Evolutionary analysis of the multigene pregnancy-specific β1-Glycoprotein family: Separation of historical and nonhistorical signals

The pregnancy-specific ₁-glycoproteins (PSG) form a large family of closely related proteins. Using newly developed methods of sequence analysis, in combination with protein modeling, we provide a framework for investigating the evolution and biological function of genes like the PSG. Evolutionary trees, based on C-terminal sequence, group PSG genes in a manner consistent with their genomic organization. Trees constructed using the N-terminal domain sequences are unreliable as an indicator of phylogeny because of non-neutral processes of sequence change. During duplication of the PSG genes, evolutionary pressures have resulted in a gradient of constrained change across each gene. The N-terminal domains show a nonrandom pattern of amino acid substitutions clustered in the immunoglobulin complementarity-determining region (CDR)-like regions, which appear to be important in the function of the protein.     

A dimorphic Alu Sb-like insertion in COL3A1 is ethnic-specific

Alu elements are a class of repetitive DNA sequences found throughout the human genome that are thought to be duplicated via an RNA intermediate in a process termed retroposition. Recently inserted Alu elements are closely related, suggesting that they are derived from a single source gene or closely related source genes. Analysis of the type III collagen gene (COL3A1) revealed a polymorphic Alu insertion in intron 8 of the gene. The Alu insertion in the COL3A1 gene had a high degree of nucleotide identity to the Sb family of Alu elements, a family of older Alu elements. The Alu sequence was less similar to the consensus sequence for the PV or Sb2 subfamilies, subfamilies of recently inserted Alu elements. These data support the observations that at least three source genes are active in the human genome, one of which is distinct from the PV and Sb2 subfamilies and predates either of these two subfamilies. Appearance of the Alu insertion in different ethnic populations suggests that the insertion may have occurred in the last 100,000 years. This Alu insert should be a useful marker for population studies and for marking COL3A1 alleles.     

Decomposition of Eucalyptus globulus leaves and three native leaf species (Alnus glutinosa, Castanea sativa and Quercus faginea) in a Portuguese low order stream

Leaf decomposition of the exotic evergreen Eucalyptus globulus (eucalyptus), and three native deciduous tree species, Alnus glutinosa (alder), Castanea sativa (chestnut) and Quercus faginea (oak), was compared in a second order stream in Central Portugal. Changes in dry weight, nitrogen and polyphenolic compounds and microbial colonization were periodically assessed for three months.Negative exponential curves fit the leaf weight loss with time for all leaf species. Mass loss rate was in the order alder (K = 0.0161) > chestnut (K = 0.0079) > eucalyptus (K = 0.0068) > oak (K = 0.0037). Microbial colonization followed the same pattern as breakdown rates. Evidence of fungal colonization was observed in alder after 3 days in the stream, whereas it took 21 days in oak leaves to have fungal colonization. Fungal diversity was leaf species-dependent and increased with time. In all cases, percent nitrogen per unit leaf weight increased, at least, at the initial stages of decay while soluble polyphenolics (expressed as percentage per unit leaf weight) decreased rapidly in the first month of leaves immersion.Intrinsic factors such as nitrogen and polyphenolic content may explain differences in leaf decomposition. The possible incorporation of eucalyptus litter into secondary production in a reasonable time span is suggested, although community balance and structure might be affected by differences in allochthonous patterns determined by eucalyptus monocultures.     

Variable effects of air-drying on leaching losses from tree leaf litter

Leaching of soluble substances may be an important first step in leaf litter decomposition in small streams, but recent research has suggested that large leaching losses (up to 30% of initial mass in 48 h) may be an artifact created by using air-dried leaves in decomposition experiments. In laboratory experiments, we compared 3 d leaching losses from freshly fallen and air-dried senescent leaves of 27 tree species from different regions across Canada. Air-dried leaves from all species leached measurable amounts of original mass (3.6–32.8% dry mass), but leaching losses from fresh leaves (0–35%) were detectable in all but two species. Air-drying increased leaching losses in many species, but in others it reduced leaching losses or had no measurable effect. Results for leaves of the same species collected in different regions or in different years were generally similar, but species within the same genus often behaved very differently. Neither moisture content (fresh or air-dried), leaf thickness, nor cuticle thickness proved of any value as predictors of leaching losses or the effect of air-drying. The propensity of autumn-fallen leaves to leach, whether fresh or air-dried, appears to be a property of the individual tree species.     

