Archaic African and Asian lineages in the genetic ancestry of modern humans.

A 3-kb region encompassing the beta-globin gene has been analyzed for allelic sequence polymorphism in nine populations from Africa, Asia, and Europe. A unique gene tree was constructed from 326 sequences of 349 in the total sample. New maximum-likelihood methods for analyzing gene trees on the basis of coalescence theory have been used. The most recent common ancestor of the beta-globin gene tree is a sequence found only in Africa and estimated to have arisen approximately 800,000 years ago. There is no evidence for an exponential expansion out of a bottlenecked founding population, and an effective population size of approximately 10,000 has been maintained. Modest differences in levels of beta-globin diversity between Africa and Asia are better explained by greater African effective population size than by greater time depth. There may have been a reduction of Asian effective population size in recent evolutionary history. Characteristically Asian ancestry is estimated to be older than 200,000 years, suggesting that the ancestral hominid population at this time was widely dispersed across Africa and Asia. Patterns of beta-globin diversity suggest extensive worldwide late Pleistocene gene flow and are not easily reconciled with a unidirectional migration out of Africa 100,000 years ago and total replacement of archaic populations in Asia.     

Involvement of enzyme-substrate charge interactions in the caseinolytic specificity of lactococcal cell envelope-associated proteinases.

Three series of oligopeptides were synthesized to investigate the proposal that a major factor in determining the differences in specificity of the lactococcal cell surface-associated proteinases against caseins is the interactions between charged amino acids in the substrate and in the enzyme. The sequences of the oligopeptides were based on two regions of kappa-casein (residues 98 to 111 and 153 to 169) which show markedly different susceptibilities to PI- and PIII-type lactococcal proteinases. In each series, one oligopeptide had an identical sequence to that of the kappa-casein region, while in the others, one or more charged residues were substituted by an amino acid of opposite charge, i.e., His<-->Glu. Generally, substitution of His by Glu in the oligopeptides corresponding to residues 98 to 111 of kappa-casein resulted in reduced cleavage of susceptible bonds by the PI-type proteinase and increased cleavage of susceptible bonds by the PIII-type proteinase. In the case of the oligopeptide corresponding to residues 153 to 169 of kappa-casein, one major cleavage site was evident, and the bond was hydrolyzed by both types of proteinase (even though this sequence in kappa-casein itself is extremely resistant to the PI-type enzyme). Substitution of Glu by His in this oligopeptide, even in the P7 position, resulted in increased cleavage of the bond by the PI-type proteinase and reduced cleavage by the PIII-type proteinase. C-terminal truncation of this oligopeptide resulted in a 100-fold decrease in the rate of hydrolysis of the susceptible bond and a change in the pattern of cleavage.(ABSTRACT TRUNCATED AT 250 WORDS)     

The phoP locus influences processing and presentation of Salmonella typhimurium antigens by activated macrophages

The destruction and processing of bacteria by activated macrophages facilitates the presentation of antigens to T cells and thereby promotes the induction of specific immunity. The PhoP-PhoQ regulatory system that controls the synthesis of many Salmonella proteins required for virulence and survival within macrophages is one mechanism that this particular intracellular pathogen has evolved to resist destruction. To address whether the phoP locus also influences antigen processing during the interaction of Salmonella typhimurium with macrophages, we tested the effect of phoP mutations on the processing and presentation of model antigens expressed by the bacteria. Activated macrophages processed phoP^? bacteria with greater efficiency than wild-type bacteria, as measured by the response of antigen-specific T-hybridoma cells; Salmonella constitutively expressing PhoP were processed even less efficiently than wild-type Salmonella. After heat-inactivation, however, both wild-type and phoP^? bacteria were efficiently processed. The altered processing and presentation efficiency was not due to differences in the level of antigen expressed by the bacteria or differences in the level of bacterial uptake by the macrophages. In addition, phoP-regulated gene expression was shown to influence processing of antigen phagocytosed independently of the bacteria. Thus, phoP-regulated gene products decrease the processing and presentation of S. typhimurium antigens, demonstrating a rote 1or this virulence locus in the inhibition of the induction of specific immunity.     

Tc(VII) reduction and accumulation by immobilized cells of Escherichia coli

Resting cells of Escherichia coli, immobilized in a flow-through bioreactor, coupled the oxidation of formate or hydrogen to Tc(VII) reduction and removal from solution. Cells, pregrown anaerobically in a hollow-fiber membrane bioreactor, were challenged with 50 muM Tc(VII) in a carrier solution of phosphate-buffered saline. The radionuclide accumulated within the membrane component of the reactor, corresponding to the localization of the cells. Negligible Tc removal was noted in a reactor containing a mutant deficient in active Tc(VII) reductase, when supplied with formate as an electron donor. Formate or hydrogen was supplied as the electron donor for Tc(VII) reduction to cells immobilized in reactors operated in transverse (crossflow) and direct (dead-end filtration) modes, respectively. Flow-rate activity relationships were used to compare the performance of the reactors. A flow rate of 2.4 mL h(-1) supported the removal of 50% of the Tc from solution in a reactor operated in transverse mode with formate as an electron donor. In contrast, a flow rate of 0.7 mL h(-1), supported comparable Tc removal when hydrogen was introduced to a reactor operated in direct mode. The reduced reactor efficiency, when hydrogen was used as an electron donor, could be attributed, in part, to poor delivery of the gas to the cells. The biocatalyst was highly stable in the reactor; no loss in activity was noted over 200 h of continuous use. (c) 1997 John Wiley & Sons Inc. Biotechnol Bioeng 55: 505-510, 1997.     

