G+C3 structuring along the genome: a common feature in prokaryotes

The heterogeneity of gene nucleotide content in prokaryotic genomes is commonly interpreted as the result of three main phenomena: (1) genes undergo different selection pressures both during and after translation (affecting codon and amino acid choice); (2) genes undergo different mutational pressure whether they are on the leading or lagging strand; and (3) genes may have different phylogenetic origins as a result of lateral transfers. However, this view neglects the necessity of organizing genetic information on a chromosome that needs to be replicated and folded, which may add constraints to single gene evolution. As a consequence, genes are potentially subjected to different mutation and selection pressures, depending on their position in the genome. In this paper, we analyze the structuring of different codon usage measures along completely sequenced bacterial genomes. We show that most of them are highly structured, suggesting that genes have different base content, depending on their location on the chromosome. A peculiar pattern of genome structure, with a tendency toward an A+T-enrichment near the replication terminus, is found in most bacterial phyla and may reflect common chromosome constraints. Several species may have lost this pattern, probably because of genome rearrangements or integration of foreign DNA. We show that in several species, this enrichment is associated with an increase of evolutionary rate and we discuss the evolutionary implications of these results. We argue that structural constraints acting on the circular chromosome are not negligible and that this natural structuring of bacterial genomes may be a cause of overestimation in lateral gene transfer predictions using codon composition indices.     

Vitamin D regulation of the renin-angiotensin system

The renin-angiotensin system (RAS) plays a central role in the regulation of blood pressure, electrolyte, and volume homeostasis. Epidemiological and clinical studies have long suggested an association of inadequate sunlight exposure or low serum 1,25-dihydroxyvitamin D(3) [1,25(OH)(2)D(3)] levels with high blood pressure and/or high plasma renin activity, but the mechanism is not understood. Our recent discovery that 1,25(OH)(2)D(3) functions as a potent negative endocrine regulator of renin gene expression provides some insights into the mechanism. The concept of vitamin D regulation of blood pressure through the RAS opens a new avenue to our understanding of the physiological functions of the vitamin D endocrine system, and provides a basis for exploring the potential use of vitamin D analogues in prevention and treatment of hypertension.     

Spatial distribution of canopy and subcanopy species along a sloping topography in a cool-temperate conifer-hardwood forest in the snowy region of Japan

The spatial distributions of canopy and subcanopy species (50cm stem length) were investigated within a plot extending from the top of a ridge to the valley bottom in a cool-temperate old-growth mixed forest, dominated by Cryptomeria japonica and Fagus crenata, in the snowy region of Japan. Based on the longitudinal profile of the slope, the study slope was divided into the relatively gentle upper slope position (US), the steep lower slope position (LS), the flat valley bottom (VB) and the boundary zone between the upper and lower slopes (BS). Spatial dispersal and the association patterns of species were analyzed in upperstory (10cm d.b.h) and understory (<10cm d.b.h) layers. Dominant species in the upperstory layer abruptly changed from Cryptomeria to Fagus at the BS site. In contrast, the understory trees of many species, including shade-intolerant and evergreen species, were independent of the location of conspecific upperstory trees or canopy gaps and extended their distributions on and around the BS site. Significant, diverse canopy and subcanopy species occurred at this site in both upperstory and understory layers. On the BS site, which is the lower margin of Cryptomeria-dominated vegetation, there were many medium-sized C.japonica that were killed by uprooting or breaking of the stems as a result of heavy snow pressure. It is suggested that the snow pressure gradient along a slope has a strong influence on community structure and the maintenance of diverse canopy and subcanopy species in this snowy mixed forest.     

