RT-PCR method to quantify vascular endothelial growth factor expression.

The vascular endothelial growth factor (VEGF) is implicated in the progression of cancers. Its expression is well correlated with tumor growth and metastases. The availability of a rapid and sensitive method to detect the amounts of VEGF mRNA in biological samples of limited size, very small biopsies, or samples containing relatively few cells could provide an interesting prognostic tool for clinicians. We have developed an RT-PCR method that allows us to detect the VEGF mRNA from as little as 3 micrograms total mRNA. We have also shown that this protocol can be generalized to all cell lines tested. This method constitutes a very potent tool for the analysis of VEGF mRNA expression in different contexts.     

Novel Multiscale Modeling Tool Applied to Pseudomonas aeruginosa Biofilm Formation

Multiscale modeling is used to represent biological systems with increasing frequency and success. Multiscale models are often hybrids of different modeling frameworks and programming languages. We present the MATLAB-NetLogo extension (MatNet) as a novel tool for multiscale modeling. We demonstrate the utility of the tool with a multiscale model of Pseudomonas aeruginosa biofilm formation that incorporates both an agent-based model (ABM) and constraint-based metabolic modeling. The hybrid model correctly recapitulates oxygen-limited biofilm metabolic activity and predicts increased growth rate via anaerobic respiration with the addition of nitrate to the growth media. In addition, a genome-wide survey of metabolic mutants and biofilm formation exemplifies the powerful analyses that are enabled by this computational modeling tool.     

Simulating tumor growth in confined heterogeneous environments

The holy grail of computational tumor modeling is to develop a simulation tool that can be utilized in the clinic to predict neoplastic progression and propose individualized optimal treatment strategies. In order to develop such a predictive model, one must account for many of the complex processes involved in tumor growth. One interaction that has not been incorporated into computational models of neoplastic progression is the impact that organ-imposed physical confinement and heterogeneity have on tumor growth. For this reason, we have taken a cellular automaton algorithm that was originally designed to simulate spherically symmetric tumor growth and generalized the algorithm to incorporate the effects of tissue shape and structure. We show that models that do not account for organ/tissue geometry and topology lead to false conclusions about tumor spread, shape and size. The impact that confinement has on tumor growth is more pronounced when a neoplasm is growing close to, versus far from, the confining boundary. Thus, any clinical simulation tool of cancer progression must not only consider the shape and structure of the organ in which a tumor is growing, but must also consider the location of the tumor within the organ if it is to accurately predict neoplastic growth dynamics.     

Neuronal growth via hybrid system of self-growing and diffusion based grammar rules: I

The formation of neuronal networks requires axonal growth towards target neutons. A simple set of grammar rules is introduced to describe axonal growth towards target cells situated both at short and long distances from the growing neuron. Growth for short distances is descrbed by growth following the highest gradient of a chemical compound (which is spread by diffusion from the targets). This approach fails to describe long-distance growth, which is addressed by adopting a graph grammar theory for growing trees. With these rules a flexible tool to draw network of neurons by computer can be developed.     

Growth stimulation of human melanocytes: identification and characterization of melanoma-derived melanocyte growth factor (M-McGF)

The melanocyte growth stimulating factor from human melanoma cells grown in vitro [Eisinger, M. et al, (1985) Science 229, 984-986] has been purified and identified as a 14 kDa peptide. The activity was shown to be sensitive to acid and heat treatments but resistant to reduction. The factor has strong affinity for heparin-Sepharose and was separated into two fractions by ion-exchange chromatography. Based on its properties, it is grouped in the family of heparin-binding growth factors. Identification of this growth factor will provide a tool for studies of growth regulation of normal and transformed human melanocytes.     

Do Bertalanffy's growth curves result from optimal resource allocation?

Bertalanffy's equation is commonly used to model indeterminate growth. Bertalanffy claimed that this growth pattern results from growth potential decreasing with age. An alternative approach provided by life history theory predicts that indeterminate growth is optimal for organisms in a seasonal environment and results not from decreasing growth potential but from allocating increasingly less energy with age into growth, and more into reproduction. Bertalanffy's curves are the result of evolutionary optimization and should not be used in optimization models as an assumption, but they can be used as a tool to describe the indeterminate growth pattern phenomenologically.     

