On the paradoxical determinations of the lacuno-canalicular permeability of bone

The lacuno-canalicular permeability has been shown to play a key role in the behavior of bone tissue. The aim of this study is, by giving an overview of the determinations of this parameter, to question the paradoxical values provided by theoretical predictions and recent experimental measurements. We propose therefore a Kozeny-like law obtained by a numerical method which relates the permeability to the textural parameters of cortical bone microstructure. Moreover, we suggest possible explanations for this paradox considering the empirical difficulties and possible multiphysical effects.     

Effect of reserpine on the differentiation of the external granular layer of the cerebellum in the chick embryo

In this work we analyse the effect produced by reserpine on the development of thickness and cell number in the external granular layer in the cerebellum of chick embryo. A striking 48-hour histogenetic delay is observed in the treated embryos relative to controls, as show by greater thickness and cell density of this layer in the former, as well as by retarded appearance of a typical radial morphological organization of the external granular layer.     

An investigation of the role of the copper in galactose oxidase.

Galactose oxidase is a metalloenzyme containing a single copper atom per molecule. The mechanism of action of galactose oxidase is studied in this paper by investigating substrate specificity and activation by peroxidase, and probing the copper site by electron spin resonance (ESR) spectroscopy. Line-shape simulation of ESR spectra are also reported and a comparison is made between observed and simulated spectra for galactose oxidase. A comparison is also reported for the enzyme from various commercial sources and enzyme isolated from a fungus in this laboratory. The results of this investigation suggest that the copper is in an environment of four in-plane nitrogens with axial symmetry.     

Telemetric system for measuring the pressure of the tongue on the palate]

The development of the upper jaw during growth is influenced by the function and position of the tongue and perioral soft tissues, and the pressures exerted by them. Accurate determination of the forces exerted by the tongue would provide relevant information about this influence. To date, our ability to obtain continuous recordings of the tongue pressure during certain functions is limited. In this paper, an easy-to-employ and accurate telemetric system for such functional measurements is presented. The system, consisting of four piezoresistive pressure sensors, a microcontroller, a telemetric module and batteries, is integrated within a removable orthodontic plate and transmits the measured data out of the oral cavity to a receiver.     

Avoiding the SCAMs

Dendrites from the same neuron usually avoid contact with one another, a behavior known as self-avoidance. In this issue of Neuron and in the upcoming May 4, 2007 issue of Cell, a pair of studies by Soba et al. and Hughes et al. and a study by Matthews et al., respectively, identify products from the highly alternatively spliced Dscam gene as central to this behavior in Drosophila. Signaling induced by adhesion between identical isoforms triggers repulsion between sister dendrites.     

Conjugative transposons: the tip of the iceberg

Elements that excise and integrate, such as prophages, and transfer by conjugation, such as plasmids, have been found in various bacteria. These elements appear to have a diversified set of characteristics including cell-to-cell contact using pili or cell aggregation, transfer of single-stranded or double-stranded DNA, low or high specificity of integration and serine or tyrosine recombinases. This has led to a highly heterogeneous nomenclature, including conjugative transposons, integrative 'plasmids', genomic islands and numerous unclassified elements. However, all these elements excise by site-specific recombination, transfer the resulting circular form by conjugation and integrate by recombination between a specific site of this circular form and a site in the genome of their host. Whereas replication of the circular form probably occurs during conjugation, this replication is not involved in the maintenance of the element. In this review, we show that these elements share very similar characteristics and, therefore, we propose to classify them as integrative and conjugative elements (ICEs). These elements evolve by acquisition or exchanges of modules with various transferable elements including at least ICEs and plasmids. The ICEs are probably widespread among the bacteria.     

Probing the role of the ATP-operated clamp in the strand-passage reaction of DNA gyrase.

The high-resolution structure of the 43 kDa N-terminal fragment of the DNA gyrase B protein shows a large cavity within the protein dimer. The approximate size of this cavity is 20 A, suggesting it could accommodate a DNA helix. Computer-modelling studies of this cavity suggest that it contains a constriction, reducing the width to approximately 13 A, principally caused by the side chain of Arg286. We have used site-directed mutagenesis to alter this residue to Gln. Gyrase bearing this mutation shows virtually no supercoiling activity and near-normal relaxation and DNA cleavage activities. The mutated protein has ATPase activity which cannot be stimulated by DNA. These data support the proposed role of the 43 kDa domain as an ATP-operated clamp which binds DNA during the supercoiling cycle. The lack of DNA-dependent ATPase of the mutant may indicate that binding of DNA within the clamp is a prerequisite for stimulation of the ATPase activity.     

