Tentacle regeneration in hydra: A quantitative methodological approach

A quantitative method is proposed for the evaluation of distal regeneration in Hydra attenuata; it is based on estimates of tentacle elongation during 10 days of regeneration, determination of a Tentacle Regeneration Index, and a statistical analysis of profiles obtained from various samples in different experiments. The results show that: polyps under normal conditions have similar regeneration patterns, regardless of individual variability; and ATxII, a neurotoxin of cnidarian origin, produces a statistically significant increase in the Tentacle Regeneration Index. The results are discussed in relation to pattern formation and growth in Hydra.     

Pattern formation in hydra tissue without developmental gradients

Ring-shaped pieces of hydra tissue were excised from a specified position on a body column of 20-30 polyps and grafted together in tandem like a chain of beads. A "tandem graft" prepared in this way has the same basic tissue organization and same tube-like morphology as a normal hydra body column, but lacks the head, foot, and developmental gradients ordinarily present. Three major types of structures were formed along the length of the tandem graft: heads, buds, and feet. The relative number of these structures produced was strongly affected by the origin of the tissue used to prepare the tandem graft. Evidence was obtained which suggests that tissue originally located outside of the budding zone in intact hydra has a strong latent capacity to form a bud, and that the level of this capacity forms a gradient from the budding zone toward the hypostome. Evidence was also obtained which is consistent with the view that the head and foot forming mechanisms cross-react positively, increasing the chances for these two structures to be formed next to each other on a tandem graft.     

A restaining method to restore faded fluorescence in tissue specimens for quantitative confocal microscopy.

The aim of this study was to develop a procedure to remove the TO-PRO-3 fluorescent dye from tissue sections and restain with TO-PRO-3, still allowing calculation of DNA content and distribution by confocal laser scanning microscopy (CLSM). This would allow repeated measurements on the same tissue sections and prevents loss of tissue material from valuable clinical samples. Thick sections (14 microm) were cut from a paraffin block of adrenal tissue and stained using TO-PRO-3. Image stacks were acquired by CLSM. Thereafter, three destaining approaches were tested based on incubation, at different temperatures and durations, in the medium that is normally used to dissolve TO-PRO-3. The same areas were imaged again to measure residual fluorescence and were subsequently restained and imaged again. The intensity of the images acquired after initial staining and restaining were compared. A number of 3-D (texture) features computed after segmentation of nuclei were compared as well. The best destaining result was obtained by incubation of sections at 37 degrees C in preheated medium twice for 20 min. On average, the 3-D feature values were comparable with those after initial staining. With the described protocol it is possible to remove TO-PRO-3 fluorescence from tissue sections that can successfully be restained with minimal influence on fluorescence intensity and nuclear chromatin distribution.     

A quantitative method for measuring protein phosphorylation

We have developed a novel method for quantitating protein phosphorylation by a variety of protein kinases. It can be used with purified kinases and their substrates in vitro or in combination with cell extracts. The method is based on the knowledge that protein kinase C (PKC) adds three phosphates to each molecule of its preferred substrate, myelin basic protein (MBP). A time course is performed in which a kinase is allowed to phosphorylate its preferred substrate or the protein under investigation in the presence of [gamma-32P]ATP. At the same time PKC is allowed to fully phosphorylate MBP. After resolving the products by SDS-PAGE, electrophoretic transfer, and determining the degree of incorporation of 32P by phosphorImager analysis, the data are converted to moles phosphate/mole protein by normalization with phosphorylated MBP. The method is both sensitive and relatively rapid and all the steps are commonly available in the biochemistry laboratory. We have used this method to confirm and extend information on the relationship of MEK1 and MAPK/Erk2 in rat lung fibroblasts exposed to V(2)O(5). A 4-h exposure to V(2)O(5) results in partial phosphorylation of MAPK/Erk2 such that 25% of the potential phosphorylation sites are occupied. We also demonstrate that despite multiple potential phosphorylation sites, recombinant human AP endonuclease is weakly phosphorylated in vitro (4% at best) by PKC, cGMP-dependent protein kinase, casein kinase II, and casein kinase I and not at all phosphorylated by MAPK. Furthermore we are unable to demonstrate phosphorylation in cell extracts from HeLa cells, mouse fibroblasts after oxidative damage with H(2)O(2) or alkylation damage with methylmethane sulfonate, or rat lung fibroblasts after oxidative damage with V(2)O(5).     

A quantitative method for separation of livingHydra cells

Summary We describe a rapid method for the isolation of large numbers of livingHydra cells of defined cell type in an isotonic cell medium (Gierer et al. 1972). Intact animals are enzymatically dissociated into a single cell suspension and the various cell types separated in less than one hour by counterflow centrifugation elutriation. Cell loss is minimal. RNA isolated from various fractions can be probed with cell type specific cDNA-clones.     

A rapid method for quantitative determination of L-tryptophan

Summary A modified colorimetric technique automatized by an Alpkem micro-continuous flow analyser was described for estimating the concentration of L-tryptophan in fermentation broth. This approach provided a convenient alternative to HPLC for L-tryptophan estimation and may help to avoid the time-consuming and laborious screening work encountered in the strain improvement programme.     

