An easy way to reduce PIT-tag loss in rodents

Passive integrated transponders (PIT-tags) have been shown to be a reliable method for individually marking rodents in field studies. The loss rates of PIT-tags vary, depending on the species, from 3.6 to 7.2%. We used PIT-tags to individually mark a population of edible dormice. Due to a relatively high loss rate of transponders in the first year (7.4%) we used a tissue adhesive to seal the punctuation wound in the second year. With this method we could reduce the tag-loss rate to 2.2%. We therefore recommend using a tissue adhesive, which is easy and fast to apply, after injecting a transponder.     

An easy way to include weak alignment constraints into NMR structure calculations

We have recently shown that an energy penalty for the incorporation of residual tensorial constraints into molecular structure calculations can be formulated without the explicit knowledge of the Saupe orientation tensor (Moltke and Grzesiek, J. Biomol. NMR, 1999, 15, 77–82). Here we report the implementation of such an algorithm into the program X-PLOR. The new algorithm is easy to use and has good convergence properties. The algorithm is used for the structure refinement of the HIV-1 Nef protein using 252 dipolar coupling restraints. The approach is compared to the conventional penalty function with explicit knowledge of the orientation tensor's amplitude and rhombicity. No significant differences are found with respect to speed, Ramachandran core quality or coordinate precision.     

Technical note: Ultraviolet reflectance-absorbance photography; An easy,inexpensive research tool

Photography in the ultraviolet wavelength is possible by use of special lenses, special filters, or both. This paper makes available pertinent information on an easy, inexpensive UV photographic technique. A comprehensive bibliography is provided. By using a flash guide number, lens apertures for various lens-subject distances can be calculated. The inexpensive technique is accomplished by simple adaptation of a Kodak Wratten 18A filter to the normal camera lens. The method is equally suited for living material, dried herbarium material, and chromatograms. The technique is useful in studies of pollination ecology, insect energetics, taxonomy, and flavonoid chemistry.     

White gels: an easy way to preserve methylene blue stained gels

Methylene blue can be used as a stain for visualizing nucleic acids in polyacrylamide gel electrophoresis. However, its relatively low sensitivity and reversible binding make it a temporary stain that diffuses from the gel relatively fast. Here we describe a very simple method for fixing methylene blue bands in nucleic acid polyacrylamide gels. The procedure makes the methylene blue stain permanent and increases the visibility of the bands, also contributing to increasing the sensitivity of methylene blue.     

An easy colorimetric assay for glycosyltransferases

Glycosyltransferases are involved in biosynthesis of both protein-bound and non-bound glycans that have multiple and important biological functions in all species. A variety of methods for assaying glycosyltransferase activity have been developed driven by the specific interests and type of information required by researchers. In this work, a novel colorimetric assay for the glycosyltransferase-catalyzed reaction was established. Compared with measuring the newly formed product, which might not exhibit visible absorption, the unreacted acceptor could be readily detected by measuring the visible absorption of the hydrolysis product. In the assay, 4-nitrophenyl-β-D-glycoside (glycosyl-β-pNP) is used as the glycosyl acceptor, which can be hydrolyzed by a special exoglycosidase to release the p-nitrophenol before glycosylation reactions. Absorbance change of the p-nitrophenolate corresponds to unreacted glycosyl acceptor that accompanied the glycosyl transfer. The assay is demonstrated to be useful in the initial characterization of recombinant glycosyltransferases for their kinetic parameters, optimal metal cofactor, and pH value. It provides a simple, sensitive, and quantitative method for assessing glycosyltransferase activity and is thus expected to have broad applications including automated high-throughput screening.     

An isotopic technique to mark mid-sized vertebrates non-invasively

Understanding the basis of habitat choice having important implications for explaining the distribution of organisms, as well as helping to differentiate between habitats of different quality for effective management. In this study, the effects of sex, age and reproductive status on habitat use patterns of cheetahs Acinonyx jubatus in the Serengeti plains were explored using Ecological Niche Factor Analysis (ENFA). Our results showed that gender and territoriality did not affect patterns of habitat use. However, females tended to be more specialized when they were young than when they were older, displaying a more restricted ecological niche. Likewise, older females without cubs were more specialized than the same adult females with young cubs. This result did not hold for younger females. Altogether, the ENFA approach allowed us to (1) use the large amount of incidental sighting data collected over 12 years on cheetah spatial distribution; (2) identify the importance of reproductive status and age on the relationship between animals and their habitat; (3) further demonstrate that ENFA is applicable in a wide range of situations, including for exploring individual variation in niche definition.     

