Genomic Consequences of Ecological Speciation in Astyanax Cavefish

The cave environment is consistently radically different than the surface environment because it lacks light, and animals adapting to cave life are subject to strong selective forces much different than those experienced by their ancestors who evolved in the presence of light. As such, their divergence from surface ancestors and eventual speciation is likely to be driven by the shift in ecology. We report here that hybrids between cave and surface Astyanax mexicanus fishes produce offspring with allelic frequencies that differ significantly from Mendelian expectations both for transmission ratios and for independent assortment of unlinked markers. Comparison of allelic content of DNA from fin clips and sperm pools show that the transmission ratio distortion likely occurs during spermatogenesis. Departures from expectations of independent assortment are essentially epistatic phenomena generating linkage disequilibrium. A novel analysis of the epistatic interactions reveals an apparent network of interactions among genes known or suspected to be involved in cave adaptation, implying that the epistasis arose as a “by product” of the divergence due to cave adaptation.     

<Superscript>15</Superscript>N natural abundance of fossil peat reflects the influence of animal-derived nitrogen on vegetation

'¹⁵N signatures of fossil peat were used to interpret past ecosystem processes on tectonically active subantarctic Macquarie Island. By comparing past vegetation reconstructed from the fossil record with present-day vegetation analogues, our evidence strongly suggests that changes in the '¹⁵N signatures of fossil peat at this location reflect mainly past changes in the proportion of plant nitrogen derived from animal sources. Associated with uplift above sea level over the past 8,500 years, fossil records in two peat deposits on the island chronicle a change from coastal vegetation with fur and elephant seal disturbance to the existing inland herbfield. Coupled with this change are synchronous changes in the '¹⁵N signatures of peat layers. At two sites ¹⁵N-enriched peat '¹⁵N signatures of up to +17‰ were associated with a high abundance of pollen of the nitrophile Callitriche antarctica (Callitrichaceae). At one site fossil seal hair was also associated with enriched peat '¹⁵N. Less ¹⁵N enriched '¹⁵N signatures (e.g. -1.9‰ to +3.9‰) were measured in peat layers which lacked animal associated C. antarctica and Acaena spp. Interpretation of a third peat profile indicates continual occupation of a ridge site by burrowing petrels for most of the Holocene. We suggest that ¹⁵N signatures of fossil peat remained relatively stable with time once deposited, providing a significant new tool for interpreting the palaeoecology.     

Bubble-Induced Cave Collapse

Conventional wisdom among cave divers is that submerged caves in aquifers, such as in Florida or the Yucatan, are unstable due to their ever-growing size from limestone dissolution in water. Cave divers occasionally noted partial cave collapses occurring while they were in the cave, attributing this to their unintentional (and frowned upon) physical contact with the cave walls or the aforementioned “natural” instability of the cave. Here, we suggest that these cave collapses do not necessarily result from cave instability or contacts with walls, but rather from divers bubbles rising to the ceiling and reducing the buoyancy acting on isolated ceiling rocks. Using familiar theories for the strength of flat and arched (un-cracked) beams, we first show that the flat ceiling of a submerged limestone cave can have a horizontal expanse of 63 meters. This is much broader than that of most submerged Florida caves (~ 10 m). Similarly, we show that an arched cave roof can have a still larger expanse of 240 meters, again implying that Florida caves are structurally stable. Using familiar bubble dynamics, fluid dynamics of bubble-induced flows, and accustomed diving practices, we show that a group of 1-3 divers submerged below a loosely connected ceiling rock will quickly trigger it to fall causing a “collapse”. We then present a set of qualitative laboratory experiments illustrating such a collapse in a circular laboratory cave (i.e., a cave with a circular cross section), with concave and convex ceilings. In these experiments, a metal ball represented the rock (attached to the cave ceiling with a magnet), and the bubbles were produced using a syringe located at the cave floor.     

