Molecular basis of beta (0)-thalassemia/HbE disease in Thailand

The molecular basis of beta(0)-thalassemia/HbE disease in 30 Thai patients was investigated using DNA amplification and dot-blot hybridization with a number of allele specific oligonucleotide probes. The mutations identified were 17 cases of 4 base-pair deletion at codons 41-42, 4 cases of amber mutation at codon 17, and one case each of an ochre mutation at codon 35, a single base substitution at position 5 of IVS-1, and a single base substitution at position 654 of IVS-2.     

A comparison of algorithms for the identification of specimens using DNA barcodes: examples from gymnosperms

In order to use DNA sequences for specimen identification (e.g., barcoding, fingerprinting) an algorithm to compare query sequences with a reference database is needed. Precision and accuracy of query sequence identification was estimated for hierarchical clustering (parsimony and neighbor joining), similarity methods (BLAST, BLAT and megaBLAST), combined clustering/similarity methods (BLAST/parsimony and BLAST/neighbor joining), diagnostic methods (DNA–BAR and DOME ID), and a new method (ATIM). We offer two novel alignment‐free algorithmic solutions (DOME ID and ATIM) to identify query sequences for the purposes of DNA barcoding. Publicly available gymnosperm nrITS 2 and plastid matK sequences were used as test data sets. On the test data sets, almost all of the methods were able to accurately identify sequences to genus; however, no method was able to accurately identify query sequences to species at a frequency that would be considered useful for routine specimen identification (42–71% unambiguously correct). Clustering methods performed the worst (perhaps due to alignment issues). Similarity methods, ATIM, DNA–BAR, and DOME ID all performed at approximately the same level. Given the relative precision of the algorithms (median = 67% unambiguous), the low accuracy of species‐level identification observed could be ascribed to the lack of correspondence between patterns of allelic similarity and species delimitations. Application of DNA barcoding to sequences of CITES listed cycads (Cycadopsida) provides an example of the potential application of DNA barcoding to enforcement of conservation laws. © The Willi Hennig Society 2006.     

Vaccine-related mumps infections in Thailand and the identification of a novel mutation in the mumps fusion protein

An outbreak of nine cases of mumps was reported from a total of 97 vaccinated nursing students at two medical colleges in Thailand in 2010, 16–26 days after administration of MMR vaccine containing the L-Zagreb mumps strain. Symptoms ranged in severity from fever and parotid swelling to orchitis. Clinical samples were obtained from seven patients and three were suitable for further study.Sequencing confirmed that the SH gene of the mumps virus in the unpassaged clinical specimens was identical to the L-Zagreb SH gene in the vaccine. Further analysis of the viral genome identified nucleotide position 5170 as a novel mutation which corresponds to an amino acid change in the fusion protein.This study provides another virologically confirmed example of mumps resulting from the L-Zagreb vaccine strain.     

Lack of Association of the HbE Variant with Protection from Cerebral Malaria in Thailand

Hemoglobin E (HbE; beta26Glu --> Lys) is the most common variant of the beta-globin gene in Southeast Asia; it has been suggested that it confers resistance against Plasmodium falciparum malaria. In this study 306 adult patients with P. falciparum malaria (198 mild and 108 cerebral malaria patients) living in northwest Thailand were investigated to examine whether the HbE variant is associated with protection from cerebral malaria. Our results revealed that the sample allele frequency of HbE was not significantly different between mild (7.3%) and cerebral malaria (7.4%) patients. Thus, the HbA/HbE polymorphism would not be a major genetic factor influencing the onset of cerebral malaria in Thailand.     

Aeroallergens of plant origin: Molecular basis and aerobiological significance

This review presents an update on the sources and molecular basis of aeroallergens of plants, derived from pollen, seeds, leaf and stem detritus and their protein molecules. These aeroallergens are a natural component of the atmosphere, either because of their natural function or human activity. Pollen is a source of allergens within the 10–200 μm size range, and while most allergenic pollen types account for only 20–30% of total annual pollen catch, during their flowering season, they are usually the dominant type. Tree pollen commences the season in winter, with birch pollen counts in Scandinavia being the highest daily pollen counts yet reported and a major allergen, a 14-kDa protein, which is similar to pathogenesis-related proteins. Grass pollen follows in spring, and is unique as its two immunodominant allergens, a 35-kDa glycoprotein and 28–32-kDa protein, are in different cellular sites: the cytosol and surface of pollen grains; and in intracellular starch granules. The allergens at the pollen surface are not inhalable and can interact only with the eyes, nasal and oral cavities. Starch granules are released to the atmospheric aerosol when grains rupture in rainwater. These are a major source of allergen-containing micronic particles, which are important because they are inhalable. At the same time, allergen molecules are present in the aerosol, and these can bind to soot particles, and so be respired deep into the airways. The major Japanese cedar pollen allergen has been detected both within the pollen and in orbicules; particles less than 1 μm that line the anther cavity and can be released into the air when dehiscence occurs. Ragweed is the major cause of late summer hayfever in eastern North America, where its pollen accounts for up to 41% of the annual pollen catch. It is a major source of aeroallergens in both respirable and non-respirable size ranges. As a result of human activity, dusts derived from seeds and cereal grains during transport, storage and milling provide a source of micronic particles, containing potent allergens that can trigger allergic disease.     