Haemozoin formation in the midgut of the blood-sucking insect Rhodnius prolixus

Malaria parasites digest haemoglobin and detoxify the free haem by its sequestration into an insoluble dark-brown pigment known as haemozoin (Hz). Until recently, this pigment could be found only in Plasmodium parasites. However, we have shown that Hz is also present in the midgut of the blood-sucking insect Rhodnius prolixus [Oliveira et al. (1999) Nature 400, 517-518]. Here we show that Hz synthesis in the midgut of this insect is promoted by a particulate fraction from intestine lumen. Haem aggregation activity is heat-labile and is inhibited in vitro by chloroquine (CLQ). Inhibition of Hz formation in vivo by feeding insects with CLQ leads to increased levels of haem in the haemolymph of the insect, which resulted in increased lipid peroxidation. Taken together, these results indicate that a factor capable of promoting Hz crystallisation is present in R. prolixus midgut and that this activity represents an important physiological defence of this insect against haem toxicity.     

On the information content of the genetic code

In living organisms 20 amino acids along with the terminator value(s) are encoded by 64 codons giving a degeneracy of the codons as described by the genetic code. A basic theoretical problem of genetic codes is to explain the particular distribution of degeneracies of partitions involved in the codes. In this work the degeneracy problem is considered in the framework of information theory. It is shown by direct numerical evaluation of a certain degeneracy information function associated with the genetic code that the degeneracy of the codes is observed to be related to the optimization of this function.     

Retrograde Traffic Out of the Yeast Vacuole to the TGN Occurs via the Prevacuolar/Endosomal Compartment

A large number of trafficking steps occur between the last compartment of the Golgi apparatus (TGN) and the vacuole of the yeast Saccharomyces cerevisiae. To date, two intracellular routes from the TGN to the vacuole have been identified. Carboxypeptidase Y (CPY) travels through a prevacuolar/endosomal compartment (PVC), and subsequently on to the vacuole, while alkaline phosphatase (ALP) bypasses this compartment to reach the same organelle. Proteins resident to the TGN achieve their localization despite a continuous flux of traffic by continually being retrieved from the distal PVC by virtue of an aromatic amino acid–containing sorting motif. In this study we report that a hybrid protein based on ALP and containing this retrieval motif reaches the PVC not by following the CPY sorting pathway, but instead by signal-dependent retrograde transport from the vacuole, an organelle previously thought of as a terminal compartment. In addition, we show that a mutation in VAC7, a gene previously identified as being required for vacuolar inheritance, blocks this trafficking step. Finally we show that Vti1p, a v-SNARE required for the delivery of both CPY and ALP to the vacuole, uses retrograde transport out of the vacuole as part of its normal cellular itinerary.     

A Blind Empiricism Against the Coevolution Theory of the Origin of the Genetic Code

Ronneberg et al. (Proc Natl Acad Sci USA 97:13690–13695, 2000) recently suggested abandoning the coevolution theory of genetic code origin on the basis of two pieces of evidence. They (1) criticize the use of several pairs of amino acids in a precursor–product relationship to support this theory and (2) suggest a new set of codes in which to investigate the statistical bases of the coevolution theory, reaching the conclusion that this theory is not statistically validated in this set. In this paper I critically analyze the robustness of these conclusions. Observations and arguments lead to the belief that the pairs of amino acids in a precursor–product relationship originally used by the coevolution theory are such, or may at least be interpreted as such, and are therefore a manifestation of this theory. Furthermore, the new set of codes that Ronneberg et al. suggest is open to criticism and is thus substituted by the set of amino acid permutation codes, in which even the pairs of amino acids they favor end up by supporting the coevolution theory. Overall, the analysis seems to show that the paper by Ronneberg et al. is of minor scientific value while the coevolution theory seems to be one of the best theories at our disposal for explaining the evolutionary organisation of the genetic code and is, contrary to their claims, statistically well validated. Received: 21 February 2001 / Accepted: 22 May 2001     

Pyruvate kinase from the thermophilic eubacterium Bacillus acidocaldarius as probe to monitor the sodium concentrations in the blood

We describe the isolation and characterization of a pyruvate kinase from the thermophilic eubacterium Bacillus acidocaldarius. This protein appears to be a tetramer composed of four 55-kDa subunits. The intrinsic tryptophan fluorescence of this protein is quenched by approximately 20% upon binding sodium, which occurs with a dissociation constant near 15 mM. Importantly, the intrinsic fluorescence of this pyruvate kinase does not appear to be affected by potassium, magnesium, and calcium at the concentrations found in whole blood. It appears that this pyruvate kinase can provide the basis for a selective protein sensor for sodium with minimal interference from other cations.     

