The apportionment of dinucleotide repeat diversity in Native Americans and Europeans: a new approach to measuring gene identity reveals asymmetric patterns of divergence

The purpose of this paper is to assess the extent of gene identity and differentiation at 33 dinucleotide repeat loci (377 total alleles) within and among three European and three Native American populations. In order to do this, we show that a maximum-likelihood method proposed for phylogenetic trees (Cavalli-Sforza and Piazza 1975) can be used to estimate gene identity (Nei 1987) with respect to any hierarchical structure. This method allows gene differentiation to be evaluated with respect to any internal node of a hierarchy. It also allows a generalization of F- and G-statistics to situations with unequal expected levels of differentiation. Our principal finding is that levels of genetic differentiation are unique to specific populations and levels of nesting. The populations of European origin show very little internal differentiation; moreover, their continental average is close to the total population defined by the aggregate of Europeans and Native Americans. By contrast, the Native American populations show moderate levels of internal differentiation, and a great distance between their continental average and the total. The results of analyses of subsets of loci that were selected to have high gene diversities in either Europeans or Native Americans closely parallel those from the total set of loci. This suggests that the principal results are unlikely to be caused by a European ascertainment bias in locus selection. In summary, our findings demonstrate that partitions of gene diversity into within- and between-populations components are heavily biased by the populations analyzed and the models fitted. Optimistically, however, more information is available to analyze population history and evolution by quantifying, as we have done, the uniqueness of patterns of differentiation.      

Preliminary studies of the impact of excreted N on cycling and uptake of N in pasture systems using natural abundance stable isotopic discrimination

The possibility of using natural abundance techniques to determine N transformations and flows after deposition of cattle dung has been examined. These preliminary results showed that ¹⁵N in dung was greater than in plants growing in association with particular pats. This, and other observational information, indicated that dung pats of different ages were being examined. There were significant variations in plant ¹⁵N signatures within and between species grown in association and away from the dung. It was probable that variation in plant ¹⁵N was brought about by changes in soil mineral N pools after transfer of N derived from the dung. This resulted in different ¹⁵N signatures in Trifolium repens (because of changes in N utilization from soil or atmospheric pools), in Lolium perenne (because of changes in ¹⁵N in soil mineral N), but not in Ranunculus repens (because the majority of active roots were outside the range of immediate influence of the deposited dung). The differences in ¹⁵N allowed the development of hypotheses for changes in soil N pools and the acquisition of N by plants from soil, dung or atmospheric sources.     

Future trends in nitrogen research

N research effort has undergone major changes over recent decades with changing emphasis because of environmental problems and issues. This driving force, coupled with a universal desire to improve N-use efficiency, appreciation of the importance of maintaining soil resource quality and a need to provide integrated landscape managements, will continue to prompt new research areas and issues for study. Already, much information has been provided and new approaches and needs defined. It will be essential in future research to take full note of the many interactions that occur and to provide a mechanistic basis so that scaling of effects can be undertaken with the appropriate simplification without being superficial. Examples of interactions, as well as fundamental gaps in the basic processes are discussed and needs for future research identified.     

Rates of nuclear and cytoplasmic mitochondrial DNA sequence divergence in mammals

Differential rates of nucleotide substitution among different gene segments and between distinct evolutionary lineages is well documented among mitochondrial genes and is likely a consequence of locus-specific selective constraints that delimit mutational divergence over evolutionary time. We compared sequence variation of 18 homologous loci (15 coding genes and 3 parts of the control region) among 10 mammalian mitochondrial DNA genomes which allowed us to describe different mitochondrial evolutionary patterns and to produce an estimation of the relative order of gene divergence. The relative rates of divergence of mitochondrial DNA genes in the family Felidae were estimated by comparing their divergence from homologous counterpart genes included in nuclear mitochondrial DNA (Numt, pronounced "new might"), a genomic fossil that represents an ancient transfer of 7.9 kb of mitochondrial DNA to the nuclear genome of an ancestral species of the domestic cat (Felis catus). Phylogenetic analyses of mitochondrial (mtDNA) sequences with multiple outgroup species were conducted to date the ancestral node common to the Numt and the cytoplasmic (Cymt) mtDNA genes and to calibrate the rate of sequence divergence of mitochondrial genes relative to nuclear homologous counterparts. By setting the fastest substitution rate as strictly mutational, an empirical "selective retardation index" is computed to quantify the sum of all constraints, selective and otherwise, that limit sequence divergence of mitochondrial gene sequences over time.      

Rapid evolution in a conserved gene family. Evolution of the actin gene family in the sea urchin genus Heliocidaris and related genera

Camarodont sea urchins possess a rapidly evolving actin gene family whose members are expressed in distinct cell lineages in a developmentally regulated fashion. Evolutionary changes in the actin gene family of echinoids include alterations in number of family members, site of expression, and gene linkage, and a dichotomy between rapidly and slowly evolving isoform-specific 3' untranslated regions. We present sequence comparisons and an analysis of the actin gene family in two congeneric sea urchins that develop in radically different modes, Heliocidaris erythrogramma and H. tuberculata. The sequences of several actin genes from the related species Lytechinus variegatus are also presented. We compare the features of the Heliocidaris and Lytechinus actin genes to those of the the actin gene families of other closely related sea urchins and discuss the nature of the evolutionary changes among sea urchin actins and their relationship to developmental mode.      

