A Julia set model of field-directed morphogenesis: developmental biology and artificial life

One paradigm used in understanding the control of morpho-geneticevents is the concept of positional information, where sub-organismiccomponents (such as cells) act in response to positional cues.It is important to determine what kinds of spatiotemporal patternsmay be obtained by such a method, and what the characteristicsof such a morphogenetic process might be. This paper presentsa computer model of morphogenesis based on gene activity drivenby interpreting a positional information field. In this model,the interactions of mutually regulating developmental genesare viewed as a map from R² to R², and are modeled by the complexnumber algebra. Functions in complex variables are used to simulategenetic interactions resulting in position-dependent differentiation.This is shown to be equivalent to computing modified Julia sets,and is seen to be sufficient to produce a very rich set of morphologieswhich are similar in appearance and several important characteristicsto those of real organisms. The properties of this model canbe used to study the potential role of fields and positionalinformation as guiding factors in morphogenesis, as the modelfacilitates the study of static images, time-series (movies)and experimental alterations of the developmental process. Itis thus shown that gene interactions can be modeled as a multi-dimensionalalgebra, and that only two interacting genes are sufficientfor (i) complex pattern formation, (ii) chaotic differentiationbehavior, and (iii) production of sharp edges from a continuouspositional information field. This model is meant to elucidatethe properties of the process of positional information-guidedbiomorphogenesis, not to serve as a simulation of any particularorganism's development. Good quantitative data are not currentlyavailable on the interplay of gene products in morphogenesis.Thus, no attempt is made to link the images produced with actualpictures of any particular real organism. A brief introductionto top-down models and positional information is followed bythe formal definition of the model. Then, the implications ofthe resulting morphologies to biological development are discussed,in terms of static shapes, parametrization studies, time series(movies made from individual frames), and behavior of the modelin light of experimental perturbations. All figures (in grayscale),formulas and parameter values needed to re-create the figuresand movies are included.     

Altered free calcium transients in pig kidney cells (LLC-PK1) cultured with penicillin/streptomycin

Summary The effect of a conventional antibiotic (penicillin/streptomycin) mixture on the widely used kidney epithelial cell line, LLC-PK₁, was investigated by measuring growth and intracellular free calcium. Free calcium concentration was the same in cells cultured for 3 to 7 wk with (“plus”) and without (“minus”) antibiotics both at rest and when challenged with high (14 mM) external calcium. When exposed to vasopressin, minus cells exhibited significantly smaller calcium transients than plus cells. A similar difference existed for transients elicited by a calcium ionophore, 4-br-A23187. After longer periods of culture (>20 wk), minus cells grew slower than plus cells but on reaching confluence (minus cells took 1 day longer) the morphologies and viabilities were indistinguishable. The finding that culture with penicillin/streptomycin reversibly modified some properties of LLC-PK₁ cells, at least partly through altered calcium homeostasis, is of importance for workers using this cell model to study drug effects and raises the general possibility of similar effects on other cultured cells.     

Intramolecular interference effects in dynamic light scattering from rigid rings

A formula for the apparent diffusion coefficient [D_app(κ)] of a rigid ring is derived from the exact first cumulant of its dynamic structure factor. D_app(κ) is expressed in terms of the ring radius, the diffusion coefficients (D_zz and D_xx) for translation parallel and perpendicular, respectively, to the symmetry axis, and the diffusion coefficients (D and D) for rotation around the symmetry and transverse axes, respectively. D_app(κ) exhibits oscillations as a function of the scattering vector k , which depend on D and the anisotropy of translational diffusion (D_zz ? D_xx). The maxima in D_app(κ) are associated with minima in the static structure factor S(κ, 0), which are due to destructive intramolecular interference. The oscillations in D_app(κ) result from periodic variations in the relative intensities of scattered light from different orientations of the ring, which manifest the various motions to different extents. The orientations contributing most to the scattered intensity are those that exhibit the least destructive interference and consequently contribute most to the decay of the dynamic structure factor. © 1993 John Wiley & Sons, Inc.     

Glycolytic enzymes in non-photosynthetic plastids of pea (Pisum sativum L.) roots

The presence of the glycolytic enzymes from hexokinase to pyruvate kinase in plastids of seedling pea (Pisum sativum L.) roots was investigated. The recoveries, latencies and specific activities of each enzyme in different fractions was compared with those of organelle marker enzymes. Tryptic-digestion experiments were performed on each enzyme to determine whether activities were bound within membranes. The results indicate that hexokinase (EC 2.7.1.2) and phosphoglyceromutase (EC 5.4.2.1) are absent from pea root plastids. The possible function of the remaining enzymes is considered.Abbreviations GADPH glyceraldehyde 3-phosphate dehydrogenase - PFK phosphofructokinase - PFP pyrophosphate: fructose 6-phosphate 1-phosphotransferase Bronwen A. Trimming gratefully acknowledges the award of a studentship from the Science and Engineering Research Council     

Vegetation Changes Following Large-scale Fence Removal Across a Protected Area Network Within the Kruger to Canyons Biosphere Reserve,South Africa

Ecosystems - In the early 1990’s, reserves adjacent to Kruger National Park (KNP) removed their fences to create a continuous landscape within the Kruger to Canyons Biosphere Reserve....     