A novel structured kinetic modeling approach for the analysis of plasmid instability in recombinant bacterial cultures

The instantaneous specific growth rate of a recombinant bacterial culture is directly calculated using a simple structured kinetic modeling approach. Foreign plasmid replication and foreign protein expression represent metabolic burdens to the host cell. The individual effects of these plasmid-mediated activities on the growth rate of plasmid-bearing cells are estimated separately. The dynamic and steady state simulations of the model equations show remarkable agreement with widely observed experimental trends in plasmid copy number and foreign protein content. The model provides an important tool for understanding and controlling plasmid instability in recombinant bacterial fermentations. The modeling framework employed here is suitable for studying the metabolism and growth of a variety of microbial cultures.     

Spatio-temporal leaf growth patterns of Arabidopsis thaliana and evidence for sugar control of the diel leaf growth cycle

Leaf growth dynamics are driven by diel rhythms. The analysis of spatio-temporal leaf growth patterns in Arabidopsis thaliana wild type and mutants of interest is a promising approach to elucidate molecular mechanisms controlling growth. The diel availability of carbohydrates is thought to affect diel growth. A digital image sequence processing (DISP)-based noninvasive technique for visualizing and quantifying highly resolved spatio-temporal leaf growth was adapted for the model plant A. thaliana. Diel growth patterns were analysed for the wild type and for a mutant with altered diel carbohydrate metabolism. A. thaliana leaves showed highest relative growth rates (RGRs) at dawn and lowest RGRs at the beginning of the night. Along the lamina, a clear basipetal gradient of growth rate distribution was found, similar to that in many other dicotyledonous species. The starch-free 1 (stf1) mutant revealed changed temporal growth patterns with reduced nocturnal, and increased afternoon, growth activity. The established DISP technique is presented as a valuable tool to detect altered temporal growth patterns in A. thaliana mutants. Endogenous changes in the diel carbohydrate availability of the starch-free mutant clearly affected its diel growth rhythms.     

THE GROWTH PATTERN OF THE FLOWERING SHOOT OF URGINEA MARITIMA L. (LILIACEAE)

The flowering shoot of Urginea maritima constitutes an interesting one-dimensional growth system. Stalk emergence from the bulb is completed in a few days and is followed by a characteristic very rapid pattern of subapical elongation, with stalk growth rates approaching 3 mm/hr. This elongation system, similar to root tips and other biological materials, has characteristics that may prove it to be a valuable tool for biological studies, as well as for investigating chemical aspects of biological elongation phenomena.     

Estimation of fungal growth using the ergosterol assay: a rapid tool in assessing the microbiological status of grains and feeds

AIM: To use ergosterol assay as a rapid tool to assess the extent of fungal contamination in grains and feeds. METHODS AND RESULTS: Ergosterol was extracted from moulds and quantified using a modified method based on Seitz et al. (1977). A good correlation coefficient of 0.9998 was obtained for ergosterol standards and a strong correlation (R(2) = 0 x 9645) was established between the ergosterol content and the growth of Aspergillus niger ATCC 24126. This shows that this assay can be used to estimate fungal growth. The ergosterol contents and amount of carbon dioxide produced in both Control and Myco CURB (brand) liquid-treated corns were measured over 36 days. Ergosterol contents of pelleted pig feeds were also determined. In both experiments, the levels of ergosterol in the control samples were significantly higher than those of the mould-inhibitor-treated samples. CONCLUSIONS: A strong positive correlation (Spearman, Rs = 0 x 7241) was observed between the ergosterol content and the degree of fungal growth. Hence, ergosterol assay can be used as a rapid tool to assess the microbiological status of grains and feeds. SIGNIFICANCE AND IMPACT OF THE STUDY: This study affirms that ergosterol assay is a rapid and accurate tool that can be used for the assessment of the feed quality.     

Modelling the effectiveness of contraception for controlling introduced populations of elephant in South Africa

Re‐introduced African elephant (Loxodonta africana Blumenbach) populations are growing at very high rates in many of southern Africa’s reserves, have attained densities higher than previously thought possible and may be exhibiting irruptive growth. Active management of such populations is necessary to prevent the potentially negative effects on habitat and biodiversity that are associated with elephant overpopulation. One potentially feasible method of elephant management is immunocontraception, but very little is known about the long‐term effectiveness of this method. Using demographic data from three South African elephant populations, we made model projections of the effects of contraception on population growth rates to determine whether contraception may be a feasible management tool for elephant. In comparison with noncontracepted populations, realistic reductions in population growth rate after 20 years of contraception were projected to be up to c. 64%, with 50% being a very feasible target. Through its ability to reduce population growth rates, immunocontraception should be an effective tool for preventing or minimizing irruption in elephants and, perhaps, other introduced ungulate species.     

