Global gene expression analysis of bovine somatic cell nuclear transfer blastocysts and cotyledons.

Low developmental competence of bovine somatic cell nuclear transfer (SCNT) embryos is a universal problem. Abnormal placentation has been commonly reported in SCNT pregnancies from a number of species. The present study employed Affymetrix bovine expression microarrays to examine global gene expression patterns of SCNT and in vivo produced (AI) blastocysts as well as cotyledons from day-70 SCNT and AI pregnancies. SCNT and AI embryos and cotyledons were analyzed for differential expression. Also in an attempt to establish a link between abnormal gene expression patterns in early embryos and cotyledons, differentially expressed genes were compared between the two studies. Microarray analysis yielded a list of 28 genes differentially expressed between SCNT and AI blastocysts and 19 differentially expressed cotyledon genes. None of the differentially expressed genes were common to both groups, although major histocompatibility complex I (MHCI) was significant in the embryo data and approached significance in the cotyledon data. This is the first study to report global gene expression patterns in bovine AI and SCNT cotyledons. The embryonic gene expression data reported here adds to a growing body of data that indicates the common occurrence of aberrant gene expression in early SCNT embryos.

Effects of amino acid substitutions in and around the arginine-glycine-aspartic acid (RGD) sequence on fertilization and parthenogenetic development in mature bovine oocytes.

Integrins have been shown to be involved in the process of fertilization and many integrin-ligand interactions are mediated through the recognition of an arginine-glycine-aspartic acid (RGD) sequence. Despite the fact the RGD domain is a principal player in determining the functional characteristics of an adhesive protein, increasing evidence has accumulated implicating the amino acids flanking the RGD sequence in determining the functional properties of the RGD-containing protein. A set of linear peptides in which the amino acid sequence in and around the RGD tri-peptide was modified was synthesized to better understand the specificity of the RGD-receptor interaction. Mature oocytes were fertilized in vitro in the presence of RGD-containing and RGD-modified peptides. Both the RGD-containing and RGD-modified peptides impaired the ability of sperm to fertilize bovine oocytes, illustrated by a reduction in cleavage. The linear modified RGD containing peptides were also examined for their ability to induce parthenogenetic development with the objective of providing a linear RGD peptide with greater biological activity than the one (GRGDSPK) used previously (Campbell et al., 2000). The data demonstrate the specificity of the receptor for the RGD sequence, further implicate the involvement of integrins in the process of bovine fertilization, and illustrate the importance of the amino acids surrounding the RGD sequence in determining the binding and functional properties of RGD-containing peptides. The data support the findings that a linear RGD peptide can block fertilization and that amino acids around the RGD sequence have an impact on the biological activity of the receptor.

Multiple-event study of bioretention for treatment of urban storm water runoff.

Bioretention is a novel best management practice for urban storm water, employed to minimize the impact of urban runoff during storm events. Bioretention consists of porous media layers that can remove pollutants from infiltrating runoff via mechanisms that include adsorption, precipitation, and filtration. However, the effectiveness of bioretention in treating repetitive inputs of runoff has not been investigated. In this study, a bioretention test column was set up and experiments proceeded once every week for a total of 12 tests. Through all 12 repetitions, the infiltration rate remained constant (0.35 cm/min). All 12 tests demonstrated excellent removal efficiency for TSS, oil/grease, and lead (99%). For total phosphorus, the removal efficiency was about 47% the system removal efficiency ranged from 2.3% to 23%. Effluent nitrate concentration became higher than the influent concentration during the first 28 days and removal efficiency ranged from 9% to 20% afterward. Some degree of denitrification was apparently proceeding in the bioretention system. Overall, the top mulch layer filtered most of TSS in the runoff and prevented the bioretention media from clogging during 12 repetitions. Runoff quality was improved by the bioretention column.

The yeast recombinational repair protein Rad59 interacts with Rad52 and stimulates single-strand annealing.

The yeast RAD52 gene is essential for homology-dependent repair of DNA double-strand breaks. In vitro, Rad52 binds to single- and double-stranded DNA and promotes annealing of complementary single-stranded DNA. Genetic studies indicate that the Rad52 and Rad59 proteins act in the same recombination pathway either as a complex or through overlapping functions. Here we demonstrate physical interaction between Rad52 and Rad59 using the yeast two-hybrid system and co-immunoprecipitation from yeast extracts. Purified Rad59 efficiently anneals complementary oligonucleotides and is able to overcome the inhibition to annealing imposed by replication protein A (RPA). Although Rad59 has strand-annealing activity by itself in vitro, this activity is insufficient to promote strand annealing in vivo in the absence of Rad52. The rfa1-D288Y allele partially suppresses the in vivo strand-annealing defect of rad52 mutants, but this is independent of RAD59. These results suggest that in vivo Rad59 is unable to compete with RPA for single-stranded DNA and therefore is unable to promote single-strand annealing. Instead, Rad59 appears to augment the activity of Rad52 in strand annealing.