Fine root demography in alfalfa (Medicago sativa L.)

In perennial forages like alfalfa (Medicago sativa L.), repeated herbage removal may alter root production and mortality which, in turn, could affect deposition of fixed N in soil. Our objective was to determine the extent and patterns of fine-diameter root production and loss during the year of alfalfa stand establishment. The experiment was conducted on a loamy sand soil (Udorthentic Haploboroll) in Minnesota, USA, using horizontally installed minirhizotrons placed directly under the seeded rows at 10, 20, and 40 cm depths in four replicate blocks. We seeded four alfalfa germplasms that differed in N₂ fixation capacity and root system architecture: Agate alfalfa, a winter hardy commercially-available cultivar; Ineffective Agate, which is a non-N₂-fixing near isoline of Agate; a new germplasm that has few fibrous roots and strong tap-rooted traits; and a new germplasm that has many fibrous roots and a strongly branched root system architecture. Video images collected biweekly throughout the initial growing season were processed using C-MAP-ROOTS software.More than one-half of all fine roots in the upper 20 cm were produced during the first 7 weeks of growth. Root production was similar among germplasms, except that the highly fibrous, branch-rooted germplasm produced 29% more fine roots at 20 cm than other germplasms. In all germplasms, about 7% of the fine roots at each depth developed into secondarily thickened roots. By the end of the first growing season, greatest fine root mortality had occurred in the uppermost depth (48%), and least occurred at 40 cm (36%). Survival of contemporaneous root cohorts was not related to soil depth in a simple fashion, although all survivorship curves could be described using only five rates of exponential decline. There was a significant reduction in fine root mortality before the first herbage harvest, followed by a pronounced loss (average 22%) of fine roots at the 10- and 20-cm depths in the 2-week period following herbage removal. Median life spans of these early-season cohorts ranged from 58 to 131 days, based on fitted exponential equations. At all depths, fine roots produced in the 4 weeks before harvest (early- to mid-August) tended to have shorter median life spans than early-season cohorts. Similar patterns of fine root mortality did not occur at the second harvest. Germplasms differed in the pattern, but not the ultimate extent, of fine root mortality. Fine root turnover during the first year of alfalfa establishment in this experiment released an estimated 830 kg C ha^–1 and 60 kg N ha^–1, with no differences due to N₂ fixation capacity or root system architecture.     

The effects of mycorrhizal roots on litter decomposition, soil biota, and nutrients in a spodosolic soil

We studied the effects of mycorrhizal pitch pine (Pinus rigida) roots on litter decomposition, microbial biomass, nematode abundance and inorganic nutrients in the E horizon material of a spodosolic soil, using field microcosms created in a regenerating pitch pine stand in the New Jersey Pinelands. Pine roots stimulated litter decomposition by 18.7% by the end of the 29 month study. Both mass loss and N and P release from the litter were always higher in the presence of roots than in their absence. Nutrient concentrations in decomposing litter were similar, however, in the presence and absence of roots, which suggests that the roots present in the with-root treatment did not withdraw nutrients directly from the litter. The soil was slightly drier in the presence of roots, but there was no discernible effect on soil microbial biomass. The effects of roots on soil extractable inorganic nutrients were inconsistent. Roots, however, were consistently associated with higher numbers of soil nematodes. These results suggest that, in soils with low total C and N contents, roots stimulate greater activity of the soil biota, which contribute, in turn, to faster litter decomposition and nutrient release.Contribution No. 95-22 from the Institute of Marine and Coastal Sciences.Contribution No. 95-22 from the Institute of Marine and Coastal Sciences.     

