Genetic variation of recent Alu insertions in human populations

The Alu family of intersperesed repeats is comprised of ovr 500,000 members which may be divided into discrete subfamilies based upon mutations held in common between members. Distinct subfamilies of Alu sequences have amplified within the human genome in recent evolutionary history. Several individual Alu family members have amplified so recently in human evolution that they are variable as to presence and absence at specific loci within different human populations. Here, we report on the distribution of six polymorphic Alu insetions in a survey of 563 individuals from 14 human population groups across several continents. Our results indicate that these polymorphic Alu insertions probably have an African origin and that there is a much smaller amount of genetic variation between European populations than that found between other populations groups. Present address: Department of Pathology, Stanley S. Scott Cancer Center, Louisiana State University Medical Center, 1901 Perdido St., New Orleans, LA 70112 Correspondence to: M.A. Batzer     

NMR Studies of Pi-Containing Extracellular and Cytoplasmic Compartments in Brain

Abstract: The inorganic phosphate (P_i) NMR peak in brain has an irregular shape, which suggests that it represents more than a single homogeneous pool of P_i. To test the ability of the Marquardt-Levenberg (M-L) nonlinear curve fit algorithm software (Peak-Fit) to separate multiple peaks, locate peak centers, and estimate peak heights, we studied simulated P_i spectra with defined peak centers, areas, and signal-to-noise (S/N) ratios ranging from ∞ to 5.8. As the S/N ratio decreased below 15, the M-L algorithm located peak centers accurately when they were detected; however, small peaks tended to grow smaller and disappear, whereas the amplitudes of larger peaks increased. We developed an in vitro three-compartment model containing a mixture of P_i buffer, phosphocreatine, phosphate diester, and phosphate monoester (PME), portions of which were adjusted to three different pHs before addition of agar. Weighed samples of each buffered gel together with phospholipid extract and bone chips were placed in an NMR tube and covered with mineral oil. Following baseline correction, it was possible to separate the P_i peaks arising from the three compartments with different pH values if each peak made up 10–35% of total P_i area. In vivo, we identified the plasma compartment by intraarterial infusion of P_i. It was assumed that intracellular compartments contained high-energy phosphates and took up glucose. Based on these assumptions we subjected the brains to complete ischemia and observed that P_i compartments at pH 6.82, 6.92, 7.03, and 7.13 increased markedly in amplitude. If the brain cells took up and phosphorylated 2-deoxyglucose (2-DG), 2-DG-6-phosphate (2-DG-6-P) would appear in the PME portion of the spectrum ionized according to pH_i. Four 2-DG-6-P peaks with calculated pH values of 6.86, 6.94, 7.04, and 7.15 did appear in the spectrum, thereby confirming that the four larger P_i peaks represented intracellular spaces.     

Fetal cells in maternal blood: recovery by charge flow separation

Fetal blood cells can be recovered from the maternal circulation by charge flow separation (CFS), a method that obviates the risks associated with amniocentesis and chorionic villus sampling. By CFS, we processed blood samples from 13 women carrying male fetuses, 2 carrying fetuses with trisomy 21, and 1 who had delivered a stillborn infant with trisomy 18. On average more than 2000 fetal nucleated red blood cells were recovered per 20-ml sample of maternal blood. Recovery of fetal cells was confirmed by fluorescence in situ hybridization with probes for chromosomes Y, 18 and 21. After culturing of CFS-processed cells, amplification by the polymerase chain reaction revealed Y-chromosomal DNA in clones from four of six women bearing male fetuses, but not in clones from three women bearing female fetuses. Received: 8 January 1996 / Revised: 22 March 1996     

Computational sequence analysis of matrix metalloproteinases

Matrix metalloproteinases (MMP) play a cardinal role in the breakdown of extracellular matrix involved in a variety of biological and pathological processes. Research on MMPs has classified and characterized these enzymes according to their matrix substrate specificity, gene and protein domain structure, and regulation of activity and expression. However, the discovery of new MMPs has introduced a need for a more comprehensive and systematic method of classification and quantitative comparison of known and newly discovered members. This study compiles a sequence alignment, constructs a dendrogram, and calculates physical data and homology percentage assignments in order to obtain further insight into MMP structure-function relationships. Thorough analysis of MMP primary sequence domains, physical data patterns, and statistical analysis of sequence homology yields higher resolution in the similarities and differences that group MMP members.     