A novel missense mutation in the factor VIII gene identified by analysis of amplified hemophilia DNA sequences.

To date the only point mutations demonstrated to cause hemophilia are C to T transitions in TaqI sites. These were detected by screening Southern blots with cloned factor VIII probes. During the development of improved methods for detecting and analyzing mutations in genomic DNA, a novel G to C transversion mutation has been identified. This rare transversion results in a missense mutation, with proline being substituted for arginine in one of the active domains of the factor VIII molecule. The results suggest that the improved methods will be useful for detecting mutations in hemophilia as well as in other genetic disorders. In this method, specific DNA sequences in genomic DNA are amplified using oligonucleotide primers and a heat-resistant DNA polymerase. Mutations are detected and localized in the amplified samples by RNase A cleavage, and the altered region is then sequenced.     

The identification of a sex-specific DNA marker in the ostrich using a random amplified polymorphic DNA (RAPD) assay

PCR-based techniques described to date for sex diagnosis in birds are not useful in ratites. We report here the identification of a W-linked marker in the ostrich (Struthio camelus) which allows gender diagnosis in chicks or juvenile birds. DNA from 10 females and 11 males was used to prepare two pools for each sex. Two-hundred different 10-mer primers of arbitrary sequence were used to screen those pools using a random amplified polymorphic DNA (RAPD) assay. One primer (D 10) generated a female-specific band. Sex specificity was confirmed by testing the 21 animals individually. The candidate DNA fragment was cloned and sequenced. Longer primers were designed to optimize a sex-specific PCR which will be useful in diagnosis.     

Molecular discrimination of six species of Bagrid catfishes from Indus river system using randomly amplified polymorphic DNA markers

Bagrid catfishes constitute a very important group of fishes having immense commercial importance in south-east countries. The phylogenetic relationships and genome specificity among six species of Bagrid catfishes (Mystus bleekeri, M. cavasius, M. vittatus, M. tengara, M. aor and M. seenghala) were investigated using RAPD markers as discriminating characters for the first time. 511 RAPD fragments were generated using ten decamer primers of arbitrary nucleotide sequences. Amplification reactions resulted in fragments ranging in length between 92 and 2,863 bp, which were assigned to 155 RAPD loci. Clearly resolved and repeatable bands were scored for their presence or absence in a binary matrix. Different RAPD profiles were observed for all the six Mystus species. In the present study three group diagnostic, eleven group exclusive and 18 species-specific markers were generated. Thus six Mystus species can be successfully differentiated on the basis of these 18 species-specific RAPD markers. UPGMA dendrogram constructed on the basis of genetic distance formed two distinct clusters, M. seenghala and M. aor form one separate cluster from other four species i.e., M. tengara, M. cavasius, M. bleekeri and M. vittatus. The inferences drawn from the above study clearly showed their genetic distinctness from the other four Mystus species and supported their inclusion into a separate genus, Sperata.     

Molecular analysis of glycogen storage disease type Ia in Iranian Azeri Turks: identification of a novel mutation

Glycogen storage diseases (GSDs) are caused by abnormalities in enzymes that are involved in the regulation of gluconeogenesis and glycogenolysis. GSD I, an autosomal recessive metabolic disorder, is the most common GSD and has four subtypes. Here, we examined GSD Ia caused by the defective glucose-6-phosphatase catalytic (G6PC) gene. We investigated the frequency of GSD Ia and clarified its molecular aspect in patients with the main clinical and biochemical characteristics of GSD, including 37 unrelated patients with a mean age of three years at the time of diagnosis. All patients belonged to the Azeri Turkish population. Hypoglycaemia and hypertriglyceridaemia were the most frequent laboratory findings. Mutations were detected by performing direct sequencing. Mutation analysis of the G6PC gene revealed that GSD Ia accounted for 11% in GSD patients with involvement of liver. Three patients were homozygous for R83C mutation. In addition, a novel stop mutation, Y85X, was identified in a patient with the typical features of GSD Ia.     