Applications of minirhizotrons to understand root function in forests and other natural ecosystems

Minirhizotrons have proved useful to understand the dynamics and function of fine roots. However, they have been used comparatively infrequently in forests and other natural plant communities. Several factors have contributed to this situation, including anomalous root distributions along the minirhizotron surface and the difficulty of extracting data from minirhizotron images. Technical and methodological advances have ameliorated some of these difficulties, and minirhizotrons have considerable potential to address some questions of long standing interest. These questions include more fully understanding the role of roots in carbon and nutrient cycling, rates of root decomposition, responses to resource availability and the functional significance of interactions between plant roots and soil organisms. Maximizing the potential for minirhizotrons to help us better understand the functional importance of fine roots in natural plant communities depends upon using them to answer only those questions appropriate to both their inherent strengths and limitations.     

A new family of dispersed repeats from Brassica nigra: characterization and localization

The 459-bp HindIII (pBN-4) and the 1732-bp Eco RI (pBNE8) fragments from the Brassica nigra genome were cloned and shown to be members of a dispersed repeat family. Of the three major diploid Brassica species, the repeat pBN-4 was found to be highly specific for the B. nigra genome. The family also hybridized to Sinapis arvensis showing that B. nigra had a closer relationship with the S. arvensis genome than with B. oleracea or B. campestris. The clone pBNE8 showed homology to a number of tRNA species indicating that this family of repeats may have originated from a tRNA sequence. The species-specific 459-bp repeat pBN-4 was localized on the B. nigra chromosomes using monosomic addition lines. In addition to the localization of pBN-4, the chromosomal distribution of two other species-specific repeats, pBN34 and pBNBH35 (reported earlier), was studied. The dispersed repeats pBN-4 and pBNBH35 were found to be present on all of the chromosomes, whereas the tandem repeat pBN34 was localized on two chromosomes.     

Fungal succession in the early decomposition process of pine cones on the floor ofPinus densiflora forests

The fungal succession on pine cones on the floor ofPinus densiflora forest was investigated in the early decomposition process (within ca. 30% decrease in dry weight). The fungal flora was examined by both washing and surface-sterilization methods on artificially placed cones and naturally fallen cones. The decomposition rates of artificially placed cones were 0.081–0.082 yr^–1. On withered cones still attached to the tree,Pestalotiopsis spp. were dominant. These fungi also occurred with higher frequencies after cones had lain on the floor and on cones in the L and FH horizons.Xylaria sp. andPhomopsis sp., which seem to colonize the interior of the tissue, occurred with higher frequencies on the cones on the tree, but their occurrence frequencies decreased after cones had lain on the forest floor. Conversely,Mortierella spp. andTrichoderma spp. newly occurred or their occurrence frequencies increased on lying cones. Of these,Trichoderma koningii increased rapidly and showed high occurrence frequencies.Thysanophora penicillioides, which prefers coniferous substrates, showed higher occurrence frequencies in the early stages of lying on the forest floor. On cones lying on the floor, the fungal flora did not significantly change during the investigation period.     

Search for rhythmicity during hibernation in the European hamster

Temporal patterns of hibernation were studied by continuous monitoring of body temperature by radiotelemetry over 6 months in European hamsters, Cricetus cricetus, at constant temperature and photoperiod. Entrances into hibernation occurred mostly at the end of the night (0000–0800 hours), while arousals were randomly distributed between day and night. This is at variance with a control of bout duration by a clock with a period of 24 h. Consequently, the timing of entrances implies a phase-resetting of the circadian clock on each arousal. Persistence of circadian rhythmicity with a period different from 24 h during deep hibernation was investigated examining whether the durations of torpor bouts were integer multiples of a constant period. A non-parametric version of the classical contingency test of periodicity was developed for this purpose. Periods ranging from 21 to 29 h were tested. Nine animals out of ten showed at least one significant period in this range (P<0.01), either below 24 h (21.8±0.5 h, n=4) or above (27.3±0.5 h, n=7). However, we have found a theoretical model of bout durations for which the contingency test of periodicity sometimes gives false significant results. This indicates that the power of the test is weak. With this reservation our results suggest that a circadian oscillator controls the duration of a bout of hibernation, which would occur after an integer, but variable and possibly temperature-dependent number of cycles.Abbreviations _b a contingency test (see Appendix) - SCN suprachiasmatic nuclei - period - T _b body temperature