Directly modelling population dynamics in the South American Arid Diagonal using 14C dates

Large anthropogenic ¹⁴C datasets are widely used to generate summed probability distributions (SPDs) as a proxy for past human population levels. However, SPDs are a poor proxy when datasets are small, bearing little relationship to true population dynamics. Instead, more robust inferences can be achieved by directly modelling the population and assessing the model likelihood given the data. We introduce the R package ADMUR which uses a continuous piecewise linear (CPL) model of population change, calculates the model likelihood given a ¹⁴C dataset, estimates credible intervals using Markov chain Monte Carlo, applies a goodness-of-fit test, and uses the Schwarz Criterion to compare CPL models. We demonstrate the efficacy of this method using toy data, showing that spurious dynamics are avoided when sample sizes are small, and true population dynamics are recovered as sample sizes increase. Finally, we use an improved ¹⁴C dataset for the South American Arid Diagonal to compare CPL modelling to current simulation methods, and identify three Holocene phases when population trajectory estimates changed from rapid initial growth of 4.15% per generation to a decline of 0.05% per generation between 10 821 and 7055 yr BP, then gently grew at 0.58% per generation until 2500 yr BP.This article is part of the theme issue ‘Cross-disciplinary approaches to prehistoric demography’.     

Anti-apoptotic gene Bcl2 is required for stapes development and hearing

In this paper we describe novel and specific roles for the apoptotic regulators Bcl2 and Bim in hearing and stapes development. Bcl2 is anti-apoptotic while Bim is pro-apoptotic. Characterization of the auditory systems of mice deficient for these molecules revealed that Bcl2^−/− mice suffered severe hearing loss. This was conductive in nature and did not affect sensory cells of the inner ear, with cochlear hair cells and neurons present and functional. Bcl2^−/− mice were found to have a malformed, often monocrural, porous stapes (the small stirrup-shaped bone of the middle ear), but a normally shaped malleus and incus. The deformed stapes was discontinuous with the incus and sometimes fused to the temporal bones. The defect was completely rescued in Bcl2^−/−Bim^−/− mice and partially rescued in Bcl2^−/−Bim^+/− mice, which displayed high-frequency hearing loss and thickening of the stapes anterior crus. The Bcl2^−/− defect arose in utero before or during the cartilage stage of stapes development. These results implicate Bcl2 and Bim in regulating survival of second pharyngeal arch or neural crest cells that give rise to the stapes during embryonic development.     

Derivation of gnotobiotic ferrets: perinatal diet and hand-rearing requirements

A procedure is described which has resulted in successful gnotobiotic derivation of the domestic ferret. The most critical element of this hand-rearing procedure was found to be diet, with ferret milk being required for at least the first 7 days. Puppy milk replacer was phased in during the next 10 days, and enriched cow's milk sufficed thereafter. Around-the-clock sip-feeding with fire-polished Pasteur pipettes was necessary at intervals gradually increasing from 1 to 1.5 hours at birth to 3 hours by day 21. Temperature regulation was accomplished with an electric heating pad placed eccentrically under towel bedding to provide a 30 degrees-40 degrees C gradient, along which the kits positioned themselves to their own comfort. Techniques are described for minimizing fatalities due to dehydration, milk-aspiration pneumonia, underfeeding, overfeeding, gut stasis and obstipation. Internal hemorrhage, the greatest single cause of mortality in this study, manifested at day 13 and involved all kits by day 17. Despite immediate vitamin K1 dietary supplementation, five of the seven remaining kits died of hemorrhage by day 19. Around day 50, the two surviving kits were weaned from milk to dry commercial cat and ferret diets supplemented with vitamins K, C, A, D, E and B-complex and were reared to adulthood on this diet.     

Cellular localization and export of the soluble haemolysin of Vibrio cholerae El Tor

Summary The cellular location of the haemolysin of Vibrio cholerae El Tor strain 017 has been analyzed. This protein is found both in the periplasmic space and the extracellular medium in Vibrio cholerae. However, when the cloned gene, present on plasmid pPM431, is introduced into E. coli K-12 this protein remains localized predominantly in the periplasmic space with no activity detected in the extracellular medium. Mutants of E. coli K-12 (tolA and tolB) which leak periplasmic proteins mimic excretion and release the haemolysin into the growth medium. Secretion of haemolysin into the periplasm is independent of perA (envZ) and in fact, mutants in perA (envZ) harbouring pPM431 show hyperproduction of periplasmic haemolysin. These results in conjunction with those for other V. cholerae extracellular proteins suggest that although E. coli K-12 can secrete these proteins into the periplasm, it lacks a specific excretion mechanism, present in V. cholerae, for the release of soluble proteins into the growth medium.     

The trajectory of a stiff rod in a curved potential energy trough. An initial result for short nucleosomal rods

The equilibrium trajectory of the axis of a rod subject to an externally imposed curved potential energy trough tends to conform to the shape of the curved trough, but also tends to be straight because of elastic resistance to bending. The actual path of the axis is a balance between the two extremes. We consider a potential energy trough centered along a circular arc of radius R. For a rod of small length compared to R, we show that the axis at equilibrium forms an arc of a circle of radius greater than R. The value of the radius of the axial path depends on the relative values of the Hooke's Law bending constant for the rod and the depth and width of the trough. Motivation for the calculation is provided by nucleosomal DNA, which conforms to the surface of a roughly cylindrical histone core at physiological ionic strength, but is observed to unwind into a partially extended conformation at very low ionic strength. We suggest that the rigidity to bending of short DNA segments becomes sufficiently great at low ionic strength to overcome attractive interactions with the histone surface. Alternately, of course, if during the cell cycle mutually attractive forces between DNA and histone core are weakened at constant ionic strength, the same type of unfolding would be expected to occur as the strength of the DNA-histone contacts drops below the level required to overcome elastic resistance to bending of the DNA rod.