Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated

It has long been known, from the distribution of multiple amino acid replacements, that not all amino acids of a sequence are replaceable. More recently, the phenomenon was observed at the nucleotide level in mitochondrial DNA even after allowing for different rates of transition and transversion substitutions. We have extended the search to globin gene sequences from various organisms, with the following results: (1) Nearly every data set showed evidence of invariable nucleotide positions. (2) In all data sets, substitution rates of transversions and transitions were never in the ratio of 2/1, and rarely was the ratio even constant. (3) Only rarely (e.g., the third codon position of beta hemoglobins) was it possible to fit the data set solely by making allowance for the number of invariable positions and for the relative rates of transversion and transition substitutions. (4) For one data set (the second codon position of beta hemoglobins) we were able to simulate the observed data by making the allowance in (3) and having the set of covariotides (concomitantly variable nucleotides) be small in number and be turned over in a stochastic manner with a probability that was appreciable. (5) The fit in the latter case suggests, if the assumptions are correct and at all common, that current procedures for estimating the total number of nucleotide substitutions in two genes since their divergence from their common ancestor could be low by as much as an order of magnitude. (6) The fact that only a small fraction of the nucleotide positions differ is no guarantee that one is not seriously underestimating the total amount of divergence (substitutions). (7) Most data sets are so heterogeneous in their number of transition and transversion differences that none of the current models of nucleotide substitution seem to fit them even after (a) segregation of coding from noncoding sequences and (b) splitting of the codon into three subsets by codon position. (8) These frequently occurring problems cannot be seen unless several reasonably divergent orthologous genes are examined together.      

Geochemical processes in the Lake Fryxell Basin (Victoria Land,Antarctica)

Major ion, nutrient, transition metal, and cadmium concentrations are presented for nine meltwater streams flowing into Lake Fryxell, a permanently stratified lake with an anoxic hypolimnion in Taylor Valley, Antarctica. For the major ions, stream compositions are considered in terms of dissolution of marine-derived salts and chemical weathering of local rocks. Although Lake Fryxell has undergone significant evaporative concentration, only calcite, of the simple salts, is predicted to precipitate. Geochemical budgets indicate, however, that large quantities of K, Mg, and SO₄ have also been removed from the lake. Reverse weathering may be an important sink for K and Mg, although magnesium removal with calcium carbonate phases is also likely. Assuming constancy of composition over recent geologic time, all of the salts in the Fryxell water column could have been delivered under present flows in about three thousand years (chloride age).Comparison of nutrient concentrations in these meltwater streams with other flowing waters in the world reveals that the Fryxell streams are strikingly deficient in NO₃-N but not PO₄-P. The apparent nitrogen deficiency in Lake Fryxell itself can be attributed to the low annual stream loadings of this nutrient.Stream concentrations and loadings are also presented for Mn, Fe, Co, Ni, Cu, and Cd. Dissolved metal concentrations correlate roughly with average crustal abundances, suggesting that chemical weathering is the major source for these elements. Vertical metal profiles within Lake Fryxell itself appear to be governed by the formation of insoluble sulfide phases, or, in the case of Mn, by MnHPO₄. However, dissolved nickel levels in sulfide-bearing waters are much higher than can be explained in terms of metal-sulfide equilibria, and we suspect that significant organic complexing of this metal is occurring in the deeper waters.     

Effects of plant height and row spacing on kenaf forage potential with multiple harvests

Kenaf (Hibiscus cannabinus L.) forage potential can be enhanced through its regrowth capacity and higher production in narrow rows. A field experiment was conducted in Matamoros, Coahuila, Mexico, during 2 growing seasons (2004 and 2005) to study the effects of plant height and row spacing on kenaf forage potential with multiple harvests. This study evaluated the effects of (1) 2 plant heights at cutting (1.0-1.2 m and 1.8-2.0 m) and (2) 4 inter row spacings (0.19, 0.38, 0.57 and 0.76 m) using a 2 x 4 factorial arrangement of treatments in a completely randomized block design with 4 replications. Dry matter (DM) and crude protein (CP) yields, DM partitioning, neutral detergent fiber (NDF) and CP concentrations were determined. Heights at cutting × row spacing interactions were not significant for the monitored variables (p>0.05). Kenaf response to treatments was only relevant for main effects (p≤0.05). Row spacing and plant height affected DM and CP yields (p≤0.05), whereas only plant height affected chemical composition and DM partitioning (p≤0.05). Dry matter (17.0%-26.0%), and CP (12.4%-15.6%) yields were higher (p≤0.05) when plant heights had reached 1.8 to 2.0 m. Row spacing reduction from 0.76 m to 0.38 and 0.19 m increased DM yield (20.4-33.4%) and CP yield (24.2-38.5%) (p≤0.05). Kenaf forage potential increases when planted in narrow rows and harvested 2 or 3 times during the growing season.     