Characterisation of castor oil by on-line and off-line non-aqueous reverse-phase high-performance liquid chromatography-mass spectrometry (APCI and UV/MALDI)

A non-aqueous reverse-phase HPLC method, based on two columns in series, has been used to separate the major triacylglycerols (TAGs) from commercial castor oil and to perform either on-line negative ion atmospheric pressure chemical ionisation (APCI), or off-line positive ion matrix-assisted laser desorption ionisation (MALDI)/MS. The resulting Mass Spectra showed chloride-attached TAG molecules [M + CI]- in the case of negative-ion APCI, and sodium-attached TAG molecules [M + Na]+ in the case of positive-ion MALDI. For MALDI time-of-flight (TOF)/MS, a liquid binary matrix system consisting of sodium ferrocyanide and glycerol was applied, resulting in excellent TAG sensitivity, which was necessary for the determination of trace amounts of TAGs in castor oil. Both techniques allowed unambiguous molecular mass determination of the intact TAG molecules with no thermal degradation. Furthermore, seamless post source decay (PSD) fragment ion analysis by means of a curved field reflector TOF mass spectrometer allowed the determination of the fatty acid composition of each individual TAG. Castor oil contained eight different TAGs which were successfully determined by both APCI and MALDI techniques. In each TAG, at least two units of 12-hydroxy-9-octadecenoic acid (ricinoleic acid) were present. The following fatty acids were determined by seamless PSD fragment ion analysis and APCI/MALDI molecular mass determination as TAG substructures: ricinoleic acid, palmitic acid, stearic acid, oleic acid, linoleic acid, linolenic acid, dihydroxy stearic acid and eicosenoic acid. Triricinolein was the dominating TAG.     

Kinetics of the dimerization of retroviral proteases: the "fireman's grip" and dimerization

All retroviral proteases belong to the family of aspartic proteases. They are active as homodimers, each unit contributing one catalytic aspartate to the active site dyad. An important feature of all aspartic proteases is a conserved complex scaffold of hydrogen bonds supporting the active site, called the "fireman's grip," which involves the hydroxyl groups of two threonine (serine) residues in the active site Asp-Thr(Ser)-Gly triplets. It was shown previously that the fireman's grip is indispensable for the dimer stability of HIV protease. The retroviral proteases harboring Ser in their active site triplet are less active and, under natural conditions, are expressed in higher enzyme/substrate ratio than those having Asp-Thr-Gly triplet. To analyze whether this observation can be attributed to the different influence of Thr or Ser on dimerization, we prepared two pairs of the wild-type and mutant proteases from HIV and myeloblastosis-associated virus harboring either Ser or Thr in their Asp-Thr(Ser)-Gly triplet. The equilibrium dimerization constants differed by an order of magnitude within the relevant pairs. The proteases with Thr in their active site triplets were found to be approximately 10 times more thermodynamically stable. The dimer association contributes to this difference more than does the dissociation. We propose that the fireman's grip might be important in the initial phases of dimer formation to help properly orientate the two subunits of a retroviral protease. The methyl group of threonine might contribute significantly to fixing such an intermediate conformation.     

Paternity success and the direction of sexual selection in a field population of a semelparous marsupial,Antechinus agilis

Antechinus agilis is a small sexually size dimorphic marsupial with a brief annual mating period of 2-3 weeks. All males die after this period, and females give birth to up to 10 young. Mating is thought to be promiscuous, however, there is no field data to confirm this. Using microsatellites, we investigated paternity patterns over two seasons in a wild population. Male weight was significantly positively related to the number of females fertilized and with the number of offspring sired, in both years. Furthermore, selection gradients indicated selection for larger males. Both results suggest that size dimorphism in A. agilis can be explained by sexual selection for larger males. The proportion of offspring sired within litters, did not relate to male size. Therefore, larger males are more successful through higher mating access, not through their sperm outcompeting that of smaller males. As expected from their known ranging behaviour, the number of offspring within litters left unassigned to a father did not depend on the grid location of the mother. Female size did not differ between successful reproducing and unsuccessful females. However, females that weaned offspring had larger heads than females that did not wean offspring. Males did not 'prefer' mating with larger females, nor did assortative mating occur. From our results, the mating system of A. agilis is clearly promiscuous. Selection for larger males occurred in both years, even though in one year the operational sex ratio was highly female biased, suggesting that the potential reproductive rate is a better predictor of the direction of sexual selection in A. agilis.     

