A simple electronic tool for assessing amino acid sequence polymorphisms within exon-2 of HLA-DPB1 alleles

2020 ◽  
Vol 81 (8) ◽  
pp. 430-436
Author(s):  
H. Clifford Sullivan ◽  
Loren Gragert ◽  
Geoffrey H. Smith ◽  
Kelsi Lindblad ◽  
Howard M. Gebel ◽  
...  
Blood ◽  
1997 ◽  
Vol 90 (7) ◽  
pp. 2634-2643 ◽  
Author(s):  
Vahid Afshar-Kharghan ◽  
José A. López

We investigated the molecular genetic and biosynthetic basis of Bernard-Soulier syndrome in a severely affected white woman. Flow cytometric analysis showed a severe deficiency of glycoprotein (GP) Ib, GP IX, and GP V on the surface of her platelets. Similarly, GP Ibα was undetectable by immunoblot analysis of platelet lysates. Surprisingly, a large quantity of a 70-kD protein (which probably represents a GP Ibα degradation product) was found in the patient's plasma in much greater quantities than in the plasma of an unaffected individual. To analyze the molecular lesion responsible for the disorder, we amplified and sequenced gene segments corresponding to the entire coding regions of the GP Ibα, GP Ibβ, and GP IX genes. The patient was homozygous for a specific GP Ibα allele that contained two tandem VNTR repeats in the region encoding the macroglycopeptide (C variant) and three differences from the published GP Ibα gene sequence. Two mutations were unlikely to be involved in the disorder: the substitution of a single base (T → C) in the second nucleotide of exon 2, which is in the 5′ untranslated region of the GP Ibα transcript, and a silent mutation in the third base of the codon for Arg342 (A → G) that does not change the amino acid sequence. The third mutation was a deletion of the last two bases of the codon for Tyr492 (TAT). This mutation causes a frameshift that alters the GP Ibα amino acid sequence, beginning within its transmembrane region. The mutant polypeptide contains 81 novel amino acids and is 38 amino acids shorter than its wild-type counterpart. The new sequence changes the hydrophobic nature of the transmembrane domain and greatly decreases the net positive charge of what had been the cytoplasmic domain. The deletion mutation was introduced into the GP Ibα cDNA, alone and in combination with the 5′ mutation, and expressed in Chinese hamster ovary (CHO) cells. The deletion alone severely reduced GP Ibα expression on the cell surface. Expression was not decreased further by addition of the 5′ mutation, confirming that the deletion was the cause of the Bernard-Soulier phenotype. Stable cell lines expressing the mutant polypeptide secreted large amounts of the polypeptide into the medium, suggesting that the mutant anchors poorly in the plasma membrane. Nevertheless, a fraction of the mutant was able to associate with GP Ibβ, as demonstrated by their coimmunoprecipitation with a GP Ibβ antibody.


2015 ◽  
Vol 8 (1) ◽  
Author(s):  
Marcelo Ramalho-Ortigão ◽  
Iliano V. Coutinho-Abreu ◽  
Valdir Q. Balbino ◽  
Carlos Alberto S. Figueiredo ◽  
Rami Mukbel ◽  
...  

Blood ◽  
1997 ◽  
Vol 90 (7) ◽  
pp. 2634-2643 ◽  
Author(s):  
Vahid Afshar-Kharghan ◽  
José A. López