Outer membrane proteins of Pseudomonas

In this review, we describe the outer membrane proteins of Pseudomonas aeruginosa and related strains from the Pseudomonas fluorescens rRNA homology group of the Pseudomonadaceae, with emphasis on the physiological function and biochemical characteristics of these proteins. The use of opr (for outer membrane protein) is proposed as the genetic designation for the P. aeruginosa outer membrane proteins and letters are assigned, in conjunction with this designation, to known outer membrane proteins. Proteins whose primary functions involve pore formation, transport of specific substrates, cell structure determination and membrane stabilization are discussed. The conservation of selected proteins in the above Pseudomonas species is also examined.     

Turnover of cell surface-bound capsular polysaccharide in Staphylococcus aureus

The capsular polysaccharide (CPS) of Staphylococcus aureus strain Smith was labelled by growth of bacteria in the presence of radioactive N-acetylglucosamine and was separated from labelled cell wall components by affinity chromatography on wheat germ agglutinin following dissolution of the cells by lysostaphin. The products were partially characterised chemically and immunochemically. Similar labelled components were found in the culture fluid during growth. In a pulse-chase experiment, cell-bound CPS was released continuously into the culture fluid at the same rate as cell wall turnover and there was no evidence of direct excretion of CPS.     

Characterization of two surface-localized antigenic sites on porin protein F of Pseudomonas aeruginosa

A rapid colony immunoblot screening procedure was used to demonstrate the surface localization of porin protein F on bacterial colonies of Pseudomonas aeruginosa. By this method, we demonstrated that protein F was accessible to four different specific monoclonal antibodies in a wide variety of both mucoid and nonmucoid P. aeruginosa strains. Controls were performed to demonstrate that, using this procedure, only surface-exposed epitopes bound monoclonal antibodies and that nonspecific binding of monoclonal antibodies either to cells lacking protein F or to mucoid exopolysaccharide did not occur. Monoclonal antibodies MA4-4, MA2-10, and MA4-10, specific for protein F, also interacted with colonies of Pseudomonas putida and Pseudomonas syringae, whereas the protein F specific monoclonal antibody MA5-8 interacted only with P. aeruginosa strains. Using the above-named monoclonal antibodies, we investigated the antigenic structure of protein F. Monoclonal antibodies MA4-4, MA2-10, and MA4-10 bound to 29-31 kilodalton proteolytic fragments produced after papain or trypsin digestion of purified protein F or of protein F in outer membranes or intact cells. Antibody MA5-8 did not interact with proteolytically digested protein F but did interact with two of the six fragments produced after partial cyanogen bromide cleavage of protein F. Antibodies MA4-4, MA2-10, and MA4-10 did not interact with protein F after reduction of its internal disulphide bonds with 2-mercaptoethanol; in contrast, the reactivity of MA5-8 was unaffected. This data suggests that there are at least two distinct highly conserved surface epitopes on porin protein F.     

EMBRYONIC GENETIC LOAD IN THE HIGHBUSH BLUEBERRY,VACCINIUM CORYMBOSUM (ERICACEAE)

Hand-pollinations of 28 autotetraploid V. corymbosum accessions from a single population resulted in lower self- than outcross seed set. Fertility varied widely, ranging from clones that were effectively female sterile to individuals with high seed yields in both matings. Self- and outcross fertility were highly correlated. A genetic load model was invoked to explain these phenomena. Reduced self-fertility was attributed to homozygosity for sublethal mutations at loci controlling embryo development, or to loss of heterotic interactions at these loci. Near zero cross-fertility in some clones may be evidence of partially dominant mutational load. Estimates of the number of lethal equivalents per zygote carried by individuals in this population ranged from 2.2 to 20.4, with a mean of 9.6. Embryonic genetic load at the individual level was significantly correlated with heterozygosity at nine enzyme loci. Low pollen viability and reduced receptivity to pollen from any source were also noted in the low fertility genotypes. It is suggested that gametic, gametophytic, and embryonic development are symptomatic of the amount of genetic load carried by individuals.     