Rapid genetic identification and mapping of enzymatically amplified ribosomal DNA from several Cryptococcus species.

Detailed restriction analyses of many samples often require substantial amounts of time and effort for DNA extraction, restriction digests, Southern blotting, and hybridization. We describe a novel approach that uses the polymerase chain reaction (PCR) for rapid simplified restriction typing and mapping of DNA from many different isolates. DNA fragments up to 2 kilobase pairs in length were efficiently amplified from crude DNA samples of several pathogenic Cryptococcus species, including C. neoformans, C. albidus, C. laurentii, and C. uniguttulatus. Digestion and electrophoresis of the PCR products by using frequent-cutting restriction enzymes produced complex restriction phenotypes (fingerprints) that were often unique for each strain or species. We used the PCR to amplify and analyze restriction pattern variation within three major portions of the ribosomal DNA (rDNA) repeats from these fungi. Detailed mapping of many restriction sites within the rDNA locus was determined by fingerprint analysis of progressively larger PCR fragments sharing a common primer site at one end. As judged by PCR fingerprints, the rDNA of 19 C. neoformans isolates showed no variation for four restriction enzymes that we surveyed. Other Cryptococcus spp. showed varying levels of restriction pattern variation within their rDNAs and were shown to be genetically distinct from C. neoformans. The PCR primers used in this study have also been successfully applied for amplification of rDNAs from other pathogenic and nonpathogenic fungi, including Candida spp., and ought to have wide applicability for clinical detection and other studies.     

Differentiation and identification of iron-oxidizing acidophilic bacteria using cultivation techniques and amplified ribosomal DNA restriction enzyme analysis

Acidophilic iron-oxidizing microorganisms are important both environmentally and in biotechnological applications. Although, as a group, they are readily detected by their ability to generate ferric iron (resulting in a distinctive color change in liquid media), these microbes highly diverse phylogenetically. Various other characteristics, such as optimum growth temperature, response to organic carbon sources, and cellular morphologies, facilitate, in some cases, identification of isolates to a genus or species level, although this approach has limitations and may give erroneous results. In this study, a combined approach of using physiological traits together with amplified ribosomal DNA restriction enzyme analysis (ARDREA) has been successful in identifying all known acidophilic iron-oxidizing bacteria to the species level. Computer-generated maps were used to identify restriction enzymes that allow the differentiation of the acidophiles, and these were confirmed experimentally using authentic bacterial strains. To test further the validity of this approach, six acidophilic moderately thermophilic iron-oxidizing bacteria isolated from Montserrat (West Indies) were analysed using the ARDREA protocol. Three of the isolates were identified as Sulfobacillus acidophilus-like, and one as Sulfobacillus thermosulfidooxidans-like bacteria. The fifth isolate gave DNA digest patterns that were distinct from all known strains of iron-oxidizing acidophiles. Subsequent sequencing of the 16S rRNA genes of these isolates confirmed the identity of the four Sulfobacillus isolates, and also that the fifth isolate was a novel species. Schematic diagrams showing how ARDREA may be used to rapidly identify all known acidophilic iron-oxidizing bacteria are presented.     

Random amplified polymorphic DNA and restriction enzyme analysis of PCR amplified rDNA in taxonomy: two identification techniques for food-borne yeasts

The random amplified polymorphic DNA (RAPD) assay and the restriction enzyme analysis of PCR amplified rDNA are compared for the identification of the common spoilage yeasts Zygosaccharomyces bailii, Z. rouxii, Saccharomyces cerevisiae, Candida valida and C. lipolytica. Both techniques proved to be adequate tools for yeast identification. Since the RAPD does provide less stable patterns than restriction enzyme analysis of PCR amplified rDNA, and a large amount of data had to be compared without data reduction, Principal Component Analysis (PCA) was applied successfully for clustering the RAPD patterns. The success of PCA is highly influenced by the primer used in RAPD and the amount of reference samples. A large amount of reference samples improves the performance of clustering in PCA. The primer of choice was shown to be important with respect to the discriminatory power of the RAPD method. Some primers used enabled discrimination on the subspecies level. The results collected with both typing methods justify the conclusion that the present typing system can be applied for taxonomical purposes.     