A method for determining tissue sulfate

A method for the determination of the inorganic sulfate present in rat liver homogenates has been developed. In order to determine sulfate, a protein-free extract is required. The classical protein precipitation methods of preparing protein-free extracts gave 2.5–40% recovery of added ³⁵SO₄^2?. Separation of the protein by ultrafiltration gave only 29% recovery when 0.15 m KCl was the homogenizing medium. A homogenization medium containing 0.154 m NH₄OH and 20 g EDTA per liter gave 102 ± 11% recovery of added ³⁵SO₄^2? when the protein was separated by ultrafiltration.     

A quantitative method for determining spatial discriminative capacity

Background  

The traditional two-point discrimination (TPD) test, a widely used tactile spatial acuity measure, has been criticized as being imprecise because it is based on subjective criteria and involves a number of non-spatial cues. The results of a recent study showed that as two stimuli were delivered simultaneously, vibrotactile amplitude discrimination became worse when the two stimuli were positioned relatively close together and was significantly degraded when the probes were within a subject's two-point limen. The impairment of amplitude discrimination with decreasing inter-probe distance suggested that the metric of amplitude discrimination could possibly provide a means of objective and quantitative measurement of spatial discrimination capacity.     

A high-throughput method for the quantitative analysis of indole-3-acetic acid and other auxins from plant tissue

To investigate novel pathways involved in auxin biosynthesis, transport, metabolism, and response, we have developed a high-throughput screen for indole-3-acetic acid (IAA) levels. Historically, the quantitative analysis of IAA has been a cumbersome and time-consuming process that does not lend itself to the screening of large numbers of samples. The method described here can be performed with or without an automated liquid handler and involves purification solely by solid-phase extraction in a 96-well format, allowing the analysis of up to 96 samples per day. In preparation for quantitative analysis by selected ion monitoring-gas chromatography-mass spectrometry, the carboxylic acid moiety of IAA is derivatized by methylation. The derivatization of the IAA described here was also done in a 96-well format in which up to 96 samples can be methylated at once, minimizing the handling of the toxic reagent, diazomethane. To this end, we have designed a custom diazomethane generator that can safely withstand high flow and accommodate larger volumes. The method for IAA analysis is robust and accurate over a range of plant tissue weights and can be used to screen for and quantify other indolic auxins and compounds including indole-3-butyric acid, 4-chloro-indole-3-acetic acid, and indole-3-propionic acid.     

A quantitative cytochemical method for ornithine decarboxylase activity

Although decarboxylases, particularly ornithine decarboxylase, are of considerable importance in cell metabolism, it has been impossible to demonstrate their activity histochemically, as this depends on trapping carbon dioxide at neutral pH values. A new reagent, lead hydroxyisobutyrate, has been shown capable of such trapping. It has been applied to the demonstration of ornithine decarboxylase activity in mouse kidney. Optimal concentrations of substrate, co-factor and trapping agent, as well as the pH optimum, have been determined for cryostat sections stabilized with a collagen polypeptide. The activity was inhibited by the specific ornithine decarboxylase inhibitor alpha-difluoromethyl ornithine.     

A quantitative genetic method for estimating developmental instability

The concept of developmental instability (DI) is frequently used in evolutionary biology, and a range of definitions has been proposed. Moreover, numerous different statistical methods have been used for estimation of DI. The common basis for all methods is that measures need to be obtained from repeated structures within organisms. In the case of fluctuating asymmetry, mirror images could be interpreted as the repeats of each other. All repeats of a trait on one organism should, from a quantitative perspective, have the same genetic foundation. Most previous methods have not accounted for the genetics of the underlying trait. It is here shown how a statistical method from quantitative genetics (the repeated records animal model) can be used for assessment of DI, based on estimation of the variance due to the permanent environment. Moreover, Gibbs sampling is used for inference of the parameters, which provides a Bayesian framework where posterior distributions easily can be calculated from any functions of the variance components. The method is applied to a real dataset from two populations of the plant Scabiosa canescens, and results shows that it works well under realistic situations.     

A non-radioactive method for inexpensive quantitative RT-PCR.

We present a novel method for quantitative RT-PCR that involves direct incorporation of digoxigenin-11-dUTP (DIG-dUTP) during amplification of cDNAs, separation of RT-PCR products by agarose gel electrophoresis, Southern transfer to a nylon membrane, and chemiluminescent detection with an anti-DIG antibody. The whole procedure can be done in about a day and has the following advantages: It is highly sensitive, specificity is confirmed by monitoring the size of the RT-PCR product, it is non-radioactive, quantitative, and does not require expensive specialized equipment.     

A quantitative Western Blot method for protein measurement

A radioimmunologic assay method for the quantitation of small amounts of protein in recombinant vaccines at the level of 20-150 ng is evaluated which uses the techniques of SDS-PAGE and electrophoretic protein transfer ("Western Blot'). Known amounts of the protein being determined are included on the same gel as the unknown. After protein blotting, the nitrocellulose membrane is treated with antibody specific for the protein being determined and subsequently with [125I] Protein A. An autoradiogram is produced which corresponds directly to the nitrocellulose blot. It can, therefore, serve as a template to locate the labeled protein which is excised from the blot and measured in a gamma counter. The technique is found especially useful for evaluating cell lysates of recombinant bacteria and yeast for the percentage of the recombinant protein in the total protein mixture.