Development and Evaluation of SoySNP50K,a High-Density Genotyping Array for Soybean

The objective of this research was to identify single nucleotide polymorphisms (SNPs) and to develop an Illumina Infinium BeadChip that contained over 50,000 SNPs from soybean (Glycine max L. Merr.). A total of 498,921,777 reads 35–45bp in length were obtained from DNA sequence analysis of reduced representation libraries from several soybean accessions which included six cultivated and two wild soybean (G. soja Sieb. et Zucc.) genotypes. These reads were mapped to the soybean whole genome sequence and 209,903 SNPs were identified. After applying several filters, a total of 146,161 of the 209,903 SNPs were determined to be ideal candidates for Illumina Infinium II BeadChip design. To equalize the distance between selected SNPs, increase assay success rate, and minimize the number of SNPs with low minor allele frequency, an iteration algorithm based on a selection index was developed and used to select 60,800 SNPs for Infinium BeadChip design. Of the 60,800 SNPs, 50,701 were targeted to euchromatic regions and 10,000 to heterochromatic regions of the 20 soybean chromosomes. In addition, 99 SNPs were targeted to unanchored sequence scaffolds. Of the 60,800 SNPs, a total of 52,041 passed Illumina’s manufacturing phase to produce the SoySNP50K iSelect BeadChip. Validation of the SoySNP50K chip with 96 landrace genotypes, 96 elite cultivars and 96 wild soybean accessions showed that 47,337 SNPs were polymorphic and generated successful SNP allele calls. In addition, 40,841 of the 47,337 SNPs (86%) had minor allele frequencies ≥10% among the landraces, elite cultivars and the wild soybean accessions. A total of 620 and 42 candidate regions which may be associated with domestication and recent selection were identified, respectively. The SoySNP50K iSelect SNP beadchip will be a powerful tool for characterizing soybean genetic diversity and linkage disequilibrium, and for constructing high resolution linkage maps to improve the soybean whole genome sequence assembly.     

Cardio-respiratory effects of chloramine-T exposure in rainbow trout

In order to establish whether the blood gas respiratory disturbances noted with exposure to chloramine-T are due to differences in the rates of uptake of O₂ and excretion of CO₂ or gill blood flow, adult rainbow trout (Oncorhynchus mykiss) were fitted with dorsal aorta and bulbus arteriosus catheters to facilitate blood pressure recordings, an ultrasonic blood flow probe and opercular impedance electrodes. Fish received either a 45-min static exposure to 9 mg l⁻¹ chloramine-T or tap water (control) and continuous recordings of blood pressure, and ventilation frequency and amplitude were made. Pre- and post-exposure arterial and venous blood samples were taken and analyzed for O₂ and CO₂ content, hemoglobin concentration and hematocrit. Chloramine-T exposure had no effect on any of the continuously recorded parameters. However, individual measurements (made immediately prior to and following exposure) of cardiac output and O₂ uptake rates increased significantly following exposure to chloramine-T compared to before exposure. CO₂ excretion rates were unaffected by chloramine-T exposure. Calculation of the perfusion convection requirement showed a significant increase for CO₂ but not for O₂. It was concluded that increases in O₂ uptake resulted from increased cardiac output but that CO₂ excretion, a diffusion-limited process, was not increased due to additional diffusive limitations caused by the irritant effect of chloramine-T.     

Antimicrobial drug use in three Canadian general hospitals.

Total amounts of antimicrobial drugs used to treat inpatients during 1975 were calculated for three Canadian general hospitals, one of them the principal teaching hospital of a medical school. Use of drugs was compared with that reported for Boston City Hospital during periods when antimicrobial therapy was and was not supervised by infectious disease consultants. Ampicillin, tetracyclines, cephalosporins, erythromycin and aminoglycosides for prophylactic oral administration were used excessively in the three hospitals. The degree of overuse was comparable to that at Boston City Hospital during years when drug use was uncontrolled. Overuse or improper choice of antimicrobial drug decreases the quality of patient care and increases its cost. More rigorous education is needed for both medical students and practising physicians in the rational use of antimicrobial drugs. Informal consultation with an infectious disease unit should be required before certain overly popular or toxic antibiotics are administered to hospitalized patients.     

Molecular Cloning and Expression of a Human Phosphodiesterase 4C

A cDNA coding for a human phosphodiesterase 4C (PDE4C2) was isolated from the mRNA prepared from the glioblastoma cell line, U87. The cDNA contained an ORF of 1818 bp corresponding to a 605 amino acid polypeptide. The sequence differed at the 5′ end from the human PDE4C previously reported (Engels, P. et al, 1995 FEBs Letters 358, 305-310) indicating that it represents a novel splice variant of the human PDE4C gene. Evidence was also obtained for a third 5′ splice variant. The PDE4C2 cDNA was transfected into both COS 1 cells and yeast cells, and shown to direct the expression of an 80 kD polypeptide by Western blotting using a PDE4C specific antiserum. The activity of cell lysates was typical of PDE4 being specific for cAMP and inhibitable by the selective inhibitor, rolipram. However, the K_m for cAMP of the enzyme produced in COS cells was 0.6 μM compared to 2.6 μM for the yeast 4C activity. In addition the COS cell PDE4 activity was much more sensitive to R rolipram than the yeast PDE4 enzyme (IC₅₀ of 23 nM compared to 1648 nM). This difference in rolipram sensitivity was associated with the detection of a high affinity [³H] R rolipram binding site on the COS cell 4C enzyme but not on the yeast expressed enzyme. The results indicate that the enzyme can adopt more than one active conformation, which are distinguished by their interaction with rolipram.