The ELLIPS suite of macromolecular conformation algorithms

This paper describes a series of four programmes for the PC based on ellipsoidal representations of macromolecular shape in solution using Universal shape functions. ELLIPS1 is based on simple ellipsoid of revolution models (where two of the three axes of the ellipsoid are fixed equal to each other). If the user types in a value for a shape function from sedimentation or other types of hydrodynamic measurement, it will return a value for the axial ratio of the ellipsoid. ELLIPS2 is based on the more general triaxial ellipsoid with the removal of the restriction of two equal axes. The user enters the three semi-axial dimensions of the molecule or the equivalent two axial ratios and ELLIPS2 returns the value of all the hydrodynamic shape functions. It also works of course for ellipsoids of revolution. ELLIPS3 and ELLIPS4 do the reverse of ELLIPS2, that is they both provide a method for the unique evaluation of the triaxial dimensions or axial ratios of a macromolecule (and without having to guess a value for the so-called „hydration”) after entering at least three pieces of hydrodynamic information: ELLIPS3 requires EITHER the intrinsic viscosity with the second virial coefficient (from sedimentation equilibrium, light scattering or osmometry) and the radius of gyration (from light or x-ray scattering) OR the intrinsic viscosity with the concentration dependence term for the sedimentation coefficient and the (harmonic mean) rotational relaxation time from fluorescence depolarisation measurements. ELLIPS4 evaluates the tri-axial shape of a macromolecule from electro-optic decay based Universal shape functions using another Universal shape function as a constraint in the extraction of the decay constants. Accepted: 1 November 1996     

SOLPRO: theory and computer program for the prediction of SOLution PROperties of rigid macromolecules and bioparticles

Single-valued hydrodynamic coefficients of a rigid particle can be calculated from existing theories and computer programs for either bead models or ellipsoids. Starting from these coefficients, we review the procedures for the calculation of complex solution properties depending on rotational diffusion, such as the decays of electric birefringence and fluorescence anisotropy. We also describe the calculation of the scattering form factor of bead models. The hydrodynamic coefficients and solution properties can be combined to give universal, shape-dependent functions, which were initially intended for ellipsoidal particles, and are extended here for the most general case. We have implemented all these developments in a new computer program, SOLPRO, for calculation of SOLution PROperties, which can be linked to existing software for bead models or ellipsoids. Accepted: 1 November 1996     

Spermiogenesis in the brush-tailed possum,Trichosurus vulpecula (Marsupialia)

Summary Acrosome development in the Australian Brush-tailed possum, Trichosurus vulpecula, displays a number of extraordinary features. This is particularly evident in the later stages of spermiogenesis, when the area of the nuclear surface bounded by the nuclear ring, and covered by the acrosome, is reduced considerable. As a result, the acrosomal material becomes located over its definitive position on the anterior third of the dorsal nuclear surface; in this process it is thrown into a series of folds, and a wide subacrosomal space is formed.Further changes around the time of spermiation result in the release of a spermatozoon in which a thin layer of acrosomal material is closely applied to the nucleus over the area of the definitive location of the acrosome, whilst its margins are greatly extended and project freely away from the nucleus. The latter feature does not appear to have been reported for the sperm of other mammals.The authors would like to thank Dr. D.J.H. Cockayne, Director of the Electron Microscope Unit, University of Sydney, for the generous provision of transmission electron microscope facilities, and Dr. M.R. Dickson, Electron Microscopist in charge, Biomedical Electron Microscope Unit, University of New South Wales, for the use of other facilities. Also, thanks are due to Miss Robin Arnold and Mrs. Eva Vassak of the Department of Histology and Embryology, University of Sydney, for their expert assistance. The assistance of the N.S.W. National Parks and Wildlife Service in the provision of permits to work on these native mammals is acknowledged     

The purification and amino acid composition of human uterus collagens, rheumatoid-arthritis-nodule collagen and ox tendon collagen

Collagens and gelatins were isolated from human post-menopausal uterus, puerperal (post-partum) uterus, rheumatoid-arthritis-nodule and ox tendon. Different means of purifying collagen were studied and a method was devised that enables highly purified collagen to be obtained, even from the uterus. This method involves the use of a number of aqueous and organic extractants as well as digestion with elastase to eliminate elastin. The purity of the collagen preparations was assessed and they were used to study the amino acid composition of collagen. The amino acid compositions of all the collagens studied were similar to those of human bone and tendon collagen, but certain small differences were noted and are discussed. The soluble collagen extracted from some of the tissues was also studied.     

LIPID DEFICIENCY IN THE CENTRAL NERVOUS SYSTEM OF LANDRACE PIGLETS AFFECTED WITH CONGENITAL TREMOR AIII, A FORM OF CEREBROSPINAL HYPOMYELINOGENESIS

—Congenital tremor, type AIII, is characterized by partial agenesis of the white matter of the CNS affecting mainly the spinal cord. The percentage water content of the fresh cord is consistently higher than normal and other parts of the CNS are sporadically affected. The total lipid content (mg/g fresh tissue) is markedly decreased in the cord but brain stem and cerebellum are less severely deficient; the cerebrum is barely deficient. Total amounts of cholesterol, cerebroside and phospholipid (mmol/part) are significantly reduced predominantly in cerebellum, brain stem and cord. Total DNA and protein contents are decreased to a significant extent only in spinal cord. Broadly similar lipid changes are found in fixed tissues. The data are consistent with sub-normal myelination, associated with a deficiency of oligodendrocytes.