Evolution of ancient satellite DNAs in sturgeon genomes

This study characterizes a repetitive DNA family of sequences in sturgeon, the PstI satellite DNA. We have found a high degree of preservation for these sequences, which are present in all 13 species analyzed, including within the genera Acipenser, Huso, and Scaphirhynchus of the family Acipenseridae. This is one of the most ancient satellite DNAs found to date, because it has been estimated to be more than 100 million years old. Alternatively, to the current view that most satellite DNAs are species-specific or preserved in a few closely related species, the PstI family and other previously characterized sturgeon satellite DNA, the HindIII, represent the most fascinating exceptions to the rapid sequence change usually undergone by satellite DNAs. Here, we compare the evolutionary pattern of these two satellite DNA families, PstI and HindIII, which differ markedly in length, sequence, and nucleotide composition. We have found that, in contrast to the situation in most other living beings, a high degree of preservation, a slow sequence change rate and slowed concerted evolution, appears to be a general rule for sturgeon satellite DNAs. The possible causes for all these features are discussed in the light of the evolutionary specifics found within these ancient organisms.     

The reproductive biology of closely related coral species: gametogenesis in<Emphasis Type="Italic"> Madracis</Emphasis> from the southern Caribbean

Reproductive patterns were studied in closely related coral species of the genus Madracis on Curaçao, Netherlands Antilles. Gonadal development of six sympatric species was examined over a 13-month period. Reproductive differences among Madracis species are small. All species are hermaphroditic brooders and show similar patterns in gamete development. Timing of gamete maturation is positively correlated with seawater temperature in all species. Oocyte development typically begins in June and precedes the development of spermaries. Mature gametes, male and female, are present from August to November when seawater temperatures reach their yearly maximum. Developmental pathways for male and female gametes are identical among species. Interspecific differences exist in the number and size of oocytes. Our data indicates that differences in gametogenic development between closely related, but ecologically different subspecies are small or absent and do not necessarily match with species separations based on morphological criteria.Communicated by Topic Editor D. Barnes     

Comparative genomics of rice and Arabidopsis. Analysis of 727 cytochrome P450 genes and pseudogenes from a monocot and a dicot

Data mining methods have been used to identify 356 Cyt P450 genes and 99 related pseudogenes in the rice (Oryza sativa) genome using sequence information available from both the indica and japonica strains. Because neither of these genomes is completely available, some genes have been identified in only one strain, and 28 genes remain incomplete. Comparison of these rice genes with the 246 P450 genes and 26 pseudogenes in the Arabidopsis genome has indicated that most of the known plant P450 families existed before the monocot-dicot divergence that occurred approximately 200 million years ago. Comparative analysis of P450s in the Pinus expressed sequence tag collections has identified P450 families that predated the separation of gymnosperms and flowering plants. Complete mapping of all available plant P450s onto the Deep Green consensus plant phylogeny highlights certain lineage-specific families maintained (CYP80 in Ranunculales) and lineage-specific families lost (CYP92 in Arabidopsis) in the course of evolution.     

Adaptive responses to static conditions in nutrient-rich cultures of luminous Ralstonia eutropha

The lux-gene fused Ralstonia eutropha, when adapting to static conditions, causes stratification of air-exposed and nutrient-rich cultures at above 0.15 mg biomass ml(-1). The O2 respiring biofilm (luminous neuston) phase, along with the dark sub-neustonic suspension phase, develops within 5-60 min. The instability of the biphasic static culture was identified as a reason for occasionally observable oscillatory bioluminescence.     

Neurological symptoms in tricolor sharkminnow Balantiocheilos melanopterus associated with Myxobolus balantiocheili n. sp. infecting the central nervous system