Growth Arrest Lines in Long Bones of the Casas Grandes Population

Abstract

One aspect of paleopathology, the examination of growth arrest lines, is suggested as a tool in archeological interpretation. Disruption of the normal growth pattern of long bones may result in the formation of transverse lines of extra-dense bone, visible in ordinary X-rays of the bone shaft. These radio opaque lines, presumed to result from temporary growth arrest caused by illness, are described for a sample of tibias and femurs from Casas Grandes, an archeological site in northern Chihuahua, Mexico. The sex and age of each individual at the time of growth arrest is noted, and the possibility of using this information to supplement or clarify archeological data is discussed.     

On-line monitoring of recombinant bacterial cultures using multi-wavelength fluorescence spectroscopy

Multi-wavelength fluorescence spectroscopy was evaluated as a tool for on-line monitoring of recombinant Escherichia coli cultivations expressing human basic fibroblast growth factor (hFGF-2). The data sets for the various combinations of the excitation and emission spectra from batch cultivations were analyzed using principal component analysis. Chemometric models (the partial least squares method) were developed for correlating the fluorescence data and the experimentally measured variables such as the biomass and glucose concentrations as well as the carbon dioxide production rate. Excellent correlations were obtained for these variables for the calibration cultivations. The predictability of these models was further tested in batch and fed-batch cultivations. The batch cultivations were well predicted by the PLS models for biomass, glucose concentrations and carbon dioxide production rate (RMSEPs were respectively 5%, 7%, 9%). However, when tested for biomass concentrations in fed-batch cultivations (with final biomass three times higher than the highest calibration data) the models had good predictability at high growth rates (RMSEPs were 3% and 4%, respectively for uninduced and induced fed-batch cultivations), which was as good as for the batch cultivations used for developing the models (RMSEPs were 3% and 5%, respectively for uninduced and induced batch cultivations). The fed-batch cultivations performed at low growth rates exhibited much higher fluorescence for fluorophores such as flavin and NAD(P)H as compared to fed-batch cultivations at high growth rate. Therefore, the PLS models tended to over-predict the biomass concentrations at low growth rates. Obviously the cells changed their concentration of biogenic fluorophores depending on the growth rate. Although multi-wavelength fluorescence spectroscopy is a valuable tool for on-line monitoring of bioprocess, care must be taken to re-calibrate the PLS models at different growth rates to improve the accuracy of predictions.     

CUSUM chart method for continuous monitoring of antifouling treatment of tubular heat exchangers in open-loop cooling seawater systems

Abstract

A CUSUM chart method is presented as an alternative tool for continuous monitoring of an electromagnetic field-based (EMF) antifouling (AF) treatment of a heat exchanger cooled by seawater. During an initial experimental phase, biofilm growth was allowed in a heat exchanger formed of four tubes until sufficient growth had been established. In two of the tubes, continuous EMF treatment was then applied. The heat transfer resistance and heat duty (heat transfer per unit time) results showed that biofilm adhesion was reduced by the EMF treatment. EMF treatments resulted in a 35% improvement in the heat transfer resistance values. The proposed CUSUM chart method showed that the EMF treatment increased the useful life of the heat exchanger by ～20?days. Thus, CUSUM charts proved to be an efficient tool for continuous monitoring of an AF treatment using data collected online and can also be used to reduce operation and maintenance costs.     

Production of a monoclonal antibody directed against the high-affinity nerve growth factor receptor.

The high-affinity nerve growth factor receptor corresponds to the tyrosine protein kinase encoded by the proto-oncogene trkA. Different findings suggest that nerve growth factor (NGF) can be operative in the growth modulation of tumor cell lines possessing high-affinity binding sites for this molecule. Using as immunizing material the SKNBE neuroblastoma cell line transfected with proto-trkA we produced a monoclonal antibody (MAb) able to recognize the high-affinity nerve growth factor receptor. The selected MAb, designated MGR12, is directed against an epitope present on the extracellular domain of the receptor since it showed reactivity on living trkA-expressing cells and was able to immunoprecipitate the proto-trkA molecule. The MGR12 MAb is directed against a non-functional epitope since it neither inhibited NGF binding nor induced receptor internalization. This new reagent appears to be an appropriate tool for analyzing the expression of high-affinity nerve growth factor receptor in tumors of different origin and for elucidating its involvement in tumor progression.     