Beta-thalassaemia in indigenous Belgian families: identification of a novel mutation

The molecular basis of β-thalassemia was investigated at the DNA level in 28 Belgians from 14 unrelated families. All the patients were heterozygous for β-thalassaemia. Seven different mutations were identified using a combination of dot-blot hybridization with allele-specific oligonucleotide probes and direct automated fluorescence-based DNA sequencing. Among these mutations, four are commonly found in the Mediterraneans – codon 8 (–AA), IVS-I-1 (G→A), IVS-I-6 (T→C) and codon 39 (C→T) – and two have occasionally been reported – initiation codon (T→C) and codon 35 (C→A). The last mutation, a –CC deletion at codons 38/39, appears to be a novel mutation and can routinely be investigated by AvaII restriction on amplified DNA. We report our findings, discuss the diversity of the mutations found in Belgium and show the usefulness of direct DNA sequencing in a population in which the molecular defects of β-thalassaemia have yet to be characterized and in which screening is hampered by the wide range of potential mutations. Received: 8 December 1995 / Revised: 7 February 1996     

Molecular analysis of Helicobacter pylori populations in antral biopsies from individual patients using randomly amplified polymorphic DNA (RAPD) fingerprinting

Abstract In the present study, randomly amplified polymorphic DNA (RAPD) fingerprinting has been used to analyse multiple single colony isolates of Helicobacter pylori from antral biopsies in an attempt to ascertain whether or not multiple strains are present in individual patients using single biopsy samples. The RAPD fingerprints derived from single colonies obtained from the same biopsy specimen were in all cases indistinguishable. The previously noted heterogeneity between H. pylori strains from different individuals was confirmed. RAPD fingerprinting, combined with a simple method of template preparation, was shown to be an excellent method for H. pylori strain differentiation. The results of this study indicate that the H. pylori population is homogeneous in individual patients at a single gastric site.     

Erythrocyte concentrates, low in buffy coat: production, preservation and evaluation of its quality

Buffy coat-poor packed red cells were prepared from fresh ACD-, ACD-AG- and EDTA-blood, than resuspended with a preservation solution, containing glucose, adenine, guanosine, sucrose, citric acid and sodium citrate and stored at 4 degrees C for 6 weeks. The survival rate of resuspended red cells from ACD-AG-blood amounted to 77% after 6 weeks of storage. The ATP content of resuspended red cells was approximately 25% lower than in ACD-AG whole blood during storage caused probably by increased ATP consuming reactions at the red cell membrane. The P2G-content of resuspended red cells from ACD- and ACD-AG-blood decreased above 50% of the normal level during the first week, as fast as in ACD- and ACD-AG whole blood. The P2G-breakdown in red cells from EDTA-blood was delayed for a week due to the higher pH as in CPD blood. Additions of xylitol, inorganic phosphate, and bicarbonate in 6, 5 and 20 mM final concentrations in the red cell suspensions and an increased pH at the same time delayed the breakdown of ATP and P2G. Packed red cells can be administered fast enough at hematocrits to 0.60 that will be achieved by adding 50 to 100 ml preservation solution. Leukocytes and thrombocytes were reduceds to 70 to 80%. With increasing rate of reduction a higher loss of red cells occured. Buffy coat-poor red cell concentrate contains only few microaggregates. It diminishes the risc of febrile transfusion reactions and delays the appearance of alloimmunisation. The circulatory overload of patients is less frequent than after transfusions of red cell resuspensions containing a large resuspension volume.     

Cell-free identification of novel N-myristoylated proteins from complementary DNA resources using bioorthogonal myristic acid analogues

To establish a non-radioactive, cell-free detection system for protein N-myristoylation, metabolic labeling in a cell-free protein synthesis system using bioorthogonal myristic acid analogues was performed. After Cu(I)-catalyzed azide–alkyne cycloaddition (CuAAC) with a biotin tag, the tagged proteins were separated by sodium dodecyl sulfate–polyacrylamide gel electrophoresis (SDS–PAGE) and blotted on a polyvinylidene fluoride (PVDF) membrane, and then protein N-myristoylation was detected by enhanced chemiluminescence (ECL) using horseradish peroxidase (HRP)-conjugated streptavidin. The results showed that metabolic labeling in an insect cell-free protein synthesis system using an azide analogue of myristic acid followed by CuAAC with alkynyl biotin was the most effective strategy for cell-free detection of protein N-myristoylation. To determine whether the newly developed detection method can be applied for the detection of novel N-myristoylated proteins from complementary DNA (cDNA) resources, four candidate cDNA clones were selected from a human cDNA resource and their susceptibility to protein N-myristoylation was evaluated using the newly developed strategy. As a result, the products of three cDNA clones were found to be novel N-myristoylated protein, and myristoylation-dependent specific intracellular localization was observed for two novel N-myristoylated proteins. Thus, the metabolic labeling in an insect cell-free protein synthesis system using bioorthogonal azide analogue of myristic acid was an effective strategy to identify novel N-myristoylated proteins from cDNA resources.     