The effects of liming an Adirondack lake watershed on downstream water chemistry

Calcite treatment of chronically acidic lakes has improved fish habitat, but the effects on downstream water quality have not previously been examined. In this study, the spatial and temporal effects of watershed CaCO₃ treatment on the chemistry of a lake outlet stream in the Adirondack Mountains of New York were examined. Before CaCO₃ treatment, the stream was chronically acidic. During spring snowmelt before treatment, pH and acid-neutralizing capacity (ANC) in the outlet stream declined, and NO ₃ ^– and inorganic monomeric aluminum (Al_IM) concentrations increased sharply. During that summer, SO ₄ ^– and NO ₃ ^– concentrations decreased downstream, and dissolved organic carbon (DOC) concentrations and ANC increased, in association with the seasonal increase in decomposition of organic matter and the attendant SO ₄ ^– -reduction process. A charge-balance ANC calculation closely matched measured downstream changes in ANC in the summer and indicated that SO ₄ ^– reduction was the major process contributing to summer increases in ANC. Increases in Ca²⁺ concentration and ANC began immediately after CaCO₃ application, and within 3 months, exceeded their pretreatment values by more than 130 eq/L. Within 2 months after treatment, downstream decreases in Ca²⁺ concentration, ANC, and pH, were noted. Stream mass balances between the lake and the sampling site 1.5 km downstream revealed that the transport of all chemical constituents was dominated by conservative mixing with tributaries and ground water; however, non-conservative processes resulted in significant Ca²⁺ losses during the 13-month period after CaCO₃ treatment. Comparison of substrate samples from the buffered outlet stream with those from its untreated tributaries showed that the percentage of cation-exchange sites occupied by Ca²⁺ as well as non-exchangeable Ca, were higher in the outlet-stream substrate than in tributary-stream substrate. Mass-balance data for Ca²⁺ H⁺, Al_IM, and DOC revealed net downstream losses of these constituents and indicated that a reasonable set of hypothesized reactions involving Al_IM, HCO ₃ ^– , Ca²⁺, SO ₄ ^– NO ₃ ^– , and DOC could have caused the measured changes in stream acid/base chemistry. In the summer, the sharp decrease in ANC continued despite significant downstream decreases in SO₄ ^2– concentrations. After CaCO₃ treatment, reduction of SO ₄ ^– was only a minor contributor to ANC changes relative to those caused by Ca²⁺ dilution from acidic tributaries and acidic ground water, and Ca²⁺ interactions with stream substrate.     

Influence of drought on competition between selected Rhizobium meliloti strains and naturalized soil rhizobia in alfalfa

Drought is an important environmental factor that can affect rhizobial competition and N₂ fixation. Three alfalfa (Medicago sativa L. and M. falcata L.) accessions were grown in pots containing soil from an irrigated (Soil 1) and a dryland (Soil 2) alfalfa field in northern Utah, USA. Mutants of three strains of Rhizobium meliloti Dang. from Pakistan (UL 136, UL 210, and UL 222) and a commercial rhizobial strain 102F51a were developed with various levels of resistance to streptomycin. Seeds inoculated with these individual streptomycin-resistant mutants were sown in the two soils containing naturalized rhizobial populations. Soils in the pots were maintained at −0.03, −0.5, and −1.0 MPa. After 10 weeks, plants were harvested and nodule isolates were cultured on agar medium with and without streptomycin to determine nodule occupancy (proportion of the nodules occupied by introduced rhizobial strains). Number of nodules, nodule occupancy, total plant dry weight, and shoot N were higher for Soil 1 than Soil 2. Number of nodules, plant dry weight, and shoot N decreased as drought increased from −0.03 to −1.0 MPa in the three alfalfa accessions. Rhizobial strains UL 136 and UL 222 were competitive with naturalized alfalfa rhizobia and were effective at symbiotic N₂ fixation under drought. These results suggest that nodulation, growth, and N₂ fixation in alfalfa can be improved by inoculation with competitive and drought-tolerant rhizobia and may be one economically feasible way to increase alfalfa production in water-limited environments. Joint contribution from USDA-ARS and the Utah Agric. Exp. Sta., Utah State Univ., Logan, UT 84322-4810, USA. Journal Paper No. 4931. Joint contribution from USDA-ARS and the Utah Agric. Exp. Sta., Utah State Univ., Logan, UT 84322-4810, USA. Journal Paper No. 4931.     

Higher level relationships of Apiales (Apiaceae and Araliaceae) based on phylogenetic analysis of rbcL sequences

The two families of the order Apiales (Apiaceae and Araliaceae) represent a classic example of the difficulty in understanding evolutionary relationships between tropical-temperate family pairs. In Apiales, this problem is further compounded by phylogenetic confusion at almost every taxonomic level, including ordinal, interfamilial, and infrafamilial, due largely to difficulties in understanding trends in morphological evolution. Phylogenetic analyses of rbcL sequences were employed to resolve relationships at the ordinal and familial levels. The results of the ordinal analysis confirm the placement of Apiales in an expanded subclass Asteridae as the sister group to Pittosporaceae, and refute the traditional alliance of Apiales with Cornales and Rosidae. This study has also resolved relationships of a number of enigmatic genera, suggesting, for example, that Melanophylla, Aralidium, Griselinia, and Toricellia are close relatives of Apiales. Clarification of phylogenetic relationships has concomitantly provided insights into trends of morphological evolution, and suggests that the ancestral apialean taxon was probably bicarpellate, simple-leaved, woody, and paleotropical. Phylogenetic analysis at the family level suggests that apiaceous subfamily Hydrocotyloideae, often envisioned as an intermediate group between Apiaceae and Araliaceae, is polyphyletic, with some hydrocotyloids closely allied with Araliaceae rather than Apiaceae. With the exception of some hydrocotyloids, Apiaceae appear to be monophyletic. The relationship between Apiaceae and Araliaceae remains problematic. Although the shortest rbcL trees suggest that Apiaceae are derived from within a paraphyletic Araliaceae, this result is only weakly supported.