Vegetal cover estimated by digital photographs related to biomass in a grassland site in northern Mexico

A regression model was used to determine the relationship between aerial herbaceous biomass and vegetation coverage estimated by digital images. Four samplings (n=36 each date) of vegetation cover and herbaceous biomass were performed during the growing season in 2011 in a grassland dominated by Bouteloua gracilis in La Cieneguilla, Municipality of Villa Hidalgo, Durango. Average production of dry biomass was 37.36 ± 9.66 g/m², and mean vegetation cover 30.02%. Dry biomass data were tested for normality using the test of Kolmogorov Smirnov, finding a lack of fit. The data were subjected to a logarithmic transformation and the model Ln(y) = 1.637926 + 0.08501X - 0.000586X² with an adjusted R² = 0.89 was found. In order to validate this model, another five samplings were carried out in 2013 at the same site during summer and autumn, using the same sampling size for each date as in 2011. Data collected in 2013 were analyzed with the model Ln (y) = β₀ + β₁X + β₂X². A comparison of regression coefficients was carried out between the 2011 and 2013 models with t (180+144-9-11-2=302, p<0.05) = 1.967. The results indicated that it is possible to use the 2011 regression model to estimate herbaceous aerial biomass from vegetation cover measurements with aerial photographs in La Cieneguilla site during summer and fall.     

Soil moisture effects on uptake of metals by Thlaspi, Alyssum, and Berkheya

Most commonly used hyperaccumulator plants for phytoextraction of metals evolved on soils where moisture is limited throughout much of the year. As these plant species are commercialized for use, they are frequently moved from the point of evolution to locations where environmental conditions may be significantly different. Greatest among these potential differences is soil moisture. The objective of this study was therefore to determine whether these plants could grow in soils with much higher soil moisture and whether they would continue to hyperaccumulate metals as soils approach saturation. We examined extractable soil metal concentrations, plant growth, and metal accumulation for the Ni hyperaccumulators, Alyssum murale and Berkheya coddii and the Zn hyperaccumulators Thlaspi caerulescens cultivars AB300 and AB336. Non-hyperaccumulating control species for each were also examined. In general, extractable soil concentrations of Ni decreased with increasing soil moisture content. Few significant effects related to Zn extractability were observed for any of the soil moisture treatments. The biomass of all tested species was generally greater at higher soil moisture and inhibited at low soil moisture. Further, plants accumulated large amounts of metals from soil at higher soil moisture. Highest foliar concentrations of Zn or Ni were found at the two highest WHCs of 80 and 100%. These results show that hyperaccumulators grow well under conditions of high soil moisture content and that they continue to hyperaccumulate metals. Thus, growing Thlaspi, Alyssum, and Berkheya for commercial phytoextraction under nonnative conditions is appropriate and suggests that this technology may be applied to a wide and diverse range of soil types, climatic conditions, and irrigation regimes.     

A novel scheme to assess factors involved in the reproducibility of DNA-microarray data

Background  

In research laboratories using DNA-microarrays, usually a number of researchers perform experiments, each generating possible sources of error. There is a need for a quick and robust method to assess data quality and sources of errors in DNA-microarray experiments. To this end, a novel and cost-effective validation scheme was devised, implemented, and employed.     