Approaches to the purification of the juvenile hormone esterase from the cabbage looper,Trichoplusia ni

Several approaches to the purification of juvenile hormone (JH) esterase from second-day last-instar larvae of Trichoplusia ni were taken, including: ammonium sulphate precipitation, polyethylene glycol precipitation, hydrophobic interaction chromatography, anion exchange chromatography, and gel filtration chromatography. The most successful procedure involved a combination of polyethylene glycol precipitation with anion exchange chromatography on DEAE Sephacel which yielded a 134-fold purification of juvenile hormone esterase. When this preparation was subjected to semi-preparative electrophoresis followed by isoelectric focusing on a polyacrylamide slab gel, a single band of apparently homogeneous enzyme was obtained. Juvenile hormone esterase activity was unstable after electrophoresis and isoelectric focusing. The stability of juvenile hormone esterase activity in a water solution is influenced by protein concentration and by agents protecting sulphydryl groups. The results of this study support the hypothesis that a single protein is responsible for the majority of the JH hydrolysis catalyzed by haemolymph from the larvae of T. ni used in this study.     

Improving the positional accuracy of the goniometer on the Philips CM series TEM

We have developed a method to improve the accuracy for absolute relocation of a target specimen using the goniometer on a Philips transmission electron microscope. We have achieved this by characterizing the performance of the Philips compustage, modeling its behavior, and using this model to calculate the goniometer movements required for accurate target relocation. This resulted in a 10-fold improvement in the positioning accuracy of the goniometer.     

Characterization of the trans Watson-Crick GU base pair located in the catalytic core of the antigenomic HDV ribozyme

The HDV ribozyme's folding pathway is, by far, the most complex folding pathway elucidated to date for a small ribozyme. It includes 6 different steps that have been shown to occur before the chemical cleavage. It is likely that other steps remain to be discovered. One of the most critical of these unknown steps is the formation of the trans Watson-Crick GU base pair within loop III. The U(23) and G(28) nucleotides that form this base pair are perfectly conserved in all natural variants of the HDV ribozyme, and therefore are considered as being part of the signature of HDV-like ribozymes. Both the formation and the transformation of this base pair have been studied mainly by crystal structure and by molecular dynamic simulations. In order to obtain physical support for the formation of this base pair in solution, a set of experiments, including direct mutagenesis, the site-specific substitution of chemical groups, kinetic studies, chemical probing and magnesium-induced cleavage, were performed with the specific goal of characterizing this trans Watson-Crick GU base pair in an antigenomic HDV ribozyme. Both U(23) and G(28) can be substituted for nucleotides that likely preserve some of the H-bond interactions present before and after the cleavage step. The formation of the more stable trans Watson-Crick base pair is shown to be a post-cleavage event, while a possibly weaker trans Watson-Crick/Hoogsteen interaction seems to form before the cleavage step. The formation of this unusually stable post-cleavage base pair may act as a driving force on the chemical cleavage by favouring the formation of a more stable ground state of the product-ribozyme complex. To our knowledge, this represents the first demonstration of a potential stabilising role of a post-cleavage conformational switch event in a ribozyme-catalyzed reaction.     

Bending the rules: the 2-mu plasmid of yeast

The replication of eukaryotic DNA is normally initiated at each origin only once per cell cycle. Yet, in spite of this restriction, the 2-mu plasmid of yeast has evolved an elegant mechanism which can allow it to rapidly amplify its copy number without initiating multiple rounds of replication. It achieves this by exploiting a plasmid-encoded site-specific recombination system in a way that is apparently unique to this plasmid. The 2-mu plasmid has also evolved a mechanism that allows effective partition of itself between mother and daughter cells. Together these processes ensure the persistence of the 2-mu plasmid within a population, even though retention of the plasmid is of no advantage to the host cell and causes a slightly slower growth rate. The success of this survival strategy is illustrated by the near ubiquity of the 2-mu plasmid in both wild-type and laboratory strains of yeast.