Laboratory study of biological retention for urban stormwater management.

Urban stormwater runoff contains a broad range of pollutants that are transported to natural water systems. A practice known as biological retention (bioretention) has been suggested to manage stormwater runoff from small, developed areas. Bioretention facilities consist of porous soil, a topping layer of hardwood mulch, and a variety of different plant species. A detailed study of the characteristics and performance of bioretention systems for the removal of several heavy metals (copper, lead, and zinc) and nutrients (phosphorus, total Kjeldahl nitrogen [TKN], ammonium, and nitrate) from a synthetic urban stormwater runoff was completed using batch and column adsorption studies along with pilot-scale laboratory systems. The roles of the soil, mulch, and plants in the removal of heavy metals and nutrients were evaluated to estimate the treatment capacity of laboratory bioretention systems. Reductions in concentrations of all metals were excellent (> 90%) with specific metal removals of 15 to 145 mg/m2 per event. Moderate reductions of TKN, ammonium, and phosphorus levels were found (60 to 80%). Little nitrate was removed, and nitrate production was noted in several cases. The importance of the mulch layer in metal removal was identified. Overall results support the use of bioretention as a stormwater best management practice and indicate the need for further research and development.

Competitive photocatalytic oxidation of Cu(II)--EDTA and Cd(II)--EDTA with illuminated TiO2.

Competitive photocatalytic oxidation (PCO) of mixtures of Cu(II)-EDTA and Cd(II)-EDTA was studied with variation of molar ratio of these two complexes (1 x 10(-4):0, 8 x 10(-5): 2 x 10(-5), 5 x 10-5:5 x 10(-5), 2 x 10-5:8 x 10(-5), 0:1 x 10(-4) M) and in the pH range of 4-8. PCO rates for each compound can be described using a combined aqueous + adsorbed pathway: -dC/dt = k1Caq(1+ k2Caq)+ kadsCads. This expression is valid under both noncompetitive and competitive conditions. Differences in rates under competition result from differences in the partitioning of the two species between the TiO2 surface and the aqueous phase. Total initial complex degradation rates (rTT), obtained by summation of the total destruction rates for Cu(II)-EDTA and Cd(II)-EDTA, were relatively constant at pH 4 and 5 for all ratios. At these pH values, contribution of adsorbed pathways to rTT was important, and rates were similar to those of the aqueous phase pathways. From pH 6 to 8, the degree of adsorption, and thus the adsorbed pathway rate, diminished. Through the adsorbed pathway, no difference in rate constants was found between Cu(II)-EDTA and Cd(II)-EDTA; Cd(II)-EDTA is somewhat more reactive through the aqueous phase pathway.

Loading estimates of lead, copper, cadmium, and zinc in urban runoff from specific sources.

Urban stormwater runoff is being recognized as a substantial source of pollutants to receiving waters. A number of investigators have found significant levels of metals in runoff from urban areas, especially in highway runoff. As an initiatory study, this work estimates lead, copper, cadmium, and zinc loadings from various sources in a developed area utilizing information available in the literature, in conjunction with controlled experimental and sampling investigations. Specific sources examined include building siding and roofs; automobile brakes, tires, and oil leakage; and wet and dry atmospheric deposition. Important sources identified are building siding for all four metals, vehicle brake emissions for copper and tire wear for zinc. Atmospheric deposition is an important source for cadmium, copper, and lead. Loadings and source distributions depend on building and automobile density assumptions and the type of materials present in the area examined. Identified important sources are targeted for future comprehensive mechanistic studies. Improved information on the metal release and distributions from the specific sources, along with detailed characterization of watershed areas will allow refinements in the predictions.

Cadmium adsorption on aluminum oxide in the presence of polyacrylic acid.

Adsorption of metals from aqueous solution onto oxide and other surfaces is known to affect trace metal transport in many natural and engineered systems. It is therefore important to understand whether dissolved metal inputs will be easily bound to particles or will be strongly complexed in solution and transported with the water phase. The effect of poly(acrylic acid) (PAA), representing a model compound for natural organic matter, on the adsorption of Cd(II) onto gamma-Al2O3 was determined using batch adsorption experiments over a pH range from 4 to 10. Initially, interactions among the individual components were evaluated. Cadmium adsorption onto alumina showed a typical S-shaped metal adsorption curve. PAA adsorption onto gamma-Al2O3 decreased with increase in pH. The affinity of PAA for Cd2+ increased strongly with pH. In ternary systems, the presence of PAA resulted in an enhancement of Cd(II) adsorption below pH 6, apparently due to ternary surface complex formation. Above pH 6, a decrease in cadmium adsorption onto gamma-Al2O3 was observed resulting from an increase in the concentration of soluble Cd-PAA complexes. Overall, results indicate that the presence of natural organic matter could have a significant impact on the distribution and mobility of cadmium in the environment. Simple surface complexation modeling was insufficient to describe behavior in the ternary systems due to the complexity of the PAA polymer.