Phosphorylation of the GABAA receptor by cAMP-dependent protein kinase and by protein kinase C: Analysis of the substrate domain

Previous work has shown that the GABA_A-receptor (GABA_A-R) could be phosphorylated by cAMP-dependent protein kinase (PKA), protein kinase C (PKC), and a receptor associated kinase. However, no clear picture has yet emerged concerning the particular subunit subtypes of the GABA_A-R that were phosphorylated by PKA and PKC. In the present report we show that an antibody raised against a 23 amino acid polypeptide corresponding to a sequence in the putative intracellular loop of the 1 subunit of the receptor blocks the in vitro phosphorylation of the purified receptor by PKA and PKC. Moreover, N-terminal sequence analysis of the principal phosphopeptide fragment obtained after proteolysis of the receptor yielded a sequence that corresponds to the 3 subunit of the receptor. Such data provide additional support for our hypothesis (Browning et al., 1990, Proc. Natl. Acad. Sci. USA 87:1315–1317) that both PKA and PKC phosphorylate the -subunit of the GABA_A-R.Special issue dedicated to Dr. Paul Greengard.     

Inhibition of Bordetella pertussis filamentous hemagglutinin-mediated cell adherence with monoclonal antibodies

Abstract Filamentous hemagglutinin (FHA), a 220-kDa protein located on the surface of Bordetella pertussis , is one of the major cell adhesins of this bacterium. We have produced three hybridoma cell lines that express monoclonal antibodies (mAbs) against FHA: X3C, X3E and X4B. The anti-FHA mAbs X3C and X3E reacted with 220-kDa FHA protein bands on Western blots. The mAb X4B, which reacted with FHA in ELISA, did not bind to FHA in a Western blot assay. All three mAbs seemed to be directed to the same epitope or to epitopes in close proximity as suggested by competition ELISAs. All three mAbs were able to inhibit the adherence of Chinese hamster ovary cells to purified FHA, and they could also inhibit the FHA-mediated agglutination of goose red blood cells. The attachment of B. pertussis to epithelial cell monolayers was inhibited by the mAb X3C. These antibodies are very useful probes to identify the presence of FHA in bordetellae species and in clinical reagents such as pertussis vaccines, and to characterize the functional domains of this important bacterial adhesin.     

Ten-year stability of EEG biofeedback results for a hyperactive boy who failed fourth grade perceptually impaired class

Ten years ago, the first successful application of a clinical,private-practice based, EEG 14-Hz biofeedback training regimen for the treatment of learning disorders was performed by the author. After the 10-year-old boy, with presenting symptomology including a developmental reading disorder, hyperactivity, and an educational classification of perceptually impaired, continued symptom free for a period oftwo years, his case was submitted for publication. Ten years after his termination from successful treatment, his ongoingly normal social and academic functioning is noted and his EEG brainwave signature examined and compared with a population of 24 used-to-be learning disabled, one-half of which had a pretreatment state including the educational classification of perceptually impaired. This 10-year follow-up confirms the long-term stability of the results of this EEG 14-Hz biofeedback regimen. Current findings on recent medical research identifying a major cerebral locus of dysfunction for hyperkinesis and how it supports the electrode placements of this clinical office setting regimen is also discussed.     

Expression of A mating type genes of Coprinus cinereus in a heterologous basidiomycete host

The A mating factor of Coprinus cinereus determines compatibility in mating by regulating part of a developmental sequence that leads to dikaryon formation. The A genes that trigger development encode two different classes of homeodomain proteins, and for a successful mating, a protein of one class, HD 1, must interact with a protein of the other class, HD 2. In this report we show that C. cinereus A genes that encode HD 2 proteins, a2-1 and b2-1, can elicit A-regulated development in the heterologous host C. bilanatus. Transformation rates were very low, suggesting that the genes were poorly transcribed. The fact that the HD 2 genes are functionally expressed implies successful heteromultimeric association of putative DNA-binding proteins coded by the two Coprinus species. This interaction was sufficient to satisfy the need for different A factors in the formation of a fertile C. bilanatus dikaryon, but fertile dikaryons were more readily produced in matings with the a2-1 gene transformants. The C. cinereus A genes, b1-1 and d1-1, which encode HD1 proteins, were either not expressed or their proteins were non-functional in C. bilanatus. These experiments raise some interesting questions regarding HD1–HD2 protein interactions.     

Design considerations for two-stage enrichment clinical trials

When there is a predictive biomarker, enrichment can focus the clinical trial on a benefiting subpopulation. We describe a two-stage enrichment design, in which the first stage is designed to efficiently estimate a threshold and the second stage is a “phase III-like” trial on the enriched population. The goal of this paper is to explore design issues: sample size in Stages 1 and 2, and re-estimation of the Stage 2 sample size following Stage 1. By treating these as separate trials, we can gain insight into how the predictive nature of the biomarker specifically impacts the sample size. We also show that failure to adequately estimate the threshold can have disastrous consequences in the second stage. While any bivariate model could be used, we assume a continuous outcome and continuous biomarker, described by a bivariate normal model. The correlation coefficient between the outcome and biomarker is the key to understanding the behavior of the design, both for predictive and prognostic biomarkers. Through a series of simulations we illustrate the impact of model misspecification, consequences of poor threshold estimation, and requisite sample sizes that depend on the predictive nature of the biomarker. Such insight should be helpful in understanding and designing enrichment trials.