electronic particle counter, and flow cytometry

An integrated measuring system was developed that directly compares the shape of size distributions of Saccharomyces cerevisiae populations obtained from either microscopic measurements, electronic particle counter, or flow cytometer. Because of its asymmetric mode of growth, a yeast population consists of two different subpopulations, parents and daughters. Although electronic particle counter and flow cytometer represent fast methods to assess the growth state of the population as a whole, the determination of important cell cycle parameters like the fraction of daughters or budded cells requires microscopic observation. We therefore adapted a semiautomatic and interactive 2D-image processing program for rapid and accurate determination of volume distributions of the different sub-populations. The program combines the capacity of image processing and volume calculation by contour-rotation, with the potential of visual evaluation of the cells. High-contrast images from electron micrographs are well suited for image analysis, but the necessary air drying caused the cells to shrink to 35% of their hydrated volume. As an alternative, hydrated cells overstained with the fluorochrome calcofluor and visualized by fluorescence light microscopy were used. Cell volumes calculated from length, and diameter measurements with the assumption of an ellipsoid cell shape were underestimated as compared to volumes derived from 2D-image analysis and contour rotation, because of a deviating cell shape, especially in the older parent cells with more than one bud scar. The bimodal volume distribution obtained from microscopic measurements was identical to the protein distribution measured with the flow cytometer using cells stained with dansylchloride, but differed significantly from the size distribution measured with the electronic particle counter. Compared with the flow cytometer, 2-D image analysis can thus provide accurate distributions with important additional information on, for instance, the distributions of subpopulations like parents, daughters, or budded cells.     

Determination of metabolic flux changes during fed-batch cultivation from measurements of intracellular amino acids by LC-MS/MS

Metabolic flux analysis using (13)C-labeled substrates is a well-developed method for investigating cellular behavior in steady-state culture condition. To extend its application, in particular to typical industrial conditions, such as batch and fed-batch cultivations, a novel method of (13)C metabolic flux analysis is proposed. An isotopomer balancing model was developed to elucidate flux distributions in the central metabolism and all amino acids synthetic pathways. A lysine-producing strain of Escherichia coli was cultivated by fed-batch mode in a growth medium containing yeast extract. Mass distribution data was derived from both intracellular free amino acids and proteinogenic amino acids measured by LC-MS/MS, and a correction parameter for the protein turnover effect on the mass distributions of intracellular amino acids was introduced. Metabolic flux distributions were determined in both exponential and stationary phases. Using this new approach, a culture phase-dependent metabolic shift was detected in the fed-batch culture. The approach presented here has great potential for investigating cellular behavior in industrial processes, independent of cultivation modes, metabolic phase and growth medium.     

Distribution of fibroblast growth factors in cultured tumor cells and their transplants

Summary The distributions of acidic fibroblast growth factor (aFGF) and basic FGF (bFGF) in extracts of various cultured mammalian cells were determined from their elution profiles on heparin-affinity chromatography, and assay of activity as ability to stimulate DNA synthesis in BALB/c3T3 cells. Only aFGF was found in extracts of mouse melanoma B 16 cell and rat Morris hepatoma cell (MH₁C₁) lines. Other tumor cell lines established from solid tumors and some normal cells contained bFGF as a main component, but blood tumor cell lines contained no aFGF or bFGF. The FGFs in extracts of solid tumor tissues derived by transplantations of these cultured tumor cells and various normal tissues of mice were also examined. Tumors formed by all cell lines, regardless of whether they produced aFGF, bFGF, or neither, contained bFGF that was probably derived from host cells including capillary endothelial cells, in addition to the tumor-derived aFGF or bFGF, if produced. The content of bFGF, possibly derived from the host, in these tumor tissues was comparable to those of various mouse organs other than thymus, lung, spleen, and testis, which have higher bFGF contents. Tumor tissues derived from cultured cells producing bFGF had relatively higher bFGF contents. Like bFGF, aFGF was distributed almost ubiquitously in normal mouse tissues.     

High‐resolution analysis of neuronal growth cone morphology by comparative atomic force and optical microscopy

Neuronal growth cones are motile sensory structures at the tip of axons, transducing guidance information into directional movements towards target cells. The morphology and dynamics of neuronal growth cones have been well characterized with optical techniques; however, very little quantitative information is available on the three‐dimensional structure and mechanical properties of distinct subregions. In the present study, we imaged the large Aplysia growth cones after chemical fixation with the atomic force microscope (AFM) and directly compared our data with images acquired by light microscopy methods. Constant force imaging in contact mode in combination with force‐distant measurements revealed an average height of 200 nm for the peripheral (P) domain, 800 nm for the transition (T) zone, and 1200 nm for the central (C) domain, respectively. The AFM images show that the filopodial F‐actin bundles are stiffer than surrounding F‐actin networks. Enlarged filopodia tips are 60 nm higher than the corresponding shafts. Measurements of the mechanical properties of the specific growth cone regions with the AFM revealed that the T zone is stiffer than the P and the C domain. Direct comparison of AFM and optical data acquired by differential interference contrast and fluorescence microscopy revealed a good correlation between these imaging methods. However, the AFM provides height and volume information at higher resolution than fluorescence methods frequently used to estimate the volume of cellular compartments. These findings suggest that AFM measurements on live growth cones will provide a quantitative understanding of how proteins can move between different growth cone regions. © 2006 Wiley Periodicals, Inc. J Neurobiol, 2006     