Neutron activation analysis of bulk and selected trace elements in bones using a low flux SLOWPOKE reactor

The mineral phase of bone is a reservoir for some biologically important ions and is the place where some toxic elements are also stored. For these reasons it is important to measure accurately and nondestructively the chemical content of bone, with respect to its main elements (Ca, P, Mg, Na) and its trace elements. We have analyzed different types of human bone by instrumental neutron activation analysis (INAA), using a SLOWPOKE reactor. We have compared our results with inductively coupled plasma emission spectroscopy (ICPES), and we have determined the limits of detection and sensitivity for the various elements, especially some biologically or toxicologically significant trace elements. Finally, we have given two examples of the use of INAA in following the penetration of an element (F) with time into bone and in characterizing nondestructively the mineral content of bone biopsies of a rare pathological condition (osteopetrosis).     

Hormonal regulation of estradiol biosynthesis, aromatase activity, and aromatase mRNA in rat ovarian follicles and corpora lutea

To determine the molecular basis for changes in aromatase (P450arom) activity in rat ovarian follicles and corpora lutea, seven clones for rat P450arom cDNA have been identified and isolated from a rat granulosa cell λgtll cDNA expression library using a 62 mer deoxyoligonucleotide probe (derived from an amino acid sequence of purified human placental aromatase) and a human placental P450arom cDNA probe. One of the rat P450arom cDNA clones contained an insert 1.2 kb in size. Both the human 1.8 kb cDNA and the rat 1.2 kb cDNA probes hybridized to a single species of P450arom mRNA that was 2.6 kb in size. Northern blot analysis revealed that corpora lutea isolated on day 15 of pregnancy contained high amounts of P450arom mRNA, whereas granulosa cells of antral follicles of hormonally primed, hypophysectomized rats (i.e., those from which mRNA was isolated to construct the cDNA library) contained only low amounts of P450arom mRNA. The lower amounts of P450arom in granulosa cells of preovulatory follicles in the estradiol-follicle-stimulating hormone primed hypophysectomized rats were unexpected because follicles incubated in medium containing testosterone substrate produce more estradiol than do corpora lutea isolated on day 15 of pregnancy and incubated under similar conditions. Additional studies will determine the hormonal events responsible for the elevated amounts and constitutive maintenance of P450arom mRNA and aromatase activity in luteal cells in vivo and in vitro.     

Metal ion size selectivity in ligands with groups containing the neutral oxygen donor atom. A crystallographic and thermodynamic study

The coordinating properties of open-chain ligands containing alcoholic or ethereal oxygen donors are examined. Addition of oxygen donors usually leads to complex stabilisation for large metal ions (Pb²⁺, Cd²⁺) and to less favourable effects on complex stability for small metal ions (Cu²⁺, Ni²⁺). The formation constants of these metal ions with the set of ligands RN(CH₂CHOH·CH₃)₂ where R is ---H, ---CH₂CHOH·CH₃, ---CH₂CH₂OCH₃, ---CH₂CH₂OCH₂CH₂OH, and ---CH₂---CHOCH₂CH₂CH₂ are reported. The largest stabilisation for each case where R is an O-donor group relative to R = H occurs for Pb²⁺, the largest metal ion, while Cu²⁺, the smallest metal ion, shows the smallest stabilisation. The crystal structure of [Ni(HOCH₂CH₂NHCH₂CH₂NH₂)₂] (NO₃)₂ is reported. The space group is P , with cell constants a = 13.098(3), b = 8.737(4), and c = 7.746(3) Å, β = 112.66(3), β = 90.65(3), and γ = 85.03(2), and Z = 2. Disorder of the nitrate anions hindered refinement, with the result that a final conventional R factor of 0.0903 was achieved. The Ni---N bond lengths average 2.06(1) (secondary nitrogen) and 2.10(2) (primary nitrogen). The Ni---O bond lengths are rather long, averaging 2.15(1) Å, which is used to support the idea that the steric effects are responsible for destabilising the complexes of small metal ions such as Ni(11) when neutral oxygen donors are present.