Nickel localization and response to increasing Ni soil levels in leaves of the Ni hyperaccumulator Alyssum murale

We have previously developed phytoremediation and phytomining technologies employing Alyssum Ni hyperaccumulators to quantitatively extract Ni from soils. Implementation of these technologies requires knowledge of Ni localization patterns for the Alyssum species/ecotypes of interest under realistic growth conditions. We investigated Ni uptake and localization in mature Alyssum murale Kotodesh and AJ9ç leaves. Seedlings were grown in potting mix with an increasing series of NiSO₄ addition (0, 5, 10, 20, 40, 80 mmol Ni kg^–1), NiC₄H₆O₄ addition (0, 5, 10, 30, 60, 90 mmol Ni kg^–1), in Ni-contaminated soil from metal refining operations, and serpentine soil. Plants at Ni levels 0, 5, 10, 20 mmolkg^–1 and in native soils grew normally. Plants at 40 mmolkg^–1 exhibited the onset of phytotoxicity, and 60, 80, and 90 mmolkg^–1 were demonstrably phytotoxic, but symptoms of phytotoxicity abated within 6 months. Cryogenic complement fractures were made from frozen hydrated samples. High-resolution scanning electron microscope (SEM) images were taken of one half. The other half was freeze-dried and examined with SEM and semi-quantitative energy dispersive x-ray analysis. Ni was highly concentrated in epidermal cell vacuoles and Ni and S counts showed a positive correlation. Trichome pedicles and the epidermal tissue from which the trichome grows were primary Ni compartments, but Ni was not distributed throughout trichomes. Palisade and spongy mesophyll and guard/substomatal cells contained lesser Ni concentrations but palisade mesophyll was an increasingly important compartment as Ni soil levels increased. Ni was virtually excluded from vascular tissue and trichome rays.     

Development of the mammary gland requires DGAT1 expression in stromal and epithelial tissues

Mammary gland development is a complex process that is dependent on interactions between the developing mammary epithelium and the surrounding stromal tissues. We show that mice lacking the triglyceride synthesis enzyme acyl CoA:diacylglycerol transferase 1 (DGAT1) have impaired mammary gland development, characterized by decreased epithelial proliferation and alveolar development, and reduced expression of markers of functional differentiation. Transplantation studies demonstrate that the impaired development results from a deficiency of DGAT1 in both the stromal and epithelial tissues. Our findings are the first to link defects in stromal lipid metabolism to impaired mammary gland development.     

Phytoextraction of Soil Cobalt Using Hyperaccumulator Plants

A greenhouse study was conducted on phytoextraction of cobalt by nickel hyperaccumulators Alyssum murale and Alyssum corsicum and by two varieties of cobalt accumulator Nyssa sylvatica compared with the nonmetal accumulator crop plant Brassica juncea. The plants were grown on Sassafras sandy loam soil (<2 mg Co and 5 mg Ni/kg dry soil), amended with 1 mmol Co/kg dry soil (58.9 mg/kg), and two Ni smelter-contaminated soils, Quarry muck with 24 mg Co and 1720 mg Ni/kg dry soil and Welland loam with 37 mg Co and 2570 mg Ni/kg dry soil. All soils were adjusted to pH 6.5 to prevent Ni phytotoxicity. Of the five plant entries tested in the study, the two Alyssum species demonstrated the most promising Co phytoextraction results. In Co-amended Sassafras soil, the maximum concentration accumulated by Alyssum murale was 1320 mg Co/kg dry weight, which was almost 60 times higher than accumulation by crop plant Brassica juncea. At a single harvest after 60 days of growth, A. murale was able to extract more than 3% of Co from Co-amended soil. As expected, both Alyssum species accumulated up to 1% Ni on dry weight basis when grown on Ni-contaminated soils.

Nyssa sylvatica showed considerable Co accumulation; foliar Co concentration in the second harvest was as high as 800 mg/kg dry weight. The first few leaves that emerged were chlorotic, both in the Co-amended soil and Ni-contaminated soils, but with growth the signs of toxicity disappeared. In the Co amended soil, Co concentration in Nyssa sylvatica leaves was 30% of that found in shoots of Alyssum species, but an order of magnitude higher than that of Brassica juncea. The leaves accumulated a higher concentration compared with the stems.

Both Alyssum species and Nyssa sylvatica offer promise for phytoextraction of Co and ⁶⁰Co from contaminated or mineralized soils.