Removal of Cu(II) and Cd(II) from aqueous solution by seafood processing waste sludge.

Dried waste slurry generated in seafood processing factories has been shown to be an effective adsorbent for the removal of heavy metals from dilute solutions. Characterization of the sludge surface with scanning electron microscope and X-ray microanalyzer were carried out to evaluate the components on the sludge surface that are related to the adsorption of metal ions. Aluminum and calcium, as well as organic carbon are distributed on the surface of sludge. Alkalimetric titration was used to characterize the surface acidity of the sludge sample. The surface acidity constants, pKa1s and pKa2s, were 5.80 and 9.55, respectively. Batch as well as dynamic adsorption studies were conducted with 10(-5) to 5 x 10(-3) M Cu(II) and Cd(II). A surface complexation model with the diffuse layer model successfully predicted Cu(II) and Cd(II) removals in single metal solutions. Predictions of sorption in binary-adsorbate systems based on single-adsorbate data fits represented competitive sorption data reasonably well over a wide range of conditions. The breakthrough capacity found from column studies was different for each metal ion and the data reflect the order of metal affinity for the adsorbent material very well.

Mutations in noncoding regions of the proteolipid protein gene in Pelizaeus-Merzbacher disease.

BACKGROUND: Pelizaeus-Merzbacher disease (PMD) is an X-linked recessive dysmyelinating disorder of the CNS. Duplications or point mutations in exons of the proteolipid protein (PLP) gene are found in most patients. OBJECTIVE: To describe five patients with PMD who have mutations in noncoding regions of the PLP gene. METHODS: Quantitative multiplex PCR and Southern blot analyses were used to detect duplication of the PLP gene, and DNA sequence analysis, including exon-intron borders, was used to detect mutation of the PLP gene. RESULTS: Duplication of the PLP gene was ruled out, and mutations were identified in noncoding regions of five patients in four families with PMD. In two brothers with a severe form of PMD, a G to T transversion at IVS6+3 was detected. This mutation resulted in skipping of exon 6 in the PLP mRNA of cultured fibroblasts. A patient who developed nystagmus at 16 months and progressive spastic ataxia at 18 months was found to have a 19-base pair (bp) deletion of a G-rich region near the 5' end of intron 3 of the PLP gene. A patient with a T to C transition at IVS3+2 and a patient with an A to G transition at IVS3+4 have the classic form of PMD. These, like the 19-bp deletion, are in intron 3, which is involved in PLP/DM20 alternative splice site selection. CONCLUSIONS: Mutations in introns of the PLP gene, even at positions that are not 100% conserved at splice sites, are an important cause of PMD.

A novel allele of RAD52 that causes severe DNA repair and recombination deficiencies only in the absence of RAD51 or RAD59.

With the use of an intrachromosomal inverted repeat as a recombination reporter, we have shown that mitotic recombination is dependent on the RAD52 gene, but reduced only fivefold by mutation of RAD51. RAD59, a component of the RAD51-independent pathway, was identified previously by screening for mutations that reduced inverted-repeat recombination in a rad51 strain. Here we describe a rad52 mutation, rad52R70K, that also reduced recombination synergistically in a rad51 background. The phenotype of the rad52R70K strain, which includes weak gamma-ray sensitivity, a fourfold reduction in the rate of inverted-repeat recombination, elevated allelic recombination, sporulation proficiency, and a reduction in the efficiency of mating-type switching and single-strand annealing, was similar to that observed for deletion of the RAD59 gene. However, rad52R70K rad59 double mutants showed synergistic defects in ionizing radiation resistance, sporulation, and mating-type switching. These results suggest that Rad52 and Rad59 have partially overlapping functions and that Rad59 can substitute for this function of Rad52 in a RAD51 rad52R70K strain.

A novel technique for rapid automated genotyping of DNA polymorphisms in the mouse.

The ability to rapidly and reliably genotype mice is an important concern. Traditional methods employ labour intensive and time consuming techniques such as test crossing, gel electrophoresis or nucleic acid hybridization. Here we show that a new molecular biology workstation, the WAVE DNA Fragment Analysis System, can easily resolve polymerase chain reaction (PCR) products that have small differences in their lengths. Analysis is fully automated and takes less than 7 min per sample. Approximately 200 samples can be analysed per day with only minutes of hands-on time after completion of the PCR. Genotyping with the WAVE DNA Fragment Analysis System is a fast and efficient method with minimal manual intervention.