High-throughput genotyping assays for identification of glycophorin B deletion variants in population studies

Glycophorins are the most abundant sialoglycoproteins on the surface of human erythrocyte membranes. Genetic variation in glycophorin region of human chromosome 4 (containing GYPA, GYPB, and GYPE genes) is of interest because the gene products serve as receptors for pathogens of major public health interest, including Plasmodium sp., Babesia sp., Influenza virus, Vibrio cholerae El Tor Hemolysin, and Escherichia coli. A large structural rearrangement and hybrid glycophorin variant, known as Dantu, which was identified in East African populations, has been linked with a 40% reduction in risk for severe malaria. Apart from Dantu, other large structural variants exist, with the most common being deletion of the whole GYPB gene and its surrounding region, resulting in multiple different deletion forms. In West Africa particularly, these deletions are estimated to account for between 5 and 15% of the variation in different populations, mostly attributed to the forms known as DEL1 and DEL2. Due to the lack of specific variant assays, little is known of the distribution of these variants. Here, we report a modification of a previous GYPB DEL1 assay and the development of a novel GYPB DEL2 assay as high-throughput PCR-RFLP assays, as well as the identification of the crossover/breakpoint for GYPB DEL2. Using 393 samples from three study sites in Ghana as well as samples from HapMap and 1000 G projects for validation, we show that our assays are sensitive and reliable for genotyping GYPB DEL1 and DEL2. To the best of our knowledge, this is the first report of such high-throughput genotyping assays by PCR-RFLP for identifying specific GYPB deletion types in populations. These assays will enable better identification of GYPB deletions for large genetic association studies and functional experiments to understand the role of this gene cluster region in susceptibility to malaria and other diseases.     

Dual effects of K ions upon the inactivation of the anomalous rectifier of the tunicate egg cell membrane

Summary Inactivation of the K inward current through the anomalous rectifier channel of the egg cell membrane of a tunicate,Halocynthia roretzi Drashe, was studied under voltage-clamp. The noise spectrum of the steady-state current recorded at hyperpolarized potentials was measured in solutions in which Na, Cs, Hydrazine, or Sr caused inactivation of the current. The unitary conductance estimated was independent of which cation caused inactivation. From the relation between the concentration of cations which caused inactivation and the extent of inactivation at fixed potentials, the binding of one inactivator to a channel was found to cause inactivation, and the potency of inactivation was Cs⁺>Hydrazine⁺>Na⁺>Li⁺, and Ba²⁺>Sr²⁺. The inactivation caused by Na⁺ was increased by K⁺ when [K] _o was lower than 20mm, but was decreased by K⁺ in higher K-ASW (artificial sea water). One K⁺ was found to inactivate the channel cooperatively with one Na⁺. Increase of inactivation by K⁺ was a dominant effect in Cs-ASW. The inactivation was explained quantitatively by a model assuming cooperative plugging by a monovalent inactivator and a K⁺.     

Keratan sulfate glycosaminoglycans in murine eosinophil-specific granules.

We examined the presence of sialyl glycoconjugates in specific granules from murine bone marrow eosinophils. Lectin cytochemistry using Maackia amurensis lectin II (MAL II) specific for sialyl alpha-2,3 galactose residues demonstrated positive labeling in both immature and mature specific granules. Pretreatment with Clostridium neuraminidase or keratanase II eliminated the positive labeling of MAL II in the specific granules. High iron diamine-thiocarbohydrazide-silver proteinate physical development (HID-TCH-SP-PD) staining, which is specific for sulfated glycoconjugates, also positively labeled immature specific granules lacking crystalloids but not mature granules with crystalloids. Pretreatment with a combination of chondroitinase ABC and keratanase, or a combination of chondroitinase ABC and keratanase II, eliminated the positive labeling obtained with HID-TCH-SP-PD. These results indicate that the sialyl residues detected by MAL II are expressed as terminal sugar residues of keratan sulfate proteoglycan, which appears to be of the corneal type in view of its sensitivity to keratanase and keratanase II. (J Histochem Cytochem 47:481-488, 1999)     

Composition of phosphoglycerides and glycosyl glycerides in castor bean mitochondria

Phosphoglycerides and glycosyl glycerides in mitochondria fromcastor bean endosperms were determined by silicic acid columnchromatography using C-A and C-M as eluting solvents and bysupplemental use of TLC. The small amount of glycosyl glyceridedetected in the mitochondrial fraction may be due to contaminationby other organelle(s). ¹Present address: Ocean Research Institute, University of Tokyo,Nakano, Tokyo 164, Japan. (Received June 13, 1974; )     

Biosynthesis of homocysteine sulfinic acid in the vitamin B6-deficient rat.

The formation of L-homocysteine sulfinic acid in the rat was examined in vivo and in vitro. This compound was rarely found, in trace amounts, in the urine and could not be detected in the tissues of various animal species studied. When L-homocysteine or methionine was given orally or intraperitoneally to rats deficient in vitamine B6, the level of homocysteine sulfinic acid in the urine increased and its synthesis could be detected in the liver.     

Characterization of disease resistance gene-like sequences in near-isogenic lines of tomato

 We examined near-isogenic lines (NILs) carrying either of the tomato mosaic virus (ToMV) resistance genes Tm-1 and Tm-2 for sequences homologous to the isolated disease-resistance genes. DNA fragments were amplified from the genomic DNA of the NILs by the polymerase chain reaction (PCR) using primers designed on the basis of sequences of certain domains conserved among some disease-resistance genes. Of ten PCR products cloned, five were identified as having homology to either of the two classes of disease-resistance genes. The first class encoded proteins containing leucine-rich repeats (LRRs) and a nucleotide-binding site (NBS), such as the RPS2 gene in Arabidopsis and the N gene in tobacco. The second class encoded proteins containing a C-terminal membrane anchor but no NBS, such as the Cf 2 and Cf 9 genes in tomato. In Southern hybridization of the genomic DNAs of the NILs carrying either Tm-1 or Tm-2 and their parental NIL carrying neither of these resistance genes, multiple bands could be detected with most of the clones used as probes. This suggests that the genomes of the NILs contain multiple copies of sequences homologous to some of the known disease-resistance genes. No evidence was obtained to show that the Tm-1 and/or Tm-2 loci encode either class of protein, since no polymorphic band patterns between the NILs were detected by Southern hybridization. Received: 15 August 1997 / Accepted: 2 September 1997