The reconstruction of side-chain conformations from protein Cα coordinates

A model of nine proteins including side-chain atoms have been built from the known C^α coordinates and amino acid sequences using a Monte Carlo Protein Building Annealing method. The Cartesian coordinates for the side-chain atoms were established with bond lengths and angles selected randomly from within previously determined ranges. A simulated annealing technique is used to generate some 300 structures with differing side-chain conformations. The atomic coordinates of the backbone atoms are fixed during the simulated annealing process. The coordinates of the side-chain atoms of 300 low energy conformations are averaged to obtain a mean structure that is minimized with the C^α atoms constrained to their position in the x-ray structure using the OPLS/AMBER force field with the GB/SA water model. The rms deviation of the main-chain atoms (without C^β) compared with the corresponding crystal structures is in the range 0.20–0.64 Å. The rms deviation of the side-chain atoms is between 1.72 and 2.71 Å and for all atoms is between 1.19 and 1.99 Å. The method is insensitive to random errors in the C^α positions and the computational requirement is modest. © 1997 John Wiley & Sons, Inc.     

Correcting eggshell indices of raptor eggs for hole size and eccentricity

Eggshell thickness is often expressed by means of an index based on the length, breadth and weight of the shell. The effect of the blow-hole and egg eccentricity on Ratcliffe's shell thickness index was investigated in a sample of 585 eggs from six raptor species. Corrections for the size of the hole and egg eccentricity are proposed, as is a combined formula to correct both sources of error at the same time. It is shown that by using these formulae, considerable improvements in estimates of shell thinning are obtained. These may be especially useful when sample sizes are small, which is often the case when working with species that have been reduced in numbers.     

Glacial refugia and reticulate evolution: the case of the Tasmanian eucalypts

Tasmania is a natural laboratory for investigating the evolutionary processes of the Quaternary. It is a large island lying 40-44 degrees S, which was repeatedly glaciated and linked to southeastern continental Australia during the Quaternary. Climate change promoted both the isolation of species in glacial refugia, and an exchange between Tasmanian and mainland floras. Eucalyptus is a complex and diverse genus, which has increased in abundance in Australia over the past 100 kyr, probably in response to higher fire frequency. Morphological evidence suggests that gene flow may have occurred between many eucalypt species after changes in their distribution during the Quaternary. This paper summarizes recent genetic evidence for migration and introgressive hybridization in Tasmanian Eucalyptus. Maternally inherited chloroplast DNA reveals a long-term persistence of eucalypts in southeastern Tasmanian refugia, coupled with introgressive hybridization involving many species. Detailed analysis of the widespread species Eucalyptus globulus suggests that migration from mainland Australia was followed by introgression involving a rare Tasmanian endemic. The data support the hypothesis that changes in distribution of interfertile species during the Quaternary have promoted reticulate evolution in Eucalyptus.     

Reproductive hormone profiles in mares during the autumn transition as determined by collection of jugular blood at 6 h intervals throughout ovulatory and anovulatory cycles

The aim was to define precisely the FSH secretion pattern in mares during the two ovulatory cycles before, and for 24 days after, the last ovulation of the season and to compare this with the profiles of other reproductive hormones and follicular growth to identify changes which may lead to the termination of follicular cycles. Jugular blood was collected every 6 h from ten light horse mares for 6 weeks in autumn. Samples were assayed for FSH, LH, prolactin, inhibin, oestrone conjugates and progesterone. Luteolysis occurred earlier and periovulatory oestrone, but not inhibin, concentrations were significantly lower in the last than in the second to last cycles. In ovulatory and anovulatory cycles, daily mean FSH concentrations were low at the expected time of ovulation and high between days 9 and 11 (day 0 = ovulation), which were usually after luteolysis. However, the periovulatory FSH nadir was prolonged in the last compared with the second to last cycles, and the difference between peak and trough values was not significant in anovulatory cycles. Between day 5 and day 8, the FSH interpulse interval was approximately 2 days, and did not vary in successive cycles. The LH profile also showed progressive changes as mares entered acyclicity; the surge terminated sooner in the last than in the second to last cycles, and failed to occur when expected in acyclicity. Sporadic prolactin pulses occurred at luteolysis in a similar proportion of ovulatory and anovulatory cycles. These results indicate that inadequate gonadotrophin stimulation in early dioestrus may be a critical event leading to suboptimal follicular and luteal development, and eventually acyclicity. Moreover, the time relationships amongst changes in pituitary and ovarian hormones and follicular growth become increasingly disrupted during the autumn transition, which may contribute to the cessation of cyclicity.     