The Growth of a Laboratory

The growth of the laboratory work in a general and teaching hospital was studied from annual statistical returns, which gave a broad general picture for the period 1922 through 1953, and permitted a more detailed analysis for 1954 through 1964. An attempt was made to analyze the growth of work in the various laboratory departments, and to explain the changes found as far as possible. It appears that knowledge of previous changes might be used as a predictive tool for estimating future work loads. A plea is made for utilization of such studies in the design, equipment, staffing and financing of laboratory work, with the recognition that growth in this department has been and is likely to continue to be disproportionately greater than in hospital work as a whole.     

CLIMTREG: Detecting temporal changes in climate–growth reactions – A computer program using intra-annual daily and yearly moving time intervals of variable width

Analysing climate–growth relationships is one of the key areas in dendrochronological research. One problem however remained unsolved – the discrepancy between the trees continuous growth over the vegetation period and the mean climate variables stretching over much longer periods. Here we present the possibility to calculate climate–growth correlations based on daily climate data using variable temporal width together with moving correlations to accommodate for short term as well as long term influences on tree growth. For the first time this offers the opportunity to acknowledge annual changes in the growing seasonal length and effects of short extreme events. Numerous outputs in data- and graphic-files allows a comparison of varying periods with significant correlations between climate and tree growth. Furthermore the use of climate scenarios is an optional tool for growth predictions.     

Coupling curvature-dependent and shear stress-stimulated neotissue growth in dynamic bioreactor cultures: a 3D computational model of a complete scaffold

The main challenge in tissue engineering consists in understanding and controlling the growth process of in vitro cultured neotissues toward obtaining functional tissues. Computational models can provide crucial information on appropriate bioreactor and scaffold design but also on the bioprocess environment and culture conditions. In this study, the development of a 3D model using the level set method to capture the growth of a microporous neotissue domain in a dynamic culture environment (perfusion bioreactor) was pursued. In our model, neotissue growth velocity was influenced by scaffold geometry as well as by flow- induced shear stresses. The neotissue was modeled as a homogenous porous medium with a given permeability, and the Brinkman equation was used to calculate the flow profile in both neotissue and void space. Neotissue growth was modeled until the scaffold void volume was filled, thus capturing already established experimental observations, in particular the differences between scaffold filling under different flow regimes. This tool is envisaged as a scaffold shape and bioprocess optimization tool with predictive capacities. It will allow controlling fluid flow during long-term culture, whereby neotissue growth alters flow patterns, in order to provide shear stress profiles and magnitudes across the whole scaffold volume influencing, in turn, the neotissue growth.     

Electrospun poly-l-lactide nanofibres as scaffolds for tissue engineering]

Tissue engineering is a promising tool for treating structural and functional defects in bone and cartilage. To provide optimal conditions for three-dimensional cell growth the use of a scaffold is necessary. The aim of the study was to test the potential application of an electrospun poly (l-lactide)-nanostructured scaffold as a matrix for tissue engineering. Matrices were seeded with human osteosarcoma MG-63 cells and cultivated for 14 days. Cells showed a clear preference for growth along the nanofibres, and demonstrated no signs of degeneration or apoptosis. The fine structure of electrospun nanofibres makes them an ideal scaffold for tissue engineering, in particular for cartilage repair. They can be "doped" with growth factors, medications, etc., and are both biocompatible and biodegradable.     

InraPorc: A model and decision support tool for the nutrition of sows

From results obtained over the last 20 years on energy and amino acid utilisation in reproductive sows, it has become possible to improve the determination of nutrient requirements (factorial approach) and the prediction of an animal's response to nutrient supplies (modelling). The objective of this project was to integrate the current state of knowledge in a nutritional model for growing pigs and for sows and make it available as a software tool to end-users, mainly nutritionists involved in the pig industry and students in animal nutrition. The aim of this paper is to describe the basis of the sow model. The sow is represented as different compartments that change over the reproductive cycle. Nutrient flows considered are those of energy and digestible amino acids. Nutrients are used with the highest priority for maintenance and uterine growth or milk production. Subsequently, deposition and/or mobilisation of body proteins and lipids are determined and used for estimating the changes in body weight and backfat thickness of the sow. A decision support tool was built from the set of equations given, with additional modules to describe animal's characteristics and adjust some model parameters to account for variations in genotypes and performance. This tool can be used to determine energy and amino acids requirements of sows according to production objectives, or to predict body composition changes according to a given feeding strategy. The use of the decision support tool is illustrated through some examples.