Interaction of synapsin I with membranes

The synapsins (I, II, and III) comprise a family of peripheral membrane proteins that are involved in both regulation of neurotransmitter release and synaptogenesis. Synapsins are concentrated at presynaptic nerve terminals and are associated with the cytoplasmic surface of synaptic vesicles. Membrane-binding of synapsins involves interaction with both protein and lipid components of synaptic vesicles. Synapsin I binds rapidly and with high affinity to liposomes containing anionic lipids. The binding of bovine synapsin I to liposomes was studied using fluoresceinphosphatidyl-ethanolamine (FPE) to measure membrane electrostatic potential. Synapsin binding to liposomes caused a rapid increase in FPE fluorescence, indicating an increase in positive charge at the membrane surface. Synapsin I binding to monolayers resulted in a substantial increase in monolayer surface pressure. At higher initial surface pressures, the synapsin-induced increase in monolayer surface pressure is dependent on the presence of anionic lipids in the monolayer. Synapsin I also induced rapid aggregation of liposomes, but did not induce leakage of entrapped carboxyfluorescein, while other aggregation-inducing agents promoted extensive leakage. These results are in agreement with the presence of amphipathic stretches of amino acids in synapsin I that exhibit both electrostatic and hydrophobic interactions with membranes, and offer a molecular explanation for the high affinity binding of synapsin I to liposomes and for stabilization of membranes by synapsin I.     

Conformational heterogeneity of cytochrome P450 3A4 revealed by high pressure spectroscopy

We applied hydrostatic pressure perturbation to study substrate-induced transitions in human cytochrome P450 3A4 (CYP3A4) with bromocriptine (BCT) as a substrate. The barotropic behavior of the purified enzyme in solution was compared with that observed in recombinant microsomes of Saccharomyces cerevisiae coexpressing CYP3A4, cytochrome b(5), (b(5)) and NADPH-cytochrome P450 reductase (CPR). Important barotropic heterogeneity of CYP3A4 was detected in both cases. Only about 70% of CYP3A4 in solution and about 50% of the microsomal enzyme were susceptible to a pressure-induced P450-->P420 transition. The results suggest that both in solution and in the membrane CYP3A4 is represented by two conformers with different positions of spin equilibrium and different barotropic properties. No interconversion between these conformers was observed within the time frame of the experiment. Importantly, a pressure-induced spin shift, which is characteristic of all cytochromes P450 studied to date, was detected in CYP3A4 in solution only; the P450-->P420 transition was the sole pressure-induced process detected in microsomes. This fact suggests unusual stabilization of the high-spin state of CYP3A4, which is assumed to reflect decreased water accessibility of the heme moiety due to specific interactions of the hemoprotein with the protein partners (b(5) and CPR) and/or membrane lipids.     

An improved method of computing the wear factor for total hip prostheses involving the variation of relative motion and contact pressure with location on the bearing surface

A new method of computing the wear factor for total hip prostheses is presented. In the conventional method, only the resultant contact force and the track drawn by the point of its application are considered so that the product of the instantaneous force and sliding increment is integrated over one motion cycle. In the present, improved, method the contact pressure distribution is discretized by a large number of smaller normal forces, and the contribution of each is summed. This is important because the relative motion and contact pressure vary strongly with location, and because the transverse pressure component is substantial. Hence, the present surface integral represents the large contact surface better than the conventional line integral. A prerequisite for the surface integral was the method of computing the relative motion correctly anywhere on the contact surface, developed and published earlier by the present authors. For the pressure discretization, the contact surface was divided into nearly equal-sized surface elements. The contact pressure was modelled with ellipsoidal, paraboloidal and sinusoidal distributions. Two load cases were studied, double-peak and static. When an ellipsoidal contact pressure distribution extending over a hemisphere was discretized by 1000 element forces, the computed wear factor for double-peak load in a biaxial hip wear simulator was 30% lower than in the conventional resultant force case. The present method can be later developed further to involve the temporal variation of size and location of the contact surface.