Abstract We investigated the molecular genetic and biosynthetic basis of Bernard-Soulier syndrome in a severely affected white woman. Flow cytometric analysis showed a severe deficiency of glycoprotein (GP) Ib, GP IX, and GP V on the surface of her platelets. Similarly, GP Ibα was undetectable by immunoblot analysis of platelet lysates. Surprisingly, a large quantity of a 70-kD protein (which probably represents a GP Ibα degradation product) was found in the patient's plasma in much greater quantities than in the plasma of an unaffected individual. To analyze the molecular lesion responsible for the disorder, we amplified and sequenced gene segments corresponding to the entire coding regions of the GP Ibα, GP Ibβ, and GP IX genes. The patient was homozygous for a specific GP Ibα allele that contained two tandem VNTR repeats in the region encoding the macroglycopeptide (C variant) and three differences from the published GP Ibα gene sequence. Two mutations were unlikely to be involved in the disorder: the substitution of a single base (T → C) in the second nucleotide of exon 2, which is in the 5′ untranslated region of the GP Ibα transcript, and a silent mutation in the third base of the codon for Arg342 (A → G) that does not change the amino acid sequence. The third mutation was a deletion of the last two bases of the codon for Tyr492 (TAT). This mutation causes a frameshift that alters the GP Ibα amino acid sequence, beginning within its transmembrane region. The mutant polypeptide contains 81 novel amino acids and is 38 amino acids shorter than its wild-type counterpart. The new sequence changes the hydrophobic nature of the transmembrane domain and greatly decreases the net positive charge of what had been the cytoplasmic domain. The deletion mutation was introduced into the GP Ibα cDNA, alone and in combination with the 5′ mutation, and expressed in Chinese hamster ovary (CHO) cells. The deletion alone severely reduced GP Ibα expression on the cell surface. Expression was not decreased further by addition of the 5′ mutation, confirming that the deletion was the cause of the Bernard-Soulier phenotype. Stable cell lines expressing the mutant polypeptide secreted large amounts of the polypeptide into the medium, suggesting that the mutant anchors poorly in the plasma membrane. Nevertheless, a fraction of the mutant was able to associate with GP Ibβ, as demonstrated by their coimmunoprecipitation with a GP Ibβ antibody.


2019 ◽  
Vol 4 (Suppl 3) ◽  
pp. A61.3-A62
Author(s):  
Roland Funwei ◽  
Catherine O Falade ◽  
Olusola Ojurongbe

BackgroundPrompt diagnosis and appropriate treatment remain the hallmark needed to reduce malaria-related mortality in areas of high transmission. Rapid diagnostic tests (RDTs) that target the Pfhrp-2 gene, are essential in resource-limited settings where microscopy is not available. However, Pfhrp-2 gene deletion is implicated in limiting RDT sensitivity. Studies evaluating Pfhrp-2 and Pfhrp-3 deletion and the amino acid sequence diversity has not been investigated in Nigeria. We therefore hypothesised that malaria parasites in Nigeria are lacking Pfhrp-2/Pfhrp-3 genes with variable amino acid repeats sequences.MethodsThe study was part of a prospective cohort study evaluating RDTs performance. We pooled 66 samples comprising false negatives (n=31) and true positives (n=35) to elucidate Pfhrp-2/Pfhrp-3 gene deletion, RDT cross-reactivity with Pfhrp-3 antigen and amino acid sequence diversity. The 18SrRNA, msp 1, msp2 and glurp genes were amplified to establish active Plasmodium falciparum infection and the exon-2 regions of Pfhrp-2 and Pfhrp-3 genes were amplified to determine the presence or absence of Pfhrp-2 and Pfhrp-3 genes. Isolates with conserved Pfhrp-2/Pfhrp-3 were sequenced.ResultsAll 66 samples were positive for 18SrRNA, msp1, msp2 and glurp, indicating active P. falciparum infection. However, 16.7% and 6.0% of the samples were lacking Pfhrp-2 and Pfhrp-3 genes. Of the false negative samples, 25.8% and 12.9% has Pfhrp-2 and Pfhrp-3 deletions. Three Pfhrp-3 conserved antigens cross reacted to give RDT positive results. An extensive diversity in the amino acid sequence was observed.ConclusionPlasmodium falciparum parasites in Nigeria lack Pfhrp-2 and Pfhrp-3 genes. However, the proportion of deletions is low compared to reports from other malaria-endemic regions. In addition, a high amino acid tandem repeat was observed. A combination of pLDH and Pfhrp-2 based RDTs is recommended for accurate malaria diagnosis.


Author(s):  
M.K. Lamvik ◽  
L.L. Klatt

Tropomyosin paracrystals have been used extensively as test specimens and magnification standards due to their clear periodic banding patterns. The paracrystal type discovered by Ohtsuki1 has been of particular interest as a test of unstained specimens because of alternating bands that differ by 50% in mass thickness. While producing specimens of this type, we came across a new paracrystal form. Since this new form displays aligned tropomyosin molecules without the overlaps that are characteristic of the Ohtsuki-type paracrystal, it presents a staining pattern that corresponds to the amino acid sequence of the molecule.


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