Genetic analysis of growth curves using the SAEM algorithm

The analysis of nonlinear function-valued characters is very important in genetic studies, especially for growth traits of agricultural and laboratory species. Inference in nonlinear mixed effects models is, however, quite complex and is usually based on likelihood approximations or Bayesian methods. The aim of this paper was to present an efficient stochastic EM procedure, namely the SAEM algorithm, which is much faster to converge than the classical Monte Carlo EM algorithm and Bayesian estimation procedures, does not require specification of prior distributions and is quite robust to the choice of starting values. The key idea is to recycle the simulated values from one iteration to the next in the EM algorithm, which considerably accelerates the convergence. A simulation study is presented which confirms the advantages of this estimation procedure in the case of a genetic analysis. The SAEM algorithm was applied to real data sets on growth measurements in beef cattle and in chickens. The proposed estimation procedure, as the classical Monte Carlo EM algorithm, provides significance tests on the parameters and likelihood based model comparison criteria to compare the nonlinear models with other longitudinal methods.     

The effects of alternate optimal solutions in constraint-based genome-scale metabolic models

Genome-scale constraint-based models of several organisms have now been constructed and are being used for model driven research. A key issue that may arise in the use of such models is the existence of alternate optimal solutions wherein the same maximal objective (e.g., growth rate) can be achieved through different flux distributions. Herein, we investigate the effects that alternate optimal solutions may have on the predicted range of flux values calculated using currently practiced linear (LP) and quadratic programming (QP) methods. An efficient LP-based strategy is described to calculate the range of flux variability that can be present in order to achieve optimal as well as suboptimal objective states. Sample results are provided for growth predictions of E. coli using glucose, acetate, and lactate as carbon substrates. These results demonstrate the extent of flux variability to be highly dependent on environmental conditions and network composition. In addition we examined the impact of alternate optima for growth under gene knockout conditions as calculated using QP-based methods. It was observed that calculations using QP-based methods can show significant variation in growth rate if the flux variability among alternate optima is high. The underlying biological significance and general source of such flux variability is further investigated through the identification of redundancies in the network (equivalent reaction sets) that lead to alternate solutions. Collectively, these results illustrate the variability inherent in metabolic flux distributions and the possible implications of this heterogeneity for constraint-based modeling approaches. These methods also provide an efficient and robust method to calculate the range of flux distributions that can be derived from quantitative fermentation data.     

Faster or slower: has growth of eastern Baltic cod changed?

Recent environmental changes have influenced the ecology and biology of eastern Baltic cod. Declining somatic condition, maturation at smaller size and restricted size distribution of the population suggest that growth rates have decreased between the early 2000s and the 2010s. Extensive age estimation problems have until now precluded testing of this hypothesis. This study presents evidence for a decrease in somatic growth rate of Baltic cod. Temporal patterns of growth, condition and maturation were analysed based on two complementary analyses: length frequency mode progression derived from DATRAS bottom trawl survey data and known-age samples, where size at age was back-calculated from daily otolith growth patterns. In the known-age samples, growth was positively related to somatic condition at capture with maturity dependent differences. Immature individuals had experienced significantly lower growth and were in lower condition at capture than mature individuals. Growth rates in the known-age samples were estimated at 9.5, 7.8 and 5.7?cm per year for age classes 1, 2 and 3 respectively. Growth between age 2 and 3 decreased significantly from 8.8?cm in the 1997 year class to 7.6?cm in the 2010 year class. While the 2001 and 2004 known-age samples were representative for the population, the 2013 sample was biased towards individuals with a higher condition and growth. Complementary length frequency analysis following the length mode of fish from age 2 to age 3 confirmed growth estimates from the early 2000s, while suggesting a 37.5% lower growth in 2013 compared with 2005.     

A Bayesian analysis of the effect of selection for growth rate on growth curves in rabbits

Gompertz growth curves were fitted to the data of 137 rabbits from control (C) and selected (S) lines. The animals came from a synthetic rabbit line selected for an increased growth rate. The embryos from generations 3 and 4 were frozen and thawed to be contemporary of rabbits born in generation 10. Group C was the offspring of generations 3 and 4, and group S was the contemporary offspring of generation 10. The animals were weighed individually twice a week during the first four weeks of life, and once a week thereafter, until 20 weeks of age. Subsequently, the males were weighed weekly until 40 weeks of age. The random samples of the posterior distributions of the growth curve parameters were drawn by using Markov Chain Monte Carlo (MCMC) methods. As a consequence of selection, the selected animals were heavier than the C animals throughout the entire growth curve. Adult body weight, estimated as a parameter of the Gompertz curve, was 7% higher in the selected line. The other parameters of the Gompertz curve were scarcely affected by selection. When selected and control growth curves are represented in a metabolic scale, all differences disappear.     

