Consensus and comprehensive linkage maps of bovine chromosome 24

This study describes development of a consensus genetic linkage map of bovine chromosome 24 (BTA24). Eight participating laboratories contributed data for 58 unique markers including a total of 25 409 meioses. Eighteen markers, which were typed in more than one reference population, were used as potential anchors to generate a consensus framework map. The framework map contained 16 loci ordered with odds greater than 1000:1 and spanned 79.3 cM. Remaining markers were included in a comprehensive map relative to these anchors. The resulting BTA24 comprehensive map was 98.3 cM in length. Average marker intervals were 6.1 and 2.5 cM for framework and comprehensive maps, respectively. Marker order was generally consistent with previously reported BTA24 linkage maps. Only one discrepancy was found when comparing the comprehensive map with the published USDA-MARC linkage map. Integration of genetic information from different maps provides a high-resolution BTA24 linkage map.     

Dauer juvenile longevity and stress tolerance in natural populations of entomopathogenic nematodes: is there a relationship?

Qualitative and quantitative genetic analysis of life span in experimental adult animals predicts that resistance to stress and longevity are positively correlated, but such studies on field populations of animals are rare. We tested this hypothesis using dauer juveniles of 15 natural populations of the entomopathogenic nematode, Heterorhabditis bacteriophora, collected from diverse localities. Dauer juvenile longevity at 25 degrees C in autoclaved tap water and tolerance to major environmental stresses including heat (survival at 40 degrees C for 2 h), ultraviolet (UV) radiation (original virulence remaining after exposure to 302 nm UV for 5 min), hypoxia (survival at approximately 0% dissolved O2 at 25 degrees C for 96 h), and desiccation (survival in 25% glycerol at 25 degrees C for 72 h) differed significantly among populations. Intrinsic dauer juvenile longevity, defined as the number of weeks to 90% mortality (LT90) estimated using probit analysis of nematode survival data at 25 degrees C varied between 6 and 16 weeks among populations. Longevity was most strongly correlated with heat followed by UV and hypoxia tolerance, respectively, but showed no correlation with desiccation tolerance. The strong positive correlation of longevity with heat tolerance was further confirmed through principal components analysis which showed almost identical variance for heat and longevity. Among the stress factors, only UV tolerance was positively correlated with heat and hypoxia tolerance. Differences in longevity and stress tolerance in nematode populations isolated from a single 200 m2 grassland locality further support another hypothesis that population structure of heterorhabditid nematodes is highly fragmented, thus suggesting the existence of metapopulation dynamics.     

Mutations in the 16S rRNA genes of Helicobacter pylori mediate resistance to tetracycline

Low-cost and rescue treatments for Helicobacter pylori infections involve combinations of several drugs including tetracycline. Resistance to tetracycline has recently emerged in H. pylori. The 16S rRNA gene sequences of two tetracycline-resistant clinical isolates (MIC = 64 microg/ml) were determined and compared to the consensus H. pylori 16S rRNA sequence. One isolate had four nucleotide substitutions, and the other had four substitutions and two deletions. Natural transformation with the 16S rRNA genes from the resistant organisms conferred tetracycline resistance on susceptible strains. 16S rRNA genes containing the individual mutations were constructed and tested for the ability to confer resistance. Only the 16S rRNA gene containing the triple mutation, AGA965-967TTC, was able to confer tetracycline resistance on H. pylori 26695. The MICs of tetracycline for the transformed strains were equivalent to those for the original clinical isolates. The two original isolates were also metronidazole resistant, but this trait was not linked to the tetracycline resistance phenotype. Serial passage of several H. pylori strains on increasing concentrations of tetracycline yielded mutants with only a very modest increase in tetracycline resistance to a MIC of 4 to 8 microg/ml. These mutants all had a deletion of G942 in the 16S rRNA genes. The mutations in the 16S rRNA are clearly responsible for tetracycline resistance in H. pylori.     

Fast biphasic regulation of type 3 inositol trisphosphate receptors by cytosolic calcium