Enhancement of polyhedrin nuclear localization during baculovirus infection.

Polyhedrin is the major component of the nuclear viral occlusions produced during replication of the baculovirus Autographa californica multicapsid nuclear polyhedrosis virus (AcMNPV). Since viral occlusions are responsible for the horizontal transmission of AcMNPV in nature, the biosynthesis, localization, and assembly of polyhedrin are important events in the viral replication cycle. We recently defined the sequence requirements for nuclear localization and assembly of polyhedrin. In this study, we examined the localization of polyhedrin at different times of infection. The results showed that nuclear localization of polyhedrin becomes more efficient as the occlusion phase of infection progresses. Several different factors were identified that might contribute to this overall effect, including a higher rate of polyhedrin nuclear localization and a higher rate of polyhedrin biosynthesis. We also examined the biosynthesis and processing of polyhedrin in cells infected with an AcMNPV few polyhedra (FP) mutant, which produces smaller numbers of viral occlusions that contain few or no virions. Compared with wild type, the FP mutant produced polyhedrin more slowly and localized it to the nucleus less efficiently at the beginning of the occlusion phase of infection (24 h postinfection). This supported the idea that the efficiency of polyhedrin nuclear localization is tightly coupled to its rate of biosynthesis. It also revealed that expression of the viral 25K gene, which is inactivated in the FP mutant, is directly or indirectly associated with an enhancement of polyhedrin biosynthesis and nuclear localization at the beginning of the occlusion phase of infection. This enhancement effect appears to be necessary to ensure the normal assembly of viral occlusions.     

An assessment of the contribution of net mineralization to N cycling in grass swards using a field incubation method

Measurements of net mineralization using a field incubation method were made over a full growing season (180 d). Soil cores, taken from cut swards which for many years had been previously grazed by cattle, were placed in jars in the field for successive incubation periods of 14 d. Acetylene was added to the incubation jars to inhibit nitrification in the soil cores and thereby prevent losses of N through denitrification. Net mineralization over 180 d amounted to 415, 321 and 310 kg N ha^–1 under grass/clover, unfertilized grass and grass receiving 420 kg N ha^–1 y^–1, respectively. At the start of the growing season, an index of potentially mineralizable N in the soil was estimated by a chemical extraction method, but this index was <50% of the estimates obtained by field incubation. The amount of N in herbage harvested regularly from the swards also under-estimated the supply of N from the soil, with apparent recoveries of 53, 82 and 74% and total yields of N of 240, 263 and 538 (kg N ha^–1) from grass/clover, unfertilized grass and fertilized grass, respectively. Mineralization rates varied significantly with seasonal soil temperature fluctuations, but the incubation method was apparently less sensitive in relation to changes in soil water content. Rates of N-turnover (as % of total soil N) were highest under grass/clover (9%), but similar under fertilized and unfertilized grass swards (approximately 5%).     

Human IgA1 blockade of IgG-initiated lysis of Neisseria meningitidis is a function of antigen-binding fragment binding to the polysaccharide capsule

We have recently shown that human IgA1 can initiate lysis of group C Neisseria meningitidis via the classical C pathway when bound to specific outer membrane proteins, but that IgA1 can also function as a blocking antibody when bound to the polysaccharide capsule of meningococci. In this report, we further characterized IgA1 blockade by examining the effect of IgA1 on IgG-initiated immune lysis of group C meningococci. We purified IgG and monomeric IgA1 from either convalescent group C meningococcal case sera or tetravalent (A, C, Y, W135) polysaccharide vaccinate sera. In the absence of IgA1, IgG initiated complete lysis (greater than 99%) of strains 118V (C:P3,4:L2,4) 126E (C:P3:L1,8), and 35E (C:P5:L2). Addition of IgA1 to the bactericidal reaction mixture completely blocked the lytic function of IgG. Removal of the Fc portion of IgA1 with either pepsin or IgA1 protease did not affect blockade. Both the F(ab')2 and Fab derivatives of IgA1 blocked lysis quantitatively as well as intact IgA1. The Fc fragment produced by IgA1 protease cleavage neither increased nor decreased Fab-mediated blockade. IgA1 and its Fab and F(ab')2 fragments blocked IgG-initiated lysis via either the classical pathway in factor B-depleted and in properdin-deficient serum, the alternative pathway in MgEGTA-chelated serum, or both pathways combined. Absorption of the IgA1 and IgG with alum-bound group C polysaccharide completely removed blocking and lytic activity, respectively, indicating that both the blocking IgA1 and the lytic IgG were specific for the group C capsule. Blocking by IgA1 was a linear function of the polysaccharide Ag-binding capacity (ABC) ratio of blocking IgA1 to lytic IgG. Complete blockade was observed at an ABC ratio of 5.5. At ABC ratios of 3.3 and 4.4, IgA1 affected significant blockade whether added previous to, concurrent with, or subsequent to sensitization of the organisms with IgG. With the use of a C polysaccharide ELISA, we found that the binding of IgA1 to the group C capsule in the presence of IgG exhibited positive cooperativity and therefore that blockade was independent of the ability of IgA1 to directly compete with IgG for binding to epitopes within the group C capsule. We conclude that IgA1, when bound to the group C polysaccharide capsule, can block IgG-initiated lysis of group C meningococci through either the classical or the alternative pathway before or after the organism is exposed to IgG, and that blockade is an Fc-independent event.