An easy way for the rapid purification of recombinant proteins from Helicobacter pylori using a newly designed expression vector

We constructed a H. pylori expression vector which consisted of both a His-tag and a GST tag as purification tools for recombinant protein and a chloramphenicol resistant cat gene as a reporter. The backbone of the vector pBKcontained an ColEI origin of replication and a kanamycin resistant gene. A set of oligos for the His-tag and the PCR product of gst (glutathione S-transferase) gene were inserted sequentially in frame in themulti-cloning site of pBK. The orf of cat was inserted downstreamof the gst to generate pBKHGC. The 3′ part of H. pylori clpB and flaA were cloned into the vector which was introduced into H. pylori. Recombinant proteins were purified by GSH affinity column, digested with thrombin and were analyzed by western blotting. The final recombinant proteins were successfully purified.     

An easy diagnostic approach to primary aldosteronism.

The infusion of 40 mEq potassium (aspartate) in 250 ml isotonic 1-fructose at a rate of 20 mEq/h into 5 patients (34-56 years old) with aldosteronoma and 2 patients with bilateral primary aldosteronism consistently raised their mean arterial pressure by 15-20 mmHg. Their pressure values returned to the baseline levels 4-5 h after the infusion. In contrast, in controls (10 patients with idiopathic arterial hypertension, matched for age, sex, and magnitude of the untreated hypertension, and 7 patients with inactive adrenal nodules as incidental findings on upper abdomen ultrasound or computerized tomography) the same procedure caused negligible arterial pressure changes. The cause of the rise in blood pressure observed uniquely in patients with primary aldosteronism after infusion of potassium (aspartate) cannot be accounted for by an increase in plasma aldosterone, blood volume, or plasma angiotensin II. The cause of this response thus remains obscure; nonetheless, this simple procedure may prove useful in differentiating primary aldosteronism from idiopathic hypertension, in excluding the adrenal disorder, and in revealing even its mildest forms.     

Breaking Caenorhabditis elegans the easy way using the Balch homogenizer: An old tool for a new application

The nematode Caenorhabditis elegans is a model organism best known for its powerful genetics. There is an increasing need in the worm community to couple genetics with biochemistry. Isolation of functionally active proteins or nucleic acids without the use of strong oxidizing denaturants or of subcellular compartments from C. elegans has, however, been challenging because of the worms’ thick surrounding cuticle. The Balch homogenizer is a tool that has found much use in mammalian cell culture biology. The interchangeable single ball-bearing design of this instrument permits rapid permeabilization, or homogenization, of cells. Here we demonstrate the utility of the Balch homogenizer for studies with C. elegans. We describe procedures for the efficient breakage and homogenization of every larval stage, including dauers, and show that the Balch homogenizer can be used to extract functionally active proteins. Enzymatic assays for catalase and dihydrolipoamide dehydrogenase show that sample preparation using the Balch homogenizer equals or outperforms conventional methods employing boiling, sonication, or Dounce homogenization. We also describe phenol-free techniques for isolation of genomic DNA and RNA. Finally, we used the tool to isolate coupled mitochondria and polysomes. The reusable Balch homogenizer represents a quick and convenient solution for undertaking biochemical studies on C. elegans.     

A ‘simple clock’ approach of circadian rhythms: An easy way to predict the clock's singularity

A graphical method is presented which allows the prediction of phase resetting curves of circadian rhythms for both type 1 and type 0 resetting, starting from one experimentally determined phase resetting curve. Calculations were based on literature data for the pupal eclosion rhythm of Drosophila pseudoobscura. The method is based on the assumption that for all practical purposes the rhythm may be approached as a “simple clock”, i.e. an oscillator with only one state variable, namely its phase or circadian time, CT. Besides predicting both “types” of phase resetting the method is capable to locate the “position” of the phase singularity and thus the transition from type 1 to type 0 resetting. This graphical method is an elaboration of the “transformation method”, developed in 1972 by A. Johnsson and H. G. Karlsson, which was effective in predicting phase resetting by “strong” stimuli, but failed in the case of “weak” stimuli. Predictions made using the extended transformation method are in good agreement with experimental results obtained with Drosophila. Also for the flesh fly, Sarcophaga argyrostoma, a prediction is made of the position of the phase singularity of the eclosion rhythm and compared with experimental results.