Extracellular matrix-associated protein Sc1 is not essential for mouse development

Sc1 is an extracellular matrix-associated protein whose function is unknown. During early embryonic development, Sc1 is widely expressed, and from embryonic day 12 (E12), Sc1 is expressed primarily in the developing nervous system. This switch in Sc1 expression at E12 suggests an importance for nervous-system development. To gain insight into Sc1 function, we used gene targeting to inactivate mouse Sc1. The Sc1-null mice showed no obvious deficits in any organs. These mice were born at the expected ratios, were fertile, and had no obvious histological abnormalities, and their long-term survival did not differ from littermate controls. Therefore, the function of Sc1 during development is not critical or, in its absence, is subserved by another protein.     

Identification of a novel phosphonocarboxylate inhibitor of Rab geranylgeranyl transferase that specifically prevents Rab prenylation in osteoclasts and macrophages

Nitrogen-containing bisphosphonate drugs inhibit bone resorption by inhibiting FPP synthase and thereby preventing the synthesis of isoprenoid lipids required for protein prenylation in bone-resorbing osteoclasts. NE10790 is a phosphonocarboxylate analogue of the potent bisphosphonate risedronate and is a weak anti-resorptive agent. Although NE10790 was a poor inhibitor of FPP synthase, it did inhibit prenylation in J774 macrophages and osteoclasts, but only of proteins of molecular mass approximately 22-26 kDa, the prenylation of which was not affected by peptidomimetic inhibitors of either farnesyl transferase (FTI-277) or geranylgeranyl transferase I (GGTI-298). These 22-26-kDa proteins were shown to be geranylgeranylated by labelling J774 cells with [(3)H]geranylgeraniol. Furthermore, NE10790 inhibited incorporation of [(14)C]mevalonic acid into Rab6, but not into H-Ras or Rap1, proteins that are modified by FTase and GGTase I, respectively. These data demonstrate that NE10790 selectively prevents Rab prenylation in intact cells. In accord, NE10790 inhibited the activity of recombinant Rab GGTase in vitro, but did not affect the activity of recombinant FTase or GGTase I. NE10790 therefore appears to be the first specific inhibitor of Rab GGTase to be identified. In contrast to risedronate, NE10790 inhibited bone resorption in vitro without markedly affecting osteoclast number or the F-actin "ring" structure in polarized osteoclasts. However, NE10790 did alter osteoclast morphology, causing the formation of large intracellular vacuoles and protrusion of the basolateral membrane into large, "domed" structures that lacked microvilli. The anti-resorptive activity of NE10790 is thus likely due to disruption of Rab-dependent intracellular membrane trafficking in osteoclasts.     

Development of the Canadian beef reference herd for gene mapping studies

A project to map quantitative trait loci (QTL), in beef cattle using a full-sib design was initiated using six Bos taurus breeds. Embryo transfer was used in a large scale, short timeframe experiment to develop this herd for gene mapping. Full-sib families allowed for genetic information to be followed through both the sire and the dam and for both parents to be slaughtered so that carcass quality data could also be obtained from both of them at close to typical slaughter ages. Repeatability of response to superovulation was significant among the 3 flushes per female. Response to superovulation was negatively correlated with backfat of the donor. Crossbred embryos were found to have higher survival than purebred embryos.     

Aquatic hotspots: speciation in ancient lakes III

The conference Speciation in Ancient Lakes (‘SIAL’) III was held in Irkutsk, Russia from 2 to 7 September2002.