Competitive exclusion along climate gradients: energy efficiency influences the distribution of two salmonid fishes

We tested the importance of thermal adaptations and energy efficiency in relation to the geographical distribution of two competing freshwater salmonid fish species. Presence–absence data for Arctic char and brown trout were obtained from 1502 Norwegian lakes embracing both temperature and productivity gradients. The distributions were contrasted with laboratory‐derived temperature scaling models for food consumption, growth and energy efficiency. Thermal performances of the two species were almost identical. However, Arctic char exhibited double the growth efficiency (per unit of food) and appear to have out‐competed brown trout from cold, low‐productivity lakes, perhaps by scramble competition. Brown trout, for which previous reports have shown to be aggressive and dominant, have likely excluded the more energy‐efficient Arctic char from relatively warm, productive lakes, perhaps by contest competition. Competitive interaction changing in outcome with lake productivity, rather than thermal performance, is likely a major determinant of the range distribution of the two species. Our study highlights the need for more focus on choice of relevant ecophysiological traits in ecological climate impact studies and species distribution modelling.     

Connection between stochastic and deterministic modelling of microbial growth

We present in this paper various links between individual and population cell growth. Deterministic models of the lag and subsequent growth of a bacterial population and their connection with stochastic models for the lag and subsequent generation times of individual cells are analysed. We derived the individual lag time distribution inherent in population growth models, which shows that the Baranyi model allows a wide range of shapes for individual lag time distribution. We demonstrate that individual cell lag time distributions cannot be retrieved from population growth data. We also present the results of our investigation on the effect of the mean and variance of the individual lag time and the initial cell number on the mean and variance of the population lag time. These relationships are analysed theoretically, and their consequence for predictive microbiology research is discussed.     

Evidence that size-selective mortality affects growth of Atlantic cod (Gadus morhua L.) in the southern Gulf of St Lawrence

The effects of size-selective fishing mortality on the growth of Atlantic cod ( Gadus morhuu L.) in the southern Gulf of St Lawrence were investigated and compared between: (1) a period when fishing mortality was relatively high, growth was relatively rapid, and abundance low (1967–1972 year classes): and (2) a period when fishing mortality was lower, growth was slow, and density high (1977–1982 year classes). Cod first entered the fishery at age 3 during both periods. The 1967–1972 year classes (fast growing) were fully recruited to the fishery by age 5 or 6 and the fishery removed over twice as many fish from the lower than upper quartiles of length-at-age distributions for cod 4 to 10 years old (disproportionately high exploitation of slow-growing fish). In contrast. the 1977–1982 year classes (slow growing) did not fully recruit to the fishery until age 9 or 10 and the fishery removed four times as many fish from the upper than lower quartiles of the length-at-age distributions for 4- to 10-year-old cod (disproportionately high exploitation of fast-growing fish). The reduced mean lengths-at-age of the 1977–1982 year classes compared with the 1967–I972 year-classes is consistent with the different patterns of exploitation of fast- and slow-growing fish for the two periods.     

Three-dimensional culture of human tumor cells under standardized medium conditions

The 3-dimensional culture of human tumor spheroids under standardized medium conditions may reveal information on specific biological parameters that could be masked in serum-supplemented media. Spheroids derived from human tumor cells are growth retarded in media free of serum. Ex-Cyte IV is a substance derived from human blood that can be used to improve growth in tissue culture. In this study the growth of spheroids from four different human tumor cell lines was studied when grown in medium free of serum, medium supplemented with varying concentrations Ex-Cyte IV, and medium supplemented with foetal calf serum (FCS). The parameters used for comparisons were growth rate, growth enhancement, clonogenicity and cell cycle distribution.The four cell lines showed different growth rates in serum-free medium, which were increased to different extents when Ex-Cyte IV or FCS were added. The growth enhancing effect induced by Ex-Cyte IV was differently concentration dependent for each cell line. The clonogenicity of cells grown as spheroids in serum-free medium was lower than in spheroids grown in supplemented media. There was no difference in clonogenicity between the differently supplemented media. All four cell lines responded to growth in serum-free medium with a drop in the S-phase and G2M phase.The present study provides a novel approach to the study of human tumor cells in 3-dimensional culture under defined conditions. The human serum derived substance Ex-Cyte IV may provide a method to obtain information on specific biological parameters that could be masked in serum-supplemented media.