Mitochondrial DNA evidence supports northeast Indian origin of the aboriginal Andamanese in the Late Paleolithic

In view of the geographically closest location to Andaman archipelago,Myanmar was suggested to be the origin place of aboriginal Andamanese.However,for lacking any genetic information from this region,which has prevented to resolve the dispute on whether the aboriginal Andamanese were originated from mainland India or Myanmar.To solve this question and better understand the origin of the aboriginal Andamanese,we screened for haplogroups M31(from which Andaman-specific lineage M31a1 branched off)and M32 among 846mitochondrial DNAs(mtDNAs)sampled across Myanmar.As a result,two Myanmar individuals belonging to haplogroup M31 were identified,and completely sequencing the entire mtDNA genomes of both samples testified that the two M31 individuals observed in Myanmar were probably attributed to the recent gene flow from northeast India populations.Since no root lineages of haplogroup M31 or M32 were observed in Myanmar,it is unlikely that Myanmar may serve as the source place of the aboriginal Andamanese.To get further insight into the origin of this unique population,the detailed phylogenetic and phylogeographic analyses were performed by including additional 7 new entire mtDNA genomes and 113 M31 mtDNAs pinpointed from South Asian populations,and the results suggested that Andaman-specific M31a1 could in fact trace its origin to northeast India.Time estimation results further indicated that the Andaman archipelago was likely settled by modern humans from northeast India via the land-bridge which connected the Andaman archipelago and Myanmar around the Last Glacial Maximum(LGM),a scenario in well agreement with the evidence from linguistic and palaeoclimate studies.     

Use of random amplified polymorphic DNA to identify several novel markers for sex identification in the crested serpent eagle and crested goshawk

The crested serpent eagle (Spilornis cheela hoya) has no distinct sexual dimorphic traits. In the current study, we report the results of an EE0.6 (EcoRI 0.6-kb fragment) sequence applied to S. cheela hoya and a novel random amplified polymorphic DNA (RAPD) marker that can be used to sex individuals within the species S. cheela hoya and Accipiter trivigatus formosae (crested goshawk). We used sex-specific primers for the avian CHD1 (chromo-helicase-DNA-binding 1) gene and the EE0.6 sequence in PCR assays to determine sex. In addition, 120 random primers were used for RAPD fingerprinting to search for novel sex-specific fragments of S. cheela hoya. The OPBB08 random primer generated a 1241-bp sex-specific fragment in all female S. cheela hoya. From the nucleotide sequence, PCR primers were designed to amplify 553-, 895-, and 194-bp sex-specific fragments present in all female S. cheela hoya. One of these primer pairs (ScBB08-7F/R) also amplified a male/female common fragment that can be used as an internal control (543 bp). Moreover, one of the primer pairs (ScBB08-5aF/5bR) could be used to identify genders of A. trivigatus formosae. In conclusion, we identified novel sex-specific DNA markers of S. cheela hoya and A. trivigatus formosae that can be used for rapid and accurate sex identification.     

Molecular basis of X-ray-induced mutation at the HPRT locus in human lymphocytes

Human lymphocytes lacking functional HPRT enzyme after a dose of 300 rad X-radiation were cloned and the monoclonal populations expanded so that sufficient genomic DNA was obtained for Southern analysis. A total of 33 mutant clones were analysed. Wild-type clones showed no evidence of changes to the HPRT gene resolvable by Southern banding patterns whereas 17 of 33 mutant clones showed changes. The alterations observed included total gene deletions (3 clones) and partial gene deletions with or without the appearance of novel bands (12 clones). Two clones showed the appearance of novel bands only. There were no changes observed in 16 of the 33 mutant clones. Three clones showed changes inconsistent with deletion of portions of the gene. In these clones inversion seems to have been the most likely cause of the mutation. The spectrum of gene alterations following ionizing radiation appears different to that previously observed for spontaneous mutations. Consequently, ionizing radiation or radiomimetic agents would appear to be aetiologic, at the most, for only a minor proportion of in vivo somatic mutations.