In cytosol-like medium (CLM) with a free [Ca(2+)] of 200 nm, a supramaximal concentration of inositol 1,4,5-trisphosphate (IP(3)) (30 microm) evoked (45)Ca(2+) release from type 3 IP(3) receptors only after a latency of 48 +/- 6 ms; this latency could not be reduced by increasing the IP(3) concentration. In CLM containing a low free [Ca(2+)] ( approximately 4 nm), 300 microm IP(3) evoked (45)Ca(2+) release after a latency of 66 +/- 11 ms; this was reduced to 14 +/- 3 ms when the [Ca(2+)] was 1 mm. Preincubation with CLM containing 100 microm Ca(2+) caused a rapid (half-time = 33 +/- 9 ms), complete, and fully reversible inhibition that could not be overcome by a high concentration of IP(3) (300 microm). Hepatic (type 2) IP(3) receptors were not inhibited by Ca(2+) once they had bound IP(3), but 100 microm Ca(2+) rapidly inhibited type 3 IP(3) receptors whether it was delivered before addition of IP(3) or at any stage during a response to IP(3). Ca(2+) increases the affinity of IP(3) for hepatic receptors by slowing IP(3) dissociation, but Ca(2+) had no effect on IP(3) binding to type 3 receptors. The rate of inhibition of type 3 IP(3) receptors by Ca(2+) was faster than the rate of IP(3) dissociation, and occurred at similar rates whether receptors had bound a high (adenophostin) or low affinity (3-deoxy-3-fluoro-IP(3)) agonist. Dissociation of agonist is not therefore required for Ca(2+) to inhibit type 3 IP(3) receptors. We conclude that type 2 and 3 IP(3) receptors are each biphasically regulated by Ca(2+), but by different mechanisms. For both, IP(3) binding causes a stimulatory Ca(2+)-binding site to be exposed allowing Ca(2+) to bind and open the channel. IP(3) binding protects type 2 receptors from Ca(2+) inhibition, but type 3 receptors are inhibited by Ca(2+) whether or not they have IP(3) bound. Increases in cytosolic [Ca(2+)] will immediately inhibit type 3 receptors, but inhibit type 2 receptors only after IP(3) has dissociated.     

Characterization of thermodynamic diversity between transmissible spongiform encephalopathy agent strains and its theoretical implications.

Some transmissible spongiform encephalopathy (TSE) (or "prion") strains, notably those derived from bovine spongiform encephalopathy, are highly resistant to total inactivation by heat. When three TSE strains derived from sheep with scrapie were heated, little inactivation took place at low temperatures, but at higher temperatures, considerable inactivation occurred. The temperature at which substantial inactivation first occurred varied according to TSE strain, and it was calculated to be 70 degrees C for the 22C strain, 84 degrees C for ME7, and 97 degrees C for 22A by fitting the data to a model based on competition between a destructive and a protective reaction. However, PrP(Sc) from mice infected with a range of TSE strains retained similar resistance to proteinase K digestion after heating to below or above these temperatures, showing that the properties of PrP(Sc) responsible for proteinase resistance do not correlate with those conferring thermostability on the TSE agent. The simplest explanation of these data is that the causal agent contains a macromolecular component that is structurally independent of the host, that it varies covalently between TSE strains, and that it is protected by other macromolecular components. The model is in accord with the virino hypothesis, which proposes a host-independent informational molecule protected by the host protein PrP.     

Amino acid encoding schemes from protein structure alignments: multi-dimensional vectors to describe residue types

Bioinformatic software has used various numerical encoding schemes to describe amino acid sequences. Orthogonal encoding, employing 20 numbers to describe the amino acid type of one protein residue, is often used with artificial neural network (ANN) models. However, this can increase the model complexity, thus leading to difficulty in implementation and poor performance. Here, we use ANNs to derive encoding schemes for the amino acid types from protein three-dimensional structure alignments. Each of the 20 amino acid types is characterized with a few real numbers. Our schemes are tested on the simulation of amino acid substitution matrices. These simplified schemes outperform the orthogonal encoding on small data sets. Using one of these encoding schemes, we generate a colouring scheme for the amino acids in which comparable amino acids are in similar colours. We expect it to be useful for visual inspection and manual editing of protein multiple sequence alignments.     

Animal flight dynamics II. Longitudinal stability in flapping flight

Stability is essential to flying and is usually assumed to be especially problematic in flapping flight. If so, problems of stability may have presented a particular hurdle to the evolution of flapping flight. In spite of this, the stability of flapping flight has never been properly analysed. Here we use quasi-static and blade element approaches to analyse the stability provided by a flapping wing. By using reduced order approximations to the natural modes of motion, we show that wing beat frequencies are generally high enough compared to the natural frequencies of motion for a quasi-static approach to be valid as a first approximation. Contrary to expectations, we find that there is noting inherently destabilizing about flapping: beating the wings faster simply amplifies any existing stability or instability, and flapping can even enhance stability compared to gliding at the same air speed. This suggests that aerodynamic stability may not have been a particular hurdle in the evolution of flapping flight. Hovering animals, like hovering helicopters, are predicted to possess neutral static stability. Flapping animals, like fixed wing aircraft, are predicted to be stable in forward flight if the mean flight force acts above and/or behind the centre of gravity. In this case, the downstroke will always be stabilizing. The stabilizing contribution may be diminished by an active upstroke with a low advance ratio and more horizontal stroke plane; other forms of the upstroke may make a small positive contribution to stability. An active upstroke could, therefore, be used to lower stability and enhance manoeuvrability. Translatory mechanisms of unsteady lift production are predicted to amplify the stability predicted by a quasi-static analysis. Non-translatory mechanisms will make little or no contribution to stability. This may be one reason why flies, and other animals which rely upon non-translatory aerodynamic mechanisms, often appear inherently unstable.