A new species, Myxobolus balantiocheili, is described from the central nervous system of wild and cultured tricolor sharkminnow Balantiocheilos melanopterus from Thailand. The infection was associated with emaciation and severe neurological symptoms, including sudden uncoordinated darting, rolling and pitching. Whitish cysts of varying shape, measuring 70 to 500 microm, were located in the brain, spinal cord and in the meninx, and were sometimes accompanied by haemorrhages. In the brain, most cysts were located in the medulla oblongata and the mesencephalon. Cysts with a segmental distribution were observed in the meninx of the spinal cord. Single di- to hexasporic pansporoblasts, and free mature spores, were frequently seen in both the white and grey matter of the brain and spinal cord, mostly associated with blood vessels. Mature spores varied in shape from oval to ellipsoid, measuring 12.3 +/- 0.59 (range 10.6 to 13.3) x 10.0 +/- 0.47 (9.2 to 10.9) x 6.9 +/- 0.20 (6.7 to 7.1) microm. Spore size and morphology, in addition to fish-host species and apparently narrow tissue tropism, clearly distinguishes this new Myxobolus. No marked inflammatory response or gliosis was associated with the lesions, but compression and degeneration of the nervous tissue surrounding large cysts was observed. We suggest that the high temperature of the fish hosts' tropical habitat may have increased the rate of development and the virulence of M. balantiocheili.     

The synthesis and SAR of 2-arylsulfanyl-phenyl piperazinyl acetic acids as glyT-1 inhibitors

Elevation of glycine levels and activation of the NMDA receptor by inhibition of the glycine transporter 1 (GlyT-1) is a potential strategy for the treatment of schizophrenia. A novel series of GlyT-1 inhibitors have been identified containing the 2-arylsulfanyl-phenylpiperazine motif. The most prominent member of this series, (R)-4-[5-chloro-2-(4-methoxy-phenylsulfanyl)-phenyl]-2-methyl-piperazin-1-yl-acetic acid (31) is a potent glycine transporter-1 inhibitor (IC(50)=150 nM), which elevated glycine levels in rat ventral hippocampus as measured by microdialysis in vivo at doses of 1.2-4.6 mg/kg s.c.     

Structure of the periplasmic chaperone Skp suggests functional similarity with cytosolic chaperones despite differing architecture

The 17-kDa protein (Skp) of Escherichia coli is a homotrimeric periplasmic chaperone for newly synthesized outer-membrane proteins. Here we present its X-ray structure at a resolution of 2.35 A. Three hairpin-shaped alpha-helical extensions reach out by approximately 60 A from a trimerization domain, which is composed of three intersubunit beta-sheets that wind around a central axis. The alpha-helical extensions approach each other at their distal turns, resulting in a fold that resembles a 'three-pronged grasping forceps'. The overall shape of Skp is reminiscent of the cytosolic chaperone prefoldin, although it is based on a radically different topology. The peculiar architecture, with apparent plasticity of the prongs and distinct electrostatic and hydrophobic surface properties, supports the recently proposed biochemical mechanism of this chaperone: formation of a Skp(3)-Omp complex protects the outer membrane protein from aggregation during passage through the bacterial periplasm.     

Structural mechanism of specific ligand recognition by a lipocalin tailored for the complexation of digoxigenin

DigA16 is an artificial digoxigenin-binding protein, which was derived from the bilin-binding protein, a lipocalin of Pieris brassicae, via reshaping of its natural ligand pocket. Here we report the crystal structures of DigA16 in the presence of either digoxigenin or digitoxigenin and for the apo-protein at resolutions below 1.9A. As a consequence of the altogether 17 amino acid substitutions within the binding site significant structural changes have occurred in the four loops that form the entrance to the ligand pocket on top of the structurally conserved beta-barrel framework. For example, one loop adopts a new alpha-helical backbone structure, which seems to be induced by few critical side-chain contacts. Digoxigenin becomes almost fully buried (by 95%) upon complexation, whereby specificity for the hydrophilic steroid is maintained through hydrogen-bonding networks and shape complementarity. The differential binding of the related steroid digitoxigenin is mainly governed by an internal histidine residue, whose side-chain undergoes significant induced fit. Among those amino acids that line the ligand pocket two tyrosine and one tryptophan residue provide the largest contacts. Interestingly, corresponding three side-chains are found with the same mutual orientation in the anti-digoxigenin antibody 26-10, even though the hapten orientation is quite different there and only 66% of the steroid surface is buried in the combining site. Hence, in the case of the engineered lipocalin DigA16 an example of convergent in vitro evolution is observed. Generally, the remarkable structural plasticity of the loop region and the role of polar residues in the binding site illustrate the potential of the lipocalin scaffold for the generation of specific receptor proteins towards a variety of ligands.